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Faculty Publication (2021)

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1. Abalos, N.A., Ebajo, V.D. Jr., Camacho, D.H., Jacinto, S.D. (2021). Cytotoxic and apoptotic activity of Aglaforbesin derivative isolated from Aglaia loheri Merr. on HCT116 human colorectal cancer cellsAsian Pacific Journal of Cancer Prevention, 22 (1), Pages 53-60. DOI:10.31557/APJCP.2021.22.1.53more

Abstract:

The genus Aglaia (Meliaceae) is an established source of many anticancer compounds. The study evaluated the leaf extracts of Aglaia loheri, a tree native to the Philippines, as potential source of anticancer compounds. Methods: Using bioassay-guided fractionation, A. loheri leaf extract was subjected to various chromatographic techniques and step-wise application of MTT assay on human colorectal carcinoma cells, HCT116, to determine the cytotoxic fractions. The most cytotoxic HPLC isolate was structurally identified using 1D and 2D NMR and its apoptotic effect was assessed by JC-1 staining, caspase 3/7 assay and TUNEL assay. Results: After stepwise chromatography fractionation, an HPLC isolate, structurally identified as aglaforbesin derivative (AFD), demonstrated potent cytotoxicity against HCT116. AFD exhibited strong toxicity (IC50 = 1.13 ±0.07 µg/mL) and high selectivity on HCT116 than normal human kidney cells (HK-2). AFD-induced toxicity to HCT116 is possibly through the stimulation of the apoptotic signaling pathway via caspase 3/7 activation and DNA fragmentation independent of mitochondrial membrane depolarization. Conclusion: AFD exhibited selective cytotoxicity and apoptotic activity to HCT116 and could be further developed as anticancer drug lead.

 

2. Almenario, F.M., Jacinto, S.D. (2021). HPLC isolate from the leaves of Kaffir Lime (Citrus hystrix DC) exhibits selective cytotoxicity against human breast adenocarcinoma cell line, MCF-7Philippine Journal of Science, 150 (1), Pages 111-121.more

Abstract:

The increasing mortality and morbidity rate caused by breast cancer warrants the need to screen for compounds ideal for chemotherapeutic application. This study evaluated the cytotoxicity of Citrus hystrix leaves utilizing a bioactivity-guided fractionation scheme. Using various chromatographic techniques, the fractions were subjected to MTT [3-(4, 5-dimethylthiazol-2- yl)-2, diphenyltetrazo-lium bromide] assay to determine cytotoxicity and bioassays to confirm apoptosis as the mode of cell death. The results revealed that the crude extract was moderately cytotoxic against human breast adenocarcinoma (MCF-7) but not to other cancer cell lines tested. Solvent partitioning of the crude extract revealed that hexane partition exhibited the highest cytotoxicity (IC50: 23 µg/mL) to MCF-7. Sequentially, vacuum liquid chromatography (VLC) of the hexane partition separated VLC 7 (IC50: 17.2 µg/mL) with the highest percent yield. Hence, VLC 7 was subjected to gravity column chromatography (GCC), where GCC 7.4 exhibited promising cytotoxicity to MCF-7 (IC50: 14.6 µg/mL). Selectivity index (SI) indicated that GCC 7.4 was highly selective against MCF-7 (SI > 2), relative to non-cancer cell lines NIH3T3, HDFn, and AA8. Interestingly, GCC 7.4 induced apoptosis as confirmed by several markers including phosphatidylserine (PS) membrane translocation, mitochondrial membrane depolarization, nuclear condensation, and DNA fragmentation. To further purify the components present in GCC 7.4, high-performance liquid chromatography (HPLC) was performed. HPLC 7.4.5 was active against MCF-7 (IC50: 5.5 µg/mL) without being cytotoxic against the non-cancer cell line NIH3T3. Overall, the results demonstrated that C. hystrix leaves possess promising compounds that are highly selective and cytotoxic against MCF-7 by inducing apoptosis.  

 

3. Amberong, A.G.T., Fidelino, J.S.,  Duco, R.A.J.,  Mimie M. Ledesma, M.M., Duya, M.V.,  Ong, P.S.†, Duya, M.R.M. (2021). Toward a Philippine Bat Call Library: Acoustic Characterization of Insectivorous bats in Bulacan, Luzon Island, PhilippinesPhilippine Journal of Science, 150 (S1), Pages 473-485. Special Issue on Biodiversity.more 

Abstract:

The diversification in call features across different echolocating bat species can provide sufficient information for reliable species identification. In the Philippines, bat bioacoustics is still a growing field. There is a need for a well-developed reference library of calls from different species of insectivorous bats, representing different habitats across each species’ geographic ranges. This study aims to contribute to the building of an echolocation call library for Philippine insectivorous bats. We describe the echolocation calls of 15 species from five families captured in Bulacan province on the island of Luzon. A total of 321 echolocation calls from 105 individuals released in an enclosure were recorded using a Pettersson Elektronik M500 USB ultrasound microphone. Using discriminant function analysis, we assessed the potential of using call parameters in classifying bat echolocation calls to species correctly. Regardless of sample size, correct overall cross-validated classification levels were 92.8% for CF-dominated calls from Hipposideridae and Rhinolophidae families, and 96.9% for FM-dominated calls from Vespertilionidae and Miniopteridae families. When variations in classification levels due to sample size were considered, 98.4% of CF-component dominated calls (four species removed due to small sample size) and 98.9% of FM-component dominated calls (one species removed due to small sample size) were successfully classified into their species. Calls from one species under the Emballonuridae family were characterized. We found some conflicts in identification between species belonging to species complexes, particularly within Hipposideridae. Nevertheless, our results have shown that echolocation calls can be a reliable method in the identification of insectivorous bat species and can complement morphometric and molecular data. The current research contributes to the bat call library we are building as a reference for future taxonomic and ecological studies in the Philippines.

 

4. Aya, FASayco, MJPGarcia, LMB. (2021). Optimum stocking density and feeding level for laboratoryreared earlystage silver therapon (Leiopotherapon plumbeus) larvaeAquac Res202152, Pages 935– 942. https://doi.org/10.1111/are.14947 more

Abstract:

Growth, survival and feeding of earlystage silver therapon Leiopotherapon plumbeus larvae reared at different stocking densities and feeding levels were examined. Larvae (8 days post hatch (dph); 0.38–0.50 mg body weight (BW); 5.33–6.90 mm in total length (TL)) were stocked at densities of 5, 15, 25 and 35 larvae/L and cofed with live food (Brachionus rotundiformis and Artemia nauplii) and formulated microdiet or fed Artemia alone for 28 days. Another batch of 8 dph silver therapon larvae (0.65 mg BW; 9.47 mm TL) were stocked at 15 larvae/L and were fed 1, 2 or 5 Artemia nauplii/mL for 28 days. Survival at lower densities (5 and 15 larvae/L) was significantly improved than in highdensity reared larvae. Furthermore, larvae fed Artemia alone showed higher survival (20.4%–81.4%) than those offered live food and formulated microdiet combined (3.5%–32.9%) in each stocking density, indicating the suitability of Artemia for earlystage silver therapon larvae. Growth parameters were significantly affected by stocking density in larvae fed Artemia alone but not in the live food and formulated microdiet cofed group. No significant differences in growth and survival were observed in silver therapon larvae reared on three feeding levels. However, higher feed intake at 5 nauplii/mL resulted in significantly higher body lipid contents than those fed 1 or 2 nauplii/mL. The results suggest that larvae held at stocking densities of 5 and 15 larvae/L and fed 5 Artemia nauplii/mL promote maximum growth, survival and higher feed intake of earlystage silver therapon larvae under laboratory conditions.

 

5. Baluyot, J.C., Reyes, E.M., Velarde, M.C. (2021). Per- and polyfluorozlkyl substances (PFAS) as contaminants of emerginc concern in Asia’s freshwater resources. Environmental Research, 197, 111122.more

Abstract:

The occurrence of per- and polyfluoroalkyl substances (PFAS) in water resources is an emerging concern because of their environmental persistence and bioaccumulation in humans. In Western countries, health advisories regarding PFAS exposure have been released to warn the public of its potential adverse effects. However, awareness regarding PFAS exposure in Asia is still at its infancy as reflected by the minimal safeguards imposed to protect the population from exposure. Here, we reviewed studies on PFAS contamination in Asia with a focus on freshwater resources to determine whether PFAS is also a concern in this part of the globe. Peer reviewed articles which included information on PFAS levels from 2000 to 2020 were compiled. The highest PFAS contamination was detected in surface water relative to ground, tap, and drinking water. PFAS levels in water resources in several countries in Asia, such as China, Japan, and South Korea, were above the recommended level, similar to that in the United States. PFAS in South and Southeast Asia were just below the recommended level, but the rise of PFAS in China in the recent decade, alongside its remarkable economic and industrial growth, suggests that increased PFAS contamination in South and Southeast Asia may soon follow, as these countries compete with the global economy. Hence, there is a need for these countries to also implement measures that will reduce the exposure of their population to PFAS.

 

6. Calayag, A.M.B., Widmer, K.W., Rivera, W.L. (2021). Antimicrobial susceptibility and prevalence of bla and qnr genes in salmonella entrica isolated from slaughtered porkResearch Square, Pages 1-15.more

Abstract:

Salmonella enterica is known as one of the most common foodborne pathogens worldwide. While salmonellosis is usually self-limiting, severe infections may require antimicrobial therapy. However, increasing resistance of Salmonella to antimicrobials, particularly uoroquinolones and cephalosporins, is of utmost concern. The present study aimed to investigate the antimicrobial susceptibility of S. enterica isolated from pork, the major contributor in Philippine livestock production. Results: Our results show that 61.2% of the isolates carried antimicrobial resistance genes qnrS and blaTEM. While qnrA (12.9%) and qnrB (39.3%) were found less frequently, co-carriage of blaTEM and one to three qnr subtypes was observed in 45.5% of the isolates. Co-carriage of blaTEM and blaCTX-M was also observed in 3.9% of the isolates. Antimicrobial susceptibility testing revealed that majority of the isolates were non-susceptible to ampicillin and trimethoprim/sulfamethoxazole, and 13.5% of the isolates were multidrug-resistant. Conclusions: High prevalence rates of S. enterica carrying antimicrobial resistance genes (ARG), specically the presence of isolates co-carrying resistance to both ß-lactams and uoroquinolones, raise a concern on antimicrobial use in the Philippine hog industry and on possible transmission of ARG to other bacteria.

 

7. Daquioag, J.E.L., Penuliar, G.M. (2021). Isolation of actinomycetes with cellulolytic and antimicrobial activities from soils collected from an urban green space in the PhilippinesInternational Journal of Microbiology, 2021, Article ID 6699430, 14 pages.  https://doi.org/10.1155/2021/6699430more

Abstract:

Actinomycetes are one of the most important groups of soil bacteria that are recognized as sources of commercially important enzymes and antimicrobials. Actinomycetes, however, are largely underestimated and uncharacterized in underexplored habitats such as green spaces in urban areas. This study aimed to isolate actinomycetes from soils in the University of the Philippines Diliman campus and determine their cellulolytic and antimicrobial activities. A total of 235 isolates were purified from the soil samples collected. Cellulolytic and antimicrobial activities were observed in 114 and 18 isolates, respectively. The cell-free supernatants of 31 isolates exhibited high cellulolytic activities. Two isolates, in particular EWLG2 and EPNA9, had 0.596 FPU and 0.885 FPU cellulolytic activity, respectively. Seven isolates exhibited antimicrobial activities in the screening methods used. The crude extracts of isolates AWLG9, AWLG8, AWLG10, AULG1, APLG2, and AWLG13 had minimum inhibitory concentrations (MIC) values ranging from 31.25µg/mL to 500µg/mL against Candida spp. Isolates AULG1 and EPLG5 were active against the bacterial test microorganisms and had MIC values ranging from 250µg/mL to 500µg/mL. DNA sequencing identified the isolates which exhibited high cellulolytic and antimicrobial activities as Bacillus sp. and Streptomyces sp., with percent identities ≥98%. This study shows that green spaces are rich sources of soil microorganisms that have cellulolytic and antimicrobial activities. It is recommended that the isolates obtained in this study be examined further for possible applications in bioethanol production and pharmacology.

 

8. Dela Peña, L.B.R.O., Vejano, M.R.A., Rivera, W.L. (2021). Molecular surveillance of Cryptosporidium spp. for microbial source tracking of fecal contamination in Laguna Lake, PhilippinesJ Water Health 2021; jwh2021059.more

Abstract:

Water quality deterioration in source waters poses increased health, environmental, and economic risks. Here, we genotyped Cryptosporidium spp. obtained from water samples of Laguna Lake, Philippines, and its tributaries for the purpose of source-tracking fecal contamination. A total of 104 surface water samples were collected over a 1-year period (March 2018 to April 2019). Detection of Cryptosporidium was carried out using genus-specific primers targeting a fragment of the small subunit (SSU) rRNA gene. The study revealed 8 (14%) tributary samples and 1 (2.77%) lake sample positive for contamination. The species were determined to be C. parvum (n = 4), C. muris (n = 2), C. hominis (n =1), C. galli (n =1), C. baileyi (n = 1), C. suis (n = 1), as well as rat genotype IV (n = 1). Two species were detected in duck (C.baileyi) and cattle (C.parvum) fecal samples. The data presented suggest that Cryptosporidium contamination is likely to come from sewage or human feces as well as various agricultural sources (i.e. cattle, swine, and poultry). This information reveals the importance of mitigating fecal pollution in the lake system and minimizing health risks due to exposure to zoonotic Cryptosporidium species.

 

9. Galano, J.B., Rodriquez, L.J. (2021). Exotic mahogany leaf litter hinders growth of Philippine native tree seedlingsProceedings of the National Institute of Ecology of the Republic of Korea, 2 (2), Pages 76-81.more

Abstract:

With continuous decline of Philippine forest cover, sustainable forest management and restoration are essential to restore destroyed forest ecosystems. Unfortunately, of ten most planted trees in reforestation projects in the Philippines, eight are exotic species, with large leaf mahogany (Swietenia macrophylla) being the most dominat. In this study, effects of Swietenia macrophylla in reforestation projects on native tree species was evaluated. Effects of S. macropylla leaf litter, frequency, and canopy on the growth of the Philippine native species Pterocarpus indicus were investigated. Results showed that S. macrophylla leaf litter significant inhibited the growth of P. indicus seedlings based on root collar-to-shoot height. The standardized growth rate of seedlings in plots without S. macrophylla leaf litter was significantly higher than the growth rate of seedlings in plots with leaf litter. Furthermore, there was no significant difference in the standardized growth rate of seedlings between plots without litter and a control plot. On the contrary, S. macrophylla tree frequency and canopy closure showed no significant effect. These results attest to the negative effect of widely planted S. macrophylla to a valuable Philippine native tree P. indicus. With accumulating scientific evidence about negative effects of S. macrophylla on native trees, discontinued use in tree planting and reforestation efforts with active management of restoration sites previously planted with large leaf mahogany are needed.

 

10. Galidon, J.M.M., Penneys, D.S., Lagunday, N.E., Tandang, D.N., Coritico, F.P., Amoroso, V.B., Fritsch, P.W. (2021). Hypericum perryongii (Hypericaceae)a new species from PhilippinesPhytotaxa478 (1), Oages 061–066. https://doi.org/10.11646/phytotaxa.478.1.4more

Abstract:

Hypericum perryongii, from Mindanao Island, Philippines, is herein described and illustrated. This new taxon closely resembles both H. geminiflorum and H. formosanum but can be easily distinguished from the former by its larger corolla and calyx lobes and higher number of stamens per fascicle, and from the latter by its terminally 1-flowered inflorescences and the subsessile and abaxially glaucous leaves.

 

11. Gigante, E.T., Lim, E.J., Crisostomo, K.G., Cornejo, P. and Rodriguez, L.J. (2021). Increase in humidity widens heat tolerance range of tropical Ceratosolen fig waspsEcological Entomology, 46, Pages 573-581.more

Abstract:

1. Fig wasps are the obligate mutualistic pollinators of fig trees, which are important components of tropical forests. The stability of these species interactions, in the face of environmental changes, relies heavily on the thermal tolerance of these wasps.

2. This study determined the upper thermal limits of three tropical Ceratosolen fig wasp species. Humidity levels and collection season were varied to determine the effect of water availability on heat tolerance.

3. Wasps were placed in incubators to simulate different temperature regimes (30–45 °C) with varying humidity conditions. Wasp populations from either the dry or wet seasons were tested. Upper lethal temperature was determined by recording wasp survival.

4. All factors (temperature, humidity, season, wasp species, and their interactions) significantly affected wasp longevity. Exposure to high temperatures resulted in a significant decrease in wasp longevity: longest at 30 °C and the ratio decreased rapidly at 40 and 45 °C. An increase in temperature from 30 to 35 °C caused at least a two-fold reduction in wasp lifespan. More surprisingly, humid conditions allowed survival for two to six times longer than non-humid conditions in high temperatures (40–45 °C). Wasps obtained during the wet season also survived longer than those from the dry season. Increased water availability (i.e. during wet season and with high humidity conditions) thus increased wasp upper thermal limits.

5. Relative humidity was a strong limiting factor in the heat tolerance of tropical wasps. Persistence of insect species that are narrowly-distributed will depend on the presence of intact, high-humidity habitats.

 

12. Jolejole, M.E., Cayetano, M.G., Magbanua, F.S. (2021). Responses of benthic macroinvertebrate communities in tropical Asian streams passing through and industrial zoneChemistry and Ecology, 37 (5), Pages 399-418.more 

Abstract:

Industrial zones have been key drivers of growth across Asia but are also the source of water quality deterioration in surrounding rivers and streams. This study examined the effects of industrial zone located at the San Cristobal sub-catchment of Laguna de Bay, the Philippines on the spatiotemporal variation in water quality and benthic macroinvertebrate communities. Sampling sites were established in upstream and downstream sections of two tributaries of San Cristobal River, and the main channel of Diezmo River, and were sampled in 2018 during dry (February and April) and rainy (June and October) seasons. Results showed significant spatial difference with declining water quality (low dissolved oxygen; high levels of ammonia-nitrogen, phosphate-phosphorus, and total suspended solids) at the downstream sites. Consequently, benthic macroinvertebrates responded via change in community structure and composition (decline in pollutionsensitive taxa from upstream through downstream) to water quality degradation related to industrial land use downstream. Furthermore, seasonal variation was observed in benthic macroinvertebrate communities due to the absence of spateinduced disturbance, allowing benthic macroinvertebrates to proliferate in the rainy season. Findings of this study reveal that benthic macroinvertebrates can be used as bioindicators in the evaluation of the ecological integrity of surface river and stream systems that pass through industrial zones.

 

13. Karki. M.,, Davies, K., Gundimeda, H., Acosta, L.A., Ausseil, A-G., Gopal S. Rawat, G., Anticamara, J.A., Youn, Y.C., Wu, N., Sellamuttu, S.S., Asha Rajvanshi, A. (2021). Biodiversity. Climate change and Economic Development in Asia-Pacific RegionWorld Scientific Encyclopedia of Climate Change, Pages 171-186.more

Abstract:

The Asia-Pacific (AP) region is one of the most diverse regions in the world in terms of its socio-cultural, biological and physical features. It has the world’s highest mountains and deepest ocean floors. Located in the region are diverse tropical, subtropical and montane forests, grasslands, wetlands, deserts, alpine and coastal ecosystems, and the largest numbers of small islands, and richest corals globally. It hosts a high number of native species, having 16 of the 36 global biodiversity hotspots and 4 of the 10 megadiverse countries. With the world’s largest and most extensive areas of coral reefs and mangroves, it has the greatest marine biodiversity globally as well (IPBES, 2018)…

 

14. Lee, D.G., Lee, J.S., Quilantang, N.G., Jacinto, S.D., Lee, S. (2021). Determination of Afzelin and Astragalin from Lespedeza cuneata on Aldose Reductase Inhibition. Journal of Chromatographic Science, bmaa127.  https://doi.org/10.1093/chromsci/bmaa127more

Abstract:

The bioactive chemicals in L. cuneata were investigated by repeated column chromatography and their effect on aldose reductase (AR), obtained from rat lenses, was examined. Results showed that the ethyl acetate and n-butanol fractions of L. cuneata exhibited potential inhibitory effect against AR with IC50 values of 0.57 and 0.49 μg/mL, respectively. Phytochemical analysis of these two fractions resulted in the isolation of five flavonoids namely, acacetin (1), afzelin (2), astragalin (3), kaempferol (4) and scutellarein 7-O-glucoside (5). The AR inhibitory effect of compounds 1-5 was explored; compounds 23 and 5 showed potential AR-inhibitory effects with IC50 values of 2.20, 1.91 and 12.87 μM, respectively. Quantitative analysis of afzelin (2) and astragalin (3) in L. cuneata by high performance liquid chromatography with ultraviolet detection revealed its content to be 0.722–11.828 and 2.054–7.006 mg/g, respectively. Overall, this study showed that L. cuneata is rich in flavonoids with promising AR-inhibitory activities, which can be utilized for the development of natural therapies for treating and managing diabetic complications.

15. Matias, D.M.S., Kim, H., Anticamara, J.A., Matias, K.M.S., Tibig, L.V. (2021). Emerging response options and scenarios of slow onset events related to climate change in Southeast AsiaCurrent Opinion in Environmental Sustainability, 50, Pages 175-184.more

Abstract:

The negative effects of slow onset events (SOEs) related to climate change are already affecting developing countries, with the resulting impacts likely to increase significantly. With an increasing urgency to act on SOEs, this paper systematically reviewed and synthesized literature on SOEs in Southeast Asia (SEA), which is a region of several highly climate vulnerable countries. With a focus on scenarios and emerging response options by affected sectors such as agriculture, fisheries, and forestry, we found that the drivers of SOEs in SEA are both indirect and direct and have confounding impacts. Only a few researches used scenarios and models for assessing SOEs in SEA, a majority of which use Representative Concentration Pathways and Shared Socioeconomic Pathways. The impacts of SOEs range from environmental, ecological, economic, and social factors and require integrated response options including mitigation or adaptation that pay attention to the complexity of the intersection between human and natural systems.

 

16. Moendeg, K.J., Leonardo, L.R., Isorena, T.G., Hilotina, F.C.A.S., Pates, I.S., Cacayorin, N.O. (2021). Prevalence and spatial distribution of heterophyidiasis in Southern PhilippinesActa Tropica, 220, 105940.more

Abstract:

Heterophyidiasis is a fish-borne zoonotic disease that is considered to be an emerging public health problem in the Philippines. This study was carried out to determine the spatial distribution and risk factors of heterophyidiasis in five selected villages in New Corella, Davao del Norte in Southern Mindanao. Of the 1,101 individuals examined, 26 (2.36% overall prevalence rate, 95% CI 1.46–3.25) were positive for heterophyid eggs. Higher infection rate was observed in males (3.85%, 95% CI 2.27–5.43) than females (0.76%, 95% CI 0.02–1.5). Mapping of cases was done to show the spatial distribution of heterophyidiasis in New Corella. Multiple logistic regression analysis showed that gender, raw freshwater fish consumption, undercooked grilled fish consumption and proximity to rivers or creeks are the risk factors significantly associated with heterophyid infection. This study confirmed the presence of heterophyid infection in humans in the surveyed villages in New Corella in Southern Philippines.

