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Rxivist combines preprints from bioRxiv with data from Twitter to help you find the papers being discussed in your field. Currently indexing 57,309 bioRxiv papers from 263,909 authors.

Most downloaded bioRxiv papers, since beginning of last month

55,912 results found. For more information, click each entry to expand.

81: Microtubules promote intercellular contractile force transmission during tissue folding
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Posted to bioRxiv 04 Feb 2019

Microtubules promote intercellular contractile force transmission during tissue folding
874 downloads developmental biology

Clint Shijun Ko, Vardges Tserunyan, Adam C Martin

During development, forces transmitted between cells are critical for sculpting epithelial tissues. Actomyosin contractility in the middle of the cell apex (medioapical) can change cell shape (e.g., apical constriction), but can also result in force transmission between cells via attachments to adherens junctions. How actomyosin networks maintain attachments to adherens junctions under tension is poorly understood. Here, we discovered that microtubules promote actomyosin intercellular attachments in epithelia during Drosophila mesoderm invagination. First, we used live imaging to show a novel arrangement of the microtubule cytoskeleton during apical constriction: medioapical Patronin (CAMSAP) foci formed by actomyosin contraction organized an apical non-centrosomal microtubule network. Microtubules were required for mesoderm invagination but were not necessary for initiating apical contractility or adherens junction assembly. Instead, microtubules promoted connections between medioapical actomyosin and adherens junctions. These results delineate a role for coordination between actin and microtubule cytoskeletal systems in intercellular force transmission during tissue morphogenesis.

82: Genome-wide rare variant analysis for thousands of phenotypes in 54,000 exomes
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Posted to bioRxiv 04 Jul 2019

Genome-wide rare variant analysis for thousands of phenotypes in 54,000 exomes
872 downloads genetics

Elizabeth T. Cirulli, Simon White, Robert W Read, Gai Elhanan, William J Metcalf, Karen A Schlauch, Joseph J Grzymski, James Lu, Nicole L Washington

Defining the effects that rare variants can have on human phenotypes is essential to advancing our understanding of human health and disease. Large-scale human genetic analyses have thus far focused on common variants, but the development of large cohorts of deeply phenotyped individuals with exome sequence data has now made comprehensive analyses of rare variants possible. We analyzed the effects of rare (MAF<0.1%) variants on 3,166 phenotypes in 40,468 exome-sequenced individuals from the UK Biobank and performed replication as well as meta-analyses with 1,067 phenotypes in 13,470 members of the Healthy Nevada Project (HNP) cohort who underwent Exome+ sequencing at Helix. Our analyses of non-benign coding and loss of function (LoF) variants identified 78 gene-based associations that passed our statistical significance threshold (p<5x10-9). These are associations in which carrying any rare coding or LoF variant in the gene is associated with an enrichment for a specific phenotype, as opposed to GWAS-based associations of strictly single variants. Importantly, our results do not suffer from the test statistic inflation that is often seen with rare variant analyses of biobank-scale data because of our rare variant-tailored methodology, which includes a step that optimizes the carrier frequency threshold for each phenotype based on prevalence. Of the 47 discovery associations whose phenotypes were represented in the replication cohort, 98% showed effects in the expected direction, and 45% attained formal replication significance (p<0.001). Six additional significant associations were identified in our meta-analysis of both cohorts. Among the results, we confirm known associations of PCSK9 and APOB variation with LDL levels; we extend knowledge of variation in the TYRP1 gene, previously associated with blonde hair color only in Solomon Islanders to blonde hair color in individuals of European ancestry; we show that PAPPA, a gene in which common variants had previously associated with height via GWAS, contains rare variants that decrease height; and we make the novel discovery that STAB1 variation is associated with blood flow in the brain. Our results are available for download and interactive browsing in an app (https://ukb.research.helix.com). This comprehensive analysis of the effects of rare variants on human phenotypes marks one of the first steps in the next big phase of human genetics, where large, deeply phenotyped cohorts with next generation sequence data will elucidate the effects of rare variants.

