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Faculty Publication (2018)

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1. Angelo, D., Ramos, E., Batomalaque, G. A., & Anticamara, J. A. (2018). Current Status of Philippine Mollusk Museum Collections and Research, and their Implications on Biodiversity Science and Conservation. Philippine Journal of Science, 147 (1), Pages 123–163.

2. Boncan, D. A. T., David, A. M. E., & Lluisma, A. . (2018). A CAZyme-Rich Genome of a Taxonomically Novel Rhodophyte-Associated Carrageenolytic Marine Bacterium. Marine Biotechnology, Article in Press, Pages 1–21.

3. Catap, E.S., Kho, M.J.L., Jimenez, M.R.R. (2018). In vivo nonspecific immunomodulatory and antispasmodic effects of common purslane (Portulaca oleracea Linn.) leaf extracts in ICR miceJournal of Ethnopharmacology, 215, Pages 191-198.  more

Abstract:

Ethnopharmacological relevance

Portulaca oleracea (common purslane) is used in traditional medicine to cure various illnesses. However, its immune-protective properties and antispasmodic effects still need more pharmacological data if the plant will be utilized in herbal and drug formulations. Therefore, the present study determined the capacity of this plant species to modulate nonspecific immune responses and to confirm its antispasmodic activity in vivo in ICR mice.

4. Daquioag, J., Almiral, R., Ayala, M., Subejano, M., & Penuliar, G. (2018). Staphylococcus aureus and methicillin-resistant S. Aureus carriage in public computer services providers and utility jeepneys in UP Diliman. Science Diliman, 30 (1).

5. Dumilag, R.V., Monotilla, W.D. (2018). Molecular diversity and biogeography of Philippine foliose Bangiales (Rhodophyta)Journal of Applied Phycology, 30 (1), Pages 173-186.more

Abstract:

Species circumscription based on phenotypes has frequently masked the actual species diversity in foliose Bangiales. Application of DNA sequence differences in this group has removed dependence on the utility of morphological characters traditionally considered for species discrimination. This study currently represents an extensive analysis of phylogeny and species discrimination of foliose Bangiales across most of their distributional range in the northern Philippines, particularly in Luzon Strait. Molecular assessment based on plastid rbcL and two mitochondrial loci, COI-5P, and cox2–3 spacer, suggested four major groups diagnostic of species lineage. As supported by the results from the four molecular species delimitation methods: PTP, bPTP, ABGD, and SPN, the confirmed Philippine foliose Bangiales species included Pyropia acanthophora, Py. tanegashimensis, and two cryptic taxa from Batanes Islands. The number of species detected in this study suggested that the true species composition of Philippine foliose Bangiales might be considerably lower than what was previously thought. It is possible however that a greater sampling effort in complete seasonal range of collections will reveal more species and extent of their actual distributions. Although the influence of northeast monsoon significantly affects the growth of foliose Bangiales in the Philippines, its role in shaping their present-day distribution remains unclear. Our molecular datasets however suggested that their current biogeographic distribution might reflect past vicariant events and is therefore more complex than have been previously regarded.

6. Espiritu, C.A.L., Justo, C.A.C., Rubio, M.J., Svobodova, M., Bashammakh, A.S., Alyoubi, A.O., Rivera, W.L., Rollon, A.P., O'Sullivan, C.K. (2018). Aptamer Selection against a Trichomonas vaginalis Adhesion Protein for Diagnostic Applications. ACS Infectious Diseases, 4 (9), Pages 1306-1315.more

Abstract:

Trichomoniasis, caused by Trichomonas vaginalis, is the leading nonviral sexually transmitted infection worldwide. We report the selection of a DNA aptamer against a T. vaginalis adhesion protein, AP65, using a microtiter plate-based in vitro combinatorial chemistry process termed systematic evolution of ligands by exponential enrichment. The enriched library pool was sequenced by next-generation sequencing, and several aptamer candidates with high affinity and specificity were identified. The aptamer with the highest affinity and specificity had a KD in the low nanomolar range, as confirmed by three different techniques: surface plasmon resonance, enzyme-linked aptamer assay, and biolayer interferometry. The selected aptamer was demonstrated to have a high specificity to the AP65 protein and to T. vaginalis cells with no cross-reactivity to other enteric and urogenital microorganisms. Current work is focused on the development of inexpensive and easy-to-use aptamer-based diagnostic assays for the reliable and rapid detection of T. vaginalis in vaginal swabs.  

7. Galidon, J.M., Pasion, B., Tongco, M.D., Fidelino, J., Duya, M.R., Ong, P.S. (2018). Plant diversity patterns in remnant forests and exotic tree species-based reforestation in active limestones quarries in the Luzon and Mindanao biogeographic sub-regions in the PhilippinesEcological Research, 33 (1), Pages 63-72.more

Abstract:

The Philippines is both a megadiversity country and a global biodiversity hotspot. The diversity patterns of three major plant groups were assessed: (1) trees (trees and palms), (2) herbs (grasses, shrubs, forbs, ferns), and (3) epiphytes (climbers and epiphytes), by determining the changes in compositional and species richness patterns in two forest conditions, i.e., remnant forests and exotic tree species-based reforested areas, in active forest over limestone quarries in the Luzon and Mindanao biogeographic sub-regions of the Philippines. We identified 458 species comprising 266 tree species, 95 herbaceous species and 97 epiphyte species. Of these, 21 species were categorized as threatened species. Species composition differed between remnant forests and exotic tree species-based reforested areas for tree species and epiphyte species, while composition differences between the Luzon and Mindanao biogeographic sub-regions were limited to tree species only. Differences in species diversity (in terms of richness) were observed between biogeographic sub-regions for all plant groups, while differences between forest conditions were found for tree and epiphyte species only. Interestingly, there were significantly fewer numbers of exotic species in bigger remnant forest sites and in older exotic tree species-based reforested sites, while larger numbers of native species occurred in older than in younger exotic tree species-based reforested sites. The results emphasize the importance of understanding forest recovery in disturbed ecosystems. Conservation attention should focus on protecting remaining forests and planting native species as part of a forest restoration strategy to enhance faster forest recovery and re-connecting remnant forest patches.

8. Ibana, J. A., Sherchand, S. P., Fontanilla, F. L., Nagamatsu, T., Schust, D. J., Quayle, A. J., & Aiyar, A. (2018). Chlamydia trachomatis-infected cells and uninfected-bystander cells exhibit diametrically opposed responses to interferon gamma. Scientific Reports, (1), 8476.

9. Kim, E.-S., Trisurat, Y., Muraoka, H., Shibata, H., Amoroso, V., Boldgiv, B., Hoshizaki, K., Kassim, A.R., Young-Sun Kim, Hong Quan Nguyen, Ohte, N., Ong, P.S., Wang, C.-P. (2018). The International Long-Term Ecological Research–East Asia–Pacific Regional Network (ILTER-EAP): history, development, and perspectivesEcological Research, 33 (1), Pages 19-34.more

Abstract:

There are growing needs to broaden and deepen our multi-faceted understanding of the ecosystems, and the networks of Long-Term Ecological Research (LTER) can play significant roles in fostering and applying ecosystem studies at regional and global scales. The International LTER Network (ILTER) is organized as a global network of field research sites and scientists to address current ecological issues such as biodiversity loss and ecosystem degradation within a globally changing environment. The ILTER East Asia–Pacific Regional Network (ILTER-EAP) is one of the four constituent ILTER regional networks. Since 1995, ILTER-EAP has been developed to promote data sharing, research collaborations and capability building in the science and to bridge gaps between societal needs and scientific imperatives on concerns in the Asia–Pacific Region. Currently, ILTER-EAP comprises nine formal ILTER members and two associate networks. Their activities involve long-term and multiple-site observations of structural, functional and developmental aspects of ecosystems, data sharing, and bridging society and ecological science. This paper presents a review of the activities of ILTER-EAP, focusing on its: (1) vision and the development following its inception, (2) scientific activities and major outputs related to selected thematic areas, (3) contributions from ILTER-EAP to the international initiatives, and (4) future challenges and opportunities relating to its development and role in facilitating regional and global research collaborations. Accordingly, regional research questions were identified that could be most effectively addressed by opening up a common research platform, integrated data management system and the network science, which is open to all interested parties.

10. LaManna, J. A., Mangan, S. A., Alonso, A., Bourg, N. A., Brockelman, W. Y., Bunyavejchewin, S., … Myers, J. A. (2018). Comment on “Plant diversity increases with the strength of negative density dependence at the global scale.” Science, 360 (6391).

11. LaManna, J. A., Mangan, S. A., Alonso, A., Bourg, N. A., Brockelman, W. Y., Bunyavejchewin, S., … Ong, P. S. (2018). Response to Comment on “ Plant diversity increases with the strength of negative density dependence at the global scale .” Science, 360 (6391).

12. Lee, J., Lee, D., Rodriguez, J., Park, J. Y., Cho, E. J., Jacinto, S. D., & Lee, S. (2018). Determination of flavonoids in Acer okamotoanum and their aldose reductase inhibitory activities. Horticulture Environment and Biotechnology, 59 (1), Pages 131–137.

13. Lutz, J. A., Furniss, T. J., Johnson, D. J., Davies, S. J., Allen, D., Alonso, A., … Zimmerman, J. K. (2018). Global importance of large-diameter trees. Global Ecology and Biogeography.

14. Matias, A.M., Hereward, J. (2018). The complete mitochondrial genome of the five-lined cardinalfish Cheilodipterus quinquelineatus (Apogonidae). Mitochondrial DNA Part B, 3 (2), Pages 521-522. more

Abstract:

Cheilopdipterus quinquelineatus (Apogonidae) is an interesting species for investigating processes driving population divergence in marine system due to its wide distribution and life-history traits. However, to date, there is a limited genetic resource available for this species, or the family Apogonidae as exemplified by the availability of only two mitogenomes. In this study, we assembled the whole mitochondrial genome of this species yielding a 16,537 bp circular assembly composed of the typical vertebrate mitochondrial features. Phylogenetic inference of the supraordinal group of C. quiquelineatus showed monophyly of the major families. 

15. Matias, A.M.A., Riginos, C. (2018). Revisiting the "Centre Hypotheses" of the Indo-West Pacific: Idiosyncratic genetic diversity of nine reef species offers weak support for the Coral Triangle as centre of genetic biodiversity. Journal of Biogeography, 45 (8), Pages 1806-1817.more

Abstract:

Aim

Several biogeographic hypotheses seek to explain the extreme species diversity of the coral reefs in the Coral Triangle (CT) of the Indo‐West Pacific (IWP). Here, we investigate processes implicit to the Centre of Origin, Centre of Overlap and Centre of Survivalhypotheses. We focus on intraspecific genetic data, where intraspecific diversity can provide information regarding directionality of past dispersal (gene flow) and changes in population size such as expansion from refugia.

 

Methods

We use existing mitochondrial DNA data augmented with new samples from the Philippines, thus filling in key sampling gaps from previous studies, to examine nine reef species. We first test if genetic diversity peaks in the CT. We then estimate gene flow between regions—CT vs. Indian Ocean (IO) and CT vs. Pacific Ocean (PO)—to assess concordance with predicted directions of movement (i.e. into the CT or out of the CT). Finally, we investigate the historical demography of these species and evaluate population expansions to ascertain whether genetic diversity is correlated with putative Pleistocene refugia.

 

Results

Genetic diversity in the CT was not greater than genetic diversity in the IO and PO, and we found highly variable spatial patterns of genetic diversity when species were evaluated individually. Gene flow estimates indicated very limited exchange between regions, consistent with peripheral isolation and/or signals of historical divergence. For some species, however, there were signals of movement out of the CT. While there was no significant correlation between genetic diversity and putative refugia, genetic patterns suggested that some populations have experienced population expansions. The locations of expansion were also variable across species. Overall, there was no signal of concordant processes shaping intraspecific genetic diversity.

 

Main conclusions

Genetic patterns across species were highly variable with some species lending weak support for processes aligned with each of the “Centre” of diversity hypotheses. But overall there was no compelling evidence for uniform processes underlying all species, which possibly indicate that processes underlying the different “Centre” have not strongly affected IWP species within the recent past.

16. Orosco, F. L., & Lluisma, A. O. (2018). Genetic diversity of Penaeus monodon (Fabricius, 1798) in the Philippines as revealed by mitochondrial Cytochrome Oxidase I (COI)(Article). Philippine Agricultural Scientist, 101 (1), Pages 84–92.

17. Pagalilauan, H. A. M., Paraoan, C. E. M., & Vital, P. G. (2018). Detection of pathogenic bioaerosols and occupational risk in a Philippine landfill site. Archives of Environmental and Occupational Health, 73 (2), Pages 107–114.

18. Pedales, R.D.C., Fontanilla, I.K.C. (2018). Forensic entomology in the Philippines: Establishing baseline data on the forensically important blow fly species Chrysomya megacephala (Fabricius, 1974)Philippine Journal of Science, 147 (1).

Abstract:

The Philippines is yet to adapt and implement guidelines and protocols in forensic entomology, particularly establishing local databases. Considering the efforts made by neighboring Southeast Asian countries in the field, the nation has been left behind in insect evidence-based investigations. Of utmost importance to forensic entomology are blow flies (Diptera: Calliphoridae), which are primary colonizers of carrion. Through knowledge of their distribution, identity, and growth rates, investigators are able to provide a post-mortem interval that is most accurate after the onset of putrefaction. The Philippines has a total of 83 blow fly species recorded, including the cosmopolitan species Chrysomya megacephala. This paper aims to establish a baseline reference in Philippine forensic entomology by mapping the distribution, providing DNA barcodes, and estimating larval growth rates from oviposition to pupariation of C. megacephala. Distribution data were mapped in QGIS using localities from fieldwork data in this study and those in the Key to the Philippine Calliphoridae by Kurahashi and Magpayo. DNA barcodes of specimens from Isabela, Quezon City, and Marinduque in the Philippines matched with C. megacephala from the database in GenBank and revealed a possible SNP in the fragment amplified. C. megacephala was reared from oviposition in a simple incubation set-up to estimate the duration of development to pupariation, which ranged 100-113 hours. This is the first study on the distribution, molecular identification, and development of C. megacephala in the Philippines. Further work is needed to distinguish among populations of the species and to construct more precise growth curves. 

19. Perez, C.M.T., Pajares, I.G., Alcantara, V.A., Simbahan, J.F. (2018). Bacterial laminarinase for application in ethanol production from brown algae Sargassum sp. using halotolerant yeastBiofuel Research Journal, 5 (1), Pages 792-797.more

Abstract:

Macroalgae are known to have many industrial applications, with current research targeting the potential of macroalgal biomass as feedstock in production of biofuels. Marine algal biomass is rich in storage carbohydrates, laminarin, and cellulose, which can be converted to fermentable sugars using appropriate enzymes, for fermentation to ethanol. This study focused on ethanol production from macroalgae using only enzymatic treatment for saccharification of algal biomass. This involved the isolation and identification of cellulase and laminarinase-producing microorganisms from mangrove area in the Philippines and production of partially purified enzymes for algal biomass saccharification. Results showed that the partially purified laminarinase produced from Bacillus sp. was capable of hydrolyzing the laminarin present in the macroalage. Fermentation of the algal hydrolysate yielded only small amount of ethanol due to lack of other pre-treatment methods, however, it was observed that higher ethanol was produced in saccharification treatments using a combination of cellulase and laminarinase which implies a possible synergistic effect between the two enzymes. 

20. Rodriguez, J. P., Lee, Y. K., Woo, D. G., Shim, J. S., Geraldino, P. J. L., Jacinto, S. D., & Lee, S. (2018). Flavonoids from Cirsium japonicum var. maackii pappus as inhibitors of aldose reductase and their simultaneous determination. Chemical Papers, 72 (1), Pages 81–88.

21. Ramos, D.A.E., Batomalaque, G.A., Anticamara, J.A. (2018). Current status of Philippine Mollusk Museum Collections and Research, and their Implications on Biodiversity Science and ConservationPhilippine Journal of Science. 147 (1), Pages 123-163.

Abstract:

Mollusks are an invaluable resource in the Philippines, but recent reviews on the status of museum collections of mollusks or research trends in the country are lacking. Such assessments can contribute to a more comprehensive evaluation of natural history museums in the Philippines, as well as biodiversity management. This review showed that local museums in the Philippines have much to improve in terms of their accessibility and geographic coverage in order to effectively cater to research and conservation needs of the country. Online access to databases was lacking for local museums, making it cumbersome to retrieve collection information. The UST museum held the most species and subspecies across all museums (4899), comparable to the national museums of countries such as the USA and France. In terms of size, there were larger Philippine mollusk collections in museums abroad. Majority of mollusk specimens come from Regions 4 and 7, while the CAR and Region 12 were least sampled. Publications on Philippine mollusks are dominated by taxonomic and biodiversity research. Around 80% of publications were on marine species. Therefore, there is a great need to (1) improve access to collections by publishing databases and collections online; (2) improve spatial coverage of mollusk sampling to have a better nationwide (and habitat) representation of Philippine mollusk diversity; (3) fill important knowledge gaps in the ecological assessment of exploited mollusks and minor taxa that will be useful in status assessment and management; and (4) build a network of functional museums to facilitate mollusk and invertebrate researches and conservation by making properly curated specimens available to more researchers nationwide.

22. Rodriguez, J.P., Lee, Y.K., Woo, D.G., Shim, J.S., Geraldino, J.L., Jacinto, S.D., Lee, S. (2018). Flavonoids from Cirsium japonicum var. maackii pappus as inhibitors of aldose reductase and their simultaneous determinationChemical Papers, 72 (1), Pages 81-88.more

Abstract:

Aldose reductase is an enzyme in the polyol pathway which is associated in the progression of diabetic complications. In this study, we evaluated the inhibitory activity of Cirsium japonicumvar. maackii pappus (CJP) against rat lens aldose reductase (RLAR). The ethanolic extract, fractions and isolated flavonoids were subjected to an RLAR assay. Isolation of chloroform (CHCl3) and ethyl acetate (EtOAc) fractions led to the identification of four flavonoids: hispidulin (1), cirsimaritin (2), apigenin (3), and cirsimarin (4). The RLAR assay results suggested that the EtOAc fraction and flavonoids 1 and 3 promoted better AR inhibition than did TMG (control). The half-maximal inhibitory concentration (IC50) of compounds 1 and 3was 0.77 and 3.19 μM, respectively. A simultaneous determination of flavonoid content using HPLC–UV indicated that CJP contained large amounts of compounds 2 and 3 (1.65 and 1.84 mg/g, respectively). Flavonoids from Cirsium species have been widely reported to show various pharmacological activities. This study indicated that CJP has the potential to prevent diabetic complications and was a potential source of flavonoids.