 

17. Pabico, L.A., Duya, M.V., Fidelino, J.S., Ong, P.S., Duya, M.R.M. (2021). Bird Feeding Guild Assemblage along a disturbance gradient in the Pantabangan-Carranglan watershed and Forest Reserve, Central Luzon Island, PhilippinesPhilippine Journal of Science, 150 (1) (Special Issues on Biodiversity), Pages 237-255.more

Abstract:

Functional groups or guilds are now becoming popular in biodiversity conservation and monitoring as representative of the condition and status of a habitat as a whole. These can provide a rich source of additional evidence that can supplement evidence from studies based on taxonomic composition. In this study, we assessed differences in bird species and feeding guild assemblages across three habitat types within the Pantabangan-Carranglan Watershed and Forest Reserve (PCWFR), a major watershed in the Philippines located in the province of Nueva Ecija on central Luzon island. We sampled three habitat types during the wet and dry seasons from 2012–2016 using ground and canopy nets. After 4084 mist-net days, we captured 1191 bird individuals of 92 species and 41 families. Both species and feeding guild assemblages differed between habitats based on PERMANOVA (p = 0.001). Nineteen species and five feeding guilds differed in abundance between habitats. Our study demonstrated significant responses of the species and feeding guild assemblages of birds within the PCWFR to a disturbance gradient. We also found that feeding guild assemblage patterns were significantly correlated to species assemblage patterns. The use of guilds in bird monitoring can, thus, help facilitate the involvement of indigenous people and local communities, whose knowledge of birds is based on their observations of the environment, including traits that define these feeding guild classifications. However, there is potential to obscure the presence of taxonomically distinct lineages, such as the many endemic species and subspecies found on Luzon island and the Philippines. This concern is especially important in a megadiverse region like the Philippines. As such, we recommend the use of a functional approach in tandem with the traditional taxonomic approach in studying bird communities.

 

18. Que,G.C.L., Widmann, I.D.L., Widmann, P., Dione Gale B. Naval, D.G.B., Fontanilla, I.K.C. (2021). Mitochondrial DNA haplotype analysis of the endemic and critically endangered Philippine Cockatoo (Cacatua haematuropygia P.L.S. Müller, 1776)Philippine Journal of Science, 150 (1) (Special Issue on Biodiversity), Pages 135-146.more

Abstract:

The Philippine cockatoo or “katala” (Cacatua haematuropygia) is a Critically Endangered parrot species endemic to the Philippines with an estimated wild population of up to 1,120 individuals. Threats to its continued existence include habitat destruction and poaching for the pet trade. While protected populations exist in Palawan under the care of the Katala Foundation Inc., no previous genetic studies aimed at quantifying genetic diversity in the protected populations have been done. This study examines two mitochondrial genes, ND2 and COX1, in protected populations of the katala. ND2 was sequenced for 101 individuals while for COX1, 103 individuals were successfully sequenced. Results show that very few haplotypes are present for both ND2 and COX1 and there is a possible reduction of genetic diversity over time. In addition, the nuclear gene TGFB2 was examined for 31 individuals. TGFB2 sequences were highly similar, further supporting the hypothesis of a possible genetic bottleneck. Future conservation work and breeding efforts for the species should consider the possible consequences of reduced genetic diversity.

 

19. Ragasa, L.R.P., Joson, S.E.A., Bagay, W.L.R., Perez, T.A., Velarde, M .C. (2021). Transcriptome analysis reveals involvement of oxidative stress response in a copper-tolerant Fusarium oxysporum strainFungal Biology.  https://doi.org/10.1016/j.funbio.2021.01.001.more

Abstract:

High amount of copper is toxic to most organisms, but endophytic fungi can develop survival strategies to tolerate and respond to environmental stressors such as heavy metal contaminants. While high copper induces oxidative stress, it is still unclear which genes are associated with copper tolerance. Here, we performed a metatranscriptome analysis of endophytic fungi isolated from a black nightshade plant Solanum nigrum L. growing on mine tailings of a gold processing area. Initial screening revealed the presence of a copper-tolerant strain of Fusarium oxysporum, designated as IB-SN1W, which tolerated up to 1000 ppm and 300 ppm copper in solid and liquid media, respectively. Differential gene expression analysis by RNA sequencing showed that 23% of contigs are uniquely expressed in the copper-treated fungus. These genes are involved in copper ion import, polyamine transport, oxidoreductase activity, and oxidative stress response. Catalase transcripts were also highly upregulated in IB-SN1W compared to a non-tolerant F. oxysporum strain. Catalase inhibition decreased copper-tolerance in IB-SN1W, while the addition of antioxidants prevented the copper-dependent growth inhibition in the non-tolerant strain. Overall, these results suggest that oxidative stress response contributes to copper tolerance in F. oxysporum.

 

20. Rodriguez, A.M.H., Reyes, M.F., Lim, N.N.S., Tolentino, J.E.M., Ipulan-Colet L.A. (2021). Effects of Binunga [Macaranga tanarius (L.) Mull.Arg.] Crude Leaf Extract on Cancer Cells, Angiogenesis, Early implantation, and EmbryogenesisPhilippine Journal of Science, 150 (2), Pages 461-471.more

Abstract:

Medicinal plants have long been known to contain an abundance of natural bioactive compounds, some of which have been studied for their anti-cancer and anti-angiogenic properties. However, testing the possible side effects of a “drug” candidate is not congruently done in vivo. Hence, the effects of these plant extracts on different biological processes are unknown. This study aims to evaluate the anti-cancer and anti-angiogenic activity of the crude leaf extract of the plant Macaranga tanarius (L.) Müll.Arg. while simultaneously assessing its safety. For anti-cancer and anti-angiogenic evaluation of the extract, MTT [3-(4,5-dimethylthiazol-2-yl)-2,5diphenyltetrazoliumbromide] and duck chorioallantoic membrane (CAM) assays were utilized, respectively. Alongside this, the detrimental effect of the leaf extract on normal biological processes was conducted by examining its effect on mice implantation and embryogenesis through morphological and histological analyses. For anti-cancer potential, crude methanolic extract of the leaves from M. tanarius was found to be cytotoxic against HCT116 at a concentration of 18.93 ug/mL. The extract also showed anti-angiogenic potential as CAM assay revealed that the extract reduced the percent area of blood vessels. In the mice implantation assay, the methanolic extracts were not able to significantly decrease the number of embryo implantations in the uterus. Furthermore, CD31 staining showed that the uterus treated with M. tanarius exhibited a significant reduction in blood vessels. Reduction of blood vessels did not affect late organogenesis since the gestation index of dams and fetal malformation index showed no significant difference between PBS- (phosphate-buffered saline solution) and extract-treated groups after additional treatment at (embryonic day) E8.5 and E9.5. This suggests that M. tanarius leaves possess bioactive compounds for anti-cancer and anti-angiogenic therapy that may not interfere with normal biological processes such as pregnancy.

 

21. Rodriguez, L.J.V., Cruaud, A., Rasplus, JY. (2021). Low sampling effort and high genetic isolation contribute to under documented diversity in Philippine fig waspsPhilippine Journal of Science, 150 (1) (Special Issues on Biodiversity), Pages 173-180.more

Abstract:

One of the unique attributes of tropical forests is the diversity of fig-fig wasp interactions. In the Philippines, there is a good estimate of the number of fig species, but none for the pollinating fig wasps. According to our review of the literature, there are only 10 described species of Ceratosolen in the Philippines, eight of which are endemic to the country (80% endemicity) out of a global count of 72 species worldwide. However, most historical collections were only from Luzon island. In this study, because of an increased sampling effort across 10 islands – coupled with morphological comparisons with described species and analysis of genomic data – we identified 29 as yet undescribed Ceratosolen species (which represents an increase of nearly 300% for the Philippine fig wasp fauna). This shows that the major factors contributing to under-documented diversity in Philippine Ceratosolen are low sampling effort and high genetic isolation between lineages. More importantly, this is probably not limited to fig wasps and we suspect underestimated diversity in most Philippine faunal lineages. Building a strong taxonomic foundation is key to the establishment of good conservation practices. It is time to start investing in Philippine biodiversity research before we lose our natural treasures.

 

22. Salmo, S.G. III. (2021).  Assessment of typhoon impacts and post-typhoon recovery in Philippine Mangroves: lessons and challenges for adaptive managementDynamic Sedimentary Environments of Mangrove Coasts, Pages 539-562. https://doi.org/10.1016/B978-0-12-816437-2.00022-7more

Abstract:

The extent and state of ecosystem health of Philippine mangroves are affected by the occurrences of typhoons (ca. 20 per year). While severe damages (and sometimes even total forest collapse) are commonly reported, there are some cases where mangroves are less damaged and easily recovered implying that some mangroves are either highly vulnerable or resilient. Most studies on effects of typhoons in mangroves (including post-typhoon recovery) are mainly focused on vegetation but rarely on changes in sediment and faunal composition and activities. Also, these studies are mostly short-term and rapid (<1 year) with suboptimal experimental designs because of the lack of baseline data and systematic assessment. In this study, a 15-year synthesis of impacts of typhoon and post-typhoon recovery in selected mangrove sites in the Philippines was discussed and compared with other typhoon-disturbed tropical/subtropical mangroves. The study covered pre- and post-typhoon changes in vegetation, sediment, and faunal assemblages and activities including the assessment of possible recovery and identification of recovery indicators. The study provides an overview of interrelationships of vegetation, sediment (including nutrients), and faunal assemblages and activities as a more integrative approach in damage and recovery assessments. Lastly, the implications of the study on research needs (e.g., systematic and sustained monitoring) and policy and management programs (e.g., effective conservation and restoration programs) for Philippine mangroves were discussed.

 

23. Suyom, L.M., Cueno, P.M.G.M., Rivera, W.L. (2021). Development of diffractive optics technology based immunoassay protocol and its application in the detection of Entamoeba hystolytica infectionsJournal of Immunological Methods, 493, 113016.more

Abstract:

Amebiasis due to infection with Entamoeba histolytica is a problematic parasitic disease in many countries. By means of a novel technology developed by Axela Biosensors, Inc., the dotLab™ system, a rapid immunoassay was developed to detect at least 5.45 cells/mL of E. histolytica, the causative agent of amebiasis, in spiked stool samples in 66 min. Regeneration of the dotLab™ sensor using 0.1 M glycine (pH 2.5) solution was established, enabling the assessment of multiple stool samples (up to 8 X) using a single sensor. This developed assay was applied to assess the health status of a community in relation to E. histolytica infections of relocated families in San Isidro, Rodriguez, Rizal, Philippines. The community was found to be 15.6% and 26.1% positive for E. histolytica using real-time polymerase chain reaction (real-time PCR) and dotLab™ methods, respectively. Compared to real-time PCR, the dotLab™ method is 94.74% sensitive and 74.79% specific. The agreement of the two methods was tested using Kappa coefficient test and it showed that dotLab™ is a reliable alternative to real-time PCR. The optimized dotLab™ assay did not cross-react with stool samples containing Escherichia coli, Blastocystis sp., Cryptosporidium sp. and Giardia intestinalis. The community had 17 X to 24 X higher infection rate than previous reports in the Philippines. Sex, age, and duration of settlement in the relocation area were not related to the rate of infection. This increase may be due to improper hygiene and sanitation in the community.

 

24. Torres, S.K.M., Santos, B.S. (2021). Genetic diversity and population structure of three Caranx species from Batangas Province, PhilippinesPhilippine Journal of Science, 150 (1) (Special Issues on Biodiversity), Pages 223-236.more

Abstract:

Species belonging to the genus Caranx, locally known as “talakitok,” belong to the economically important fish in the Philippines. The popularity of these species makes them prone to overexploitation, which may result to a decline in their population in the wild. Despite these circumstances, stock assessment and population genetic variation studies are scarce. In this study, three species from this genus (C. ignobilis, C. papuensis, C. ignobilis) from the Batangas region were subjected to genetic diversity and population structure analyses using the cytochrome b (cyt b) gene of the mitochondrial DNA (mtDNA) to address these information gaps. High haplotype and high nucleotide diversity were noted in C. ignobilis, which may indicate that the population is still large and stable. However, C. papuensis and C. sexfasciatus populations had a low nucleotide diversity and high haplotype diversity, which could mean a possible genetic bottleneck in the recent past. Likewise, each of these three species showed no genetic differentiation between marine and freshwater specimens, which can be attributed to their life history and biology. Analysis of molecular variance (AMOVA) revealed weak genetic structure, indicated by low percentage value between populations. Based on neutrality tests and mismatch distribution analysis, the three species may have possibly undergone demographic expansion. This study provides the genetic profile of Caranx species found in the Batangas region before the recent Taal Volcano eruption (January 2020), which can be used to investigate the effects of this eruption on the population of this species. Likewise, results obtained from this study served as preliminary data for the population genetics of Caranx spp. found in Batangas, Philippines.

 

25. Verdera, A.B., Montecillo, A.D., Obusan, M.C.M. (2021). Draft Genome Sequence of Streptomyces sp. Isolate H28 from the Meycauayan River, PhilippinesMicrobiology Resource Announcements, 10 (1), e01269-20. DOI: 10.1128/MRA.01269-20more

Abstract:

In this paper, we report the draft genome sequence of Streptomyces sp. isolate H28, isolated from sediments of the Meycauayan River in the Philippines. This species exhibits production of melanin as well as the ability to utilize and degrade both high-density polyethylene (HDPE) and low-density polyethylene (LDPE).

 

 Chemistry logo

1. Amoroso, V.B., Mendez, R.A., Junio, H.A., Molino, R.J.E.J., Pescadero, I.R. and Villalobos, A.P. (2021). Characterization of a Natural Fungicide from an Indigenous Plant Tasmannia piperita (Hook.f.) Miers Extract: Stability, Metabolomics, and In silico StudiesPhilippine Journal of Science, 150 (2), Pages 355-370. more

Abstract:

Many indigenous plants are rich in secondary metabolites with fungicidal activity. Based on literature and focus group discussions (FGDs), seven species of indigenous plants as potential sources of fungicide were collected in several places in Mindanao Island and tested for phytochemicals. Among the seven species, Tasmannia piperita (Hook.f.) Miers showed the highest amount of phenolic and flavonoid content and was chosen for further studies. Consistency of the extraction, active ingredient characterization, thermostability, and photostability of T. piperita leaf methanolic extract (TPLME) was determined using high-performance liquid chromatography (HPLC) while secondary metabolites profiling was conducted using ultrahigh performance liquid chromatography high-resolution mass spectrometry (UHPLC-HRMS). Molecular docking studies and in silico absorption, distribution, metabolism, and excretion analysis (ADME) were carried out for the identified compounds. HPLC trace of fresh methanolic extract shows consistency of extraction from batch to batch while that of the 12-mo-old methanolic extract indicates real-time stability. Results from thermo- and photo-stability indicate stability for at least one year at room temperature. Secondary metabolite profiles indicate the presence of flavonoids, glycosylated flavonoids, polyphenols, sesquiterpene lactones, glycerides, phosphocholines, and pigments. Molecular docking study of these compounds against Arg-X-Leu-Arg (RXLR) effector proteins of the fungal phytopathogen Phytophthora infestans (PDB ID: 2NAR, 3ZRG, and 5L7S) showed 3-genistein-8-C-glucoside (7) and rhoifolin (8) with the highest docking score against 2NAR while cyranoside (6), trihydroxyisoflavone (10), and apigenin-7-O-glucuronide (12) have the highest docking score against 3ZRG. Rhoifolin (8) also showed the highest docking score against 5L7S, supporting the high activity of these T. piperita methanolic extract against P. infestans. In silico ADME analysis revealed drug-likeness of the identified compounds based on Lipinski’s rule of five. All these results provide a scientific basis for the use of the methanolic extract in the development of a natural fungicide from the indigenous plant T. piperita.

 

2. Bruzon, D.A.V., Tapang, G.A. and Martinez, I.S. (2021). An electrochemical setup designed for carbon dioxide solubility measurements in ionic liquids.  Review of Scientific Instruments, 92 (2), 024102.more

Abstract:

An electrochemical setup was designed and built to evaluate carbon dioxide solubility in ionic liquids. The setup can simultaneously measure amounts of CO2 in the gas and in the ionic liquid phase, making it very useful for in situ electrochemical measurements. The home-built glass cell is able to withstand high vacuum allowing the ionic liquid samples to be properly evacuated before characterization and kept free of contaminants during experiments. A pressure gauge attached to the setup enables continuous monitoring of gas added to the system. This kind of configuration can measure gas solubility in ionic liquids expressed as Henry’s constants determined from generated plots of dissolved gas concentration in the ionic liquid vs headspace gas pressure. It also serves as a more economical alternative to other gas solubility measurement techniques, as it is predominantly made of glass, and requires minimal sample amounts. The setup can be useful in determining the solubility of various gases in ionic liquids.

 

3. Budlayan, M.L., Lagare-Oracion, J.P., Dela Rosa, L., Rodriguez, M.J., Manigo, J., Alguno, A., Austria, E., Arco, S.,  Patricio, J., Deocaris, C., Basilia, B. and Capangpangan, R. (2021). Gold nanoparticles-decorated paper-based sensor for rapid cyanide detection in waterAdvances in Natural Sciences: Nanoscience and Nanotechnology, 12 ( 2), 025007. more

Abstract:

In this study, a versatile sensing platform based on a commercially available filter paper for the development of a colorimetric sensor using label-free gold nanoparticles (AuNPs) for the detection of cyanide in water is presented. The developed sensor can be applied for the direct detection of cyanide from an aqueous sample efficiently in a wide concentration range. The synthesised AuNPs were found to have an average size of about 13.2 ± 2.65 nm with a surface plasmon resonance peak at around 525 nm. Successful integration of AuNPs on the WFP substrate was observed through the FESEM-EDX analysis and supported by the presence of an absorbance peak at about 528 nm on the spectrum of the WFP-AuNPs composite. The colour of the WFP-AuNPs composite changed from purple-red to white in the presence of cyanide. Using the paper-based sensor, the limit of detection is calculated to be 7.68 × 10−6 M (0.5 ppm). The said sensitivity is good enough for the determination of cyanide in industrial wastewater samples. The developed sensor also showed excellent selectivity towards cyanide over other ions, demonstrating its practical applicability to monitor cyanide contamination in different environmental samples. Furthermore, the applicability of the sensor was demonstrated using several real water samples spiked with cyanide, including creek and tap water. Notably, the sensor showed great promise for the rapid, cost-effective, and versatile monitoring of cyanide contamination in various aqueous samples.

 

4. Granada, J.R.N., Yago,  A.C.C., and Solis, J.S. (2021).  Adsorption of Cadmium (II) onto Oxidized Activated Carbon Derived from Mahogany (Swietenia macrophylla King) Pericarp: Equilibrium, Thermodynamics, and KineticsPhilippine Journal of Science, 150 (1), Pages 291-305. more

Abstract:

The thermodynamics and kinetics of the adsorption of Cd(II) ions onto oxidized activated carbon derived from mahogany pericarp were studied. The activated carbon was prepared via initial carbonization and activation by phosphoric acid, followed by oxidization using different concentrations of nitric acid (HNO3; 2.5 M, 5.0 M, and 10.0 M). With increasing concentration of HNO3, the number of carboxylic acid groups increased while the number of phenolic groups decreased. Adsorption equilibrium studies revealed that the maximum adsorption capacity for Cd(II) increased with the increasing degree of oxidation of carbon material. The adsorption of Cd2+ ions onto the oxidized carbon was best described by the Freundlich model. Results of kinetic studies showed that the adsorption of Cd(II) ions onto the oxidized activated carbon is limited by film diffusion; for the unmodified carbon, Cd(II) adsorption was limited by intraparticle diffusion. The adsorption process onto the oxidized activated carbon materials was determined to be spontaneous, at the temperature range studied (25–50 °C).

 

5. Heng, J. Z. X., Tang, K. Y., Regulacio, M. D., Lin, M., Loh, X. J., Li, Z., & Ye, E. (2021). Solar-Powered Photodegradation of Pollutant Dyes Using Silver-Embedded Porous TiO2 NanofibersNanomaterials, 11 (4), Page 856.more

Abstract:

Titanium dioxide (TiO2) nanomaterials have been ubiquitously investigated as a photocatalyst for organic contaminant treatment in wastewater due to their exemplary semiconductor properties. However, their huge band gap remains a barrier for visible light absorption, limiting their utility in practical applications. The incorporation of noble metals in the TiO2 scaffold would help mitigate the problem via plasmonic resonance enhancements. Silver (Ag) is the chosen noble metal as it is relatively cheap and has great plasmonic effects. In this study, the use of electrospun Ag-embedded TiO2 nanofibers as a photocatalyst is shown to be effective in decomposing rhodamine B and methyl orange dyes under a solar simulator in 3 h, which is more efficacious as opposed to pristine TiO2 nanofibers. This showcases the potential of a simple and economic wastewater treatment system for the removal of organic pollutants.

 

6. Junio, J.B., Chirawatkul, P., Conato, M.T. and Mercado, C.C. (2021). Substitution of Ca2+ in Calcite by Sn2+ and Sr2+ cations through ion exchange characterized by X-ray absorption and photoelectron spectroscopiesMRS Advances. https://doi.org/10.1557/s43580-021-00061-wmore

Abstract:

Tin (Sn2+) and strontium (Sr2+), two potential alternatives to lead (Pb2+) in perovskite formation, were explored in transforming calcium carbonate (CaCO3) into a leaving group in a cation exchange reaction. This is the first part of a sequential ion exchange process in transforming calcite into a Pb-free perovskite material for perovskite solar cell applications. Calcite, a polymorph of CaCO3, was successfully transformed into strontianite (SrCO3) through a cation exchange reaction. In the Sn substitution reaction on the other hand, no SnCO3 formation was noted. Instead, oxides of Sn were formed. The wider spaces in between Ca2+ cations in (100) orientation account for the higher atomic Sn2+ and Sr2+ concentrations as compared to (001) orientation, where the cation movement is restricted. X-ray absorption and photoelectron spectroscopies were used to investigate the ion-exchange transformation of calcite towards the formation of an intermediate carbonate material.

 

7. Labasan, K.B., Lin, HJ., Baskoro, F., Togonon, J.J.H., Wong, H.Q., Chang, C.W., Arco, S.D., and Yen, H.J. (2021). Dicyanotriphenylamine-Based Polyimides as High-Performance Electrodes for Next Generation Organic Lithium-Ion BatteriesACS Applied Materials & Interfaces, 13 (15),  Pages 17467-17477.more

Abstract:

Aromatic polyimide (PI) derivatives have recently been investigated as redox-active electrode materials for Li-ion batteries because of their high thermal stability and thermo-oxidative stability complemented by excellent solvent resistance, good electrical and mechanical properties, and chemical resistance. In this work, we report two PI derivatives from a newly synthesized 4,4′-diamino-3″,4″-dicyanotriphenylamine (DiCN-TPA) monomer and two dianhydrides, pyromellitic dianhydride (PMDA) and 1,4,5,8-naphthalenetetracarboxylic dianhydride (NTCDA); designated as TPA-PMPI and TPA-NTCPI, respectively, as electrode materials for Li-ion batteries. Characterizations of the PIs reveal excellent thermal stability and bipolar property. The incorporation of DiCN-TPA into the polymer structure resulted to a disordered chain arrangement, thus giving high glass transition temperatures (Tg). Electrochemical performance tests reveal that TPA-NTCPI cathode delivered a reversible specific capacity of 150 mAh g–1 at 0.1 A g–1 and exhibited a stability up to 1000 cycles. On the other hand, TPA-PMPI anode delivered a high specific capacity of up to 1600 mAh g–1 at 0.1 A g–1 after 100 cycles. The electrochemical performance of TPA-NTCPI cathode and TPA-PMPI anode are both among the best compared with other reported aromatic PI-based electrodes. The long cycle lifetime and excellent battery performance further suggest that TPA-NTCPI and TPA-PMPI are promising organic electrode materials for next generation Li-ion batteries.

