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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 67,594 bioRxiv papers from 298,341 authors.

Most downloaded bioRxiv papers, since beginning of last month

66,293 results found. For more information, click each entry to expand.

1: Kinetic fingerprint of antibody therapies predicts outcomes of Alzheimer clinical trials
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Posted to bioRxiv 22 Oct 2019

Kinetic fingerprint of antibody therapies predicts outcomes of Alzheimer clinical trials
24,776 downloads biophysics

Sara Linse, Tom Scheidt, Katja Bernfur, Michele Vendruscolo, Christopher M. Dobson, Samuel IA Cohen, Eimantas Sileikis, Martin Lundquist, Fang Qian, Tiernan O'Malley, Thierry Bussiere, Paul H Weinreb, Catherine K Xu, Georg Meisl, Sean Devenish, Tuomas P. J. Knowles, Oskar Hansson

Alzheimer's disease affects nearly 50 million people worldwide with an overall cost of over 1% of the global economy. The amyloid cascade hypothesis, according to which the misfolding and aggregation of the amyloid-β peptide (Aβ) triggers a series of pathological processes that eventually result in massive brain tissue loss, has driven many therapeutic efforts for the past 20 years. Repeated failures, however, have highlighted the challenges of characterizing the molecular mechanisms of therapeutic candidates targeting Aβ, and connecting them to the outcomes of clinical trials. Here, we determine the mechanism of action of four clinical stage antibodies (aducanumab, gantenerumab, bapineuzumab and solanezumab). We quantify the dramatic differences that these antibodies have on the aggregation kinetics and on the production of oligomeric aggregates, and link these effects to the affinity and stoichiometry of each antibody for the monomeric and fibrillar forms of Aβ. We show that the binding parameters of each antibody correlate with the corresponding level of amyloid clearance in clinical trials and that the reduction in oligomer flux correlates with the cognitive improvement. We reveal that, uniquely amongst these four antibodies, aducanumab dramatically reduces the flux of oligomeric forms of Aβ. These results demonstrate the power of quantitative molecular analysis in predicting the outcomes of clinical trials.

2: Quantitative translation of dog-to-human aging by conserved remodeling of epigenetic networks
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Posted to bioRxiv 04 Nov 2019

Quantitative translation of dog-to-human aging by conserved remodeling of epigenetic networks
12,696 downloads evolutionary biology

Tina Wang, Jianzhu Ma, Andrew N. Hogan, Samson Fong, Katherine Licon, Brian Tsui, Jason F Kreisberg, Peter D. Adams, Anne-Ruxandra Carvunis, Danika L. Bannasch, Elaine A. Ostrander, Trey Ideker

Mammals progress through similar physiological stages during life, from early development to puberty, aging, and death. Yet, the extent to which this conserved physiology reflects conserved molecular events is unclear. Here, we map common epigenetic changes experienced by mammalian genomes as they age, focusing on evolutionary comparisons of humans to dogs, an emerging model of aging. Using targeted sequencing, we characterize the methylomes of 104 Labrador retrievers spanning a 16 year age range, achieving >150X coverage within mammalian syntenic blocks. Comparison with human methylomes reveals a nonlinear relationship which translates dog to human years, aligns the timing of major physiological milestones between the two species, and extends to mice. Conserved changes center on specific developmental gene networks which are sufficient to capture the effects of anti-aging interventions in multiple mammals. These results establish methylation not only as a diagnostic age readout but as a cross-species translator of physiological aging milestones.

3: An integrated brain-machine interface platform with thousands of channels
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Posted to bioRxiv 17 Jul 2019

An integrated brain-machine interface platform with thousands of channels
9,490 downloads neuroscience

Elon Musk, Neuralink

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.

4: Natural image reconstruction from brain waves: a novel visual BCI system with native feedback
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Posted to bioRxiv 01 Oct 2019

Natural image reconstruction from brain waves: a novel visual BCI system with native feedback
7,045 downloads neuroscience

Grigory Rashkov, Anatoly Bobe, Dmitry Fastovets, Maria Komarova

Here we hypothesize that observing the visual stimuli of different categories trigger distinct brain states that can be decoded from noninvasive EEG recordings. We introduce an effective closed-loop BCI system that reconstructs the observed or imagined stimuli images from the co-occurring brain wave parameters. The reconstructed images are presented to the subject as a visual feedback. The developed system is applicable to training BCI-naive subjects because of the user-friendly and intuitive way the visual patterns are employed to modify the brain states.

