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Currently indexing 62,232 bioRxiv papers from 276,288 authors.

Most downloaded bioRxiv papers, since beginning of last month

Results 1 through 20 out of 49529

 

1: An integrated brain-machine interface platform with thousands of channels

Elon Musk, Neuralink

11,301 downloads (posted 17 Jul 2019) neuroscience

Brain-machine interfaces (BMIs) hold promise for the restoration of sensory and motor function and the treatment of neurological disorders, but clinical BMIs have not yet been widely adopted, in part because modest channel counts have limited their potential. In this white paper, we describe Neuralink’s first steps toward a scalable high-bandwidth BMI system. We have built arrays of small and flexible electrode “threads”, with as many as 3,072 electrodes per array distributed across 96 threads. We have also built a neurosurgical robot capable of inserting six threads (192 electrodes) per minute. Each thread can be individually inserted into the brain with micron precision for avoidance of surface vasculature and targeting specific brain regions. The electrode array is packaged into a small implantable device that contains custom chips for low-power on-board amplification and digitization: the package for 3,072 channels occupies less than (23 × 18.5 × 2) mm3. A single USB-C cable provides full-bandwidth data streaming from the device, recording from all channels simultaneously. This system has achieved a spiking yield of up to 70% in chronically implanted electrodes. Neuralink’s approach to BMI has unprecedented packaging density and scalability in a clinically relevant package.

https://rxivist.org/papers/55953
https://doi.org/10.1101/703801

2: Mammalian Y RNAs are modified at discrete guanosine residues with N-glycans

Ryan A. Flynn, Benjamin A. H. Smith et al.

7,005 downloads (posted 30 Sep 2019) molecular biology

Glycans modify lipids and proteins to mediate inter- and intramolecular interactions across all domains of life. RNA, another multifaceted biopolymer, is not thought to be a major target of glycosylation. Here, we challenge this view with evidence that mammalian cells use RNA as a third scaffold for glycosylation in the secretory pathway. Using a battery of chemical and biochemical approaches, we find that a select group of small noncoding RNAs including Y RNAs are modified with complex, sialylated N-glycans (glycoRNAs)...

https://rxivist.org/papers/62015
https://doi.org/10.1101/787614

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

Anna Wiik, Tommy R Lundberg et al.

6,950 downloads (posted 26 Sep 2019) physiology

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 T1...

https://rxivist.org/papers/61827
https://doi.org/10.1101/782557

4: The Genomic Formation of South and Central Asia

Vagheesh M Narasimhan, Nick Patterson et al.

3,826 downloads (posted 31 Mar 2018) genomics

The genetic formation of Central and South Asian populations has been unclear because of an absence of ancient DNA. To address this gap, we generated genome-wide data from 362 ancient individuals, including the first from eastern Iran, Turan (Uzbekistan, Turkmenistan, and Tajikistan), Bronze Age Kazakhstan, and South Asia. Our data reveal a complex set of genetic sources that ultimately combined to form the ancestry of South Asians today. We document a southward spread of genetic ancestry from the Eurasian Steppe, corre...

https://rxivist.org/papers/6917
https://doi.org/10.1101/292581

5: Prefrontal cortex as a meta-reinforcement learning system

Jane X Wang, Zeb Kurth-Nelson et al.

3,086 downloads (posted 06 Apr 2018) neuroscience

Over the past twenty years, neuroscience research on reward-based learning has converged on a canonical model, under which the neurotransmitter dopamine 'stamps in' associations between situations, actions and rewards by modulating the strength of synaptic connections between neurons. However, a growing number of recent findings have placed this standard model under strain. In the present work, we draw on recent advances in artificial intelligence to introduce a new theory of reward-based learning. Here, the dopamine sy...

https://rxivist.org/papers/13080
https://doi.org/10.1101/295964

6: LeafByte: A mobile application that measures leaf area and herbivory quickly and accurately

Zoe L Getman-Pickering, Adam Campbell et al.

3,043 downloads (posted 23 Sep 2019) ecology

1. In both basic and applied studies, quantification of herbivory on foliage is a key metric in characterizing plant-herbivore interactions, which underpin many ecological, evolutionary, and agricultural processes. Current methods of quantifying herbivory are slow or inaccurate. We present LeafByte, a free iOS application for measuring leaf area and herbivory. LeafByte can save data automatically, read and record barcodes, handle both light and dark colored plant tissue, and be used non-destructively. 2. We evaluate ...

https://rxivist.org/papers/61478
https://doi.org/10.1101/777516

7: An association between sexes of successive siblings in the data from Demographic and Health Survey program

Mikhail Monakhov

2,733 downloads (posted 12 Nov 2015) physiology

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 chi...

https://rxivist.org/papers/20443
https://doi.org/10.1101/031344

8: Molecular Atlas Of The Adult Mouse Brain

Cantin Ortiz, Jose Fernandez Navarro et al.