 

8. Lim, J.P.L., Braza, M.K.E., and Nellas, R.B. (2021). The effect of ligand affinity to the contact dynamics of the ligand binding domain of thyroid hormone receptor - retinoid X receptorJournal of Molecular Graphics and Modelling, 104, art. no. 107829. more

Abstract:

Ligand-based allostery has been gaining attention for its importance in protein regulation and implication in drug design. One of the interesting cases of protein allostery is the thyroid hormone receptor - retinoid x receptor (TR:RXR), which regulates the gene expression of important physiological processes, such as development and metabolism. It is regulated by the TR native ligand triiodothyronine (T3), which displays anticooperative behavior to the RXR ligand 9-cis retinoic acid (9C). In contrast to this anticooperative behavior, 9C has been shown to increase the activity of TR:RXR. Here we probed the influence of the affinity and the interactions of the TR ligand to the allostery of the TR:RXR through contact dynamics and residue networks. The TR ligand analogs were designed to have higher (G2) and lower (N1) binding energies than T3 when docked to the TR:RXR(9C) complex. The aqueous TR(N1/T3/G2):RXR(9C) complexes were subjected to 30 ns all-atom simulations using theNAMD. The program CAMERRA was used to capture the subtle perturbations of TR:RXR by mapping the residue contact dynamics. Various parts of the TR ligands; including the hydrophilic head, the iodine substituents, and the ligand tail; have been probed for their significance in ligand affinity. The results on the T3 and G2 complexes suggest that ligand affinity can be utilized as a predictor for anticooperative systems on which ligand is more likely to dissociate or remain bound. All 3 complexes also display distinct contact networks for cross-dimer signalling and ligand communication. Understanding ligand-based allostery could potentially unveil secrets of ligand-regulated protein dynamics, a foundation for the design of better and more efficient allosteric drugs.

 

9. Molino,  R.J.E.J. and Junio HA. (2021). Profiling the Philippine Blue: Liquid Chromatography / Mass Spectrometry-based metabolomics study on Philippine IndigoferaRapid Communications Mass Spectrometry. 35 (7): e9037.more

Abstract:

Rationale

High-throughput liquid chromatography/mass spectrometry (LC/MS) analysis presents an interesting platform for natural dyes research. A particular example is the assessment of the dynamic changes in fermentation mixtures of Philippine Indigofera, and in the investigation of commercially available indigo prepared using traditional and optimized methods.

Methods

Leaves from Indigofera tinctoria and Indigofera suffruticosa were subjected to methanolic extraction and aqueous fermentation for 48 h. Indigo powders prepared following 2-day and 15-day fermentation were also subjected to profiling using ultra-high-performance liquid chromatography/quadrupole time-of-flight mass spectrometry (UHPLC/QTOF-MS). MS2 spectra were annotated through a library search in the community-curated Global Natural Products Social Molecular Networking (GNPS). Spectra with no library hits in GNPS were annotated by analysis of their fragmentation pathways.

Results

UHPLC/MS-based detection and fragmentation analysis led to characterization of leucoindigo and the unreported tryptanthrin intermediate, 5a-hydroxy-5,5a-dihydroindolo[2,1-b]quinazoline-6,12-dione, in the fermentation extract of I. tinctoria leaves. Indigo-associated metabolites were absent in an Indigofera specimen in Laguna Province, which explained why it did not produce blue dye. Locally produced indigo was abundant in indigotin and indirubin, differentiated based on product ions with the corresponding predicted fragmentation pattern. The relative intensity of indigotin, however, decreased with the traditional process of extended fermentation to produce indigo.

Conclusions

The study is the first to demonstrate simultaneous MS-based analysis of reaction intermediates, indigotin dye, side products, and catabolites on actively transforming fermentation extracts of I. tinctoria. New results include annotated mass spectra for leucoindigo, and for the unreported 5a-hydroxy-5,5a-dihydroindolo[2,1-b]quinazoline-6,12-dione, which is probably an intermediate in tryptranthrin synthesis. The proposed fragmentation schemes could guide the annotation of analogous compounds in complex mixtures.

 

10. Oracion, J.P.L., De La Rosa, L.B. , Budlayan, M.L.M., Rodriguez, M.J.D., Manigo, J.P. , Patricio, J.N., Arco, S.D., Austria, E.S., Alguno, A.C., Deocaris, C.C. and Capangpangan, R.Y. (2021). Simple one-pot in situ synthesis of gold and silver nanoparticles on bacterial cellulose membrane using polyethyleneimineJournal of Applied Science and Engineering, 24 (3), Pages 351-357. more

Abstract:

Immobilization of metallic nanoparticles on bacterial cellulose (BC) matrix is widely used in fabricating materials with significant importance in emerging technologies for sensing, catalysis, and biomedical applications. Although reports on in situ integration of nanoparticles have been widely explored, commonly employed methods utilize numerous reagents and tedious synthesis routes. In this work, a one-pot, in situ reductions of gold and silver nanoparticles (AuNPs and AgNPs) was done using polyethyleneimine on a BC matrix obtained from Acetobacter xylinum. The surface chemistry of the BC membrane was studied using FT-IR spectroscopy, and the formation of nanoparticles onto the nanocellulose network was examined using FESEM-EDX analysis, obtaining 30.6 and 4.4 wt. % for Au and Ag, respectively. UV-Vis analysis showed that the SPR peaks were found at 546 nm for AuNPs and 401 nm for AgNPs. Moreover, stability tests confirmed the stable integration of the in situ-synthesized nanoparticles on the BC membrane. This study demonstrated a facile one-pot, in situ synthesis of AuNPs and AgNPs on the BC membrane, providing new insights on nanoparticle-impregnated cellulosic material for further applications.

 

11. Ramos, R.M.C.R. and Regulacio, M.D. (2021). Controllable Synthesis of Bimetallic Nanostructures Using Biogenic Reagents: A Green PerspectiveACS Omega DOI: 10.1021/acsomega.1c00692 more

Abstract:

Bimetallic nanostructures are emerging as a significant class of metal nanomaterials due to their exceptional properties that are useful in various areas of science and technology. When used for catalysis and sensing applications, bimetallic nanostructures have been noted to exhibit better performance relative to their monometallic counterparts owing to synergistic effects. Furthermore, their dual metal composition and configuration can be modulated to achieve optimal activity for the desired functions. However, as with other nanostructured metals, bimetallic nanostructures are usually prepared through wet chemical routes that involve the use of harsh reducing agents and hazardous stabilizing agents. In response to intensifying concerns over the toxicity of chemicals used in nanomaterial synthesis, the scientific community has increasingly turned its attention toward environmentally and biologically compatible reagents that can enable green and sustainable nanofabrication processes. This article aims to provide an evaluation of the green synthetic methods of constructing bimetallic nanostructures, with emphasis on the use of biogenic resources (e.g., plant extracts, DNA, proteins) as safe and practical reagents. Special attention is devoted to biogenic synthetic protocols that demonstrate controllable nanoscale features, such as size, composition, morphology, and configuration. The potential use of these biogenically prepared bimetallic nanostructures as catalysts and sensors is also discussed. It is hoped that this article will serve as a valuable reference on bimetallic nanostructures and will help fuel new ideas for the development of more eco-friendly strategies for the controllable synthesis of various types of nanostructured bimetallic systems. 

 

12. Regulacio M.D. and Hans E.D.R. (2021). Dual Plasmonic Au-Cu2-xS Nanocomposites: Design Strategies and Photothermal PropertiesChemistry — A European Journal.   DOI: 10.1002/chem.202101392more

Abstract:

Coupling two different materials to create a hybrid nanostructured system is a powerful strategy for achieving synergistically enhanced properties and advanced functionalities. In the case of Au and Cu 2– x S, their combination at the nanoscale results in dual plasmonic Au–Cu 2– x S nanocomposites that exhibit intense photon absorption in both the visible and the near-infrared spectral range. Their strong light-absorbing property translates to superior photothermal transduction efficiency, rendering them attractive in photothermal-based applications. There are several nanostructure configurations that are possible for the Au–Cu 2– x S system, and the successful fabrication of a particular architecture often requires a carefully planned synthetic strategy. In this Minireview, we present the different synthetic approaches that can be employed to produce rationally designed Au–Cu 2– x S nanocomposites, with focus on the experimental protocols that can lead to heterodimer, core−shell, reverse core−shell, and yolk−shell configurations. We also discuss the photothermal behavior of these materials and provide a glimpse of their potential use as photothermally active agents in therapeutic and theranostic applications.

 

13. Regulacio, M. D., Nguyen, D.‐T., Horia, R., Seh, Z. W. (2021). Designing Nanostructured Metal Chalcogenides as Cathode Materials for Rechargeable Magnesium Batteries.  Nano- Micro Small: 2007683.more

Abstract:

Rechargeable magnesium batteries (RMBs) are regarded as promising candidates for beyond-lithium-ion batteries owing to their high energy density. Moreover, as Mg metal is earth-abundant and has low propensity for dendritic growth, RMBs have the advantages of being more affordable and safer than the currently used lithium-ion batteries. However, the commercial viability of RMBs has been negatively impacted by slow diffusion kinetics in most cathode materials due to the high charge density and strongly polarizing nature of the Mg2+ ion. Nanostructuring of potential cathode materials such as metal chalcogenides offers an effective means of addressing these challenges by providing larger surface area and shorter migration routes. In this article, a review of recent research on the design of metal chalcogenide nanostructures for RMBs’ cathode materials is provided. The different types and structures of metal chalcogenide cathodes are discussed, and the synthetic strategies through which nanostructuring of these materials can be achieved are described. An organized summary of their electrochemical performance is also presented, along with an analysis of the current challenges and future directions. Although particular focus is placed on RMBs, many of the nanostructuring concepts that are discussed here can be carried forward to other next-generation energy storage systems.

 

14. Rosales, C.M.F., Lamorena, R.B. (2021). In silico study of possible roles of relative humidity in chemical speciation on ambient particulate matter using PHREEQCInternational Journal of Environmental Science and Technology https://doi.org/10.1007/s13762-021-03134-3more

Abstract:

One of the components of ambient particulate matter (PM) that contributes to its possible toxicity are metals. Moreover, other factors in the environment, such as the presence of water as indoor humidity, can also affect the behavior of PM either physically or chemically. Chemically, the presence of water may affect the forms or species in which the metal is present. The present study aims to utilize PHREEQC, a geochemical modeling software, in the evaluation of species formation of metals in particulate matter. From all these runs, it was found that the possible roles of water in metal speciation in particulate matter are as follows: (1) in the presence of water as relative humidity (RH), metals in PM may be hydroxylated, which may facilitate further uptake of water and affect the reactivity of the PM, (2) in addition to the RH, the volume of the room may affect the species concentrations present, and (3) inferences may be made regarding the possible initial form of the metals, which may be oxides, as shown by the formation of hydroxylated metals upon exposure of metals to water vapor. These observations give a brief insight into how water may possibly interact and affect the possible toxicity of metal species in PM.

 

15. Sta Ana, K.M., Madriaga, J. and Espino, M.P. (2021). β-Lactam antibiotics and antibiotic resistance in Asian lakes and rivers: An overview of contamination, sources and detection methodsEnvironmental Pollution, 275, 116624.more

Abstract:

Lakes and rivers are sources of livelihood, food and water in many parts of the world. Lakes provide natural resources and valuable ecosystem services. These aquatic ecosystems are also vulnerable to known and new environmental pollutants. Emerging water contaminants are now being studied including antibiotics because of the global phenomenon on antibiotic resistance. β-Lactam antibiotics are widely used in human and animal disease prevention or treatment. The emergence of antibiotic resistance is a public health threat when bacteria become more resistant and infections consequently increase requiring treatment using last resort drugs that are more expensive. This review summarizes the key findings on the occurrence, contamination sources, and determination of β-lactam antibiotics and β-lactam antibiotic resistant bacteria and genes in the Asian lake and river waters. The current methods in the analytical measurements of β-lactam antibiotics in water involving solid-phase extraction and liquid chromatography-mass spectrometry are discussed. Also described is the determination of antibiotic resistance genes which is primarily based on a polymerase chain reaction method. To date, β-lactam antibiotics in the Asian aquatic environments are reported in the ng/L concentrations. Studies on β-lactam resistant bacteria and resistance genes were mostly conducted in China. The occurrence of these emerging contaminants is largely uncharted because many aquatic systems in the Asian region remain to be studied. Comprehensive investigations encompassing the environmental behavior of β-lactam antibiotics, emergence of resistant bacteria, transfer of resistance genes to non-resistant bacteria, multiple antibiotic resistance, and effects on aquatic biota are needed particularly in rivers and lakes that are eventual sinks of these water contaminants.

 

16. Tang, K.Y., Chen, J.X., Legaspi, E.D.R., Owh, C., Lin, M., Tee, I.S.Y., Kai, D., Loh, X.J., Li, Z., Regulacio, M.D. and Ye, E. (2021). Gold-decorated TiO2 nanofibrous hybrid for improved solar-driven photocatalytic pollutant degradationChemosphere, 265, 129114. more

Abstract:

TiO2-based nanomaterials are among the most promising photocatalysts for degrading organic dye pollutants. In this work, Au–TiO2 nanofibers were fabricated by the electrospinning technique, followed by calcination in air at 500 °C. Morphological and structural analyses revealed that the composite consists of TiO2 nanofibers with embedded Au nanoparticles that are extensively distributed throughout the porous fibrous structure of TiO2. The photocatalytic performance of these Au-embedded TiO2 nanofibers was evaluated in the photodegradation of Rhodamine B and methylene blue under solar simulator irradiation. Compared with pristine TiO2 nanofibers, the Au-embedded TiO2 nanofibers displayed far better photocatalytic degradation efficiency. The plasmon resonance absorption of Au nanoparticles in the visible spectral region and the effective charge separation at the heterojunction of the Au–TiO2 hybrid are the key factors that have led to the considerable enhancement of the photocatalytic activity. The results of this study clearly demonstrate the potential of Au–TiO2 electrospun nanofibers as solar-light-responsive photocatalysts for the effective removal of dye contaminants from aquatic environments.

 

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1. Bagtasa, G. (2021). Analog forecasting of tropical cyclone rainfall in the PhilippinesWeather and Climate Extremes, 32: 100323. https://doi.org/10.1016/j.wace.2021.100323more

Abstract:

Tropical cyclone (TC) rainfall results in damages to properties and loss of lives. It is also a significant source of freshwater in the Philippines. This study describes a method in forecasting accumulated TC rainfall using analogous TCs from historical datasets. A TC rainfall database where precipitation within 5 of TC centers was created for all landfalling TCs from 1951 to 2015. To predict TC rainfall, the mean rainfall of all past TCs with similar tracks included in the database, referred to as analog TCs, is calculated. Landfalling TCs from 2016 to 2018 are used to optimize the selection of past analog TCs. Each past TC member was also adjusted according to a target TC's intensity and movement speed. The optimized analog method is then applied to landfalling TCs from 2019 to November 2020. Results show that the composite rainfall from past TCs within 1.8 of the forecast TC yields the best hit rate of intense rainfall. The analog TC rainfall forecast generally has a similar spatial distribution as the observed TC rain. However, this method tends to miss extreme rainfall values due to a “smoothing” effect caused by the variability of extreme rain locations of each TC member and constraints in the rainfall data used in the database. Nevertheless, forecast assessment results show that analog TC rainfall forecasting performed better than the WRF model in predicting intense and inland rainfall. In addition to it being computationally inexpensive, it can complement the inherent biases of dynamical models.

 

2. lgodon, M., Takahashi, Y., Sato, M., Kubota, H., Ishida, T., Yamashita, K., Castro, E., Perez, G. J., Marciano, J. J., Matsumoto, J., Hamada, J., Tsuboki, K., and Yamada, H. (2021). 3D Reconstruction of Typhoon and Thunderstorm Cloud Top Using Airborne CameraEGU General Assembly 2021, online, 19–30 Apr 2021, EGU21-14160, https://doi.org/10.5194/egusphere-egu21-14160, 2021more

Abstract:

Typhoons are extreme weather phenomena that inflict damages and casualties around globe. These phenomena are difficult to study because of their chaotic behaviour but the capacity to measure their intensity can help mitigate the hazards that they bring. In the past, several attempts have been done to relate typhoon's intensity with the structural evolution of its eye. This suggests the possible relation between the typhoon intensity with typhoon eye altitude. In this research, we visualize Typhoon Trami’s structure by reconstructing the three-dimensional model inside its eye and analyze the information of its cloud top altitude. An experiment was conducted under the SATREPS/ULAT project (SATREPS: Science and Technology Research Partnership for Sustainable Development, ULAT: Understanding Lightning and Thunderstorm) where images of Typhoon Trami were taken from an aircraft last September 26, 2018. Aircraft images were used to reconstruct the 3D model inside the typhoon eye because they provide closer views of the typhoon than that of geostationary satellite images, making it easier to reconstruct a 3D model. The 3D reconstruction generated covers 43 km region of the typhoon eye at 20.2 m/pixel spatial resolution. Three cross-sections of the 3D model were analyzed, and the resulting altitude distribution was compared with the cloud-top altitude estimated by mapping the brightness temperature of the Himawari Thermal Infrared Band 13 with cloud-top height as measured by NOAA sonde data. From the 3D model, the altitude distribution ranges from 5.3 km to 14.3 km which corresponds with the altitude estimated from the brightness temperature of 6.5 km to 14.3 km. However, regions of altitude difference can also be observed between the two methods. This study shows that a three-dimensional model could be a good mode of typhoon visualization as it shows a more detailed typhoon structure such as the stairstep structures that was detected at some regions within the typhoon eye. This research was supported by SATREPS, funded by Japan Science and Technology Agency (JST) / Japan International Cooperation Agency (JICA).

 

3. Jolejole, M.E., Cayetano, M.G., Magbanua, F.S. (2021). Responses of benthic macroinvertebrate communities in tropical Asian streams passing through an industrial zone. Chemistry and Ecologyhttps://doi.org/10.1080/02757540.2021.1888935more

Abstract:

Industrial zones have been key drivers of growth across Asia but are also the source of water quality deterioration in surrounding rivers and streams. This study examined the effects of industrial zone located at the San Cristobal sub-catchment of Laguna de Bay, the Philippines on the spatiotemporal variation in water quality and benthic macroinvertebrate communities. Sampling sites were established in upstream and downstream sections of two tributaries of San Cristobal River, and the main channel of Diezmo River, and were sampled in 2018 during dry (February and April) and rainy (June and October) seasons. Results showed significant spatial difference with declining water quality (low dissolved oxygen; high levels of ammonia-nitrogen, phosphate-phosphorus, and total suspended solids) at the downstream sites. Consequently, benthic macroinvertebrates responded via change in community structure and composition (decline in pollution-sensitive taxa from upstream through downstream) to water quality degradation related to industrial land use downstream. Furthermore, seasonal variation was observed in benthic macroinvertebrate communities due to the absence of spate-induced disturbance, allowing benthic macroinvertebrates to proliferate in the rainy season. Findings of this study reveal that benthic macroinvertebrates can be used as bioindicators in the evaluation of the ecological integrity of surface river and stream systems that pass through industrial zones.

 

4. Kim S., Kwon Y.S., Pyo J., Ligaray M., Min J. -H., Ahn J.M., Baek S. -S.,Cho K.H. (2021). Developing a clou d -based toolbox for sensitivity analysis of a water quality modelEnvironmental Modelling and Software, 141, Article number 105068. DOI: https://doi.org/10.1016/j.envsoft.2021.105068more

Abstract:

The complexity associated with water quality models (WQMs) has increased owing to the introduction of numerous physical and biological mechanisms in the models. Sensitivity analysis (SA) is conducted to identify influential parameters in these mechanisms. However, enormous computational power and time are required to obtain numerical solutions from thousands of model simulations. Therefore, a cloud-based toolbox is developed for performing SA of WQMs by implementing a cloud computing system using grab sampling data and hyperspectral images (HSI) of waterbodies. Cloud computing can provide high-performance computation by adjusting the scale of the computational power according to user preference. The developed toolbox with the cloud system can reduce the computation time for SA by approximately 20 times compared to that of a desktop computer.

 

5. Macalalad, R.V., Badilla, R.A., Cabrera, O.C., Bagtasa, G. (2021). Hydrological response of the pampanga river basin in the Philippines to intense tropical cyclone rainfallJournal of Hydrometeorology, 22 (4), Pages 781-794. DOI: https://doi.org/10.1175/JHM-D-20-0184.1more

Abstract:

The Philippines is frequently affected by tropical cyclones (TCs), and understanding the flood response of the Pampanga River basin (PRB) from TC-induced rain is needed in effective disaster risk management. As large uncertainties remain in TC rain forecasting, we propose a simple checklist method for flood forecasting of the PRB that depends on the general TC track, season, and accumulated rainfall. To this end, flood events were selected based on the alert, alarm, and critical river height levels established by the Philippine Atmospheric, Geophysical and Astronomical Services Administration (PAGASA). Results show that all flood events in the PRB were induced by TCs. All intense TCs that directly traversed the PRB resulted in critical-level floods. These TCs also had the shortest flood onset of 7–27 h from alert to critical level. Flooding from distant landfalling TCs, on the other hand, are dependent on season. TCs traversing north (south) of the PRB induced flooding only during the southwest (northeast) monsoon season. These TCs can raise water levels from alert to critical in 11–48 h. Remote precipitation from non-landfalling TCs can also induce critical-level flooding but with a longer onset time of 59 h. These results indicate that a simple checklist method can serve as a useful tool for flood forecasting in regions with limited data and forecasting resources.

 

6. Minjeong Kim, Ligaray, M., Yong Sung Kwon, Soobin Kim, Sangsoo Baek, Jong Cheol Pyo, Gahyun Baek, Jingyeong Shin, Jaai Kim, Changsoo Lee, Young Mo Kim, Kyung Hwa Cho. (2021). Designing a marine outfall to reduce microbial risk on a recreational beach: Field experiment and modelingJournal of Hazardous Materials, 409, 124587.  https://doi.org/10.1016/j.jhazmat.2020.124587more

Abstract:

A marine outfall can be a wastewater management system that discharges sewage and stormwater into the sea; hence, it is a source of microbial pollution on recreational beaches, including antibiotic resistant genes (ARGs), which lead to an increase in untreatable diseases. In this regard, a marine outfall must be efficiently located to mitigate these risks. This study aimed to 1) investigate the spatiotemporal variability of Escherichia coli (E. coli) and ARGs on a recreational beach and 2) design marine outfalls to reduce microbial risks. For this purpose, E. coli and ARGs with influential environmental variables were intensively monitored on Gwangalli beach, South Korea in this study. Environmental fluid dynamic code (EFDC) was used and calibrated using the monitoring data, and 12 outfall extension scenarios were explored (6 locations at 2 depths). The results revealed that repositioning the marine outfall can significantly reduce the concentrations of E. coli and ARGs on the beach by 46–99%. Offshore extended outfalls at the bottom of the sea reduced concentrations of E. coli and ARGs on the beach more effectively than onshore outfalls at the sea surface. These findings could be helpful in establishing microbial pollution management plans at recreational beaches in the future.