83: On the discovery of population-specific state transitions from multi-sample multi-condition single-cell RNA sequencing data
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Posted to bioRxiv 26 Jul 2019

On the discovery of population-specific state transitions from multi-sample multi-condition single-cell RNA sequencing data
870 downloads bioinformatics

Helena L Crowell, Charlotte Soneson, Pierre-Luc Germain, Daniela Calini, Ludovic Collin, Catarina Raposo, Dheeraj Malhotra, Mark D Robinson

Single-cell RNA sequencing (scRNA-seq) has quickly become an empowering technology to profile the transcriptomes of individual cells on a large scale. Many early analyses of differential expression have aimed at identifying differences between subpopulations, and thus are focused on finding markers for cell populations either in a single sample or across multiple samples. More generally, such methods can compare expression levels in multiple sets of cells, thus leading to cross-condition analyses. However, given the emergence of replicated multi-condition scRNA-seq datasets, an area of increasing focus is making sample-level inferences, termed here as differential state analysis. For example, one could investigate the condition-specific responses of cell populations measured from patients from each condition; however, it is not clear which statistical framework best handles this situation. In this work, we surveyed the methods available to perform cross-condition differential state analyses, including cell-level mixed models and methods based on aggregated pseudobulk data. We developed a flexible simulation platform that mimics both single and multi-sample scRNA-seq data and provide robust tools for multi-condition analysis within the muscat R package.

84: Single-cell genomic atlas of great ape cerebral organoids uncovers human-specific features of brain development
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Posted to bioRxiv 27 Jun 2019

Single-cell genomic atlas of great ape cerebral organoids uncovers human-specific features of brain development
869 downloads developmental biology

Sabina Kanton, Michael James Boyle, Zhisong He, Malgorzata Santel, Anne Weigert, Fatima Sanchis Calleja, Leila Sidow, Jonas Fleck, Patricia Guijarro, Dingding Han, Zhengzong Qian, Michael Heide, Wieland Huttner, Philipp Khaitovich, Svante Pääbo, Barbara Treutlein, J. Gray Camp

The human brain has changed dramatically since humans diverged from our closest living relatives, chimpanzees and the other great apes. However, the genetic and developmental programs underlying this divergence are not fully understood. Here, we have analyzed stem cell-derived cerebral organoids using single-cell transcriptomics (scRNA-seq) and accessible chromatin profiling (scATAC-seq) to explore gene regulatory changes that are specific to humans. We first analyze cell composition and reconstruct differentiation trajectories over the entire course of human cerebral organoid development from pluripotency, through neuroectoderm and neuroepithelial stages, followed by divergence into neuronal fates within the dorsal and ventral forebrain, midbrain and hindbrain regions. We find that brain region composition varies in organoids from different iPSC lines, yet regional gene expression patterns are largely reproducible across individuals. We then analyze chimpanzee and macaque cerebral organoids and find that human neuronal development proceeds at a delayed pace relative to the other two primates. Through pseudotemporal alignment of differentiation paths, we identify human-specific gene expression resolved to distinct cell states along progenitor to neuron lineages in the cortex. We find that chromatin accessibility is dynamic during cortex development, and identify instances of accessibility divergence between human and chimpanzee that correlate with human-specific gene expression and genetic change. Finally, we map human-specific expression in adult prefrontal cortex using single-nucleus RNA-seq and find developmental differences that persist into adulthood, as well as cell state-specific changes that occur exclusively in the adult brain. Our data provide a temporal cell atlas of great ape forebrain development, and illuminate dynamic gene regulatory features that are unique to humans.

85: Why we publish where we do: Faculty publishing values and their relationship to review, promotion and tenure expectations
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Posted to bioRxiv 21 Jul 2019

Why we publish where we do: Faculty publishing values and their relationship to review, promotion and tenure expectations
867 downloads scientific communication and education

Meredith T Niles, Lesley A Schimanski, Erin C. McKiernan, Juan Pablo Alperin

Using an online survey of academics at 55 randomly selected institutions across the US and Canada, we explore priorities for publishing decisions and their perceived importance within review, promotion, and tenure (RPT). We find that respondents most value journal readership, while they believe their peers most value prestige and related metrics such as impact factor when submitting their work for publication. Respondents indicated that total number of publications, number of publications per year, and journal name recognition were the most valued factors in RPT. Older and tenured respondents (most likely to serve on RPT committees) were less likely to value journal prestige and metrics for publishing, while untenured respondents were more likely to value these factors. These results suggest disconnects between what academics value versus what they think their peers value, and between the importance of journal prestige and metrics for tenured versus untenured faculty in publishing and RPT perceptions.

