PLoS Computational Biology最新文献

{"title":"What constrains food webs? A maximum entropy framework for predicting their structure with minimal biases.","authors":"Francis Banville,&nbsp;Dominique Gravel,&nbsp;Timothée Poisot","doi":"10.1371/journal.pcbi.1011458","DOIUrl":"10.1371/journal.pcbi.1011458","url":null,"abstract":"<p><p>Food webs are complex ecological networks whose structure is both ecologically and statistically constrained, with many network properties being correlated with each other. Despite the recognition of these invariable relationships in food webs, the use of the principle of maximum entropy (MaxEnt) in network ecology is still rare. This is surprising considering that MaxEnt is a statistical tool precisely designed for understanding and predicting many types of constrained systems. This principle asserts that the least-biased probability distribution of a system's property, constrained by prior knowledge about that system, is the one with maximum information entropy. MaxEnt has been proven useful in many ecological modeling problems, but its application in food webs and other ecological networks is limited. Here we show how MaxEnt can be used to derive many food-web properties both analytically and heuristically. First, we show how the joint degree distribution (the joint probability distribution of the numbers of prey and predators for each species in the network) can be derived analytically using the number of species and the number of interactions in food webs. Second, we present a heuristic and flexible approach of finding a network's adjacency matrix (the network's representation in matrix format) based on simulated annealing and SVD entropy. We built two heuristic models using the connectance and the joint degree sequence as statistical constraints, respectively. We compared both models' predictions against corresponding null and neutral models commonly used in network ecology using open access data of terrestrial and aquatic food webs sampled globally (N = 257). We found that the heuristic model constrained by the joint degree sequence was a good predictor of many measures of food-web structure, especially the nestedness and motifs distribution. Specifically, our results suggest that the structure of terrestrial and aquatic food webs is mainly driven by their joint degree distribution.</p>","PeriodicalId":49688,"journal":{"name":"PLoS Computational Biology","volume":"19 9","pages":"e1011458"},"PeriodicalIF":4.3,"publicationDate":"2023-09-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10503755/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10286131","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"An automated interface for sedimentation velocity analysis in SEDFIT.","authors":"Peter Schuck, Samuel C To, Huaying Zhao","doi":"10.1371/journal.pcbi.1011454","DOIUrl":"10.1371/journal.pcbi.1011454","url":null,"abstract":"<p><p>Sedimentation velocity analytical ultracentrifugation (SV-AUC) is an indispensable tool for the study of particle size distributions in biopharmaceutical industry, for example, to characterize protein therapeutics and vaccine products. In particular, the diffusion-deconvoluted sedimentation coefficient distribution analysis, in the software SEDFIT, has found widespread applications due to its relatively high resolution and sensitivity. However, a lack of suitable software compatible with Good Manufacturing Practices (GMP) has hampered the use of SV-AUC in this regulatory environment. To address this, we have created an interface for SEDFIT so that it can serve as an automatically spawned module with controlled data input through command line parameters and output of key results in files. The interface can be integrated in custom GMP compatible software, and in scripts that provide documentation and meta-analyses for replicate or related samples, for example, to streamline analysis of large families of experimental data, such as binding isotherm analyses in the study of protein interactions. To test and demonstrate this approach we provide a MATLAB script mlSEDFIT.</p>","PeriodicalId":49688,"journal":{"name":"PLoS Computational Biology","volume":"19 9","pages":"e1011454"},"PeriodicalIF":4.3,"publicationDate":"2023-09-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10503714/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10336367","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"The inhibitory control of traveling waves in cortical networks.","authors":"Grishma Palkar,&nbsp;Jian-Young Wu,&nbsp;Bard Ermentrout","doi":"10.1371/journal.pcbi.1010697","DOIUrl":"10.1371/journal.pcbi.1010697","url":null,"abstract":"<p><p>Propagating waves of activity can be evoked and can occur spontaneously in vivo and in vitro in cerebral cortex. These waves are thought to be instrumental in the propagation of information across cortical regions and as a means to modulate the sensitivity of neurons to subsequent stimuli. In normal tissue, the waves are sparse and tightly controlled by inhibition and other negative feedback processes. However, alterations of this balance between excitation and inhibition