journal
https://read.qxmd.com/read/38394341/shared-input-and-recurrency-in-neural-networks-for-metabolically-efficient-information-transmission
#1
JOURNAL ARTICLE
Tomas Barta, Lubomir Kostal
Shared input to a population of neurons induces noise correlations, which can decrease the information carried by a population activity. Inhibitory feedback in recurrent neural networks can reduce the noise correlations and thus increase the information carried by the population activity. However, the activity of inhibitory neurons is costly. This inhibitory feedback decreases the gain of the population. Thus, depolarization of its neurons requires stronger excitatory synaptic input, which is associated with higher ATP consumption...
February 23, 2024: PLoS Computational Biology
https://read.qxmd.com/read/38394339/a-biologically-inspired-repair-mechanism-for-neuronal-reconstructions-with-a-focus-on-human-dendrites
#2
JOURNAL ARTICLE
Moritz Groden, Hannah M Moessinger, Barbara Schaffran, Javier DeFelipe, Ruth Benavides-Piccione, Hermann Cuntz, Peter Jedlicka
Investigating and modelling the functionality of human neurons remains challenging due to the technical limitations, resulting in scarce and incomplete 3D anatomical reconstructions. Here we used a morphological modelling approach based on optimal wiring to repair the parts of a dendritic morphology that were lost due to incomplete tissue samples. In Drosophila, where dendritic regrowth has been studied experimentally using laser ablation, we found that modelling the regrowth reproduced a bimodal distribution between regeneration of cut branches and invasion by neighbouring branches...
February 23, 2024: PLoS Computational Biology
https://read.qxmd.com/read/38394308/a-simulation-framework-to-determine-optimal-strength-training-and-musculoskeletal-geometry-for-sprinting-and-distance-running
#3
JOURNAL ARTICLE
Tom Van Wouwe, Jennifer Hicks, Scott Delp, Karen C Liu
Musculoskeletal geometry and muscle volumes vary widely in the population and are intricately linked to the performance of tasks ranging from walking and running to jumping and sprinting. As an alternative to experimental approaches, where it is difficult to isolate factors and establish causal relationships, simulations can be used to independently vary musculoskeletal geometry and muscle volumes, and develop a fundamental understanding. However, our ability to understand how these parameters affect task performance has been limited due to the high computational cost of modelling the necessary complexity of the musculoskeletal system and solving the requisite multi-dimensional optimization problem...
February 23, 2024: PLoS Computational Biology
https://read.qxmd.com/read/38386700/a-novel-batch-effect-correction-method-for-scrna-seq-data-based-on-adversarial-information-factorization
#4
JOURNAL ARTICLE
Lily Monnier, Paul-Henry Cournède
Single-cell RNA sequencing (scRNA-seq) technology produces an unprecedented resolution at the level of a unique cell, raising great hopes in medicine. Nevertheless, scRNA-seq data suffer from high variations due to the experimental conditions, called batch effects, preventing any aggregated downstream analysis. Adversarial Information Factorization provides a robust batch-effect correction method that does not rely on prior knowledge of the cell types nor a specific normalization strategy while being adapted to any downstream analysis task...
February 22, 2024: PLoS Computational Biology
https://read.qxmd.com/read/38386693/age-dependent-ventilator-induced-lung-injury-mathematical-modeling-experimental-data-and-statistical-analysis
#5
JOURNAL ARTICLE
Quintessa Hay, Christopher Grubb, Sarah Minucci, Michael S Valentine, Jennifer Van Mullekom, Rebecca L Heise, Angela M Reynolds
A variety of pulmonary insults can prompt the need for life-saving mechanical ventilation; however, misuse, prolonged use, or an excessive inflammatory response, can result in ventilator-induced lung injury. Past research has observed an increased instance of respiratory distress in older patients and differences in the inflammatory response. To address this, we performed high pressure ventilation on young (2-3 months) and old (20-25 months) mice for 2 hours and collected data for macrophage phenotypes and lung tissue integrity...