86: m6A-binding YTHDF proteins promote stress granule formation by modulating phase separation of stress granule proteins
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Posted to bioRxiv 07 Jul 2019

m6A-binding YTHDF proteins promote stress granule formation by modulating phase separation of stress granule proteins
863 downloads biochemistry

Ye Fu, Xiaowei Zhuang

Diverse RNAs and RNA-binding proteins form phase-separated, membraneless granules in cells under stress conditions. However, the role of the prevalent mRNA methylation, m6A, and its binding proteins in stress granule (SG) assembly remain unclear. Here, we show that m6A-modified mRNAs are enriched in SGs, and that m6A-binding YTHDF proteins are critical for SG formation. Depletion of YTHDF1/3 inhibits SG formation and recruitment of m6A-modified mRNAs to SGs. Both the N-terminal intrinsically disordered region and the C-terminal m6A-binding YTH domain of YTHDF proteins are crucial for SG formation. Super-resolution imaging further reveals that YTHDF proteins are in a super-saturated state, forming clusters that reside in the periphery of and at the junctions between SG core clusters, and promote SG phase separation by reducing the activation energy barrier and critical size for condensate formation. Our results reveal a new function and mechanistic insights of the m6A-binding YTHDF proteins in regulating phase separation.

87: Structures of virus-like capsids formed by the drosophila neuronal Arc proteins
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Posted to bioRxiv 10 Jul 2019

Structures of virus-like capsids formed by the drosophila neuronal Arc proteins
862 downloads neuroscience

Simon Erlendsson, Dustin R Morado, Jason R Shepherd, John A. G. Briggs

The neuronal protein Arc is a critical mediator of synaptic plasticity. Arc originated in tetrapods and flies through domestication of retrotransposon Gag genes. Recent studies have suggested that Arc mediates intercellular mRNA transfer, and, like Gag, can form capsid-like structures. Here we report that drosophila proteins dArc1 and dArc2 assemble virus-like capsids. We determine the capsid structures to 2.8 Å and 3.7 Å resolution, respectively, finding similarity to capsids of retroviruses and retrotransposons. Differences between dArc1 and dArc2 capsids, including the presence of a structured zinc-finger pair in dArc1, are consistent with differential RNA binding specificity. Our data support a model in which ancestral capsid-forming and RNA-binding properties of Arc remain under positive selection pressure and have been repurposed to function in neuronal signalling.

88: Innovations in Primate Interneuron Repertoire
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Posted to bioRxiv 23 Jul 2019

Innovations in Primate Interneuron Repertoire
862 downloads neuroscience

Fenna M Krienen, Melissa Goldman, Qiangge Zhang, Ricardo del Rosario, Marta Florio, Robert Machold, Arpiar Saunders, Kirsten Levandowski, Heather Zaniewski, Benjamin Schuman, Carolyn Wu, Alyssa Lutservitz, Christopher D Mullally, Nora Reed, Elizabeth Bien, Laura Bortolin, Marian Fernandez-Otero, Jessica Lin, Alec Wysoker, James Nemesh, David Kulp, Monika Burns, Victor Tkachev, Richard Smith, Chistopher A. Walsh, Jordane Dimidschstein, Bernardo Rudy, Leslie Kean, Sabina Berretta, Gordon Fishell, Guoping Feng, Steven A McCarroll