23. Romana-Eguia, M.R.R., Santos, B.S., Ikeda, M., Basiao, Z.U., Kijima, A. (2018). Genetic assessment of milkfish (Chanos chanos Forsskal) stocks based on novel short tandem repeats for marker‐aided broodstock managementAquaculture Research, 49 (4), Pages 1557-1568.more

Abstract:

Milkfish hatchery broodstock are either from on‐grown wild‐caught or hatchery‐produced fry/juveniles. To determine if a marker‐assisted management scheme can be formulated for improved milkfish hatchery production, milkfish stocks were genetically characterized using nine novel short tandem repeats or microsatellites. Eight wild‐bred Philippine stocks (CLA, CUR, CAM, SIH, SBH‐I1, HH, PAL and ZH‐P0), four hatchery‐bred stocks (SBH‐I2, SBH‐D, BoH and ZH‐F1), two farm stocks of known mixed lineages (SPH and BDH) and one Indonesian hatchery‐bred stock (WJH) were assessed. WJH was included since milkfish fingerlings from Indonesia reared in Philippine farms could be developed into future broodstock. Mean allelic richness (Ar) was highest in wild‐bred stocks (9.5) and lowest in hatchery‐bred spawners (9.1). Mean expected heterozygosities (He) were relatively similar in all stocks with wild‐bred stocks slightly higher (0.67) than the others. An analysis of molecular variance indicated significant yet low genetic differentiation among stocks (FST = 0.013; p = .000) where variation (98.6%) was explained by intra‐stock differences. In some of the domesticated stocks, reductions in mean allelic richness were observed in first generation hatchery broodstock (e.g. ZH‐F1; Ar = 8.3), compared with their founder stock (e.g. ZH‐P0; Ar = 9.4). The Indonesian stock was similar to local wild‐bred stocks based on genetic variability indices; thus, it might be likely that the local stocks’ fitness traits could be comparable with the imported milkfish stock which has been perceived to be better. The quality of locally available farmed milkfish and prospects of formulating a broodstock management scheme for the production of good quality milkfish seedstock are herewith discussed.

24. Salas, R. L., Garcia, J. K. D. L., Miranda, A. C. R., Rivera, W. L., Nellas, R. B., & Sabido, P. M. G. (2018). Effects of truncation of the peptide chain on the secondary structure and bioactivities of palmitoylated anoplin. Peptides, 104, Pages 7–14.

25. Salvador, J.M., Apaga, D.L.T., Delfin, F.C., Calacal, G.C., Dennis, S.E., De Ungria, M.C.A. (2018). Filipino DNA variation at 12 X-Chromosome short tandem repeat markers. Forensic Science International: Genetics, 36, Pages e8-e12.more

Abstract:

Demands for solving complex kinship scenarios where only distant relatives are available for testing have risen in the past years. In these instances, other genetic markers such as X-chromosome short tandem repeat (X-STR) markers are employed to supplement autosomal and Y-chromosomal STR DNA typing. However, prior to use, the degree of STR polymorphism in the population requires evaluation through generation of an allele or haplotype frequency population database. This population database is also used for statistical evaluation of DNA typing results. Here, we report X-STR data from 143 unrelated Filipino male individuals who were genotyped via conventional polymerase chain reaction-capillary electrophoresis (PCR-CE) using the 12 X-STR loci included in the Investigator® Argus X-12 kit (Qiagen) and via massively parallel sequencing (MPS) of seven X-STR loci included in the ForenSeq™ DNA Signature Prep kit of the MiSeq® FGx™ Forensic Genomics System (Illumina). Allele calls between PCR-CE and MPS systems were consistent (100% concordance) across seven overlapping X-STRs. Allele and haplotype frequencies and other parameters of forensic interest were calculated based on length (PCR-CE, 12 X-STRs) and sequence (MPS, seven X-STRs) variations observed in the population. Results of our study indicate that the 12 X-STRs in the PCR-CE system are highly informative for the Filipino population. MPS of seven X-STR loci identified 73 X-STR alleles compared with 55 X-STR alleles that were identified solely by length via PCR-CE. Of the 73 sequence-based alleles observed, six alleles have not been reported in the literature. The population data presented here may serve as a reference Philippine frequency database of X-STRs for forensic casework applications.    

26. Tamayo, N.C.A., Anticamara, J.A. , Acosta-Michlik, L. (2018). National estimates of values of Philippine Reefs' Ecosystem ServicesEcological Economics, 146, Pages 633-644.more

Abstract:

Ecosystem Services (ES) – the direct (e.g., food and natural medicines) and indirect (e.g., cultural diversity and aesthetic values) benefits people obtain from various ecosystems – need to be assessed to aid decision makers and concerned public in creating policies that ensure continuous flow of ES to their beneficiaries (e.g., fisheries, food, income, livelihood, and traditional way of life to fishers and consumers). However, to date, ES assessments in Philippine reefs are mostly concentrated only on fisheries and tourism or on few areas in the Philippines (e.g., Pangasinan and Bohol Marine Triangle). This study fills research gaps by assessing coral reefs across 15 regions in the Philippines by estimating the following: (1) potential reef fisheries and Willingness-To-Pay (WTP) biodiversity values using underwater surveys and literature data, (2) reef fisheries value using Bureau of Fisheries and Aquatic Resources (BFAR) and literature data, (3) tourism value using Department of Tourism (DOT) and literature data, and (4) Total Economic Value (TEV). The TEV of Philippine reefs' ES amounted to 4 billion US$/yr or 140,000 US$/km2/yr. Furthermore, in each region of the Philippines, annual TEV ranged from 100 to 800 million US$, with potential reef fisheries value contributing the most in the TEV, followed by reef fisheries, tourism, and WTP biodiversity values. In addition, the Visayas regions have the highest values of benefits from coral reefs. Although the Philippines is deriving millions to billions of dollars of economic benefits from coral reefs, the observed degradation and temporal decline in coastal ecosystems could lead to a decline in the potential reef fisheries value, subsequently the TEV. The Philippines need to improve accounting and managing the derived benefits from coral reefs to ensure the sustainability and continuous flow of these benefits for present and future Filipino beneficiaries.

27. Tayaban, K.M.M., Pintor, K.L., Vital, P.G. (2018). Detection of potencial harmful algal bloom-causing microalgae from freshwater prawn farms in Central Luzon, Philippines, for bloom monitoring and prediction. Environment, Developmental and Sustainability, 20 (3), Pages1311-1328. more

Abstract:

Prawn aquaculture industry is one of the developing economic activities in the Philippines. Generally, a wide range of microalgae typically grow and proliferate in many aquaculture ponds. However, certain species of microalgae have the ability to form harmful algal blooms (HABs) which often bring damaging consequences to the aquaculture industry, food safety, and the environment. The study aims to identify and characterize the composition of microalgae (particularly Cyanophyta) that are capable of forming HABs in selected freshwater prawn culture ponds in Central Luzon, Philippines, using morphological, ultrastructural, and molecular characterizations. From water samples collected in ten selected ponds across Central Luzon (Bulacan, Nueva Ecija, Pampanga, Tarlac, and Zambales), potential HAB formers such as Oscillatoria agardhii, O. princeps, Microcystis aeruginosa, and M. wesenbergii were observed to have occurred mostly, while Anabaena circinalis was only observed in one site. Both morphological and ultrastructural methods brought upon some challenges and limitations while molecular methods using 16S rRNA gene and phylogenetic analysis which were optimized in this study offered better and more efficient ways of identification and were helpful in resolving genus-level and species-level relationships. The influence of physicochemical properties of pond water, especially nutrient levels (nitrate, nitrite, and orthophosphate) on the occurrence of these cyanobacteria was also analyzed. As a pioneering study on freshwater HABs in aquaculture ponds in the country, results of the study can provide information to improve the knowledge in bloom occurrence and prediction, and to develop freshwater HAB prevention and control methods.

28. Tiongson, J. K. A., Bruzon, D. A. V., Tapang, G. A., & Martinez, I. S. (2018). Syntheses and Properties of Methoxy and Nitrile Functionalized Imidazolium Tris(pentafluoroethyl)trifluorophosphate Ionic Liquids. Journal of Chemical and Engineering Data, 63 (5), Pages 1135–1145. 

29. Vital, P.G., Zara, E.S., Paraoan, C.E.M., Dimasupil, M.A.Z., Abello, J.J.M., Santos, I.T.G., Rivera, W.L. (2018). Antibiotic resistance and extended-spectrum beta-lactamase production of Escherichia coli isolated from irrigation waters in selected urban farms in Metro Manila, Philippines. Water, 10 (5), Page 548. more

Abstract:

Highly-polluted surface waters are increasingly used for irrigation in different agricultural settings because they have high nutrient content and are readily available. However, studies showed that they are reservoirs for the emergence and dissemination of antibiotic-resistant bacteria in the environment. In this study, the resistance of 212 Escherichia coli isolates from irrigation water, soil, and vegetables in selected urban farms in Metro Manila, Philippines was evaluated. Results showed that antibiotic resistance was more prevalent in water (67.3%) compared to soil (56.4%) and vegetable (61.5%) isolates. Resistance to tetracycline was the highest among water (45.6%) and vegetable (42.3%) isolates while ampicillin resistance was the highest among soil isolates (33.3%). Multidrug-resistant (MDR) isolates were also observed and they were more prevalent in water (25.3%) compared to soil (2.8%) and vegetable (8.4%) isolates. Interestingly, there are patterns of antibiotic resistance that were common to isolates from different samples. Extended-spectrum beta-lactamase production (ESBL) was also investigated and genes were observed to be present in 13 isolates. This provides circumstantial evidence that highly-polluted surface waters harbor antibiotic-resistant and MDRE. coli that may be potentially transferred to primary production environments during their application for irrigation purposes.

 

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1. Agulto, V.C., Empizo, M.J.F.,  Kawano, K.  Minami, Y., Yamanoi, K., Sarukura, N., Yago, A.C. and  Sarmago, R.V. (2018). Two-step fabrication of ZnO-PVP composites with tunable visible emissionsOptical Materials, 76, Pages 317-322.more

Abstract:

We report a two-step fabrication of zinc oxide-polyvinylpyrrolidone (ZnO-PVP) composites for potential phosphor-based applications. The composites are fabricated by initially preparing ZnO microrods using hydrothermal growth method and then dip-coating the microrods into aqueous PVP solutions with varying molar concentrations. The as-prepared ZnO microrods exhibit smooth surfaces and broad visible emissions, while the ZnO-PVP composites have pitted surfaces with shifted and reduced visible emissions. These changes in the structural and optical properties, which are found to depend on the PVP concentration, are attributed to the adsorption of PVP on the microrod surface. Although the surface morphology and visible emission are modified by PVP, the composites still maintain a hexagonal wurtzite crystal structure and near-band-edge ultraviolet (UV) emission similar with the as-prepared microrods. Our results therefore suggest that the ZnO-PVP composites can be used as phosphors that offer not only properties found in both ZnO and PVP but also tunable visible emissions which can be controlled during material fabrication.

2.Aseem, A., Jeba, G. G., Conato, M. T., Rimer, J. D., & Harold, M. P. (2018). Oxidative coupling of methane over mixed metal oxide catalysts: Steady state multiplicity and catalyst durability. Chemical Engineering Journal, 331, Pages 132–143.

3. Atayde, E.C. Jr., Montalbo, R.C.K., and Arco, S.D. (2018). Temperature- and pH-dependent drug release of block copolymers of methacrylic acid and Poly (Ethylene Glycol) methyl ether methacrylates. Philippine Journal of Science, 147 (3), Pages, 363-372.more

Abstract:

The block copolymers, poly(methacrylic acid)-b-poly(di(ethylene glycol) methyl ether methacrylate) (Block-D) and poly(methacrylic acid)-b-poly(poly(ethylene glycol) methyl ether methacrylate) (Block-P) were synthesized via reversible addition-fragmentation chain transfer (RAFT) polymerization towards the development of stimuli-responsive carriers of poorly water-soluble drugs. The structures of the copolymers and the confirmation of successful block copolymerization were studied using proton nuclear magnetic resonance (1H-NMR) spectroscopy. Data from gel permeation chromatography (GPC) then showed polydispersity indices (PDI) close to 1.0, characteristic of RAFT polymerization. Stimuli-response studies revealed Block-D was responsive at pH 5.15 and 26°C while Block-P was responsive at pH 5.15 and 72°C. The corresponding micelles had particle sizes of 92.95-201.4 nm, as determined by dynamic light scattering (DLS), with critical micelle concentration (CMC) at about 10-1 mg/ mL, per fluorescence studies. Using ibuprofen as the model drug, the drug loading content reached 11.76%, at 66.65% efficiency. In vitro release profiles then demonstrated 18% drug release within 5 h at stomach-like conditions, and 65% release within 5 h at small intestine-like conditions. Ultimately, cell viability assays of the blank and loaded micelles confirmed that neither is cytotoxic. These results show the immense potential and capability of the synthesized material as a drug delivery system for poorly water-insoluble drugs.

4. Atayde, E., Patricio, J., Marquez, M., and Arco, S. (2018). Investigating the electrochemical window of 1-methylimidazolium acetate and its effect as dopant to electrospun polyacrylonitrile fibers. In AIP Conference Proceedings, Vol. 2004 (1), Pages 040001-1 – 040001-5.more

Abstract:

Ionic liquids are a special class of materials that are currently being studied for their potential application as electrolytes for supercapacitors due to their thermal and electrochemical stability. In this study, we report the synthesis and characterization of an ionic liquid, 1-methylimidazolium acetate (MIMOAc), its electrochemical properties and its amenability as dopant in the electrospinning of polyacrylonitrile (PAN) fiber, a material commonly utilized as separator membrane for energy storage devices. MIMOAc was synthesized via solventless sonochemical reaction involving 1methylimidazole and acetic acid. The synthesized IL was then analyzed by cyclic voltammetry to determine its electrochemical window, the range in which no visible oxidation and reduction of the material occurs. It was found out that MIMOAc has a wide potential window of 3.6 V rendering it a formidable candidate as electrolyte for supercapacitors.  Furthermore, the IL was used as dopant in the electrospinning of PAN solution in the production of fibers. Based from AFM and SEM data, it was observed that the ionic liquid facilitated in the formation of thinner and consistent PAN fibers as compared to the undoped ones. 

 

5. Austria, E.S., Nuesca, G.M. and Lamorena, R.B. (2018). Spectral fitting approach for the determination of enrichment and contamination factors in mining sediments using laser-induced breakdown spectroscopy. Environmental Science and Pollution Research, Pages 1-9. more

Abstract:

Monitoring of pollution index values in sediments is crucial in assessing the environmental impacts of toxic metals in a given location. These indices are typically acquired using elaborate and tedious calibration curve-dependent techniques such as (inductively coupled plasma – optical emission spectroscopy) ICP-OES and (atomic absorption spectroscopy) AAS. In this study, laser-induced breakdown spectroscopy (LIBS) was used as a simple and fast alternative method for estimating enrichment factor (EF) and contamination factor (CF) of the sediment samples obtained from selected mining sites. Quantitative analyses of three metal targets (Cd, Pb, and Zn) were done using a calibration-free LIBS method based on the Boltzmann population distribution. Both the EF and CF values calculated from classical ICP-OES method provided significantly high correspondence with the respective EF (R2 = 0.8862–0.9770, p < 0.01–0.05) and CF (R2 = 0.9454–0.9714, p < 0.01) obtained from the developed LIBS method. The intensity-based LIBS approach identified samples AC2 and CCC as the ones with the highest and lowest pollution index values, respectively. The same observation was seen using the concentration-based ICP-OES technique which showed good correlation between the two methods. The correlation results showed the potential of the curve-fitting LIBS analysis in evaluating the level of metal contamination in an area without the preparation of matrix-matched calibration curves.

6. Belleza, O. J. V., Naraga, A. M. ., & Villaraza, A. J. L. (2018). Relative Ligand Exchange Rates in Gd-based MRI Contrast Agent Formation as Probed by Gd–XO Complex. Journal of the Chinese Chemical Society, 65 (5), Pages 561–566.

7. Briones, A.T. and Chichioco-Hernandez, C.L. (2018). Lipase inhibitory activity of Carica papayaChrysophyllum cainitoCorcorus olitoriusCympogon citrates and Syzgium cumini extractsFood Research, 2 (1), Pages 51-55.more

Abstract:

The lipase inhibitory action of Carica papaya, Chrysophyllum cainito, Corcorus olitorius,  Cymbopogon citrates and Syzygium cumini were evaluated to explore for the presence of  anti-obesity compounds and their potential weight-lowering activity. Enzyme inhibition results of the alcoholic extracts of the five plants showed that C. cainito has the highest percent inhibition at 74.91% while S. cumini, C. citratus, C. olitorius and C. papaya obtained less than 50% average inhibition. C. cainito was partitioned using hexane and ethyl acetate to further concentrate the bioactive compounds. The lipase inhibition assay of hexane and ethyl acetate extracts showed 92.11% inhibition and 21.9% inhibition, respectively. The greater activity in the former may imply that majority of potential anti lipase constituents are found in the hexane portion.

8. Buenaventura, A. G. E., Yago, A. C. C., Buenaventura, A. G. E., & Yago, A. C. C. (2018). Facile Electrochemical Pretreatment of Multiwalled Carbon Nanotube - Polydimethylsiloxane Paste Electrode for Enhanced Detection of Dopamine and Uric Acid. In AIP Conference Proceedings, Vol. 1958, Article number 020029.

9. Buenviaje, S. C., Usman, K. A. S., Payawan, L. M., Buenviaje, S. C., Usman, A. S., & Payawan, L. M. (2018). Synthesis and Characterization of Titanium Dioxide- Polypyrrole Nanocomposites for the Photodegradation of Bromophenol Blue. In AIP Conference Proceedings, Vol. 1958, Article number 020015.

10. Calangian, M. F., Ildefonzo, A. B., Manzano, V. K. S., Agcaoili, G. J. T., Ganado, R. J. J., Yago, A. C. C., Magdaluyo, E.R. Jr., Vasquez, R.D., and Franco, F. C. Jr. (2018). Facile Synthesis of Biologically Derived Fluorescent Carbon Nanoparticles (Fcnps) from an Abundant Marine Alga and its Biological Activities. Oriental Journal of Chemistry, 34 (2), Pages 791–799.

11. Denna, M.C.F.J., Camitan, R.A.B., Yabut, D.A., Rivera, B.A. and  Coo, L.dlC. (2018). Determination of Cu (II) in environmental water samples using polymer inclusion membrane- TAC optode in a continuous flow system.  Sensors and Actuators B: Chemical, 260, Pages 445-451.more

Abstract:

This study describes the selective determination of copper (II) using the recently developed polymer inclusion membrane (PIM) in a river water system via a continuous flow (CF) system. The PIM is composed of 42% di(2-ethlyhexyl) phosphoric acid (D2EHPA) as the carrier, 8% dioctyl phthalate (DOP) as the plasticizer and 49% poly(vinyl chloride) (PVC) as the base polymer. The colorimetric reagent that is used for the spectrophotometric determination of copper (II) is 1% 2-(2-thiazolylazo)-p-cresol (TAC). In this system, copper (II) is extracted into the PIM as the copper-D2EHPA complex which afterwards reacts with TAC producing green copper −TAC complex. The quantitative measurements are conducted by using light emitting diode (LED) and light dependent resistor (LDR) connected to a voltmeter. Results are obtained through the voltage readout on the computer. Under optimal conditions, the sensor has a limit of detection (LOD) of 0.10 mg L−1 and a limit of quantitation (LOQ) of 0.35 mg L−1. The CF-PIM-TAC system was successfully used in the determination of Cu(II) in river systems near mining sites.

12. Doederer, K., De Vera, G.A., Espino, M.P., Pype, M.-L., Gale, D. and Keller, J. (2018). MIB and geosmin removal during adsorption and biodegradation phases of GAC filtration. Water Science and Technology: Water Supply, 18 (4), Pages 1449-455.

13. Espenilla, M. B. L., Magyaya, R. C. S., Conato, M. T., Espenilla, M. B. L., Magyaya, R. C. S., Conato, M. T., & Ph, D. (2018). N / Fe-TiO 2 Doped Nanoparticles Loaded on Bentonite for Increased Photocatalytic Activity for the Degradation of Organic Pollutants. In AIP Conference Proceedings, Vol. 1958, Article number 020019.