February 22, 2024: PLoS Computational Biology
https://read.qxmd.com/read/38386690/diverse-mutant-selection-windows-shape-spatial-heterogeneity-in-evolving-populations
#6
JOURNAL ARTICLE
Eshan S King, Dagim S Tadele, Beck Pierce, Michael Hinczewski, Jacob G Scott
Mutant selection windows (MSWs), the range of drug concentrations that select for drug-resistant mutants, have long been used as a model for predicting drug resistance and designing optimal dosing strategies in infectious disease. The canonical MSW model offers comparisons between two subtypes at a time: drug-sensitive and drug-resistant. In contrast, the fitness landscape model with N alleles, which maps genotype to fitness, allows comparisons between N genotypes simultaneously, but does not encode continuous drug response data...
February 22, 2024: PLoS Computational Biology
https://read.qxmd.com/read/38386685/genome-scale-metabolic-network-modelling-for-metabolic-profile-predictions
#7
JOURNAL ARTICLE
Juliette Cooke, Maxime Delmas, Cecilia Wieder, Pablo Rodríguez Mier, Clément Frainay, Florence Vinson, Timothy Ebbels, Nathalie Poupin, Fabien Jourdan
Metabolic profiling (metabolomics) aims at measuring small molecules (metabolites) in complex samples like blood or urine for human health studies. While biomarker-based assessment often relies on a single molecule, metabolic profiling combines several metabolites to create a more complex and more specific fingerprint of the disease. However, in contrast to genomics, there is no unique metabolomics setup able to measure the entire metabolome. This challenge leads to tedious and resource consuming preliminary studies to be able to design the right metabolomics experiment...
February 22, 2024: PLoS Computational Biology
https://read.qxmd.com/read/38381804/epinest-an-agent-based-model-to-simulate-epidemic-dynamics-in-large-scale-poultry-production-and-distribution-networks
#8
JOURNAL ARTICLE
Francesco Pinotti, José Lourenço, Sunetra Gupta, Suman Das Gupta, Joerg Henning, Damer Blake, Fiona Tomley, Tony Barnett, Dirk Pfeiffer, Md Ahasanul Hoque, Guillaume Fournié
The rapid intensification of poultry production raises important concerns about the associated risks of zoonotic infections. Here, we introduce EPINEST (EPIdemic NEtwork Simulation in poultry Transportation systems): an agent-based modelling framework designed to simulate pathogen transmission within realistic poultry production and distribution networks. We provide example applications to broiler production in Bangladesh, but the modular structure of the model allows for easy parameterization to suit specific countries and system configurations...
February 21, 2024: PLoS Computational Biology
https://read.qxmd.com/read/38377165/denoising-diffusion-probabilistic-models-for-generation-of-realistic-fully-annotated-microscopy-image-datasets
#9
JOURNAL ARTICLE
Dennis Eschweiler, Rüveyda Yilmaz, Matisse Baumann, Ina Laube, Rijo Roy, Abin Jose, Daniel Brückner, Johannes Stegmaier
Recent advances in computer vision have led to significant progress in the generation of realistic image data, with denoising diffusion probabilistic models proving to be a particularly effective method. In this study, we demonstrate that diffusion models can effectively generate fully-annotated microscopy image data sets through an unsupervised and intuitive approach, using rough sketches of desired structures as the starting point. The proposed pipeline helps to reduce the reliance on manual annotations when training deep learning-based segmentation approaches and enables the segmentation of diverse datasets without the need for human annotations...
February 20, 2024: PLoS Computational Biology
https://read.qxmd.com/read/38377147/intra-ripple-frequency-accommodation-in-an-inhibitory-network-model-for-hippocampal-ripple-oscillations
#10
JOURNAL ARTICLE
Natalie Schieferstein, Tilo Schwalger, Benjamin Lindner, Richard Kempter
Hippocampal ripple oscillations have been implicated in important cognitive functions such as memory consolidation and planning. Multiple computational models have been proposed to explain the emergence of ripple oscillations, relying either on excitation or inhibition as the main pacemaker. Nevertheless, the generating mechanism of ripples remains unclear. An interesting dynamical feature of experimentally measured ripples, which may advance model selection, is intra-ripple frequency accommodation (IFA): a decay of the instantaneous ripple frequency over the course of a ripple event...
