Subjects -> BIOLOGY (Total: 3174 journals)
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    - ORNITHOLOGY (26 journals)
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    - ZOOLOGY (117 journals)

BIOLOGY (1491 journals)            First | 1 2 3 4 5 6 7 8 | Last

Showing 201 - 400 of 1720 Journals sorted alphabetically
Biological Research     Open Access   (Followers: 1)
Biological Rhythm Research     Hybrid Journal   (Followers: 1)
Biological Theory     Hybrid Journal   (Followers: 3)
Biological Trace Element Research     Hybrid Journal  
Biologicals     Full-text available via subscription   (Followers: 7)
Biologics: Targets & Therapy     Open Access   (Followers: 1)
Biologie Aujourd'hui     Full-text available via subscription  
Biologie in Unserer Zeit (Biuz)     Hybrid Journal   (Followers: 36)
Biologija     Open Access  
Biology     Open Access   (Followers: 3)
Biology and Philosophy     Hybrid Journal   (Followers: 18)
Biology Bulletin     Hybrid Journal   (Followers: 1)
Biology Bulletin Reviews     Hybrid Journal  
Biology Direct     Open Access   (Followers: 9)
Biology Letters     Full-text available via subscription   (Followers: 44)
Biology Methods and Protocols     Open Access  
Biology of Sex Differences     Open Access   (Followers: 1)
Biology of the Cell     Full-text available via subscription   (Followers: 9)
Biology Open     Open Access  
Biology, Medicine, & Natural Product Chemistry     Open Access   (Followers: 2)
Bioma : Jurnal Ilmiah Biologi     Open Access  
Biomacromolecules     Hybrid Journal   (Followers: 23)
Biomarker Insights     Open Access   (Followers: 2)
Biomarkers     Hybrid Journal   (Followers: 4)
Biomass and Bioenergy     Partially Free   (Followers: 8)
Biomaterials     Hybrid Journal   (Followers: 55)
Biomaterials Advances     Full-text available via subscription   (Followers: 19)
Biomath     Open Access  
Biomatter     Open Access  
Biomechanics and Modeling in Mechanobiology     Hybrid Journal   (Followers: 8)
Biomedical Chromatography     Hybrid Journal   (Followers: 6)
Biomedical Engineering     Hybrid Journal   (Followers: 11)
Biomedical Engineering and Computational Biology     Open Access   (Followers: 11)
BioMedical Engineering OnLine     Open Access   (Followers: 4)
Biomedical Engineering: Applications, Basis and Communications     Hybrid Journal   (Followers: 4)
Biomedical Journal     Open Access   (Followers: 5)
Biomedical Science and Engineering     Open Access   (Followers: 5)
Biomedical Signal Processing and Control     Hybrid Journal   (Followers: 9)
BioMetals     Hybrid Journal   (Followers: 1)
Biometrical Letters     Open Access  
Biometrics     Hybrid Journal   (Followers: 51)
Biometrika     Hybrid Journal   (Followers: 21)
Biomimetic Intelligence and Robotics     Open Access  
Biomolecular NMR Assignments     Hybrid Journal   (Followers: 3)
Biomolecules     Open Access   (Followers: 1)
BioNanoScience     Partially Free   (Followers: 3)
Bionature     Open Access   (Followers: 1)
Biopreservation and Biobanking     Hybrid Journal   (Followers: 2)
Bioprocess and Biosystems Engineering     Hybrid Journal   (Followers: 9)
Bioresource Technology     Partially Free   (Followers: 9)
BioRisk     Open Access   (Followers: 2)
Biosaintifika : Journal of Biology & Biology Education     Open Access  
BioScience     Hybrid Journal   (Followers: 27)
Biosecurity and Bioterrorism: Biodefense Strategy, Practice, and Science     Hybrid Journal   (Followers: 3)
Biosemiotics     Hybrid Journal   (Followers: 1)
Biosensors     Open Access   (Followers: 3)
Biosensors and Bioelectronics     Hybrid Journal   (Followers: 27)
Biosensors and Bioelectronics : X     Open Access   (Followers: 2)
Bioseparation     Hybrid Journal   (Followers: 1)
Biosfer : Jurnal Biologi dan Pendidikan Biologi     Open Access  
Biosfer : Jurnal Tadris Biologi     Open Access  
BioSocieties     Hybrid Journal   (Followers: 3)