14. Hung, S.C., Yeh, C.J., Ku, C.C., Lin, W.C., Fan, C.Y., Zulueta, M., Manabe, Y., Fukase, K., Li, Y.K. (2018). Single-step per-O-sulfonation and 1,6-Anhydro-bridge formation of sugar oligomers for fibroblast growth factor interactions. Chembiochem. DOI: 10.1002/cbic.201800464. more

Abstract:

Many circulating cancer-related proteins, such as fibroblast growth factors (FGFs), associate with glycosaminoglycans, particularly heparan sulfate, in the cell surface. Disaccharide analogues of heparan sulfate were previously identified as the shortest component of the sugar that bind to FGF-1 and FGF-2. Herein we conceived per-O-sulfonated analogues of such disaccharides taking note of the typical pose of L-iduronic acid and devised a single-step per-O-sulfonation and 1,6-anhydro-bridge formation of unprotected sugars to achieve such compounds by directly using SO3·Et3N as sulfonation reagent and dimethylformamide as solvent. The synthesized sugars based on the oligomaltose backbone bound FGF-1 and FGF-2 mostly in the submicromolar level, with the tetrasaccharide analogue reaching a low nanomolar binding with FGF-2.

15. Khakzad, N., Martinez, I. S., Kwon, H.-M., Stewart, C., Perera, R., & Reniers, G. (2018). Security risk assessment and management in chemical plants: Challenges and new trends. Process Safety Progress, 37 (2), Pages 211–220.

16. Kue, K.Y., Claudio, G.C. and Hsu, C.P. (2018). Hamiltonian-independent generalization of the fragment excitation difference scheme.  J. Chem. Theory Comput., 14, Pages, 1304−1310. more

Abstract:

The fragment excitation difference (FED) scheme is a useful method for calculating the complete diabatic couplings of various energy transfer systems. The lack of a good definition for the transformation of the transition density matrix to the off-diagonal FED matrix elements limits FED to single-excitation methods. We have developed a generalized FED scheme called the θ-optimized FED (θ-FED) scheme which does not require transforming the transition density matrices. In θ-FED, two states of interest are linearly transformed by a mixing angle θ into two mixed states. The excitation difference of each mixed state is evaluated and optimized numerically to determine the mixing angle. This approach allows for finding diabatic states and the corresponding couplings for a general set of Hamiltonians.

17. Martin, Z.N.Z., Martinez, I.S., and Nellas, R.B. (2018). Surface tension data of n-propane, n-octane and n-dodecane from nucleation simulations. Tellus, Series B: Chemical and Physical Meteorology, 70 (1). more

Abstract:

The Classical Nucleation Theory (CNT) has been a dominant model in understanding the self-assembly of new thermodynamic phases. CNT provides significant explanations to processes such as aerosol formation and cloud condensation. In this work, we generated the nucleation free energy profiles of normal alkanes (n-propane, n-octane and n-dodecane) at five different temperatures using the grand-canonical version of the nucleation algorithm. From these free energy profiles, characteristic   (  ) values were obtained. Using the density,   values from United-Atom Transferable Potentials for Phase Equilibria (TraPPE-UA) force field and the obtained   values, we calculated the corresponding surface tension,   values of these n-alkane systems at different temperatures. Values obtained are within reasonable agreement with experimental data.

18. Paderes, M. C., Siau, W. Y., Rong, Z., & Zhao, Y. (2018). Catalytic and Enantioselective Direct α-Alkylation of 3-Aryl and 3-Alkyl Oxindole Using Quinine-Derived Urea Catalyst. ChemistrySelect, (22), Pages 6160–6164.

19. Pagtalunan, C. A. M., Sumera, F. C. and Conato, M. T. (2018). Synthesis and Characterization of 12-Aminolauric Acid- Modified Montmorillonite for Catalytic Application. In AIP Conference Proceedings, Vol. 1958, Article number 020021.

20. Ramos, P. C. L., & Conato, M. T. (2018). Hydrothermal synthesis, crystal structures, and enantioselective adsorption property of bis(L-histidinato)nickel(II) monohydrate Hydrothermal Synthesis, Crystal Structures, and Enantioselective Adsorption Property of Bis(L- histidinato)nickel(II) Monohydr. AIP Conference Proceedings, Vol. 1958, Article number 020017.

21. Rellin, K.F.B., Dasmarinas, D.D. and Junio, H.A. (2018). Untargeted Metabolite Profiling of Philippine-grown Crescentia cujete and its Commercial Fruit Juice using GC-MS and UPLC-HRMS. Philippine Journal of Science, 147 (4), Pages 647-658.more

Abstract:

Calabash fruit (Crescentia cujete L.) juice has gained traction in Southern Philippines for its miraculous effect against stroke, diabetes, and cancer. Metabolite profile of local C. cujete fruit pulp and the commercial fruit juice were established using gas chromatography mass spectrometry (GC-MS) and ultra-high performance liquid chromatography high-resolution mass spectrometry (UPLC-HRMS). Putative hits to the NIST Mass Spectral Library included methyl salicylate, (+)-δ-cadinene, benzene and its derivatives such as toluene and o-xylene. Toluene and o-xylene are known air pollutants. Results indicated that the fruit has the potential to bioaccumulate small organic molecules. Volatile organic compounds detected in the fruit pulp were absent from the processed commercial juice. Other benzenoid compounds – thiazole and (+)-δ-cadinene, which are important biosynthetic precursors – were identified from the juice sample. Molecular networking analysis of the tandem MS data of the ethanol extract of the juice putatively identified the presence of 1-kestose and sucrose. 1-Kestose is considered as an essential prebiotic compound associated with boosting metabolism and immunity. Other kestose isomers were also indicated to be present in the juice based on the elution profile and MS/MS data. Preliminary activity tested for both samples yielded positive result against Candida albicans using disc diffusion asay. Only the juice sample yielded significant activity against Escherichia coli.

22. Salas, R.L., Garcia, J.K.DL, Miranda, A.C.R., Rivera, W.L., Nellas, R.B., and Sabido, P.M.G. (2018). Effects of truncation of the peptide chain on the secondary structure and bioactivities of palmitoylated anoplin. Peptides 104, Pages 7-14. more

Abstract:

Anoplin (GLLKRIKTLL-NH2) is of current interest due to its short sequence and specificity towards bacteria. Recent studies on anoplin have shown that truncation and acylation compromises its antimicrobial activity and specificity, respectively. In this study, truncated analogues (pal-ano-9 to pal-ano-5) of palmitoylated anoplin (pal-anoplin) were synthesized to determine the effects of C-truncation on its bioactivities. Moreover, secondary structure of each analogue using circular dichroism (CD) spectroscopy was determined to correlate with bioactivities. Interestingly, pal-anoplin, pal-ano-9 and pal-ano-6 were helical in water, unlike anoplin. In contrast, pal-ano-8, pal-ano-7 and pal-ano-5, with polar amino acid residues at the C-terminus, were random coil in water. Nevertheless, all the peptides folded into helical structures in 30% trifluoroethanol/water (TFE/H2O) except for the shortest analogue pal-ano-5. Hydrophobicity played a significant role in the enhancement of activity against bacteria E. coli and S. aureus as all lipopeptides including the random coil pal-ano-5 were more active than the parent anoplin. Meanwhile, the greatest improvement in activity against the fungus C. albicans was observed for pal-anoplin analogues (pal-ano-9 and pal-ano-6) that were helical in water. Although, hydrophobicity is a major factor in the secondary structure and antimicrobial activity, it appears that the nature of amino acids at the C-terminus also influence folding of lipopeptides in water and its antifungal activity. Moreover, the hemolytic activity of the analogues was found to correlate with hydrophobicity, except the least hemolytic pal-ano-5. Since most of the analogues are more potent and shorter than anoplin, they are promising drug candidates for further development.

23. Sibal, L.N. and Espino, M.P.B. (2018). Heavy metals in lake water: a review on occurrence and analytical determination. International Journal of Environmental Analytical Chemistry, DOI:10.1080/03067319.2018.1481212.

24.Tiongson, J.K.A., Bruzon, D.A.V., Tapang, G.A., and Martinez, I.S. (2018). Syntheses and properties of methoxy and nitrile functionalized imidazolium tris(pentafluoroethyl) trifluorophosphate ionic liquids. Journal of Chemical and Engineering Data, 63 (5), Pages 1135-1145. more

Abstract:

An alternative and more benign method was employed to synthesize tris(pentafluoroethyl)trifluorophosphate (FAP) ionic liquids (ILs). Ion exchange chromatography was used instead of the typical electrochemical fluorination developed by Ignat'ev and co-workers. The resulting procedure is simple and can be readily performed, as the use of corrosive hydrofluoric acid and the production of toxic and explosive byproducts were circumvented. Functionalization of the alkyl group of the imidazolium cation with a methoxy and a nitrile moiety was employed to observe changes in properties. The success of the synthesis was confirmed by 1H, 19F, and 31P NMR, IR, and UV-vis spectroscopy techniques. Quantitative product yields of approximately 80% (w/w) were obtained. The water content and viscosity values of the synthesized FAP-based ILs were found to be lower compared to other fluorine-containing ionic liquids. Thermal analyses resulted in high thermal degradation temperatures greater than 573.15 K. Electrochemical analyses showed potential windows of values greater than 5.0 V, indicating electrochemical stability. On the basis of the basic properties observed, the FAP-based ILs synthesized in this study may be useful as gas absorbents, electrolytes, and other applications, especially those involving extended temperature ranges.

25. Tutor, J.T. and Chichioco-Hernandez, C.L. (2018). Angiotensin-converting enzyme inhibition of fractions from Eleusine indica leaf extractsPharmacogn J., 10 (1), Pages 25-28. more

Abstract:

Solvent fractions and decoction of Eleusine indica leaves were tested for their ability to inhibit angiotensin-converting enzyme (ACE), an important component of the Renin-Angiotensin- Aldosterone System which is a critical regulator of arterial blood pressure. The ACE inhibitory activity of each fraction was measured by employing a colorimetric assay based on the hydrolysis of histidyl-hippuryl-leucine (HHL) by ACE. Preliminary assay results revealed that the ethyl acetate fraction exhibited the highest antihypertensive activity with a percent inhibition of 51.51%. This fraction was considered for further isolation using a bioassay-guided fractionation scheme. 

26. Usman, K. A. S., Buenviaje, S. C., Razal, J. M., Conato, M. T., & Payawan, L. M. J. (2018). Synthesis and characterization of zinc adeninate metal-organic frameworks (bioMOF1) as potential anti-inflammatory drug delivery material. In 8TH International Conference on Nanoscience and Nanotechnology 2017 (NANO-SciTech 2017).

27. Zulueta, M.M.L., Chyan, C.L. and Hung, S.C. (2018). Structural analysis of synthetic heparan sulfate oligosaccharides with fibroblast growth factors and heparin-binding hemagglutininCurrent Opinion in Structural Biology, 50, Pages 126-133.more

Abstract:

Heparan sulfate interacts with a variety of proteins at the cell surface. These proteins are primarily attracted to the high negative charge distribution brought by sulfate, sulfamate, and carboxylate functionalities along the sugar chain. Apart from electrostatic interactions, hydrogen bonding and even hydrophobic interactions contribute to the complex formation. While additional sulfate/sulfamate groups are often tolerated as long as the main structural requirements are met, occasionally, certain extra sulfate groups may be detrimental to the binding affinity. Here, we show these binding characteristics using the binding of fibroblast growth factors and heparin-binding hemagglutinin to synthetic heparan sulfate oligosaccharides as examples. Insights into the binding characteristics of these proteins may benefit future therapeutic interventions.

IESM logo

1. Bagtasa, G., Cayetano, M.G., Yuan, C.-S. (2018). Seasonal variation and chemical characterization of PM2.5 in northwestern Philippines. Atmospheric Chemistry and Physics, 18 (7), Pages 4965-4980. more

Abstract:

The seasonal and chemical characteristics of fine particulate matter (PM2.5) were investigated in Burgos, Ilocos Norte, located at the northwestern edge of the Philippines. Each 24gh sample of fine aerosol was collected for four seasons. Fine particulate in the region shows strong seasonal variation in both concentration and composition. Highest mass concentration was seen during the boreal spring season with a mean mass concentration of 21.6g±g6.6g3, and lowest was in fall with a mean concentration of 8.4g±g2.3g3. Three-day wind back trajectory analysis of air mass reveals the influence of the northwestern Pacific monsoon regimes on PM2.5 concentration. During southwest monsoon, sea salt was the dominant component of fine aerosols carried by moist air from the South China Sea. During northeast monsoon, on the other hand, both wind and receptor model analysis showed that higher particulate concentration was due to the long-range transport (LRT) of anthropogenic emissions from northern East Asia. Overall, sea salt and soil comprise 33g% of total PM2.5 concentration, while local biomass burning makes up 33g%. LRT of industrial emission, solid waste burning and secondary sulfate from East Asia have a mean contribution of 34g% to the total fine particulate for the whole sampling period.

2. Ishida, T., Kurihara, J., Viray, F.A., Namuco, S.B., Paringit, E.C., Perez, G.J., Takahashi, Y., Marciano, J.J., Jr. (2018). A novel approach for vegetation classification using UAV-based hyperspectral imagingComputers and Electronics in Agriculture, 144, Pages 80-85.more

Abstract:

The use of unmanned aerial vehicle (UAV)-based spectral imaging offers considerable advantages in high-resolution remote-sensing applications. However, the number of sensors mountable on a UAV is limited, and selecting the optimal combination of spectral bands is complex but crucial for conventional UAV-based multi spectral imaging systems. To overcome these limitations, we adopted a liquid crystal tunable filter (LCTF), which can transmit selected wavelengths without the need to exchange optical filters. For calibration and validation of the LCTF-based hyperspectral imaging system, a field campaign was conducted in the Philippines during March 28-April 3, 2016. In this campaign, UAV-based hyperspectral imaging was performed in several vegetated areas, and the spectral reflectances of 14 different ground objects were measured. Additionally, the machine learning (ML) approach using a support vector machine (SVM) model was applied to the obtained dataset, and a high resolution classification map was then produced from the aerial hyperspectral images. The results clearly showed that a large amount of misclassification occurred in shaded areas due to the difference in spectral reflectance between sunlit and shaded areas. It was also found that the classification accuracy was drastically improved by training the SVM model with both sunlit and shaded spectral data. As a result, we achieved a classification accuracy of 94.5% in vegetated areas.

3. Macatangay, R. C. (2018). Project MANTRA: Multi-platform Analysis of Trace Gases and Aerosols with a Focus on Atmospheric CO2 Measurements for Southeast Asia. In Land-Atmospheric Research Applications in South and Southeast Asia.

4. Rodrigo, S.M.T., Villanoy, C.L., Briones, J.C., Bilgera, P.H.T., Cabrera, O.C., Narisma, G.T.T. (2018). The mapping of storm surge-prone areas and characterizing surge-producing cyclones in Leyte Gulf, PhilippinesNatural Hazards, Pages 1-16. more

Abstract:

Historically, Leyte Gulf in central eastern Philippines has received catastrophic damage due to storm surges, the most recent of which was during Typhoon Haiyan in 2013. A city-level risk assessment was performed on Leyte Gulf through synthetic storm generation, high-resolution ocean modeling, and decision tree analyses. Cyclones were generated through a combination of a Poisson point process and Monte Carlo simulations. Wind and pressure fields generated from the cyclones were used in a storm surge model of Leyte Gulf developed on Delft3D. The output of these simulations was a synthetic record of extreme sea level events, which were used to estimate maximum surge heights for different return periods and to characterize surge-producing storm characteristics using decision tree analyses. The results showed that the area most prone to surges is the Tacloban–Basey area with a 2.8 ± 0.3 m surge occurring at a frequency of every 50 years. Nearby Palo area will likely receive a surge of 1.9 ± 0.4 m every 50 years while Giporlos–Salcedo area a surge of 1.0 ± 0.1 m. The decision tree analysis performed for each of these areas showed that for surges of 3–4 m, high-velocity winds (> 30 m/s) are consistently the main determining factor. For the areas, Tacloban, Basey, and Giporlos–Salcedo, wind speed was also the main determining factor for surge > 4 m.

 

IM

1. Agong, Louis Anthony; Amarra, Carmen; Caughman, John S.; Herman, AJ (Herman, Ari J). (2018). On the girth and diameter of generalized Johnson graphs.  Discrete Mathematics, 341 (1), Pages 138-142.more

Abstract:

Let v > k > i be non-negative integers. The generalized Johnson graph, J(v, k, i), is the graph whose vertices are the k-subsets of a v-set, where vertices A and B are adjacent whenever vertical bar A boolean AND B vertical bar = i. In this article, we derive general formulas for the girth and diameter of J(v, k, i). Additionally, we provide a formula for the distance between any two vertices A and B in terms of the cardinality of their intersection.

2. Akiyama, Shigeki, Caalim, Jonathan, Imai, Katsunobu, Kaneko, Hajime (2018). Corona Limits of Tilings: Periodic Case. Discrete & Computational Geometry, Pages 1-27. DOI: https://doi.org/10.1007/s00454-018-0033-x.more

Abstract:

We study the limit shape of successive coronas of a tiling, which models the growth of crystals. We define basic terminologies and discuss the existence and uniqueness of corona limits, and then prove that corona limits are completely characterized by directional speeds. As an application, we give another proof that the corona limit of a periodic tiling is a centrally symmetric convex polyhedron [see Zhuravlev (St Petersbg Math J 13(2):201–220, 2002) and Maleev and Shutov (Layer-by-layer growth model for partitions, packings, and graphs, Tranzit-X, Vladimir, 2011)].

3. Amarra, C. (2018). Graphs and Combinatorics. DOI: https://doi.org/10.1007/s00373-018-1948-y.more

Abstract:

We consider latin square graphs Γ=LSG(H) of the Cayley table of a given finite group H. We characterize all pairs (Γ,G), where G is a subgroup of autoparatopisms of the Cayley table of H such that G acts arc-transitively on Γ and all nontrivial G-normal quotient graphs of Γ are complete. We show that H must be elementary abelian and determine the number k of complete normal quotients. This yields new infinite families of diameter two arc-transitive graphs with k=1 or k=2.

4. Arceo, C.P.P., Jose, E.C., Lao, A.R., Mendoza, E.R. (2018). Reactant subspaces and kinetics of chemical reaction networksJournal of Mathematical Chemistry, 56 (2), Pages 395-422.more

Abstract:

This paper studies a chemical reaction network’s (CRN) reactant subspace, i.e. the linear subspace generated by its reactant complexes, to elucidate its role in the system’s kinetic behaviour. We introduce concepts such as reactant rank and reactant deficiency and compare them with their analogues currently used in chemical reaction network theory. We construct a classification of CRNs based on the type of intersection between the reactant subspace R and the stoichiometric subspace S and identify the subnetwork of S-complexes, i.e. complexes which, when viewed as vectors, are contained in S, as a tool to study the network classes, which play a key role in the kinetic behaviour. Our main results on new connections between reactant subspaces and kinetic properties are (1) determination of kinetic characteristics of CRNs with zero reactant deficiency by considering the difference between (network) deficiency and reactant deficiency, (2) resolution of the coincidence problem between the reactant and kinetic subspaces for complex factorizable kinetics via an analogue of the generalized Feinberg–Horn theorem, and (3) construction of an appropriate subspace for the parametrization and uniqueness of positive equilibria for complex factorizable power law kinetics, extending the work of Müller and Regensburger.

