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Rxivist uses download data on preprints from bioRxiv to help you find the papers being discussed in your field. Currently indexing 101,433 bioRxiv papers from 428,488 authors.

Most tweeted bioRxiv papers, last 7 days

386 results found. For more information, click each entry to expand.

41: Alleloscope: Integrative single cell analysis of allele-specific copy number alterations and chromatin accessibility in cancer
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Posted to bioRxiv 25 Oct 2020

Alleloscope: Integrative single cell analysis of allele-specific copy number alterations and chromatin accessibility in cancer
5 tweets bioinformatics

Chi-Yun Wu, Billy T. Lau, Heonseok Kim, Anuja Sathe, Susan M Grimes, Hanlee P. Ji, Nancy R Zhang

Cancer progression is driven by both somatic copy number aberrations (CNAs) and chromatin remodeling, yet little is known about the interplay between these two classes of events in shaping the clonal diversity of cancers. We present Alleloscope, a method for allele-specific copy number estimation that can be applied to single cell DNA and ATAC sequencing data, either separately or in combination. This approach allows for integrative multi-omic analysis of allele-specific copy number and chromatin accessibility on the same cell. On scDNA-seq data from gastric, colorectal, and breast cancer samples, with extensive validation using matched linked-read sequencing, Alleloscope finds pervasive occurrence of highly complex, multi-allelic copy number aberrations, where cells that carry varying allelic configurations adding to the same total copy number co-evolve within a tumor. The contributions of such allele-specific events to intratumor heterogeneity have been under-reported and under-studied due to the lack of methods for their detection. On scATAC-seq from two basal cell carcinoma samples and a gastric cancer cell line, Alleloscope detects multi-allelic copy number events and copy neutral loss-of-heterozygosity, enabling the dissection of the contributions of chromosomal instability and chromatin remodeling in tumor evolution. ### Competing Interest Statement The authors have declared no competing interest.

42: Orbitofrontal cortex and learning predictions of state transitions
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Posted to bioRxiv 20 Sep 2020

Orbitofrontal cortex and learning predictions of state transitions
5 tweets neuroscience

Stephanie C.Y. Chan, Nicolas W. Schuck, Nina Lopatina, Geoffrey Schoenbaum, Yael Niv

Learning the transition structure of the environment – the probabilities of transitioning from one environmental state to another – is a key prerequisite for goal-directed planning and model-based decision making. To investigate the role of the orbitofrontal cortex (OFC) in goal-directed planning and decision making, we used fMRI to assess univariate and multivariate activity in the OFC while humans experienced state transitions that varied in degree of surprise. In convergence with recent evidence, we found that OFC activity was related to greater learning about transition structure, both across subjects and on a trial-by-trial basis. However, this relationship was inconsistent with a straightforward interpretation of OFC activity as representing a state prediction error that would facilitate learning of transitions via error-correcting mechanisms. The state prediction error hypothesis predicts that OFC activity at the time of observing an outcome should increase expectation of that observed outcome on subsequent trials. Instead, our results showed that OFC activity was associated with increased expectation of the more probable outcome; that is, with more optimal predictions. Our findings add to the evidence of OFC involvement in learning state-to-state transition structure, while providing new constraints for algorithmic hypotheses regarding how these transitions are learned. Significance Statement The orbitofrontal cortex (OFC) has been implicated in model-based decision making—the kind of decisions that result from planning using an “environment model” of how current actions affect our future states. However, the widely suggested role of the OFC in representing expected values of future states is not sufficient to explain why the OFC would be critical for planning in particular. A new line of evidence implicates the OFC in learning about transition structure of the environment – a key component of the “environment model” used for planning. We investigate this function, adding to the growing literature on the role of the OFC in learning and decision making, while unveiling new questions about the algorithmic role of OFC in goal-directed planning. ### Competing Interest Statement The authors have declared no competing interest.

