34 results on '"Jomar F. Rabajante"'
Search Results
2. Using Constrained Optimization for the Allocation of COVID-19 Vaccines in the Philippines
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Christian Alvin H. Buhat, Kemuel M. Quindala, Dylan Antonio S. J. Talabis, Mary Grace P. Recreo, Jerrold M. Tubay, Destiny Sm Lutero, Monica C Torres, Yancee H. Olave, and Jomar F. Rabajante
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Economics and Econometrics ,COVID-19 Vaccines ,Coronavirus disease 2019 (COVID-19) ,Philippines ,Population ,Distribution (economics) ,Health administration ,03 medical and health sciences ,0302 clinical medicine ,Humans ,Original Research Article ,030212 general & internal medicine ,education ,education.field_of_study ,Government ,Health Care Rationing ,Health economics ,Actuarial science ,business.industry ,030503 health policy & services ,Health Policy ,Vaccination ,Constrained optimization ,COVID-19 ,General Medicine ,Models, Theoretical ,Business ,0305 other medical science - Abstract
Background Vaccine allocation is a national concern especially for countries such as the Philippines that have limited resources in acquiring COVID-19 vaccines. As such, certain groups are suggested to be prioritized for vaccination to protect the most vulnerable before vaccinating others. Objective The study aims to determine an optimal and equitable allocation of COVID-19 vaccines in the Philippines that will minimize the projected number of additional COVID-19 deaths while satisfying the priority groups for immediate vaccination. Methods In this study, a linear programming model is formulated to determine an allocation of vaccines such that COVID-19 deaths are minimized while the prioritization framework set by the government is satisfied. Data used were collected up to November 2020. Total vaccine supply, vaccine effectiveness, vaccine cost, and projected deaths are analyzed. Results of the model are also compared to other allocation approaches. Results Results of the model show that a vaccine coverage of around 60–70% of the population can be enough for a community with limited supplies, and an increase in vaccine supply is beneficial if the initial coverage is less than the specified target range. Additionally, among the vaccines considered in the study, the one with 89.9% effectiveness and a 183 Philippine peso price per dose projected the lowest number of deaths. Compared with other model variations and common allocation approaches, the model has achieved both an optimal and equitable allocation. Conclusions Having a 100% coverage for vaccination with a 100% effectiveness rate of vaccine is ideal for all countries. However, some countries have limited resources. Therefore, the results of our study can be used by policymakers to determine an optimal and equitable distribution of COVID-19 vaccines for a country/community. Supplementary Information The online version contains supplementary material available at 10.1007/s40258-021-00667-z.
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- 2021
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3. An Integrated Mass Spectrometry-Based Glycomics-Driven Glycoproteomics Analytical Platform to Functionally Characterize Glycosylation Inhibitors
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Michael Russelle S. Alvarez, Qingwen Zhou, Sheryl Joyce B. Grijaldo, Carlito B. Lebrilla, Ruel C. Nacario, Francisco M. Heralde, Jomar F. Rabajante, and Gladys C. Completo
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Integrins ,Lung Neoplasms ,Glycosylation ,glycomics ,glycoproteomics ,glycosylation ,proteomics ,in silico docking ,network pharmacology ,non-small cell lung cancer ,Pharmaceutical Science ,Mass Spectrometry ,Analytical Chemistry ,Medicinal and Biomolecular Chemistry ,Polysaccharides ,Theoretical and Computational Chemistry ,Drug Discovery ,Humans ,2.1 Biological and endogenous factors ,Physical and Theoretical Chemistry ,Aetiology ,Glycomics ,Lung ,Glycoproteins ,Cancer ,Organic Chemistry ,carbohydrates (lipids) ,Chemistry (miscellaneous) ,Molecular Medicine ,Mannose - Abstract
Cancer progression is linked to aberrant protein glycosylation due to the overexpression of several glycosylation enzymes. These enzymes are underexploited as potential anticancer drug targets and the development of rapid-screening methods and identification of glycosylation inhibitors are highly sought. An integrated bioinformatics and mass spectrometry-based glycomics-driven glycoproteomics analysis pipeline was performed to identify an N-glycan inhibitor against lung cancer cells. Combined network pharmacology and in silico screening approaches were used to identify a potential inhibitor, pictilisib, against several glycosylation-related proteins, such as Alpha1-6FucT, GlcNAcT-V, and Alpha2,6-ST-I. A glycomics assay of lung cancer cells treated with pictilisib showed a significant reduction in the fucosylation and sialylation of N-glycans, with an increase in high mannose-type glycans. Proteomics analysis and in vitro assays also showed significant upregulation of the proteins involved in apoptosis and cell adhesion, and the downregulation of proteins involved in cell cycle regulation, mRNA processing, and protein translation. Site-specific glycoproteomics analysis further showed that glycoproteins with reduced fucosylation and sialylation were involved in apoptosis, cell adhesion, DNA damage repair, and chemical response processes. To determine how the alterations in N-glycosylation impact glycoprotein dynamics, modeling of changes in glycan interactions of the ITGA5–ITGB1 (Integrin alpha 5-Integrin beta-1) complex revealed specific glycosites at the interface of these proteins that, when highly fucosylated and sialylated, such as in untreated A549 cells, form greater hydrogen bonding interactions compared to the high mannose-types in pictilisib-treated A549 cells. This study highlights the use of mass spectrometry to identify a potential glycosylation inhibitor and assessment of its impact on cell surface glycoprotein abundance and protein–protein interaction.