5: Evidence supporting a viral origin of the eukaryotic nucleus
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Posted to bioRxiv 21 Jun 2019

Evidence supporting a viral origin of the eukaryotic nucleus
3,899 downloads evolutionary biology

Philip JL Bell

The defining feature of the eukaryotic cell is the possession of a nucleus that uncouples transcription from translation. This uncoupling of transcription from translation depends on a complex process employing hundreds of eukaryotic specific genes acting in concert and requires the 7-methylguanylate (m7G) cap to prime eukaryotic mRNA for splicing, nuclear export, and cytoplasmic translation. The origin of this complex system is currently a paradox since it is not found or needed in prokaryotic cells which lack nuclei, yet it was apparently present and fully functional in the Last Eukaryotic Common Ancestor (LECA). According to the Viral Eukaryogenesis (VE) hypothesis the abrupt appearance of the nucleus in the eukaryotic lineage occurred because the nucleus descends from the viral factory of a DNA phage that infected the archaeal ancestor of the eukaryotes. Consequently, the system for uncoupling of transcription from translation in eukaryotes is predicted by the VE hypothesis to be viral in origin. In support of this hypothesis it is shown here that m7G capping apparatus that primes the uncoupling of transcription from translation in eukaryotes is present in viruses of the Mimiviridae but absent from bona-fide archaeal relatives of the eukaryotes such as Lokiarchaeota. Furthermore, phylogenetic analysis of the m7G capping pathway indicates that eukaryotic nuclei and Mimiviridae obtained this pathway from a common ancestral source that predated the origin of LECA. These results support the VE hypothesis and suggest the eukaryotic nucleus and the Mimiviridae descend from a common First Eukaryotic Nuclear Ancestor (FENA).

6: Variability in the analysis of a single neuroimaging dataset by many teams
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Posted to bioRxiv 15 Nov 2019

Variability in the analysis of a single neuroimaging dataset by many teams
3,718 downloads neuroscience