Biospecies     Open Access  
BIOspektrum     Hybrid Journal   (Followers: 5)
Biostatistics     Hybrid Journal   (Followers: 18)
Biosystematics and Ecology     Open Access   (Followers: 3)
Biosystems     Hybrid Journal   (Followers: 3)
Biosystems Diversity     Open Access  
Biota Amazônia     Open Access  
Biota Neotropica     Open Access  
Biotechnology Advances     Hybrid Journal   (Followers: 34)
Biotropia : The Southeast Asian Journal of Tropical Biology     Open Access  
Biotropica     Hybrid Journal   (Followers: 19)
Birth Defects Research     Hybrid Journal  
BJHM Open Research     Full-text available via subscription   (Followers: 1)
BMC Bioinformatics     Open Access   (Followers: 111)
BMC Biology     Open Access   (Followers: 50)
BMC Developmental Biology     Open Access   (Followers: 13)
BMC Evolutionary Biology     Open Access   (Followers: 58)
BMC Genomics     Open Access   (Followers: 69)
BMC Molecular and Cell Biology     Open Access   (Followers: 40)
BMC Proceedings     Full-text available via subscription   (Followers: 2)
BMC Research Notes     Open Access   (Followers: 3)
BMC Structural Biology     Open Access   (Followers: 8)
BMC Systems Biology     Open Access   (Followers: 16)
Boletín Científico : Centro de Museos. Museo de Historia Natural     Open Access  
Boletín del Centro de Investigaciones Biológicas     Open Access  
Boletín Micológico     Open Access  
Bone Reports     Open Access  
Bonorowo Wetlands     Open Access  
Borneo Journal of Resource Science and Technology     Open Access  
Bothalia : African Biodiversity & Conservation     Open Access  
Brain Science Advances     Open Access  
Brazilian Journal of Biological Sciences     Open Access  
Breastfeeding Medicine     Hybrid Journal   (Followers: 20)
Briefings in Bioinformatics     Hybrid Journal   (Followers: 43)
Briefings in Functional Genomics     Hybrid Journal   (Followers: 3)
British Poultry Abstracts     Hybrid Journal   (Followers: 3)
Brittonia     Hybrid Journal  
Bulletin de la Société Royale des Sciences de Liège     Open Access  
Bulletin of Experimental Biology and Medicine     Hybrid Journal  
Bulletin of Mathematical Biology     Hybrid Journal   (Followers: 9)
Bulletin of the Ecological Society of America     Open Access   (Followers: 4)
Bulletin of the Lebedev Physics Institute     Hybrid Journal  
Butlletí de la Institució Catalana d'Història Natural     Open Access  
CABI Agriculture and Bioscience     Open Access   (Followers: 1)
Caldasia     Open Access  
Cameroon Journal of Experimental Biology     Open Access  
Canadian Journal of Bioethics     Open Access  
Canadian Journal of Plant Pathology     Hybrid Journal   (Followers: 3)
Çanakkale Onsekiz Mart University Journal of Marine Sciences and Fisheries     Open Access  
Cancer Biology & Therapy     Open Access   (Followers: 11)
Cancer Cell International     Open Access   (Followers: 7)
Carbon Capture Science & Technology     Open Access  
Carbon Management     Hybrid Journal   (Followers: 5)
Carbon Resources Conversion     Open Access   (Followers: 2)
Caryologia : International Journal of Cytology, Cytosystematics and Cytogenetics     Partially Free  
Caucasiana     Open Access  
Cell     Full-text available via subscription   (Followers: 1145)
Cell Adhesion & Migration     Open Access   (Followers: 9)
Cell and Tissue Banking     Hybrid Journal   (Followers: 1)
Cell and Tissue Biology     Hybrid Journal   (Followers: 4)
Cell and Tissue Research     Hybrid Journal   (Followers: 5)
Cell Biochemistry and Function     Hybrid Journal   (Followers: 8)
Cell Biology and Development     Open Access   (Followers: 2)
Cell Biology and Toxicology     Hybrid Journal   (Followers: 10)
Cell Biology Education     Free   (Followers: 4)
Cell Biology International     Hybrid Journal   (Followers: 4)
Cell Biology International Reports     Hybrid Journal   (Followers: 2)
Cell Calcium     Hybrid Journal   (Followers: 2)
