bluuebunny/crossref_metadata_2025_split huggingface dataset:
Functional Connectome Fingerprinting Using Shallow Feedforward Neural Networks
Authors: Sarar Gokce , Rao Bhaskar , Liu Thomas 
Published: October 2020

ABSTRACTAlthough individual subjects can be identified with high accuracy using correlation matrices computed from resting-state functional magnetic resonance imaging (rsfMRI) data, the performance significantly degrades as the scan duration is decreased. Recurrent neural networks can achieve high accuracy with short duration (72s) data segments but are designed to use temporal features not present in the correlation matrices. Here we show that shallow feedforward neural networks that rely solely on the information in rsfMRI correlation matrices can achieve state-of-the-art identification accuracies (≥ 99.5%) with data segments as short as 20s and across a range of input data-size combinations when the total number of data points (# regions × # time points) is on the order of 10,000.
Mice alternate between discrete strategies during perceptual decision-making
Authors: Ashwood Zoe C. , Roy Nicholas A. , Stone Iris R. ,   The International Brain Laboratory, Urai Anne E. , Churchland Anne K. , Pouget Alexandre , Pillow Jonathan W. 
Published: October 2020

AbstractClassical models of perceptual decision-making assume that subjects use a single, consistent strategy to form decisions, or that strategies evolve slowly over time. Here we present new analyses suggesting that this common view is incorrect. We analyzed data from mouse and human decision-making experiments and found that choice behavior relies on an interplay between multiple interleaved strategies. These strategies, characterized by states in a hidden Markov model, persist for tens to hundreds of trials before switching, and may alternate multiple times within a session. The identified mouse decision-making strategies were highly consistent across individuals and comprised a single “engaged” state, in which decisions relied heavily on the sensory stimulus, and several biased states in which errors frequently occurred. These results provide a powerful alternate explanation for “lapses” often observed in rodent psychophysical experiments, and suggest that standard measures of performance mask the presence of dramatic changes in strategy across trials.
Population-based prevalence surveys during the COVID-19 pandemic: a systematic review
Authors: Franceschi Vinícius Bonetti , Santos Andressa Schneiders , Glaeser Andressa Barreto , Paiz Janini Cristina , Caldana Gabriel Dickin , Machado Lessa Carem Luana , de Menezes Mayer Amanda , Küchle Julia Gonçalves , Gazzola Zen Paulo Ricardo , Vigo Alvaro , Winck Ana Trindade , Rotta Liane Nanci , Thompson Claudia Elizabeth 
Published: October 2020

AbstractPopulation-based prevalence surveys of COVID-19 contribute to establish the burden and epidemiology of infection, the role of asymptomatic and mild infections in transmission, and allow more precise decisions about reopen policies. We performed a systematic review to evaluate qualitative aspects of these studies, their reliability, and biases. The available data described 37 surveys from 19 countries, mostly from Europe and America and using antibody testing. They reached highly heterogeneous sample sizes and prevalence estimates. Disproportional prevalence was observed in minority communities. Important risk of bias was detected in four domains: sample size, data analysis with sufficient coverage, measurements in standard way, and response rate. The correspondence analysis showed few consistent patterns for high risk of bias. Intermediate risk of bias was related to American and European studies, blood samples and prevalence >1%. Low risk of bias was related to Asian studies, RT-PCR tests and prevalence <1%.One sentence summaryPopulation-based prevalence surveys of COVID-19 until September 2020 were mostly conducted in Europe and Americas, used antibody testing, and had important risks of bias.
Leveraging AutoML to provide NAFLD screening diagnosis: Proposed machine learning models
Authors: Bangash Ali Haider 
Published: October 2020