43: The case for formal methodology in scientific reform
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Posted to bioRxiv 28 Apr 2020

The case for formal methodology in scientific reform
5 tweets scientific communication and education

Berna Devezer, Danielle J. Navarro, Joachim Vandekerckhove, Erkan Ozge Buzbas

Current attempts at methodological reform in sciences come in response to an overall lack of rigor in methodological and scientific practices in experimental sciences. However, some of these reform attempts suffer from the same mistakes and over-generalizations they purport to address. Considering the costs of allowing false claims to become canonized, we argue for more rigor and nuance in methodological reform. By way of example, we present a formal analysis of three common claims in the metascientific literature: (a) That reproducibility is the cornerstone of science; (b) That data must not be used twice in any analysis; and (c) That exploratory projects lead to bad statistical inference. We show that none of these three claims are correct in general and we explore when they do and do not hold. ### Competing Interest Statement The authors have declared no competing interest.

44: MOSTWAS: Multi-Omic Strategies for Transcriptome-Wide Association Studies
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Posted to bioRxiv 18 Apr 2020

MOSTWAS: Multi-Omic Strategies for Transcriptome-Wide Association Studies
5 tweets genetics

Arjun Bhattacharya, Yun Li, Michael I. Love

Traditional predictive models for transcriptome-wide association studies (TWAS) consider only single nucleotide polymorphisms (SNPs) local to genes of interest and perform parameter shrinkage with a regularization process. These approaches ignore the effect of distal-SNPs or other molecular effects underlying the SNP-gene association. Here, we outline multi-omics strategies for transcriptome imputation from germline genetics to allow more powerful testing of gene-trait associations by prioritizing distal-SNPs to the gene of interest. In one extension, we identify mediating biomarkers (CpG sites, microRNAs, and transcription factors) highly associated with gene expression and train predictive models for these mediators using their local SNPs. Imputed values for mediators are then incorporated into the final predictive model of gene expression, along with local SNPs. In the second extension, we assess distal-eQTLs (SNPs associated with genes not in a local window around it) for their mediation effect through mediating biomarkers local to these distal-eSNPs. Distal-eSNPs with large indirect mediation effects are then included in the transcriptomic prediction model with the local SNPs around the gene of interest. Using simulations and real data from ROS/MAP brain tissue and TCGA breast tumors, we show considerable gains of percent variance explained (1-2% additive increase) of gene expression and TWAS power to detect gene-trait associations. This integrative approach to transcriptome-wide imputation and association studies aids in identifying the complex interactions underlying genetic regulation within a tissue and important risk genes for various traits and disorders. ### Competing Interest Statement The authors have declared no competing interest.

45: Pyronaridine and artesunate are potential antiviral drugs against COVID-19 and influenza
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Posted to bioRxiv 28 Jul 2020

Pyronaridine and artesunate are potential antiviral drugs against COVID-19 and influenza
5 tweets microbiology

Joon-Yong Bae, Gee Eun Lee, Heedo Park, Juyoung Cho, Yung-Eui Kim, Joo-Yeon Lee, Chung Ju, Won-Ki Kim, Jin Il Kim, Man-Seong Park

Since the first human case was reported in Wuhan Province, China in December 2019, SARS-CoV-2 has caused millions of human infections in more than 200 countries worldwide with an approximately 4.01% case-fatality rate (as of 27 July, 2020; based on a WHO situation report), and COVID-19 pandemic has paralyzed our global community. Even though a few candidate drugs, such as remdesivir (a broad antiviral prodrug) and hydroxychloroquine, have been investigated in human clinical trials, their therapeutic efficacy needs to be clarified further to be used to treat COVID-19 patients. Here we show that pyronaridine and artesunate, which are the chemical components of anti-malarial drug Pyramax, exhibit antiviral activity against SARS-CoV-2 and influenza viruses. In human lung epithelial (Calu-3) cells, pyronaridine and artesunate were highly effective against SARS-CoV-2 while hydroxychloroquine did not show any effect at concentrations of less than 100 μM. In viral growth kinetics, both pyronaridine and artesunate inhibited the growth of SARS-CoV-2 and seasonal influenza A virus in Calu-3 cells. Taken together, we suggest that artesunate and pyronaridine might be effective drug candidates for use in human patients with COVID-19 and/or influenza, which may co-circulate during this coming winter season. ### Competing Interest Statement The authors have declared no competing interest.