Rotem Botvinik-Nezer, Felix Holzmeister, Colin F. Camerer, Anna Dreber, Juergen Huber, David I. Laibson, Michael Kirchler, Roni Iwanir, Jeanette A. Mumford, Alison Adcock, Paolo Avesani, Blazej Baczkowski, Aahana Bajracharya, Leah Bakst, Sheryl Ball, Marco Barilari, Nadège Bault, Derek Beaton, Julia Beitner, Roland Benoit, Ruud Berkers, Jamil Bhanji, Bharat Biswal, Sebastian Bobadilla-Suarez, Tiago Bortolini, Katherine Bottenhorn, Alexander Bowring, Senne Braem, Hayley Brooks, Emily Brudner, Cristian Calderon, Julia Camilleri, Jaime Castrellon, Luca Cecchetti, Edna Cieslik, Zachary Cole, Olivier Collignon, Robert Cox, William Cunningham, Stefan Czoschke, Kamalaker Dadi, Charles Davis, Alberto De Luca, Mauricio Delgado, Lysia Demetriou, Jeffrey Dennison, Xin Di, Erin Dickie, Ekaterina Dobryakova, Claire Donnat, Juergen Dukart, Niall W Duncan, Joke Durnez, Amr Eed, Simon Eickhoff, Andrew Erhart, Laura Fontanesi, G. Matthew Fricke, Adriana Galvan, Remi Gau, Sarah Genon, Tristan Glatard, Enrico Glerean, Jelle Goeman, Sergej Golowin, Carlos González-García, Krzysztof Gorgolewski, Cheryl Grady, Mikella Green, João Guassi Moreira, Olivia Guest, Shabnam Hakimi, J. Paul Hamilton, Roeland Hancock, Giacomo Handjaras, Bronson Harry, Colin Hawco, Peer Herholz, Gabrielle Herman, Stephan Heunis, Felix Hoffstaedter, Jeremy Hogeveen, Susan Holmes, Chuan-Peng Hu, Scott Huettel, Matthew Hughes, Vittorio Iacovella, Alexandru Iordan, Peder Isager, Ayse Ilkay Isik, Andrew Jahn, Matthew Johnson, Tom Johnstone, Michael Joseph, Anthony Juliano, Joseph Kable, Michalis Kassinopoulos, Cemal Koba, Xiang-Zhen Kong, Timothy Koscik, Nuri Erkut Kucukboyaci, Brice Kuhl, Sebastian Kupek, Angela Laird, Claus Lamm, Robert Langner, Nina Lauharatanahirun, Hongmi Lee, Sangil Lee, Alexander Leemans, Andrea Leo, Elise Lesage, Flora Li, Monica Li, Phui Cheng Lim, Evan Lintz, Schuyler Liphardt, Annabel Losecaat Vermeer, Bradley Love, Michael Mack, Norberto Malpica, Theo Marins, Camille Maumet, Kelsey McDonald, Joseph McGuire, Helena Melero, Adriana Méndez Leal, Benjamin Meyer, Kristin Meyer, Paul Mihai, Georgios Mitsis, Jorge Moll, Dylan Nielson, Gustav Nilsonne, Michael Notter, Emanuele Olivetti, Adrian Onicas, Paolo Papale, Kaustubh Patil, Jonathan E. Peelle, Alexandre Pérez, Doris Pischedda, Jean-Baptiste Poline, Yanina Prystauka, Shruti Ray, Patricia Reuter-Lorenz, Richard Reynolds, Emiliano Ricciardi, Jenny Rieck, Anais Rodriguez-Thompson, Anthony Romyn, Taylor Salo, Gregory Samanez-Larkin, Emilio Sanz-Morales, Margaret Schlichting, Douglas Schultz, Qiang Shen, Margaret Sheridan, Fu Shiguang, Jennifer Silvers, Kenny Skagerlund, Alec Smith, David Smith, Peter Sokol-Hessner, Simon Steinkamp, Sarah Tashjian, Bertrand Thirion, John Thorp, Gustav Tinghög, Loreen Tisdall, Steven Tompson, Claudio Toro-Serey, Juan Torre, Leonardo Tozzi, Vuong Truong, Luca Turella, Anna E. van’t Veer, Tom Verguts, Jean Vettel, Sagana Vijayarajah, Khoi Vo, Matthew Wall, Wouter D. Weeda, Susanne Weis, David White, David Wisniewski, Alba Xifra-Porxas, Emily Yearling, Sangsuk Yoon, Rui Yuan, Kenneth Yuen, Lei Zhang, Xu Zhang, Joshua Zosky, Thomas E. Nichols, Russell A. Poldrack, Tom Schonberg

Data analysis workflows in many scientific domains have become increasingly complex and flexible. To assess the impact of this flexibility on functional magnetic resonance imaging (fMRI) results, the same dataset was independently analyzed by 70 teams, testing nine ex-ante hypotheses. The flexibility of analytic approaches is exemplified by the fact that no two teams chose identical workflows to analyze the data. This flexibility resulted in sizeable variation in hypothesis test results, even for teams whose statistical maps were highly correlated at intermediate stages of their analysis pipeline. Variation in reported results was related to several aspects of analysis methodology. Importantly, meta-analytic approaches that aggregated information across teams yielded significant consensus in activated regions across teams. Furthermore, prediction markets of researchers in the field revealed an overestimation of the likelihood of significant findings, even by researchers with direct knowledge of the dataset. Our findings show that analytic flexibility can have substantial effects on scientific conclusions, and demonstrate factors related to variability in fMRI. The results emphasize the importance of validating and sharing complex analysis workflows, and demonstrate the need for multiple analyses of the same data. Potential approaches to mitigate issues related to analytical variability are discussed.

7: In situ cryo-electron tomography reveals filamentous actin within the microtubule lumen
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Posted to bioRxiv 18 Nov 2019

In situ cryo-electron tomography reveals filamentous actin within the microtubule lumen
3,313 downloads cell biology

Danielle M Paul, Judith Mantell, Ufuk Borucu, Jennifer Coombs, Katherine J Surridge, John M Squire, Paul Verkade, Mark P Dodding

Microtubules and filamentous (F-) actin engage in complex interactions to drive many cellular processes from subcellular organisation to cell division and migration. This is thought to be largely controlled by proteins that interface between the two structurally distinct cytoskeletal components. Here, we use cryo-electron tomography to demonstrate that the microtubule lumen can be occupied by extended segments of F-actin in small-molecule induced, microtubule-based cellular projections. We uncover an unexpected versatility in cytoskeletal form that may prompt a significant development of our current models of cellular architecture and offer a new experimental approach for the in-situ study of microtubule structure and contents.