Cell Communication & Adhesion     Hybrid Journal   (Followers: 2)
Cell Cycle     Full-text available via subscription   (Followers: 5)
Cell Death and Differentiation     Hybrid Journal   (Followers: 7)
Cell Discovery     Open Access   (Followers: 2)
Cell Division     Open Access   (Followers: 1)
Cell Genomics     Full-text available via subscription   (Followers: 2)
Cell Metabolism     Full-text available via subscription   (Followers: 58)
Cell Proliferation     Open Access  
Cell Reports     Open Access   (Followers: 61)
Cell Reports Medicine     Open Access   (Followers: 3)
Cell Reports Methods     Open Access   (Followers: 1)
Cell Research     Hybrid Journal   (Followers: 11)
Cell Stress and Chaperones     Hybrid Journal   (Followers: 1)
Cell Surface     Open Access  
Cell Systems     Hybrid Journal   (Followers: 7)
Cells     Open Access   (Followers: 2)
Cells & Development     Hybrid Journal   (Followers: 3)
Cells Tissues Organs     Full-text available via subscription   (Followers: 1)
Cellular Immunology     Hybrid Journal   (Followers: 29)
Cellular Logistics     Full-text available via subscription  
Cellular Microbiology     Hybrid Journal   (Followers: 12)
Cellular Oncology     Hybrid Journal   (Followers: 3)
Cellular Reprogramming     Hybrid Journal  
Cellular Signalling     Hybrid Journal   (Followers: 10)
Ceylon Journal of Science     Open Access  
Channels     Open Access   (Followers: 1)
Check List : The Journal of Biodiversity Data     Open Access   (Followers: 2)
Chem     Hybrid Journal  
ChemBioEng Reviews     Full-text available via subscription   (Followers: 3)
Chemosensory Perception     Hybrid Journal  
Chirality     Hybrid Journal  
Chromosoma     Hybrid Journal  
Chromosome Research     Hybrid Journal   (Followers: 2)
Ciencia     Open Access  
Ciencia Amazónica (Iquitos)     Open Access  
Ciência ET Praxis     Open Access  
CienciaUAT     Open Access  
Cladistics     Hybrid Journal   (Followers: 7)
Climate Change Ecology     Open Access   (Followers: 16)
Clinical Dysmorphology     Hybrid Journal  
Clinical Phytoscience     Open Access  
Clinical Proteomics     Open Access   (Followers: 3)
Clinical Spectroscopy     Open Access   (Followers: 1)
Coevolution     Open Access  
Cogent Biology     Open Access  
Cognitive Neurodynamics     Hybrid Journal   (Followers: 2)
Cold Spring Harbor Perspectives in Biology     Full-text available via subscription   (Followers: 3)
Cold Spring Harbor Protocols     Full-text available via subscription   (Followers: 4)
Communication in Biomathematical Sciences     Open Access   (Followers: 2)
Communications Biology     Open Access  
Communications in Applied Sciences     Open Access  
Communications Materials     Open Access  
Communicative & Integrative Biology     Open Access  
Community Ecology     Full-text available via subscription   (Followers: 27)
Comparative Medicine     Full-text available via subscription   (Followers: 5)
Composite Interfaces     Hybrid Journal   (Followers: 6)
Comptes Rendus : Chimie     Open Access  
Comptes Rendus Biologies     Open Access   (Followers: 1)
Computational Biology Journal     Open Access   (Followers: 6)
Computational Mathematics and Mathematical Physics     Hybrid Journal   (Followers: 5)
Computer Methods in Biomechanics and Biomedical Engineering     Hybrid Journal   (Followers: 10)
Computer Methods in Biomechanics and Biomedical Engineering : Imaging & Visualization     Hybrid Journal  
Computers in Biology and Medicine     Hybrid Journal   (Followers: 11)
Connective Tissue Research     Hybrid Journal  
Contact (CTC)     Open Access  
Contributions to Plasma Physics     Hybrid Journal   (Followers: 3)
CRISPR Journal     Hybrid Journal  
Critical Reviews in Clinical Laboratory Sciences     Hybrid Journal   (Followers: 19)
Crustaceana     Hybrid Journal   (Followers: 6)
Cryobiology     Hybrid Journal   (Followers: 3)