46: Flexible working memory through selective gating and attentional tagging
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Posted to bioRxiv 18 Nov 2019

Flexible working memory through selective gating and attentional tagging
5 tweets neuroscience

Wouter Kruijne, Sander M. Bohte, Pieter R. Roelfsema, Christian N.L. Olivers

Working memory is essential for intelligent behavior as it serves to guide behavior of humans and nonhuman primates when task-relevant stimuli are no longer present to the senses. Moreover, complex tasks often require that multiple working memory representations can be flexibly and independently maintained, prioritized, and updated according to changing task demands. Thus far, neural network models of working memory have been unable to offer an integrative account of how such control mechanisms are implemented in the brain and how they can be acquired in a biologically plausible manner. Here, we present WorkMATe, a neural network architecture that models cognitive control over working memory content and learns the appropriate control operations needed to solve complex working memory tasks. Key components of the model include a gated memory circuit that is controlled by internal actions, encoding sensory information through untrained connections, and a neural circuit that matches sensory inputs to memory content. The network is trained by means of a biologically plausible reinforcement learning rule that relies on attentional feedback and reward prediction errors to guide synaptic updates. We demonstrate that the model successfully acquires policies to solve classical working memory tasks, such as delayed match-to-sample and delayed pro-saccade/antisaccade tasks. In addition, the model solves much more complex tasks including the hierarchical 12-AX task or the ABAB ordered recognition task, which both demand an agent to independently store and updated multiple items separately in memory. Furthermore, the control strategies that the model acquires for these tasks subsequently generalize to new task contexts with novel stimuli. As such, WorkMATe provides a new solution for the neural implementation of flexible memory control.

47: In vivo visualization of propagating α-synuclein pathologies in mouse and marmoset models by a bimodal imaging probe, C05-05
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Posted to bioRxiv 23 Oct 2020

In vivo visualization of propagating α-synuclein pathologies in mouse and marmoset models by a bimodal imaging probe, C05-05
5 tweets neuroscience

Maiko Ono, Manami Takahashi, Aki Shimozawa, Masayuki Fujinaga, Wakana Mori, Yuji Nagai, Koki Mimura, Takeharu Minamihisamatsu, Shoko Uchida, Masafumi Shimojo, Yuhei Takado, Hiroyuki Takuwa, Naruhiko Sahara, Ming-Rong Zhang, Takafumi Minamimoto, Masato Hasegawa, Makoto Higuchi

Deposition of intracellular α-synuclein fibrils is implicated in neurodegenerative parkinsonian disorders, while high-contrast in vivo detection of α-synuclein depositions has been unsuccessful in animal models and humans. Here, we have developed a bimodal imaging probe, C05-05, for visualizing α-synuclein inclusions in the brains of living animals modeling α-synuclein propagation. In vivo optical and PET imaging of a mouse model demonstrated sensitive detection of α-synuclein aggregates by C05-05, revealing a dynamic propagation of fibrillogenesis along neural pathways followed by disruptions of these structures. Moreover, longitudinal 18F-C05-05-PET of a marmoset model captured widespread dissemination of fibrillary pathologies accompanied by neurodegeneration detected by dopamine transporter PET. In addition, in vitro assays demonstrated the high-affinity binding of 18F-C05-05 to α-synuclein versus other protein pathologies in human brain tissues. Collectively, we propose a new imaging technology enabling etiological and therapeutic assessments of α-synuclein pathogenesis at nonclinical levels, highlighting the applicability of C05-05 to clinical PET. ### Competing Interest Statement The authors have declared no competing interest.

48: Chi.Bio: An open-source automated experimental platform for biological science research
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Posted to bioRxiv 07 Oct 2019

Chi.Bio: An open-source automated experimental platform for biological science research
5 tweets bioengineering

Harrison Steel, Robert Habgood, Ciarán Kelly, Antonis Papachristodoulou

The precise characterisation and manipulation of in vivo biological systems is critical to their study. However, in many experimental frameworks this is made challenging by non-static environments during cell growth, as well as variability introduced by manual sampling and measurement protocols. To address these challenges we present Chi.Bio, a parallelised open-source platform that offers a new experimental paradigm in which all measurement and control actions can be applied to a bulk culture in situ. In addition to continuous-culturing capabilities (turbidostat functionality, heating, stirring) it incorporates tunable light outputs of varying wavelengths and spectrometry. We demonstrate its application to studies of cell growth and biofilm formation, automated in silico control of optogenetic systems, and readout of multiple orthogonal fluorescent proteins. By combining capabilities from many laboratory tools into a single low-cost platform, Chi.Bio facilitates novel studies in synthetic, systems, and evolutionary biology, and broadens access to cutting-edge research capabilities.