1,978 downloads (posted 27 Sep 2019) neuroscience

Brain maps are essential for integrating information and interpreting the structure-function relationship of circuits and behavior. We aimed to generate a systematic classification of the adult mouse brain organization based on unbiased extraction of spatially-defining features. Applying whole-brain spatial transcriptomics, we captured the gene expression signatures to define the spatial organization of molecularly discrete subregions. We found that the molecular code contained sufficiently detailed information to direc...

https://rxivist.org/papers/61950
https://doi.org/10.1101/784181

9: A guide to performing Polygenic Risk Score analyses

Shing Wan Choi, Timothy Mak et al.

1,942 downloads (posted 14 Sep 2018) genomics

The application of polygenic risk scores (PRS) has become routine in genetic epidemiological studies. Among a range of applications, PRS are commonly used to assess shared aetiology among different phenotypes and to evaluate the predictive power of genetic data, while they are also now being exploited as part of study design, in which experiments are performed on individuals, or their biological samples (eg. tissues, cells), at the tails of the PRS distribution and contrasted. As GWAS sample sizes increase and PRS becom...

https://rxivist.org/papers/32683
https://doi.org/10.1101/416545

10: Sex Chromosome Dosage Effects On Gene Expression In Humans

Armin Raznahan, Neelroop Parikshak et al.

1,893 downloads (posted 14 May 2017) genomics

A fundamental question in the biology of sex-differences has eluded direct study in humans: how does sex chromosome dosage (SCD) shape genome function? To address this, we developed a systematic map of SCD effects on gene function by analyzing genome-wide expression data in humans with diverse sex chromosome aneuploidies (XO, XXX, XXY, XYY, XXYY). For sex chromosomes, we demonstrate a pattern of obligate dosage sensitivity amongst evolutionarily preserved X-Y homologs, and update prevailing theoretical models for SCD co...

https://rxivist.org/papers/7313
https://doi.org/10.1101/137752

11: GeneWalk identifies relevant gene functions for a biological context using network representation learning

Robert Ietswaart, Benjamin M Gyori et al.

1,843 downloads (posted 05 Sep 2019) bioinformatics

The primary bottleneck in high-throughput genomics experiments is identifying the most important genes and their relevant functions from a list of gene hits. Existing methods such as Gene Ontology (GO) enrichment analysis provide insight at the gene set level. For individual genes, GO annotations are static and biological context can only be added by manual literature searches. Here, we introduce GeneWalk (github.com/churchmanlab/genewalk), a method that identifies individual genes and their relevant functions under a p...

https://rxivist.org/papers/59888
https://doi.org/10.1101/755579

12: Quantifying the tradeoff between sequencing depth and cell number in single-cell RNA-seq

Valentine Svensson, Eduardo da Veiga Beltrame et al.

1,823 downloads (posted 09 Sep 2019) genomics

The allocation of a sequencing budget when designing single cell RNA-seq experiments requires consideration of the tradeoff between number of cells sequenced and the read depth per cell. One approach to the problem is to perform a power analysis for a univariate objective such as differential expression. However, many of the goals of single-cell analysis requires consideration of the multivariate structure of gene expression, such as clustering. We introduce an approach to quantifying the impact of sequencing depth and ...

https://rxivist.org/papers/60246
https://doi.org/10.1101/762773

13: Normalization and variance stabilization of single-cell RNA-seq data using regularized negative binomial regression

Christoph Hafemeister, Rahul Satija

1,701 downloads (posted 14 Mar 2019) genomics

Single-cell RNA-seq (scRNA-seq) data exhibits significant cell-to-cell variation due to technical factors, including the number of molecules detected in each cell, which can confound biological heterogeneity with technical effects. To address this, we present a modeling framework for the normalization and variance stabilization of molecular count data from scRNA-seq experiments. We propose that the Pearson residuals from 'regularized negative binomial regression', where cellular sequencing depth is utilized as a covaria...

https://rxivist.org/papers/46065
https://doi.org/10.1101/576827

14: The Tolman-Eichenbaum Machine: Unifying space and relational memory through generalisation in the hippocampal formation

James C.R. Whittington, Timothy H. Muller et al.