Primates and rodents, which descended from a common ancestor more than 90 million years ago, exhibit profound differences in behavior and cognitive capacity. Modifications, specializations, and innovations to brain cell types may have occurred along each lineage. We used Drop-seq to profile RNA expression in more than 184,000 individual telencephalic interneurons from humans, macaques, marmosets, and mice. Conserved interneuron types varied significantly in abundance and RNA expression between mice and primates, but varied much more modestly among primates. In adult primates, the expression patterns of dozens of genes exhibited spatial expression gradients among neocortical interneurons, suggesting that adult neocortical interneurons are imprinted by their local cortical context. In addition, we found that an interneuron type previously associated with the mouse hippocampus--the "ivy cell", which has neurogliaform characteristics--has become abundant across the neocortex of humans, macaques, and marmosets. The most striking innovation was subcortical: we identified an abundant striatal interneuron type in primates that had no molecularly homologous cell population in mouse striatum, cortex, thalamus, or hippocampus. These interneurons, which expressed a unique combination of transcription factors, receptors, and neuropeptides, including the neuropeptide TAC3, constituted almost 30% of striatal interneurons in marmosets and humans. Understanding how gene and cell-type attributes changed or persisted over the evolutionary divergence of primates and rodents will guide the choice of models for human brain disorders and mutations and help to identify the cellular substrates of expanded cognition in humans and other primates.

89: An N-terminal motif in NLR immune receptors is functionally conserved across distantly related plant species
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Posted to bioRxiv 04 Jul 2019

An N-terminal motif in NLR immune receptors is functionally conserved across distantly related plant species
861 downloads plant biology

Hiroaki Adachi, Mauricio Contreras, Adeline Harant, Chih-Hang Wu, Lida Derevnina, Toshiyuki Sakai, Cian Duggan, Eleonora Moratto, Tolga Osman Bozkurt, Abbas Maqbool, Joe Win, Sophien Kamoun

The molecular codes underpinning the functions of plant NLR immune receptors are poorly understood. We used in vitro Mu transposition to generate a random truncation library and identify the minimal functional region of NLRs. We applied this method to NRC4, a helper NLR that functions with multiple sensor NLRs within a Solanaceae receptor network. This revealed that the NRC4 N-terminal 29 amino acids are sufficient to induce hypersensitive cell death. This region is defined by the consensus MADAxVSFxVxKLxxLLxxEx (MADA motif) that is conserved at the N-termini of NRC family proteins and ~20% of coiled-coil (CC)-type plant NLRs. The MADA motif matches the N-terminal α1 helix of Arabidopsis NLR protein ZAR1, which undergoes a conformational switch during resistosome activation. Immunoassays revealed that the MADA motif is functionally conserved across NLRs from distantly related plant species. NRC-dependent sensor NLRs lack MADA sequences indicating that this motif has degenerated in sensor NLRs over evolutionary time.

90: The Spatio-Temporal Control of Zygotic Genome Activation
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Posted to bioRxiv 06 Dec 2018

The Spatio-Temporal Control of Zygotic Genome Activation
855 downloads developmental biology

George Gentsch, Nick D L Owens, James C Smith

One of the earliest and most significant events in embryonic development is zygotic genome activation (ZGA). In several species, bulk transcription begins at the mid-blastula transition (MBT) when, after a certain number of cleavages, the embryo attains a particular nuclear-to-cytoplasmic (N/C) ratio, maternal repressors become sufficiently diluted, and the cell cycle slows down. Here we resolve the frog ZGA in time and space by profiling RNA polymerase II (RNAPII) engagement and its transcriptional readout. We detect a gradual increase in both the quantity and the length of RNAPII elongation before the MBT, revealing that >1,000 zygotic genes disregard the N/C timer for their activation, and that the sizes of newly transcribed genes are not necessarily constrained by cell cycle duration. We also find that Wnt, Nodal and BMP signaling together generate most of the spatio-temporal dynamics of regional ZGA, directing the formation of orthogonal body axes and proportionate germ layers.

