Metric information in cognitive maps: Euclidean embedding of non-Euclidean environments
by Tristan Baumann, Hanspeter A. Mallot
The structure of the internal representation of surrounding space, the so-calledcognitive map, has long been debated. A Euclidean metric map is the most straight-forward hypothesis, but human navigation has been shown to systematically deviate from the Euclidean ground truth. Vector navigation based on non-metric models can better explain the observed behavior, but also discards useful geometric properties such as fast shortcut estimation and cue integration.
Here, we propose another alternative, a Euclidean metric map that is systematically distorted to account for the observed beh...
Source: PLoS Computational Biology - December 27, 2023 Category: Biology Authors: Tristan Baumann Source Type: research
Time warping between main epidemic time series in epidemiological surveillance
by Jean-David Morel, Jean-Michel Morel, Luis Alvarez
The most common reported epidemic time series in epidemiological surveillance are the daily or weekly incidence of new cases, the hospital admission count, the ICU admission count, and the death toll, which played such a prominent role in the struggle to monitor the Covid-19 pandemic. We show that pairs of such curves are related to each other by a generalized renewal equation depending on a smooth time varying delay and a smooth ratio generalizing the reproduction number. Such a functional relation is also explored for pairs of simultaneous curves measuring the same in...
Source: PLoS Computational Biology - December 27, 2023 Category: Biology Authors: Jean-David Morel Source Type: research
PyRates —A code-generation tool for modeling dynamical systems in biology and beyond
by Richard Gast, Thomas R. Kn ösche, Ann Kennedy
The mathematical study of real-world dynamical systems relies on models composed of differential equations. Numerical methods for solving and analyzing differential equation systems are essential when complex biological problems have to be studied, such as the spreading of a virus, the evolution of competing species in an ecosystem, or the dynamics of neurons in the brain.
Here we presentPyRates, a Python-based software for modeling and analyzing differential equation systems via numerical methods.PyRates is specifically designed to account for the inherent complexity of b...
Source: PLoS Computational Biology - December 27, 2023 Category: Biology Authors: Richard Gast Source Type: research
Estimating neuronal firing density: A quantitative analysis of firing rate map algorithms
by Roddy M. Grieves
The analysis of neurons that exhibit receptive fields dependent on an organism ’s spatial location, such as grid, place or boundary cells typically begins by mapping their activity in space using firing rate maps. However, mapping approaches are varied and depend on multiple tuning parameters that are usually chosen qualitatively by the experimenter and thus vary significant ly across studies. Small changes in parameters such as these can impact results significantly, yet, to date a quantitative investigation of firing rate maps has not been attempted. Using simulated datasets, we examined how tuning...
Source: PLoS Computational Biology - December 27, 2023 Category: Biology Authors: Roddy M. Grieves Source Type: research
Optimizing COVID-19 testing strategies on college campuses: Evaluation of the health and economic costs
by Kaitlyn E. Johnson, Remy Pasco, Spencer Woody, Michael Lachmann, Maureen Johnson-Leon, Darlene Bhavnani, Jessica Klima, A. David Paltiel, Spencer J. Fox, Lauren Ancel Meyers
Colleges and universities in the US struggled to provide safe in-person education throughout the COVID-19 pandemic. Testing coupled with isolation is a nimble intervention strategy that can be tailored to mitigate the changing health and economic risks associated with SARS-CoV-2. We developed a decision-support tool to aid in the design of university-based screening strategies using a mathematical model of SARS-CoV-2 transmission. Applying this fra...
Source: PLoS Computational Biology - December 22, 2023 Category: Biology Authors: Kaitlyn E. Johnson Source Type: research
Method to determine whether sleep phenotypes are driven by endogenous circadian rhythms or environmental light by combining longitudinal data and personalised mathematical models
by Anne C. Skeldon, Thalia Rodriguez Garcia, Sean F. Cleator, Ciro della Monica, Kiran K. G. Ravindran, Victoria L. Revell, Derk-Jan Dijk
Sleep timing varies between individuals and can be altered in mental and physical health conditions. Sleep and circadian sleep phenotypes, including circadian rhythm sleep-wake disorders, may be driven by endogenous physiological processes, exogeneous environmental light exposure along with social constraints and behavioural factors. Identifying the relative contributions of these driving factors to different phenotypes is essential for the design of personalised interventions.
The timi...
Source: PLoS Computational Biology - December 22, 2023 Category: Biology Authors: Anne C. Skeldon Source Type: research
Insights to HIV-1 coreceptor usage by estimating HLA adaptation with Bayesian generalized linear mixed models
by Anna Hake, Anja Germann, Corena de Beer, Alexander Thielen, Martin D äumer, Wolfgang Preiser, Hagen von Briesen, Nico Pfeifer
The mechanisms triggering the human immunodeficiency virus type I (HIV-1) to switch the coreceptor usage from CCR5 to CXCR4 during the course of infection are not entirely understood. While low CD4+ T cell counts are associated with CXCR4 usage, a predominance of CXCR4 usage with still high CD4+ T cell counts remains puzzling. Here, we explore the hypothesis that viral adaptation to the human leukocyte antigen (HLA) complex, especially to the HLA class II alleles, contributes to the coreceptor ...