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Similar Journals
Journal Cover
Bulletin of Mathematical Biology
Journal Prestige (SJR): 0.717
Citation Impact (citeScore): 1
Number of Followers: 9  
 
  Hybrid Journal Hybrid journal (It can contain Open Access articles)
ISSN (Print) 1522-9602 - ISSN (Online) 0092-8240
Published by Springer-Verlag Homepage  [2469 journals]
  • Derivation and Analysis of a Discrete Predator–Prey Model

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      Abstract: Abstract We derive a discrete predator–prey model from first principles, assuming that the prey population grows to carrying capacity in the absence of predators and that the predator population requires prey in order to grow. The proposed derivation method exploits a technique known from economics that describes the relationship between continuous and discrete compounding of bonds. We extend standard phase plane analysis by introducing the next iterate root-curve associated with the nontrivial prey nullcline. Using this curve in combination with the nullclines and direction field, we show that the prey-only equilibrium is globally asymptotic stability if the prey consumption-energy rate of the predator is below a certain threshold that implies that the maximal rate of change of the predator is negative. We also use a Lyapunov function to provide an alternative proof. If the prey consumption-energy rate is above this threshold, and hence the maximal rate of change of the predator is positive, the discrete phase plane method introduced is used to show that the coexistence equilibrium exists and solutions oscillate around it. We provide the parameter values for which the coexistence equilibrium exists and determine when it is locally asymptotically stable and when it destabilizes by means of a supercritical Neimark–Sacker bifurcation. We bound the amplitude of the closed invariant curves born from the Neimark–Sacker bifurcation as a function of the model parameters.
      PubDate: 2022-05-21
       
  • Testing and Isolation Efficacy: Insights from a Simple Epidemic Model

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      Abstract: Abstract Testing individuals for pathogens can affect the spread of epidemics. Understanding how individual-level processes of sampling and reporting test results can affect community- or population-level spread is a dynamical modeling question. The effect of testing processes on epidemic dynamics depends on factors underlying implementation, particularly testing intensity and on whom testing is focused. Here, we use a simple model to explore how the individual-level effects of testing might directly impact population-level spread. Our model development was motivated by the COVID-19 epidemic, but has generic epidemiological and testing structures. To the classic SIR framework we have added a per capita testing intensity, and compartment-specific testing weights, which can be adjusted to reflect different testing emphases—surveillance, diagnosis, or control. We derive an analytic expression for the relative reduction in the basic reproductive number due to testing, test-reporting and related isolation behaviours. Intensive testing and fast test reporting are expected to be beneficial at the community level because they can provide a rapid assessment of the situation, identify hot spots, and may enable rapid contact-tracing. Direct effects of fast testing at the individual level are less clear, and may depend on how individuals’ behaviour is affected by testing information. Our simple model shows that under some circumstances both increased testing intensity and faster test reporting can reduce the effectiveness of control, and allows us to explore the conditions under which this occurs. Conversely, we find that focusing testing on infected individuals always acts to increase effectiveness of control.
      PubDate: 2022-05-13
       
  • Multistationarity in Cyclic Sequestration-Transmutation Networks

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      Abstract: Abstract We consider a natural class of reaction networks which consist of reactions where either two species can inactivate each other (i.e., sequestration), or some species can be transformed into another (i.e., transmutation), in a way that gives rise to a feedback cycle. We completely characterize the capacity of multistationarity of these networks. This is especially interesting because such networks provide simple examples of “atoms of multistationarity”, i.e., minimal networks that can give rise to multiple positive steady states.
      PubDate: 2022-05-11
       
  • Slow–Fast Model and Therapy Optimization for Oncolytic Treatment of
           Tumors

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      Abstract: Abstract The present work studies models of oncolytic virotherapy without space variable in which virus replication occurs at a faster time scale than tumor growth. We address the questions of the modeling of virus injection in this slow–fast system and of the optimal timing for different treatment strategies. To this aim, we first derive the asymptotic of a three-species slow–fast model and obtain a two-species dynamical system, where the variables are tumor cells and infected tumor cells. We fully characterize the behavior of this system depending on the various biological parameters. In the second part, we address the modeling of virus injection and its expression in the two-species system, where the amount of virus does not appear explicitly. We prove that the injection can be described by an instantaneous jump in the phase plane, where a certain amount of tumors cells are transformed instantly into infected tumor cells. This description allows discussing qualitatively the timing of different injections in the frame of successive treatment strategies. This work is illustrated by numerical simulations. The timing and amount of injected virus may have counterintuitive optimal values; nevertheless, the understanding is clear from the phase space analysis.
      PubDate: 2022-05-10
       
  • Effect of Human Mobility on the Spatial Spread of Airborne Diseases: An
           Epidemic Model with Indirect Transmission

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      Abstract: Abstract We extended a class of coupled PDE–ODE models for studying the spatial spread of airborne diseases by incorporating human mobility. Human populations are modeled with patches, and a Lagrangian perspective is used to keep track of individuals’ places of residence. The movement of pathogens in the air is modeled with linear diffusion and coupled to the SIR dynamics of each human population through an integral of the density of pathogens around the population patches. In the limit of fast diffusion pathogens, the method of matched asymptotic analysis is used to reduce the coupled PDE–ODE model to a nonlinear system of ODEs for the average density of pathogens in the air. The reduced system of ODEs is used to derive the basic reproduction number and the final size relation for the model. Numerical simulations of the full PDE–ODE model and the reduced system of ODEs are used to assess the impact of human mobility, together with the diffusion of pathogens on the dynamics of the disease. Results from the two models are consistent and show that human mobility significantly affects disease dynamics. In addition, we show that an increase in the diffusion rate of pathogen leads to a lower epidemic.
      PubDate: 2022-05-04
       