5. Babierra, A.L. & Reyes, Noli N.  (2018). A new characterization of the generalized inverse using projections on level setsJournal of Approximation Theory, 236, Pages 23-35.more   

Abstract:

We give a new characterization of the Moore–Penrose generalized inverse using projections on level sets. Our results may be used to obtain explicit approximations to metric projections on level sets. We illustrate our results in the setting of frames and annihilating subspaces.

6. Bacani, Dennis B., Lope, Jose Ernie C., Tahara, Hidetoshi (2018). On the unique solvability of nonlinear fuchsia partial differential equationsTokyo J. of Math., Advance publication (2018), 15 pages.more

Abstract:

We consider a singular nonlinear partial differential equation of the form

(tt)mu=F(t,x,{(tt)jαxu}(j,α)Im)

with arbitrary order mm and Im={(j,α)N×Nn;j+|α|≤m,j<m}Im={(j,α)N×Nn;j+|α|m,j<m} under the condition that F(t,x,{zj,α}(j,α)Im)F(t,x,{zj,α}(j,α)Im) is continuous in ttand holomorphic in the other variables, and it satisfies F(0,x,0)≡0F(0,x,0)≡0 and (∂F/∂zj,α)(0,x,0)≡0(∂F/∂zj,α)(0,x,0)≡0 for any (j,α)Im∩{|α|>0}(j,α)Im{|α|>0}. In this case, the equation is said to be a nonlinear Fuchsian partial differential equation. We show that if F(t,x,0)F(t,x,0) vanishes at a certain order as tttends to 00 then the equation has a unique solution with the same decay order.

 

7. Betty, R., Nemenzo, F., & Vasquez, T. (2018). Mass formula for self-dual codes over Fq+uFq+u2FqJournal of Applied Math and Computing, 57, Pages 523-546.more

Abstract:

In this paper, we establish a mass formula for self-dual codes over the finite chain ring Fq+uFq+u2FqFq+uFq+u2Fq, where FqFq is the finite field of order q and u3=0u3=0. We also give a classification of self-dual codes over Fq+uFq+u2FqFq+uFq+u2Fq, for q=2,3,4,5,7,8,9q=2,3,4,5,7,8,9, with lengths 2 and 4.

8. Caalim, Jonathan, Canlubo, Clarisson, Tanaka, Yui-Ichi. (2018). On the Lie algebra associated to S-unitary matrices. Linear algebra and its applications, 553, 167-181. DOI: 10.1016/j.laa.2018.05.010.more

Abstract:

A natural generalization of unitary groups arising from sesquilinear forms which are assumed neither Hermitian nor skew-Hermitian is considered. Let SMn(C). An S-unitary matrix A is a matrix AGLn(C) such that ASA=S. The set US of all S-unitary matrices is a matrix Lie group. A formula for the real dimension of the associated Lie algebra uS when S is nonsingular and normal is derived. When S is invertible and unitary, it is shown that uS is the direct sum of some Lie algebras associated to the indefinite unitary groups. Finally, the dimension formula is applied to a class of permutation matrices.

9. Cortez, Mark Jayson, Nazareno, Allen Lamarca, Mendoza, Eduardo R.  (2018). A computational approach to linear conjugacy in a class of power law kinetic systemsJournal of Mathematical Chemistry, 56 (2 & 1), Pages 336-357.  more

Abstract:

This paper studies linear conjugacy of PL-RDK systems, which are kinetic systems with power law rate functions whose kinetic orders are identical for branching reactions, i.e. reactions with the same reactant complex. Mass action kinetics (MAK) systems are the best known examples of such systems with reactant-determined kinetic orders (RDK). We specify their kinetics with their rate vector and T matrix. The T matrix is formed from the kinetic order matrix by replacing the reactions with their reactant complexes as row indices (thus compressing identical rows of branching reactions of a reactant complex to one) and taking the transpose of the resulting matrix. The T matrix is hence the kinetic analogue of the network’s matrix of complexes Y with the latter’s columns of non-reactant complexes truncated away. For MAK systems, the T matrix and the truncated Y matrix are identical. We show that, on non-branching networks, a necessary condition for linear conjugacy of MAK systems and, more generally, of PL-FSK (power law factor span surjective kinetics) systems, i.e. those whose T matrix columns are pairwise different, is T= T′, i.e. equality of their T matrices. This motivated our inclusion of the condition T= T′ in exploring extension of results from MAK to PL-RDK systems. We extend the Johnston–Siegel Criterion for linear conjugacy from MAK to PL-RDK systems satisfying the additional assumption of T= T′ and adapt the MILP algorithms of Johnston et al. and Szederkenyi to search for linear conjugates of such systems. We conclude by illustrating the results with several examples and an outlook on further research.

10. de la Cruz, R.J., Granario, D.Q. (2018). Products of symplectic normal matricesLinear Algebra and Its Applications, 543, Pages 162-172.more

Abstract:

A matrix A∈M2n(C) is symplectic if AT[0In−In0]A=[0In−In0]. We show that every symplectic matrix is a product of a symplectic unitary and a symplectic skew-Hermitian matrix. We show that every symplectic matrix is a product of four symplectic skew-Hermitian matrices or a product of four symplectic Hermitian matrices. We give the possible Jordan canonical forms of symplectic matrices which can be written as a product of a symplectic Hermitian and a matrix which is either symplectic Hermitian or symplectic skew-Hermitian.

11. Dela Rosa, K.L., Merino, D.I., Paras, A.T. (2018). The subspaces spanned by Householder vectors associated with an orthogonal or a symplectic matrixLinear Algebra and Its Applications, 546, Pages 37-49.more

Abstract:

The Cartan–Dieudonné–Scherk Theorem guarantees that every complex orthogonal matrix can be written as a product of matrices of the form HS,u≡I−uuTS, where S=I and uCn satisfies uTu=2; moreover, every complex symplectic matrix can be written as a product of matrices of the form HS,u≡I−uuTS where S=J=[0I−I0] and u≠0. Let a nonempty VCn be given. The S-orthogonal complement of V is VS={zCn | wTSz=0 for all wV}. The image of an n-by-n complex matrix A is the set of all zCn for which there is an xCn such that z=Ax and is denoted by Im(A). Let S=I or S=J. Suppose that Q=HS,u1HS,u2HS,ur. Set U=span{u1,u2,…,ur}. We study the relationship between Q, U, and Im(Q−I). Suppose that r is minimal. We show that if dim(U)=r, then Im(Q−I)=U. We also show that S(Q−I) is not skew symmetric if and only if dim(U)=r. Let W=Im(Q−I). We show that a relationship between W and WS determines the Jordan structure of Q, in particular, we show that (Q−I)2=0 if and only if WWS.

12. Hui, Shyamal Kumar & Lemence, Richard. (2018). On generalized ϕ-recurrent kenmotsu manifolds with respect to quarter-symmetric metric connection. Kyungpook Mathematical Journal, 58 (2), Pages 347-359.more

Abstract:

A Kenmotsu manifold Mn(φ, ξ, η, g), (n = 2m+1 > 3) is called a generalized φ-recurrent if its curvature tensor R satisfies

φ2((WR)(X,Y)Z)=A(W)R(X,Y)Z+B(W)G(X,Y)Z

for all X, Y, Z, W χ(M), where denotes the operator of covariant differentiation with respect to the metric g, i.e. is the Riemannian connection, A, B are non-vanishing 1-forms and G is given by G(X, Y )Z = g(Y, Z)X −g(X, Z)Y. In particular, if A = 0 = B then the manifold is called a φ-symmetric. Now, a Kenmotsu manifold Mn(φ, ξ, η, g), (n = 2m + 1 > 3) is said to be generalized φ-Ricci recurrent if it satisfies

φ2((WQ)(Y))=A(X)QY+B(X)Y

for any vector field X, Y χ(M), where Q is the Ricci operator, i.e., g(QX, Y ) = S(X, Y ) for all X, Y. In this paper, we study generalized φ-recurrent and generalized φ-Ricci recurrent Kenmotsu manifolds with respect to quarter-symmetric metric connection and obtain a necessary and sufficient condition of a generalized φ-recurrent Kenmotsu manifold with respect to quarter symmetric metric connection to be generalized Ricci recurrent Kenmotsu manifold with respect to quarter symmetric metric connection.

13. Kim, S., de los Reyes, A.A., Jung, E.  (2018). Mathematical model and intervention strategies for mitigating tuberculosis in the Philippines. Journal of Theoretical Biology, 443 (14), Pages 100-112. more

Abstract:

Tuberculosis (TB) is the sixth leading cause of morbidity and mortality in the Philippines. Although significant progress has been made in the detection and cure of TB under the Directly Observed Treatment Short Course, battling against the disease is still a burdensome task. It demands a concerted effort for specific and effective interventions. In this work, a mathematical TB model fitted to the Philippine data is developed to understand its transmission dynamics. Different control strategies such as distancing, latent case finding, case holding, active case finding controls, and combinations thereof are investigated within the framework of optimal control theory. This study proposes optimal control strategies for reducing the number of high-risk latent and infectious TB patients with minimum intervention implementation costs. Results suggest that distancing control is the most efficient control strategy when a single intervention is utilized. However, full scale employment of the distancing control measure is a daunting task. This burden can be circumvented by the combination of other control interventions. Our noble finding in this study is that enhancing active case finding control instead of case holding control together with distancing and latent case finding control is shown to have significant potential for curtailing the spread of TB in the Philippines.

14. Lope, J. E. C., Sato, R., & Vernescu, B. (2018). Well-posedness of steady state Navier–Stokes equations with slip boundary conditions. Applicable Analysis, 6811, Pages 1–15.more

Abstract:

We study the motion of a viscous incompressible fluid in a bounded region of (Formula presented.) containing finitely many rigid solid particles of small size. On the boundary of the particles, we prescribe the slip boundary condition of the form developed in Fujita H. [A mathematical analysis of motions of viscous incompressible fluid under leak or slip boundary conditions. Mathematical fluid mechanics and modeling (Kyoto, 1994). Srikaisekikenkysho Kkyroku No. 888; 1994. p. 199–216] and Le Roux C, Tani A. [Steady solutions of the Navier–Stokes equations with threshold slip boundary conditions. Math Methods Appl Sci. 2007;30(5):595–624]. We derive a weak formulation of the problem and obtain an equivalent variational inequality formulation. Sufficient conditions for existence, uniqueness, and continuous dependence on data are obtained.

15. Magdalena, Ikha, Roque, Marian P.  (2018).  Analytical and numerical solution for wave reflection from a porous wave absorberJournal of Physics: Conference Series, 974 (1). more

Abstract:

In this paper, wave reflection from a porous wave absorber is investigated theoretically and numerically. The equations that we used are based on shallow water type model. Modification of motion inside the absorber is by including linearized friction term in momentum equation and introducing a filtered velocity. Here, an analytical solution for wave reflection coefficient from a porous wave absorber over a flat bottom is derived. Numerically, we solve the equations using the finite volume method on a staggered grid. To validate our numerical model, comparison of the numerical reflection coefficient is made against the analytical solution. Further, we implement our numerical scheme to study the evolution of surface waves pass through a porous absorber over varied bottom topography.  

16. Paguio, Victoria May E., Kappel, Franz, Kotanko, Peter. (2018). A model of vascular refilling with inflammationMathematical Biosciences, 303, 101-114.  DOI: 10.1016/j.mbs.2018.06.007.more

Abstract:

Inflammation is prevalent in hemodialysis patients and is believed to significantly contribute to cardiovascular disease progression in end stage renal disease patients undergoing hemodialysis. Increased vascular permeability associated with inflammation is likely to influence the capillary wall properties, affecting vascular refilling during hemodialysis. In this paper, we present a model that incorporates inflammation into a vascular refilling model. We investigate how inflammation may affect the fluid volume and protein concentration dynamics in the plasma and interstitial spaces. In our work, we quantify inflammation by considering the concentration of the inflammatory biomarker C-reactive protein (CRP). Traditional sensitivity functions and subset selection based on asymptotic standard errors were used to aid in parameter identification. Estimates of the parameters were calculated from numerically generated measurements for fluid flux and hematocrit. Observations on the capillary wall properties, filtration and reflection coefficients, were done using data on mean CRP and serum albumin from a large population of European hemodialysis patients in their terminal two years before death and patients surviving for at least four years after dialysis initiation.

 

17. Palines, Herbert S. Jitman, Somphong & Dela Cruz, Romar (2018). Hermitian self-dual quasi-abelian codes. Journal of Algebra Combinatorics Discrete Structures and Applications, 5 (1), Pages 5-18.more

Abstract:

Quasi-abelian codes constitute an important class of linear codes containing theoretically and practically interesting codes such as quasi-cyclic codes, abelian codes, and cyclic codes. In particular, the sub-class consisting of 1-generator quasi-abelian codes contains large families of good codes. Based on the well-known decomposition of quasi-abelian codes, the characterization and enumeration of Hermitian self-dual quasi-abelian codes are given. In the case of 1-generator quasi-abelian codes, we offer necessary and sufficient conditions for such codes to be Hermitian self-dual and give a formula for the number of these codes. In the case where the underlying groups are some p-groups, the actual number of resulting Hermitian self-dual quasi-abelian codes are determined.

 

18. Talabis, D.A.S.J., Arceo, C.P.P., Mendoza, E.R. (2018). Positive equilibria of a class of power-law kineticsJournal of Mathematical Chemistry, 56 (2), Pages 358-394.more

Abstract:

This paper studies a class of power-law kinetics, PL-ILK, for whose subset, PL-TIK, analogues of the Deficiency Zero Theorem and the Deficiency One Theorem (DOT) for mass action systems are valid. The DOT also includes the necessary and sufficient condition of Boros for uniqueness in the non-weakly reversible case. To our knowledge, this is the first set of kinetics beyond mass action kinetics (MAK) for which the DOT has been shown to be valid. A further interesting property of PL-TIK is a certain “robustness” relative to dependence of linkage classes: existence of a positive equilibrium for each linkage class implies the existence of a positive equilibrium for the whole network. For MAK systems, the PL-ILK property is equivalent to the reactant deficiency of the linkage class containing the zero complex being one, and zero for all other linkage classes. As shown in the Supplementary Materials, an initial survey of MAK and BST systems already reveals numerous examples with PL-ILK kinetics.

 

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1. Agulto, V. C., Empizo, M. J. F., Kawano, K., Minami, Y., Yamanoi, K., Sarukura, N., Yago, A.C.C., Sarmago, R. V. (2018). Two-step fabrication of ZnO-PVP composites with tunable visible emissions. Optical Materials, 76, Pages 317–322.more

Abstract:

We report a two-step fabrication of zinc oxide-polyvinylpyrrolidone (ZnO-PVP) composites for potential phosphor-based applications. The composites are fabricated by initially preparing ZnO microrods using hydrothermal growth method and then dip-coating the microrods into aqueous PVP solutions with varying molar concentrations. The as-prepared ZnO microrods exhibit smooth surfaces and broad visible emissions, while the ZnO-PVP composites have pitted surfaces with shifted and reduced visible emissions. These changes in the structural and optical properties, which are found to depend on the PVP concentration, are attributed to the adsorption of PVP on the microrod surface. Although the surface morphology and visible emission are modified by PVP, the composites still maintain a hexagonal wurtzite crystal structure and near-band-edge ultraviolet (UV) emission similar with the as-prepared microrods. Our results therefore suggest that the ZnO-PVP composites can be used as phosphors that offer not only properties found in both ZnO and PVP but also tunable visible emissions which can be controlled during material fabrication.

2. Angub, M. C. M., Vergara, C. J. T., Husay, H. A. F., Salvador, A. A., Empizo, M. J. F., Kawano, K., Minami, Y., Shimizu, T., Sarukura, N., Somintac, A. S. (2018). Hydrothermal growth of vertically aligned ZnO nanorods as potential scintillator materials for radiation detectors. Journal of Luminescence, 203, Pages 427-435.more

Abstract:

We investigate the hydrothermal growth of zinc oxide (ZnO) nanorods to realize their potential scintillator applications. Vertically aligned ZnO nanorods were successfully fabricated on seeded silicon (Si) substrates at a relatively low temperature of 85 °C using different hexamethylenetetramine [(CH2)6N4, HMTA] and zinc acetate dihydrate [Zn(CH3COO)2·2H2O, ZnAc] concentration ratios. Varying the precursor concentration ratio affects the nanorod dimensions which, in turn, influence the apparent densities and observed emissions. But regardless of the HMTA and ZnAc concentration ratio used, the fabricated nanorods exhibit well-defined morphologies, hexagonal crystal structure, preferential -axis orientation, and 24–120-ps ultraviolet (UV) emissions. With these excellent structural and optical properties, the hydrothermal-grown ZnO nanorods are suggested to be used as scintillator materials which offer not only fast scintillation response but also high spatial resolution for future radiation detectors.

3. Austria, E.S., J., Nuesca, G. M., & Lamorena, R. . (2018). Spectral fitting approach for the determination of enrichment and contamination factors in mining sediments using laser-induced breakdown spectroscopy. Environmental Science and Pollution Research, Article in press.

 

4. Bardolaza, H. R., Vasquez, J. D. E., Bacaoco, M. Y., de los Reyes, A. E., Lopez, L.P., J., Somintac, A. S., Salvador, A.A., Estacio, E.S., Sarmago, R. V. (2018). Temperature dependence of THz emission and junction electric field of GaAs–AlGaAs modulation-doped heterostructures with different i-AlGaAs spacer layer thicknesses. Journal of Materials Science: Materials in Electronics, 29 (10), Pages 8760–8766.more

Abstract:

Photocarrier dynamics in GaAs/AlGaAs modulation-doped heterostructures (MDH) having i-AlGaAs spacer layers of different thicknesses were investigated using temperature-dependent terahertz time-domain spectroscopy (THz-TDS) and photoreflectance spectroscopy. In particular, results are discussed in the framework of the temperature dependence of the heterojunction electric field and photocarrier velocity for two i-AlGaAs spacer layer thickness values. The junction electric field, THz emission intensity and bandwidth of the MDH samples all decrease as temperature decreases. In contrast, the THz emission intensity and bandwidth of a reference bulk undoped GaAs does not significantly vary with temperature. These results imply that THz emission of MDH’s originates primarily from carrier drift due to the GaAs/AlGaAs junction electric field. A general decrease in the THz emission bandwidth of the MDH’s is attributed to a decrease in carrier velocity at lower temperatures, presumably due to the weaker electric field. Moreover, the MDH sample with thinner spacer layer exhibited a higher junction electric field. This work demonstrates the study of temperature-dependent photocarrier transport and junction electric field measurements. The results may provide useful insights in the design of MDH-based devices.

5. Buenviaje, S. C., Usman, K. A. S., Payawan, L. M., Buenviaje, S. C., Usman, A. S., & Payawan, L. M. (2018). Synthesis and Characterization of Titanium Dioxide- Polypyrrole Nanocomposites for the Photodegradation of Bromophenol Blue. In AIP Conference Proceedings, Vol. 1958, Article number 020015.more

Abstract:

Titania (TiO2) nanoparticles were synthesized through sol-gel method and stabilized by polypyrrole through photopolymerization. The titania-polypyrrole (TP) nanocomposites were then characterized on the basis of particle size, stability, dispersity, band gap energy, and surface morphology. Using dynamic light scattering, TP products of varied mole ratios were found to be all nano in size with bare TiO2 having 66.6 nm and the rest with 90 nm. These materials were also found to be stable in water with Zeta potentials all above 25 mV. The band gap energies of TP products were precise and accurate relative to the 3.52 eV of bare TiO2 using ultraviolet-visible spectra. The particles were also monodisperse enough with PDI values of 0.450. The TP material was also drop-casted on mica, and found to have cone-shaped peaks at 60 nm and almost uniform surface using atomic force microscopy. Photodegradation of bromophenol blue was also optimized and found to have 97.53% efficiency in the presence of TP as photocatalyst and at pH 7.

