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Currently indexing 63,068 bioRxiv papers from 279,747 authors.

Most downloaded bioRxiv papers, since beginning of last month

Results 1 through 20 out of 61421


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.


2: Insights from a survey-based analysis of the academic job market

Jason D Fernandes, Sarvenaz Sarabipour et al.

9,400 downloads (posted 09 Oct 2019) scientific communication and education

Many postdoctoral fellows in the STEM fields enter the academic job market with little knowledge of the process and expectations, and without any means to assess their qualifications relative to the general applicant pool. Demystifying this process is critical, as there is little information publicly available. In this work, we provide insight into the process of academic job searches by gathering data to establish background metrics for typical faculty job applicants, and further correlate these metrics with job search...


3: 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)...


4: 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...


5: Toxicity of JUUL Fluids and Aerosols Correlates Strongly with Nicotine and Some Flavor Chemical Concentrations

Esther Omaiye, Kevin J McWhirter et al.

4,632 downloads (posted 09 Dec 2018) pharmacology and toxicology

While JUUL electronic cigarettes (ECs) have captured the majority of the EC market with a large fraction of their sales going to adolescents, little is known about their cytotoxicity and potential effects on health. The purpose of this study was to determine flavor chemical and nicotine concentrations in the eight currently marketed pre-filled JUUL EC cartridges (pods) and to evaluate the cytotoxicity of the different variants (e.g., Cool Mint and Creme Brulee) using in vitro assays. Nicotine and flavor chemicals were a...


6: The Genomic Formation of South and Central Asia

Vagheesh M Narasimhan, Nick Patterson et al.

3,997 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...


7: A proximity biotinylation map of a human cell

Christopher D Go, James D R Knight et al.

3,582 downloads (posted 07 Oct 2019) molecular biology

Compartmentalization is an essential characteristic of eukaryotic cells, ensuring that cellular processes are partitioned to defined subcellular locations. High throughput microscopy and biochemical fractionation coupled with mass spectrometry have helped to define the proteomes of multiple organelles and macromolecular structures. However, many compartments have remained refractory to such methods, partly due to lysis and purification artefacts and poor subcompartment resolution. Recently developed proximity-dependent ...


8: 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...


9: 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 ...


10: Correlative three-dimensional super-resolution and block face electron microscopy of whole vitreously frozen cells

David P Hoffman, Gleb Shtengel et al.

2,910 downloads (posted 18 Sep 2019) cell biology

Living cells function through the spatial compartmentalization of thousands of distinct proteins serving a multitude of diverse biochemical needs. Correlative super-resolution (SR) fluorescence and electron microscopy (EM) has emerged as a pathway to directly view nanoscale protein relationships to the underlying global ultrastructure, but has traditionally suffered from tradeoffs of structure preservation, fluorescence retention, resolution, and field of view. We developed a platform for three-dimensional correlative c...


11: 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...


12: A guide to performing Polygenic Risk Score analyses

Shing Wan Choi, Timothy Mak et al.

2,625 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...


13: Isolation of an archaeon at the prokaryote-eukaryote interface

Hiroyuki Imachi, Masaru K Nobu et al.

2,416 downloads (posted 06 Aug 2019) microbiology

The origin of eukaryotes remains enigmatic. Current data suggests that eukaryotes may have risen from an archaeal lineage known as "Asgard archaea". Despite the eukaryote-like genomic features found in these archaea, the evolutionary transition from archaea to eukaryotes remains unclear due to the lack of cultured representatives and corresponding physiological insight. Here we report the decade-long isolation of a Lokiarchaeota-related Asgard archaeon from deep marine sediment. The archaeon, " Candidatus Prometheoarcha...


14: Report of Partial findings from the National Toxicology Program Carcinogenesis Studies of Cell Phone Radiofrequency Radiation in Hsd: Sprague Dawley® SD rats (Whole Body Exposure)

Michael Wyde, Mark Cesta et al.

2,302 downloads (posted 26 May 2016) cancer biology

The U.S. National Toxicology Program (NTP) has carried out extensive rodent toxicology and carcinogenesis studies of radiofrequency radiation (RFR) at frequencies and modulations used in the U.S. telecommunications industry. This report presents partial findings from these studies. The occurrences of two tumor types in male Harlan Sprague Dawley rats exposed to RFR, malignant gliomas in the brain and schwannomas of the heart, were considered of particular interest and are the subject of this report. The findings in this...


15: The GTEx Consortium atlas of genetic regulatory effects across human tissues

Francois Aguet, Alvaro N Barbeira et al.

2,250 downloads (posted 03 Oct 2019) genetics

The Genotype-Tissue Expression (GTEx) project was established to characterize genetic effects on the transcriptome across human tissues, and to link these regulatory mechanisms to trait and disease associations. Here, we present analyses of the v8 data, based on 17,382 RNA-sequencing samples from 54 tissues of 948 post-mortem donors. We comprehensively characterize genetic associations for gene expression and splicing in cis and trans, showing that regulatory associations are found for almost all genes, and describe the...


16: The Future of OA: A large-scale analysis projecting Open Access publication and readership

Heather Piwowar, Jason Priem et al.

2,023 downloads (posted 09 Oct 2019) scientific communication and education

Understanding the growth of open access (OA) is important for deciding funder policy, subscription allocation, and infrastructure planning. This study analyses the number of papers available as OA over time. The models includes both OA embargo data and the relative growth rates of different OA types over time, based on the OA status of 70 million journal articles published between 1950 and 2019. The study also looks at article usage data, analyzing the proportion of views to OA articles vs views to articles which are cl...


17: 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...


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

Robert Ietswaart, Benjamin M Gyori et al.

1,942 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...


19: Comprehensive integration of single cell data

Tim Stuart, Andrew Butler et al.

1,931 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...


20: 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...