AbstractNAFLD is reported to be the only hepatic ailment increasing in its prevalence concurrently with both; obesity & T2DM. In the wake of a massive strain on global health resources due to COVID 19 pandemic, NAFLD is bound to be neglected & shelved. Abdominal ultrasonography is done for NAFLD screening diagnosis which has a high monetary cost associated with it. We utilized MLjar, an autoML web platform, to propose machine learning models that require no coding whatsoever & take in only easy-to-measure anthropometric measures for coming up with a screening diagnosis for NAFLD with considerably high AUC. Further studies are suggested to validate the generalization of the presented models.
From miRNA target gene network to miRNA function: miR-375 might regulate apoptosis and actin dynamics in the heart muscle via Rho-GTPases-dependent pathways
Authors: Osmak German , Kiselev Ivan , Baulina Natalia , Favorova Olga 
Published: October 2020

AbstractMicroRNAs (miRNAs) are short single-stranded non-coding RNA molecules, which are involved in regulation of main biological processes, such as apoptosis, cell proliferation and differentiation, through sequence-specific interaction with target mRNAs. In this study we propose a workflow for predicting miRNAs function by analyzing the structure of the network of their target genes. This workflow was applied to study the functional role of miR-375 in the heart muscle (myocardium), since this miRNA was previously shown to be associated with heart diseases and data on its function in myocardium are mostly unclear. We identifiedPIK3CA, RHOA, MAPK3, PAFAH1B1, CTNNB1, MYC, PRKCA, ERBB2, andCDC42as key genes in the miR-375 regulated network and predicted the possible function of miR-375 in the heart muscle, consisting mainly in the regulation of the Rho-GTPases-dependent signalling pathways.We implemented our algorithm for miRNA function prediction into Python module, which is available at GitHub (https://github.com/GJOsmak/miRNET)
Molecular forms ofAnopheles subpictus s.l.andAnopheles sundaicus s.l.in the Indian subcontinent
Authors: Sindhania Ankita , Das Manoj K. , Sharma Gunjan , Surendran Sinnathamby N. , Kaushal B.R. , Lohani Himanshu P. , Singh Om P. 
Published: October 2020

AbstractBackgroundAnopheles subpictus s.l.andAnopheles sundaicus s.l.are closely related species, each comprising of several sibling species. Ambiguities exist in the classification of these two nominal species and the specific status of members ofAn. subpictuscomplex. Identifying fixed molecular forms and mapping their spatial distribution will help in resolving the taxonomic ambiguities and understanding their relative epidemiological significance.MethodsDNA sequencing of Internal Transcribed Spacer-2 (ITS2), 28S-rDNA (D1-to-D3 domains) andcytochrome oxidase-IIof morphologically identified specimens of two nominal species,An. subpictus s.l.andAn. sundaicus s.l.collected from the Indian subcontinent, was performed and subjected to genetic distance and molecular phylogenetic analyses.ResultsMolecular characterization of mosquitoes for rDNA revealed the presence of two molecular forms ofAn. sundaicus s.l.(identified asAn. epiroticus s.s.andAn. sundaicusD) and three molecular forms ofAn. subpictus s.l.(provisionally designated as Form A, B and C) in the Indian subcontinent. Phylogenetic analyses revealed two distinct clades: (i) subpictus clade, with a single molecular form ofAn. subpictus(Form A) prevalent in mainland India and Sri Lanka, and (ii) sundaicus clade, comprising of members of Sundaicus Complex., two molecular forms ofAn. subpictus s.l., (Form B and C) prevalent in coastal areas or islands, and molecular forms reported from Thailand and Indonesia. Based on the number of float-ridges on eggs, allAn. subpictusmolecular Form B were classified as Species B whereas majority (80%) of the molecular Form A were classified as sibling species C. Fixed intragenomic sequence variation in ITS2 with the presence of two haplotypes was found in molecular Form A throughout its distribution.ConclusionA total of three molecular forms ofAn. subpictus s.l.and two molecular forms ofAn. sundaicus s.l.were recorded in the Indian subcontinent. Phylogenetically, two forms ofAn. subpictus s.l., (Form B and C) prevalent in coastal areas or islands in the Indian subcontinent and molecular forms reported from Southeast Asia are members of Sundaicus Complex. Molecular Form A ofAn. subpictusis distantly related to all other forms and deserve a distinct specific status. Presence ofAn. epiroticusin Indian territory is recorded for the first time.
Dual-view light-sheet imaging through tilted glass interface using a deformable mirror
Authors: Vladimirov N , Preusser F , Wisniewski J , Yaniv Z , Desai RA , Woehler A , Preibisch S 
Published: October 2020

