Methods and considerations for estimating parameters in biophysically detailed neural models with simulation based inference
PLOS Computational Biology
by Nicholas Tolley, Pedro L. C. Rodrigues, Alexandre Gramfort, Stephanie R. Jones
17h ago
by Nicholas Tolley, Pedro L. C. Rodrigues, Alexandre Gramfort, Stephanie R. Jones Biophysically detailed neural models are a powerful technique to study neural dynamics in health and disease with a growing number of established and openly available models. A major challenge in the use of such models is that parameter inference is an inherently difficult and unsolved problem. Identifying unique parameter distributions that can account for observed neural dynamics, and differences across experimental conditions, is essential to their meaningful use. Recently, simulation based inference (SBI) has ..read more
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Disentangled deep generative models reveal coding principles of the human face processing network
PLOS Computational Biology
by Paul Soulos, Leyla Isik
17h ago
by Paul Soulos, Leyla Isik Despite decades of research, much is still unknown about the computations carried out in the human face processing network. Recently, deep networks have been proposed as a computational account of human visual processing, but while they provide a good match to neural data throughout visual cortex, they lack interpretability. We introduce a method for interpreting brain activity using a new class of deep generative models, disentangled representation learning models, which learn a low-dimensional latent space that “disentangles” different semantically meaningful dimen ..read more
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Circadian regulation of sinoatrial nodal cell pacemaking function: Dissecting the roles of autonomic control, body temperature, and local circadian rhythmicity
PLOS Computational Biology
by Pan Li, Jae Kyoung Kim
17h ago
by Pan Li, Jae Kyoung Kim Strong circadian (~24h) rhythms in heart rate (HR) are critical for flexible regulation of cardiac pacemaking function throughout the day. While this circadian flexibility in HR is sustained in diverse conditions, it declines with age, accompanied by reduced maximal HR performance. The intricate regulation of circadian HR involves the orchestration of the autonomic nervous system (ANS), circadian rhythms of body temperature (CRBT), and local circadian rhythmicity (LCR), which has not been fully understood. Here, we developed a mathematical model describing ANS, CRBT ..read more
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A simulation framework to determine optimal strength training and musculoskeletal geometry for sprinting and distance running
PLOS Computational Biology
by Tom Van Wouwe, Jennifer Hicks, Scott Delp, Karen C. Liu
4d ago
by 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 d ..read more
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Shared input and recurrency in neural networks for metabolically efficient information transmission
PLOS Computational Biology
by Tomas Barta, Lubomir Kostal
4d ago
by 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. Given that the goal of neural p ..read more
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Age-dependent ventilator-induced lung injury: Mathematical modeling, experimental data, and statistical analysis
PLOS Computational Biology
by Quintessa Hay, Christopher Grubb, Sarah Minucci, Michael S. Valentine, Jennifer Van Mullekom, Rebecca L. Heise, Angela M. Reynolds
6d ago
by 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 ..read more
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Genome scale metabolic network modelling for metabolic profile predictions
PLOS Computational Biology
by Juliette Cooke, Maxime Delmas, Cecilia Wieder, Pablo Rodríguez Mier, Clément Frainay, Florence Vinson, Timothy Ebbels, Nathalie Poupin, Fabien Jourdan
6d ago
by 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 ..read more
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Diverse mutant selection windows shape spatial heterogeneity in evolving populations
PLOS Computational Biology
by Eshan S. King, Dagim S. Tadele, Beck Pierce, Michael Hinczewski, Jacob G. Scott
6d ago
by 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 d ..read more
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A novel batch-effect correction method for scRNA-seq data based on Adversarial Information Factorization
PLOS Computational Biology
by Lily Monnier, Paul-Henry Cournède
6d ago
by 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. It compares to a ..read more
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EPINEST, an agent-based model to simulate epidemic dynamics in large-scale poultry production and distribution networks
PLOS Computational Biology
by Francesco Pinotti, José Lourenço, Sunetra Gupta, Suman Das Gupta, Joerg Henning, Damer Blake, Fiona Tomley, Tony Barnett, Dirk Pfeiffer, Md. Ahasanul Hoque, Guillaume Fournié
6d ago
by 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 Banglad ..read more
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