49: Quantifying the contribution of Neanderthal introgression to the heritability of complex traits
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Posted to bioRxiv 08 Jun 2020

Quantifying the contribution of Neanderthal introgression to the heritability of complex traits
5 tweets evolutionary biology

Evonne McArthur, David C. Rinker, John A. Capra

Background: Nearly all Eurasians have ~2% Neanderthal ancestry due to several events of inbreeding between anatomically modern humans and archaic hominins. Previous studies characterizing the legacy of Neanderthal ancestry in modern Eurasians have identified examples of both adaptive and deleterious effects of admixture. However, we lack a comprehensive understanding of the genome-wide influence of Neanderthal introgression on modern human diseases and traits. Results: We integrate recent maps of Neanderthal ancestry with well-powered association studies for more than 400 diverse traits to estimate heritability enrichment patterns in regions of the human genome tolerant of Neanderthal ancestry and in introgressed Neanderthal variants themselves. First, we find that variants in regions tolerant of Neanderthal ancestry are depleted of heritability for all traits considered, except skin and hair-related traits. Second, the introgressed variants remaining in modern Europeans are depleted of heritability for most traits; however, we discover that they are enriched for heritability of several traits with potential relevance to human adaptation to non-African environments, including hair and skin traits, autoimmunity, chronotype, bone density, lung capacity, and menopause age. To better understand the phenotypic consequences of these enrichments, we adapt recent methods to test for consistent directional effects of introgressed alleles, and we find directionality for several traits. Finally, we use a direction-of-effect-aware approach to highlight novel candidate introgressed variants that influence risk for disease. Conclusion: Our results demonstrate that genomic regions retaining Neanderthal ancestry are not only less functional at the molecular-level, but are also depleted for variation influencing a diverse array of complex traits in modern humans. In spite of this depletion, we identify traits where introgression has an outsized effect. Integrating our results, we propose a framework for using quantification of trait heritability and direction of effect in introgressed regions to understand how Neanderthals were different from modern humans, how selection acted on different traits, and how introgression may have facilitated adaptation to non-African environments. ### Competing Interest Statement The authors have declared no competing interest.

50: The association between pain-induced autonomic reactivity and descending pain control is mediated by the periaqueductal grey
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Posted to bioRxiv 27 Oct 2020

The association between pain-induced autonomic reactivity and descending pain control is mediated by the periaqueductal grey
4 tweets neuroscience

Elena Makovac, Alessandra Venezia, David Hohenschurz-Schmidt, Ottavia Dipasquale, Jade B. Jackson, Sonia Medina, Owen O'Daly, Steve CR Williams, Stephen B McMahon, Matthew A. Howard

There is a strict interaction between the autonomic nervous system (ANS) and pain, which might involve descending pain modulatory mechanisms. The periaqueductal grey (PAG) is involved both in descending pain modulation and ANS, but its role in mediating this relationship has not yet been explored. Here, we sought to determine brain regions mediating ANS and descending pain control associations. 30 participants underwent Conditioned Pain Modulation (CPM) assessments, in which they rated painful pressure stimuli applied to their thumbnail, either alone or with a painful cold contralateral stimulation. Differences in pain ratings between 'pressure-only' and 'pressure+cold' stimuli provided a measure of descending pain control. In 18 of the 30 participants, structural scans and two functional MRI assessments, one pain-free and one during cold-pain, were acquired. Heart Rate Variability (HRV) was simultaneously recorded. Low frequency HRV (LF-HRV) and the CPM score were negatively correlated; individuals with higher LF-HRV during pain reported reductions in pain during CPM. PAG-frontal medial cortex (FMC) and PAG-rostral ventro-medial medulla (RVM) functional connectivity correlated negatively with the CPM. Importantly, PAG-FMC functional connectivity mediated the strength of HRV-CPM association. CPM response magnitude was also negatively associated with PAG and positively associated with FMC grey matter volumes. Our multi-modal approach, using behavioral, physiological and MRI measures, provides important new evidence of interactions between ANS and descending pain mechanisms. ANS dysregulation and dysfunctional descending pain modulation are characteristics of chronic pain. We suggest that further investigation of body-brain interactions in chronic pain patients may catalyse the development of new treatments. ### Competing Interest Statement The authors have declared no competing interest.