AbstractLight-sheet microscopy has become one of the primary tools for imaging live developing organisms because of its high speed, low phototoxicity, and optical sectioning capabilities. Detection from multiple sides (multi-view imaging) additionally allows nearly isotropic resolution via computational merging of the views. However, conventional light-sheet microscopes require that the sample is suspended in a gel to allow optical access from two or more sides. At the same time, the use of microfluidic devices is highly desirable for many experiments, but geometric constrains and strong optical aberrations caused by the coverslip titled relative to objectives make the use of multi-view lightsheet challenging for microfluidics.In this paper we describe the use of adaptive optics (AO) to enable multi-view light-sheet microscopy in such microfluidic setup by correcting optical aberrations introduced by the tilted coverslip. The optimal shape of deformable mirror is computed by an iterative stochastic gradient-descent algorithm that optimizes PSF in two orthogonal planes simultaneously. Simultaneous AO correction in two optical arms is achieved via a knife-edge mirror that splits excitation path and combines the detection path.We characterize the performance of this novel microscope setup and, by dual-view light-sheet imaging ofC.elegansinside a microfluidic channel, demonstrate a drastic improvement of image quality due to AO and dual-view reconstruction. Our microscope design allows multi-view light-sheet microscopy with microfluidic devices for precisely controlled experimental conditions and high-content screening.
ESCO: single cell expression simulation incorporating gene co-expression
Authors: Tian Jinjin , Wang Jiebiao , Roeder Kathryn 
Published: October 2020

AbstractMotivationGene-gene co-expression networks (GCN) are of biological interest for the useful information they provide for understanding gene-gene interactions. The advent of single cell RNA-sequencing allows us to examine more subtle gene co-expression occurring within a cell type. Many imputation and denoising methods have been developed to deal with the technical challenges observed in single cell data; meanwhile, several simulators have been developed for benchmarking and assessing these methods. Most of these simulators, however, either do not incorporate gene co-expression or generate co-expression in an inconvenient manner.ResultsTherefore, with the focus on gene co-expression, we propose a new simulator, ESCO, which adopts the idea of the copula to impose gene co-expression, while preserving the highlights of available simulators, which perform well for simulation of gene expression marginally. Using ESCO, we assess the performance of imputation methods on GCN recovery and find that imputation generally helps GCN recovery when the data are not too sparse, and the ensemble imputation method works best among leading methods. In contrast, imputation fails to help in the presence of an excessive fraction of zero counts, where simple data aggregating methods are a better choice. These findings are further verified with mouse and human brain cell data.AvailabilityThe ESCO implementation is available as R packageSplatterESCO(https://github.com/JINJINT/SplatterESCO).Contactroeder@andrew.cmu.edu
Mutational meltdown of microbial altruists inStreptomyces coelicolorcolonies
Authors: Zhang Zheren , Shitut Shraddha , Claushuis Bart , Claessen Dennis , Rozen Daniel E. 
Published: October 2020

AbstractIn colonies of the filamentous multicellular bacteriumStreptomyces coelicolor, a sub-population of cells arise that hyper-produce metabolically costly antibiotics, resulting in division of labor that maximizes colony fitness. Because these cells contain large genomic deletions that cause massive reductions to individual fitness, their behavior is altruistic, much like worker castes in social insects or somatic cells in multicellular organisms. To understand the reproductive and genomic fate of these mutant cells after their emergence, we use experimental evolution by serially transferring populations via spore-to-spore transfer for 25 cycles, reflective of the natural mode of bottlenecked transmission for these spore-forming bacteria. We show that, in contrast to wild-type cells, altruistic mutant cells continue to significantly decline in fitness during transfer while they delete larger and larger fragments from their chromosome ends. In addition, altruistic mutants acquire a roughly 10-fold increase in their base-substitution rates possibly due to mutations in genes for DNA replication and repair. Ecological damage, caused by reduced sporulation, coupled with irreversible DNA damage due to point mutations and deletions, leads to an inevitable and irreversible type of mutational meltdown in these cells. Taken together, these results suggest that the altruistic cells arising in this division of labor are analogous to reproductively sterile castes of social insects.
Asymmetries around the visual field: From retina to cortex to behavior
Authors: Kupers Eline R. , Benson Noah C. , Carrasco Marisa , Winawer Jonathan 
Published: October 2020