91: Effects and Feasibility of Hyperthermic Baths for Patients with Depressive Disorder: A Randomized Controlled Clinical Pilot Trial
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Posted to bioRxiv 12 Sep 2018

Effects and Feasibility of Hyperthermic Baths for Patients with Depressive Disorder: A Randomized Controlled Clinical Pilot Trial
836 downloads clinical trials

Johannes Naumann, Catharina Sadaghiani, Iris Kruza, Luisa Denkel, Gunver Kienle, Roman Huber

Background: Evaluation of efficacy, safety and feasibility of hyperthermic baths (HTB; head-out-of-water-immersion in 40°C), twice a week, compared to a physical exercise program (PEP; moderate intensity aerobic exercises) in moderate to severe depression. Method: Single-site, open-label randomized controlled 8-week parallel-group pilot study at an university outpatient clinic as part of usual depression care. Medically stable outpatients with depressive disorder (ICD-10: F32/F33) as determined by the 17-item Hamilton Depression Rating Scale (HAM-D) score ≥18 and a score ≥2 on item 1 (Depressed Mood) were randomly assigned to receive either two sessions of HTB or PEP per week (40-45 min) provided by two trained doctoral students. An independent biometric center used computer-generated tables to allocate treatments. Primary outcome measure was the change in HAM-D total score from baseline (T0) to the 2-week time point (T1). Linear regression analyses, adjusted for baseline values, were performed to estimate intervention effects on an intention-to-treat (ITT) principle. Findings: 45 patients (HTB n = 22; PEP n = 23) were randomized and analyzed according to ITT (mean age = 48.4 years, SD = 11.3, mean HAM-D score = 21.7, SD = 3.2). Baseline-adjusted mean difference was 4.3 points in the HAM-D score in favor of HTB (p<0.001). This improvement was achieved after two weeks. Compliance with the intervention and follow-up was far better in the HTB group (2 vs 13 dropouts). There were no treatment-related serious adverse events. Main limitation: the number of dropouts in the PEP group (13 of 23) was far higher than in other trials investigating exercise in depression (18.1 % dropouts). Conclusions: HTB seems to be a fast-acting, safe and easy accessible method leading to clinically relevant improvement in depressive disorder after two weeks; it is also suitable for persons who have problems performing exercise training. Clinical Trial registration ID #DRKS00011013.

92: Altering the temporal regulation of one transcription factor drives sensory trade-offs
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Posted to bioRxiv 15 Jun 2018

Altering the temporal regulation of one transcription factor drives sensory trade-offs
833 downloads developmental biology

Ariane Ramaekers, Simon Weinberger, Annelies Claeys, Martin Kapun, Jiekun Yan, Reinhard Wolf, Thomas Flatt, Erich Buchner, Bassem A Hassan

Size trade-offs of visual versus olfactory organs is a pervasive feature of animal evolution. Comparing Drosophila species, we find that larger eyes correlate with smaller antennae, where olfactory organs reside, and narrower faces. We demonstrate that this trade-off arises through differential subdivision of the head primordium into visual versus non-visual fields. Specification of the visual field requires a highly-conserved eye development gene called eyeless in flies and Pax6 in humans. We discover that changes in the temporal regulation of eyeless expression during development is a conserved mechanism for sensory trade-offs within and between Drosophila species. We identify a natural single nucleotide polymorphism in the cis-regulatory region of eyeless that is sufficient to alter its temporal regulation and eye size. Because Pax6 is a conserved regulator of sensory placode subdivision, we propose that alterations in the mutual repression between sensory territories is a conserved mechanism for sensory trade-offs in animals.

93: Highly-accurate long-read sequencing improves variant detection and assembly of a human genome
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Posted to bioRxiv 13 Jan 2019

Highly-accurate long-read sequencing improves variant detection and assembly of a human genome
822 downloads genomics

Aaron M Wenger, Paul Peluso, William J Rowell, Pi-Chuan Chang, Richard Hall, Gregory T. Concepcion, Jana Ebler, Arkarachai Fungtammasan, Alexey Kolesnikov, Nathan D Olson, Armin Toepfer, Michael Alonge, Medhat Mahmoud, Yufeng Qian, Chen-Shan Chin, Adam M Phillippy, Michael C. Schatz, Gene Myers, Mark A. DePristo, Jue Ruan, Tobias Marschall, Fritz J. Sedlazeck, Justin M Zook, Heng Li, Sergey Koren, Andrew Carroll, David R Rank, Michael W Hunkapiller