  • Effect of Population Partitioning on the Probability of Silent Circulation
           of Poliovirus

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      Abstract: Abstract Polio can circulate unobserved in regions that are challenging to monitor. To assess the probability of silent circulation, simulation models can be used to understand transmission dynamics when detection is unreliable. Model assumptions, however, impact the estimated probability of silent circulation. Here, we examine the impact of having distinct populations, rather than a single well-mixed population, with a discrete-individual model including environmental surveillance. We show that partitioning a well-mixed population into networks of distinct communities may result in a higher probability of silent circulation as a result of the time it takes for the detection of a circulation event. Population structure should be considered when assessing polio control in a region with many loosely interacting communities.
      PubDate: 2022-05-04
       
  • Evaluating Strategies For Tuberculosis to Achieve the Goals of WHO in
           China: A Seasonal Age-Structured Model Study

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      Abstract: Abstract Although great progress has been made in the prevention and mitigation of TB in the past 20 years, China is still the third largest contributor to the global burden of new TB cases, accounting for 833,000 new cases in 2019. Improved mitigation strategies, such as vaccines, diagnostics, and treatment, are needed to meet goals of WHO. Given the huge variability in the prevalence of TB across age-groups in China, the vaccination, diagnostic techniques, and treatment for different age-groups may have different effects. Moreover, the statistics data of TB cases show significant seasonal fluctuations in China. In view of the above facts, we propose a non-autonomous differential equation model with age structure and seasonal transmission rate. We derive the basic reproduction number, \({\mathcal {R}}_{0}\) , and prove that the unique disease-free periodic solution, \({\mathcal {P}}_{0}\) is globally asymptotically stable when \({\mathcal {R}}_{0}<1\) , while the disease is uniformly persistent and at least one positive periodic solution exists when \({\mathcal {R}}_{0}>1\) . We estimate that the basic reproduction number \({\mathcal {R}}_{0}=1.3935\) ( \(95\%\text{ CI }:(1.3729, 1.4087)\) ), which means that TB is uniformly persistent. Our results demonstrate that vaccinating susceptible individuals whose ages are over 65 and between 20 and 24 is much more effective in reducing the prevalence of TB, and each of the improved vaccination strategy, diagnostic strategy, and treatment strategy leads to substantial reductions in the prevalence of TB per 100,000 individuals compared with current approaches, and the combination of the three strategies is more effective. Scenario A (i.e., coverage rate \(85\%\) , diagnosis rate \(5\theta _{k}\) , relapse rate \(0.1\chi _{k}\) ) is the best and can reduce the prevalence of TB per 100,000 individuals by \(98.91\%\) and \(99.07\%\) in 2035 and 2050, respectively. Although the improved strategies will significantly reduce the incidence rate of TB, it is challenging to achieve the goal of WHO in 2050. Our findings can provide guidance for public health authorities in projecting effective mitigation strategies of TB.
      PubDate: 2022-04-29
       
  • Allee Effects Plus Noise Induce Population Dynamics Resembling Binary
           Markov Highs and Lows

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      Abstract: Abstract We show that the combination of Allee effects and noise can produce a stochastic process with alternating sudden decline to a low population phase, followed, after a random time, by abrupt increase in population density. We introduce a new, flexible, deterministic model of attenuated Allee effects, which interpolates between the logistic and a usual Allee model. Into this model, we incorporate environmental and demographic noise. The solution of the resulting Kolmogorov forward equation shows a dichotomous distribution of residence times with heavy occupation of high, near saturation, and low population states. Investigation of simulated sample paths reveals that indeed attenuated Allee effects and noise, acting together, produce alternating, sustained, low and high population levels. We find that the transition times between the two types of states are approximately exponentially distributed, with different parameters, rendering the embedded hi-low process approximately Markov.
      PubDate: 2022-04-24
       
  • A Refunding Scheme to Incentivize Narrow-Spectrum Antibiotic Development

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      Abstract: Abstract The rapid rise of antibiotic resistance is a serious threat to global public health. The situation is exacerbated by the “antibiotics dilemma”: Developing narrow-spectrum antibiotics against resistant bacteria is most beneficial for society, but least attractive for companies, since their usage and sales volumes are more limited than for broad-spectrum drugs. After developing a general mathematical framework for the study of antibiotic resistance dynamics with an arbitrary number of antibiotics, we identify efficient treatment protocols. Then, we introduce a market-based refunding scheme that incentivizes pharmaceutical companies to develop new antibiotics against resistant bacteria and, in particular, narrow-spectrum antibiotics that target specific bacterial strains. We illustrate how such a refunding scheme can solve the antibiotics dilemma and cope with various sources of uncertainty that impede antibiotic R &D. Finally, connecting our refunding approach to the recently established Antimicrobial Resistance (AMR) Action Fund, we discuss how our proposed incentivization scheme could be financed.
      PubDate: 2022-04-22
       