can lead to pathological behavior such as seizure-type dynamics (with low inhibition) or failure to propagate (with high inhibition). We develop a spiking one-dimensional network of neurons to explore the reliability and control of evoked waves and compare this to a cortical slice preparation where the excitability can be pharmacologically manipulated. We show that the waves enhance sensitivity of the cortical network to stimuli in specific spatial and temporal ways. To gain further insight into the mechanisms of propagation and transitions to pathological behavior, we derive a mean-field model for the synaptic activity. We analyze the mean-field model and a piece-wise constant approximation of it and study the stability of the propagating waves as spatial and temporal properties of the inhibition are altered. We show that that the transition to seizure-like activity is gradual but that the loss of propagation is abrupt and can occur via either the loss of existence of the wave or through a loss of stability leading to complex patterns of propagation.</p>","PeriodicalId":49688,"journal":{"name":"PLoS Computational Biology","volume":"19 9","pages":"e1010697"},"PeriodicalIF":4.3,"publicationDate":"2023-09-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10503768/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10336368","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"RSim: A reference-based normalization method via rank similarity.","authors":"Bo Yuan,&nbsp;Shulei Wang","doi":"10.1371/journal.pcbi.1011447","DOIUrl":"10.1371/journal.pcbi.1011447","url":null,"abstract":"<p><p>Microbiome sequencing data normalization is crucial for eliminating technical bias and ensuring accurate downstream analysis. However, this process can be challenging due to the high frequency of zero counts in microbiome data. We propose a novel reference-based normalization method called normalization via rank similarity (RSim) that corrects sample-specific biases, even in the presence of many zero counts. Unlike other normalization methods, RSim does not require additional assumptions or treatments for the high prevalence of zero counts. This makes it robust and minimizes potential bias resulting from procedures that address zero counts, such as pseudo-counts. Our numerical experiments demonstrate that RSim reduces false discoveries, improves detection power, and reveals true biological signals in downstream tasks such as PCoA plotting, association analysis, and differential abundance analysis.</p>","PeriodicalId":49688,"journal":{"name":"PLoS Computational Biology","volume":"19 9","pages":"e1011447"},"PeriodicalIF":4.3,"publicationDate":"2023-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10501661/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10296905","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"A multi-layer mean-field model of the cerebellum embedding microstructure and population-specific dynamics.","authors":"Roberta Maria Lorenzi,&nbsp;Alice Geminiani,&nbsp;Yann Zerlaut,&nbsp;Marialaura De Grazia,&nbsp;Alain Destexhe,&nbsp;Claudia A M Gandini Wheeler-Kingshott,&nbsp;Fulvia Palesi,&nbsp;Claudia Casellato,&nbsp;Egidio D'Angelo","doi":"10.1371/journal.pcbi.1011434","DOIUrl":"10.1371/journal.pcbi.1011434","url":null,"abstract":"<p><p>Mean-field (MF) models are computational formalism used to summarize in a few statistical parameters the salient biophysical properties of an inter-wired neuronal network. Their formalism normally incorporates different types of neurons and synapses along with their topological organization. MFs are crucial to efficiently implement the computational modules of large-scale models of brain function, maintaining the specificity of local cortical microcircuits. While MFs have been generated for the isocortex, they are still missing for other parts of the brain. Here we have designed and simulated a multi-layer MF of the cerebellar microcircuit (including Granule Cells, Golgi Cells, Molecular Layer Interneurons, and Purkinje Cells) and validated it against experimental data and the corresponding spiking neural network (SNN) microcircuit model. The cerebellar MF was built using a system of equations, where properties of neuronal populations and topological parameters are embedded in inter-dependent transfer functions. The model time constant was optimised using local field potentials recorded experimentally from acute mouse cerebellar slices as a template. The MF reproduced the average dynamics of different neuronal populations in response to various input patterns and predicted the modulation of the Purkinje Cells firing depending on cortical plasticity, which drives learning in associative tasks, and the level of feedforward inhibition. The cerebellar MF provides a computationally efficient tool for future investigations of the causal relationship between microscopic neuronal properties and ensemble brain activity in virtual brain models addressing both physiological and pathological conditions.