 

7. Park, S., Ligaray, M., Kim, Y., Chon, K., Son, M., Cho, K.H. (2021). Investigating the influence of catholyte salinity on seawater battery desalinationDesalination, 506, Article number 115018. DOI: https://doi.org/10.1016/j.desal.2021.115018more

Abstract:

The seawater battery (SWB) is a promising desalination technology that utilizes abundant sodium ions as an energy storage medium. Recently, the alternative desalination system, seawater battery desalination (SWB-D), was developed by placing an SWB next to the desalination compartment. This SWB-D system can desalt water while charging the SWB next to it. However, only a fixed catholyte solution has been investigated, although the catholytes impact the overall SWB-D performance. Therefore, we evaluated the effect of different catholytes on the desalination performance. High-saline reverse osmosis (RO) concentrate or brackish water exhibited excellent salt removal capability (>85.3% of sodium and >76.6% of chloride ions) with relatively short operation times (36.4 h for RO concentrate and 39.5 h for brackish water) upon charging, whereas the relatively low-saline river water showed the longest operation time (81.0 h), implying that river water should be excluded as a potential catholyte. The amount of desalinated water was marginally reduced due to osmosis through the anion exchange membrane; however, the amount of treated salt was >82.9% even after the reduction in water volume. These findings suggest that the catholyte with a resistance of >0.041 kΩ·cm can be ideal for the SWB-D.

 

8. Racoma, B.A., Klingaman, N., Holloway, C., Schiemann, R., Bagtasa, G. (2021). Tropical Cyclone Characteristics Associated with Extreme Precipitation in the Northern PhilippinesEGU General Assembly 2021, Issue EGU21-15486. DOI: https://doi.org/10.5194/egusphere-egu21-15486more

Abstract:

The Philippines is exposed to Tropical Cyclones (TCs) throughout the year due to its location in the western North Pacific. While these TCs provide much-needed precipitation for the country’s hydrological cycle, extreme precipitation from TCs may also cause damaging hazards such as floods and landslides. This study examines the relationship between TC extreme precipitation and TC characteristics, including movement speed, intensity, and season, for westward-moving TCs crossing Luzon, northern Philippines. We measure extreme precipitation by the Weighted Precipitation Exceedance (WPE), calculated against a 95th percentile threshold, which considers both the magnitude and spatial extent of TC-related extreme precipitation.

WPE has a significant, moderate positive relationship with TC intensity and a significant, weak negative relationship with TC movement speed. When TCs are classified by pre-landfall intensity, Typhoons (1-minute maximum sustained wind speed > 64 knots) tend to yield higher WPE than non-Typhoons (< 64 knots). On the other hand, when TCs are classified by pre-landfall speed, Slow TCs (movement speed < 11.38 knots) tend to yield higher WPE than Fast TCs (movement speed > 11.38 knots). However, while distributions of WPE are similar between the Southwest Monsoon (June-September) and Northeast Monsoon (October-December) seasons, the relationship between pre-landfall TC intensity and WPE is more pronounced during June-September. These results suggest that it is important to consider the pre-landfall cyclone movement speed, intensity, and season to anticipate extreme precipitation of incoming TCs. A decision table considering these factors is devised to aid in TC extreme precipitation forecasting.

 

9. Suwa, R., Rollon, R., Sharma, S., Yoshikai, M., Albano, G.M.G., Ono, K., Adi, N.S., Ati, R.N.A., Kusumaningtyas, M.A., Kepel, T.L., Maliao, R.J., Primavera-Tirol, Y.H., Blanco, A.C., Nadaoka, K. (2021). Mangrove biomass estimation using canopy height and wood density in the South East and East Asian regions. Estuarine, Coastal and Shelf Science, 248, Article number 106937. https://doi.org/10.1016/j.ecss.2020.106937more

Abstract:

Mangroves aboveground biomass (ABG) estimation at a large scale is a crucial to understand their role in mitigating climate change. The large-scale estimation of AGB is generally conducted with remote sensing techniques using stand characteristics such as canopy height and species composition. In the present study, we employed Lorey's mean canopy height (Hm) and basal area weighted mean wood density (ρm) to develop models for estimating AGB of mangroves in Asian regions such as Indonesia, Philippines and Japan, considering its application toward large-scale AGB estimation covering different climatic zones of subtropical zone in the Eastern Asia and tropical zone in the Southeastern Asia. The best power function model for AGB estimation with Hm as a single explanatory variable was selected based on AIC ranks. The Hm – AGB relationship model varied significantly among study sites. We successfully developed common allometric model to estimate AGB for closed-canopy mangroves in the Asian regions. The common allometric model of the Hm – AGB relationship tended to show underestimation for old growth mangroves having AGB > ca. 400 Mg ha−1. The common allometric model showed a similar trend with a previously developed model for mangroves in Bangladesh. On the other hand, the common allometric model for mangroves showed distinct difference from the model for terrestrial tropical forests, i.e. the range of Hm was narrower in mangroves than in terrestrial tropical forests, and AGB was quite higher in mangroves than in terrestrial tropical forests at a same range of Hm. The difference of AGB specific to Hm was explained by higher ρm and cumulative basal area (BA) in mangroves than that in terrestrial tropical forests. In particular, mangrove showed quite high BA in a comparison with terrestrial tropical forests. This study confirmed that developing mangrove specific biomass model is important since mangroves showed its unique characteristics through comparisons with terrestrial tropical forests, and limitations of the use of Hm as a single variable. It should be noted that old growth mangrove AGB is underestimated with the developed common allometric models. For old growth mangroves, carbon stock should be fairly evaluated with more accurate models otherwise their contribution to blue carbon would be overlooked, which could lead insufficient efforts for conservation of old growth mangroves. Further accurate models for estimating mangrove AGB at large scale are urgently required.

 

10. Takahashi, Y., Sato, M., Kubota, H., Ishida, T., Castro, E., Algodon, M., Perez, G., and Marciano, J. (2021). Coordinated observation system for extreme weathers consisting of AWS network with lightning sensor and micro-satellitesEGU General Assembly 2021, online, 19–30 Apr 2021, EGU21-14649, https://doi.org/10.5194/egusphere-egu21-14649more

Abstract:

In order to predict the intensity and location of extreme weathers, such as torrential rainfall by individual thunderstorm or typhoon, we are developing the new methodology of weather monitoring using a ground AWS network with lightning sensors and micro-satellites weighting about 50kg, which will realize quasi-real-time thunderstorm monitoring with broad coverage. Based on the AWS network data, we plan to operate micro-satellites in nearly real-time, manipulating the attitude of satellite for capturing the most dangerous or important cloud images for 3D reconstruction. We have developed and launched several micro-satellites and been improving the target pointing operation for this decade. We succeeded in obtaining the images of the typhoon center at a resolution of 60-100 m for Typhoon Trami in 2018 and Typhoon Maysak in 2020. Using 4 or a few 10s images captured from different angles by one micro-satellite when it passed over the typhoon area, 3D models of typhoon eye were reconstructed, which have a ground resolution of ~100 m. Due to the unusual temperature profile around typhoon eye, it’s very difficult to estimate the heigh distribution of cloud top only with a thermal infrared image at a resolution of 2 km taken by geostationary meteorological satellite. This is one of the biggest limitations in estimating the precise intensity of typhoons, namely, the center pressure or the maximum wind velocity. The on-demand flexible operation of micro-satellite will achieve the high accuracy estimation of typhoon intensity as well as the speed estimation of individual thunderstorm development, which can be applied to disaster management. This research was conducted by a mixed team of Japan and the Philippines, supported by Science and Technology Research Partnership for Sustainable Development (SATREPS), which is funded by Japan Science and Technology Agency (JST) / Japan International Cooperation Agency (JICA).

 

11. Tolentino, J.T., Bagtasa, G. (2021). Calibration of Kain–Fritsch cumulus scheme in Weather Research and Forecasting (WRF) model over Western Luzon, PhilippinesMeteorology and Atmospheric Physics. (Article in Press)more

Abstract:

Calibration of the cumulus parameterization scheme for localized areas is one method that can improve numerical weather prediction rainfall forecast accuracy. Calibration for model development, however, is a time-consuming procedure that requires numerous simulations. The utilization of an efficient method for calibrating complex dynamical models can help mitigate the heavy computational costs involved. In this study, five parameters in the Weather Research and Forecasting (WRF) Kain–Fritsch cumulus scheme were calibrated based on rainfall verification in the northwest and the southeast regions of the Philippines. Two optimization methods—Multiple Very Fast Simulated Annealing (MVFSA) and Adaptive Surrogate Modeling-Based Optimization (ASMO)—were used to find the best parameter set values. Both methods generated a higher coefficient of downdraft (Pd), lower entrainment (Pe), and longer convective available potential energy (CAPE) consumption time (Pc), which were found to result in better skill scores than the default WRF. Precipitation amount in both calibrated models decreased leading to an overall less wet bias. Precipitation skill score in the northwestern Philippines significantly improved by 35%, while that of the southeastern Philippines only increased by 3%. In addition, model calibration had no significant effect on the simulated temperature and wind speed. The results show that calibration of the cumulus parameterization scheme yields better results for convective rainfall rather than rain from stratiform clouds, which is expected since the cumulus parameterization scheme represents the effects of sub-grid-scale convective processes.

 

12. Yoshikai, M., Nakamura, T., Suwa, R., Argamosa, R., Okamoto, T., Rollon, R., Basina, R., Primavera-Tirol, Y.H., Blanco, A.C., Adi, N.S., Nadaoka, K. (2021). Scaling relations and substrate conditions controlling the complexity of Rhizophora prop root systemEstuarine, Coastal and Shelf Science, 248, Article number 107014. DOI: https://doi.org/10.1016/j.ecss.2020.107014more

Abstract:

The complex structures of the prop root system of the mangrove genus Rhizophora attenuate storm surges and tsunamis and promote sedimentation. While quantification of the mangrove's drag force is essential for assessing the mangroves' ability to reduce the risk of disaster and vulnerability to rising sea-level, the projected area of prop root system having multiple orders of prop roots (e.g., first-, second-, and third-order prop roots, where the root order indicates the level of branching from the stem) are still unexplored. To contribute to the quantitative evaluation of the mangrove's drag force, we investigated the vertical profile of whole-tree prop root projected area and the number of prop roots of 156 trees sampled from Indonesia, the Philippines, and Japan. Our results showed that prop roots above the first-order contribute up to 80% of the whole-tree prop root projected area, highlighting the importance of the presence of second-, third-, and even higher-order prop roots on the drag force exerted by mangroves. Based on field data, an empirical model for the prop root system, described by a scaling factor (S), and maximum and minimum root heights (HRmax, HRmin), was developed by assuming that the size distribution of prop roots follows a constant scaling factor S. S and HRmax showed significant correlations with stem diameter at breast height suggesting the scaling relations in the prop root system. The model, which employs the site- and species-specific regression models for S and HRmax, reproduced the vertical distribution of the number of prop roots – a good predictor of the prop root projected area – with reasonable accuracy. However, the site- and species-specific scaling relations are highly variable depending on the environment, suggesting morphological plasticity in the prop root system. Rhizophora trees that grow on a shallow sediment layer (around 0.1 m thickness) tend to produce more prop roots compared with those on a thicker sediment layer suggesting a morphological response of the prop root system to increase below-ground root biomass where below-ground root development is physically constrained. Multivariate analysis indicated that hard substrate also possibly contributes to higher complexity of prop root system. However, prediction of the site- and species-specific scaling relations from these environmental variables still needs to be improved. Further research is needed to explain the mechanisms of morphological response of prop root systems to environmental gradients and to establish a generalized model for predicting the prop root system in various environments.

 

13. Yun, D., Abbas, A., Jeon, J., Ligaray, M., Baek, S.S., Cho, K. H. (2021). Developing a deep learning model for the simulation of micro-pollutants in a watershedJournal of Cleaner Production, Volume 300, 1 June 2021, 126858.more

Abstract:

In recent years, as agricultural activities and types of crops have become diverse, the occurrence of micro-pollutants has been reported more frequently in rural areas. These pollutants have detrimental effects on human health and ecological systems; thus, it is important to manage and monitor their presence in the environment. The modeling approach could be an effective way to understand and manage these pollutants. This study predicts the concentrations of micro-pollutants (MPs) using deep learning (DL) models, and the results are then compared with simulation results obtained from the soil water assessment tool (SWAT) model. The SWAT model showed an unacceptable performance owing to the resulting negative Nash–Sutcliffe efficiency (NSE) values for the simulations. This may be caused by the limitations of SWAT, which pertains to adopting simplified equations to simulate micro-pollutants. In addition, the ambiguous plan of pesticide application increased the model uncertainty, thereby deteriorating the model result. Here, we developed two different DL models: long short-term memory (LSTM) and convolutional neural network (CNN). LSTM exhibited the highest model performance, with NSE values of 0.99 and 0.75 for the training and validation steps, respectively. In the multi-target MP model, the error decreased as the number of simulated pollutants increased. The simulation of the four pollutants had the highest error, while the six-target simulation had the lowest error. In conclusion, this study demonstrated that the LSTM model has the potential to improve the prediction of MPs in aquatic systems.

 

IM

1. Avila, J., Cabarrubias, B. (2021). Homogenization of a quasilinear elliptic problem in domains with small holesApplicable Analysis. DOI: 10.1080/00036811.2021.1884226.more

Abstract:

This work aims to provide the asymptotic behavior of some class of quasilinear problems posed in a domain with small holes in RNRN for N>2, as ϵ0ϵ→0. A nonlinear Robin boundary condition is prescribed on some of the holes, while a Dirichlet boundary one is imposed on the other holes as well as on the outer boundary. We apply the Periodic Unfolding Method for the homogenization of this problem.

 

2. Caalim, J., & John De La Cruz, R. (2021). 2n-by-2n symplectic completions of matrices of order 2n-1. Asian-European Journal of Mathematics, 14 (4). doi:10.1142/S1793557121500650.more

Abstract:

Let be a field. Set J:= [0-InIn0. A matrix X  F2n×2n is symplectic if XJ-1XTJ = I. We say that a matrix P  F2n-1×2n-1 has a symplectic completion of order 2n if there exist x,y  F2n-1×1 and a scalar α  F such that [PyTxα] is symplectic. If P is nonsingular, we give necessary and sufficient conditions such that P has a symplectic completion of order 2n. We give an implicit characterization of all matrices of order 3 which have symplectic completions of order 4. 

 

3. Darbas, Marion, Heleine, Jérémy, Mendoza, Renier, Velasco, Arrianne Crystal. (2021). Sensitivity analysis of the complete electrode model for electrical impedance tomography[J]. AIMS Mathematics 6(7): 7333-7366. doi: 10.3934/math.2021431more

Abstract:

Electrical impedance tomography (EIT) is an imaging technique that reconstructs the conductivity distribution in the interior of an object using electrical measurements from the electrodes that are attached around the boundary. The Complete Electrode Model (CEM) accurately incorporates the electrode size, shape, and effective contact impedance into the forward problem for EIT. In this work, the effect of the conductivity distribution and the electrode contact impedance on the solution of the forward problem is addressed. In particular, the sensitivity of the electric potential with respect to a small-amplitude perturbation in the conductivity, and with respect to some defective electrodes is studied. The Gâteaux derivative is introduced as a tool for the sensitivity analysis and the Gâteaux differentiability of the electric potential with respect to the conductivity and to the contact impedance of the electrodes is proved. The derivative is then expressed as the unique solution to a variational problem and the discretization is performed with Finite Elements of type P1. Numerical simulations for different 2D and 3D configurations are presented. This study illustrates the impact of the presence of perturbations in the parameters of CEM on EIT measurements. Finally, the 2D inverse conductivity problem for EIT is numerically solved for some configurations and the results confirm the conclusions of the numerical sensitivity analysis.

 

4. de la Cruz, R. J., & Saltenberger, P. (2021). Simple forms for perplectic and symplectic normal matrices. Linear Algebra and its Applications, 620, Pages 201-227. doi:10.1016/j.laa.2021.03.003.more

Abstract:

Let B=J2n or B=Rn for the matrices given by J2n=[In−In]M2n(C)orRn=[11]Mn(C). A matrix A is called B-normal if AA=AA holds for A and its adjoint matrix A:=B−1AHB. In addition, a matrix Q is called B-unitary, if QHBQ=B. We develop sparse simple forms for nondefective (i.e. diagonalizable) J2n/Rn-normal matrices under J2n/Rn-unitary similarity transformations. For both cases we show that these forms exist for an open and dense subset of J2n/Rn-normal matrices. This implies that these forms can be seen as topologically ‘generic’ since they exist for all J2n/Rn-normal matrices except a nowhere dense subset. 

 

5. Dimabayao, J. T. (2021). Jeśmanowicz’ conjecture for polynomials. Periodica Mathematica Hungarica, 82 (1), Pages 29-38. doi:10.1007/s10998-020-00339-w. more

Abstract:

Let (a, b, c) be pairwise relatively prime integers such that a2+ b2= c2. In 1956, Jeśmanowicz conjectured that the only solution of ax+ by= cz in positive integers is (x, y, z) = (2 , 2 , 2). In this note we prove a polynomial analogue of this conjecture. 

 

6. Fulgencio, R. G., & Guibé, O. (2021). Quasilinear elliptic problems in a two-component domain with l 1 data. doi:10.1007/978-3-030-62030-1_4. more

Abstract:

In this chapter, we consider the following class of quasilinear equations: {−div(B(x,u1)u1)=finΩ1,−div(B(x,u2)u2)=finΩ2u1=0on∂Ω,(B(x,u1)u1)ν1=(B(x,u2)u2)ν1onΓ,(B(x,u1)u1)ν1=−h(x)(u1−u2)onΓ. $$\displaystyle \begin {cases} -\operatorname {div} (B(x,u_1)\nabla u_1) = f \quad &amp;amp;\mbox{in }\varOmega _1,\\ -\operatorname {div} (B(x,u_2)\nabla u_2) = f \quad &amp;amp;\mbox{in }\varOmega _2\\ u_1=0\quad &amp;amp;\mbox{on }\partial \varOmega,\\ (B(x,u_1)\nabla u_1)\nu _1 = (B(x,u_2)\nabla u_2)\nu _1 \quad &amp;amp;\mbox{on }\varGamma,\\ (B(x,u_1)\nabla u_1)\nu _1 = -h(x)(u_1-u_2) \quad &amp;amp;\mbox{on }\varGamma. \end {cases} $$ The domain Ω is composed of two components, Ω1 and Ω2, with Γ denoting the interface between them. The given function f belongs to L1(Ω). We first present a definition of a renormalized solution for this class of equations. The main result of this chapter is the existence of such a solution. 

 

7. Kim, J. -., Kim, Y. -., Galvez, L. E., & Kim, M. J. (2021). A modified dual-ouroboros public-key encryption using gabidulin codes. Applicable Algebra in Engineering, Communications and Computing, 32 (2), Pages 147-156. doi:10.1007/s00200-019-00406-x. more

Abstract:

Dual-Ouroboros is a code-based public-key encryption scheme which is a modification of McNie and a dual version of Ouroboros-R. In this paper, we present a modification of Dual-Ouroboros, using a class of rank metric codes called Gabidulin codes. By using Gabidulin codes, we eliminate the probability of decoding failure, which is one of the limitations of Dual-Ouroboros since it uses LRPC codes with probabilistic decoding. We also prove that our proposed cryptosystem is IND-CPA secure. Suggested parameters are also given which provides lower key sizes compared to other known code-based cryptosystems with zero decryption failure probability. 

 

8. Magpantay, D. M., Hernandez, B. S., de los Reyes, A. A. V., Mendoza, E. R., & Nocon, E. G. (2021). A computational approach to multistationarity in poly-PL kinetic systems. Match, 85 (3), Pages 605-634. more

Abstract:

One important question that interests those who work in chemical reaction network theory (CRNT) is this: Does the system obtained from a reaction network admit a positive equilibrium and if it does, can there be more than one within a stoichiometric class? The higher deficiency algorithm (HDA) of Ji and Feinberg provided a method of determining the multistationarity capacity of a CRN with mass action kinetics (MAK). An extension of this, called Multistationarity Algorithm (MSA), recently came into the scene tackling CRNs with power law kinetics (PLK), a kinetic system which is more general (having MAK systems as a special case). For this paper, we provide a computational approach to study the multistationarity feature of reaction networks endowed with kinetics which are non-negative linear combinations of power law functions called poly-PL kinetics (PYK). The idea is to use MSA and combine it with a transformation called STAR-MSC (i.e., Sinvariant Termwise Addition of Reactions via Maximal Stoichiometric Coefficients) producing PLKs that are dynamically equivalent to PYKs. This leads us to being able to determinine the multistationarity capacity of a much larger class of kinetic systems. We show that if the transformed dynamically equivalent PLK system is multistationary for a stoichiometric class for a set of particular rate constants, then so is its original corresponding PYK system. Moreover, the monostationarity property of the transformed PLK system also implies the monostationarity property of the original PYK system. 

 

9. Pino R, Mendoza R, Sambayan R. (2021). Optical character recognition system for Baybayin scripts using support vector machine.  PeerJ Computer Science, 7: e360. https://doi.org/10.7717/peerj-cs.360more

Abstract:

In 2018, the Philippine Congress signed House Bill 1022 declaring the Baybayin script as the Philippines’ national writing system. In this regard, it is highly probable that the Baybayin and Latin scripts would appear in a single document. In this work, we propose a system that discriminates the characters of both scripts. The proposed system considers the normalization of an individual character to identify if it belongs to Baybayin or Latin script and further classify them as to what unit they represent. This gives us four classification problems, namely: (1) Baybayin and Latin script recognition, (2) Baybayin character classification, (3) Latin character classification, and (4) Baybayin diacritical marks classification. To the best of our knowledge, this is the first study that makes use of Support Vector Machine (SVM) for Baybayin script recognition. This work also provides a new dataset for Baybayin, its diacritics, and Latin characters. Classification problems (1) and (4) use binary SVM while (2) and (3) apply the multiclass SVM classification. On average, our numerical experiments yield satisfactory results: (1) has 98.5% accuracy, 98.5% precision, 98.49% recall, and 98.5% F1 Score; (2) has 96.51% accuracy, 95.62% precision, 95.61% recall, and 95.62% F1 Score; (3) has 95.8% accuracy, 95.85% precision, 95.8% recall, and 95.83% F1 Score; and (4) has 100% accuracy, 100% precision, 100% recall, and 100% F1 Score.

 

10. Pino R, Mendoza R, Sambayan R. (2021). A Baybayin word recognition systemPeerJ Computer Science, 7: e596. https://doi.org/10.7717/peerj-cs.596more

Abstract:

Baybayin is a pre-Hispanic Philippine writing system used in Luzon island. With the effort in reintroducing the script, in 2018, the Committee on Basic Education and Culture of the Philippine Congress approved House Bill 1022 or the ”National Writing System Act,” which declares the Baybayin script as the Philippines’ national writing system. Since then, Baybayin OCR has become a field of research interest. Numerous works have proposed different techniques in recognizing Baybayin scripts. However, all those studies anchored on the classification and recognition at the character level. In this work, we propose an algorithm that provides the Latin transliteration of a Baybayin word in an image. The proposed system relies on a Baybayin character classifier generated using the Support Vector Machine (SVM). The method involves isolation of each Baybayin character, then classifying each character according to its equivalent syllable in Latin script, and finally concatenate each result to form the transliterated word. The system was tested using a novel dataset of Baybayin word images and achieved a competitive 97.9% recognition accuracy. Based on our review of the literature, this is the first work that recognizes Baybayin scripts at the word level. The proposed system can be used in automated transliterations of Baybayin texts transcribed in old books, tattoos, signage, graphic designs, and documents, among others.