  • Mathematical Modeling of Tumor and Cancer Stem Cells Treated with CAR-T
           Therapy and Inhibition of TGF- $$\beta $$ β

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      Abstract: Abstract The stem cell hypothesis suggests that there is a small group of malignant cells, the cancer stem cells, that initiate the development of tumors, encourage its growth, and may even be the cause of metastases. Traditional treatments, such as chemotherapy and radiation, primarily target the tumor cells leaving the stem cells to potentially cause a recurrence. Chimeric antigen receptor (CAR) T-cell therapy is a form of immunotherapy where the immune cells are genetically modified to fight the tumor cells. Traditionally, the CAR T-cell therapy has been used to treat blood cancers and only recently has shown promising results against solid tumors. We create an ordinary differential equations model which allows for the infusion of trained CAR-T cells to specifically attack the cancer stem cells that are present in the solid tumor microenvironment. Additionally, we incorporate the influence of TGF- \(\beta \) which inhibits the CAR-T cells and thus promotes the growth of the tumor. We verify the model by comparing it to available data and then examine combinations of CAR-T cell treatment targeting both non-stem and stem cancer cells and a treatment that reduces the effectiveness of TGF- \(\beta \) to determine the scenarios that eliminate the tumor.
      PubDate: 2022-04-16
       
  • A Hypothesis-Free Bridging of Disease Dynamics and Non-pharmaceutical
           Policies

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      Abstract: Abstract Accurate prediction of the number of daily or weekly confirmed cases of COVID-19 is critical to the control of the pandemic. Existing mechanistic models nicely capture the disease dynamics. However, to forecast the future, they require the transmission rate to be known, limiting their prediction power. Typically, a hypothesis is made on the form of the transmission rate with respect to time. Yet the real form is too complex to be mechanistically modeled due to the unknown dynamics of many influential factors. We tackle this problem by using a hypothesis-free machine-learning algorithm to estimate the transmission rate from data on non-pharmaceutical policies, and in turn forecast the confirmed cases using a mechanistic disease model. More specifically, we build a hybrid model consisting of a mechanistic ordinary differential equation (ODE) model and a gradient boosting model (GBM). To calibrate the parameters, we develop an “inverse method” that obtains the transmission rate inversely from the other variables in the ODE model and then feed it into the GBM to connect with the policy data. The resulting model forecasted the number of daily confirmed cases up to 35 days in the future in the USA with an averaged mean absolute percentage error of 27%. It can identify the most informative predictive variables, which can be helpful in designing improved forecasters as well as informing policymakers.
      PubDate: 2022-04-08
       
  • Mathematical Modelling Highlights the Potential for Genetic Manipulation
           as an Adjuvant to Counter Efflux-Mediated MDR in Salmonella

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      Abstract: Abstract Bacteria have developed resistance to antibiotics by various mechanisms, notable amongst these is the use of permeation barriers and the expulsion of antibiotics via efflux pumps. The resistance-nodulation-division (RND) family of efflux pumps is found in Gram-negative bacteria and a major contributor to multidrug resistance (MDR). In particular, Salmonella encodes five RND efflux pump systems: AcrAB, AcrAD, AcrEF, MdsAB and MdtAB which have different substrate ranges including many antibiotics. We produce a spatial partial differential equation (PDE) model governing the diffusion and efflux of antibiotic in Salmonella, via these RND efflux pumps. Using parameter fitting techniques on experimental data, we are able to establish the behaviour of multiple wild-type and efflux mutant Salmonella strains, which enables us to produce efflux profiles for each individual efflux pump system. By combining the model with a gene regulatory network (GRN) model of efflux regulation, we simulate how the bacteria respond to their environment. Finally, performing a parameter sensitivity analysis, we look into various different targets to inhibit the efflux pumps. The model provides an in silico framework with which to test these potential adjuvants to counter MDR.
      PubDate: 2022-04-05
       
  • The Effects of Migration and Limited Medical Resources of the Transmission
           of SARS-CoV-2 Model with Two Patches