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- 2022
4. Optimal strategies and cost-benefit analysis of the $${\varvec{n}}$$-player weightlifting game
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Diane Carmeliza N. Cuaresma, Erika Chiba, Jerrold M. Tubay, Jomar F. Rabajante, Maica Krizna A. Gavina, Jin Yoshimura, Hiromu Ito, Takuya Okabe, and Satoru Morita
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Multidisciplinary - Abstract
The study of cooperation has been extensively studied in game theory. Especially, two-player two-strategy games have been categorized according to their equilibrium strategies and fully analysed. Recently, a grand unified game covering all types of two-player two-strategy games, i.e., the weightlifting game, was proposed. In the present study, we extend this two-player weightlifting game into an $$n$$ n -player game. We investigate the conditions for pure strategy Nash equilibria and for Pareto optimal strategies, expressed in terms of the success probability and benefit-to-cost ratio of the weightlifting game. We also present a general characterization of $$n$$ n -player games in terms of the proposed game. In terms of a concrete example, we present diagrams showing how the game category varies depending on the benefit-to-cost ratio. As a general rule, cooperation becomes difficult to achieve as group size increases because the success probability of weightlifting saturates towards unity. The present study provides insights into achieving behavioural cooperation in a large group by means of a cost–benefit analysis.
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- 2022
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5. Spatiotemporal modeling of parasite aggregation among fish hosts in a lentic ecosystem
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Christian Alvin H. Buhat, Jomar F. Rabajante, and Vachel Gay V. Paller
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0106 biological sciences ,education.field_of_study ,Ecology ,Host (biology) ,010604 marine biology & hydrobiology ,fungi ,Population ,Lake ecosystem ,Biology ,010603 evolutionary biology ,01 natural sciences ,Parasite load ,Zooplankton ,Parasite hosting ,Macroparasite ,Ecosystem ,Computers in Earth Sciences ,Statistics, Probability and Uncertainty ,General Agricultural and Biological Sciences ,education ,General Environmental Science - Abstract
Parasite aggregation is a frequently occurring phenomenon where majority of the parasites accumulate in the smaller fraction of the host population while many individual hosts have low parasite load. One of the mechanisms of parasite aggregation is heterogeneity in the host-parasite interaction. Here, we aim to develop and analyze a spatiotemporal model to explain the details of this mechanism. We construct an agent-based simulation involving fish hosts that forage on zooplanktons harboring macroparasites. In this study, we restrict our simulations to a lentic ecosystem, i.e., still, closed freshwater environment. Our simulations show that (i) the initial sizes of the population of both the fish and zooplanktons have minimal effect on the aggregation of parasites; (ii) increasing the probabilities of reproduction of both fish and zooplankton lead to parasite aggregation among fish hosts; and (iii) aggregation occurs either by decreasing the size of the infection area or increasing the size of the zooplankton-free area in the lentic ecosystem. Our results can be used to provide insights and visualization of the underlying processes leading to aggregation. These can also be used to aid experimentalists in determining the statistical distribution of parasites in hosts for disease prevention and control.
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- 2020
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6. Optimal strategies and cost-benefit analysis of the [Formula: see text]-player weightlifting game
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Diane Carmeliza N, Cuaresma, Erika, Chiba, Jerrold M, Tubay, Jomar F, Rabajante, Maica Krizna A, Gavina, Jin, Yoshimura, Hiromu, Ito, Takuya, Okabe, and Satoru, Morita
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Game Theory ,Weight Lifting ,Cost-Benefit Analysis ,Biological Evolution ,Probability - Abstract
The study of cooperation has been extensively studied in game theory. Especially, two-player two-strategy games have been categorized according to their equilibrium strategies and fully analysed. Recently, a grand unified game covering all types of two-player two-strategy games, i.e., the weightlifting game, was proposed. In the present study, we extend this two-player weightlifting game into an [Formula: see text]-player game. We investigate the conditions for pure strategy Nash equilibria and for Pareto optimal strategies, expressed in terms of the success probability and benefit-to-cost ratio of the weightlifting game. We also present a general characterization of [Formula: see text]-player games in terms of the proposed game. In terms of a concrete example, we present diagrams showing how the game category varies depending on the benefit-to-cost ratio. As a general rule, cooperation becomes difficult to achieve as group size increases because the success probability of weightlifting saturates towards unity. The present study provides insights into achieving behavioural cooperation in a large group by means of a cost-benefit analysis.
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- 2022
7. Pollinator diversity and density measures: survey and indexing standard to model, detect, and assess pollinator deficits
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Jomar F. Rabajante, Cleofas R. Cervancia, Editha C. Jose, and Jerrold M. Tubay
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0106 biological sciences ,Agroecosystem ,education.field_of_study ,Pollination ,010604 marine biology & hydrobiology ,Population ,Foraging ,Survey sampling ,Nectar secretion ,010603 evolutionary biology ,01 natural sciences ,Geography ,Pollinator ,Statistics ,Ecosystem ,Computers in Earth Sciences ,Statistics, Probability and Uncertainty ,General Agricultural and Biological Sciences ,education ,General Environmental Science - Abstract
In response to the need to derive empirical data on the status of pollinators, we have developed a protocol to assess the pollinator population in managed and natural ecosystems, especially in Asia where there is no harmonized initiative for pollination research. This protocol is helpful in assessing organic and non-organic farming since pollinator persistence can be an indicator of good and sustainable practices. The three important steps in the protocol are planning, implementation of the survey, and computation of indices. In the planning step, experts rank and classify the pollinator hotspots in various ecosystem types based on the seasonality and likelihood of having high number of flowers and pollinators. Two-stage sampling and mapping of each hotspots are designed. The number of sample hotspots is computed according to sampling precision and confidence levels assigned per class per ecosystem type. In each sample hotspot, sample survey sites are randomly selected according to the agreed sampling precision and confidence levels. In the second step, for orchard or agroecosystem, a grid map with 100 m2 divisions is surveyed. For natural vegetation, survey sites are randomly selected according to the location of pollinator nesting sites. All sampling surveys are conducted during the blooming period of the plants, with consideration of the peak of anthesis, because this is the period when the pollinators are actively foraging, the pollen viability is high, and the nectar secretion is at its peak. Moreover, a template is created to compute for diversity measures and our proposed pollination matching measures (P-to-P ratio and index).