51: Three-dimensional residual channel attention networks denoise and sharpen fluorescence microscopy image volumes
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Posted to bioRxiv 28 Aug 2020

Three-dimensional residual channel attention networks denoise and sharpen fluorescence microscopy image volumes
4 tweets bioengineering

Jiji Chen, Hideki Sasaki, Hoyin Lai, Yijun Su, Jiamin Liu, Yicong Wu, Alexander Zhovmer, Christian A Combs, Ivan Rey-Suarez, Hungyu Chang, Chi Chou Huang, Xuesong Li, Min Guo, Srineil Nizambad, Arpita Upadhyaya, Luciano A.G. Lucas, Shih-Jong J Lee, Hari Shroff

We demonstrate residual channel attention networks (RCAN) for restoring and enhancing volumetric time-lapse (4D) fluorescence microscopy data. First, we modify RCAN to handle image volumes, showing that our network enables denoising competitive with three other state-of-the-art neural networks. We use RCAN to restore noisy 4D super-resolution data, enabling image capture over tens of thousands of images (thousands of volumes) without apparent photobleaching. Second, using simulations we show that RCAN enables class-leading resolution enhancement, superior to other networks. Third, we exploit RCAN for denoising and resolution improvement in confocal microscopy, enabling ~2.5-fold lateral resolution enhancement using stimulated emission depletion (STED) microscopy ground truth. Fourth, we develop methods to improve spatial resolution in structured illumination microscopy using expansion microscopy ground truth, achieving improvements of ~1.4-fold laterally and ~3.4-fold axially. Finally, we characterize the limits of denoising and resolution enhancement, suggesting practical benchmarks for evaluating and further enhancing network performance. ### Competing Interest Statement H.Sasaki, H.L., H.C., C.C.H., S-J J.L., L.A.G.L. are employees of DRVISION, LLC, a machine vision company. They have developed Aivia (a commercial software platform) that offers the 3D RCAN developed here.

52: Synonymous mutations and the molecular evolution of SARS-Cov-2 origins
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Posted to bioRxiv 21 Apr 2020

Synonymous mutations and the molecular evolution of SARS-Cov-2 origins
4 tweets evolutionary biology

Hongru Wang, Lenore Pipes, Rasmus Nielsen

Human severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is most closely related, by average genetic distance, to two coronaviruses isolated from bats, RaTG13 and RmYN02. However, there is a segment of high amino acid similarity between human SARS-CoV-2 and a pangolin isolated strain, GD410721, in the receptor binding domain (RBD) of the spike protein, a pattern that can be caused by either recombination or by convergent amino acid evolution driven by natural selection. We perform a detailed analysis of the synonymous divergence, which is less likely to be affected by selection than amino acid divergence, between human SARS-CoV-2 and related strains. We show that the synonymous divergence between the bat derived viruses and SARS-CoV-2 is larger than between GD410721 and SARS-CoV-2 in the RBD, providing strong additional support for the recombination hypothesis. However, the synonymous divergence between pangolin strain and SARS-CoV-2 is also relatively high, which is not consistent with a recent recombination between them, instead it suggests a recombination into RaTG13. We also find a 14-fold increase in the dN/dS ratio from the lineage leading to SARS-CoV-2 to the strains of the current pandemic, suggesting that the vast majority of non-synonymous mutations currently segregating within the human strains have a negative impact on viral fitness. Finally, we estimate that the time to the most recent common ancestor of SARS-CoV-2 and RaTG13 or RmYN02 based on synonymous divergence, is 51.71 years (95% C.I., 28.11-75.31) and 37.02 years (95% C.I., 18.19-55.85), respectively. ### Competing Interest Statement The authors have declared no competing interest.