The major DNA sequencing technologies in use today produce either highly-accurate short reads or noisy long reads. We developed a protocol based on single-molecule, circular consensus sequencing (CCS) to generate highly-accurate (99.8%) long reads averaging 13.5 kb and applied it to sequence the well-characterized human HG002/NA24385. We optimized existing tools to comprehensively detect variants, achieving precision and recall above 99.91% for SNVs, 95.98% for indels, and 95.99% for structural variants. We estimate that 2,434 discordances are correctable mistakes in the high-quality Genome in a Bottle benchmark. Nearly all (99.64%) variants are phased into haplotypes, which further improves variant detection. De novo assembly produces a highly contiguous and accurate genome with contig N50 above 15 Mb and concordance of 99.998%. CCS reads match short reads for small variant detection, while enabling structural variant detection and de novo assembly at similar contiguity and markedly higher concordance than noisy long reads.

94: Evaluation of UMAP as an alternative to t-SNE for single-cell data
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Posted to bioRxiv 10 Apr 2018

Evaluation of UMAP as an alternative to t-SNE for single-cell data
818 downloads bioinformatics

Etienne Becht, Charles-Antoine Dutertre, Immanuel W. H. Kwok, Lai Guan Ng, Florent Ginhoux, Evan W Newell

Uniform Manifold Approximation and Projection (UMAP) is a recently-published non-linear dimensionality reduction technique. Another such algorithm, t-SNE, has been the default method for such task in the past years. Herein we comment on the usefulness of UMAP high-dimensional cytometry and single-cell RNA sequencing, notably highlighting faster runtime and consistency, meaningful organization of cell clusters and preservation of continuums in UMAP compared to t-SNE.

95: An association between sexes of successive siblings in the data from Demographic and Health Survey program
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Posted to bioRxiv 12 Nov 2015

An association between sexes of successive siblings in the data from Demographic and Health Survey program
806 downloads physiology

Mikhail Monakhov

The prediction of future child's sex is a question of keen public interest. The probability of having a child of either sex is close to 50%, although multiple factors may slightly change this value. Some demographic studies suggested that sex determination can be influenced by previous pregnancies, although this hypothesis was not commonly accepted. This paper explores the correlations between siblings' sexes using data from the Demographic and Health Survey program. In the sample of about 2,214,601 women (7,985,855 children), the frequencies of sibships with multiple siblings of the same sex were significantly higher than can be expected by chance. A formal modelling demonstrated that sexes of the children were dependent on three kinds of sex ratio variation: a variation between families (Lexian), a variation within a family (Poisson) and a variation contingent upon the sex of preceding sibling (Markovian). There was a positive correlation between the sexes of successive siblings (coefficient = 0.067, p < 0.001), i.e. a child was more likely to be of the same sex as its preceding sibling. This correlation could be caused by secondary sex ratio adjustment in utero since the effect was decreasing with the length of birth-to-birth interval, and the birth-to-birth interval was longer for siblings with unlike sex.

96: End-to-end differentiable learning of protein structure
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Posted to bioRxiv 14 Feb 2018

End-to-end differentiable learning of protein structure
803 downloads bioinformatics

Mohammed AlQuraishi

Accurate prediction of protein structure is one of the central challenges of biochemistry. Despite significant progress made by co-evolution methods to predict protein structure from signatures of residue-residue coupling found in the evolutionary record, a direct and explicit mapping between protein sequence and structure remains elusive, with no substantial recent progress. Meanwhile, rapid developments in deep learning, which have found remarkable success in computer vision, natural language processing, and quantum chemistry raise the question of whether a deep learning based approach to protein structure could yield similar advancements. A key ingredient of the success of deep learning is the reformulation of complex, human-designed, multi-stage pipelines with differentiable models that can be jointly optimized end-to-end. We report the development of such a model, which reformulates the entire structure prediction pipeline using differentiable primitives. Achieving this required combining four technical ideas: (1) the adoption of a recurrent neural architecture to encode the internal representation of protein sequence, (2) the parameterization of (local) protein structure by torsional angles, which provides a way to reason over protein conformations without violating the covalent chemistry of protein chains, (3) the coupling of local protein structure to its global representation via recurrent geometric units, and (4) the use of a differentiable loss function to capture deviations between predicted and experimental structures. To our knowledge this is the first end-to-end differentiable model for learning of protein structure. We test the effectiveness of this approach using two challenging tasks: the prediction of novel protein folds without the use of co-evolutionary information, and the prediction of known protein folds without the use of structural templates. On the first task the model achieves state-of-the-art performance, even when compared to methods that rely on co-evolutionary data. On the second task the model is competitive with methods that use experimental protein structures as templates, achieving 3-7Å accuracy despite being template-free. Beyond protein structure prediction, end-to-end differentiable models of proteins represent a new paradigm for learning and modeling protein structure, with potential applications in docking, molecular dynamics, and protein design.