 

11. Velasco, Arrianne Crystal, Darbas, Marion, Mendoza, Renier. (2021). Numerical Resolution of the Electrical Impedance Tomography Inverse Problem with Fixed InclusionsInternational Journal of Mathematics and Computer Science, 16 (3), Pages 1063–1076.more

Abstract:

Electrical Impedance Tomography or EIT is an imaging technique that reconstructs the conductivity distribution in the interior of an object using electric currents. In this paper, we study the continuum model for EIT in a domain where the geometric inclusions are fixed and only the conductivity values inside these inclusions are unknown. We show analytically and numerically how the BroydenFletcher-Goldfarb-Shanno (BFGS) algorithm, a quasi-Newton method, can be effective in solving this inverse conductivity problem for EIT.

 

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1. Gonzales, K. C., Prieto, E. A., Catindig, G. A., De, A., Reyes, L., Faustino, M. A., Tumanguil - Quitoras, M. A., Husay, H. A., Vasquez, J.D., Somintac, A., Estacio, E., & Salvador, A. (2021). Terahertz emission increase in GaAs films exhibiting structural defects grown onSi (100) substrates using a two-layered LTG-GaAs buffer system. Journal of Materials Science: Materials in Electronics, 32 (!0), Pages 13825 – 13836. DOI: https://doi.org/10.1007/s10854-021-05958-8more

Abstract:

Terahertz (THz) emission increase is observed for GaAs thin films that exhibit structural defects. The GaAs epilayers are grown by molecular beam epitaxy on exactly oriented Si (100) substrates at three different temperatures (Ts = 320 °C, 520 °C and 630 °C). The growth method involves the deposition of two low-temperature-grown (LTG)-GaAs buffers with subsequent in-situ thermal annealing at Ts = 600 °C. Reflection high energy electron diffraction confirms the layer-by-layer growth mode of the GaAs on Si. X-ray diffraction shows the improvement in crystallinity as growth temperature is increased. The THz time-domain spectroscopy is performed in reflection and transmission excitation geometries. At Ts = 320 °C, the low crystallinity of GaAs on Si makes it an inferior THz emitter in reflection geometry, over a GaAs grown at the same temperature on a semi-insulating GaAs substrate. However, in transmission geometry, the GaAs on Si exhibits less absorption losses. At higher Ts, the GaAs on Si thin films emerge as promising THz emitters despite the presence of antiphase boundaries and threading dislocations as identified from scanning electron microscopy and Raman spectroscopy. An intense THz emission in reflection and transmission excitation geometries is observed for the GaAs on Si grown at Ts = 520 °C, suggesting the existence of an optimal growth temperature for GaAs on Si at which the THz emission is most efficient in both excitation geometries. The results are significant in the growth design and fabrication of GaAs on Si material system intended for future THz photoconductive antenna emitter devices.

 

2. Rosete, M.M., Zosa, M.H., Sarmago, R.V. (2021). Improved Fabrication of Electrophoretically Deposited Bi2Sr2CaCu2O8 Films via Supporting Electrolyte Optimization in EthanolJournal of Superconductivity and Novel Magnetism, 34 (1), Pages 55-61. https://doi.org/10.1007/s10948-020-05668-ymore

Abstract:

This paper describes the effect of the addition of supporting electrolytes sodium chloride (NaCl), potassium chloride (KCl), and lithium chloride (LiCl) on the stability of Bi2Sr2CaCu2O8 (Bi-2212) suspension for improved electrophoretic deposition (EPD) of Bi-2212 films. The optimal concentrations are found to be 7.15, 5.21, and 8.09 wt% for NaCl, KCl, and LiCl, respectively. They exhibit characteristic high zeta potential, small particle size, and low settling velocity entailing that well-stabilized Bi-2212 suspensions are produced. The resulting films possess a relatively smooth surface, high transition temperature (Tc), and high c-axis orientation. Further analysis shows that LiCl is the most suitable supporting electrolyte for the Bi-2212 suspension. The mechanism of action of this supporting electrolyte is influenced by the Hofmeister effects, which yields an electrostatic stabilization mechanism. The synthesized film using the optimal LiCl concentration demonstrates the highest Tc (87.25 K) and is c-axis oriented and well-textured.

 

  

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1. Amedo-Repollo, C.A., Flores-Vidal, X., Chavanne, C., Villanoy, C.L., Flament, P. (2021). Barotropic and baroclinic tides in Panay Strait, PhilippinesRegional Studies in Marine Science, 41.more

Abstract:

The Panay Strait constitutes a bathymetrically complex system with intense tidal currents. The four major tidal constituents in the total energy spectra inferred from sea level and current profiles are K1,O1,M2, andS2. Spatially, O1andM2dominate overK1andS2, respectively. The diurnal tide accounts for highest amplitude variability over the shallow shelf while semi-diurnal tides over the deeper channel of the strait. Rotary spectra of surface currents shows inertial frequency peaks and exhibit an unusually broad peak in both the clockwise (CW) and counterclockwise (CCW) rotating components, indicating frequency shift by the vorticity of sub-inertial currents prevalent in the region. Vertically, variance of the horizontal velocity explained by the major tidal constituents peaks in two distinct depth bands; the upper layer centered at 110 m (11% variance) dominated by semi-diurnal tide (M2) and the lower layer at 470 m (26% variance) dominated by diurnal tides (O1). Semi-diurnal tidal current ellipses (M2andS2) exhibit a dominance of CW motions at near-surface depth (110 m), indicative of downward energy propagation and implying a surface energy source. These features from Acoustic Doppler Current Profiler (ADCP) deployed close to the sill is consistent with the dominant semi-diurnal tide (M2) over the channel of the strait from the High Frequency Doppler Radar (HFDR). Comparison of incoherent to coherent tidal energy showsK1dominated the incoherent tidal band. Spatially, incoherent energy is dominant over the channel particularly near the sill and the constricted part of the strait. The incoherent portion of the tide is presumably attributable to the surface expression of the internal tide which seems to be generated near the sill and then topographically steered westover the edge of the shallow shelf where incoherent energy is dominant. 

 

2. Ayalon, I., Rosenberg, Y., Benichou, J. I. C., Campos, C. L. D., Sayco, S. L. G., Nada, M. A. L., Baquiran, J. I. P., Ligson, C. A., Avisar, D., Conaco, C., Kuechly, H. U., Kyba, C. C. M., Cabaitan, P. C., & Levy, O. (2021). Coral gametogenesis collapse under artificial light pollutionCurrent Biology, 31 (2), Pages 413-419.more

Abstract:

Artificial light at night (ALAN) can have negative impacts on the health of humans and ecosystems. 1234 Marine organisms, including coral reefs in particular, rely on the natural light cycles of sunlight and moonlight to regulate various physiological, biological, and behavioral processes.5678 Here, we demonstrate that light pollution caused delayed gametogenesis and unsynchronized gamete release in two coral species, Acropora millepora and Acropora digitifera, from the Indo-Pacific Ocean. Given the urbanization along major coasts, light pollution could thus further threaten coral communities’ populations, which are already under severe degradation. A worldwide-modeled light pollution impact assessment is provided, which can help incorporate an important variable in coral reef conservation planning.

 

3. Baird, A. H., Guest, J. R., Edwards, A. J., Bauman, A. G., Bouwmeester, J., Mera, H., Abrego, D., Alvarez-Noriega, M., Babcock, R. C., Barbosa, M. B.,Bonito, V. Burt, J., Cabaitan, P. C., Chang, C.-F., Chavanich, S., Chen, C. A., Chen, C.-J., Chen, W.-J., Chung, F.-C., Connolly, S. R., Cumbo, V. R., Dornelas, M., Doropoulos, C., Eyal, G., Eyal-Shaham, L., Fadli, N., Figueiredo, J. Flot, J.-F., Gan, S.-Z. Gomez, E. J.,  Graham, E. M., Grinblat, M., Gutiérrez-Isaza, N., Harii, S., Harrison, P. L., Hatta, M., Ho, N. A. J., Hoarau, G. Hoogenboom, M., Howells, E. J., Iguchi, A., Isomura, N., Jamodiong, E. A., Jandang, S., Keyse, J., Kitanobo, S., Kongjandtre, N., Kuo, C.-Y., Ligson, A., Lin, C.-H., Low, J., Loya, Y., Maboloc, E. A., Madin, J. S., Mezaki, J., Min, C., Morita, M., Moya, a., Neo, S.-H., Nitschke, M. R., Nojima, S., Nozawa, Y., Piromvaragorn, S., Plathong, S., Puill-Stephan, S., Quigley, K., Ramirez-Portilla, C., Ricardo, G., Sakai, K., Sampayo, E., Shlesinger, T., Sikim, L., Simpson, C., Sims, C. A., Sinniger, F., Spiji, D. A., Tabalanza, T., Tan, C.-H., Terraneo, T. I., Torda, G., True, J., Tun, K., Vicentuan, K., Viyakarn, V., Waheed, Z., Ward, S., Willis, B., Woods, R. M., Woolsey, E. S., Yamamoto, H. H. & Yusuf, S.(2021). An indo-pacific coral spawning databaseScientific Data, 8 (1). more

Abstract:

The discovery of multi-species synchronous spawning of scleractinian corals on the Great Barrier Reef in the 1980s stimulated an extraordinary effort to document spawning times in other parts of the globe. Unfortunately, most of these data remain unpublished which limits our understanding of regional and global reproductive patterns. The Coral Spawning Database (CSD) collates much of these disparate data into a single place. The CSD includes 6178 observations (3085 of which were unpublished) of the time or day of spawning for over 300 scleractinian species in 61 genera from 101 sites in the Indo-Pacific. The goal of the CSD is to provide open access to coral spawning data to accelerate our understanding of coral reproductive biology and to provide a baseline against which to evaluate any future changes in reproductive phenology.

 

4. Bautista VII, A. T., Limlingan, S. J. M., Bauyon, M. M. T., Jagonoy, A. M., Racho, J. M. D., Valdez, J. D. G., Monsada, A. M., Salon, B. J. T., Tabuso, A. J. E., Valerio, J. K. C., Dumalagan, E. E., & Siringan, F. P. (2021). 3D X-ray computed tomography gray value and age model datasets of coral cores Baler 2 and 3 (Philippines)Data in Brief, 34.more

Abstract:

The datasets here contain the 3D X-ray computed tomography (3DXCT) gray values and age models of coral cores Baler 2 and 3, taken from Baler, Aurora, Philippines. 3DXCT was used to analyze 5 mm-thick slabs of the coral cores. From the resulting 3DXCT images, gray values were determined per pixel from top to bottom of the slabs. The gray value profiles across the length of the slabs were then matched with records of sea surface temperature (SST) of the Baler site to construct the age model of the coral cores. Daily SST records from October 2018 to February 1982 were from the Optimum Interpolation Sea Surface Temperature or OISST [1,2], while monthly SST records from February 1982 to May 1945 were from the Extended Reconstructed Sea Surface Temperature or ERSST [3]. The gray value datasets of coral cores Baler 2 and 3 present historical records of the corals' response to changing environments through the years and may be used in studies related to such. An example of this can be seen in the relationship between coral gray values and SST. Furthermore, the age model datasets of Baler 2 and 3 serve as the basis for interpretation for all current and future studies on these coral cores. These datasets were originally produced for the research work titled “A historical record of the impact of nuclear activities based on 129I in coral cores in Baler, Philippines: an update”.

 

5. Bautista, A. T., Limlingan, S. J. M., Bauyon, M. M. T., Jagonoy, A. M., Racho, J. M. D., Valdez, J. D. G., Salon, B.J.T., Tabuso, A.J.E., Valerio, J.H.C., Dumalagan, E.E. Jr., Kusuno, H., Siringan, F.P., & Matsuzaki, H. (2021). A historical record of the impact of nuclear activities based on 129I in coral cores in Baler, Philippines: An updateJournal of Environmental Radioactivity, 227.more

Abstract:

In a previous study in 2016, we presented how 129I in coral cores from the east (Baler) and west (Parola) sides of the Philippines recorded the impacts of human nuclear activities, including nuclear weapons testing, nuclear fuel reprocessing, and nuclear accidents. However, the 2016 Baler dataset only had a two-year time resolution and a crude age model based on growth band counting. Here we present a new 2020 Baler 129I/127I atomic ratio dataset that features at least annual time resolution and a more accurate age model constructed using 3D X-ray Computed Tomography. Results show that the bomb peaks in Baler primarily came from the Pacific Proving Grounds or PPG with a time lag of about 1.8 years (or more specifically, between 1.3 and 2.4 years). Moreover, a review of the Parola dataset shows that PPG signals may have been transported to Parola in the West Philippine Sea via two pathways: the northward and southward bifurcations of the North Equatorial Current, reaching Parola about 4.5 and 8.5 years after detonation, respectively. Moreover, a prominent peak in the year 2014.7 in Baler possibly came from the 2011 Fukushima Accident, transported by the Kuroshio Recirculation Gyre and the North Pacific Mode Waters with a 3.5-year time lag. This study contributes to the understanding of the impact and transport of human-made radionuclides to the Philippines and the relevant oceanographic processes in the Western Equatorial Pacific region.

 

6. Deauna, J. D. L., Yatco, K. M. B., Villanoy, C. L., & Juinio-Meñez, M. A. (2021). Identification of priority sites to support management of commercially important sea cucumber species by applying infomap and habitat filters to larval dispersal dataFrontiers in Marine Science, 7. more

Abstract:

Stocks of commercially valuable sea cucumber species have declined in most tropical countries, which supply majority of the global demand. This work aimed to locate priority sites for the management of Holothuria scabra and Stichopus horrens in the western central Philippines. A passive larval dispersal model was run under four monsoonal regimes (Northeast monsoon, dry-transition, Southwest monsoon, and early Northeast monsoon), and the results subjected to the Infomap network detection algorithm. Three clusters of closely related geographical nodes were identified [southeastern Palawan (Group I), western Panay and eastern Mindoro (Group II), and northern and western Palawan with western Mindoro (Group III)]. Remotely sensed habitat data were used to parameterize the degree of connectivity observed among sites (H. scabra spawning and settlement requires the presence of seagrass and mangrove, while S. horrens requires corals and seagrass). Local retention, self-recruitment, settlement success and sink diversity were then calculated for each node with suitable habitat. The locations were ranked according to each metric and those with higher larval export rates, a higher diversity of larval sources and a high degree of successful larval contribution to other sites were deemed crucial for the management of wild populations. Sixteen high-priority sites were identified, distributed mainly along northern Palawan and western Panay. Six sites were common for both species at different seasons, and no single location fulfilled all stated criteria across the four seasons and both sea cucumber species considered. The priority sites for management could serve as broodstock selection and juvenile restocking areas for aquaculture production clusters, which when properly implemented, could lead to an increase in sea cucumber production and contribute to natural populations. On a broader scale, the designation of closely related clusters and incorporation of habitat requirements to dispersal data provided critical input for the delineation of ecologically meaningful management units for sea cucumbers within the region.

 

7. dela Peña, L.B.R.O., Tejada, A.J.P., Quijano, J.B.Q., Alonzo, K.H., Gernanto, E.G., Caril, A., Dela Cruz, M.A.M.D., & Onda, D.F.L. (2021). Diversity of marine eukaryotic picophytoplankton communities with emphasis on mamiellophyceae in Northwestern PhilippinesPhilippine Journal of Science, 150 (1), Pages 27-42.more

Abstract:

Eukaryotic picophytoplankton (EPP) play vital roles in primary productivity and biogeochemical cycling in the marine environment. In this study, we explored the diversity of EPP communities in two different embayments and the shifts in their community structuring during monsoonal reversal in the northwestern Philippines. Water samples were collected weekly from late northeast (NE) monsoon to intermonsoon (IM) or summer periods (February-April 2019) in Bolinao, Pangasinan, and once in January in Masinloc, Zambales. EPP community profiling was done through targeted sequencing of the V4 region of the 18S rRNA gene. Grouping of samples based on physicochemical parameters was consistent with that of community beta diversity, suggesting strong clustering between late NE and IM periods. This exhibits short-term community shifts of EPPs possibly associated with the monsoonal transition. Specifically, overall EPP alpha diversity increased towards summer coupled with increased temperature and lower nutrient concentrations. NE monsoon samples from Bolinao and Masinloc were dominated by Chlorophyta and Stramenopiles, while Prymnesiophyta, Rhizaria, and Picozoa dominated the IM period samples in Bolinao. Specifically, the prasinophytes (Chlorophyta) Ostreococcus and Nannochloris distinguished the late NE communities of Masinloc and Bolinao, respectively. Phylogenetic analysis of dominant photosynthetic EPP further revealed the presence of Clades B5 and A1 of Micromonas, as well as Clades B and E of Ostreococcus. Tree topology of Ostreococcus diversity suggests the presence of a clade distinct from other established clades, possibly indicating novel diversity in the West Philippine Sea. This is the first report of these major picophytoplankton in Philippine waters, suggesting their significance and potential "hidden" diversity, which warrants further studies.

 

8. Gallentes, A. T., Manglicmot, M. T., Gong, S. -., Hu, H. -., Shen, C. -., & Siringan, F. P. (2021). Coral boulder transport and gravel bar formation by storms in Lumaniag Village, Batangas, northwestern PhilippinesGeomorphology, 376.more

Abstract:

The contribution of tropical storms to a carbonate gravel bar formation is presented for Lumaniag village, northwestern Philippines, based on field measurements, high-precision U_Th dating of Porites sp. coral boulders (longest axis > 1 m), historical records of tsunamigenic earthquakes and typhoons, and anecdotal accounts. Results of U_Th dating suggest that the events which transported the sampled fully exposed boulders found on the gravel bar occurred during the 1960s to early 1970s; the underlying rubble are presumed to have been deposited by older inundation events. The U_Th ages are consistent with anecdotal accounts and records of typhoon tracks and damage reports from typhoons Dading (international name Winnie; 1964), Welming (international name: Emma; 1967), and several other strong typhoons in early 1970s. Hydrodynamic calculations estimate a minimum flow velocity of 3.2 m/s to initiate translocation of the largest coral boulders in the area. Potential shift in storm frequency and intensity over the next few decades suggests that the gravel bar will further accumulate carbonate sediments. With the mangroves contributing to its stability, the storm-deposited island-like feature contributes to the dissipation of approaching storm waves and provides natural protection for the nearby coastal community. The ridge will likely provide an effective buffer for extreme waves in the term unless destroyed by anthropogenic activities or an oversized extreme event.

 

9. Gorospe, J. R., Juinio-Meñez, M. A., & Southgate, P. C. (2021). Is culture performance of juvenile sandfish, Holothuria scabra, in ocean-based nursery systems influenced by proximity to milkfish (Chanos chanos) farms and hapa net mesh sizeAquaculture, 531.more

Abstract:

The impacts of proximity to milkfish farms (i.e. ‘close’, ‘intermediate’ and ‘distant’) and different hapa net mesh sizes (i.e. 400 μm and 1 mm) on periphyton characteristics and growth performance of sandfish, Holothuria scabra, juveniles (4.6 ± 0.1 mm), were evaluated in a 30-day field experiment in the Guiguiwanen Channel at Bolinao, North-western Philippines. Growth and survival of sandfish juveniles were determined twice, and chlorophyll a and ash-free dry weight (AFDW) of periphyton were monitored every 5 days during the study. Opisthobranchs that recruited inside the hapa nets were identified and counted during monitoring. Survival of sandfish juveniles differed significantly between sites but was not influenced by mesh size by day 15. Survival was significantly higher at the intermediate site by day 15. Juvenile survival was significantly higher in 400 μm mesh hapa nets across all sites by day 30. Result showed that mean length and absolute growth rates (AGR) of sandfish juveniles were significantly influenced by mesh size but not by site at day 15. Juveniles reared in the 1 mm mesh hapa nets were larger and grew faster by day 15. However, by day 30, mean length and AGR of sandfish juveniles were significantly affected by site but not mesh size. Juveniles reared at the close site were significantly larger and grew faster than those reared at the intermediate site while mean length and AGR of juveniles reared at the distant site were not significantly different to those cultured at either the close or intermediate sites. Growth rates of juveniles were lower on day 30 compared to day 15 possibly resulting from reduced food availability, as indicated by lower periphyton AFDW, resulting from inter- and intraspecific competition. A positive correlation was found between AGR and the number of surviving sandfish juveniles by day 15, while no correlation between the two parameters was observed by day 30 indicating that reduced growth rates were not mediated by interspecific stocking density, but most likely resulted from high intraspecific grazing pressure. Chlorophyll a content of periphyton was higher during the second half of the experiment; however, total periphyton biomass (as AFDW) generally decreased overtime. This reduced food availability coincided with the higher number of opisthobranchs in the hapa nets by day 30. Results showed that sandfish juveniles can grow in an environment with varying levels of nutrient enrichment, however, areas close to mariculture activity may support improved growth because of resulting increases in periphyton biomass. Additionally, the use of finer mesh (400 μm) hapa nets positively impacted juvenile survival and would support earlier transfer of juveniles from the hatchery to the ocean reducing husbandry inputs and costs.

 

10. Labrador, K., Agmata, A., Palermo, J. D., Ravago-Gotanco, R., & Pante, M. J. (2021). Mitochondrial DNA reveals genetically structured haplogroups of Bali sardinella (Sardinella lemuru) in Philippine watersRegional Studies in Marine Science, 41.more

Abstract:

Population genetic structure of Sardinella lemuru in Philippine waters was examined using mitochondrial DNA markers, control region (CR) and cytochrome oxidase I (COI). The sampling effort was focused along the northern coast of Mindanao where the species was previously reported to have regionally structured stocks. Sequences from online databases were included to expand geographic coverage of the analyses. Phylogeographic and population genetic inferences revealed the presence of genetically structured sympatric haplogroups across the archipelago (CR: n  493, K  3, between-group genetic distance = 0.038 – 0.054, global p < 0.001; COI: n   159, K  2, between-group genetic distance = 0.012, global , p  0.001). In contrast, little to no genetic differentiation was inferred when samples were assigned based on geographic location (CR global , p < 0.05; COI global , p > 0.05). These results suggest that (1) gene flow occurs across space, but is limited among sympatric haplogroups, (2) these sympatric haplogroups do not correspond to cryptic species, and (3) differences in mutation rates between the two markers may have led to a different number of haplogroups being recovered. High haplotype diversity (H; H.798), low nucleotide diversity (; ), and significantly negative Fu’s F values implied demographic expansion for all haplogroups. The mismatch distribution and Bayesian Skyline plot indicated that expansion occurred during the late Pleistocene. Based on our results, we hypothesize that the Philippines is a secondary contact zone for S. lemuru, and testing this requires that samples be obtained from the entire habitat range of the species along the Indo-West Pacific Region.