</p>","PeriodicalId":49688,"journal":{"name":"PLoS Computational Biology","volume":"19 9","pages":"e1011434"},"PeriodicalIF":4.3,"publicationDate":"2023-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10501640/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10283349","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Self-loops in evolutionary graph theory: Friends or foes?","authors":"Nikhil Sharma, Sedigheh Yagoobi, Arne Traulsen","doi":"10.1371/journal.pcbi.1011387","DOIUrl":"10.1371/journal.pcbi.1011387","url":null,"abstract":"<p><p>Evolutionary dynamics in spatially structured populations has been studied for a long time. More recently, the focus has been to construct structures that amplify selection by fixing beneficial mutations with higher probability than the well-mixed population and lower probability of fixation for deleterious mutations. It has been shown that for a structure to substantially amplify selection, self-loops are necessary when mutants appear predominately in nodes that change often. As a result, for low mutation rates, self-looped amplifiers attain higher steady-state average fitness in the mutation-selection balance than well-mixed populations. But what happens when the mutation rate increases such that fixation probabilities alone no longer describe the dynamics? We show that self-loops effects are detrimental outside the low mutation rate regime. In the intermediate and high mutation rate regime, amplifiers of selection attain lower steady-state average fitness than the complete graph and suppressors of selection. We also provide an estimate of the mutation rate beyond which the mutation-selection dynamics on a graph deviates from the weak mutation rate approximation. It involves computing average fixation time scaling with respect to the population sizes for several graphs.</p>","PeriodicalId":49688,"journal":{"name":"PLoS Computational Biology","volume":"19 9","pages":"e1011387"},"PeriodicalIF":4.3,"publicationDate":"2023-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10501642/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10283341","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Dynamical modelling of viral infection and cooperative immune protection in COVID-19 patients.","authors":"Zhengqing Zhou, Dianjie Li, Ziheng Zhao, Shuyu Shi, Jianghua Wu, Jianwei Li, Jingpeng Zhang, Ke Gui, Yu Zhang, Qi Ouyang, Heng Mei, Yu Hu, Fangting Li","doi":"10.1371/journal.pcbi.1011383","DOIUrl":"10.1371/journal.pcbi.1011383","url":null,"abstract":"<p><p>Once challenged by the SARS-CoV-2 virus, the human host immune system triggers a dynamic process against infection. We constructed a mathematical model to describe host innate and adaptive immune response to viral challenge. Based on the dynamic properties of viral load and immune response, we classified the resulting dynamics into four modes, reflecting increasing severity of COVID-19 disease. We found the numerical product of immune system's ability to clear the virus and to kill the infected cells, namely immune efficacy, to be predictive of disease severity. We also investigated vaccine-induced protection against SARS-CoV-2 infection. Results suggested that immune efficacy based on memory T cells and neutralizing antibody titers could be used to predict population vaccine protection rates. Finally, we analyzed infection dynamics of SARS-CoV-2 variants within the construct of our mathematical model. Overall, our results provide a systematic framework for understanding the dynamics of host response upon challenge by SARS-CoV-2 infection, and this framework can be used to predict vaccine protection and perform clinical diagnosis.</p>","PeriodicalId":49688,"journal":{"name":"PLoS Computational Biology","volume":"19 9","pages":"e1011383"},"PeriodicalIF":4.3,"publicationDate":"2023-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10501599/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10648897","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Evaluating the impact of test-trace-isolate for COVID-19 management and alternative strategies.","authors":"Kun Zhang,&nbsp;Zhichu Xia,&nbsp;Shudong Huang,&nbsp;Gui-Quan Sun,&nbsp;Jiancheng Lv,&nbsp;Marco Ajelli,&nbsp;Keisuke Ejima,&nbsp;Quan-Hui Liu","doi":"10.1371/journal.pcbi.1011423","DOIUrl":"10.1371/journal.pcbi.1011423","url":null,"abstract":"<p><p>There are many contrasting results concerning the effectiveness of Test-Trace-Isolate (TTI) strategies in mitigating SARS-CoV-2 spread. To shed light on this debate, we developed a novel static-temporal multiplex network characterizing both the regular (static) and random (temporal) contact patterns of individuals and a SARS-CoV-2 transmission model calibrated with historical COVID-19 epidemiological data. We estimated that the TTI strategy alone could not control the disease spread: assuming R0 = 2.5, the infection attack rate would be reduced by 24.5%. Increased test capacity and improved contact trace efficiency only slightly improved the effectiveness of the TTI. We thus investigated the effectiveness of the TTI strategy when coupled with reactive social distancing policies. Limiting contacts on the temporal contact layer would be insufficient to control an epidemic and contacts on both layers would need to be limited simultaneously. For example, the infection attack rate would be reduced by 68.1% when the reactive distancing policy disconnects 30% and 50% of contacts on static and temporal layers, respectively. Our findings highlight that, to reduce the overall transmission, it is important to limit contacts regardless of their types in addition to identifying infected individuals through contact tracing, given the substantial proportion of asymptomatic and pre-symptomatic SARS-CoV-2 transmission.