97: Octopi: Open configurable high-throughput imaging platform for infectious disease diagnosis in the field
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Posted to bioRxiv 27 Jun 2019

Octopi: Open configurable high-throughput imaging platform for infectious disease diagnosis in the field
796 downloads bioengineering

Hongquan Li, Hazel Soto-Montoya, Maxime Voisin, Lucas Fuentes Valenzuela, Manu Prakash

Access to quantitative, robust, yet affordable diagnostic tools is necessary to reduce global infectious disease burden. Manual microscopy has served as a bedrock for diagnostics with wide adaptability, although at a cost of tedious labor and human errors. Automated robotic microscopes are poised to enable a new era of smart field microscopy but current platforms remain cost prohibitive and largely inflexible, especially for resource poor and field settings. Here we present Octopi, a low-cost ($250-$500) and reconfigurable autonomous microscopy platform capable of automated slide scanning and correlated bright-field and fluorescence imaging. Being highly modular, it also provides a framework for new disease-specific modules to be developed. We demonstrate the power of the platform by applying it to automated detection of malaria parasites in blood smears. Specifically, we discovered a spectral shift on the order of 10 nm for DAPI-stained Plasmodium falciparum malaria parasites. This shift allowed us to detect the parasites with a low magnification (equivalent to 10x) large field of view (2.56 mm^2) module. Combined with automated slide scanning, real time computer vision and machine learning-based classification, Octopi is able to screen more than 1.5 million red blood cells per minute for parasitemia quantification, with estimated diagnostic sensitivity and specificity exceeding 90% at parasitemia of 50/ul and 100% for parasitemia higher than 150/μl. With different modules, we further showed imaging of tissue slice and sputum sample on the platform. With roughly two orders of magnitude in cost reduction, Octopi opens up the possibility of a large robotic microscope network for improved disease diagnosis while providing an avenue for collective efforts for development of modular instruments.

98: The Dreem Headband as an Alternative to Polysomnography for EEG Signal Acquisition and Sleep Staging
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Posted to bioRxiv 10 Jun 2019

The Dreem Headband as an Alternative to Polysomnography for EEG Signal Acquisition and Sleep Staging
793 downloads neuroscience

Pierrick J Arnal, Valentin Thorey, Michael E. Ballard, Albert Bou Hernandez, Antoine Guillot, Hugo Jourde, Mason Harris, Mathias Guillard, Pascal Van Beers, Mounir Chennaoui, Fabien Sauvet

Despite the central role of sleep in our lives and the high prevalence of sleep disorders, sleep is still poorly understood. The development of ambulatory technologies capable of monitoring brain activity during sleep longitudinally is critical to advancing sleep science and facilitating the diagnosis of sleep disorders. We introduced the Dreem headband (DH) as an affordable, comfortable, and user-friendly alternative to polysomnography (PSG). The purpose of this study was to assess the signal acquisition of the DH and the performance of its embedded automatic sleep staging algorithms compared to the gold-standard clinical PSG scored by 5 sleep experts. Thirty-one subjects completed an over-night sleep study at a sleep center while wearing both a PSG and the DH simultaneously. We assessed 1) the EEG signal quality between the DH and the PSG, 2) the heart rate, breathing frequency, and respiration rate variability (RRV) agreement between the DH and the PSG, and 3) the performance of the DH's automatic sleep staging according to AASM guidelines vs. PSG sleep experts manual scoring. Results demonstrate a strong correlation between the EEG signals acquired by the DH and those from the PSG, and the signals acquired by the DH enable monitoring of alpha (r= 0.71 ± 0.13), beta (r= 0.71 ± 0.18), delta (r = 0.76 ± 0.14), and theta (r = 0.61 ± 0.12) frequencies during sleep. The mean absolute error for heart rate, breathing frequency and RRV was 1.2 ± 0.5 bpm, 0.3 ± 0.2 cpm and 3.2 ± 0.6%, respectively. Automatic Sleep Staging reached an overall accuracy of 83.5 ± 6.4% (F1 score : 83.8 ± 6.3) for the DH to be compared with an average of 86.4 ± 8.0% (F1 score: 86.3 ± 7.4) for the five sleep experts. These results demonstrate the capacity of the DH to both precisely monitor sleep-related physiological signals and process them accurately into sleep stages. This device paves the way for high-quality, large-scale, longitudinal sleep studies.