February 20, 2024: PLoS Computational Biology
https://read.qxmd.com/read/38377134/connectivity-matrix-seriation-via-relaxation
#11
JOURNAL ARTICLE
Alexander Borst
Volume electron microscopy together with computer-based image analysis are yielding neural circuit diagrams of ever larger regions of the brain. These datasets are usually represented in a cell-to-cell connectivity matrix and contain important information about prevalent circuit motifs allowing to directly test various theories on the computation in that brain structure. Of particular interest are the detection of cell assemblies and the quantification of feedback, which can profoundly change circuit properties...
February 20, 2024: PLoS Computational Biology
https://read.qxmd.com/read/38377113/ecological-and-evolutionary-dynamics-of-cell-virus-virophage-systems
#12
JOURNAL ARTICLE
Jose Gabriel Nino Barreat, Aris Katzourakis
Microbial eukaryotes, giant viruses and virophages form a unique hyperparasitic system. Virophages are parasites of the virus transcription machinery and can interfere with virus replication, resulting in a benefit to the eukaryotic host population. Surprisingly, virophages can integrate into the genomes of their cell or virus hosts, and have been shown to reactivate during coinfection. This raises questions about the role of integration in the dynamics of cell-virus-virophage systems. We use mathematical models and computational simulations to understand the effect of virophage integration on populations of cells and viruses...
February 20, 2024: PLoS Computational Biology
https://read.qxmd.com/read/38377112/fast-adaptation-to-rule-switching-using-neuronal-surprise
#13
JOURNAL ARTICLE
Martin L L R Barry, Wulfram Gerstner
In humans and animals, surprise is a physiological reaction to an unexpected event, but how surprise can be linked to plausible models of neuronal activity is an open problem. We propose a self-supervised spiking neural network model where a surprise signal is extracted from an increase in neural activity after an imbalance of excitation and inhibition. The surprise signal modulates synaptic plasticity via a three-factor learning rule which increases plasticity at moments of surprise. The surprise signal remains small when transitions between sensory events follow a previously learned rule but increases immediately after rule switching...
February 20, 2024: PLoS Computational Biology
https://read.qxmd.com/read/38377108/robust-and-consistent-measures-of-pattern-separation-based-on-information-theory-and-demonstrated-in-the-dentate-gyrus
#14
JOURNAL ARTICLE
Alexander D Bird, Hermann Cuntz, Peter Jedlicka
Pattern separation is a valuable computational function performed by neuronal circuits, such as the dentate gyrus, where dissimilarity between inputs is increased, reducing noise and increasing the storage capacity of downstream networks. Pattern separation is studied from both in vivo experimental and computational perspectives and, a number of different measures (such as orthogonalisation, decorrelation, or spike train distance) have been applied to quantify the process of pattern separation. However, these are known to give conclusions that can differ qualitatively depending on the choice of measure and the parameters used to calculate it...
February 20, 2024: PLoS Computational Biology
https://read.qxmd.com/read/38377074/the-successor-representation-subserves-hierarchical-abstraction-for-goal-directed-behavior
#15
JOURNAL ARTICLE
Sven Wientjes, Clay B Holroyd
Humans have the ability to craft abstract, temporally extended and hierarchically organized plans. For instance, when considering how to make spaghetti for dinner, we typically concern ourselves with useful "subgoals" in the task, such as cutting onions, boiling pasta, and cooking a sauce, rather than particulars such as how many cuts to make to the onion, or exactly which muscles to contract. A core question is how such decomposition of a more abstract task into logical subtasks happens in the first place...