</p>","PeriodicalId":49688,"journal":{"name":"PLoS Computational Biology","volume":"19 9","pages":"e1011423"},"PeriodicalIF":4.3,"publicationDate":"2023-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10501547/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10283342","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Bayesian inference for spatio-temporal stochastic transmission of plant disease in the presence of roguing: A case study to characterise the dispersal of Flavescence dorée.","authors":"Hola K Adrakey,&nbsp;Gavin J Gibson,&nbsp;Sandrine Eveillard,&nbsp;Sylvie Malembic-Maher,&nbsp;Frederic Fabre","doi":"10.1371/journal.pcbi.1011399","DOIUrl":"10.1371/journal.pcbi.1011399","url":null,"abstract":"<p><p>Estimating the distance at which pathogens disperse from one season to the next is crucial for designing efficient control strategies for invasive plant pathogens and a major milestone in the reduction of pesticide use in agriculture. However, we still lack such estimates for many diseases, especially for insect-vectored pathogens, such as Flavescence dorée (FD). FD is a quarantine disease threatening European vineyards. Its management is based on mandatory insecticide treatments and the removal of infected plants identified during annual surveys. This paper introduces a general statistical framework to model the epidemiological dynamics of FD in a mechanistic manner that can take into account missing hosts in surveyed fields (resulting from infected plant removals). We parameterized the model using Markov chain Monte Carlo (MCMC) and data augmentation from surveillance data gathered in Bordeaux vineyards. The data mainly consist of two snapshot maps of the infectious status of all the plants in three adjacent fields during two consecutive years. We demonstrate that heavy-tailed dispersal kernels best fit the spread of FD and that on average, 50% (resp. 80%) of new infection occurs within 10.5 m (resp. 22.2 m) of the source plant. These values are in agreement with estimates of the flying capacity of Scaphoideus titanus, the leafhopper vector of FD, reported in the literature using mark-capture techniques. Simulations of simple removal scenarios using the fitted model suggest that cryptic infection hampered FD management. Future efforts should explore whether strategies relying on reactive host removal can improve FD management.</p>","PeriodicalId":49688,"journal":{"name":"PLoS Computational Biology","volume":"19 9","pages":"e1011399"},"PeriodicalIF":4.3,"publicationDate":"2023-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10501664/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10648898","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"E(3) equivariant graph neural networks for robust and accurate protein-protein interaction site prediction.","authors":"Rahmatullah Roche,&nbsp;Bernard Moussad,&nbsp;Md Hossain Shuvo,&nbsp;Debswapna Bhattacharya","doi":"10.1371/journal.pcbi.1011435","DOIUrl":"10.1371/journal.pcbi.1011435","url":null,"abstract":"<p><p>Artificial intelligence-powered protein structure prediction methods have led to a paradigm-shift in computational structural biology, yet contemporary approaches for predicting the interfacial residues (i.e., sites) of protein-protein interaction (PPI) still rely on experimental structures. Recent studies have demonstrated benefits of employing graph convolution for PPI site prediction, but ignore symmetries naturally occurring in 3-dimensional space and act only on experimental coordinates. Here we present EquiPPIS, an E(3) equivariant graph neural network approach for PPI site prediction. EquiPPIS employs symmetry-aware graph convolutions that transform equivariantly with translation, rotation, and reflection in 3D space, providing richer representations for molecular data compared to invariant convolutions. EquiPPIS substantially outperforms state-of-the-art approaches based on the same experimental input, and exhibits remarkable robustness by attaining better accuracy with predicted structural models from AlphaFold2 than what existing methods can achieve even with experimental structures. Freely available at https://github.com/Bhattacharya-Lab/EquiPPIS, EquiPPIS enables accurate PPI site prediction at scale.</p>","PeriodicalId":49688,"journal":{"name":"PLoS Computational Biology","volume":"19 8","pages":"e1011435"},"PeriodicalIF":4.3,"publicationDate":"2023-08-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10499216/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10587086","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}