Ten simple rules for starting FAIR discussions in your community
by Fr édérique Belliard, Angelica Maria Maineri, Esther Plomp, Andrés Felipe Ramos Padilla, Junzi Sun, Maryam Zare Jeddi
This work presents 10 rules that provide guidance and recommendations on how to start up discussions around the implementation of the FAIR (Findable, Accessible, Interoperable, Reusable) principles and creation of standardised ways of working. These recommendations will be particularly relevant if you are unsure where to start, who to involve, what the benefits and barriers of standardisation are, and if little work has been done in your discipline to standardise research workflows. When applied, the...
Source: PLoS Computational Biology - December 14, 2023 Category: Biology Authors: Fr édérique Belliard Source Type: research
Time-resolved dynamic computational modeling of human EEG recordings reveals gradients of generative mechanisms for the MMN response
by Arnaud Poublan-Couzardot, Fran çoise Lecaignard, Enrico Fucci, Richard J. Davidson, Jérémie Mattout, Antoine Lutz, Oussama Abdoun
Despite attempts to unify the different theoretical accounts of the mismatch negativity (MMN), there is still an ongoing debate on the neurophysiological mechanisms underlying this complex brain response. On one hand, neuronal adaptation to recurrent stimuli is able to explain many of the observed properties of the MMN, such as its sensitivity to controlled experimental parameters. On the other hand, several modeling studies reported evidence in favor of Bayesian learning models for expla...
Source: PLoS Computational Biology - December 13, 2023 Category: Biology Authors: Arnaud Poublan-Couzardot Source Type: research
A combined computational and experimental investigation of the filtration function of splenic macrophages in sickle cell disease
by Guansheng Li, Yuhao Qiang, He Li, Xuejin Li, Pierre A. Buffet, Ming Dao, George Em Karniadakis
Being the largest lymphatic organ in the body, the spleen also constantly controls the quality of red blood cells (RBCs) in circulation through its two major filtration components, namely interendothelial slits (IES) and red pulp macrophages. In contrast to the extensive studies in understanding the filtration function of IES, fewer works investigate how the splenic macrophages retain the aged and diseased RBCs, i.e., RBCs in sickle cell disease (SCD). Herein, we perform a computational study informed by companion experiments...
Source: PLoS Computational Biology - December 13, 2023 Category: Biology Authors: Guansheng Li Source Type: research
From dawn till dusk: Time-adaptive bayesian optimization for neurostimulation
by John E. Fleming, Ines Pont Sanchis, Oscar Lemmens, Angus Denison-Smith, Timothy O. West, Timothy Denison, Hayriye Cagnan
Stimulation optimization has garnered considerable interest in recent years in order to efficiently parametrize neuromodulation-based therapies. To date, efforts focused on automatically identifying settings from parameter spaces that do not change over time. A limitation of these approaches, however, is that they lack consideration for time dependent factors that may influence therapy outcomes. Disease progression and biological rhythmicity are two sources of variation that may influence optimal sti...
Source: PLoS Computational Biology - December 13, 2023 Category: Biology Authors: John E. Fleming Source Type: research
Machine learning identification of < i > Pseudomonas aeruginosa < /i > strains from colony image data
by Jennifer B. Rattray, Ryan J. Lowhorn, Ryan Walden, Pedro M árquez-Zacarías, Evgeniya Molotkova, Gabriel Perron, Claudia Solis-Lemus, Daniel Pimentel Alarcon, Sam P. Brown
When grown on agar surfaces, microbes can produce distinct multicellular spatial structures called colonies, which contain characteristic sizes, shapes, edges, textures, and degrees of opacity and color. For over one hundred years, researchers have used these morphology cues to classify bacteria and guide more targeted treatment of pathogens. Advances in genome sequencing technology have revolutionized our ability to classify bacterial isolates and ...
Source: PLoS Computational Biology - December 13, 2023 Category: Biology Authors: Jennifer B. Rattray Source Type: research
Sequence representation as an early step in the evolution of language
by Anna Jon-And, Markus Jonsson, Johan Lind, Stefano Ghirlanda, Magnus Enquist
Human language is unique in its compositional, open-ended, and sequential form, and its evolution is often solely explained by advantages of communication. However, it has proven challenging to identify an evolutionary trajectory from a world without language to a world with language, especially while at the same time explaining why such an advantageous phenomenon has not evolved in other animals. Decoding sequential information is necessary for language, making domain-general sequence representation a tentative basic requirement for the evolut...
Source: PLoS Computational Biology - December 13, 2023 Category: Biology Authors: Anna Jon-And Source Type: research
Generalized Michaelis –Menten rate law with time-varying molecular concentrations
by Roktaek Lim, Thomas L. P. Martin, Junghun Chae, WooJoong Kim, Cheol-Min Ghim, Pan-Jun Kim
The Michaelis –Menten (MM) rate law has been the dominant paradigm of modeling biochemical rate processes for over a century with applications in biochemistry, biophysics, cell biology, systems biology, and chemical engineering. The MM rate law and its remedied form stand on the assumption that the concentratio n of the complex of interacting molecules, at each moment, approaches an equilibrium (quasi-steady state) much faster than the molecular concentrations change. Yet, this assumption is not always justified. Here, we relax ...
Source: PLoS Computational Biology - December 11, 2023 Category: Biology Authors: Roktaek Lim Source Type: research
How well do rudimentary plasticity rules predict adult visual object learning?
by Michael J. Lee, James J. DiCarlo
A core problem in visual object learning is using a finite number of images of a new object to accurately identify that object in future, novel images.