 

11. Onda, D.F.L., Sharief, K.M. (2021) Identification of Microorganisms Related to Microplastics. IN: Rocha-Santos T., Costa M., Mouneyrac C. (eds) Handbook of Microplastics in the Environment. Springer, Cham.more

Abstract:

The potential of plastic debris to serve as alternative substrates for various biota have gained interest in recent years. In particular, studies on microbial colonization revealed their impacts and roles on the fate and potential risks of the plastic material, giving rise to the field of “plastisphere” research. These microbes have been shown to change the buoyancy of the material and promote sinking, increase the dispersal of attaching species, facilitate ingestion by changing its chemosensory properties, enhance biodeterioration and biodegradation, and even influence local biogeochemical cycles and ecological functions. Thus, exploring plastic-associated communities is important in helping us understand the full extent of the ecological impacts of plastics and microplastics pollution. However, the era of plastisphere research has just started to take off and many aspects of its “ecology” are yet to be explored, which also translates to more opportunities for researchers. This chapter focuses on the implications of microbial colonization of the plastics surface and the challenges in studying this unique association. Specifically, we assess the common themes in plastisphere research and summarize the current methods, from sample collection to analysis, that have been commonly employed in studying these communities. Although great advances have been made, standardization of protocols for future work might still be needed to enable more informative and meaningful comparisons among plastisphere studies.

 

12. Reich, H. G., Tu, W. -., Rodriguez, I. B., Chou, Y., Keister, E. F., Kemp, D. W., LaJeunesse T. C. & Ho, T. -. (2021). Iron availability modulates the response of endosymbiotic dinoflagellates to heat stressJournal of Phycology, 57 (1), Pages 3-13.more

Abstract:

Warming and nutrient limitation are stressors known to weaken the health of microalgae. In situations of stress, access to energy reserves can minimize physiological damage. Because of its widespread requirements in biochemical processes, iron is an important trace metal, especially for photosynthetic organisms. Lowered iron availability in oceans experiencing rising temperatures may contribute to the thermal sensitivity of reef‐building corals, which rely on mutualisms with dinoflagellates to survive. To test the influence of iron concentration on thermal sensitivity, the physiological responses of cultured symbiotic dinoflagellates (genus Breviolum; family Symbiodiniaceae) were evaluated when exposed to increasing temperatures (26 to 30°C) and iron concentrations ranging from replete (500 pM Fe’) to limiting (50 pM Fe’) under a diurnal light cycle with saturating radiance. Declines in photosynthetic efficiency at elevated temperatures indicated sensitivity to heat stress. Furthermore, five times the amount of iron was needed to reach exponential growth during heat stress (50 pM Fe′ at 26–28°C vs. 250 pM Fe′ at 30°C). In treatments where exponential growth was reached, Breviolum psygmophilum grew faster than B.minutum, possibly due to greater cellular contents of iron and other trace metals. The metal composition of B.psygmophilumshifted only at the highest temperature (30°C), whereas changes in B.minutum were observed at lower temperatures (28°C). The influence of iron availability in modulating each alga’s response to thermal stress suggests the importance of trace metals to the health of coral‐algal mutualisms. Ultimately, a greater ability to acquire scarce metals may improve the tolerance of corals to physiological stressors and contribute to the differences in performance associated with hosting one symbiont species over another.

 

13. Requilme, J.N.C, Conaco, C., Sayco, S.L.G., Roa-Quiaoit, H.A., Cabaitan, P.C. (2021). Using citizen science and survey data to determine the recruitment envelope of the giant clam, Tridacna gigas (Cardiidae: Tridacninae)Ocean and Coastal Management, 202.more

Abstract:

Restocking of giant clams, particularly Tridacna gigas, aims to reestablish breeding populations that have long been decimated by overexploitation. In Camiguin, southern Philippines, T. gigas juveniles that were restocked in 2001 have reached reproductive maturity and recruits have been observed on the reefs. To help document T. gigas recruits in Camiguin, the Cantaan Centennial Multi-purpose Cooperative (CCMPC) initiated a program to encourage local fishers to report any sightings of giant clams, in the surrounding reefs. The fishers would mark the location of any giant clam recruits they encountered during their regular fishing trips using makeshift buoys. Personnel from CCMP would then visit the marked sites to collect GPS data. The giant clams would later be relocated to an ocean-based nursery at the CCMP marine protected area (MPA) to ensure their protection. A total of 26 T. gigas recruits with a mean shell length of 17.8 ± 1.5 cm were found 0.2 km–2.3 km away from the restocking site between 2015 and 2017. Twenty-three of these individuals were reported by fishers while 3 were encountered during field surveys. It is highly probable that these T. gigas recruits are the progeny of the restocked individuals because there are no local populations of wild T. gigas in the area and no artificial spawning events had been conducted at the site. These results suggest that the reefs near Camiguin are suitable for giant clam recruitment and indicate that the recruitment envelope of T. gigas can extend up to several kilometers. Importantly, these findings highlight the value of a strong commitment by local organizations and collaboration with fishers as citizen scientists to enhance the sustainability of giant clam conservation efforts.

 

14. Roleda, M.Y., Lage, S., Aluwini, D.F., Rebours, C., Brurberg, M.B., Gentili, F.G. (2021). Chemical profiling of the Arctic sea lettuce Ulva lactuca (Chlorophyta) mass-cultivated on land under controlled conditions for food applicationsFood Chemistry, 341.more

Abstract:

The increasing use of seaweeds in European cuisine led to cultivation initiatives funded by the European Union. Ulva lactuca, commonly known as sea lettuce, is a fast growing seaweed in the North Atlantic that chefs are bringing into the local cuisine. Here, different strains of Arctic U. lactuca were mass-cultivated under controlled conditions for up to 10 months. We quantified various chemical constituents associated with both health benefits (carbohydrates, protein, fatty acids, minerals) and health risks (heavy metals). Chemical analyses showed that long-term cultivation provided biomass of consistently high food quality and nutritional value. Concentrations of macroelements (C, N, P, Ca, Na, K, Mg) and micronutrients (Fe, Zn, Co, Mn, I) were sufficient to contribute to daily dietary mineral intake. Heavy metals (As, Cd, Hg and Pb) were found at low levels to pose health risk. The nutritional value of Ulva in terms of carbohydrates, protein and fatty acids is comparable to some selected fruits, vegetables, nuts and grains.

 

15. Roleda, M. Y., Lage, S., Fonn Aluwini, D., Rebours, C., Brurberg, M.B, Nitschke, U., & Gentili, F. G. (2021). Corrigendum to “Chemical profiling of the arctic sea lettuce Ulva lactuca (Chlorophyta) mass-cultivated on land under controlled conditions for food applications” [Food Chemistry, 341 (2021) 127999]Food Chemistry, 347, 129059.more

Abstract:

In this regard, the title of this publication should read “Chemical profiling of the Arctic sea lettuce Ulva fenestrata (Chlorophyta) mass- cultivated on land under controlled conditions for food applications”. Moreover, reference to the sea lettuce species in this study should be Ulva fenestrata throughout the manuscript.

 

 

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1. Claro, S. B. D., Ramos, N. T., Fernando, A. G. S., Ishimura, D., Switzer, A. D. (2021). Sedimentological evidence of washover deposits from extreme wave events in Zamboanga del Sur, Mindanao, southern PhilippinesMarine Geology, 438, Article 106535. https://doi.org/10.1016/j.margeo.2021.106535more

Abstract:

The Philippines' active tectonic setting and vulnerability to tsunami hazards underscore the necessity to understand tsunami sources and their impacts. Several tsunamigenic earthquakes have devastated coastal communities in the past but geological evidence of these infrequent extreme wave events (EWEs) have yet to be described and analyzed in detail. This study documents and establishes evidence of potential tsunami deposits preserved in a mangrove environment in western Mindanao Island, which was inundated by the 1976 Moro Gulf tsunami. The 1976 Moro Gulf tsunami, by far the worst tsunami disaster in the Philippines, is associated with a Mw 8.1 earthquake along the Cotabato subduction zone. The sedimentological characteristics of potential tsunami deposits in three coastal sites bordering Pagadian and Illana Bays in Zamboanga del Sur, Mindanao, southern Philippines were analyzed and compared to describe the preservation of washover deposits in different coastal systems. The potential washover deposits of the 1976 tsunami were identified based on their sedimentary characteristics and features that contrast with the background (pre-tsunami event) sediments. The potential 1976 tsunami deposits are predominantly sand-sized and coarser than the background sediments. They also contain mud rip-up clasts, magnetite lamina, and an erosive base, similar to reported washover deposits elsewhere. The thickness of the washover deposits ranges from 7 to 12 cm. The thickest sand layer was observed in a mangrove swamp, implying that local topography influenced the distribution and preservation of the deposit. A potentially older EWE deposit was also observed in Pagadian City. The background sediments in both the mangrove swamps and coastal plains are mud to fine sand. While scarcity in historical data and rapidly changing environmental conditions pose challenges in studying washover deposits in a tropical setting, this study highlights essential information and lessons for future researchers of washover deposits in the Philippines. Sedimentological data on the potential EWE washover deposits in western Mindanao Island serve as fundamental information in understanding the processes and mechanisms of extreme wave events in this region. This study further establishes geological evidence of the country's worst historical tsunami, the 1976 Moro Gulf tsunami, which contributes to our knowledge of tsunami deposits in tropical settings.

 

2. Custado, M. J. G., David, C.P. C. (2021). Influence of runoff on coastal chlorophyll-a concentration in selected Philippine upwelling sitesPhilippine Science Letters, 14 (1), Pages 108-118.more

 

Abstract:

 Space-time variations in chlorophyll a (Chl a ) concentrations in the surface water of upwelling regions along the Polish coast of the Baltic Sea were analysed. Carried out between 1998 and 2002 in the warmer season (from April till October), the measurements were targeted mainly at the Hel upwelling. Satellite-derived sea surface temperature (AVHRR) and Chl a data (SeaWiFS) were used. Generally speaking, the Chl a concentration increased in the upwelling plume, except along the Hel Peninsula, where two scenarios took place: a reduction in Chl a concentration in spring and an increase in autumn.

 

3. Doyongan, Y.I.L., and Fernando, A.G.S. (2021). Data report: refinement of calcareous nannofossil biostratigraphy from the late Oligocene to the Pleistocene, IODP Expedition 363 Hole U1490AIn Y. Rosenthal, A.E. Holbourn, D.K. Kulhanek, and the Expedition 363 Scientists, Proceedings of the International Ocean Discovery Program, 363. publications.iodp.org.  https://doi.org/10.14379/iodp.proc.363.204.2021more

Abstract:

An Oligocene to recent sedimentary sequence was recovered in Hole U1490A in the northern portion of the Eauripik Rise (western Pacific Ocean) during International Ocean Discovery Program Expedition 363. High-resolution sampling and moderate to good calcareous nannofossil preservation allowed us to adjust the depths for nannofossil events reported shipboard. This study identified 22 zonal boundary markers and 30 secondary calcareous nannofossil events. Because of better preservation of the calcareous nannofossils in the Pliocene–Pleistocene units, more calcareous nannofossil events were observed in that interval than in the older units. In the Miocene units, the discoasters and helicosphaerids (which are important zonal boundary markers) are poorly preserved (fragmented and recrystallized), making iT difficult to identify nannofossil zones. In lieu of zonal boundary markers, secondary calcareous nannofossil events were used to refine the biostratigraphy in the Miocene interval.

 

4. Faustino-Eslava, D. V., Shibuya, H., Dimalanta, C. B., Yumul, G. P., Jr., & Macuroy, J. T. (2021). Persistent shallow magnetic inclination in the past 5 million years with implications for regional tectonics in the philippines. Journal of Asian Earth Sciences: X, doi:10.1016/j.jaesx.2021.100048more

Abstract:

Despite the growing knowledge on geomagnetic paleosecular variations, the region around the Philippine archipelago remains to be a huge data gap in this regard. This work looked into rock magnetic information from <5 Ma volcanic rocks of Luzon Island to provide data for the statistical characterization of the time-averaged field in the region. A total of 21 sites with ages from 1 ka to 4.3 Ma yielded 13 normal, 7 reversed, and 1 intermediate polarity dataset. These were aggregated with previously published work to form a combined dataset of 59 normal + reversed sites with a mean virtual geomagnetic pole at 321.1°E and 83.7°N with α95 = 3.4, and an angular standard deviation of about 14.6°. This amount of scatter is slightly larger than that predicted by Model G but relatively comparable with other near-equatorial regions such as Java and Ecuador. This work is a first examination of paleomagnetic data from the Philippines in relation to the long-term behavior of the magnetic field in this part of Southeast Asia. The long-ranging shallow inclination observed may also have implications on how paleomagnetic data are interpreted for tectonic studies in the region.

 

5. Hernández, P.A., Melián, G.V. Asensio-Ramos, M., Padrón, E., Sumino, H. Perez, N. M., Padilla, G. D., Barrancos, J., Rodriguez, F., Amonte, C., Arcilla, C., Lagmay, A.M. (2021). Geochemical and isotopic evidence of volcanic plumbing system processes from fumarolic gases of Taal volcano, Philippines, prior to the January 2020 eruptionChemical Geology, 574, 120216.  https://doi.org/10.1016/j.chemgeo.2021.120216more 

Abstract:

Significant changes in the chemical and isotopic composition of Taal fumarolic gas have been recorded observed before the January 2020 eruption, during the periods 2011 and 2016–2018. Increasing CO2/St, He/CO2, CO/CO2 and CO2/CH4 ratios were recorded during 2011 whereas increasing SO2/H2S, H2/CO2 ratios were recorded during the period 2017–2018. A decreasing on the CO2/CH4 and CO2/St ratios was observed for 2017–2018. These changes are attributed to an increased contribution of magmatic fluids to the hydrothermal system in both periods. Observed changes in H2 and CO contents suggest increases in temperature and pressure in the upper parts of the hydrothermal system of Taal volcano. The 3He/4He ratios corrected (Rc/Ra), and δ13C of fumarolic gases also increased during the periods 2010–2011 and 2017–2018 before the eruption onset. These variations were produced by two episodes of magmatic intrusion which favored degassing of a gas-rich magma at depth. During the 2010–2011 the magmatic intrusion of volatile-rich magma might have occurred from the mid-crustal storage region at shallower depths producing important he observed changes in pressure and temperature conditions, whereas a new injection of more degassed magma into the deepest zone of the hydrothermal system occurring in 2017–2018 might have favored the accumulation of gases in the subsurface, promoting conditions leading to a phreatic eruption.

 

6. Hoey, T., Tolentino, P., Guardian, E., Williams, R., Boothroyd, R., David, C. P., and Paringit, E. (2021). Flood estimation for ungauged catchments in the Philippines using multiple archival data recordsEGU General Assembly 2021, online, 19–30 Apr 2021, EGU21-4905. https://doi.org/10.5194/egusphere-egu21-4905, 2021more

Abstract:

Assessment of flood and drought risks, and changes to these risks under climate change, is a critical issue worldwide. Statistical methods are commonly used in data-rich regions to estimate the magnitudes of river floods of specified return period at ungauged sites. However, data availability can be a major constraint on reliable estimation of flood and drought magnitudes, particularly in the Global South. Statistical flood and drought magnitude estimation methods rely on the availability of sufficiently long data records from sites that are representative of the hydrological region of interest. In the Philippines, although over 1000 locations have been identified where flow records have been collected at some time, very few records exist of over 20 years duration and only a limited number of sites are currently being gauged. We collated data from three archival sources: (1) Division of Irrigation, Surface Water Supply (SWS) (1908-22; 257 sites in total); (2) Japan International Cooperation Agency (JICA) (1955-91; 90 sites); and, (3) Bureau of Research and Standards (BRS) (1957-2018; 181 sites). From these data sets, 176 contained sufficiently long and high quality records to be analysed. Series of annual maximum floods were fit using L-moments with Weibull, Log-Pearson Type III and Generalised Logistic Distributions, the best-fit of these being used to estimate 2-, 10- and 100-year flood events, Q2, Q10 and Q100. Predictive equations were developed using catchment area, several measures of annual and extreme precipitation, catchment geometry and land-use. Analysis took place nationally, and also for groups of hydrologically similar regions, based on similar flood growth curve shapes, across the Philippines. Overall, the best fit equations use a combination of two predictor variables, catchment area and the median annual maximum daily rainfall. The national equations have R2 of 0.55-0.65, being higher for shorter return periods, and regional groupings R2 are 0.60-0.77 for Q10. These coefficients of determination, R2, are lower than in some comprehensive studies worldwide reflecting in part the short individual flow records. Standard errors of residuals for the equations are between 0.19 and 0.51 (log10 units), which lead to significant uncertainty in flood estimation for water resource and flood risk management purposes. Improving the predictions requires further analysis of hydrograph shape across the different climate types, defined by seasonal rainfall distributions, in the Philippines and between catchments of different size. The results here represent the most comprehensive study to date of flood magnitudes in the Philippines and are being incorporated into guidance for river managers alongside new assessments of river channel change across the country. The analysis illustrates the potential, and the limitations, for combining information from multiple data sources and short individual records to generate reliable estimates of flow extremes.

 

7. Ibarra, D.E., David, C. P. C., and Tolentino, P. L. M. (2021). Technical note: Evaluation and bias correction of an observation-based global runoff dataset using streamflow observations from small tropical catchments in the PhilippinesHydrology and Earth System Sciences, 25 (5), Pages 2805–2820. https://doi.org/10.5194/hess-25-2805-2021more

Abstract:

Even in relatively wet tropical regions, seasonal fluctuations in the water cycle affect the consistent and reliable supply of water for urban, industrial, and agricultural uses. Historic streamflow monitoring datasets are crucial in assessing our ability to model and subsequently plan for future hydrologic changes. In this technical note, we evaluate a new observation-based global product of monthly runoff (GRUN; Ghiggi et al., 2019) for 55 small tropical catchments in the Philippines with at least 10 years of data, extending back to 1946 in some cases. Since GRUN did not use discharge data from the Philippines to train or calibrate their models, the data presented in this study, 11 915 monthly data points, provide an independent evaluation of this product. We demonstrate across all observations a significant but weak correlation (r2=0.372) between the GRUN-predicted values and observed river discharge, as well as somewhat skillful prediction (volumetric efficiency = 0.363 and log(Nash–Sutcliffe efficiency) = 0.453). GRUN performs best among catchments located in climate types III (no pronounced maximum rainfall with short dry season) and IV (evenly distributed rainfall, no dry season). There was a weak negative correlation between volumetric efficiency and catchment area, and there was a positive correlation between volumetric efficiency and mean observed runoff. Further, analysis for individual rivers demonstrates systematic biases (over- and underestimation) of baseflow during the dry season and underprediction of peak flow during some wet months for most catchments. To correct for underprediction during wet months, we applied a log-transform bias correction which greatly improves the nationwide root mean square error between GRUN and the observations by an order of magnitude (2.648 mm d−1 vs. 0.292 mm d−1). This technical note demonstrates the importance of performing such corrections when determining the proportional contribution of smaller catchments or tropical islands such as the Philippines to global tabulations of discharge. These results also demonstrate the potential use of GRUN and future data products of this nature after consideration and correction of systematic biases to (1) assess trends in regional-scale runoff over the past century, (2) validate hydrologic models for unmonitored catchments in the Philippines, and (3) assess the impact of hydrometeorological phenomena to seasonal water supply in this wet but drought-prone archipelago.

 

8. Lagmay, A. M. F. A., Santiago, J., Pulhin, J. M. (2021). Mainstreaming CCA-DRVRM using probabilistic multi-scenario hazard maps for future resilience in Haiyan-affected areas. In J. M. Pulhin, M. Inoue, R. Shaw (Eds.) Climate Change, Disaster Risks, and Human Security (243-263). Springer.more

Abstract:

For the past century, climate change impacts and disaster risks have resulted not only in millions of deaths but also in a long-term compromise on human security at various scales, from local to global. Theoretical and empirical bases both reveal how the intertwining relationship of climate change and disaster risk compromises the freedom of people for a decent and dignified life. Particularly imperiled are the livelihoods, health, food, safety, and even the culture of the vulnerable population. Asia, in particular, has been the world’s most vulnerable region in terms of quantity and magnitude of impacts from various forms of disasters, climate-induced or otherwise. Amid the escalating threats, the region continues to adapt and innovate building on the lessons it gained from its vast experiences in pursuit of resiliency and security. This chapter elaborates on the interrelationship of climate change, disaster risk, and human security gleaned through the experiences of Asia while also providing a grounded analysis of the key concepts to bridge the major gap in understanding their linkages, hence, embodying the unifying theme of the book.

 

9. Lai, C. -., Xia, X. -., Hall, R., Meffre, S., Tsikouras, B., Balangue-Tarriela, M. I. R., Idrus, A., Ifandi, E., Norazme, N. '. (2021). Cenozoic evolution of the sulu sea arc-basin system: An overviewTectonics, 40 (2). https://doi.org/10.1029/2020TC006630more

Abstract:

The Cenozoic Sulu Sea arc-basin system is situated in the tectonic junction between the South China Sea (SCS), northern Borneo, Palawan Continental Terrane, Philippine Mobile Belt, and Celebes Sea. We compare new/published geochronological and geochemical data from across the circum-Sulu Sea region, and summarize seven major magmatic phases from the Middle Eocene to Pleistocene. The Middle Eocene (42.65 Ma) Sabah ophiolite and Eocene-Oligocene (34-33 Ma) Central Palawan ophiolite have MORB-IAT-transitional features, representing an intraoceanic subduction setting in the Paleogene northern Borneo and central-southern Palawan. After the SCS opening (32 Ma) and ridge jump (25 Ma), late-stage Proto-SCS subduction (24-21 Ma) may have formed the Panay arc andesite and the BABB magmatism in SW Zamboanga peninsula. Starting of final convergence between the Palawan Continental Terrane and northern Borneo-SW Philippines (21 Ma) likely caused regional uplift/thrusting, forming the Top Crocker Unconformity and triggering the NW-dipping Celebes Sea subduction. The subduction may have formed arc magmatism (21-18 Ma) in the Cagayan ridge and its continuation in Panay and NE Sabah, and opened the NW Sulu Sea back-arc basin through continental crust attenuation. Subduction rollback likely occurred in 17-14 Ma and 13-9 Ma, shifting arc magmatism southeast to the Sulu ridge and opening the SE Sulu Sea back-arc basin. NW-dipping Celebes Sea subduction largely ceased after 9 Ma, followed by extension-related uplift/exhumation and 4-0.2 Ma intraplate volcanism in northern Borneo. SE-dipping Sulu Sea subduction likely occurred along the Negros-Sulu trenches, and produced arc volcanism from 4 Ma.