Source: PLoS Computational Biology - December 21, 2023 Category: Biology Authors: Anna Hake Source Type: research
Know-how of holding a Bioinformatics competition: Structure, model, overview, and perspectives
by Elvira C. A. Hor ácio, Lucas M. de Carvalho, Gustavo G. Pereira, Mayla C. Abrahim, Mônica P. Coelho, Deivid A. De Jesus, Glen J. Y. García, Raquel C. de Melo-Minardi, Sheila T. Nagamatsu
The article presents a framework for a Bioinformatics competition that focuses on 4 key aspects: structure, model, overview, and perspectives. Structure represents the organizational framework employed to coordinate the main tasks involved in the competition. Model showcases the competition design, which encompasses 3 phases. Overview presents our case study, the League of Brazilian Bioinformatics (LBB) 2nd Edition. Finally, the sec...
Source: PLoS Computational Biology - December 21, 2023 Category: Biology Authors: Elvira C. A. Hor ácio Source Type: research
Ten simple rules for writing a < i > PLOS Computational Biology < /i > quick tips article
by Patricia M. Palagi, Russell Schwartz, Scott Markel, B. F. Francis Ouellette (Source: PLoS Computational Biology)
Source: PLoS Computational Biology - December 21, 2023 Category: Biology Authors: Patricia M. Palagi Source Type: research
Ten simple rules for humane data science
by Hassan Masum, Philip E. Bourne (Source: PLoS Computational Biology)
Source: PLoS Computational Biology - December 21, 2023 Category: Biology Authors: Hassan Masum Source Type: research
Ten quick tips for fuzzy logic modeling of biomedical systems
by Davide Chicco, Simone Spolaor, Marco S. Nobile
Fuzzy logic is useful tool to describe and represent biological or medical scenarios, where often states and outcomes are not only completely true or completely false, but rather partially true or partially false. Despite its usefulness and spread, fuzzy logic modeling might easily be done in the wrong way, especially by beginners and unexperienced researchers, who might overlook some important aspects or might make common mistakes. Malpractices and pitfalls, in turn, can lead to wrong or overoptimistic, inflated results, with negative consequences to the biomedical resear...
Source: PLoS Computational Biology - December 21, 2023 Category: Biology Authors: Davide Chicco Source Type: research
Affect-congruent attention modulates generalized reward expectations
by Daniel Bennett, Angela Radulescu, Sam Zorowitz, Valkyrie Felso, Yael Niv
Positive and negative affective states are respectively associated with optimistic and pessimistic expectations regarding future reward. One mechanism that might underlie these affect-related expectation biases is attention to positive- versus negative-valence features (e.g., attending to the positive reviews of a restaurant versus its expensive price). Here we tested the effects of experimentally induced positive and negative affect on feature-based attention in 120 participants completing a compound-generalization task with eye-tracking. We foun...
Source: PLoS Computational Biology - December 21, 2023 Category: Biology Authors: Daniel Bennett Source Type: research
Transcript assembly and annotations: Bias and adjustment
by Qimin Zhang, Mingfu Shao
Transcript annotations play a critical role in gene expression analysis as they serve as a reference for quantifying isoform-level expression. The two main sources of annotations are RefSeq and Ensembl/GENCODE, but discrepancies between their methodologies and information resources can lead to significant differences. It has been demonstrated that the choice of annotation can have a significant impact on gene expression analysis. Furthermore, transcript assembly is closely linked to annotations, as assembling large-scale available RNA-seq data is an effective data-driven way to construct annota...
Source: PLoS Computational Biology - December 21, 2023 Category: Biology Authors: Qimin Zhang Source Type: research
An agent-based modeling approach for lung fibrosis in response to COVID-19
by Mohammad Aminul Islam, Michael Getz, Paul Macklin, Ashlee N. Ford Versypt
The severity of the COVID-19 pandemic has created an emerging need to investigate the long-term effects of infection on patients. Many individuals are at risk of suffering pulmonary fibrosis due to the pathogenesis of lung injury and impairment in the healing mechanism. Fibroblasts are the central mediators of extracellular matrix (ECM) deposition during tissue regeneration, regulated by anti-inflammatory cytokines including transforming growth factor beta (TGF- β). The TGF-β-dependent accumulation of fibroblasts at the damaged site and excess ...
Source: PLoS Computational Biology - December 21, 2023 Category: Biology Authors: Mohammad Aminul Islam Source Type: research
Protection promotes energetically efficient structures in marine communities
by Andrea Tabi, Luis J. Gilarranz, Spencer A. Wood, Jennifer A. Dunne, Serguei Saavedra
The sustainability of marine communities is critical for supporting many biophysical processes that provide ecosystem services that promote human well-being. It is expected that anthropogenic disturbances such as climate change and human activities will tend to create less energetically-efficient ecosystems that support less biomass per unit energy flow. It is debated, however, whether this expected development should translate into bottom-heavy (with small basal species being the most abundant) or top-heavy communities (where more bio...
Source: PLoS Computational Biology - December 21, 2023 Category: Biology Authors: Andrea Tabi Source Type: research