99: A general approach to engineer positive-going eFRET voltage indicators
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Posted to bioRxiv 03 Jul 2019

A general approach to engineer positive-going eFRET voltage indicators
787 downloads neuroscience

Ahmed S. Abdelfattah, Rosario Valenti, Allan Wong, Minoru Koyama, Douglas S. Douglas S. Kim, Eric R Schreiter

Genetically encoded voltage indicators (GEVIs) enable cell-type-specific monitoring of electrical activity at subcellular resolution in neurons. Coupling bright fluorophores to rhodopsin-based GEVIs via electrochromic fluorescence resonance energy transfer (eFRET) enhances their brightness but results in 'negative-going' (brighter when hyperpolarized) signals. Further improvements of eFRET GEVIs are limited by the high background fluorescence inherent to negative-going sensors. Here we report a strategy for producing eFRET GEVIs with a positive-going fluorescence response, through rational manipulation of the native proton transport pathway in microbial rhodopsins. We used this strategy to transform the state-of-the-art eFRET GEVI Voltron into a positive-going sensor, Positron, with equivalent kinetics and sensitivity. We used Positron to image spiking and subthreshold voltage signals from several neurons simultaneously in zebrafish. We further applied our general approach to GEVIs containing different voltage sensitive rhodopsin domains and various fluorescent dye and fluorescent protein reporters. These sensors represent the first bright, positive-going GEVIs with sub-millisecond response kinetics.

100: Aging is associated with a systemic length-driven transcriptome imbalance
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Posted to bioRxiv 03 Jul 2019

Aging is associated with a systemic length-driven transcriptome imbalance
786 downloads systems biology

Thomas Stoeger, Rogan A. Grant, Alexandra C. McQuattie-Pimentel, Kishore Anekalla, Sophia S Liu, Heliodoro Tejedor-Navarro, Benjamin D. Singer, Hiam Abdala-Valencia, Michael Schwake, Marie-Pier Tetreault, Harris Perlman, William E Balch, Navdeep Chandel, Karen Ridge, Jacob I. Sznajder, Richard I. Morimoto, Alexander V. Misharin, GR Scott Budinger, Luis A Nunes Amaral

Aging manifests itself through a decline in organismal homeostasis and a multitude of cellular and physiological functions. Efforts to identify a common basis for vertebrate aging face many challenges; for example, while there have been documented changes in the expression of many hundreds of mRNAs, the results across tissues and species have been inconsistent. We therefore analyzed age-resolved transcriptomic data from 17 mouse organs and 51 human organs using unsupervised machine learning to identify the architectural and regulatory characteristics most informative on the differential expression of genes with age. We report a hitherto unknown phenomenon, a systemic age-dependent length-driven transcriptome imbalance that for older organisms disrupts the homeostatic balance between short and long transcript molecules for mice, rats, killifishes, and humans. We also demonstrate that in a mouse model of healthy aging, length-driven transcriptome imbalance correlates with changes in expression of splicing factor proline and glutamine rich (Sfpq), which regulates transcriptional elongation according to gene length. Furthermore, we demonstrate that length-driven transcriptome imbalance can be triggered by environmental hazards and pathogens. Our findings reinforce the picture of aging as a systemic homeostasis breakdown and suggest a promising explanation for why diverse insults affect multiple age-dependent phenotypes in a similar manner.

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