 

10. Olfindo, V. S. V., Payot, B. D., Valera, G. T. V., & Arai, S. (2021). Petrogenesis of heterogeneous mantle peridotites with ni-rich olivine from the pujada ophiolite, philippines. Journal of Asian Earth Sciences, 205. doi:10.1016/j.jseaes.2020.104596more

Abstract:

Nickel (Ni) enrichment (>0.40 wt%) in olivine was previously recognized in mantle xenoliths and volcanic rocks. Though this enrichment is often attributed to subarc metasomatic processes, the occurrence of Nirich olivines in mantle peridotites remains to be established. We found peridotites that randomly contain unusually high Ni olivines (up to Ni = 0.53 wt%) from the mantle section of the Pujada Ophiolite, Philippines. The Pujada mantle peridotites can be classified into three groups based on their occurrence and spinel Cr#: Group I - massive lherzolites and harzburgites with Cr# =0.10–0.40, Group II - lherzolite-dunite and harzburgite-dunite interlayers with Cr# =0.10–0.40, and Group III - interlayered harzburgites and dunites with Cr# >0.40. Rare earth element composition of clinopyroxenes shows general light rare earth element (LREE) depletion and relatively flat heavy rare earth element (HREE) with minor LREE enrichment. The high-Ni olivines are associated with the occurrence of secondary orthopyroxenes, high modal abundance of orthopyroxenes (>30%) and LREE enrichment. The Ni enrichment in olivine is the result of the diffusion of Ni from a pyroxenitic melt. The crystallization of a hybridized melt from the combination of pyroxenitic melt, primitive MORB melt and hydrous silicate melt beneath an arc is reported to account for the high Ni-olivine phenocrysts in alkali basalts from Hawaii, Kamchatka and the Mexican Volcanic Belt. 

 

11. Payot, B. D., Ishimaru, S., Tamura, A., Dimalanta, C. B., Yumul, G. P. Jr., Arai, S. (2021). Remarkably fresh abyssal peridotites from Sibuyan island, Romblon Island Group, Philippines: Markers of young arc-continent collisionJournal of Asian Earth Sciences: X.https://doi.org/10.1016/j.jaesx.2021.100051more

Abstract:

The bulk of Sibuyan island in the Romblon Island Group, Philippines is underlain by remarkably fresh spinel lherzolites, harzburgites and dunites collectively called as the Sibuyan Ultramafics. Based on petrographic and geochemical characteristics, the Sibuyan Ultramafics can be classified into: (1) Group I peridotites composed of spinel lherzolites and harzburgites with spinel Cr# < 0.35, (2) Group II harzburgites and dunites with intermediate spinel Cr# = 0.40–0.65, and (3) Group III dunites with very high spinel Cr# (>0.75). Increase in spinel Cr# is accompanied by decreasing Al2O3 contents and increasing Mg# in the pyroxenes from the Group I to Group II and Group III peridotites. Chondrite-normalized clinopyroxene data revealed various trace-element patterns for the three groups suggestive of different processes (e.g. anhydrous and hydrous melting, mantle-melt interaction) involved in their formation. The Sibuyan Ultramafics is closely associated with the similarly fresh Calaton Hill metamorphic/plutonic complex in Tablas island which is thought to be representative of the lower crust of the Philippine island arc. At a more regional context, the Sibuyan Ultramafics and the Calaton Hill metamorphic/plutonic complex can be used as markers for the young arc-continent collision in western Philippines. Rapid uplift and emplacement due to the collision of the Philippine Mobile Belt and the Palawan Microcontinental Block during the Miocene or even later may have led to the remarkably fresh state of these lithologies. This occurrence is similar to the Horoman peridotite complex in the Hidaka metamorphic belt in Northern Japan. The Sibuyan Ultramafics and the Calaton Hill metamorphic/plutonic complex therefore provide a rare and fresh glimpse into the upper mantle and lower crust in the Philippines due to their young ages of emplacement.

 

12. Payot, B. D., Rau, R.-J. (2021). Preface for the “Evolution of arc systems: New findings and perspectives” special issueJournal of Asian Earth Sciences: X, 5. https://doi.org/10.1016/j.jaesx.2021.100058more

Abstract:

The geology of the Philippines and Taiwan is largely governed by the collision of an island arc with fragments from the Asian continental margin. The Philippines and Taiwan are excellent laboratories to understand what Earth processes led to these complex present day conditions, and how these may affect these areas in the future. Moreover, their vulnerability to geologic and meteorological hazards makes the Philippines and Taiwan the perfect analogues to explore new approaches and integrate various fields such as geophysics, geochemistry, tectonics, paleontology, meteorology, and environmental science, among others. Since 2007, Filipino and Taiwanese geoscientists have actively collaborated on research initiatives to address common scientific issues, which are not only relevant and applicable to the region but also at a global scale. The decision to come up with this special issue to highlight the ongoing research collaborations was made during the Philippines-Taiwan Earth Sciences International Conference (PTESIC) in Clark, Pampanga, Philippines last May 20–23, 2019. This scientific conference forms part of the Collaboration on Geosciences implemented by the Philippines Department of Science and Technology and Taiwan Ministry of Science and Technology.

This special issue is divided into two parts. Part I features papers on how island arcs formed due to tectonic and collision-related processes. Papers in Part II focus on the growth of an island arc by characterizing its basement as well as its associated magmatism and mineralization.

 

13. Qin, H.-B., Yang, S. Tanaka, M., Sanematsu, K., Arcilla, C., Takahashi, Y.  (2021). Scandium immobilization by goethite: Surface adsorption versus structural incorporationGeochimica et Cosmochimica Acta, 294, Pages 255-272. doi:10.1016/j.gca.2020.11.020more

Abstract:

Several recent studies have reported a strong association between Sc and goethite (α-FeOOH) in synthetic analogs and natural samples. However, the mechanism of Sc immobilization by goethite and controlling factors remain unclear. This study investigated the adsorption behavior and molecular-scale immobilization mechanisms of Sc at water/goethite interfaces through a combination of batch adsorption and desorption experiments, X-ray absorption fine structure (XAFS) analyses, and density functional theory (DFT) calculations. Results indicate that Sc is preferentially adsorbed on goethite with the formation of bidentate-binuclear inner-sphere complexes at the corner-sharing sites. Bulk Sc K-edge XAFS analyses suggest that Sc is incorporated into the goethite structure by substituting for Fe(III) within the crystal in synthetic Sc-substituted goethite, which is further confirmed in natural goethite particles in the laterite by using micro-focused XAFS (μ-XAFS). Furthermore, we demonstrate that the adsorbed Sc on the goethite surface can be structurally incorporated into the goethite lattice in the presence of aqueous Fe(II) possibly through goethite recrystallization induced by aqueous Fe(II). This process may affect the (re)partitioning of Sc between the goethite surface and the mineral bulk, which could be used to rationally explain disparate Sc speciation in laterites from different regions. Our study elucidates the molecular-scale mechanisms underlying Sc adsorption on and structural incorporation into goethite, providing critical insights into the understanding of geochemical behavior and environmental fates of Sc.

 

14. Soberano, O. B., Gabo-Ratio, J. A. S., Queaño, K. L., Dimalanta, C. B., Yumul, G. P., Jr., Andal, E. S., Yonezu, K., Boyce, A. J. (2021). Mineral chemistry, fluid inclusion and stable isotope studies of the suyoc epithermal veins: Insights to au-cu mineralization in southern mankayan mineral district, philippines. Ore Geology Reviews, 131 doi:10.1016/j.oregeorev.2021.104035more

Abstract:

The Suyoc prospect is an epithermal vein-type mineralization located at the southern part of the Mankayan Mineral District, Northern Luzon, Philippines. The prospect's epithermal veins are hosted in volcaniclastic rocks and conglomerate, which belong to the Late Oligocene to Early Miocene Balili Formation and the Middle to Late Miocene Suyoc Conglomerate, respectively. These veins are classified into three major types: quartz vein, quartz-sulfide vein, and quartz-carbonate vein. The quartz vein exhibits massive and cockade textures associated with pyrite + chalcopyrite. The quartz-sulfide vein consists of massive and comb quartz associated with pyrite + chalcopyrite + sphalerite. The quartz-carbonate vein has massive quartz associated with rhodochrosite and chalcopyrite + sphalerite + galena + Au/Ag ± bournonite. In addition, massive gypsum ± pyrite occurs as a minor vein-type. Fluid inclusion measurements in quartz from the three major vein-types revealed 230–250 °C formation temperatures and 1.0–3.5 wt. % NaCl equivalent salinity, which are values consistent with epithermal deposits. Quartz textures (e.g., massive, cockade, comb, crustiform) and dominance of liquid-rich fluid inclusions do not suggest that boiling is a primary mechanism of vein deposition. Possible mechanisms are inferred as meteoric water dilution based on homogenization versus salinity trend in quartz vein and presence of rhodochrosite in quartz-carbonate vein, and wall rock interaction based on FeS trend in sphalerite crystals of the quartz-carbonate vein. The presence of pyrite and chalcopyrite in the major vein-types and the FeS mole percent values (0.51 to 8.30) in quartz-carbonate vein indicate an intermediate sulfidation state. The alteration minerals illite, chlorite, pyrite and quartz indicate near-neutral pH condition. δ34S values, which vary from −1.1 to +3.9‰, suggest reduced condition when compared to the representative bulk δ34S value for the Mankayan Mineral District. The characteristics and conditions strongly indicate an intermediate sulfidation epithermal (ISE) style of mineralization. Moreover, the δDwater (−63 to −66‰) and δ18Owater (−3.9 to −1.1‰) values from the major vein-types suggest late stage formation in a magmatic-hydrothermal system similar to other ISE deposits in the Northern Luzon Segment (e.g., Victoria, Acupan and Antamok). Given these, the presence of the Suyoc ISE veins in the underexplored southern part of the Mankayan Mineral District implies potential presence of undiscovered cogenetic porphyry Cu and high sulfidation epithermal mineralization in the area. 

 

15. Ybanez, R. L., Ybanez, A. A. B., Lagmay, A. M. F. A., Aurelio, M. A. (2021). Imaging ground surface deformations in post-disaster settings via small UAVsGeoscience Letters 8, Article 23. https://doi.org/10.1186/s40562-021-00194-8more

Abstract:

Small unmanned aerial vehicles have been seeing increased deployment in field surveys in recent years. Their portability, maneuverability, and high-resolution imaging are useful in mapping surface features that satellite- and plane-mounted imaging systems could not access. In this study, we develop and apply a workplan for implementing UAV surveys in post-disaster settings to optimize the flights for the needs of the scientific team and first responders. Three disasters caused by geophysical hazards and their associated surface deformation impacts were studied implementing this workplan and was optimized based on the target features and environmental conditions. An earthquake that caused lateral spreading and damaged houses and roads near riverine areas were observed in drone images to have lengths of up to 40 m and vertical displacements of 60 cm. Drone surveys captured 2D aerial raster images and 3D point clouds leading to the preservation of these features in soft-sedimentary ground which were found to be tilled over after only 3 months. The point cloud provided a stored 3D environment where further analysis of the mechanisms leading to these fissures is possible. In another earthquake-devastated locale, areas hypothesized to contain the suspected source fault zone necessitated low-altitude UAV imaging below the treeline capturing Riedel shears with centimetric accuracy that supported the existence of extensional surface deformation due to fault movement. In the aftermath of a phreatomagmatic eruption and the formation of sub-metric fissures in nearby towns, high-altitude flights allowed for the identification of the location and dominant NE–SW trend of these fissures suggesting horst-and-graben structures. The workplan implemented and refined during these deployments will prove useful in surveying other post-disaster settings around the world, optimizing data collection while minimizing risk to the drone and the drone operators.

 

nimbb

1. Danac, J.M.C., Garcia, R.L. (2021). CircPVT1 attenuates negative regulation of NRAS by let-7 and drives cancer cells towards oncogenicitySci Rep 11, 9021. https://doi.org/10.1038/s41598-021-88539-3more

Abstract:

Circular RNAs have emerged as functional regulatory molecules whose aberrant expression has been linked to diverse pathophysiological processes. Here, we report that circPVT1 interferes with let-7 binding to NRAS, confirming this axis as one route by which circPVT1 can instigate an oncogenic program in A549 lung cancer cells and HCT116 colorectal cancer cells. CircPVT1 knockdown significantly reduced NRAS levels and attenuated cancer hallmark phenotypes such as proliferation, migration, resistance to apoptosis, cytoskeletal disorganization, and epithelial-mesenchymal transition. The effects of circPVT1 knockdown were at least partially rescued by blocking binding of let-7 to NRAS 3′UTR with a target protector, suggesting that a circPVT1/let-7/NRAS axis exists and acts in cells to reverse NRAS downregulation and favor oncogenicity. While the phenotypic effects of circPVT1 knockdown may be attributable to the global action of circPVT1, the target protection assays resolved the relative contribution of the circPVT1/let-7/NRAS axis specifically.

 

2. Danac, J.M., Uy, A.G., & Garcia, R.L. (2021). Exosomal microRNAs in colorectal cancer: Overcoming barriers of the metastatic cascade (Review)International Journal of Molecular Medicine, 47, 112. https://doi.org/10.3892/ijmm.2021.4945more

Abstract:

The journey of cancer cells from a primary tumor to distant sites is a multistep process that involves cellular reprogramming, the breaking or breaching of physical barriers and the preparation of a premetastatic niche for colonization. The loss of adhesion between cells, cytoskeletal remodeling, the reduction in size and change in cell shape, the destruction of the extracellular matrix, and the modification of the tumor microenvironment facilitate migration and invasion into surrounding tissues. The promotion of vascular leakiness enables intraand extravasation, while angiogenesis and immune suppression help metastasizing cells become established in the new site. Tumorderived exosomes have long been known to harbor microRNAs (miRNAs or miRs) that help prepare secondary sites for metastasis; however, their roles in the early and intermediate steps of the metastatic cascade are only beginning to be characterized. The present review article presents a summary and discussion of the miRNAs that form part of colorectal cancer (CRC)derived exosomal cargoes and which play distinct roles in epithelial to mesenchymal plasticity and metastatic organotropism. First, an overview of epithelialtomesenchymal transition (EMT), metastatic organotropism, as well as exosome biogenesis, cargo sorting and uptake by recipient cells is presented. Lastly, the potential of these exosomal miRNAs as prognostic biomarkers for metastatic CRC, and the blocking of these as a possible therapeutic intervention is discussed.

 

3. Koh, R.B.L., Barbosa, C.F.C., Aquino, V.M., Galvez, L.C. (2021). Extraction of high molecular weight DNA suitable for next-generation sequencing from the fiber crop abacaIndustrial Crops and Products, 161, 113194. https://doi.org/10.1016/j.indcrop.2020.113194more

Abstract:

Deoxyribonucleic acid (DNA) extraction in abaca (Musa textilis Née), the source of the strongest natural fiber (Manila hemp), is difficult due to its fibrous nature, high cellulose content, and polyphenol compounds. Thus an optimized DNA extraction method is required for extracting high quality abaca DNA for next-generation sequencing applications. This study, hence, aimed to test and compare five different methods for the extraction of high molecular weight DNA from abaca leaves. The methods are the traditional cetyl trimethylammonium bromide (CTAB) method (Protocol 1), the CTAB with polyvinylpyrrolidone (PVP) method (Protocol 2), the CTAB with 0.3 % β-mercaptoethanol method (Protocol 3), sodium dodecyl sulfate method (Protocol 4), and CTAB with Triton X-100 and PVP method (Protocol 5). The use of a high throughput homogenizer (TissueLyserII) was also tested in tandem with select extraction protocols for applications in high-throughput DNA extraction. DNA from two abaca varieties were extracted via Protocol 3 and were sent for sequencing based on the Illumina Novaseq platform. After passing the quality control parameters for library preparation, Protocol 3 was found to be the simplest and most consistent method for extracting average yield DNA with high quality for next-generation sequencing applications, while Protocol 4 was determined to have the shortest processing time. Together with TissueLyserII-facilitated homogenization, Protocol 4 is the most appropriate combination for high-throughput extraction of abaca samples which will be useful for genotyping-by-sequencing (GBS) strategies as a molecular tool for plant breeding.

 

4. Pardilla, K.P. and Hedreyda, C.T. (2021). Sequence Analysis of the Complete Gene for Endoglucanase from Strains of Thermotolerant BacillusPhilippine Journal of Science, 150 (2), Pages 535-543. more

Abstract:

Three thermotolerant Bacillus isolates from the Philippines – identified as Bacillus subtilis (1280), Bacillus velezensis (1573), and Bacillus amyloliquefaciens (10105) – exhibited cellulase activity in carboxymethylcellulose (CMC) agar plate. Moreover, the expected size (approximately 1,500 bp) putative endoglucanase gene was amplified from all three local isolates. The endoglucanase gene amplified from a Bacillus licheniformis isolate (1320) was also used in the gene sequence analysis. A colorimetric dinitrosalicylic (DNS) acid assay revealed that the total endoglucanase activity of B. velezensis 1573 at 0.168 μM reducing sugar/min is significantly higher than the endoglucanase activity of the B. subtilis 1280 at 0.0673 μM rs/min and B. amyloliquefaciens 10105 at 0.0579 μM rs/min. Endoglucanase gene sequence analysis showed the highest pairwise identity between the endoglucanase gene of B. velezensis 1573 and B. amyloliquefaciens 10105 at 97.4%. The endoglucanase gene of B. licheniformis 1320 has the lowest pairwise identity at 74.6%, 76.2%, and 75.4% with B. amyloliquefaciens 10105, B. subtilis 1280, and B. velezensis 1573, respectively. Predicted amino acid sequences of the endoglucanases revealed variations at the signal peptide, catalytic core (CC) domain, linker, and carbohydrate-binding module (CBM). The endoglucanase of B. subtilis 1280 has a 506D insertion at the CBM domain. None of these variations, however, are located in regions implicated in catalytic reaction and substrate binding. Although the predicted protein structures using MODELLER revealed endoglucanases with good fit and high homology, variations in amino acid sequences may have resulted in the differences in enzyme activity and stability. The study generated gene and protein sequences as well as amplified genes that can be used as a starting template for enzyme improvement by rational design and site-specific mutagenesis or directed evolution using DNA shuffling.

 

5. Prieto, E.I., Mojares, E.B.A., Cortez, J.J.M. and Vasquez, M.R. Jr. (2021). Electrospun nanofiber scaffolds for the propagation and analysis of breast cancer stem cells in vitroBiomedical Materials, 16 (3), 035004. https://doi.org/10.1088/1748-605X/abc3ddmore

Abstract:

Despite advances in cancer treatment, breast cancer remains the second foremost cause of cancer mortality among women, with a high rate of relapse after initial treatment success. A subpopulation of highly malignant cancer cells, known as cancer stem cells (CSCs), is suspected to be linked to metastasis and relapse. Targeting of CSCs may therefore provide a means of addressing cancer-related mortality. However, due to their low population in vivo and a lack of proper culture platform for their propagation, much of the CSC biology remains unknown. Since maintenance of CSCs is heavily influenced by the tumor microenvironment, this study developed a 3D culture platform that mimics the metastatic tumor extracellular matrix (ECM) to effectively increase CSC population in vitro and allow CSC analysis. Through electrospinning, nanofibers that were aligned, porous, and collagen-coated were fabricated from polycaprolactone to recreate the metastatic tumor ECM assemblage. Breast cancer cells seeded onto the nanofiber scaffolds exhibited gross morphology and cytoskeletal phenotype similar to invasive cancer cells. Moreover, the population of breast cancer stem cells increased in nanofiber scaffolds. Analysis of breast cancer cells grown on the nanofiber scaffolds demonstrated an upregulation of mesenchymal markers and an increase in cell invasiveness suggesting the cells have undergone epithelial-mesenchymal transition. These results indicate that the fabricated nanofiber scaffolds effectively mimicked the tumor microenvironment that maintains the cancer stem cell population, offering a platform to enrich and analyze CSCs in vitro.

 

6. Sacdalan DL, Garcia RL, Diwa MH, Sacdalan DB. (2021). Clinicopathologic Factors Associated with Mismatch Repair Status Among Filipino Patients with Young-Onset Colorectal CancerCancer Management and Research, Volume 2021 (13), Pages 2105—2115. https://doi.org/10.2147/CMAR.S286618 more

Abstract:

Introduction: Young-onset colorectal cancer is recognized as a distinct disease that may be sporadic or hereditary in nature. Microsatellite instability testing is recommended as a routine procedure in evaluating colorectal cancer specimens, especially in young-onset disease, because of implications in management. Immunohistochemistry of mismatch repair proteins serves as an inexpensive alternative to microsatellite instability testing with the added advantage of monitoring protein expression levels that may suggest underlying genetic or epigenetic alterations. This descriptive study aimed to determine the frequencies of proficient and deficient mismatch repair status among Filipino young-onset colorectal cancer patients, and to investigate their clinicopathologic profile.

Methods: Tumor tissues were prospectively collected from patients from two tertiary hospitals in the Philippines. Patients of age ≤ 45 years with resected adenocarcinoma of the colon or rectum were recruited.

Results: Seventy-seven out of 124 patients had tumor samples sent for immunohistochemistry. Of these, 61 samples (79%) were found to have proficient status while 16 samples (21%) had deficient status. Mismatch repair protein deficiencies, when present, more commonly involved MSH2 and MSH6 (9%) rather than MLH1 and PMS2 (5%). The deficient group had a mean age of 37.1 years and a female preponderance (56.25%), presenting as locally advanced ascending or descending colon tumors with mucinous histology in half of the population. The mismatch repair proficient group presented as locally advanced rectal and sigmoid tumors but with fewer mucinous adenocarcinomas (26.2%) compared to the deficient group. In both the mismatch repair proficient and deficient patients with family history reports, most did not have any known relative with cancer (75.4% and 68.75%, respectively).

Conclusion: This is the first attempt to perform mismatch repair testing among young-onset colorectal cancer patients in the Philippines and to gather data on their clinicopathologic characteristics. However, the limited sample size precludes conclusive results for the associations of mismatch repair with clinicopathologic features.

 

7. Tan, A.P.S., Aquino, V.M. and Hedreyda, C.T. (2021). Recombinant Expression of Alkane-1-Monooxygenase (AlkM) and Catechol 1,2-Dioxygenase (CatA) from Environmental Strains of Acinetobacter baumanniiPhilippine Journal of Science, 150 (2), Pages 445-452. more

Abstract:

Genes for the hydrocarbon-degrading enzymes – alkane 1-monooxygenase (AlkM) and catechol 1,2-dioxygenase (CatA) – were amplified from three environmental strains of Acinetobacter baumannii from Pasig River and oil sludge sample. Each gene has been previously cloned into a pBAD/Thio-TOPO plasmid expression vector and the recombinant pBAD/Thio-TOPO plasmids were introduced into E. coli TOP10 cells via transformation. This study was conducted to determine if AlkM and CatA proteins will be expressed by the recombinant E. coli TOP10 cells, to determine the optimized conditions for protein expression, and to perform purification of expressed AlkM and CatA fusion proteins. The pilot expression resulted in the production of the putative 62 kDa AlkM-thioredoxin and the 50 kDa CatA-thioredoxin fusion proteins, and the identity of the expressed proteins was verified to be AlkM and CatA using Western blotting. The study showed that best AlkM and CatA expression was observed when recombinant cells were grown in Super broth using 6-h post-induction time with at least 0.2% arabinose. Purified AlkM and CatA fusion proteins were obtained using affinity chromatography and subsequent size exclusion chromatography with Sephadex G-75 column. The preliminary activity of the purified CatA fusion enzyme observed at 1.128 units/mg was much lower than activities reported for other species, while an AlkM activity assay could not be performed because AlkM fusion proteins from recombinant E. coli did not solubilize after purification. These suggest the need to perform an extensive study to address AlkM solubility problem and optimize parameters for enzyme activity of expressed CatA and AlkM. Successful expression of AlkM and Cat A genes from a human bacterial pathogen in non-pathogenic E. coli host cells is an initial step to the possible use of recombinant cells in producing AlkM and CatA enzymes from a pathogenic bacterial species in addressing problems of oil contamination.