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- 2019
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8. Sustainability of nonlinear consumption schemes in resource dynamics with Allee and crowding effects
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Jomar F. Rabajante and Kyrell Vann B. Verano
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Consumption (economics) ,Mathematical optimization ,Environmental Engineering ,Renewable Energy, Sustainability and the Environment ,Computer science ,020209 energy ,02 engineering and technology ,010501 environmental sciences ,01 natural sciences ,Industrial and Manufacturing Engineering ,symbols.namesake ,Complex dynamics ,Resource (project management) ,Sustainable management ,Sustainability ,0202 electrical engineering, electronic engineering, information engineering ,symbols ,Environmental Chemistry ,Sustainable consumption ,Production (economics) ,0105 earth and related environmental sciences ,Allee effect - Abstract
Mathematical models of production and consumption are useful in devising policies for sustainable management of renewable resources. Analysis of simple but not too naive models of resource dynamics can provide initial or supplementary insights in formulating comprehensive policies. In these models, density-dependence of resources, nonlinearities in consumption schemes, and uncertainties in parameters are essential to be considered to account for the temporal complex dynamics of the resource. Here, we study minimal ordinary differential equation models which are compartmentalized into production and consumption functions. We propose density-dependent production functions with Allee and crowding effects, and nonlinear consumption functions that are hyperbolic and sigmoidal. We identify scenarios where our results differ from the existing classical logistic models with linear consumption scheme, and determine quantitative conditions leading to sustainable consumption. Our results propose conditions in which consumption efforts will not cause eventual depletion of the resource under specific assumptions. Furthermore, we analyze how delay and stochasticity affect the derived sustainability conditions. Our results can be used as initial input in formulating strategies to properly manage renewable resources, especially in the absence of models requiring extensive data availability.
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- 2019
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9. Optimal Allocation of COVID-19 Vaccines in the Philippines
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Christian Alvin H. Buhat, Monica C Torres, Mary Grace P. Recreo, Destiny Sm Lutero, Jomar F. Rabajante, Yancee H Olave, Jerrold M. Tubay, Kemuel M. Quindala, and Dylan Antonio S. J. Talabis
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Prioritization ,Vaccination ,education.field_of_study ,Actuarial science ,Coronavirus disease 2019 (COVID-19) ,business.industry ,Population ,Optimal allocation ,Distribution (economics) ,Business ,education ,Target range ,Limited resources - Abstract
Vaccine allocation is a national concern especially for countries such as the Philippines that have limited resources in acquiring COVID-19 vaccines. As such, certain groups are suggested to be prioritized for vaccination to protect the most vulnerable before vaccinating others. Our model suggests an allocation of vaccines such that COVID-19 deaths are minimized while the prioritization framework is satisfied. Results of the model show that a vaccine coverage of at least 50 to 70% of the population can be enough for a community with limited supplies, and an increase in vaccine supply is beneficial if initial coverage is less than the specified target range. Also, among the vaccines considered in the study, the one with 89.9% effectiveness and has a 183 Philippine peso (Php) price per dose projected the least number of deaths. Compared to other model variations and common allocation approaches, the model has achieved both an optimal and equitable allocation. This will be helpful for policymakers in determining a vaccine distribution for a resource-constrained community.
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- 2021
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10. Cost–Benefit Analysis of Face-to-Face Closure of Schools to Control COVID-19 in the Philippines
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Xylee Javier, Ludigil Garces, Jomar F. Rabajante, David A. Raitzer, Rouselle F. Lavado, and Glenita Amorantoa
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Finance ,Face-to-face ,Cost–benefit analysis ,Higher education ,business.industry ,Economic cost ,Closure (psychology) ,business ,Alternative education ,Inclusion (education) ,Waste disposal - Published
- 2020
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11. Modeling the Transmission of Respiratory Infectious Diseases in Mass Transportation Systems
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Christian Alvin H. Buhat, Destiny Sm Lutero, Jomar F. Rabajante, Monica C Torres, and Yancee H. Olave
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Infectious disease (medical specialty) ,Distancing ,Social distance ,Environmental health ,Pandemic ,Outbreak ,Business ,Disease ,Seating capacity ,Mass transportation - Abstract
Mass transportation is one of the areas that are badly hit by respiratory infectious disease outbreaks due to moderate to high exposure risk to pathogens brought about by the interaction among commuters. Here, we formulate agent-based models that simulate the spread of a respiratory infectious disease in a train wagon in the Manila Light Rail Transit System, and in a 49-seater public utility bus. We consider preventive measures such as implementation of social distancing, and limitation of interaction or movement among the commuters to investigate how these measures will inhibit disease transmission. We also consider the effect of protective gears and practices, crowd density, and prevalence of disease in the community on the possible number of newly-infected individuals. Our simulations show that (i) individuals must have protection with more than 90% effectiveness to inhibit transmission of the disease; (ii) social or physical distancing by more than 1m distance reduces the risk of being infected; (iii) minimizing movement or interaction with other passengers reduces the risk of transmission by 50%; (iv) passenger capacity should be less than 10-50% of the maximum seating capacity to reduce the number of infections depending on the level of imposed social distancing and passenger interaction; (v) vehicles with greater number of occupied seating capacity generate higher number of infections but vehicles with smaller dimensions have faster disease transmissions; and (vi) ideal set-up for a 24-seater train wagon (49-seater bus) is to allow a maximum of 12 (24) passengers, with little to no interaction among passengers, with social distancing of more than 1m distance apart, and each person has a protection with 90% effectiveness as much as possible. These results can aid policy makers in determining optimal strategies to minimize infections while maintaining transportation services during pandemics or disease outbreaks.