8: Genomics of a complete butterfly continent
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Posted to bioRxiv 04 Nov 2019

Genomics of a complete butterfly continent
2,985 downloads genomics

Jing Zhang, Qian Cong, Jinhui Shen, Paul A Opler, Nick V Grishin

Never before have we had the luxury of choosing a continent, picking a large phylogenetic group of animals, and obtaining genomic data for its every species. Here, we sequence all 845 species of butterflies recorded from North America north of Mexico. Our comprehensive approach reveals the pattern of diversification and adaptation occurring in this phylogenetic lineage as it has spread over the continent, which cannot be seen on a sample of selected species. We observe bursts of diversification that generated taxonomic ranks: subfamily, tribe, subtribe, genus, and species. The older burst around 70 Mya resulted in the butterfly subfamilies, with the major evolutionary inventions being unique phenotypic traits shaped by high positive selection and gene duplications. The recent burst around 5 Mya is caused by explosive radiation in diverse butterfly groups associated with diversification in transcription and mRNA regulation, morphogenesis, and mate selection. Rapid radiation correlates with more frequent introgression of speciation-promoting and beneficial genes among radiating species. Radiation and extinction patterns over the last 100 million years suggest the following general model of animal evolution. A population spreads over the land, adapts to various conditions through mutations, and diversifies into several species. Occasional hybridization between these species results in accumulation of beneficial alleles in one, which eventually survives, while others become extinct. Not only butterflies, but also the hominids may have followed this path.

9: Does training method matter?: Evidence for the negative impact of aversive-based methods on companion dog welfare
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Posted to bioRxiv 29 Oct 2019

Does training method matter?: Evidence for the negative impact of aversive-based methods on companion dog welfare
2,695 downloads animal behavior and cognition

Ana Catarina Vieira de Castro, Danielle Fuchs, Stefania Pastur, Liliana de Sousa, Anna Olsson

There is a growing number of dogs kept as companion animals, and the methods by which they are trained range broadly from those using mostly positive punishment and negative reinforcement (aversive-based methods) to those using primarily positive reinforcement (reward-based methods). Although the use of aversive-based methods has been strongly criticized for negatively affecting dog welfare, these claims do not find support in solid scientific evidence. Previous research on the subject lacks companion dog-focused research, investigation of the entire range of aversive-based techniques (beyond shock-collars), objective measures of welfare, and long-term welfare studies. The aim of the present study was to perform a comprehensive evaluation of the short- and long-term effects of aversive- and reward-based training methods on companion dog welfare. Ninety-two companion dogs were recruited from three reward-based (Group Reward, n=42) and four aversive-based (Group Aversive, n=50) dog training schools. For the short-term welfare assessment, dogs were video recorded for three training sessions and six saliva samples were collected, three at home (baseline levels) and three after the training sessions (post-training levels). Video recordings were then used to examine the frequency of stress-related behaviors (e.g., lip lick, yawn) and the overall behavioral state of the dog (e.g., tense, relaxed), and saliva samples were analyzed for cortisol concentration. For the long-term welfare assessment, dogs performed a cognitive bias task. Dogs from Group Aversive displayed more stress-related behaviors, spent more time in tense and low behavioral states and more time panting during the training sessions, showed higher elevations in cortisol levels after training and were more ‘pessimistic’ in the cognitive bias task than dogs from Group Reward. These findings indicate that the use of aversive-based methods compromises the welfare of companion dogs in both the short- and the long-term.

10: Integrated computational and experimental identification of p53, KRAS and VHL mutant selection associated with CRISPR-Cas9 editing
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Posted to bioRxiv 03 Sep 2018

Integrated computational and experimental identification of p53, KRAS and VHL mutant selection associated with CRISPR-Cas9 editing
2,658 downloads cancer biology

Sanju Sinha, Karina Barbosa Guerra, Kuoyuan Cheng, Mark DM Leiserson, David M Wilson, Bríd M Ryan, Ze’ev A. Ronai, Joo Sang Lee, Aniruddha J Deshpande, Eytan Ruppin

