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Journal of Theoretical Biology

Philip B Greenspoon, Sydney Banton, Nicole Mideo
Predators may be limited in their ability to kill prey (i.e., have type II or III functional responses), an insight that has had far-reaching consequences in the ecological literature. With few exceptions, however, this possibility has not been extended to the behaviour of immune cells, which kill pathogens much as predators kill their prey. Rather, models of the within-host environment have tended to tacitly assume that immune cells have an unlimited ability to target and kill pathogens (i.e., a type I functional response)...
March 16, 2018: Journal of Theoretical Biology
Kalle Parvinen, Ulf Dieckmann
The number of regulating variables n in a given system is an upper bound to the number of coexisting species at equilibrium according to the competitive exclusion principle. However, it may be possible to formulate the model with a lower number of regulating variables, the smallest number of which is the dimension of the environmental feedback. Here we investigate how that dimension can be determined by analysing the two parts of environmental feedback: The impact map describes how the extant species affect the regulating variables, and the sensitivity map describes how population growth depends on the regulating variables...
March 15, 2018: Journal of Theoretical Biology
Clement Aldebert, Bob W Kooi, David Nerini, Jean-Christophe Poggiale
Many current issues in ecology require predictions made by mathematical models, which are built on somewhat arbitrary choices. Their consequences are quantified by sensitivity analysis to quantify how changes in model parameters propagate into an uncertainty in model predictions. An extension called structural sensitivity analysis deals with changes in the mathematical description of complex processes like predation. Such processes are described at the population scale by a specific mathematical function taken among similar ones, a choice that can strongly drive model predictions...
March 14, 2018: Journal of Theoretical Biology
Alfonso Ruiz-Herrera, Pedro J Torres
This paper analyzes the effects of diffusion on the overall population size of the different species of a metacommunity. Depending on precise thresholds, we determine whether increasing the dispersal rate of a species has a positive or negative effect on population abundance. These thresholds depend on the interaction type of the species and the quality of the patches. The motivation for researching this issue is that spatial structure is a source of new biological insights with management interest. For instance, in a metacommunity of two competitors, the movement of a competitor could lead to a decrease of the overall population size of both species...
March 14, 2018: Journal of Theoretical Biology
Tanja Stadler, Alexandra Gavryushkina, Rachel C M Warnock, Alexei J Drummond, Tracy A Heath
A birth-death-sampling model gives rise to phylogenetic trees with samples from the past and the present. Interpreting "birth" as branching speciation, "death" as extinction, and "sampling" as fossil preservation and recovery, this model - also referred to as the fossilized birth-death (FBD) model - gives rise to phylogenetic trees on extant and fossil samples. The model has been mathematically analyzed and successfully applied to a range of datasets on different taxonomic levels, such as penguins, plants, and insects...
March 14, 2018: Journal of Theoretical Biology
Weiping Ding, Sen Liu, Shibo Li, Duobiao Ge, Fenfen Li, Dayong Gao
The liver is one of the common metastatic sites for many cancers. The obstruction of sinusoids by circulating tumor cells changes liver microenvironments and is thus considered a source of hepatic metastases. To date, few studies provide detailed information, either experimentally or theoretically, concerning the changes in blood and oxygen distributions induced by the obstruction of sinusoids. In this study, we utilized a 3D porous medium-vascular tree geometric structure to mimic the hepatic lobule and studied theoretical blood flow and oxygen transport in the lobule...
March 13, 2018: Journal of Theoretical Biology
Andrew Francis, Vincent Moulton
Phylogenetic networks are an extension of phylogenetic trees which are used to represent evolutionary histories in which reticulation events (such as recombination and hybridization) have occurred. A central question for such networks is that of identifiability, which essentially asks under what circumstances can we reliably identify the phylogenetic network that gave rise to the observed data? Recently, identifiability results have appeared for networks relative to a model of sequence evolution that generalizes the standard Markov models used for phylogenetic trees...