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- 2020
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12. A COVID-19 Infection Risk Model for Frontline Health Care Workers
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Jomar F. Rabajante and Louie Florendo Dy
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Crowd dynamics ,Infection risk ,Coronavirus disease 2019 (COVID-19) ,Urology ,Short Communication ,Philippines ,Compartmentalization (information security) ,Health informatics ,03 medical and health sciences ,0302 clinical medicine ,Health care ,Medicine ,Duration (project management) ,030304 developmental biology ,0303 health sciences ,SARS-CoV-2 ,business.industry ,Social distance ,Healthcare ,COVID-19 ,medicine.disease ,Interaction time ,Frontliner ,Work shift ,030220 oncology & carcinogenesis ,Public transport ,Medical emergency ,Crowd density ,Risk assessment ,business - Abstract
The number of confirmed COVID-19 cases admitted in hospitals is continuously increasing in the Philippines. Frontline health care workers are faced with imminent risks of getting infected. In this study, we formulate a theoretical model to calculate the risk of being infected in health care facilities considering the following factors: the average number of encounters with a suspected COVID-19 patient per hour; interaction time for each encounter; work shift duration or exposure time; crowd density, which may depend on the amount of space available in a given location; and availability and effectiveness of protective gears and facilities provided for the frontline health care workers. Based on the simulation results, a set of risk assessment criteria is proposed to classify risks as ‘low’, ‘moderate’, or ‘high’. We recommend the following: (i) decrease the rate of patient encounter per frontline health care worker, e.g., maximum of three encounters per hour in a 12-hour work shift duration; (ii) decrease the interaction time between the frontline health care worker and the patients, e.g., less than 40 minutes for the whole day; (iii) increase the clean and safe space for social distancing, e.g., maximum of 10% crowd density, and if possible, implement compartmentalization of patients; and/or (iv) provide effective protective gears and facilities, e.g., 95% effective, that the frontline health care workers can use during their shift. Moreover, the formulated model can be used for other similar scenarios, such as identifying infection risk in public transportation, school classroom settings, offices, and mass gatherings.
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- 2020
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13. Long-term persistence of agricultural pest insects by risk-spreading dispersal
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Satoru Morita, Genki Ichinose, Kotaro Aoki, Maica Krizna Areja Gavina, Hiromu Ito, Jin Yoshimura, Jomar F. Rabajante, and Vincent A. A. Jansen
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0106 biological sciences ,Reproductive success ,business.industry ,Ecology ,Pest control ,Biology ,Fecundity ,010603 evolutionary biology ,01 natural sciences ,Life history theory ,010602 entomology ,Habitat ,Agriculture ,Biological dispersal ,PEST analysis ,business ,Ecology, Evolution, Behavior and Systematics - Abstract
Insects are the most diverse organisms on earth consisting of more than 900 thousand species. However, only few of them are considered agricultural pests. Life history traits such as high fecundity, fast population growth, and high dispersal ability have been used to characterize agricultural pest insects. However, many other non-pest insects also share these traits, which indicates that there has not been a decisive condition characterizing agricultural pest insects. Agricultural habitats are risky and ephemeral to pests because of pest control and harvesting. The usual arithmetic mean fitness cannot be used to measure the persistence of these pests, because the maximal mean fitness is achieved only when they exhibit no dispersal, but that leads to immediate extinction. Using a geometric mean fitness model, we propose a quantitative measure of long-term reproductive success for agricultural pest insects. By using this approach, we can evaluate the trade-off between long-distance dispersal and high reproduction correctly and estimate the condition for the long-term persistence of pest insects in agricultural habitats. We discuss some general perspectives of pest control from the proposed characterization.
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- 2018
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14. From epigenetic landscape to phenotypic fitness landscape: Evolutionary effect of pathogens on host traits
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Jomar F. Rabajante, Mark Jayson V. Cortez, Jerrold M. Tubay, and Ariel L. Babierra
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0106 biological sciences ,0301 basic medicine ,Microbiology (medical) ,Fitness landscape ,Gene regulatory network ,Parasitism ,Biology ,010603 evolutionary biology ,01 natural sciences ,Microbiology ,Epigenesis, Genetic ,Host-Parasite Interactions ,03 medical and health sciences ,Quantitative Trait, Heritable ,Genetics ,Animals ,Cell Lineage ,Computer Simulation ,Gene Regulatory Networks ,Epigenetics ,Selection, Genetic ,Molecular Biology ,Ecology, Evolution, Behavior and Systematics ,Selection (genetic algorithm) ,Regulation of gene expression ,Phenotypic plasticity ,Models, Genetic ,Biological Evolution ,Phenotype ,Eukaryotic Cells ,030104 developmental biology ,Infectious Diseases ,Evolutionary biology - Abstract
The epigenetic landscape illustrates how cells differentiate into different types through the control of gene regulatory networks. Numerous studies have investigated epigenetic gene regulation but there are limited studies on how the epigenetic landscape and the presence of pathogens influence the evolution of host traits. Here we formulate a multistable decision-switch model involving many possible phenotypes with the antagonistic influence of parasitism. As expected, pathogens can drive dominant (common) phenotypes to become inferior, such as through negative frequency-dependent selection. Furthermore, novel predictions of our model show that parasitism can steer the dynamics of phenotype specification from multistable equilibrium convergence to oscillations. This oscillatory behavior could explain pathogen-mediated epimutations and excessive phenotypic plasticity. The Red Queen dynamics also occur in certain parameter space of the model, which demonstrates winnerless cyclic phenotype-switching in hosts and in pathogens. The results of our simulations elucidate how epigenetic landscape is associated with the phenotypic fitness landscape and how parasitism facilitates non-genetic phenotypic diversity.