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      Abstract: Abstract The sudden outbreak of SARS-CoV-2 has caused the shortage of medical resources around the world, especially in developing countries and underdeveloped regions. With the continuous increase in the duration of this disease, the control of migration of humans between regions or countries has to be relaxed. Based on this, we propose a two-patches mathematical model to simulate the transmission of SARS-CoV-2 among two-patches, asymptomatic infected humans and symptomatic infected humans, where a half-saturated detection rate function is also introduced to describe the effect of medical resources. By applying the methods of linearization and constructing a suitable Lyapunov function, the local and global stability of the disease-free equilibrium of this model without migration is obtained. Further, the existence of forward/backward bifurcation is analyzed, which is caused by the limited medical resources. This means that the elimination or prevalence of the disease no longer depends on the basic reproduction number but is closely related to the initial state of asymptomatic and symptomatic infected humans and the supply of medical resources. Finally, the global dynamics of the full model are discussed, and some numerical simulations are carried to explain the main results and the effects of migration and supply of medical resources on the transmission of disease.
      PubDate: 2022-04-04
       
  • Phage–Antibiotic Synergy Inhibited by Temperate and Chronic Virus
           Competition

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      Abstract: Abstract As antibiotic resistance grows more frequent for common bacterial infections, alternative treatment strategies such as phage therapy have become more widely studied in the medical field. While many studies have explored the efficacy of antibiotics, phage therapy, or synergistic combinations of phages and antibiotics, the impact of virus competition on the efficacy of antibiotic treatment has not yet been considered. Here, we model the synergy between antibiotics and two viral types, temperate and chronic, in controlling bacterial infections. We demonstrate that while combinations of antibiotic and temperate viruses exhibit synergy, competition between temperate and chronic viruses inhibits bacterial control with antibiotics. In fact, our model reveals that antibiotic treatment may counterintuitively increase the bacterial load when a large fraction of the bacteria are antibiotic resistant, and both chronic and temperate phages are present.
      PubDate: 2022-03-22
       
  • Weak Selection and the Separation of Eco-evo Time Scales using
           Perturbation Analysis

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      Abstract: Abstract We show that under the assumption of weak frequency-dependent selection a wide class of population dynamical models can be analysed using perturbation theory. The inner solution corresponds to the ecological dynamics, where to zeroth order, the genotype frequencies remain constant. The outer solution provides the evolutionary dynamics and corresponds, to zeroth order, to a generalisation of the replicator equation. We apply this method to a model of public goods dynamics and construct, using matched asymptotic expansions, a composite solution valid for all times. We also analyse a Lotka–Volterra model of predator competition and show that to zeroth order the fraction of wild-type predators follows a replicator equation with a constant selection coefficient given by the predator death rate. For both models, we investigate how the error between approximate solutions and the solution to the full model depend on the order of the approximation and show using numerical comparison, for \(k=1\) and 2, that the error scales according to \(\varepsilon ^{k+1}\) , where \(\varepsilon \) is the strength of selection and k is the order of the approximation.
      PubDate: 2022-03-19
       
  • Identifiable Paths and Cycles in Linear Compartmental Models

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      Abstract: Abstract We introduce a class of linear compartmental models called identifiable path/cycle models which have the property that all of the monomial functions of parameters associated to the directed cycles and paths from input compartments to output compartments are identifiable and give sufficient conditions to obtain an identifiable path/cycle model. Removing leaks, we then show how one can obtain a locally identifiable model from an identifiable path/cycle model. These identifiable path/cycle models yield the only identifiable models with certain conditions on their graph structure and thus we provide necessary and sufficient conditions for identifiable models with certain graph properties. A sufficient condition based on the graph structure of the model is also provided so that one can test if a model is an identifiable path/cycle model by examining the graph itself. We also provide some necessary conditions for identifiability based on graph structure. Our proofs use algebraic and combinatorial techniques.
      PubDate: 2022-03-19
       
  • Correction to: Systematic Analysis of Emergent Collective Motion Produced
           by a 3D Hybrid Zonal Model

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      PubDate: 2022-03-16
       
  • Predator–Prey Evolution from an Eco-evolutionary Trade-off Model: The
           Role of Trait Differentiation