6. Gili, M., Latag, G., & Balela, M. (2018). In-situ deposition of hematite (α-Fe 2 O 3 ) microcubes on cotton cellulose via hydrothermal method. Journal of Physics: Conference Series, 985, 12027.

 

7. Sadia, C. P., Lopez, L. P., delos Santos, R. M., Muldera, J. E., delos Reyes, A., Tumanguil, M. A. C., Somintac, A.S., Estacio, E.S., Salvador, A. A. (2018). Epitaxial growth of p-InAs on GaSb with intense terahertz emission under 1.55- μ m femtosecond laser excitation. Thin Solid Films, 648, Pages 46–49.more

Abstract:

We report the molecular beam epitaxy growth of high-quality p-InAs thin films evaluated in the context of 1.55 μm femtosecond laser-excited THz emission efficiency. The presence of p-InAs is confirmed via scanning electron microscopy and X-ray diffraction. Using a GaAs buffer layer, the epitaxial growth of p-InAs layers was successfully achieved. Initiating GaAs deposition by growth interruption, we find that GaAs adheres to the GaSb substrate and provides a quasi-planar surface for the subsequent layers. We also find a significant enhancement in the THz radiation intensity of p-InAs films that is approximately twice compared to that of bulk p-InAs for 1.55 μm wavelength.

8. Usman, K. A. S., Buenviaje, S. C., Razal, J. M., Conato, M. T., & Payawan, L. M. J. (2018). Synthesis and characterization of zinc adeninate metal-organic frameworks (bioMOF1) as potential anti-inflammatory drug delivery material. In 8TH International Conference on Nanoscience and Nanotechnology 2017 (NANO-SciTech 2017).more

Abstract:

Zn8(ad)4(BPDC)6O•2Me2NH2 (bioMOF1), a porous metal–organic framework with zinc-adeninate secondary building units (SBUs), interconnected via biphenyldicarboxylate linkers, shows great potential for drug delivery applications due to its non-toxic and biocompatible components (zinc and adenine). In this study, bioMOF1 crystals synthesized solvothermally at 130°C for 24 hours, were characterized thoroughly and loaded with a known anti-inflammatory drug, nimesulide (NIM). The crystalline nature of the material was confirmed using powder x-ray diffraction crystallography (PXRD) along with morphology assessment using focused-ion beam/field emission scanning electron microscopy (FIB/FESEM). NIM was introduced to the crystals via solvent exchange accompanied with vigorous stirring and quantified using thermogravimetric analysis (TGA) with loading saturation of 30% attained during the 2nd to 3rd day of drug immersion. Drug release in phosphate buffer saline and in deionized water was done to monitor the kinetic of drug release in vitro. The drug release showed a controlled discharge profile which slowed down at the 24th and 48th hour of release. Drug release in buffer showed a faster release of drug from the material, which means that the presence of cations in the solution could further trigger the release of drug. Slow drug release was observed for all of the set-ups with maximum % drug release of 24.47%, and 16.14% for the bioMOF1 in buffer and bioMOF1 in water respectively for the span of 48 hours.

 

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1. Abesamis, R. A., Langlois, T., Birt, M., Thillainath, E., Bucol, A. A., Arceo, H. O., & Russ, G. R. (2018). Benthic habitat and fish assemblage structure from shallow to mesophotic depths in a storm-impacted marine protected area. Coral Reefs, 37 (1).more

 

2. Azcuna, M., Tun, J. O., Yap, H. T., & Concepcion, G. P. (2018). Callyspongia samarensis (Porifera) extracts exhibit anticancer activity and induce bleaching in Porites cylindrica (Scleractinia). Chemistry and Ecology, 34 (5), Pages 397–411.more

 

3. Boncan, D. A. T., David, A. M. ., & Lluisma, A. . (2018). A CAZyme-Rich Genome of a Taxonomically Novel Rhodophyte-Associated Carrageenolytic Marine Bacterium. Marine Biotechnology, 1–21. Article in Press.

 

4. Breitburg, D., Levin, L. A., Oschlies, A., Grégoire, M., Chavez, F. P., Conley, D. J., … Zhang, J. (2018). Declining oxygen in the global ocean and coastal waters. Science, 359 (6371), Article number eaam7240.more

 

5. Cabaitan, P. C., Malvicini, C., Sabban, F., & Conaco, C. (2018). Versatile habitat conditioning by damselfish cultivating turf algae on giant clams. Hydrobiologia, 805 (1), Pages 89–96.more

 

6. Cai, W., Salvador-Reyes, L. A., Zhang, W., Chen, Q.-Y., Matthew, S., Ratnayake, R., … Luesch, H. (2018). Apratyramide, a Marine-Derived Peptidic Stimulator of VEGF-A and Other Growth Factors with Potential Application in Wound Healing. ACS Chemical Biology, 13 (1), Pages 91–99.more

 

7. Dumilag, R. V., & Monotilla, W. D. (2018). Molecular diversity and biogeography of Philippine foliose Bangiales (Rhodophyta). Journal of Applied Phycology, 30 (1), Pages 173–186.more

 

8. Fernández, P. A., Roleda, M. Y., Rautenberger, R., & Hurd, C. L. (2018). Carbonic anhydrase activity in seaweeds: overview and recommendations for measuring activity with an electrometric method, using Macrocystis pyrifera as a model species. Marine Biology, 165 (5), Article number 88.more

 

9. Ferrera, C., Jacinto, G. S., Chen, C.-T. A., & Lui, H.-K. (2018). Organic Carbon Concentrations in High- and Low-Productivity Areas of the Sulu Sea. Sustainability (Switzerland), 10 (6), Article number 1867.more

 

10. Fortes, M. D., Ooi, J. L. ., Tan, Y. M., Prathep, A., Bujang, J. S., & Yaakub, S. M. (2018). Seagrass in Southeast Asia: A review of status and knowledge gaps, and a road map for conservation. Botanica Marina, 61 (3), Pages 269–288.more

 

11. Fortes, M. D. (2018). Seagrass ecosystem conservation in Southeast Asia needs to link science to policy and practice. Ocean and Coastal Management, 159, Pages 51–56.

 

12. Gajigan, A. P., Yñiguez, A. T., Villanoy, C. L., San, M. L., Jacinto, G. S., & Conaco, C. (2018). Diversity and community structure of marine microbes around the Benham Rise underwater plateau , northeastern PhilippinesPeer J, Pages 1–17.more

 

13. Guzman, C., Shinzato, C., Lu, T. M., & Conaco, C. (2018). Transcriptome analysis of the reef-building octocoral, Heliopora coerulea. Scientific Reports, Pages 1–11.more

 

14. Orosco, F. L., & Lluisma, A. O. (2018). Genetic diversity of Penaeus monodon (Fabricius, 1798) in the Philippines as revealed by mitochondrial Cytochrome Oxidase I (COI). Philippine Agricultural Scientist, 101 (1), Pages 84–92.

 

15. Quimpo, T. J. R., Cabaitan, P. C., Olavides, R. D. D., Dumalagan, E.E., J., Munar, J., & Siringan, F. P. (2018). Preliminary observations of macrobenthic invertebrates and megafauna communities in the upper mesophotic coral ecosystems in apo reef natural park, Philippines. Raffles Bulletin of Zoology, 66, Pages 1-11.

 

16. Ravago-Gotanco, R., de la Cruz, T. L., Josefa Pante, M., & Borsa, P. (2018). Cryptic genetic diversity in the mottled rabbitfish Siganus fuscescens with mitochondrial introgression at a contact zone in the South China Sea. PLoS ONE, 13 (2), Pages 1–27.more

 

17. Rodrigo, S. M. T., Villanoy, C. L., Briones, J. C., Bilgera, P. H. T., Cabrera, O. C., & Narisma, G. T. T. (2018). The mapping of storm surge-prone areas and characterizing surge-producing cyclones in Leyte Gulf, Philippines. Natural Hazards, Article in Press.

 

18. Santianez, W. J. E., Lee, K. M., Uwai, S., Kurihara, A., Geraldino, P. J. L., Ganzon-Fortes, E. T., & Boo, K. (2018). Untangling nets: elucidating the diversity and phylogeny of the clathrate brown algal genus Hydroclathrus, with the description of a new genus Tronoella (Scytosiphonaceae, Phaeophyceae). Phycologia, 57 (1), Pages 61–78.

 

19. Siringan, F. P., Racasa, E. D. R., David, C. P. C., & Saban, R. C. (2018). Increase in Dissolved Silica of Rivers Due to a Volcanic Eruption in an Estuarine Bay (Sorsogon Bay, Philippines). Estuaries and Coasts, Pages 1–12.more

 

20. Soria, J. L. A., Switzer, A. D., Pilarczyk, J. E., Tang, H., Weiss, R., Siringan, F., … Koh, T. W. L. (2018). Surf beat-induced overwash during Typhoon Haiyan deposited two distinct sediment assemblages on the carbonate coast of Hernani, Samar, central Philippines. Marine Geology, 396, Pages 215–230.more

 

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1. Arcilla, C.A., Gibaga, C. R. (2018, June). Young volcanism in Cuyo Islands, Palawan, Philippines: Example of an intra-plate magmatism in the Palawan Continental Block. Poster session presented at 15th Annual Meeting Asia Oceania Geosciences Society, Honolulu, Hawaii.more

Description:

Palawan Continental Block (PCB) is a continental unit separated from the rest of Eurasia due to the opening of the South China Sea in the Oligocene. It collided with the rest of the Philippine Mobile Belt during the Middle Miocene. Located to the east of Palawan Continental Block, Cuyo Islands is an archipelago of about 50 volcanic islands in Sulu Sea. The absence of a west-dipping subducting oceanic plate on the western side of the PCB makes volcanism in Cuyo Island a perfect example of an intra-plate magmatism. With an area of around 6,000 km2, it is also the largest non-subduction related volcanism in the Philippines. This study is the first to describe the occurrence, petrology, and geochemistry of the volcanic rocks in Cuyo Island. Volcanic rocks of Cuyo Island exhibit a predominant Ocean Island Basalt (OIB) like geochemical signature, confirming the non-subduction origin of these rocks. These findings are relevant, not only to the origins of the volcanism in Cuyo, but also to the geodynamic history of the PCB.

2. Dimalanta, C. B., Faustino-Eslava, D. V., Padrones, J. T., Queaño, K. L., Concepcion, R. A. B., Suzuki, S., Yumul, G.P. (2018).Cathaysian slivers in the Philippine island arc: geochronologic and geochemical evidence from sedimentary formations of the west Central PhilippinesAustralian Journal of Earth Sciences, 65 (1), Pages 93-108.

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Abstract:

The use of geodynamic information contained in sedimentary rocks has only recently been extended into the tectonic reconstruction studies of the Philippine archipelago vis-a-vis the rest of the Southeast Asian region. We present here a comparative assessment of clastic units from the western Central Philippines, particularly from the islands of Mindoro, Panay and Palawan, and propose their likely association with sources of Cathaysian origin. Geochronological data from sedimentary formations in the study areas register U-Pb dating peaks at 185-140 Ma, 140-120 Ma and 112-90 Ma. These are similar to those observed of detrital zircons from rocks of Cathaysian origin in Taiwan and Southern China that chronicle the Yanshanian magmatic events. These same formations also record an older intercept at 1.9-1.85 Ga that likely corresponds to a regional continental orogenic episode recorded in the late Paleoproterozoic Cathaysian block. Major (e.g. Al2O3/TiO2) and trace-element (e.g. Y/Ni vs Cr/V) signatures of these sedimentary formations reflect stronger influences from granitic sources than mafic-ultramafic inputs that should otherwise be expected, considering their current oceanic island arc settings. Their La/Th and Th-Co-Zr/10 ratios also reveal continental island arc and active or passive continental margin depositional settings typical of rocks from the Palawan Microcontinental Block. New geochronological and geochemical data from the clastic rocks of northwest Mindoro, in addition to those already published for the other regions of the Palawan Microcontinental Block, provide further evidence for the amalgamation of fragments of Cathaysian origin within the Philippine island arc system.

 

3. Guotana, J. M. R., Payot, B. D., Dimalanta, C. B., Ramos, N. T., Faustino-Eslava, D. V., Queaño, K. L., & Yumul, G.P., J. (2018). Petrological and geochemical characteristics of the Samar Ophiolite ultramafic section: implications on the origins of the ophiolites in Samar and Leyte Islands, Philippines. International Geology Review, 60 (4), Pages 401-417.more

Abstract:

Cretaceous ophiolites and ophiolitic fragments occur in the Samar and Leyte islands in eastern central Philippines. The Samar Ophiolite is a complete crust-mantle sequence exposed in southern Samar, whereas the Tacloban and Malitbog ophiolite complexes are, respectively, located in the northeastern and southwestern portions of the nearby Leyte island. Despite the close proximity of these islands, the genetic relationship of these ophiolites and ophiolitic complexes, if any, remains to be elucidated. We present here new petrographic and geochemical data on the harzburgites and dunites of the ultramafic section of the Samar Ophiolite. These mantle peridotites are highly depleted residues which have low modal pyroxene content, high spinel Cr# (=0.62-0.79), and slightly enriched light rare earth element abundance with depletion in Zr and Ti. Such characteristics are typical of supra-subduction zone peridotites and strongly contrast with the abyssal signatures of the Tacloban and Malitbog ophiolite complexes. The absence of a structure between these adjacent ophiolite fragments initially hints that they form a single oceanic crust. However, with our new results, we suggest other possible mechanisms that could explain the relationship of these ophiolites.

 

4. Ilao, K., Morley, C. K., Aurelio, M. A. (2018). 3D seismic investigation of the structural and stratigraphic characteristics of the Pagasa Wedge, Southwest Palawan Basin, Philippines, and their tectonic implicationsJournal of Asian Earth Sciences, 154, Pages 213-237.more

Abstract:

The Pagasa Wedge is a poorly imaged deepwater orogenic wedge that has been variously interpreted as representing an accretionary prism, a former accretionary prism modified by thrusting onto a thinned continental margin, and a gravity-driven fold-thrust belt. This study, using 2D and 3D seismic data, together with well information indicates that at least the external part of the wedge is dominantly composed of mass transport complexes, capped by syn-kinematic sediments that have thrusts and normal faults superimposed upon them. Drilling shows that despite stratigraphic repetition of Eocene Middle Miocene units, there is stratigraphic omission of Oligocene and Early Miocene units. This absence suggests that mass transport processes have introduced the Eocene section into the wedge rather than tectonic thrusting. The accretionary prism stage (Oligocene) of the Central Palawan Ophiolite history appears to be marked by predominantly north-vergent deformation. The Deep Regional Unconformity (17 Ma) likely indicates the approximate time when obduction ceased in Palawan. The Pagasa Wedge is a late-stage product of the convergence history that was active in its final phase sometime above the top of the Nido Limestone (16 Ma) and the base of the Tabon Limestone in the Aboabo-A1X well (9 Ma). The top of the wedge is traditionally associated with the Middle Miocene Unconformity (MMU), However the presence of multiple unconformities, diachronous formation tops, local tectonic unconformities and regional diachronous events (e.g. migrating forebulges) all suggest simply giving a single age (or assigning a single unconformity, such as the MMU as defining the top of the Pagasa Wedge is inappropriate. The overall NE-SW trend of the wedge, and the dominant NW transport of structures within the wedge diverge from the more northerly transport direction determined from outcrops in Palawan, and also from the Nido Limestone in the SW part of the Pagasa Wedge. Possibly this NW transport direction is more related to gravity-driven structures responding to uplift of NE-SW Dangerous Grounds margin during the Middle Miocene (related to slab breakoff?) than it is to thrusting rooted in a plate boundary. The final modification of the wedge occurred when the effects of compression deformation on the wedge had largely ended, but gravity processes (in particular mass transport and normal faulting) still operated.

5. Kong, H., Li, H., Wu, Q.-H., Xi, X.-S., Dick, J. M., & Gabo-Ratio, J. A. S. (2018). Co-development of Jurassic I-type and A-type granites in southern Hunan, South China: Dual control by plate subduction and intraplate mantle upwelling. Chemie Der Erde. In Press, Corrected Proof. doi:10.1016/j.chemer.2018.08.002.more

Abstract:

Two types of spatially and temporally associated Jurassic granitic rocks, I-type and A-type, occur as pluton pairs in several locations in southern Hunan Province, South China. This paper aims to investigate the genetic relationships and tectonic mechanisms of the co-development of distinct granitic rocks through petrological, geochemical and geochronological studies. Zircon LA-ICPMS dating results yielded concordant U–Pb ages ranging from 180 to 148 Ma for the Baoshan and Tongshanling I-type granodiorites, and from 180 to 158 Ma for the counterpart Huangshaping and Tuling A-type granites. Petrologically, the I-type granodiorites consist of mafic minerals such as hornblende whereas the A-type granites are dominated by felsic minerals (e.g., quartz, K-feldspar and plagioclase). Major and trace element analyses indicate that the I-type granodiorites have relatively low SiO2 (64.5–71.0%) and relatively high TiO2 (0.28–0.51%), Al2O3 (13.8–15.5%), total FeO (2.3–4.7%), MgO (1.3–2.6%) and P2O5 (0.10–0.23%) contents, and the A-type granites are characterized by high concentrations of Rb (212–1499 ppm), Th (18.3–52.6 ppm), U (11.8–33.6 ppm), Ga (20.0–36.6 ppm), Y (27.1–134.0 ppm) and HREE (20.3–70.0 ppm), with pronounced negative Eu anomalies (Eu/Eu* = 0.01–0.15). Moreover, the I-type granodiorites are classified as collision-related granites emplaced under a compressional environment, whereas the A-type granites are within-plate granites generated in an extensional setting. Zircon Hf isotopic compositions vary substantially for these granitic rocks. The I-type granodiorites are characterized by relatively young Hf model ages (TDM1 = 1065–1302 Ma, TDMC =1589–2061 Ma) and moderately negative εHf(t) values (–5.9 to –11.5), whereas the A-type granites have very old model ages (TDM1 = 1454–2215 Ma, TDMC = 2211–2974 Ma) and pronounced negative εHf(t) values (–15.8 to –28.3). These petrochemical and isotopic characteristics indicate that the I-type granodiorites may have been derived from a deep source involving mantle-derived juvenile (basaltic) and crustal (pelitic) components, whereas the A-type granites may have been sourced from melting of meta-greywacke in the crust. This study proposes that the pressure and temperature differences in the source regions caused by combined effects of intra-plate mantle upwelling and plate subduction are the major controlling factors of the co-development of the two different types of magmas. Crustal anatexis related to lithospheric delamination and upwelling of hot asthenosphere under a high pressure and temperature environment led to the formation of the I-type magmas. On the other hand, the A-type magmas were formed from melting of the shallower part of the crust, where extensional stress was dominant and mantle-crust interaction was relatively weak. Rifts and faults caused by mantle upwelling developed from surface to depth and successively became channels for the ascending I- and A-type magmas, resulting in the emplacement of magmas in adjacent areas from sources at different depths.