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- 2017
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15. On the mechanistic roots of an ecological law: parasite aggregation
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Chaitanya S. Gokhale, Jomar F. Rabajante, and Elizabeth L. Anzia
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education.field_of_study ,Ecology ,Law ,Ecology (disciplines) ,Population ,Macroparasite ,Parasite hosting ,Biology ,education - Abstract
Parasite aggregation, a recurring pattern in macroparasite infections, is considered one of the “laws” of parasite ecology. Few hosts have a large number of parasites while most hosts have a low number of parasites. Phenomenological models of host-parasite systems thus use the negative-binomial distribution. However, to infer the mechanisms of aggregation, a mechanistic model that does not make any a priori assumptions is essential. Here we formulate a mechanistic model of parasite aggregation in hosts without assuming a negative-binomial distribution. Our results show that a simple model of parasite accumulation still results in an aggregated pattern, as shown by the derived mean and variance of the parasite distribution. By incorporating the derived statistics in host-parasite interactions, we can predict how aggregation affects the population dynamics of the hosts and parasites through time. Thus, our results can directly be applied to observed data as well as can inform the designing of statistical sampling procedures. Overall, we have shown how a plausible mechanistic process can result in the often observed phenomenon of parasite aggregation occurring in numerous ecological scenarios, thus providing a basis for a “law” of ecology.
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- 2019
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16. Mathematical Modeling on Competition and Cooperation of Species Using Hill-type Function
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Jose Maria L. Escaner, Racquel U. Tabornal, and Jomar F. Rabajante
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education.field_of_study ,Extinction ,Ecology (disciplines) ,media_common.quotation_subject ,Population ,Biodiversity ,Stability (learning theory) ,Ethology ,Competition (biology) ,Microeconomics ,Economics ,education ,Function (engineering) ,media_common - Abstract
Competition and cooperation play an important role in society. It drives the species to survive and it enables to balance and maintain the biodiversity in communities. These concepts are important in many fields, such as in ethology, economics, ecology, and evolutionary theory. In this paper, we develop a mathematical model that describes the dynamics of the population of a species that simultaneously interact with a competitor and/or with a cooperator. This modeling study uses a Hill-type function rather than the classical Lotka-Volterra equations. Numerical simulations are done on this model. Heat maps are used to describe different cases by varying the competition coefficient δ and cooperation coefficient γ. Our model has demonstrated not just coexistence but also exclusion or extinction of the population of species. This means that even if competition and cooperation are done simultaneously by a species, it is not a guarantee that they will always survive in the long run. It depends on how much the strength of competition and cooperation they exerted towards its co-competitor or co-cooperator. Moreover, cooperating species are most likely to survive as compared to the competing species. This modeling study enables us to look possibly for ways to control δ and γ, and consequently, control populations in our ecosystem. This will be useful not only for biologists and ecologists but also for researchers who are interested in studying the competitive and cooperative interactions of species in societies.
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- 2019
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17. Modeling Long ncRNA-Mediated Regulation in the Mammalian Cell Cycle
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Jomar F, Rabajante and Ricardo C H, Del Rosario
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Gene Expression Regulation ,Models, Genetic ,Cell Cycle ,Animals ,Humans ,Cell Cycle Proteins ,RNA, Long Noncoding ,DNA Damage - Abstract
Long noncoding RNAs (lncRNAs) are transcripts longer than 200 nucleotides that are not translated into proteins. They have recently gained widespread attention due to the finding that tens of thousands of lncRNAs reside in the human genome, and due to an increasing number of lncRNAs that are found to be associated with disease. Some lncRNAs, including disease-associated ones, play different roles in regulating the cell cycle. Mathematical models of the cell cycle have been useful in better understanding this biological system, such as how it could be robust to some perturbations and how the cell cycle checkpoints could act as a switch. Here, we discuss mathematical modeling techniques for studying lncRNA regulation of the mammalian cell cycle. We present examples on how modeling via network analysis and differential equations can provide novel predictions toward understanding cell cycle regulation in response to perturbations such as DNA damage.
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- 2019
18. Modeling Long ncRNA-Mediated Regulation in the Mammalian Cell Cycle
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Jomar F. Rabajante and Ricardo C.H. del Rosario
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0301 basic medicine ,03 medical and health sciences ,030104 developmental biology ,0302 clinical medicine ,DNA damage ,030220 oncology & carcinogenesis ,Mammalian cell ,Human genome ,Long ncRNA ,Computational biology ,Biology ,Cell cycle - Abstract
Long noncoding RNAs (lncRNAs) are transcripts longer than 200 nucleotides that are not translated into proteins. They have recently gained widespread attention due to the finding that tens of thousands of lncRNAs reside in the human genome, and due to an increasing number of lncRNAs that are found to be associated with disease. Some lncRNAs, including disease-associated ones, play different roles in regulating the cell cycle. Mathematical models of the cell cycle have been useful in better understanding this biological system, such as how it could be robust to some perturbations and how the cell cycle checkpoints could act as a switch. Here, we discuss mathematical modeling techniques for studying lncRNA regulation of the mammalian cell cycle. We present examples on how modeling via network analysis and differential equations can provide novel predictions toward understanding cell cycle regulation in response to perturbations such as DNA damage.