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      Abstract: Abstract We develop a novel eco-evolutionary modelling framework and demonstrate its efficacy by simulating the evolution of trait distributions in predator and prey populations. The eco-evolutionary modelling framework assumes that population traits have beta distributions and defines canonical equations for the dynamics of each total population size, the population’s average trait value, and a measure of the population’s trait differentiation. The trait differentiation is included in the modelling framework as a phenotype analogue, Q, of Wright’s fixation index \(F_\mathrm{ST}\) , which is inversely related to the sum of the beta distribution shape parameters. The canonical equations may be used as templates to describe the evolution of population trait distributions in many ecosystems that are subject to stabilising selection. The solutions of the “population model” are compared with those of a “phenotype model” that simulates the growth of each phenotype as it interacts with every other phenotype under the same trade-offs. The models assume no sources of new phenotypic variance, such as mutation or gene flow. We examine a predator–prey system in which each population trades off growth against mortality: the prey optimises devoting resources to growth or defence against predation; and the predator trades off increasing its attack rate against increased mortality. Computer solutions with stabilising selection reveal very close agreement between the phenotype and population model results, which both predict that evolution operates to stabilise an initially oscillatory system. The population model reduces the number of equations required to simulate the eco-evolutionary system by several orders of magnitude, without losing verisimilitude for the overarching population properties. The population model also allows insights into the properties of the system that are not available from the equivalent phenotype model.
      PubDate: 2022-03-07
      DOI: 10.1007/s11538-022-01004-8
       
  • A Continuum Mathematical Model of Substrate-Mediated Tissue Growth

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      Abstract: Abstract We consider a continuum mathematical model of biological tissue formation inspired by recent experiments describing thin tissue growth in 3D-printed bioscaffolds. The continuum model, which we call the substrate model, involves a partial differential equation describing the density of tissue, \({\hat{u}}(\hat{{\mathbf {x}}},{\hat{t}})\) that is coupled to the concentration of an immobile extracellular substrate, \({\hat{s}}(\hat{{\mathbf {x}}},{\hat{t}})\) . Cell migration is modelled with a nonlinear diffusion term, where the diffusive flux is proportional to \({\hat{s}}\) , while a logistic growth term models cell proliferation. The extracellular substrate \({\hat{s}}\) is produced by cells and undergoes linear decay. Preliminary numerical simulations show that this mathematical model is able to recapitulate key features of recent tissue growth experiments, including the formation of sharp fronts. To provide a deeper understanding of the model we analyse travelling wave solutions of the substrate model, showing that the model supports both sharp-fronted travelling wave solutions that move with a minimum wave speed, \(c = c_{\mathrm{min}}\) , as well as smooth-fronted travelling wave solutions that move with a faster travelling wave speed, \(c > c_{\mathrm{min}}\) . We provide a geometric interpretation that explains the difference between smooth and sharp-fronted travelling wave solutions that is based on a slow manifold reduction of the desingularised three-dimensional phase space. In addition, we also develop and test a series of useful approximations that describe the shape of the travelling wave solutions in various limits. These approximations apply to both the sharp-fronted and smooth-fronted travelling wave solutions. Software to implement all calculations is available at GitHub.
      PubDate: 2022-03-02
      DOI: 10.1007/s11538-022-01005-7
       
  • Modeling the Dynamics of Heroin and Illicit Opioid Use Disorder,
           Treatment, and Recovery

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      Abstract: Abstract Opioid use disorder (OUD) has become a serious leading health issue in the USA leading to addiction, disability, or death by overdose. Research has shown that OUD can lead to a chronic lifelong disorder with greater risk for relapse and accidental overdose deaths. While the prescription opioid epidemic is a relatively new phenomenon, illicit opioid use via heroin has been around for decades. Recently, additional illicit opioids such as fentanyl have become increasingly available and problematic. We propose a mathematical model that focuses on illicit OUD and includes a class for recovered users but allows for individuals to either remain in or relapse back to the illicit OUD class. Therefore, in our model, individuals may cycle in and out of three different classes: illicit OUD, treatment, and recovered. We additionally include a treatment function with saturation, as it has been shown there is limited accessibility to specialty treatment facilities. We used 2002–2019 SAMHSA and CDC data for the US population, scaled to a medium-sized city, to obtain parameter estimates for the specific case of heroin. We found that the overdose death rate has been increasing linearly since around 2011, likely due to the increased presence of fentanyl in the heroin supply. Extrapolation of this overdose death rate, together with the obtained parameter estimates, predict that by 2038 no endemic equilibrium will exist and the only stable equilibrium will correspond to the absence of heroin use disorder in the population. There is a range of parameter values that will give rise to a backward bifurcation above a critical saturation of treatment availability. We show this for a range of overdose death rate values, thus illustrating the critical role played by the availability of specialty treatment facilities. Sensitivity analysis consistently shows the significant role of people entering treatment on their own accord, which suggests the importance of removing two of the most prevalent SAMHSA-determined reasons that individuals do not enter treatment: financial constraints and the stigma of seeking treatment for heroin use disorder.
      PubDate: 2022-03-02
      DOI: 10.1007/s11538-022-01002-w
       
 
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