March 13, 2018: Journal of Theoretical Biology
Elena Piretto, Marcello Delitala, Mario Ferraro
Drug resistance is one of the major obstacles to a successful treatment of cancer and, in turn, has been recognized to be linked to intratumoral heterogeneity, which increases the probability of the emergence of a cancer clones refractory to treatment. Combination therapies have been introduced to overcome resistance, but the design of successful combined protocols is still an open problem. In order to provide some indications on the effectiveness of medical treatments, a mathematical model is proposed, comprising two cancer populations competing for resources and with different susceptibilities to the action of immune system cells and therapies: the focus is on the effects of chemotherapy and immunotherapy, used singularly or in combination...
March 13, 2018: Journal of Theoretical Biology
Nguyen Trong Hieu, Timothée Brochier, Pierre Auger, Trinh Viet Duoc, Patrice Brehmer
An idealized system of a shared fish stock associated with different exclusive economic zones (EEZ) is modelled. Parameterisation were estimated for the case of the small pelagic fisheries shared between Southern Morocco, Mauritania and the Senegambia. Two models of fishing effort distribution were explored. The first one considers independent national fisheries in each EEZ, with a cost per unit of fishing effort that depends on local fishery policy. The second one consider the case of a fully cooperative fisheries performed by an international fleet freely moving across the borders...
March 13, 2018: Journal of Theoretical Biology
Daniel John Cleather
The patella is traditionally understood to be a "joint spacer" that increases the moment arm of the patellar tendon. This characterisation is unsatisfactory as it fails to explain the more interesting characteristics of the patella: 1) that the changing pivot point of the patella causes the ratio of quadriceps to patellar tendon force to almost double as the knee flexes; 2) that the patellar tendon exerts an anteriorly directed force on the tibia when the knee is extended but this switches to a posterior draw as the knee flexes; and 3) that the presence of the patella allows the quadriceps to exert different moments on the femur and tibia...
March 13, 2018: Journal of Theoretical Biology
Gottfried Sachs, Henri Weimerskirch
Investigating the unique ability of frigatebirds of flying inside clouds, it is shown that they achieve a large energy gain by ascents to high altitudes in strong updrafts of trade cumulus clouds. Frigatebirds often perform that kind of flight, at daytime as well as in the night. This suggests that they are capable of flying inside clouds in a controlled and stabilized manner. The control requirements for ascents in terms of a circling flight in updrafts of trade cumulus clouds are analyzed, and the necessary aerodynamic control moments are determined...
March 13, 2018: Journal of Theoretical Biology
Hemachander Subramanian, Robert A Gatenby
Due to the asymmetric nature of the nucleotides, the extant informational biomolecule, DNA, is constrained to replicate unidirectionally on a template. As a product of molecular evolution that sought to maximize replicative potential, DNA's unidirectional replication poses a mystery since symmetric bidirectional self-replicators obviously would replicate faster than unidirectional self-replicators and hence would have been evolutionarily more successful. Here we carefully examine the physico-chemical requirements for evolutionarily successful primordial self-replicators and theoretically show that at low monomer concentrations that possibly prevailed in the primordial oceans, asymmetric unidirectional self-replicators would have an evolutionary advantage over bidirectional self-replicators...
March 12, 2018: Journal of Theoretical Biology
Abhishek Kumar Tiwari, Rakesh Kumar, Dharmendra Tripathi, Subham Badhyal
In vivo studies suggest that cyclic and low-magnitude loading can be useful over pharmaceutical drugs in normalizing bone loss as it encourages osteogenesis (i.e. new bone formation) at the sites of elevated strain magnitude. In silico models assumed normal strain or strain energy density (SED) as the stimulus to predict loading-induced osteogenesis, however, these models may have limited success in fitting the in vivo new bone formation at several instances. For example, rest-inserted cyclic loading amplifies the new bone formation as compared to continuous-cyclic loading even though similar strain magnitude were induced in both the cases...