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- 2019
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19. Site selection for new green mussel culture area expansion in Buguey estuary, Cagayan, Philippines
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Eunice A. Layugan, John Philip B. Tabasin, Marlon Alejos, Lorebelle E. Pidoy, Jomar F. Rabajante, and Ricardo P. Babaran
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bepress|Business ,bepress|Life Sciences|Agriculture ,bepress|Life Sciences ,bepress|Business|Agribusiness ,AgriXiv|Life Sciences|Agriculture ,AgriXiv|Business ,AgriXiv|Business|Agribusiness ,AgriXiv|Life Sciences - Abstract
Currently, there is limited data on the suitability of estuaries in Cagayan province, Philippines for aquaculture. In this brief report, we discuss the overall assessment score of Buguey estuary in the municipality of Buguey, Cagayan as potential spot for the culture of green mussel ( Perna viridis ), locally known in the Philippines as "tahong". The score is mainly based on salinity and water temperature. We also present the condition of dissolved oxygen and pH levels in the estuary but these factors do not have major effect on mussel growth compared to salinity and water temperature. The reference ideal values for a suitable culture site are 27 to 35 psu for salinity; 27 to 30°C for water temperature; >5 mg/L for dissolved oxygen; and 7.7 to 8.4 for pH. Based on this reference values, areas in Buguey estuary have acceptable possibility of success for green mussel culture, which is qualitatively equivalent to having "good" suitability. This translates to a production estimate of 81% to 90% of cultured mussels will have a marketable size. However, these ratings may vary due to competition with existing oyster farming, water depth of the chosen site (since several areas in Buguey estuary are shallow), and other factors.
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- 2018
20. Equilibrium switching and mathematical properties of nonlinear interaction networks with concurrent antagonism and self-stimulation
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Cherryl O. Talaue and Jomar F. Rabajante
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Physics ,General Mathematics ,Applied Mathematics ,Mathematical properties ,General Physics and Astronomy ,Statistical and Nonlinear Physics ,Sigmoid function ,Nonlinear system ,Gene interaction ,Control theory ,Growth rate ,Shut down ,Reciprocal ,Repressilator - Abstract
Concurrent decision-making model (CDM) of interaction networks with more than two antagonistic components represents various biological systems, such as gene interaction, species competition and mental cognition. The CDM model assumes sigmoid kinetics where every component stimulates itself but concurrently represses the others. Here we prove generic mathematical properties (e.g., location and stability of steady states) of n -dimensional CDM with either symmetric or asymmetric reciprocal antagonism between components. Significant modifications in parameter values serve as biological regulators for inducing steady state switching by driving a temporal state to escape an undesirable equilibrium. Increasing the maximal growth rate and decreasing the decay rate can expand the basin of attraction of a steady state that contains the desired dominant component. Perpetually adding an external stimulus could shut down multi-stability of the system which increases the robustness of the system against stochastic noise. We further show that asymmetric interaction forming a repressilator-type network generates oscillatory behavior.
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- 2015
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21. Asymptotic stability of a modified Lotka-Volterra model with small immigrations
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Jomar F. Rabajante, Takuya Okabe, Akira Shimizu, Takeru Tahara, Tatsuya Togashi, Takenori Kawano, Hiromu Ito, Maica Krizna Areja Gavina, Genki Ichinose, Jerrold M. Tubay, Takashi Nagatani, Kei-ichi Tainaka, Jin Yoshimura, and Satoru Morita
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0106 biological sciences ,Science ,Population ,Population Dynamics ,Volterra equations ,010603 evolutionary biology ,01 natural sciences ,Stability (probability) ,Article ,Exponential stability ,Convergence (routing) ,Animals ,Statistical physics ,education ,Mathematics ,education.field_of_study ,Multidisciplinary ,Extinction ,Oscillation ,Small number ,Models, Theoretical ,010601 ecology ,Predatory Behavior ,Medicine ,Animal Migration ,Algorithms - Abstract
Predator-prey systems have been studied intensively for over a hundred years. These studies have demonstrated that the dynamics of Lotka-Volterra (LV) systems are not stable, that is, exhibiting either cyclic oscillation or divergent extinction of one species. Stochastic versions of the deterministic cyclic oscillations also exhibit divergent extinction. Thus, we have no solution for asymptotic stability in predator-prey systems, unlike most natural predator-prey interactions that sometimes exhibit stable and persistent coexistence. Here, we demonstrate that adding a small immigration into the prey or predator population can stabilize the LV system. Although LV systems have been studied intensively, there is no study on the non-linear modifications that we have tested. We also checked the effect of the inclusion of non-linear interaction term to the stability of the LV system. Our results show that small immigrations invoke stable convergence in the LV system with three types of functional responses. This means that natural predator-prey populations can be stabilized by a small number of sporadic immigrants.
- Published
- 2017
22. Mathematical Programming Models for Determining the Optimal Location of Beehives
- Author
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Maica Krizna Areja Gavina, Cleofas R. Cervancia, and Jomar F. Rabajante
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Pharmacology ,Operations Research ,Beekeeping ,Mathematical optimization ,Apiary ,Pollination ,Linear programming ,General Mathematics ,General Neuroscience ,Pollination management ,Immunology ,Probabilistic logic ,Agriculture ,Bees ,Models, Theoretical ,Biology ,General Biochemistry, Genetics and Molecular Biology ,Computational Theory and Mathematics ,Pollinator ,Animals ,Humans ,Nectar ,General Agricultural and Biological Sciences ,General Environmental Science - Abstract
Farmers frequently decide where to locate the colonies of their domesticated eusocial bees, especially given the following mutually exclusive scenarios: (i) there are limited nectar and pollen sources within the vicinity of the apiary that cause competition among foragers; and (ii) there are fewer pollinators compared to the number of inflorescence that may lead to suboptimal pollination of crops. We hypothesize that optimally distributing the beehives in the apiary can help address the two scenarios stated above. In this paper, we develop quantitative models (specifically using linear programming) for addressing the two given scenarios. We formulate models involving the following factors: (i) fuzzy preference of the beekeeper; (ii) number of available colonies; (iii) unknown-but-bounded strength of colonies; (iv) probabilistic carrying capacity of the plant clusters; and (v) spatial orientation of the apiary.