53: HCR-FlowFISH: A flexible CRISPR screening method to identify cis-regulatory elements and their target genes
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Posted to bioRxiv 12 May 2020

HCR-FlowFISH: A flexible CRISPR screening method to identify cis-regulatory elements and their target genes
4 tweets genomics

SK Reilly, SJ Gosai, A Gutierrez, Jacob C. Ulirsch, Masahiro Kanai, D Berenzy, S Kales, GB Butler, A Gladden-Young, Hilary K. Finucane, Mohsan Saeed, R Tewhey

CRISPR screens for cis-regulatory elements (CREs) have shown unprecedented power to endogenously characterize the non-coding genome. To characterize CREs we developed HCR-FlowFISH (Hybridization Chain Reaction Fluorescent In-Situ Hybridization coupled with Flow Cytometry), which directly quantifies native transcripts within their endogenous loci following CRISPR perturbations of regulatory elements, eliminating the need for restrictive phenotypic assays such as growth or transcript-tagging. HCR-FlowFISH accurately quantifies gene expression across a wide range of transcript levels and cell types. We also developed CASA (CRISPR Activity Screen Analysis), a hierarchical Bayesian model to identify and quantify CRE activity. Using >270,000 perturbations, we identified CREs for GATA1, HDAC6, ERP29, LMO2, MEF2C, CD164, NMU, FEN1 and the FADS gene cluster. Our methods detect subtle gene expression changes and identify CREs regulating multiple genes, sometimes at different magnitudes and directions. We demonstrate the power of HCR-FlowFISH to parse genome-wide association signals by nominating causal variants and target genes. ### Competing Interest Statement PCS is a co-founder of and consultant to Sherlock Biosciences and Board Member of Danaher Corporation.

54: The Defensive Activation theory: dreaming as a mechanism to prevent takeover of the visual cortex
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Posted to bioRxiv 24 Jul 2020

The Defensive Activation theory: dreaming as a mechanism to prevent takeover of the visual cortex
4 tweets neuroscience

David M Eagleman, Don A Vaughn

Regions of the brain maintain their territory with continuous activity: if activity slows or stops (e.g., because of blindness), the territory tends to be taken over by its neighbors. A surprise in recent years has been the speed of takeover, which is measurable within an hour. These findings lead us to a new hypothesis on the origin of dream sleep. We hypothesize that the circuitry underlying dreaming serves to amplify the visual system's activity periodically throughout the night, allowing it to defend its territory against takeover from other senses. We find that measures of plasticity across 25 species of primates correlate positively with the proportion of rapid eye movement (REM) sleep. We further find that plasticity and REM sleep increase in lockstep with evolutionary recency to humans. Finally, our hypothesis is consistent with the decrease in REM sleep and parallel decrease in neuroplasticity with aging. ### Competing Interest Statement The authors have declared no competing interest.

55: Evaluation of Cell Type Annotation R Packages on Single Cell RNA-seq Data
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Posted to bioRxiv 01 Nov 2019

Evaluation of Cell Type Annotation R Packages on Single Cell RNA-seq Data
4 tweets bioinformatics

Qianhui Huang, Yu Liu, Yuheng Du, Lana X. Garmire

Annotating cell types is a critical step in single cell RNA-Seq (scRNA-Seq) data analysis. Some supervised/semi-supervised classification methods have recently emerged to enable automated cell type identification. However, comprehensive evaluations of these methods are lacking to provide practical guidelines. Moreover, it is not clear whether some classification methods originally designed for analyzing other bulk omics data are adaptable to scRNA-Seq analysis. In this study, we evaluated ten cell-type annotation methods publicly available as R packages. Eight of them are popular methods developed specifically for single cell research (Seurat, scmap, SingleR, CHETAH, SingleCellNet, scID, Garnett, SCINA). The other two methods are repurposed from deconvoluting DNA methylation data: Linear Constrained Projection (CP) and Robust Partial Correlations (RPC). We conducted systematic comparisons on a wide variety of public scRNA-seq datasets as well as simulation data. We assessed the accuracy through intra-dataset and inter-dataset predictions, the robustness over practical challenges such as gene filtering, high similarity among cell types, and increased classification labels, as well as the capabilities on rare and unknown cell-type detection. Overall, methods such as Seurat, SingleR, CP, RPC and SingleCellNet performed well, with Seurat being the best at annotating major cell types. Also, Seurat, SingleR, CP and RPC are more robust against down-sampling. However, Seurat does have a major drawback at predicting rare cell populations, and it is suboptimal at differentiating cell types that are highly similar to each other, while SingleR and RPC are much better in these aspects. All the codes and data are available at: [https://github.com/qianhuiSenn/scRNA\_cell\_deconv_benchmark][1]. [1]: https://github.com/qianhuiSenn/scRNA_cell_deconv_benchmark