One longstanding, conceptual hypothesis asserts that this core problem is solved by adult brains through two connected mechanisms: 1) the re-representation of incoming retinal images as points in a fixed, multidimensional neural space, and 2) the optimization of linear decision boundaries in that space, via simple plasticity rules applied to a single downstream layer.
Though this scheme is biologically plausible, the extent to which it e...
Source: PLoS Computational Biology - December 11, 2023 Category: Biology Authors: Michael J. Lee Source Type: research
Learning context shapes bimanual control strategy and generalization of novel dynamics
by Jonathan Orschiedt, David W. Franklin
Bimanual movements are fundamental components of everyday actions, yet the underlying mechanisms coordinating adaptation of the two hands remain unclear. Although previous studies highlighted the contextual effect of kinematics of both arms on internal model formation, we do not know how the sensorimotor control system associates the learned memory with the experienced states in bimanual movements. More specifically, can, and if so, how, does the sensorimotor control system combine multiple states from different effectors to create and adapt a motor memory? Here, we tested motor me...
Source: PLoS Computational Biology - December 8, 2023 Category: Biology Authors: Jonathan Orschiedt Source Type: research
The neurocognitive role of working memory load when Pavlovian motivational control affects instrumental learning
by Heesun Park, Hoyoung Doh, Eunhwi Lee, Harhim Park, Woo-Young Ahn
Research suggests that a fast, capacity-limited working memory (WM) system and a slow, incremental reinforcement learning (RL) system jointly contribute to instrumental learning. Thus, situations that strain WM resources alter instrumental learning: under WM loads, learning becomes slow and incremental, the reliance on computationally efficient learning increases, and action selection becomes more random. It is also suggested that Pavlovian learning influences people ’s behavior during instrumental learning by providing hard-wired instinctive responses ...
Source: PLoS Computational Biology - December 8, 2023 Category: Biology Authors: Heesun Park Source Type: research
SPIN-CGNN: Improved fixed backbone protein design with contact map-based graph construction and contact graph neural network
by Xing Zhang, Hongmei Yin, Fei Ling, Jian Zhan, Yaoqi Zhou
Recent advances in deep learning have significantly improved the ability to infer protein sequences directly from protein structures for the fix-backbone design. The methods have evolved from the early use of multi-layer perceptrons to convolutional neural networks, transformers, and graph neural networks (GNN). However, the conventional approach of constructing K-nearest-neighbors (KNN) graph for GNN has limited the utilization of edge information, which plays a critical role in network performance. Here we introduced SPIN-CGNN based on protein contact maps for ...
Source: PLoS Computational Biology - December 7, 2023 Category: Biology Authors: Xing Zhang Source Type: research
Motoneuron-driven computational muscle modelling with motor unit resolution and subject-specific musculoskeletal anatomy
by Arnault H. Caillet, Andrew T. M. Phillips, Dario Farina, Luca Modenese
The computational simulation of human voluntary muscle contraction is possible with EMG-driven Hill-type models of whole muscles. Despite impactful applications in numerous fields, the neuromechanical information and the physiological accuracy such models provide remain limited because of multiscale simplifications that limit comprehensive description of muscle internal dynamics during contraction. We addressed this limitation by developing a novel motoneuron-driven neuromuscular model, that describes the force-generating dynamics of a population of...
Source: PLoS Computational Biology - December 7, 2023 Category: Biology Authors: Arnault H. Caillet Source Type: research
From policy to practice: Lessons learned from an open science funding initiative
by Sonya B. Dumanis, Kristen Ratan, Souad McIntosh, Hetal V. Shah, Matt Lewis, Timothy H. Vines, Randy Schekman, Ekemini A. Riley (Source: PLoS Computational Biology)
Source: PLoS Computational Biology - December 7, 2023 Category: Biology Authors: Sonya B. Dumanis Source Type: research
Ten simple rules for managing laboratory information
by Casey-Tyler Berezin, Luis U. Aguilera, Sonja Billerbeck, Philip E. Bourne, Douglas Densmore, Paul Freemont, Thomas E. Gorochowski, Sarah I. Hernandez, Nathan J. Hillson, Connor R. King, Michael K öpke, Shuyi Ma, Katie M. Miller, Tae Seok Moon, Jason H. Moore, Brian Munsky, Chris J. Myers, Dequina A. Nicholas, Samuel J. Peccoud, Wen Zhou, Jean Peccoud
Author summary: Information is the cornerstone of research, from experimental (meta)data and computational processes to complex inventories of reagents and equipment. These 10 simple rules discuss best practices for leveraging laboratory information management systems to t...
Source: PLoS Computational Biology - December 7, 2023 Category: Biology Authors: Casey-Tyler Berezin Source Type: research
Dissolution of spiral wave ’s core using cardiac optogenetics
by Sayedeh Hussaini, Sarah L. L ädke, Johannes Schröder-Schetelig, Vishalini Venkatesan, Raúl A. Quiñonez Uribe, Claudia Richter, Rupamanjari Majumder, Stefan Luther
Rotating spiral waves in the heart are associated with life-threatening cardiac arrhythmias such as ventricular tachycardia and fibrillation. These arrhythmias are treated by a process called defibrillation, which forces electrical resynchronization of the heart tissue by delivering a single global high-voltage shock directly to the heart. This method leads to immediate termination of spiral waves. However, this may not be the only mechanism underlying su...
Source: PLoS Computational Biology - December 7, 2023 Category: Biology Authors: Sayedeh Hussaini Source Type: research