- Published
- 2014
- Full Text
- View/download PDF
23. Producing oscillatory decisions
- Author
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Maica Krizna Areja Gavina and Jomar F. Rabajante
- Subjects
Cognitive science ,Mathematical model ,Cognition ,Psychology ,Developmental psychology - Abstract
Mathematical models in neuroscience have led to the formulation of new theories of cognition. Several models have focused on equilibrium-converging cognitive activities but human and artificial cognition are frequently dynamic. Here we present some of the models that produce dynamic behavior of cognition, specifically those that produce temporal oscillations in decision-making.
- Published
- 2016
- Full Text
- View/download PDF
24. Poster: Host-Parasite Red Queen Dynamics with Phase-Locked Rare Genotypes
- Author
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Jomar F Rabajante and Tubay, Jerrold M
- Published
- 2016
- Full Text
- View/download PDF
25. OSCILLATION PROPAGATION IN A TWO-DIMENSIONAL LATTICE OF MUTUALLY-REPRESSIVE NODES
- Author
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Cueno, Anthony L, Jomar F Rabajante, and Maica Krizna A Gavina
- Published
- 2016
- Full Text
- View/download PDF
26. Mathematical modeling of cell-fate specification: From simple to complex epigenetics
- Author
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Jerrold M. Tubay, Jomar F. Rabajante, Ariel L. Babierra, and Editha C. Jose
- Subjects
Root (linguistics) ,business.industry ,Mind map ,Applied mathematics ,Epigenetics ,Biology ,Cell fate determination ,Software engineering ,business ,Field (computer science) ,Simple (philosophy) - Abstract
Modern biology will never be the same without mathematical and computational tools. Using mind map with “epigenetics” as the root, we discuss the current advancement in the field of biomathematics for modeling cell-fate specification. In the discussions, we also present possible directions for future research.
- Published
- 2015
- Full Text
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27. Branching and oscillations in the epigenetic landscape of cell-fate determination
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Ariel L. Babierra and Jomar F. Rabajante
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Regulation of gene expression ,State variable ,Bistability ,Models, Genetic ,Ecology ,Systems biology ,Cellular differentiation ,Transdifferentiation ,Biophysics ,Gene regulatory network ,Gene Expression Regulation, Developmental ,Cell Differentiation ,Biology ,Cell fate determination ,Evolutionary biology ,Biological Clocks ,Animals ,Humans ,Computer Simulation ,Epigenetics ,Molecular Biology ,Reprogramming ,Transcription Factors - Abstract
The well-known Waddington?s epigenetic landscape of cell-fate determination is not static but varies because of the dynamic gene regulation during development. However, existing mathematical models with few state variables and fixed parameters are inadequate in characterizing the temporal transformation of the landscape. Here we simulate a decision-switch model of gene regulation with more than two state variables and with time-varying repression among regulatory factors. We are able to demonstrate multi-lineage differentiation at different timescales that portrays the branching canals in Waddington?s illustration. We also present a repressilator-type system that activates suppressed genes via sustained oscillations in a flattened landscape, hence providing an alternative scheme for cellular reprogramming. The time-dependent parameters governed by gradient-based dynamics regulate cell differentiation, dedifferentiation and transdifferentiation. Our prediction integrates the theories of branching and structural oscillations in cell-fate determination, which reveals key temporal patterns of cell differentiation and associated diseases, such as cancer. Keywords: gene regulatory network, stem cells, pluripotency, synthetic biology, multistability, attractor Note: This paper has been accepted for publication in Progress in Biophysics and Molecular Biology (Elsevier). DOI of the peer-reviewed manuscript: 10.1016/j.pbiomolbio.2015.01.006
- Published
- 2014
28. Equilibrium switching in nonlinear biological interaction networks with concurrent antagonism
- Author
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Jomar F. Rabajante and Cherryl O. Talaue
- Subjects
Nonlinear system ,Computer science ,Biological system ,Antagonism - Abstract
Concurrent decision-making model (CDM) of interaction networks involving more than two antagonistic components can represent various biological systems, such as gene interaction, species competition and mental perception. The model assumes sigmoid kinetics where every component stimulates itself but concurrently represses the others. Here we prove general dynamical properties of the CDM (e.g., location and stability of steady states) for any dimension of the state space even if the reciprocal antagonism between two components is asymmetric. Significant modifications in parameter values serve as biological regulators for inducing steady state switching by leading a temporal state to escape an undesired equilibrium. Increasing the maximal growth rate and decreasing the decay rate expand the basin of attraction of a steady state with the desired dominant component. Perpetually adding an external stimulus can shut down multi-stability of the system that increases the robustness of the system against stochastic noise. We further show that asymmetric interaction that forms a repressilator-type network generates oscillatory behavior.
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- 2014
- Full Text
- View/download PDF
29. Equilibrium switching in nonlinear interaction networks with concurrent antagonism
- Author
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Jomar F. Rabajante
- Subjects
Nonlinear system ,Theoretical computer science ,Computer science ,Antagonism - Abstract
In this paper, we examine a nonlinear concurrent decision-making model (CDM) of interaction networks that involve more than two antagonistic components (e.g., proteins, species, communities, mental choices). The model assumes sigmoid kinetics where every component stimulates itself but represses all others. We are able to prove general dynamical properties of the CDM (e.g., location and stability of steady states) for any dimension of the state space even if the reciprocal antagonism between two components is asymmetric. There are cases where asymmetric interaction generates oscillatory behavior. Some parameters can serve as biological regulators for inducing steady state switching by leading a temporal state to escape an undesired equilibrium. Increasing the maximal growth rate and decreasing the decay rate can expand the basin of attraction of a steady state with the desired component having the dominant value. We further show that perpetually adding an external stimulus can shutdown multi-stability of the system that increases the robustness of the system against stochastic noise.