March 10, 2018: Journal of Theoretical Biology
J M López, J Herrero, D Puigjaner, G Fortuny
No abstract text is available yet for this article.
March 10, 2018: Journal of Theoretical Biology
D Calvetti, G Capo Rangel, L Gerardo Giorda, E Somersalo
The human brain is a small organ which uses a disproportional amount of the total metabolic energy production in the body. While it is well understood that the most significant energy sink is the maintenance of the neuronal membrane potential during the brain signaling activity, the role of astrocytes in the energy balance continues to be the topic of a lot of research. A key function of astrocytes, besides clearing glutamate from the synaptic clefts, is the potassium clearing after neuronal activation. Extracellular potassium plays a significant role in triggering neuronal firing, and elevated concentration of potassium may lead to abnormal firing pattern, e...
March 9, 2018: Journal of Theoretical Biology
Jinyou Yang, Yuji Shimogonya, Takuji Ishikawa
Microbial flora in the intestine has been thoroughly investigated, as it plays an important role in the health of the host. Jemielita et al. (2014) showed experimentally that Aeromonas bacteria in the intestine of zebrafish larvae have a heterogeneous spatial distribution. Although bacterial aggregation is important biologically and clinically, there is no mathematical model describing the phenomenon and its mechanism remains largely unknown. In this study, we developed a computational model to describe the heterogeneous distribution of bacteria in the intestine of zebrafish larvae...
March 8, 2018: Journal of Theoretical Biology
Nicolas Houy, François Le Grand
PURPOSE: We compare the Maximum Tolerated Dose (MTD) and Metronomic Chemotherapy (MC) protocols for temozolomide administration. We develop an innovative methodology for characterizing optimal chemotherapy regimens. METHODS: We use a PK/PD model based on Faivre and coauthors (Faivre et al., 2013) for the pharmacokinetics of temozolomide, as well as the pharmacodynamics of its efficacy. For toxicity, which is measured by the nadir of the normalized absolute neutrophil count, we formalize the myelosuppression effect of temozolomide with the physiological model of Panetta and coauthors (Panetta et al...
March 8, 2018: Journal of Theoretical Biology
Ruth Bowness, Mark A J Chaplain, Gibin G Powathil, Stephen H Gillespie
If improvements are to be made in tuberculosis (TB) treatment, an increased understanding of disease in the lung is needed. Studies have shown that bacteria in a less metabolically active state, associated with the presence of lipid bodies, are less susceptible to antibiotics, and recent results have highlighted the disparity in concentration of different compounds into lesions. Treatment success therefore depends critically on the responses of the individual bacteria that constitute the infection. We propose a hybrid, individual-based approach that analyses spatio-temporal dynamics at the cellular level, linking the behaviour of individual bacteria and host cells with the macroscopic behaviour of the microenvironment...
March 7, 2018: Journal of Theoretical Biology
Chuanyan Wu, Rui Gao, Yang De Marinis, Yusen Zhang
Advances in sequencing technologies led to rapid increase in the number and diversity of biological sequences, which facilitated development in the sequence research. In this paper, we present a new method for analyzing protein sequence similarity. We calculated the spectral radii of 20 amino acids (AAs) and put forward a novel 2-D graphical representation of protein sequences. To characterize protein sequences numerically, three groups of features were extracted and related to statistical, dynamics measurements and fluctuation complexity of the sequences...
March 7, 2018: Journal of Theoretical Biology
Ryan Nikin-Beers, Julie C Blackwood, Lauren M Childs, Stanca M Ciupe
Dengue virus causes worldwide concern with nearly 100 million infected cases reported annually. The within-host dynamics differ between primary and secondary infections, where secondary infections with a different virus serotype typically last longer, produce higher viral loads, and induce more severe disease. We build upon the variable within-host virus dynamics during infections resulting in mild dengue fever and severe dengue hemorrhagic fever. We couple these within-host virus dynamics to a population-level model through a system of partial differential equations creating an immuno-epidemiological model...
March 6, 2018: Journal of Theoretical Biology
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