 

8. Wang T, Zhou J, Zou J, Shi Y, Zhou W, Shao P, Yu T, Cui W, Li X, Wu X, Ye J, Yan X, Naman CB, Lazaro JEH and He S (2021). Discovery of Cymopolyphenols A–F From a Marine Mesophotic Zone Aaptos Sponge-Associated Fungus Cymostachys sp. NBUF082Front. Microbiol. 12:638610. https://doi.org/10.3389/fmicb.2021.638610more

Abstract:

Mesophotic coral ecosystems (MCEs) have complex but understudied biodiversity, especially for natural products discovery. Untargeted metabolomics research on 80 extracts prepared from marine sponge-associated fungi, half from shallow reefs (<30 m) and half from MCEs (30–150 m), facilitated prioritization for further study a Cymostachys fungus from a 103 m deep Aaptos sponge. LC-MS target-directed isolation yielded a series of new compounds, cymopolyphenols A−F (1–6), and two known phenylspirodrimanes, F1839-I (7) and stachybotrylactone (8). This is the first report of natural products from the recently described genus, Cymostachys. Compounds 1–6 and 8 contain a dihydroisobenzofuran moiety, and 4–6 are low-order polymers of 1 with novel scaffolds. The structures of the compounds were established by spectroscopic and spectrometric data interpretation, with further support from X-ray crystallography studies of 3 and 4. Compound 3 undergoes facile racemization in solution and was found to crystalize as a racemic mixture. Compound 5 was also obtained in racemic form, and after chiral chromatography, both separated enantiomers racemized in solution by a presumed keto-enol tautomerization. Compounds 1 and 3–6 were found to be weakly antimicrobial (MIC 16–64 μg/ml) in vitro against several Gram-positive and Gram-negative human or aquatic pathogens, compound 5 was shown to chelate iron in vitro at 10 μM, and 8 activated plant disease resistance in vivo in a transgenic model organism.

 

9. Zhou, J.; Zhang, H.; Ye, J.; Wu, X.; Wang, W.; Lin, H.; Yan, X.; Lazaro, J.E.H.; Wang, T.; Naman, C.B.; He, S. (2021). Cytotoxic Polyketide Metabolites from a Marine Mesophotic Zone Chalinidae Sponge-Associated Fungus Pleosporales sp. NBUF144Mar. Drugs, 19, 186. https://doi.org/10.3390/md19040186more

Abstract:

Two new polyketide natural products, globosuxanthone F (1), and 2′-hydroxy bisdechlorogeodin (2), were isolated from the fungus Pleosporales sp. NBUF144, which was derived from a 62 m deep Chalinidae family sponge together with four known metabolites, 3,4-dihydroglobosuxanthone A (3), 8-hydroxy-3-methylxanthone-1-carboxylate (4), crosphaeropsone C (5), and 4-megastigmen-3,9-dione (6). The structures of these compounds were elucidated on the basis of extensive spectroscopic analysis, including 1D and 2D NMR and high-resolution electrospray ionization mass spectra (HRESIMS) data. The absolute configuration of 1 was further established by single-crystal X-ray diffraction studies. Compounds 1-5 were evaluated for cytotoxicity towards CCRF-CEM human acute lymphatic leukemia cells, and it was found that 1 had an IC50 value of 0.46 µM.

 

nip 

1. Abac, A.G., Esguerra, J.P.H., Otadoy, R.E.S. (2021). Modified structure equations and mass–radius relations of white dwarfs arising from the linear generalized uncertainty principleInternational Journal of Modern Physics D, 30 (1), Article number  2150005.more

Abstract:

The generalized uncertainty principle (GUP) is a common feature among several approaches related to quantum gravity. An approach to GUP was recently developed that contains both linear and quadratic terms of momenta, from which an infinitesimal phase space volume was derived up to the linear term of momenta. We studied the effects of this linear GUP approach on the structure equations and mass–radius relation of zero-temperature white dwarfs. We formulated a linear GUP-modified Chandrasekhar equation of state (EoS) by deriving exact forms of the thermodynamic properties of ideal Fermi gases. This was then used to obtain the analytical form of the modified Newtonian structure equations for the white dwarfs. By imposing a constraint on the momenta of the particles in the white dwarf due to linear GUP, the structure equations were solved and the modified mass–radius relation of the white dwarfs were obtained. This was then extended in the context of general relativity (GR), which, like linear GUP, affects white dwarfs significantly in the high-mass regime. We found that linear GUP displays a similar overall effect as in GR — linear GUP supports gravitational collapse of the white dwarf, by decreasing its limiting (maximum) mass and increasing its corresponding limiting (minimum radius). We also found that GUP effects become evident only at large values of the GUP parameter, but these values are still within the estimated bounds. This effect gets more prominent as we increase the as-of-yet unestablished value of the parameter.

 

2. Abella, A.P. (2021). Vorticity of wave-based octupole metamaterialsMaterials Letters, 283, Article number 128720. https://doi.org/10.1016/j.matlet.2020.128720more

Abstract:

In this study, the vertical vorticity of octupole metamaterials generated by nonlinear surface waves is investigated experimentally. An analytical model developed takes into account two contributions, one from the classical Stokes drift vorticity, and another one added to match experiments. The additional contribution is the Stokes drift vorticity multiplied by a dimensionless scaling prefactor. It is found that the optimal prefactor decreases as the wave steepness increases. When this additional contribution is set to zero, the dominant vorticity decay time closely matches the wave decay time. Overall, the results imply that both the Stokes drift and the additional vorticity contributions are necessary to characterize these octupole metamaterials.

 

3. Afalla, J., Prieto, E.A., Husay, H. A., Gonzales, K.C., Catindig, G., Abulikemu, A., Somintac, A., Salvador, A., Estacio, E., Tani, M., Hase, M. (2021). Effect of heteroepitaxial growth on LT-GaAs: ultrafast optical propertiesJournal of Physics Condensed Matter. https://doi.org/10.1088/1361-648X/ac04ccmore

Abstract:

Epitaxial low temperature grown GaAs (LT-GaAs) on silicon (LT-GaAs/Si) has the potential for terahertz (THz) photoconductive antenna applications. However, crystalline, optical and electrical properties of heteroepitaxial grown LT-GaAs/Si can be very different from those grown on semi-insulating GaAs substrates ("reference"). In this study, we investigate optical properties of an epitaxial grown LT-GaAs/Si sample, compared to a reference grown under the same substrate temperature, and with the same layer thickness. Anti-phase domains and some crystal misorientation are present in the LT-GaAs/Si. From coherent phonon spectroscopy, the intrinsic carrier densities are estimated to be 1015cm-3 for either sample. Strong plasmon damping is also observed. Carrier dynamics, measured by time-resolved THz spectroscopy at high excitation fluence, reveals markedly different responses between samples. Below saturation, both samples exhibit the desired fast response. Under optical fluences ‒54 µ J/cm2, the reference LT-GaAs layer shows saturation of electron trapping states leading to non-exponential behavior, but the LT-GaAs/Si maintains a double exponential decay. The difference is attributed to the formation of As-As and Ga-Ga bonds during the heteroepitaxial growth of LT-GaAs/Si, effectively leading to a much lower density of As-related electron traps.

 

4. Almerol, J.L.O., Bantang, J.Y., Liponhay, M.P. (2021). Mixing and segregation of freely-falling granular materials through a vertical pipeGranular Matter, 23 (2), Article number 18. https://doi.org/10.1007/s10035-020-01061-7more

Abstract:

Mixing and segregation of binary mixtures of freely-falling grains are demonstrated in a cylindrical pipe with an obstacle. Previously, the same setup was used to spatially focus monodisperse granular materials. As each grain is dropped one at a time from a random position at the entrance of the cylindrical pipe, it may collide with a steady or oscillating obstacle and the wall. We performed a time-driven multi-scale simulation and use Routh’s impact model for collisions to show that the focusing of grains for monodisperse granular materials is dependent on the geometry of the pipe, the elastic properties of the grain, and the amplitude of oscillation of the obstacle. For binary granular mixtures, segregation may be achieved when the elastic properties of the grain species have a big difference. However, the efficiency of segregation is diminished when the amplitude of obstacle oscillation is increased, leading to granular mixing. Just as a high degree of segregation can be attained with a stationary obstacle, a high degree of mixing can be obtained with a moving obstacle. 

 

5. Balmeo, M.M., Dizon, J.S.C., Empizo, M.J.F., Solibet, E.J.C.D., Agulto, V.C., Salvador, A.A., Sarukura, N., Nakanishi, H., Kasai, H., Padama, A.A.B. (2021). Density functional theory-based investigation of hydrogen adsorption on zinc oxide (101¯0) surface: RevisitedSurface Science, 703, Article number 121726. https://doi.org/10.1016/j.susc.2020.121726 more

Abstract:

Density functional theory based calculations with Hubbard correction (DFT + U) were performed to investigate the effects of varying coverage and different adsorption sites on hydrogen (H) adsorption on zinc oxide (ZnO) (101¯0) surface. Results show that H adsorption on top of oxygen (O) at low coverage (0.25 monolayer, ML) shifts the conduction band below the Fermi level and narrows the band gap. These phenomena are attributed to the charge transfer between H and the surface zinc (Zn) and O atoms. On the other hand, the H adsorption on top of Zn at low coverage (0.25 ML) shows an overlapping of H, Zn, and O states while maintaining the semiconductor nature of the system. At high coverage (1.0 ML), a charge accumulation layer on the surface forms, and the mechanisms that govern the interactions of H atoms when adsorbed exclusively on top of Zn or top of O are found to be similar with the low coverage cases. Lastly, at full coverage (2.0 ML), the effect of H on top of Zn is more evident as the system retained its semiconducting property. The adsorption energy is enhanced due to the reinforced overlapping of the H, Zn, and O states and due to the possible attraction between the adsorbed H atoms. The properties and stability of full-coverage adsorption were explained based on the findings on high- and low- coverages adsorption. The findings of the study will aid in understanding the interaction of H with the ZnO surface toward the further development of ZnO's optoelectronic applications.

 

6. Bruzon, D.A.V., Tapang, G.A., Martinez, I.S. (2021). An electrochemical setup designed for carbon dioxide solubility measurements in ionic liquidsReview of Scientific Instruments, 92 (2), Article number 024102. https://doi.org/10.1063/5.0019479 more

Abstract:

An electrochemical setup was designed and built to evaluate carbon dioxide solubility in ionic liquids. The setup can simultaneously measure amounts of CO2 in the gas and in the ionic liquid phase, making it very useful for in situ electrochemical measurements. The home-built glass cell is able to withstand high vacuum allowing the ionic liquid samples to be properly evacuated before characterization and kept free of contaminants during experiments. A pressure gauge attached to the setup enables continuous monitoring of gas added to the system. This kind of configuration can measure gas solubility in ionic liquids expressed as Henry’s constants determined from generated plots of dissolved gas concentration in the ionic liquid vs headspace gas pressure. It also serves as a more economical alternative to other gas solubility measurement techniques, as it is predominantly made of glass, and requires minimal sample amounts. The setup can be useful in determining the solubility of various gases in ionic liquids.

 

7. Georges, C., Cosme, J.G., Keßler, H., Mathey, L., Hemmerich, A. (2021). Dynamical density wave order in an atom-cavity system.New Journal of Physics, 23 (2), Article number 023003. https://doi.org/10.1088/1367-2630/abdf9cmore

Abstract:

We theoretically and experimentally explore the emergence of a dynamical density wave (DW) order in a driven dissipative atom-cavity system. A Bose-Einstein condensate is placed inside a high finesse optical resonator and pumped sideways by an optical standing wave. The pump strength is chosen to induce a stationary superradiant checkerboard DW order of the atoms stabilized by a strong intracavity light field. We show theoretically that, when the pump is modulated with sufficient strength at a frequency ω d close to a systemic resonance frequency ω >, a dynamical DW order emerges, which oscillates at the two frequencies ω > and ω < = ω d - ω >. This order is associated with a characteristic momentum spectrum, also found in experiments in addition to remnants of the oscillatory dynamics presumably damped by on-site interaction and heating, not included in the calculations. The oscillating density grating, associated with this order, suppresses pump-induced light scattering into the cavity. Similar mechanisms might be conceivable in light-driven electronic matter.

 

8. Gonzales K.C., Prieto E.A., Catindig G.A., De Los Reyes A., Faustino M.A., Tumanguil-Quitoras M.A., Husay H.A., Vasquez J.D., Somintac A., Estacio E., Salvador A. (2021). Terahertz emission increase in GaAs films exhibiting structural defects grown on Si (100) substrates using a two-layered LTG-GaAs buffer systemJournal of Materials Science: Materials in Electronics. https://doi.org /10.1007/s10854-021-05958-8more

Abstract:

Terahertz (THz) emission increase is observed for GaAs thin films that exhibit structural defects. The GaAs epilayers are grown by molecular beam epitaxy on exactly oriented Si (100) substrates at three different temperatures (Ts = 320 °C, 520 °C and 630 °C). The growth method involves the deposition of two low-temperature-grown (LTG)-GaAs buffers with subsequent in-situ thermal annealing at Ts = 600 °C. Reflection high energy electron diffraction confirms the layer-by-layer growth mode of the GaAs on Si. X-ray diffraction shows the improvement in crystallinity as growth temperature is increased. The THz time-domain spectroscopy is performed in reflection and transmission excitation geometries. At Ts = 320 °C, the low crystallinity of GaAs on Si makes it an inferior THz emitter in reflection geometry, over a GaAs grown at the same temperature on a semi-insulating GaAs substrate. However, in transmission geometry, the GaAs on Si exhibits less absorption losses. At higher Ts, the GaAs on Si thin films emerge as promising THz emitters despite the presence of antiphase boundaries and threading dislocations as identified from scanning electron microscopy and Raman spectroscopy. An intense THz emission in reflection and transmission excitation geometries is observed for the GaAs on Si grown at Ts = 520 °C, suggesting the existence of an optimal growth temperature for GaAs on Si at which the THz emission is most efficient in both excitation geometries. The results are significant in the growth design and fabrication of GaAs on Si material system intended for future THz photoconductive antenna emitter devices.

 

9. Rosete, M.M., Zosa, Ma. H., Sarmago, R. V. (2021). Improved Fabrication of Electrophoretically Deposited Bi2Sr2CaCu2O8 Films via Supporting Electrolyte Optimization in EthanolJournal of Superconductivity and Novel Magnetism, 34 (1), Pages 55-61. https://doi.org/10.1007/s10948-020-05668-ymore

Abstract:

This paper describes the effect of the addition of supporting electrolytes sodium chloride (NaCl), potassium chloride (KCl), and lithium chloride (LiCl) on the stability of Bi2Sr2CaCu2O8 (Bi-2212) suspension for improved electrophoretic deposition (EPD) of Bi-2212 films. The optimal concentrations are found to be 7.15, 5.21, and 8.09 wt% for NaCl, KCl, and LiCl, respectively. They exhibit characteristic high zeta potential, small particle size, and low settling velocity entailing that well-stabilized Bi-2212 suspensions are produced. The resulting films possess a relatively smooth surface, high transition temperature (Tc), and high c-axis orientation. Further analysis shows that LiCl is the most suitable supporting electrolyte for the Bi-2212 suspension. The mechanism of action of this supporting electrolyte is influenced by the Hofmeister effects, which yields an electrostatic stabilization mechanism. The synthesized film using the optimal LiCl concentration demonstrates the highest Tc (87.25 K) and is c-axis oriented and well-textured.

 

10. Sombillo, N.I.,  Banzon, R.S., Villagonzalo, C. (2021). Optimal fixed-point quantum search in an interacting Ising spin systemQuantum Information Processing, 20 (3), Article number 90. https://doi.org/10.1007/s11128-021-03023-1more

Abstract:

In Grover’s search algorithm, a priori knowledge of the number of target states is needed to effectively find a solution. This is due to the inherent oscillatory nature of unitary gates in the algorithm. A fixed-point quantum search is introduced in T. J. Yoder, G. H. Low and I. L. Chuang, (Phys. Rev. Lett.)113, 210501 [9] to mitigate this oscillation even without knowing the size of the target space. This is done by modifying the phase inversion and oracle of the original Grover’s algorithm so that the phase can assume intermediate values in [ - π, π]. Naturally, qubits in a quantum computer are interacting among themselves and this might introduce an error in the phase assignment. In this work, we used the Ising spin chain to simulate the interactions among the qubits and demonstrate how to implement the fixed-point quantum search. By inspecting the state vectors after some finite number of iterations, we found that the error is primarily due to the phase difference of the ideal target state with that of the final state. Further investigation shows that high fidelity between the ideal and real evolution can be achieved by using a low Rabi frequency. 

 

11. Villanueva, L.L., Galapon, E.A. (2021). Finite-part integration in the presence of competing singularities: Transformation equations for the hypergeometric functions arising from finite-part integrationJournal of Mathematical Physics, 62 (4), Article number 043505. https://doi.org/10.1063/5.0038274more

Abstract:

Finite-part integration is a recently introduced method of evaluating convergent integrals by means of the finite-part of divergent integrals [E. A. Galapon, Proc. R. Soc., A 473, 20160567 (2017)]. Current application of the method involves exact and asymptotic evaluation of the generalized Stieltjes transform 0af(x)/(ω+x)ρdx under the assumption that the extension of f(x) in the complex plane is entire. In this paper, the method is elaborated further and extended to accommodate the presence of competing singularities of the complex extension of f(x). Finite-part integration is then applied to derive consequences of known Stieltjes integral representations of the Gauss function and the generalized hypergeometric function that involve Stieltjes transforms of functions with complex extensions having singularities in the complex plane. Transformation equations for the Gauss function are obtained from which known transformation equations are shown to follow. In addition, building on the results for the Gauss function, transformation equations involving the generalized hypergeometric function 3F2 are derived.

 

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1. Bacus, Michael G., Buenaventura, Sheryl Grace C., Mamites, Allan Michael C., Elizagaque, Hannah G., Labrador, Christian C., Delfin, Frederick C., Eng, Ma. Noreen J., Lagare, Arlene P, Marquez, Gloria N., Murao, Lyre Anni E. (2021). Genome-based local dynamics of canine rabies virus epidemiology, transmission, and evolution in Davao City, Philippines, 2018–2019. Infection, Genetics and Evolution, 92. https://doi.org/10.1016/j.meegid.2021.104868more

Abstract:

Rabies is a fatal zoonotic and neglected tropical disease caused by the rabies virus (RABV) and is associated with neuronal dysfunction and death, with dogs as the predominant carrier. The Philippines plans to eradicate rabies by 2022, but this is challenged with sub-optimal coverage of vaccination programs coupled with sustained transmission chains, making it unable to eradicate the disease. We investigated the dynamics of canine rabies in the highly urbanized Davao City of the Philippines and its neighboring localities by assessing genetic relationships, transmission patterns, selection pressure, and recombination events using the whole genome sequence of 49 RABV cases from June 2018 to May 2019, majority of which (46%) were from the district of Talomo, Davao City. Although phylogeographic clustering was observed, local variants also exhibited genetic sub-lineages. Phylogenetic and spatial transmission analysis provided evidence for intra- and inter-city transmission predominantly through the Talomo district of Davao City. Around 84% of the cases were owned dogs, but the genetic similiarity of RABVs from stray and owned dogs further alluded to the role of the former as transmission vectors. The high rate of improper vaccination among the affected dogs (80%) was also a likely contributor to transmission. The RABV population under Investigation is generally under strong purifying selection with no evidence of vaccine evasion due to the genetic homogeneity of viruses from vaccinated and improperly vaccinated dogs. However, some homologous recombination (HR) events were identified along the G and L genes, also predominantly associated with viruses from Talomo. The complementary findings on epidemiology, transmission, and recombination for Talomo suggest that high incidence areas can be seeds for virus dispersal and evolution. We recommend further Investigations on the possibility of HR in future large-scale genome studies. Finally, districts associated with these phenomena can be targeted for evidence-based local strategies that can help break RABV transmission chains and prevent emergence of novel strains in Davao City.

 

2. Fortajada, Enrykie B., Fontanilla, Ian Kendrich C. and De Ungria, Maria Corazon A. (2021). Incorporating animal forensics in routine meat inspection in the Philippines. Forensic Science International: Animals and Environments, 1. https://doi.org/10.1016/j.fsiae.2021.100020more

Abstract:

Robust species identification of unprocessed and processed meat is essential to ensure the safety and quality of food products. Meat adulteration results from the wrong identification of animal sources, contamination of different meats during processing, or intentional meat substitution using those from other species and non-meat products of lower economic value. This review discusses the potential applications of DNA barcoding in routine meat inspections in the Philippines. Developing mini-barcode primer sets to enhance the utility of conventional techniques is critical in adopting DNA barcoding technology as a robust tool for routine inspections of meat sold commercially, including those intended for the halal meat industry. Increasing the ability of the Philippine National Meat Inspection Service to document the number, types, and scope of meat fraud is a step forward in finally using animal forensic science as a valuable component of its regulatory functions for the protection of the meat-consuming public.

 

3. Jose, Jose M., De Ungria, Maria Corazon (2021).  Bringing the science back into forensic science in death investigations in the Philippines during the COVID-19 pandemicForensic Science International: Reports, 3. https://doi.org/10.1016/j.fsir.2021.100185more

Abstract:

After a pandemic-filled 2020 had finally come to an end, many were looking forward to a new year filled with renewed hope and fresh beginnings. Unfortunately for a 23-year old Filipina, the first day of the year would turn out to be her last day on earth. While a single individual’s death on New Year’s day would typically not be a newsworthy event in the Philippines, this particular case sparked a media frenzy. It exposed the flaws of a death investigation system still reeling from the many unsolved cases of extrajudicial killings brought about by the war on drugs. To date, the Philippines does not have an independent, science-based medico-legal death investigation system. This commentary aims to provide a case narrative to highlight the urgency of adopting a systematic death investigation system, seek justice for the victim’s family, reduce the possibilities of wrongful accusations and convictions, and maximize the use of limited and costly forensic resources in the Philippines.

 

4. Rodriguez, Jae Joseph Russell B., Laude, Rita P., De Ungria, Maria Corazon (2021). An integrated system for forensic DNA testing of sexual assault cases in the PhilippinesForensic Science International: Synergy, 3. https://doi.org/10.1016/j.fsisyn.2021.100133more

Abstract:

In the Philippines, more than 7000 cases of sexual assault are reported annually. DNA technology is a powerful tool in identifying assailants. However, it is not routinely used in sexual assault investigations due to insufficient government support to cover the high cost of DNA testing and the absence of a national system for sample collection, handling, storage, and DNA testing of biological evidence. In itself, the nature of sexual assault samples containing DNA mixtures presents challenges to laboratory methods and interpretation of results. The sample recovered from the victim may only contain trace amounts of the assailant’s DNA, may have degraded due to prolonged storage in ambient conditions which is warm and humid in the tropics, or contaminated with inhibitors, such as in anal swabs. Hence, a closer evaluation of the processes of evidence collection and DNA testing is needed to increase the likelihood of success in generating conclusive results. In this paper, we propose an integrated system for DNA testing of biological samples collected from sexual assault victims considering the limitations of resources and the prevailing warm climate. Recommendations in this work should provide basis for formulating national guidelines for DNA analysis in aid of criminal investigations. The proposed scheme can be adopted by forensic DNA laboratories in the Philippines and in other countries facing similar challenges.