February 20, 2024: PLoS Computational Biology
https://read.qxmd.com/read/38363808/linear-motifs-regulating-protein-secretion-sorting-and-autophagy-in-leishmania-parasites-are-diverged-with-respect-to-their-host-equivalents
#16
JOURNAL ARTICLE
Andras Zeke, Toby J Gibson, Laszlo Dobson
The pathogenic, tropical Leishmania flagellates belong to an early-branching eukaryotic lineage (Kinetoplastida) with several unique features. Unfortunately, they are poorly understood from a molecular biology perspective, making development of mechanistically novel and selective drugs difficult. Here, we explore three functionally critical targeting short linear motif systems as well as their receptors in depth, using a combination of structural modeling, evolutionary sequence divergence and deep learning...
February 16, 2024: PLoS Computational Biology
https://read.qxmd.com/read/38363799/enhanced-perfusion-following-exposure-to-radiotherapy-a-theoretical-investigation
#17
JOURNAL ARTICLE
Jakub Köry, Vedang Narain, Bernadette J Stolz, Jakob Kaeppler, Bostjan Markelc, Ruth J Muschel, Philip K Maini, Joe M Pitt-Francis, Helen M Byrne
Tumour angiogenesis leads to the formation of blood vessels that are structurally and spatially heterogeneous. Poor blood perfusion, in conjunction with increased hypoxia and oxygen heterogeneity, impairs a tumour's response to radiotherapy. The optimal strategy for enhancing tumour perfusion remains unclear, preventing its regular deployment in combination therapies. In this work, we first identify vascular architectural features that correlate with enhanced perfusion following radiotherapy, using in vivo imaging data from vascular tumours...
February 16, 2024: PLoS Computational Biology
https://read.qxmd.com/read/38354202/enhancing-predictive-performance-for-spectroscopic-studies-in-wildlife-science-through-a-multi-model-approach-a-case-study-for-species-classification-of-live-amphibians
#18
JOURNAL ARTICLE
Li-Dunn Chen, Michael A Caprio, Devin M Chen, Andy J Kouba, Carrie K Kouba
Near infrared spectroscopy coupled with predictive modeling is a growing field of study for addressing questions in wildlife science aimed at improving management strategies and conservation outcomes for managed and threatened fauna. To date, the majority of spectroscopic studies in wildlife and fisheries applied chemometrics and predictive modeling with a single-algorithm approach. By contrast, multi-model approaches are used routinely for analyzing spectroscopic datasets across many major industries (e.g...
February 14, 2024: PLoS Computational Biology
https://read.qxmd.com/read/38346086/stressme-unified-computing-framework-of-escherichia-coli-metabolism-gene-expression-and-stress-responses
#19
JOURNAL ARTICLE
Jiao Zhao, Ke Chen, Bernhard O Palsson, Laurence Yang
Generalist microbes have adapted to a multitude of environmental stresses through their integrated stress response system. Individual stress responses have been quantified by E. coli metabolism and expression (ME) models under thermal, oxidative and acid stress, respectively. However, the systematic quantification of cross-stress & cross-talk among these stress responses remains lacking. Here, we present StressME: the unified stress response model of E. coli combining thermal (FoldME), oxidative (OxidizeME) and acid (AcidifyME) stress responses...
February 12, 2024: PLoS Computational Biology
https://read.qxmd.com/read/38346082/accounting-for-isoform-expression-increases-power-to-identify-genetic-regulation-of-gene-expression
#20
JOURNAL ARTICLE
Nathan LaPierre, Harold Pimentel
A core problem in genetics is molecular quantitative trait locus (QTL) mapping, in which genetic variants associated with changes in the molecular phenotypes are identified. One of the most-studied molecular QTL mapping problems is expression QTL (eQTL) mapping, in which the molecular phenotype is gene expression. It is common in eQTL mapping to compute gene expression by aggregating the expression levels of individual isoforms from the same gene and then performing linear regression between SNPs and this aggregated gene expression level...
February 12, 2024: PLoS Computational Biology
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