6. Lagmay, A. M. F. A. (2018). An open data law for climate resilience and disaster risk reduction.more

Abstract:

A clear policy on Open Data for Climate Resilience and Disaster Risk Reduction through legislation is necessary if we are to achieve the Philippines’ sustainable development goals and save lives of Filipinos. Legislation of an Open Data Act will ensure strict compliance with Open Data standards by publicly funded institutions, in particular agencies that hold data concerning the safety and well-being of Filipinos. Defining the standards in an Open Data Law will mandate compliance to the key elements of Open Data, which include: 1) availability in digital format of data, downloadable via the internet in bulk for ease of use; 2) amenability to intermixing with other datasets through interoperable format structure and machine readability of digital files; 3) freedom to use, reuse and redistribute, even on commercial basis; and 4) a “no conditions” rule on the use of Open Data, except for appropriate citation for due credit. The value of Open Data for publicly-funded activities is recognized worldwide. Policies on open access have been adopted in the Unites States, United Kingdom, Germany, Netherlands, Finland, Brazil and many more. Their adoption of a policy for free access to government data is based on the concept that goods and services that should be freely available to everyone as determined by society, must be made available as free data for “the public good”. While these services to collect and make available the data are not actually free, they are, nonetheless, funded with public money. The broad use of such services benefits all of society so the cost to each individual user is largely borne by all. Open Data is critical for effective hazards management. When raw data is made publicly accessible without conditions, we build new information and derive knowledge personalized to the needs of a person or a community. It is a process that turns information into knowledgeable choices for individuals, families and local government units for building risk information. Such knowledge, acquired in timely fashion because data is openly accessible, is critical to effective disaster prevention and mitigation efforts. The National Government has pushed for an Open- Data policy since 2011 and is now enshrined in the Philippine Development Plan 2017-2022 and the Philippine Open Government Partnership Action Plan. Although laudable, the efforts on Open Data, as reflected in the Philippine Open Data Portal, leaves much to be desired. Agency officials and employees, until today, argue on the basis of issues on national security, cost recovery, sustainability and intellectual property, in order to withhold their data. These issues have long been answered by those countries which have adopted an Open Data policy, including the Philippines.

7. Maxwell, K. V., Ramos, N. T., Tsutsumi, H., Chou, Y.-C., Duan, F., & Shen, C.-C. (2018). Late Quaternary uplift across northwest Luzon Island, Philippines constrained from emergent coral reef terraces. Earth Surface Processes and Landforms. https://doi.org/10.1002/esp.4474. more

Abstract:

Emergent coral reef terraces in northwest Luzon Island, Philippines are studied to understand relative sea level (RSL) changes and uplift along the Manila Trench forearc region during the Late Quaternary. Coral reef sequences in Currimao, Badoc, and Badoc Island were mapped and were described based on geomorphological characteristics, elevation patterns, and ages. The lower emergent coral reef terraces, which are dated Holocene, are subdivided into three to possibly four terrace steps (TI–TIV in ascending order) with the highest terrace (TIII–TIV) rising up to ~7–9 m amsl. The well‐preserved staircase morphology and meter‐scale terrace risers possibly imply episodes of abrupt RSL changes that resulted from coseismic uplift during the mid‐Holocene. Around 6.8 kyr BP, ~3 m of rapid uplift (possibly coseismic) is inferred to account for the vertical separation of TI (6.2 kyr BP at 3.5 m amsl) and TII (6.8 kyr BP at 6.6 m amsl) in Currimao site. A subsequent episode of RSL fall occurred at 6 kyr BP, based on dated coral samples, and has emerged the lowest terraces in the study sites. New geomorphic and radiometric data suggest that the mid‐Holocene sea‐level highstand in northwest Luzon occurred at around 7–6 kyr BP. From the elevation and thorium‐230 age of dated terrace surfaces, we estimated Holocene uplift rates from 0.17 ± 0.12 to 0.82 ± 0.15 mm/yr across the three study sites. The estimated uplift rates of northwest Luzon are relatively lower than the uplift rates reported in similar tectonically active regions of the west Pacific such as Papua New Guinea, Taiwan, New Zealand, and Japan. The geomorphological characteristics and age of emergent coral reef terraces reported in this study offer insights on the preservation of long‐term deformation along the northwest Luzon coastal plain that is bordered by a subduction zone and upper‐plate faults.

8. Meyer-Dombard, D. R., Casar, C. P., Simon, A.G., Cardace, D., Shrenk, M. O., Arcilla, C. A. (2018). Biofilm formation and potential for iron cycling in sepentinization-influenced ground water of the Zambales and Coast Range ophiolites. Extremophiles, 22 (3), 407-431.more

Abstract:

Terrestrial serpentinizing systems harbor microbial subsurface life. Passive or active microbially mediated iron transformations at alkaline conditions in deep biosphere serpentinizing ecosystems are understudied. We explore these processes in the Zambales (Philippines) and Coast Range (CA, USA) ophiolites, and associated surface ecosystems by probing the relevance of samples acquired at the surface to in situ, subsurface ecosystems, and the nature of microbe–mineral associations in the subsurface. In this pilot study, we use microcosm experiments and batch culturing directed at iron redox transformations to confirm thermodynamically based predictions that iron transformations may be important in subsurface serpentinizing ecosystems. Biofilms formed on rock cores from the Zambales ophiolite on surface and in-pit associations, confirming that organisms from serpentinizing systems can form biofilms in subsurface environments. Analysis by XPS and FTIR confirmed that enrichment culturing utilizing ferric iron growth substrates produced reduced, magnetic solids containing siderite, spinels, and FeO minerals. Microcosms and enrichment cultures supported organisms whose near relatives participate in iron redox transformations. Further, a potential ‘principal’ microbial community common to solid samples in serpentinizing systems was identified. These results indicate collectively that iron redox transformations should be more thoroughly and universally considered when assessing the function of terrestrial subsurface ecosystems driven by serpentinization.

 

9. Pearson, P. N. and IODP Expedition 363 Shipboard Scientific Party … Fernando, A.G.S. (2018). A deep-sea agglutinated foraminifer tube constructed with planktonic foraminifer shells of a single species. Journal of Micropalaeontology, 37, 97-104.more

Abstract:

Agglutinated foraminifera are marine protists that show apparently complex behaviour in constructing their shells, involving selecting suitable sedimentary grains from their environment, manipulating them in three dimensions, and cementing them precisely into position. Here we illustrate a striking and previously undescribed example of complex organisation in fragments of a tube-like foraminifer (questionably assigned to Rhabdammina) from 1466 m water depth on the northwest Australian margin. The tube is constructed from well-cemented siliciclastic grains which form a matrix into which hundreds of planktonic foraminifer shells are regularly spaced in apparently helical bands. These shells are of a single species, Turborotalita clarkei, which has been selected to the exclusion of all other bioclasts. The majority of shells are set horizontally in the matrix with the umbilical side upward. This mode of construction, as is the case with other agglutinated tests, seems to require either an extraordinarily selective trial-and-error process at the site of cementation or an active sensory and decision-making system within the cell.

 

10. Pubellier, M., Aurelio, M. and Sautter, B. (2018). The life of a marginal basin depicted in a structural map of the South China Sea. Episodes 41(3).

Abstract:

The South China Sea (SCS) is presented here as a case example to demonstrate the evolution of basins developed at convergent boundaries. The structural map published in 2017 by CGMW at the 1:3 million scale allows to visualize the location of the rifting faults from a normal to hyper-extended crust, the shape and structure of the oceanic crust and their late involvement in a convergent margin. It highlights the reactivation of the Mesozoic tectono-stratigraphic setting such as broad folds and granitic plutons during the rifting, and the effect of the resulting architecture on the NW Borneo accretionary wedge.

11. Racasa E., Lloren, R., Manglicmot, M., Jago-on, K. A. B., Balangue, M. I. R. D., Taniguchi, M., Siringan, F. P.  (2018). Lacustrine groundwater discharge in southern Laguna de Bay, Philippines. In: A. Endo, T. Oh. (eds.) The Water-Energy-Food Nexus. Global Environmental Studies. Singapore: Springer. Pages 87-100.more

Abstract:

Although a major potential contributor to water and nutrient budgets, lacustrine groundwater discharge (LGD) is often neglected in most lake studies. Through electrical resistivity profiling surveys, the authors examined the possible occurrence of LGD in southern Laguna de Bay, the largest freshwater lake in the Philippines. Discrete and dispersed LGDs were identified. Discrete LGDs were inferred from narrow highly resistive zones that cut vertically across the lake floor. These discrete LGDs line-up with projections of lineaments on land and are thus deemed to be fault-controlled. Dispersed LGDs, interpreted from wide swaths of resistivity signals cutting across the lake floor, were found to occur more commonly in shallower areas. Findings from radon concentrations, nutrient concentrations, and chlorophyll a analyses support the perceived patterns of LGD occurrences. Nutrient input through LGD is probably contributing to the lake’s current eutrophic condition however where discrete LGDs occur, the fisheries appear to be enhanced.

12Siringan, F. P., Racasa, E. D. R., David, C. P. C., & Saban, R. C. . (2018). Increase in Dissolved Silica of Rivers Due to a Volcanic Eruption in an Estuarine Bay (Sorsogon Bay, Philippines). Estuaries and Coasts, Pages 1–12.more

Abstract:

Mount Bulusan, the Philippines’ fourth most active volcano, erupted in February 21, 2011, sending volcanic ash and pyroclastic materials to its surrounding rivers. The waters drained into the estuary of harmful algal blooms plagued Sorsogon Bay. We aim to determine the impact of the 2011 volcanic eruption and the preceding volcanic ash emissions to the dissolved silica concentration of rivers draining the flanks of Mt. Bulusan and its possible implications to the phytoplankton assemblage of the bay. Six river water sampling periods from August 2010 to October 2012 overlapped with Mt. Bulusan’s active phase of volcanism. Our data shows that mean river silica from pre-eruption levels of ~ 500 μM increased by more than 200% during and post-eruption. Highest Si concentration of 2270 μM was measured from Cadacan River in August 2011. Here, we argue that the sustained general increase of dissolved silica is due to the silica-containing materials from Mt. Bulusan’s eruption and that their concentration in river waters is also a function of watershed lithology and precipitation. Increase in dissolved silica and other nutrients caused a shift to diatom domination and, possibly, termination of Pyrodinium bahamense var. compressum blooms. Silica load increase in embayments is a natural process that controls the dominance of algae. Our study also highlights the importance of Philippine rivers to the global ocean silica budget as a function of high precipitation, tectonics in general, and volcanism in particular.

13. Sun, H.-S., Li, H., Algeo, T. J., Gabo-Ratio, J. A. S., Yang, H., Wu, J.-H., & Wu, P. (2018). Geochronology and geochemistry of volcanic rocks from the Tanjianshan Group, NW China: Implications for the early Palaeozoic tectonic evolution of the North Qaidam Orogen. Geological Journal. doi:10.1002/gj.3268. more

Abstract:

The widely exposed Tanjianshan volcanic rocks in the North Qaidam Orogen (NW China) encode abundant information about early Palaeozoic magma origin and tectonic evolution. This research utilizes petrological, geochemical, and geochronological methods to investigate the last volcanic cycle (Formation d) of the Tangjianshan Group, aiming to reveal the tectonic evolutionary processes of the North Qaidam Orogen. Formation d can be further divided into two major volcanic sequences, that is, Formation d‐1/d‐4 and Formation d‐3. Formation d‐1/d‐4 is a set of intermediate–basic volcaniclastic rocks intercalated with volcanic lava and contemporary hypabyssal diabase–gabbro intrusive rocks. The rocks are characterized by high average concentrations of Al2O3, K2O, Na2O, and P2O5, pronounced differentiation of light (LREE) and heavy rare earth elements (HREE) and enrichment of LREEs and light‐ion lithophile elements (LILE), showing continental arc affiliation and enriched mid‐ocean‐ridge basalt (E‐MORB) characteristics. They have positive zircon εHf (t) values (7.5 to 16.1) and variable whole‐rock εNd (t) values (−2.7 to 7.0), with crustal Hf model ages (TDMC) and two‐stage Nd model ages (T2DM) ranging from 428 to 970 Ma and from 618 to 1,410 Ma, respectively. The magma may have originated from an enriched mantle source and experienced crustal contamination in a continental back‐arc basin. In contrast, Formation d‐3 is composed of volcaniclastic rocks intercalated with layered basaltic andesite and basalts. It has higher average concentrations of CaO, FeOT, and MgO, lower ΣREE and flatter REE patterns, lower average 87Sr/86Sr ratios (0.70557), higher average 143Nd/144Nd ratios (0.51285), and exclusively positive εNd (t) values (1.3 to 5.0), consistent with normal mid‐ocean‐ridge basalt (N‐MORB) influence. The magma may have been derived from a normal mantle source without significant modification, which probably formed in a rift‐related tectonic setting or even a mid‐ocean ridge that developed within a back‐arc basin. Magmatic zircons from Formation d‐1/d‐4 yield U–Pb ages mostly at 460–440 Ma, whereas zircons modified by continental exhumation‐related orogenic fluids are mainly dated at 430–420 Ma. Magmatic zircons from Formation d‐3 mainly have U–Pb ages of 440–430 Ma. Integrating the magma genesis and rock affiliation interpretations of this study with geological information for the study area and adjacent regions, a four‐stage tectonic evolutionary model is proposed for the early Palaeozoic North Qaidam Orogen: (a) oceanic subduction with arc magmatism (520–460 Ma), (b) continental collision with back‐arc magmatism (Formation d‐1/d‐4) (460–440 Ma), (c) mid‐ocean ridge extension with rift‐related magmatism (Formation d‐3) (440–430 Ma), and (d) continental exhumation with orogenic fluid modification (430–420 Ma).

14. Vacquand, C., Deville, E., Beaumont, V., Guyot, F. Sissmann, O., Pillot, D., Arcilla, C., Prinzhofer, A. (2018). Reduced gas seepages in ophiolitic complexes: evidences for multiple origins of the H2-CH4-N2 gas mixturesGeochimica et Cosmochimica Acta, 223, Pages 437-461.more

Abstract:

This paper proposes a comparative study of reduced gas seepages occurring in ultrabasic to basic rocks outcropping in ophiolitic complexes based on the study of seepages from Oman, the Philippines, Turkey and New Caledonia. This study is based on analyses of the gas chemical composition, noble gases contents, stable isotopes of carbon, hydrogen and nitrogen. These seepages are mostly made of mixtures of three main components which are H2, CH4 and N2 in various proportions. The relative contents of the three main gas components show 4 distinct types of gas mixtures (H2-rich, N2-rich, N2-H2-CH4 and H2-CH4). These types are interpreted as reflecting different zones of gas generation within or below the ophiolitic complexes. In the H2-rich type, associated noble gases display signatures close to the value of air. In addition to the atmospheric component, mantle and crustal contributions are present in the N2-rich, N2-H2-CH4 and H2-CH4 types. H2-bearing gases are either associated with ultra-basic (pH 10–12) spring waters or they seep directly in fracture systems from the ophiolitic rocks. In ophiolitic contexts, ultrabasic rocks provide an adequate environment with available Fe2+ and alkaline conditions that favor H2 production. CH4 is produced either directly by reaction of dissolved CO2 with basic-ultrabasic rocks during the serpentinization process or in a second step by H2-CO2 interaction. H2 is present in the gas when no more carbon is available in the system to generate CH4. The N2-rich type is notably associated with relatively high contents of crustal 4He and in this gas type N2 is interpreted as issued mainly from sediments located below the ophiolitic units.

 

15. Yan, Y., Yao, D., Tian, Z., Huang, C., Chen, W., Santosh, M., Yumul, G. P. Jr., Dimalanta, C. B., Li, Z. (2018). Zircon U-Pb chronology and hf isotope from the Palawan-Mindoro block, Philippines: Implication to provenance and tectonic evolution of the South China Sea. Tectonics, 37 (4), Pages 1063-1076. more

Abstract:

The continental margin of Southeast Asia evolved from a dominantly Andean-type active margin during Mesozoic to a Western Pacific-type since Late Cretaceous. With the spreading of the South China Sea, the Palawan-Mindoro Block drifted from mainland Asia and the Cenozoic strata provide an excellent window to gain insights into the tectonic evolution of the margin of Southeast Asia. Here we present U-Pb age and Hf isotopic data on detrital zircon grains from Cenozoic sedimentary rocks in the Palawan-Mindoro Block, Philippines, to evaluate the provenance and tectonic evolution of the South China Sea. Zircon grains in Eocene-Miocene sedimentary rocks from the Palawan-Mindoro Block show a wide range in age from 60 to 2700 Ma, with four major age groups of 80–120 Ma, 160–180 Ma, 1600–2100 Ma, and 2200–2700 Ma. The εHf(t) of the zircon grains of the samples from Mindoro Island range from −39 to +13.7, and similar Hf isotopic composition is recorded in Paleogene and Neogene strata. Zircon U-Pb ages and Hf isotopic data of the Eocene samples from the Palawan-Mindoro Block show a similar pattern with those from Taiwan, which suggests that the Palawan-Mindoro Block was attached to the margin of South China during Late Cretaceous-Eocene times. The difference of zircon U-Pb age composition in the Miocene samples between the Palawan-Mindoro Block and Taiwan reflects southward drifting of the Palawan-Mindoro Block and seafloor spreading of the South China Sea at that time. 

16. Yang, Y.H., Tsai, M.C., Hu, J.C., Aurelio, M.A., Hashimoto, M., Escudero, J.A.P., Su, Z., & Chen Q. (2018). Coseismic slip deficit of the 2017 Mw 6.5 Ormoc earthquake that occurred along a creeping segment and geothermal field of the Philippine Fault. Geophysical Research Letters March 2018.more

Abstract:

Coseismic surface deformation imaged through Interferometric Synthetic Aperture Radar (InSAR) measurements was used to estimate the fault geometry and slip distribution of the 2017 Mw 6.5 Ormoc Earthquake along a creeping segment of the Philippine Fault on Leyte Island. Our best fitting faulting model suggests that the coseismic rupture occurred on a fault plane with high dip angle of 78.5° and strike angle of 325.8°, and the estimated maximum fault slip of 2.3 m is located at 6.5 km east-northeast of the town of Kananga. The recognized insignificant slip in the Tongonan geothermal field zone implies that the plastic behavior caused by high geothermal gradient underneath the Tongonan geothermal field could prevent the coseismic failure in heated rock mass in this zone. The predicted Coulomb failure stress (CFS) change shows that a significant positive CFS change occurred along the SE segment of central Philippine fault with insignificant coseismic slip and infrequent aftershocks, which suggests an increasing risk for future seismic hazard. 

17. Ybañez, R. L., Racoma, B. A. B., Ybañez, A. A. B., Balangue-Tarriela, M. I. R. D. (2018). Flood susceptibility assessment of Mt. Makiling, Philippines using two-dimensional meteorological and hydrological modelling. Philippine Journal of Science 147(3): 463-471.

more

Abstract:

In a data-poor, hazard-prone country like the Philippines, interpolating distant data points and computer modelling have become the go-to methods for determining the hazards that may affect an area. The absence of monitoring stations and gauges necessitates the application of modelling techniques to build on the little data available and generate reliable hazard maps. In this study-the devastating Sep 2009 Tropical Cyclone Ketsana (local name: Ondoy) event, its atmospheric characteristics, and its effects near Mt. Makiling, Laguna-is analyzed utilizing two modelling software: the Weather Research and Forecasting (WRF) model to assess the amount of rainfall, and FLO-2D to map the flood hazard areas around the volcano using the output of the WRF. A lone meteorological observation station on Mt. Makiling provided rainfall data for comparison with the results of the meteorological and hydrological models. The WRF model yielded a mean rainfall amount in the study area of 129.92 mm over 24 h for the storm against the observed rainfall amount for the same duration at 182.3 mm from the meteorological station. The flood model using the WRF data yielded minimal inundated areas, while the flood model of the observed rainfall data showed several low-lying urban areas inundated by up to 1.5 m of floodwaters. Comparison with flood data collected by responding agencies and groups after the event shows good correlation of affected areas and flood heights, with discrepancies being attributed to the swelling of Laguna de Bay because of excess runoff from other surrounding provinces-a factor that the models could not consider. Despite this, the WRF model generated from global atmospheric data and the flood model using the WRF product appears as a feasible substitute in the absence of on-site observation points and monitoring stations.