1,668 downloads (posted 16 Sep 2019) neuroscience

The hippocampal-entorhinal system is important for spatial and relational memory tasks. We formally link these domains; provide a mechanistic understanding of the hippocampal role in generalisation; and offer unifying principles underlying many entorhinal and hippocampal cell-types. We propose medial entorhinal cells form a basis describing structural knowledge, and hippocampal cells link this basis with sensory representations. Adopting these principles, we introduce the Tolman-Eichenbaum machine (TEM). After learning,...

https://rxivist.org/papers/60878
https://doi.org/10.1101/770495

15: Pan-cancer classifications of tumor histological images using deep learning

Javad Noorbakhsh, Saman Farahmand et al.

1,639 downloads (posted 26 Jul 2019) bioinformatics

Histopathological images are essential for the diagnosis of cancer type and selection of optimal treatment. However, the current clinical process of manual inspection of images is time consuming and prone to intra- and inter-observer variability. Here we show that key aspects of cancer image analysis can be performed by deep convolutional neural networks (CNNs) across a wide spectrum of cancer types. In particular, we implement CNN architectures based on Google Inception v3 transfer learning to analyze 27815 H&E slides ...

https://rxivist.org/papers/56771
https://doi.org/10.1101/715656

16: Comprehensive integration of single cell data

Tim Stuart, Andrew Butler et al.

1,635 downloads (posted 02 Nov 2018) genomics

Single cell transcriptomics (scRNA-seq) has transformed our ability to discover and annotate cell types and states, but deep biological understanding requires more than a taxonomic listing of clusters. As new methods arise to measure distinct cellular modalities, including high-dimensional immunophenotypes, chromatin accessibility, and spatial positioning, a key analytical challenge is to integrate these datasets into a harmonized atlas that can be used to better understand cellular identity and function. Here, we devel...

https://rxivist.org/papers/35822
https://doi.org/10.1101/460147

17: A molecular cell atlas of the human lung from single cell RNA sequencing

Kyle J Travaglini, Ahmad N Nabhan et al.

1,565 downloads (posted 27 Aug 2019) genomics

Although single cell RNA sequencing studies have begun providing compendia of cell expression profiles, it has proven more difficult to systematically identify and localize all molecular cell types in individual organs to create a full molecular cell atlas. Here we describe droplet- and plate-based single cell RNA sequencing applied to ~70,000 human lung and blood cells, combined with a multi-pronged cell annotation approach, which have allowed us to define the gene expression profiles and anatomical locations of 58 cel...

https://rxivist.org/papers/59113
https://doi.org/10.1101/742320

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

Hongquan Li, Hazel Soto-Montoya et al.

1,520 downloads (posted 27 Jun 2019) bioengineering

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 reconfigura...

https://rxivist.org/papers/54308
https://doi.org/10.1101/684423

19: A single-cell and single-nucleus RNA-seq toolbox for fresh and frozen human tumors

Michal Slyper, Caroline B. M. Porter et al.

1,511 downloads (posted 12 Sep 2019) genomics

Single cell genomics is essential to chart the complex tumor ecosystem. While single cell RNA-Seq (scRNA-Seq) profiles RNA from cells dissociated from fresh tumor tissues, single nucleus RNA-Seq (snRNA-Seq) is needed to profile frozen or hard-to-dissociate tumors. Each strategy requires modifications to fit the unique characteristics of different tissue and tumor types, posing a barrier to adoption. Here, we developed a systematic toolbox for profiling fresh and frozen clinical tumor samples using scRNA-Seq and snRNA-Se...

https://rxivist.org/papers/60662
https://doi.org/10.1101/761429

20: Reversal of ageing- and injury-induced vision loss by Tet-dependent epigenetic reprogramming

Yuancheng Lu, Anitha Krishnan et al.

1,433 downloads (posted 31 Jul 2019) molecular biology

Ageing is a degenerative process leading to tissue dysfunction and death. A proposed cause of ageing is the accumulation of epigenetic noise, which disrupts youthful gene expression patterns that are required for cells to function optimally and recover from damage. Changes to DNA methylation patterns over time form the basis of an 'ageing clock', but whether old individuals retain information to reset the clock and, if so, whether this would improve tissue function is not known. Of all the tissues in the body, the centr...

https://rxivist.org/papers/57084
https://doi.org/10.1101/710210