AbstractVisual performance varies around the visual field. It is best near the fovea compared to the periphery, and at iso-eccentric locations it is best on the horizontal, intermediate on the lower, and poorest on the upper meridian. The fovea-to-periphery performance decline is linked to the decreases in cone density, retinal ganglion cell (RGC) density, and V1 cortical magnification factor (CMF) as eccentricity increases. The origins of polar angle asymmetries are not well understood. Optical quality and cone density vary across the retina, but recent computational modeling has shown that these factors can only account for a small percentage of behavior. Here, we investigate how visual processing beyond the cone photon absorptions contributes to polar angle asymmetries in performance. First, we quantify the extent of asymmetries in cone density, midget RGC density, and V1 CMF. We find that both polar angle asymmetries and eccentricity gradients increase from cones to mRGCs, and from mRGCs to cortex. Second, we extend our previously published computational observer model to quantify the contribution of phototransduction by the cones and spatial filtering by mRGCs to behavioral asymmetries. Starting with photons emitted by a visual display, the model simulates the effect of human optics, cone isomerizations, phototransduction, and mRGC spatial filtering. The model performs a forced choice orientation discrimination task on mRGC responses using a linear support vector machine classifier. The model shows that asymmetries in a decision-maker’s performance across polar angle are greater when assessing the photocurrents than when assessing isomerizations and are greater still when assessing mRGC signals. Nonetheless, the polar angle asymmetries of the mRGC outputs are still considerably smaller than those observed from human performance. We conclude that cone isomerizations, phototransduction and the spatial filtering properties of mRGCs contribute to polar angle performance differences, but that a full account of these differences will entail additional contribution from cortical representations.
Speech categorization is better described by induced rather than evoked neural activity
Authors: Mahmud Md Sultan , Yeasin Mohammed , Bidelman Gavin M. 
Published: October 2020

ABSTRACTCategorical perception (CP) describes how the human brain categorizes speech despite inherent acoustic variability. We examined neural correlates of CP in both evoked and induced EEG activity to evaluate which mode best describes the process of speech categorization. Using source reconstructed EEG, we used band-specific evoked and induced neural activity to build parameter optimized support vector machine (SVMs) model to assess how well listeners’ speech categorization could be decoded via whole-brain and hemisphere-specific responses. We found whole-brain evoked β-band activity decoded prototypical from ambiguous speech sounds with ~70% accuracy. However, induced γ-band oscillations showed better decoding of speech categories with ~95% accuracy compared to evoked β-band activity (~70% accuracy). Induced high frequency (γ-band) oscillations dominated CP decoding in the left hemisphere, whereas lower frequency (θ-band) dominated decoding in the right hemisphere. Moreover, feature selection identified 14 brain regions carrying induced activity and 22 regions of evoked activity that were most salient in describing category-level speech representations. Among the areas and neural regimes explored, we found that induced γ-band modulations were most strongly associated with listeners’ behavioral CP. Our data suggest that the category-level organization of speech is dominated by relatively high frequency induced brain rhythms.
Epistatic interactions shape the interplay between beneficial alleles and gain or loss of pathways in the evolution of novel metabolism
Authors: Bruger Eric L. , Chubiz Lon M. , Rojas Echenique José I. , Renshaw Caleb J. , Espericueta N. Victoria , Draghi Jeremy A. , Marx Christopher J. 
Published: October 2020