 

nimbb

1. Bascos, N.A.D., Emralino, F.L.C., Liu, F.C., Conception, C.P., Altamia, M., Huang, Y.C., Hsieh, Y.C., Chen, C.J., Palmes-Saloma, C. (2018). Biophysical and functional characterization of asFP504, a novel fluorescent protein from the PhilippinesPhilippine Journal of Science, 147 (1), Pages 65-74.  more

Abstract:

Fluorescent proteins have proven to be invaluable for a myriad of applications in scientific research. The discovery and characterization of novel fluorescent proteins promises to expand this range even further.  This report focuses on the biophysical and functional characterization of a novel green fluorescent protein cloned from a Philippine soft coral species. The asFP504 protein showed peak excitation at 471 nm and at 494 nm (λE1= 471 nm; λE2=494 nm), its emission maximum from 471 nm excitation was observed at 504 nm. The fluorescence was observed to be related to its oligomeric state.  Both fluorescence and oligomerization were robustly maintained for a range of temperatures, pH conditions, treatment with chaotropic agents, and proteolysis. X-ray crystallography documented a molecular packing of three dimers within each asymmetric unit for the asFP504 protein. The observed absorbance and fluorescence properties are comparable to that of commercially available fluorescence proteins. Despite its lower absorbance, asFP504 has higher quantum yield than mCitrine. In addition, the stability of asFP504 in the presence of multiple denaturants presents the potential of this protein – the first fluorescent protein from the Philippines – for use in many different research applications.

2. Boncan, D. A. T., David, A. M. ., & Lluisma, A. O. (2018). A CAZyme-Rich Genome of a Taxonomically Novel Rhodophyte-Associated Carrageenolytic Marine Bacterium. Marine Biotechnology, Article in, Pages 1–21. more

Abstract:

Carbohydrate-active enzymes (CAZymes) have significant biotechnological potential as agents for degradation or modification of polysaccharides/glycans. As marine macroalgae are known to be rich in various types of polysaccharides, seaweed-associated bacteria are likely to be a good source of these CAZymes. A genomics approach can be used to explore CAZyme abundance and diversity, but it can also provide deep insights into the biology of CAZyme producers and, in particular, into molecular mechanisms that mediate their interaction with their hosts. In this study, a Gram-negative, aerobic, rod-shaped, carrageenolytic, and culturable marine bacterium designated as AOL6 was isolated from a diseased thallus of a carrageenan-producing farmed rhodophyte, Kappaphycus alvarezii (Gigartinales, Rhodophyta). The whole genome of this bacterium was sequenced and characterized. Sequence reads were assembled producing a high-quality genome assembly. The estimated genome size of the bacterium is 4.4 Mb and a G+C content of 52%. Molecular phylogenetic analysis based on a complete sequence of 16S rRNA, rpoB, and a set of 38 single-copy genes suggests that the bacterium is an unknown species and represents a novel genus in the family Cellvibrionaceae that is most closely related to the genera Teredinibacter and Saccharophagus. Genome comparison with T. turnerae T7901 and S. degradans 2-40 reveals several features shared by the three species, including a large number of CAZymes that comprised > 5% of the total number of protein-coding genes. The high proportion of CAZymes found in the AOL6 genome exceeds that of other known carbohydrate degraders, suggesting a significant capacity to degrade a range of polysaccharides including κ-carrageenan; 34% of these CAZymes have signal peptide sequences for secretion. Three putative κ-carrageenase-encoding genes were identified from the genome of the bacterium via in silico analysis, consistent with the results of the zymography assay (with κ-carrageenan as substrate). Genome analysis also indicated that AOL6 relies exclusively on type 2 secretion system (T2SS) for secreting proteins (possibly including glycoside hydrolases). In relation to T2SS, the product of the pilZ gene was predicted to be highly expressed, suggesting specialization for cell adhesion and secretion of virulence factors. The assignment of proteins to clusters of orthologous groups (COGs) revealed a pattern characteristic of r-strategists. Majority of two-component system proteins identified in the AOL6 genome were also predicted to be involved in chemotaxis and surface colonization. These genomic features suggest that AOL6 is an opportunistic pathogen, adapted to colonizing polysaccharide-rich hosts, including carrageenophytes.

3. Dumilag, R.V., Monotilla, W.D. (2018). Molecular diversity and biogeography of Philippine foliose Bangiales (Rhodophyta)Journal of Applied Phycology, 30 (1), Pages 173-186.more

Abstract:

Species circumscription based on phenotypes has frequently masked the actual species diversity in foliose Bangiales. Application of DNA sequence differences in this group has removed dependence on the utility of morphological characters traditionally considered for species discrimination. This study currently represents an extensive analysis of phylogeny and species discrimination of foliose Bangiales across most of their distributional range in the northern Philippines, particularly in Luzon Strait. Molecular assessment based on plastid rbcL and two mitochondrial loci, COI-5P, and cox2–3 spacer, suggested four major groups diagnostic of species lineage. As supported by the results from the four molecular species delimitation methods: PTP, bPTP, ABGD, and SPN, the confirmed Philippine foliose Bangiales species included Pyropia acanthophora, Py. tanegashimensis, and two cryptic taxa from Batanes Islands. The number of species detected in this study suggested that the true species composition of Philippine foliose Bangiales might be considerably lower than what was previously thought. It is possible however that a greater sampling effort in complete seasonal range of collections will reveal more species and extent of their actual distributions. Although the influence of northeast monsoon significantly affects the growth of foliose Bangiales in the Philippines, its role in shaping their present-day distribution remains unclear. Our molecular datasets however suggested that their current biogeographic distribution might reflect past vicariant events and is therefore more complex than have been previously regarded.

4. Hampton, H.G., Jackson, S.A., Fagerlund, R.D., Vogel, A.I.M., Dy, R.L., Blower, T.R., Fineran, P.C. (2018). AbiEi Binds Cooperatively to the Type IV abiE Toxin–Antitoxin Operator Via a Positively-Charged Surface and Causes DNA Bending and Negative Autoregulation. Journal of Molecular Biology, 430 (8), Pages 1141-1156.more

Abstract:

Bacteria resist phage infection using multiple strategies, including CRISPR-Cas and abortive infection (Abi) systems. Abi systems provide population-level protection from phage predation, via “altruistic” cell suicide. It has recently been shown that some Abi systems function via a toxin–antitoxin mechanism, such as the widespread AbiE family. The Streptococcus agalactiae AbiE system consists of a bicistronic operon encoding the AbiEi antitoxin and AbiEii toxin, which function as a Type IV toxin–antitoxin system. Here we examine the AbiEi antitoxin, which belongs to a large family of transcriptional regulators with a conserved N-terminal winged helix-turn-helix domain. This winged helix-turn-helix is essential for transcriptional repression of the abiE operon. The function of the AbiEi C-terminal domain is poorly characterized, but it contributes to transcriptional repression and is sufficient for toxin neutralization. We demonstrate that a conserved charged surface on one face of the C-terminal domain assists sequence-specific DNA binding and negative autoregulation, without influencing antitoxicity. Furthermore, AbiEi binds cooperatively to two inverted repeats within the abiE promoter and bends the DNA by 72°. These findings demonstrate that the mechanism of DNA binding by the widespread family of AbiEi antitoxins and transcriptional regulators can contribute to negative autoregulation.

5. Malit, J.J.L. and Hedreyda, C.T. (2018). Detection and Sequence Analysis of Enzyme Genes of Four Thermo-tolerant Bacillus pumilus Strains from the PhilippinesPhilippine Journal of Science, 147 (2).more

Abstract:

The Philippines boasts of diversity in bacterial species that can be explored in producing industrially significant enzymes to help reduce the country’s dependence on enzyme importation. This study was focused on four thermotolerant strains of Bacillus pumilus, a species reported to produce serine alkaline protease, lipase, pectate lyase, and laccase. Enzyme gene targeted polymerase chain reaction (PCR) and gene sequence analysis confirmed the presence of four enzyme genes in all strains studied.  Preliminary enzyme assays revealed that all strains except 1271, tested positive for protease, pectate lyase, and lipase activities. Only strain 1271, however, exhibited positive laccase activity.  These initial results could be the basis for pursuing studies on laccase using strain 1271 and studies on protease, pectate lyase and lipase enzymes from the other three strains. Partial amino acid sequence of the serine alkaline protease gene in strain 1271 revealed five amino acid variations from the other three strains and the variations resulted in protein conformational changes. The translated partial laccase gene sequence of strain 1271 exhibited ten amino acid variations from partial laccase enzymes of the other three strains but the amino acid variations did not result in enzyme conformation change. The amino acid sequences in the complete lipase genes showed five amino acid variations in isolate 1271 compared with enzymes from other three strains but no change in the predicted protein model was observed. Sixteen variations in the amino acid sequences of the pectate lyase enzyme observed among strains resulted in a unique pectate lyase protein conformation for each isolate. The role of enzyme conformation variation as well as other factors that could have led to the enzyme assay results in this study, could be further elucidated with optimized quantitative enzyme assays, gene expression studies and mutagenesis.

6. Maralit, B.A., Phattarunda Jareea, Pakpoom Boonchuen, Anchalee Tassanakajon, Kunlaya Somboonwiwat. (2018). Differentially expressed genes in hemocytes of Litopenaeus vannamei challenged with Vibrio parahaemolyticus AHPND (VPAHPND) and VPAHPND toxin. Fish & Shellfish Immunology, 81, Pages 284-296.more

Abstract:

While toxin-harboring Vibrio parahaemolyticus has been previously established as the causative agent of early mortality syndrome (EMS) or acute hepatopancreatic necrosis disease (AHPND) in shrimp, information on the mechanistic processes that happen in the host during infection is still lacking. Here, we examined the expression responses of the shrimp hemocyte transcriptome to V. parahaemolyticus AHPND (VPAHPND) by RNA sequencing (RNA-seq). Using libraries (SRA accession number SRP137285) prepared from shrimp hemocytes under experimental conditions, a reference library was de novo assembled for gene expression analysis of VPAHPND-challenged samples at 0, 3/6, and 48 h post infection (hpi). Using the library from 0-hpi as the control, 359 transcripts were found to be differentially expressed in the 3/6-hpi library, while 429 were differentially expressed in the 48-hpi library. The expression patterns reported in the RNA-seq of 9 representative genes such as anti-lipopolysaccharide factor (LvALF), crustin p (CRU), serpin 3 (SER), C-type lectin 3 (CTL), clottable protein 2 (CLO), mitogen-activated protein kinase kinase 4 (MKK4), P38 mitogen-activated protein kinase (P38), protein kinase A regulatory subunit 1 (PKA) and DNAJ homolog subfamily C member 1-like (DNJ) were validated by qRT-PCR. The expression of these genes was also analyzed in shrimp that were injected with the partially purified VPAHPND toxin. A VPAHPND toxin-responsive gene, LvALF was identified, and its function was characterized by RNA interference. LvALF knockdown resulted in significantly rapid increase of shrimp mortality caused by toxin injection. Protein-protein interaction analysis by molecular docking suggested that LvALF possibly neutralizes VPAHPND toxin through its LPS-binding domain. The data generated in this study provide preliminary insights into the differences in the immune response of shrimp to the bacterial and toxic aspect of VPAHPND as a disease.

 

7. Perera, D.,  Magbanua, Z.V.,  Thummasuwan, S.,  Mukherjee, D.,  Arick, M., II,  Chouvarine, P.,  Nairn, C.J.,  Schmutz, J.,  Grimwood, J.,  Dean, J.F.D.,  Peterson, D.G. (2018). Exploring the loblolly pine (Pinus taeda L.) genome by BAC sequencing and Cot analysisGene, 663, Pages 165-177.more

Abstract:

Loblolly pine (LP; Pinus taeda L.) is an economically and ecologically important tree in the southeastern U.S. To advance understanding of the loblolly pine (LP; Pinus taeda L.) genome, we sequenced and analyzed 100 BAC clones and performed a Cot analysis. The Cot analysis indicates that the genome is composed of 57, 24, and 10% highly-repetitive, moderately-repetitive, and single/low-copy sequences, respectively (the remaining 9% of the genome is a combination of fold back and damaged DNA). Although single/low-copy DNA only accounts for 10% of the LP genome, the amount of single/low-copy DNA in LP is still 14 times the size of the Arabidopsis genome. Since gene numbers in LP are similar to those in Arabidopsis, much of the single/low-copy DNA of LP would appear to be composed of DNA that is both gene- and repeat-poor. Macroarrays prepared from a LP bacterial artificial chromosome (BAC) library were hybridized with probes designed from cell wall synthesis/wood development cDNAs, and 50 of the “targeted” clones were selected for further analysis. An additional 25 clones were selected because they contained few repeats, while 25 more clones were selected at random. The 100 BAC clones were Sanger sequenced and assembled. Of the targeted BACs, 80% contained all or part of the cDNA used to target them. One targeted BAC was found to contain fungal DNA and was eliminated from further analysis. Combinations of similarity-based and ab initio gene prediction approaches were utilized to identify and characterize potential coding regions in the 99 BACs containing LP DNA. From this analysis, we identified 154 gene models (GMs) representing both putative protein-coding genes and likely pseudogenes. Ten of the GMs (all of which were specifically targeted) had enough support to be classified as intact genes. Interestingly, the 154 GMs had statistically indistinguishable (α = 0.05) distributions in the targeted and random BAC clones (15.18 and 12.61 GM/Mb, respectively), whereas the low-repeat BACs contained significantly fewer GMs (7.08 GM/Mb). However, when GM length was considered, the targeted BACs had a significantly greater percentage of their length in GMs (3.26%) when compared to random (1.63%) and low-repeat (0.62%) BACs. The results of our study provide insight into LP evolution and inform ongoing efforts to produce a reference genome sequence for LP, while characterization of genes involved in cell wall production highlights carbon metabolism pathways that can be leveraged for increasing wood production.

8. Vasquez, M.R., Jr.,  Prieto, E.I.,  Wada, M. (2018). Radio-frequency plasma-induced biocompatibility of polyimide substratesPlasma Medicine, 8 (1), Pages 35-44.more

Abstract:

Surfaces of polyimide (PI) sheets were modified using 13.56-MHz radio-frequency discharges to enhance their affinity with fibroblast cells. Physico-chemical analysis of pristine and plasma-treated PI sheets showed different responses against argon (Ar), oxygen (O2), and nitrogen (N2) as the plasma process gases. Overall, hydrophilicity of treated PI surfaces was enhanced, and its surface free energy increased from 53 dyn/cm to at least 73 dyn/ cm. Surface roughness values also increased from 1.3 to 40.8 nm, as demonstrated by atomic force microscopy analyses. Infrared spectral analyses showed a decrease of imide functional group peak intensities on plasma exposure, corresponding to chemical surface structural changes. In addition, plasma-treated surfaces significantly increased cell adhesion and proliferation compared to pristine samples. N2-containing plasma exhibited the greatest increase among the test gases, due to the possible inclusion of N2-based functional groups that enhance biochemical affinity of fibroblast cells.

 

nip 

1. Agulto, V.C., Empizo, M.J.F.,  Kawano, K.  Minami, Y., Yamanoi, K., Sarukura, N., Yago, A.C. and  Sarmago, R.V. (2018). Two-step fabrication of ZnO-PVP composites with tunable visible emissionsOptical Materials, 76, Pages 317-322.more

Abstract:

We report a two-step fabrication of zinc oxide-polyvinylpyrrolidone (ZnO-PVP) composites for potential phosphor-based applications. The composites are fabricated by initially preparing ZnO microrods using hydrothermal growth method and then dip-coating the microrods into aqueous PVP solutions with varying molar concentrations. The as-prepared ZnO microrods exhibit smooth surfaces and broad visible emissions, while the ZnO-PVP composites have pitted surfaces with shifted and reduced visible emissions. These changes in the structural and optical properties, which are found to depend on the PVP concentration, are attributed to the adsorption of PVP on the microrod surface. Although the surface morphology and visible emission are modified by PVP, the composites still maintain a hexagonal wurtzite crystal structure and near-band-edge ultraviolet (UV) emission similar with the as-prepared microrods. Our results therefore suggest that the ZnO-PVP composites can be used as phosphors that offer not only properties found in both ZnO and PVP but also tunable visible emissions which can be controlled during material fabrication.

2. Angub, M.C.M., Vergara, C.J.T., Husay, H.A.F., Salvador, A.A., Empizo, M.J.F., Kawano, K., Minami, Y., Shimizu, T., Sarukura, N., Somintac, A.S. (2018). Hydrothermal growth of vertically aligned ZnO nanorods as potential scintillator materials for radiation detectors. Journal of Luminescence, 203, Pages 427-435.more

Abstract:

We investigate the hydrothermal growth of zinc oxide (ZnO) nanorods to realize their potential scintillator applications. Vertically aligned ZnO nanorods were successfully fabricated on seeded silicon (Si) substrates at a relatively low temperature of 85 °C using different hexamethylenetetramine [(CH2)6N4, HMTA] and zinc acetate dihydrate [Zn(CH3COO)2·2H2O, ZnAc] concentration ratios. Varying the precursor concentration ratio affects the nanorod dimensions which, in turn, influence the apparent densities and observed emissions. But regardless of the HMTA and ZnAc concentration ratio used, the fabricated nanorods exhibit well-defined morphologies, hexagonal crystal structure, preferential c-axis orientation, and 24–120-ps ultraviolet (UV) emissions. With these excellent structural and optical properties, the hydrothermal-grown ZnO nanorods are suggested to be used as scintillator materials which offer not only fast scintillation response but also high spatial resolution for future radiation detectors.

 

3. Balgos, M. H., Jaculbia, R., Prieto, E. A., Mag-usara, V. K., Tani, M., Salvador, A., … Somintac, A. (2018). Surface effect of n-GaAs cap on the THz emission in LT-GaAs. Journal of Materials Science: Materials in Electronics, Pages 1–7.

 

4. Balista, J.A.F., Saloma, C. (2018). Modified inelastic bouncing ball model of the Brazil nut effect and its reverse. Granular Matter, 20(47). more

Abstract:

We developed the modified inelastic bouncing ball model (mIBBM) to describe the emergence of the Brazil nut effect (BNE) and its reverse (RBNE) in a vertically-vibrated binary granular mixture. The mIBBM incorporates the container-to-grains force-transmission efficiency (transmissibility) Tr to quantify the dimensionless mean void lifetime ωδt that acts as the segregation phase indicator where ω is the vibration angular frequency. The mixture is represented as two non-interacting inelastic balls, Ball A and Ball B. Each ball bounces with a time-of-flight τA (or τB) that depends on transmissibility TrA (or TrB) and the dimensionless container acceleration Γ, i.e., τA = τA(Γ, TrA) and τB = τB(Γ, TrB). The ball dynamics are described by the bifurcation diagrams of the dimensionless times-of-flight, ωτA(Γ, TrA) and ωτB(Γ, TrB). The probability-weighted difference ωδt between branches of the two diagrams is computed and interpreted as follows: ωδt>0 (occurrence of BNE), ωδt<0 (RBNE) and ωδt = 0 (no segregation). Segregation phases are revealed as varying shifts and widths of ωδt across the Γ axis. The phase boundaries in the ωδt-versus-Γ diagram are sensitive to changes in TrA, TrB and ΔTr = (TrA − TrB). The mIBBM explains why the BNE is a more likely than the RBNE and predicts a segregation phase sequence that is generally consistent with related experimental results taken over a limited ω-range. Additional experiments are needed to enable a more comprehensive and precise evaluation of the mIBBM.