56: On statistical tests of functional connectome fingerprinting
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Posted to bioRxiv 15 Oct 2018

On statistical tests of functional connectome fingerprinting
4 tweets neuroscience

Zeyi Wang, Haris Sair, Ciprian Crainiceanu, Martin Lindquist, Bennett A. Landman, Susan Resnick, Joshua T. Vogelstein, Brian Caffo

Fingerprinting of functional connectomes is an increasingly standard measure of reproducibility in functional magnetic resonance imaging connectomics. In such studies, one attempts to match a subject's first session image with their second, in a blinded fashion, in a group of subjects measured twice. The number or percentage of correct matches is usually reported as a statistic. In this manuscript, we investigate the statistical tests of matching based on exchangeability assumption in the fingerprinting analysis. We show that a nearly universal Poisson(1) approximation applies for different matching schemes. We theoretically investigate the permutation tests and explore the issue that the test is overly sensitive to uninteresting directions in the alternative hypothesis, such as clustering due to familial status or demographics. We perform a numerical study on two functional magnetic resonance imaging (fMRI) resting state datasets, the Human Connectome Project (HCP) and the Baltimore Longitudinal Study of Aging (BLSA). These datasets are instructive, as the HCP includes techinical replications of long scans and includes monozygotic and dyzogotic twins as well as non-twin siblings. In contrast, the BLSA study incorporates more typical length resting state scans in a longitudinal study. Finally, a study of single regional connections is performed on the HCP data.

57: Osmolarity-independent electrical cues guide rapid response to injury in zebrafish epidermis
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Posted to bioRxiv 05 Aug 2020

Osmolarity-independent electrical cues guide rapid response to injury in zebrafish epidermis
4 tweets cell biology

Andrew S. Kennard, Julie A. Theriot

The ability of epithelial tissues to heal after injury is essential for animal life, yet the mechanisms by which epithelial cells sense tissue damage are incompletely understood. In aquatic organisms such as zebrafish, osmotic shock following injury is believed to be an early and potent activator of a wound response. We find that, in addition to sensing osmolarity, basal skin cells in zebrafish larvae are also sensitive to changes in the particular ionic composition of their surroundings after wounding, specifically the concentration of sodium chloride in the immediate vicinity of the wound. This sodium chloride-specific wound detection mechanism is independent of cell swelling, and instead is suggestive of a mechanism by which cells sense changes in the transepithelial electrical potential generated by the transport of sodium and chloride ions across the skin. Consistent with this hypothesis, we show that electric fields directly applied within the skin are sufficient to initiate actin polarization and migration of basal cells in their native epithelial context in vivo, even overriding endogenous wound signaling. This suggests that, in order to mount a robust wound response, skin cells respond to both osmotic and electrical perturbations arising from tissue injury. ### Competing Interest Statement The authors have declared no competing interest.

58: Muscle strength, size and composition following 12 months of gender-affirming treatment in transgender individuals: retained advantage for the transwomen
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Posted to bioRxiv 26 Sep 2019

Muscle strength, size and composition following 12 months of gender-affirming treatment in transgender individuals: retained advantage for the transwomen
4 tweets physiology

A Wiik, TR Lundberg, E Rullman, DP Andersson, M Holmberg, M Mandić, TB Brismar, O Dahlqvist Leinhard, S Chanpen, J Flanagan, S Arver, T Gustafsson

Objectives: This study explored the effects of gender-affirming treatment, which includes inhibition of endogenous sex hormones and replacement with cross-sex hormones, on muscle function, size and composition in 11 transwomen (TW) and 12 transmen (TM). Methods: Isokinetic knee extensor and flexor muscle strength was assessed at baseline (T00), 4 weeks after gonadal suppression of endogenous hormones but before hormone replacement (T0), and 3 (T3) and 11 (T12) months after hormone replacement. In addition, at T00 and T12, we assessed lower-limb muscle volume using MRI, and cross-sectional area (CSA) and radiological density using CT. Results: Thigh muscle volume increased (15%) in TM, which was paralleled by increased quadriceps CSA (15%) and radiological density (6%). In TW, the corresponding parameters decreased by -5% (muscle volume) and -4% (CSA), while density remained unaltered. The TM increased strength over the assessment period, while the TW generally maintained or slightly increased in strength. Baseline muscle volume correlated highly with strength (R>0.75), yet the relative change in muscle volume and strength correlated only moderately (R=0.65 in TW and R=0.32 in TM). The absolute levels of muscle volume and knee extension strength after the intervention still favored the TW. Conclusion: Cross-sex hormone treatment markedly affects muscle strength, size and composition in transgender individuals. Despite the robust increases in muscle mass and strength in TM, the TW were still stronger and had more muscle mass following 12 months of treatment. These findings add new knowledge that could be relevant when evaluating transwomen's eligibility to compete in the women's category of athletic competitions.