- Published
- 2014
- Full Text
- View/download PDF
30. A Numerical Model of Philippine Population Growth: Child Policy, Quantitative Insights and Challenges
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Ariel L. Babierra, Dylan Antonio S. J. Talabis, Erick Justine V. Manay, Jabez Joshua M. Flores, and Jomar F. Rabajante
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education.field_of_study ,Ecology ,Population size ,Population ,Populations and Evolution (q-bio.PE) ,Per capita income ,Quantitative Biology - Quantitative Methods ,Birth rate ,jel:J13 ,jel:J1 ,jel:J11 ,Family planning ,jel:J18 ,FOS: Biological sciences ,Population projection ,Economics ,Population growth ,Carrying capacity ,Demographic economics ,Quantitative Biology - Populations and Evolution ,education ,demography, population projection, child policy, zero growth, economy, logistic, carrying capacity, age-structured model, Philippines ,Quantitative Methods (q-bio.QM) ,91D20, 92D25 - Abstract
In this study, we forecast the population of the Philippines using a discrete age-structured compartmental model. We estimated the future population structure of the Philippines if the government imposes an n-child policy on top of the declining current birth and death rate trend of the country., Comment: 22 pages
- Published
- 2013
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31. Investigating the Propagation and Death of Information in Human Subpopulation Networks
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Jomar F. Rabajante
- Subjects
Social group ,Information propagation ,Theoretical computer science ,Ordinary differential equation ,Control (management) ,Belief system ,Information flow (information theory) ,Inflow ,Mathematics - Abstract
We introduce a conceptual-mathematical model that simulates the spread of information. We represent the states of the actors in the information flow using compartments. The compartment diagram is translated into a system of coupled ordinary differential equations. The diversity of social groups (subpopulations) is incorporated in the model, and the model is applicable for a heterogeneous community. We determine four possible spots that can be influenced to control the information propagation such as (1) controlling the inflow and outflow of people in each subpopulation, (2) regulating the media of communication, (3) influencing the belief system of the actors, and (4) introducing an antithesis to the circulating information.
- Published
- 2012
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32. OPTIMAL DEPLOYMENT OF COMMUNITY POLICE FORCE
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Jomar F Rabajante
- Published
- 2008
- Full Text
- View/download PDF
33. A Mathematical Model of Intra-Colony Spread of American Foulbrood in European Honeybees (Apis mellifera L.)
- Author
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Editha C. Jose, Alejandro C. Fajardo, Jomar F. Rabajante, Eduardo O. Jatulan, and C. G. B. Banaay
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American foulbrood ,lcsh:Medicine ,System stability ,Biology ,Animal Diseases ,Microbiology ,Honey Bees ,fluids and secretions ,Colony Collapse ,Infected cell ,Animals ,lcsh:Science ,Gram-Positive Bacterial Infections ,Paenibacillus larvae ,Multidisciplinary ,Transmission (medicine) ,lcsh:R ,fungi ,Bees ,Models, Theoretical ,bacterial infections and mycoses ,respiratory tract diseases ,lcsh:Q ,Paenibacillus ,Algorithms ,Research Article - Abstract
American foulbrood (AFB) is one of the severe infectious diseases of European honeybees (Apis mellifera L.) and other Apis species. This disease is caused by a gram-positive, spore-forming bacterium Paenibacillus larvae. In this paper, a compartmental (SI framework) model is constructed to represent the spread of AFB within a colony. The model is analyzed to determine the long-term fate of the colony once exposed to AFB spores. It was found out that without effective and efficient treatment, AFB infection eventually leads to colony collapse. Furthermore, infection thresholds were predicted based on the stability of the equilibrium states. The number of infected cell combs is one of the factors that drive disease spread. Our results can be used to forecast the transmission timeline of AFB infection and to evaluate the control strategies for minimizing a possible epidemic.
- Published
- 2015
- Full Text
- View/download PDF
34. Red Queen dynamics in multi-host and multi-parasite interaction system
- Author
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Jerrold M. Tubay, Jomar F. Rabajante, Jin Yoshimura, Takashi Uehara, Satoru Morita, and Dieter Ebert
- Subjects
Population Density ,Dominant types ,Infectivity ,Multidisciplinary ,Behavior, Animal ,Zoology ,Models, Theoretical ,Biology ,Article ,Host-Parasite Interactions ,Red queen ,Animals ,Parasite hosting ,Parasites - Abstract
In host-parasite systems, dominant host types are expected to be eventually replaced by other hosts due to the elevated potency of their specific parasites. This leads to changes in the abundance of both hosts and parasites exhibiting cycles of alternating dominance called Red Queen dynamics. Host-parasite models with less than three hosts and parasites have been demonstrated to exhibit Red Queen cycles, but natural host-parasite interactions typically involve many host and parasite types resulting in an intractable system with many parameters. Here we present numerical simulations of Red Queen dynamics with more than ten hosts and specialist parasites under the condition of no super-host nor super-parasite. The parameter region where the Red Queen cycles arise contracts as the number of interacting host and parasite types increases. The interplay between inter-host competition and parasite infectivity influences the condition for the Red Queen dynamics. Relatively large host carrying capacity and intermediate rates of parasite mortality result in never-ending cycles of dominant types.
- Published
- 2015
- Full Text
- View/download PDF
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