 

5. Bardolaza, H. R., Vasquez, J. D. E., Bacaoco, M. Y., de los Reyes, A. E., Lopez, L.P., J., Somintac, A. S., … Sarmago, R. V. (2018). Temperature dependence of THz emission and junction electric field of GaAs–AlGaAs modulation-doped heterostructures with different i-AlGaAs spacer layer thicknesses. Journal of Materials Science: Materials in Electronics, 29 (10), Pages 8760–8766.

 

6. Bernardo, R. C. S., & Esguerra, J. P. H. (2018). Maximally-localized position, Euclidean path-integral, and thermodynamics in GUP quantum mechanics. Annals of Physics, 391, Pages 293–311.

 

7. Castillo, J., Vega, I., Wardell, B. (2018)Self-force on a scalar charge in a circular orbit about a Reissner-Nordström black hole. Physical Review D, 98(2), Article number 024024.

Abstract:

Motivated by applications to the study of self-force effects in scalar-tensor theories of gravity, we calculate the self-force exerted on a scalar charge in a circular orbit about a Reissner-Nordström black hole. We obtain the self-force via a mode-sum calculation and find that our results differ from recent post-Newtonian calculations even in the slow-motion regime. We compute the radiative fluxes toward infinity and down the black hole and verify that they are balanced by energy dissipated through the local self-force—in contrast to the reported post-Newtonian results. The self-force and radiative fluxes depend solely on the black hole’s charge-to-mass ratio, the controlling parameter of the Reissner-Nordström geometry. They both monotonically decrease as the black hole approaches extremality. With respect to an extremality parameter ε, the energy flux through the event horizon is found to scale as ε5/4 as ε→0.

 

8. Dasallas, L.L.Garcia, W.O. (2018). Numerical simulation of femtosecond pulsed laser ablation of copper for oblique angle of incidence through two-temperature modelMaterials Research Express, 5 (1).more

Abstract:

We propose a numerical model to describe laser ablation of a copper target by a femtosecond laser pulse at an oblique angle of incidence. The model is based on the two temperature model and improved to include laser fluence, laser spot size, and dynamic changes in reflectivity of the target. Numerical results show that the electron and lattice temperatures decrease with the angle of incidence. The dependency of the maximum temperature with angle of incidence follow a cosine power law. The threshold laser fluence, ablation depth and crater size depend on the polarization and angle of the incident laser beam. Our model is supported by the experimental results reported by other group working in femtosecond pulsed laser ablation. 

9. Dasallas, L.L., Jaculbia, R.B., Balois, M.V., Garcia, W.O., Hayazawa, N. (2018). Position, orientation, and relative quantum yield ratio determination of fluorescent nanoemitters via combined laser scanning microscopy and polarization measurements. Optical Materials Express, 8 (5), Pages 1290-1304. more

Abstract:

We present a universal method of determining the position, 3D orientation, and relative quantum yield ratio (RQYR) of fluorescent nanoemitters (ZnS coated CdSe quantum dots) in a glass slide by combining laser scanning microscopy (LSM) and polarization measurements. The quantum dots were located through LSM intensity maps using azimuthal, radial, and linear incident polarizations. LSM imaging was not sufficient to determine the orientation of the quantum dots due to the isotropic absorption dipole moment. The 3D orientation was obtained through polarization measurement. By combining LSM and polarization measurements, the RQYR of a single molecule was evaluated, allowing us to compare the quantum yield of the nanoemitters. 

10. Dasallas, L. L., & Garcia, W. O. (2018). Numerical simulation of femtosecond pulsed laser ablation of copper for oblique angle of incidence through two-temperature model. Materials Research Express, (1), Article Number: 016518.

 

11. De Vero, J.C., Lee, D., Shin, H., Namuco, S.B., Hwang, I., Sarmago, R.V., Song, J.H. (2018). Influence of deposition conditions on the growth of micron-thick highly c-axis textured superconducting GdBa2Cu3O7-δ films on SrTiO3 (100). Journal of Vacuum Science and Technology A: Vacuum, Surfaces and Films, 36 (3). 

Abstract:

A fundamental understanding of film processing conditions and its effect on the microstructure, crystallinity, and electrical properties of thick layers of a GdBa2Cu3O7-δ (GdBaCuO) superconductor is necessary to optimize material requirements for its applications. In this work, the authors investigated the surface microstructure, crystalline quality, and superconducting properties of GdBaCuO thick films on (100) SrTiO3 single crystal substrates prepared by pulsed laser deposition (PLD). To clarify the effect of PLD growth conditions the substrate temperature, oxygen partial pressure, and laser fluence were systematically varied, then their impact was correlated on the microstructure and superconducting properties of thick layers of GdBaCuO films. By optimizing these growth conditions, the authors successfully obtained preferentially c-axis textured and superconducting films with a uniform and homogeneous layer up to 3.8 μm thick. Based on these results, the authors provide a key guiding principle in achieving thick highly c-axis textured superconducting GdBaCuO films using PLD.

12. delos Santos, R., Mag-usara, V., Tuico, A., Copa, V., Salvador, A., Yamamoto, K., Somintac, A., Kurihara, K., Kitahara, H., Tani, M., Estacio, E.  (2018). Metal-Coated <100>-Cut GaAs Coupled to Tapered Parallel-Plate Waveguide for Cherenkov-Phase-Matched Terahertz Detection: Influence of Crystal Thickness. Journal of Infrared, Millimeter, and Terahertz Waves, 39(6), Pages 514-520. more

Abstract:

The influence of crystal thickness of metal-coated <100>-cut GaAs (M-G-M) on Cherenkov-phase-matched terahertz (THz) pulse detection was studied. The M-G-M detectors were utilized in conjunction with a metallic tapered parallel-plate waveguide (TPPWG). Polarization-sensitive measurements were carried out to exemplify the efficacy of GaAs in detecting transverse magnetic (TM)- and transverse electric (TE)-polarized THz waves. The reduction of GaAs’ thickness increased the THz amplitude spectra of the detected TM-polarized THz electro-optic (EO) signal due to enhanced electric field associated with a more tightly-focused and well-concentrated THz radiation on the thinner M-G-M. The higher-fluence THz beam coupled to the thinner M-G-M improved the integrated intensity of the detected THz amplitude spectrum. This trend was not observed for TE-polarized THz waves, wherein the integrated intensities were almost comparable. Nevertheless, good agreement of spectral line shapes of the superposed TM- and TE-polarized THz-EO signals with that of elliptically polarized THz-EO signal demonstrates excellent polarization-resolved detection capabilities of M-G-M via Cherenkov-phase-matched EO sampling technique. 

13. Gabriel, A.A., Ballesteros, M.L.P., Rosario, L.M.D., Tumlos,R.B., Ramos, H.J. (2018). Elimination of Salmonella enterica on common stainless steel food contact surfaces using UV-C and atmospheric pressure plasma jetFood Control, 86, Pages 90-100.more

Abstract: 

This study aimed to evaluate the efficacy of ultraviolet-C irradiation and atmospheric pressure plasma jet treatment as inactivation methods of Salmonella spp. on stainless steel surfaces commonly used as food contact surfaces. Two types of stainless steel namely 304 and 316, were used as test surfaces with each type having three different finishes: 2B, Hair line (HL), and Mirror (MR). A cocktail of 7 serovars of S. enterica at mid stationary phase (17 h) cells were allowed to adhere onto the surfaces (4h) prior to UV-C and plasma treatment. Results showed that the test organism exhibited a biphasic UV-C inactivation composed of a fast log linear inactivation phase followed by a slower inactivation tail on all test surfaces. The D values calculated from the faster log linear inactivation phase ranged from 2.54 (316 2B and 316 HL) to 4.31 s (304 2B). The maximum population reduction calculated before the inactivation tail ranged from 3.32 (316 HL) to 4.97 log CFU/in2 (304 MR). Plasma treatment of metal surfaces resulted in abrupt increase in surface temperature, reaching up to 180 °C within 15 s of treatment, and led to log linear inactivation in all surfaces treated with atmospheric plasma jet. The D values ranged from 2.66 (304 2B) to 3.43 s (316 MR). Both metal type and surface finish were observed not to affect the efficacies of UV-C inactivation and atmospheric pressure plasma jet treatment. The results obtained in the study demonstrated the potential of the tested physical treatments as alternatives to commonly used food contact surface chemical sanitation protocols.

14. Lee, H.V., J., Rosario, L. M. D., Tumlos, R. B., Ramos, H. J., Bo-Ot, L. M. T., & Soriano, M. N. (2018). Excitation of O(1S) auroral green line from ambient air in a microwave-induced plasma jet at atmospheric pressure. Japanese Journal of Applied Physics, 57 (6), Article number 066102.

 

15. Narag, J., Hermosa, N.  (2018) Diffraction of polygonal slits using catastrophe optics. Journal of Applied Physics, 124(3), Article number 034902.more

Abstract: 

Young's boundary wave theory provides an alternative view of diffraction being an interference of a geometric wave and a boundary wave. Here, we show theoretically and experimentally that the transverse structure of a plane wave diffracted through slits originates solely from the boundary waves. For polygonal slits, we demonstrate that the concept of the ordinary evolute is ill-defined, and we solve this problem by taking the limit of the evolute as the curvature goes to zero. We show that light focuses not on caustic as ordinarily described in catastrophe optics but on regions which we define as second order evolutes. Experimentally, we show that these second order evolutes still correspond to the brightest regions of the diffraction because of the boundary waves at the vertices of the polygon. This research is valuable in the study of diffraction of slits in general and in optical self-healing where the reconstruction of the transverse structure is investigated.

 

16. Prieto, E., Vizcara, S., Lopez, L., Vasquez, J., Balgos, M., Hashizume, D., … Estacio, E. S. (2018). Intense THz emission in high quality MBE-grown GaAs film with a thin n-doped buffer. Optical Materials Express, (6), 1463.

 

17. Sadiaa, C.P., Lopez Jr., L.P., delos Santos, R.M., Muldera, J.E., De Los Reyes, A.E.,Tumanguil, M.A.C., Que, C.T., Mag-usara,V.K., Tani, M., Somintac, A.S., Estacio, E.S., Salvador, A.S. (2018). Epitaxial growth of p-InAs on GaSb with intense terahertz emission under 1.55- μ m femtosecond laser excitationThin Solid Films, 648, Pages 46-49.more

Abstract: 

We report the molecular beam epitaxy growth of high-quality p-InAs thin films evaluated in the context of 1.55 μm femtosecond laser-excited THz emission efficiency. The presence of p-InAs is confirmed via scanning electron microscopy and X-ray diffraction. Using a GaAs buffer layer, the epitaxial growth of p-InAs layers was successfully achieved. Initiating GaAs deposition by growth interruption, we find that GaAs adheres to the GaSb substrate and provides a quasi-planar surface for the subsequent layers. We also find a significant enhancement in the THz radiation intensity of p-InAs films that is approximately twice compared to that of bulk p-InAs for 1.55 μm wavelength.

18. Sombillo, D. L. B., & Galapon, E. A. (2018). Barrier-traversal-time operator and the time-energy uncertainty relation. Physical Review A - Atomic, Molecular, and Optical Physics, 97(6), Article number 062127.more

Abstract:

A general barrier-traversal-time operator is constructed using the time-of-arrival formalism. We study the operator's dynamics and determine the role played by the time-energy commutation relation. It turns out that similar dynamics is observed whether the traversal-time operator is canonically conjugate to the system Hamiltonian or not. We also use the barrier-traversal-time operator to calculate the traversal-time distributions for different cases (free case, and above-the-barrier and under-the-barrier traversals). The peak of the traversal-time distributions coincides with the classical expected traversal times for the free case and the above-the-barrier case. We then present our interpretation of the time-energy uncertainty relation that is consistent with the different traversal-time distributions.

19. Tica, C.D., Galapon, E.A. (2018). Finite-part integration of the generalized Stieltjes transform and its dominant asymptotic behavior for small values of the parameter. I. Integer ordersJournal of Mathematical Physics, 59 (2).more

Abstract:

The paper addresses the exact evaluation of the generalized Stieltjes transform Sn[f]=0 f(x)(ω+x)-ndx of integral order n = 1, 2, 3,  about ω = 0 from which the asymptotic behavior of Sn[f] for small parameters ω is directly extracted. An attempt to evaluate the integral by expanding the integrand (ω + x)-n about ω = 0 and then naively integrating the resulting infinite series term by term leads to an infinite series whose terms are divergent integrals. Assigning values to the divergent integrals, say, by analytic continuation or by Hadamard's finite part is known to reproduce only some of the correct terms of the expansion but completely misses out a group of terms. Here we evaluate explicitly the generalized Stieltjes transform by means of finite-part integration recently introduced in Galapon [Proc. R. Soc. A 473, 20160567 (2017)]. It is shown that, when f(x) does not vanish or has zero of order m at the origin such that (n - m) ≥ 1, the dominant terms of Sn[f] as ω → 0 come from contributions arising from the poles and branch points of the complex valued function f(z)(ω + z)-n. These dominant terms are precisely the terms missed out by naive term by term integration. Furthermore, it is demonstrated how finite-part integration leads to new series representations of special functions by exploiting their known Stieltjes integral representations. Finally, the application of finite part integration in obtaining asymptotic expansions of the effective diffusivity in the limit of high Peclet number, the Green-Kubo formula for the self-diffusion coefficient, and the antisymmetric part of the diffusion tensor in the weak noise limit is discussed.

20. Tiongson, J.K.A., Bruzon, D.A.V., Tapang, G.A., Martinez, I.S. (2018). Syntheses and Properties of Methoxy and Nitrile Functionalized Imidazolium Tris(pentafluoroethyl)trifluorophosphate Ionic Liquids. Journal of Chemical and Engineering Data, 63 (5), Pages 1135-1145. more

Abstract:

An alternative and more benign method was employed to synthesize tris(pentafluoroethyl)trifluorophosphate (FAP) ionic liquids (ILs). Ion exchange chromatography was used instead of the typical electrochemical fluorination developed by Ignat'ev and co-workers. The resulting procedure is simple and can be readily performed, as the use of corrosive hydrofluoric acid and the production of toxic and explosive byproducts were circumvented. Functionalization of the alkyl group of the imidazolium cation with a methoxy and a nitrile moiety was employed to observe changes in properties. The success of the synthesis was confirmed by 1H, 19F, and 31P NMR, IR, and UV-vis spectroscopy techniques. Quantitative product yields of approximately 80% (w/w) were obtained. The water content and viscosity values of the synthesized FAP-based ILs were found to be lower compared to other fluorine-containing ionic liquids. Thermal analyses resulted in high thermal degradation temperatures greater than 573.15 K. Electrochemical analyses showed potential windows of values greater than 5.0 V, indicating electrochemical stability. On the basis of the basic properties observed, the FAP-based ILs synthesized in this study may be useful as gas absorbents, electrolytes, and other applications, especially those involving extended temperature ranges.

 

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1. Buenaventura, A. G. E., Yago, A. C. C., Buenaventura, A. G. E., & Yago, A. C. C. (2018). Facile Electrochemical Pretreatment of Multiwalled Carbon Nanotube - Polydimethylsiloxane Paste Electrode for Enhanced Detection of Dopamine and Uric Acid. In AIP Conference Proceedings, Vol. 1958, Article number 020029.

 

2. Buenviaje, S. C., Usman, K. A. S., Payawan, L. M., Buenviaje, S. C., Usman, A. S., & Payawan, L. M. (2018). Synthesis and Characterization of Titanium Dioxide- Polypyrrole Nanocomposites for the Photodegradation of Bromophenol Blue. In AIP Conference Proceedings, Vol. 1958, Article number 020015.

 

3. Calacal, G. C., Salvador, J. M., Sagum, M. S., Fortun, R. D., & De Ungria, M. C. A. (2018). Pathology and DNA Analysis of Exhumed Human Remains Three-years Post-mortem. Philippine Journal of Science, 147 (1), Pages 9–16.

 

4. Catap, E. S., Kho, M. J. L., & Jimenez, M. R. R. (2018). In vivo nonspecific immunomodulatory and antispasmodic effects of common purslane (Portulaca oleracea Linn.) leaf extracts in ICR mice. Journal of Ethnopharmacology, 215, Pages 191–198.

 

5. Martin, Z. N. Z., Martinez, I. S., & Nellas, R. B. (2018). Surface tension data of n-propane, n-octane and n-dodecane from nucleation simulations. Tellus, Series B: Chemical and Physical Meteorology, 70 (1), Pages 1–5.

 

6. Pagalilauan, H. A. M., Paraoan, C. E. M., & Vital, P. G. (2018). Detection of pathogenic bioaerosols and occupational risk in a Philippine landfill site. Archives of Environmental and Occupational Health, 73 (2), Pages 107–114.

 

7. Pedales, R. D. C., & Fontanilla, I. K. C. (2018). Forensic entomology in the Philippines : Establishing Baseline Data on the Forensically Important Blow Fly Species Chrysomya megacephala ( Fabricius , 1794 ). Philippine Journal of Science, 147 (1), Pages 17–25.

 

8. Ramos, P. C. L., & Conato, M. T. (2018). Hydrothermal synthesis, crystal structures, and enantioselective adsorption property of bis(L-histidinato)nickel(II) monohydrate Hydrothermal Synthesis, Crystal Structures, and Enantioselective Adsorption Property of Bis(L- histidinato)nickel(II) Monohydr. AIP Conference Proceedings, 1958, Article number 020017.

 

9. Salas, R. L., Garcia, J. K. D. L., Miranda, A. C. R., Rivera, W. L., Nellas, R. B., & Sabido, P. M. G. (2018). Effects of truncation of the peptide chain on the secondary structure and bioactivities of palmitoylated anoplin. Peptides, 104, Pages 7–14.

 

10. Salvador, J. M., Apaga, D. L. T., Delfin, F. C., Calacal, G. C., Dennis, S. E., & De Ungria, M. C. A. (2018). Filipino DNA variation at 12 X-chromosome short tandem repeat markers. Forensic Science International: Genetics.

 

11. Tiongson, J. K. A., Bruzon, D. A. V., Tapang, G. A., & Martinez, I. S. (2018). Syntheses and Properties of Methoxy and Nitrile Functionalized Imidazolium Tris(pentafluoroethyl)trifluorophosphate Ionic Liquids. Journal of Chemical and Engineering Data, 63 (5), Pages 1135–1145.

 

12. Usman, K. A. S., Buenviaje, S. C., Razal, J. M., Conato, M. T., & Payawan, L. M. J. (2018). Synthesis and characterization of zinc adeninate metal-organic frameworks (bioMOF1) as potential anti-inflammatory drug delivery material. In 8TH International Conference on Nanoscience and Nanotechnology 2017 (NANO-SciTech 2017).

 

13. Vital, P. G., Zara, E. S., Paraoan, C. E. M., Dimasupil, M. A. Z., Abello, J. J. M., Santos, I. T. G., & Rivera, W. L. (2018). Antibiotic Resistance and Extended-Spectrum Beta-Lactamase Production of Escherichia coli Isolated from Irrigation Waters in Selected Urban Farms in Metro Manila , Philippines. Water (Switzerland), 10 (5), Article number 548.