59: The Clostridioides difficile species problem: global phylogenomic analysis uncovers three ancient, toxigenic, genomospecies
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Posted to bioRxiv 22 Sep 2020

The Clostridioides difficile species problem: global phylogenomic analysis uncovers three ancient, toxigenic, genomospecies
3 tweets microbiology

Daniel R. Knight, Korakrit Imwattana, Brian Kullin, Enzo Guerrero-Araya, Daniel Paredes-Sabja, Xavier Didelot, Kate E. Dingle, David W. Eyre, César Rodríguez, Thomas V. Riley

Clostridioides difficile infection (CDI) remains an urgent global One Health threat. The genetic heterogeneity seen across C. difficile underscores its wide ecological versatility and has driven the significant changes in CDI epidemiology seen in the last 20 years. We analysed an international collection of over 12,000 C. difficile genomes spanning the eight currently defined phylogenetic clades. Through whole-genome average nucleotide identity, pangenomic and Bayesian analyses, we identified major taxonomic incoherence with clear species boundaries for each of the recently described cryptic clades CI-III. The emergence of these three novel genomospecies predates clades C1-5 by millions of years, rewriting the global population structure of C. difficile specifically and taxonomy of the Peptostreptococcaceae in general. These genomospecies all show unique and highly divergent toxin gene architecture, advancing our understanding of the evolution of C. difficile and close relatives. Beyond the taxonomic ramifications, this work impacts the diagnosis of CDI worldwide. ### Competing Interest Statement DWE declares lecture fees from Gilead, outside the submitted work. No other author has a conflict of interest to declare.

60: Cross-reactive serum and memory B cell responses to spike protein in SARS-CoV-2 and endemic coronavirus infection
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Posted to bioRxiv 23 Sep 2020

Cross-reactive serum and memory B cell responses to spike protein in SARS-CoV-2 and endemic coronavirus infection
3 tweets immunology

Ge Song, Wan-ting He, Sean Callaghan, Fabio Anzanello, Deli Huang, James Ricketts, Jonathan L. Torres, Nathan Beutler, Linghang Peng, Sirena Vargas, Jon Cassell, Mara Parren, Linlin Yang, Caroline Ignacio, Davey M. Smith, James E. Voss, David Nemazee, Andrew B Ward, Thomas Rogers, Dennis R. Burton, Raiees Andrabi

Pre-existing immune responses to seasonal endemic coronaviruses could have profound consequences for antibody responses to SARS-CoV-2, either induced in natural infection or through vaccination. Such consequences are well established in the influenza and flavivirus fields. A first step to establish whether pre-existing responses can impact SARS-CoV-2 infection is to understand the nature and extent of cross-reactivity in humans to coronaviruses. We compared serum antibody and memory B cell responses to coronavirus spike (S) proteins from pre-pandemic and SARS-CoV-2 convalescent donors using a series of binding and functional assays. We found weak evidence of pre-existing SARS-CoV-2 cross-reactive serum antibodies in pre-pandemic donors. However, we found stronger evidence of pre-existing cross-reactive memory B cells that were activated on SARS-CoV-2 infection. Monoclonal antibodies (mAbs) isolated from the donors showed varying degrees of cross-reactivity with betacoronaviruses, including SARS and endemic coronaviruses. None of the cross-reactive mAbs were neutralizing except for one that targeted the S2 subunit of the S protein. The results suggest that pre-existing immunity to endemic coronaviruses should be considered in evaluating antibody responses to SARS-CoV-2. ### Competing Interest Statement R.A., G.S., W.H., T.F.R., and D.R.B. are listed as inventors on pending patent applications describing the SARS-CoV-2 and HCoV-HKU1 cross-reactive antibodies. D.R.B. is a consultant for IAVI. All other authors have no competing interests to declare.

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