AbstractFitness landscapes are often invoked to interpret the effects of allele substitutions and their interactions; however, evolution also includes larger changes like gene loss and acquisition. Previous work with the methylotrophic bacteriumMethylorubrum extorquensAM1 identified strongly beneficial mutations in a strain evolved to utilize a novel,Foreignpathway in place of its native central metabolic pathway for growth on methanol. These mutations were consistently beneficial, regardless of the order in which they arose. Here we extend this analysis to consider loss or acquisition of metabolic pathways by examining strains relying upon either theNativepathway, or both (‘Dual’) pathways present. Unlike in theForeignpathway context in which they evolved, these alleles were often deleterious in these alternative genetic backgrounds, following patterns that were strongly contingent on the specific pathways and other evolved alleles present. Landscapes for these alternative pathway backgrounds altered which genotypes correspond to local fitness peaks and would restrict the set of accessible evolutionary trajectories. These epistatic interactions negatively impact the probability of maintaining multiple degenerate pathways, making it more difficult for these pathways to coevolve. Together, our results highlight the uncertainty of retaining novel functions acquired via horizontal gene transfer (HGT), and that the potential for cells to either adopt novel functions or to maintain degenerate pathways together in a genome is heavily dependent upon the underlying epistatic interactions between them.Author SummaryThe evolution of physiology in microbes has important impacts ranging from global cycling of elements to the emergence and spread of pathogens and their resistance to antibiotics. While genetic interactions between mutations in evolving lineages of microbes have been investigated, these have not included the acquisition of novel genes on elements like plasmids, and thus how these elements interact with existing alleles. The dynamics of novel gene retention are of interest from both positive (e.g., biotechnology) and negative (e.g., antimicrobial resistance) practical impacts. We find that the patterns of interactions between evolved alleles appear substantially different, and generally much less positive, when moved into novel genetic backgrounds. Additionally, these preexisting alleles were found to have strong impacts on the ability of genotypes to maintain – and in rare cases coevolve with – novel genes and pathways. These results show that even though they evolved separately, the particular alleles in a genetic background, and importantly the physiological impacts they confer, weigh heavily on whether genes for novel metabolic processes are maintained.
orfipy: a fast and flexible tool for extracting ORFs
Authors: Singh Urminder , Wurtele Eve Syrkin 
Published: October 2020

SummarySearching for ORFs in transcripts is a critical step prior to annotating coding regions in newly-sequenced genomes and to search for alternative reading frames within known genes. With the tremendous increase in RNA-Seq data, faster tools are needed to handle large input datasets. These tools should be versatile enough to fine-tune search criteria and allow efficient downstream analysis. Here we present a new python based tool,orfipy, which allows the user to flexibly search for open reading frames in fasta sequences. The search is rapid and is fully customizable, with a choice of Fasta and BED output formats.Availability and implementationorfipyis implemented in python and is compatible with python v3.6 and higher. Source code:https://github.com/urmi-21/orfipy. Installation: from the source, or via PyPi (https://pypi.org/project/orfipy) or bioconda (https://anaconda.org/bioconda/orfipy).Contactusingh@iastate.edu,mash@iastate.eduSupplementary informationSupplementary data are available athttps://github.com/urmi-21/orfipy
Direct visualization of epithelial microvilli biogenesis
Authors: Gaeta Isabella M. , Meenderink Leslie M. , Postema Meagan M. , Cencer Caroline S. , Tyska Matthew J. 
Published: October 2020

SUMMARYMicrovilli are actin bundle supported surface protrusions that play essential roles in diverse epithelial cell functions. To develop our understanding of microvilli biogenesis, we used live imaging to directly visualize protrusion growth at early stages of epithelial differentiation. Time-lapse data revealed that an “initiation complex” enriched in EPS8 and IRTKS appears at future sites of microvillus growth minutes before core actin bundle assembly. Elongation of a new core bundle occurs in parallel with the arrival of EZRIN and plasma membrane encapsulation. In addition tode novogrowth, we also observed that new microvilli emerge from pre-existing protrusions. Additionally, we found that new microvilli can also collapse, characterized first by loss of membrane wrapping and Ezrin enrichment, followed by a sharp decrease in distal tip EPS8 and IRTKS. These studies are the first to offer a temporally resolved microvillus growth mechanism and highlight critical factors that drive this process.