PLOS Computational Biology
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#1Thibault Lagache (MBL: Marine Biological Laboratory)H-Index: 17
#2Alison Hanson (MBL: Marine Biological Laboratory)H-Index: 1
Last. Rafael Yuste (MBL: Marine Biological Laboratory)H-Index: 109
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Measuring the activity of neuronal populations with calcium imaging can capture emergent functional properties of neuronal circuits with single cell resolution. However, the motion of freely behaving animals, together with the intermittent detectability of calcium sensors, can hinder automatic monitoring of neuronal activity and their subsequent functional characterization. We report the development and open-source implementation of a multi-step cellular tracking algorithm (Elastic Motion Correc...
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#1Rupamanjari Majumder (MPG: Max Planck Society)H-Index: 8
#2Sayedeh Hussaini (MPG: Max Planck Society)H-Index: 2
Last. Eberhard Bodenschatz (MPG: Max Planck Society)H-Index: 63
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Interruptions in nonlinear wave propagation, commonly referred to as wave breaks, are typical of many complex excitable systems. In the heart they lead to lethal rhythm disorders, the so-called arrhythmias, which are one of the main causes of sudden death in the industrialized world. Progress in the treatment and therapy of cardiac arrhythmias requires a detailed understanding of the triggers and dynamics of these wave breaks. In particular, two very important questions are: 1) What determines t...
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Self-deception, paranoia, and overconfidence involve misbeliefs about the self, others, and world. They are often considered mistaken. Here we explore whether they might be adaptive, and further, whether they might be explicable in Bayesian terms. We administered a difficult perceptual judgment task with and without social influence (suggestions from a cooperating or competing partner). Crucially, the social influence was uninformative. We found that participants heeded the suggestions most unde...
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#1Jason Bennett (La Jolla Institute for Allergy and Immunology)
#2Mikhail Pomaznoy (La Jolla Institute for Allergy and Immunology)H-Index: 4
Last. Bjoern Peters (La Jolla Institute for Allergy and Immunology)H-Index: 87
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Recent technological advances have made the gathering of comprehensive gene expression datasets a commodity. This has shifted the limiting step of transcriptomic studies from the accumulation of data to their analyses and interpretation. The main problem in analyzing transcriptomics data is that the number of independent samples is typically much lower ( 14,000). To address this, it would be desirable to reduce the gathered data’s dimensionality without losing information. Clustering genes into ...
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#1Jurasz J (GUT: Gdańsk University of Technology)
#2Maciej Baginski (GUT: Gdańsk University of Technology)H-Index: 9
Last. Miłosz Wieczór (GUT: Gdańsk University of Technology)H-Index: 9
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The current surge in bacterial multi-drug resistance (MDR) is one of the largest challenges to public health, threatening to render ineffective many therapies we rely on for treatment of serious infections. Understanding different factors that contribute to MDR is hence crucial from the global "one health" perspective. In this contribution, we focus on the prototypical broad-selectivity proton-coupled antiporter EmrE, one of the smallest known ligand transporters that confers resistance to aroma...
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#1Daniel Mattox (Dartmouth College)H-Index: 4
#2Chris Bailey-Kellogg (Dartmouth College)H-Index: 33
Lectin-glycan interactions facilitate inter- and intracellular communication in many processes including protein trafficking, host-pathogen recognition, and tumorigenesis promotion. Specific recognition of glycans by lectins is also the basis for a wide range of applications in areas including glycobiology research, cancer screening, and antiviral therapeutics. To provide a better understanding of the determinants of lectin-glycan interaction specificity and support such applications, this study...
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#1Ramzan Umarov (Hiroshima University)H-Index: 8
#2Yu Li (CUHK: The Chinese University of Hong Kong)H-Index: 19
Last. Erik Arner (Hiroshima University)H-Index: 3
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Drug treatment induces cell type specific transcriptional programs, and as the number of combinations of drugs and cell types grows, the cost for exhaustive screens measuring the transcriptional drug response becomes intractable. We developed DeepCellState, a deep learning autoencoder-based framework, for predicting the induced transcriptional state in a cell type after drug treatment, based on the drug response in another cell type. Training the method on a large collection of transcriptional d...
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#1Bikash K. Bhandari (University of Otago)H-Index: 3
#2Chun Shen Lim (University of Otago)H-Index: 6
Last. Paul P. Gardner (University of Otago)H-Index: 36
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Recombinant protein production is a key process in generating proteins of interest in the pharmaceutical industry and biomedical research. However, about 50% of recombinant proteins fail to be expressed in a variety of host cells. Here we show that the accessibility of translation initiation sites modelled using the mRNA base-unpairing across the Boltzmann’s ensemble significantly outperforms alternative features. This approach accurately predicts the successes or failures of expression experime...
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#1Junior Samuel Lopez-Yepez (AU: Aarhus University)
#2Juliane Martin (AU: Aarhus University)
Last. Duda Kvitsiani (AU: Aarhus University)H-Index: 5
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Choice history effects describe how future choices depend on the history of past choices. In experimental tasks this is typically framed as a bias because it often diminishes the experienced reward rates. However, in natural habitats, choices made in the past constrain choices that can be made in the future. For foraging animals, the probability of earning a reward in a given patch depends on the degree to which the animals have exploited the patch in the past. One problem with many experimental...
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#1Lorenzo Ferrucci (Sapienza University of Rome)H-Index: 3
#2Aldo Genovesio (Sapienza University of Rome)H-Index: 24
Last. Encarni Marcos (Universidad Miguel Hernández de Elche)H-Index: 11
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A standard view in the literature is that decisions are the result of a process that accumulates evidence in favor of each alternative until such accumulation reaches a threshold and a decision is made. However, this view has been recently questioned by an alternative proposal that suggests that, instead of accumulated, evidence is combined with an urgency signal. Both theories have been mathematically formalized and supported by a variety of decision-making tasks with constant information. Howe...
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