Recent studies have reported that CRISPR-Cas9 gene editing induces a p53 -dependent DNA damage response in primary cells, which may select for cells with oncogenic p53 mutations[11][1],[12][2]. It is unclear whether these CRISPR-induced changes are applicable to different cell types, and whether CRISPR gene editing may select for other oncogenic mutations. Addressing these questions, we analyzed genome-wide CRISPR and RNAi screens to systematically chart the mutation selection potential of CRISPR knockouts across the whole exome. Our analysis suggests that CRISPR gene editing can select for mutants of KRAS and VHL , at a level comparable to that reported for p53 . These predictions were further validated in a genome-wide manner by analyzing independent CRISPR screens and patients’ tumor data. Finally, we performed a new set of pooled and arrayed CRISPR screens to evaluate the competition between CRISPR-edited isogenic p53 WT and mutant cell lines, which further validated our predictions. In summary, our study systematically charts and points to the potential selection of specific cancer driver mutations during CRISPR-Cas9 gene editing. [1]: #ref-11 [2]: #ref-12

11: 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)
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Posted to bioRxiv 26 May 2016

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)
2,614 downloads cancer biology

Michael Wyde, Mark Cesta, Chad Blystone, Susan Elmore, Paul Foster, Michelle Hooth, Grace Kissling, David Malarkey, Robert Sills, Matthew Stout, Nigel Walker, Kristine Witt, Mary Wolfe, John Bucher

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 report were reviewed by expert peer reviewers selected by the NTP and National Institutes of Health (NIH). These reviews and responses to comments are included as appendices to this report, and revisions to the current document have incorporated and addressed these comments. When the studies are completed, they will undergo additional peer review before publication in full as part of the NTP's Toxicology and Carcinogenesis Technical Reports Series. No portion of this work has been submitted for publication in a scientific journal. Supplemental information in the form of four additional manuscripts has or will soon be submitted for publication. These manuscripts describe in detail the designs and performance of the RFR exposure system, the dosimetry of RFR exposures in rats and mice, the results to a series of pilot studies establishing the ability of the animals to thermoregulate during RFR exposures, and studies of DNA damage. (1) Capstick M, Kuster N, Kuhn S, Berdinas-Torres V, Wilson P, Ladbury J, Koepke G, McCormick D, Gauger J, and Melnick R. A radio frequency radiation reverberation chamber exposure system for rodents; (2) Yijian G, Capstick M, McCormick D, Gauger J, Horn T, Wilson P, Melnick RL, and Kuster N. Life time dosimetric assessment for mice and rats exposed to cell phone radiation; (3) Wyde ME, Horn TL, Capstick M, Ladbury J, Koepke G, Wilson P, Stout MD, Kuster N, Melnick R, Bucher JR, and McCormick D. Pilot studies of the National Toxicology Program's cell phone radiofrequency radiation reverberation chamber exposure system; (4) Smith-Roe SL, Wyde ME, Stout MD, Winters J, Hobbs CA, Shepard KG, Green A, Kissling GE, Tice RR, Bucher JR, and Witt KL. Evaluation of the genotoxicity of cell phone radiofrequency radiation in male and female rats and mice following subchronic exposure.

12: A genetic map of the response to DNA damage in human cells
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Posted to bioRxiv 18 Nov 2019

A genetic map of the response to DNA damage in human cells
2,479 downloads cancer biology

Michele Olivieri, Tiffany Cho, Alejandro Álvarez-Quilón, Kejiao Li, Matthew J Schellenberg, Michal Zimmermann, Nicole Hustedt, Silvia Emma Rossi, Salomé Adam, Henrique Melo, Anne Margriet Heijink, Guillermo Sastre-Moreno, Nathalie Moatti, Rachel Szilard, Andrea McEwan, Alexanda K Ling, Almudena Serrano-Benitez, Tajinder Ubhi, Irene Delgado-Sainz, Michael W Ferguson, Grant W Brown, Felipe Cortés-Ledesma, R. Scott Williams, Alberto Martin, Dongyi Xu, Daniel Durocher

The response to DNA damage is critical for cellular homeostasis, tumor suppression, immunity and gametogenesis. In order to provide an unbiased and global view of the DNA damage response in human cells, we undertook 28 CRISPR/Cas9 screens against 25 genotoxic agents in the retinal pigment epithelium-1 (RPE1) cell line. These screens identified 840 genes whose loss causes either sensitivity or resistance to DNA damaging agents. Mining this dataset, we uncovered that ERCC6L2, which is mutated in a bone-marrow failure syndrome, codes for a canonical non-homologous end-joining pathway factor; that the RNA polymerase II component ELOF1 modulates the response to transcription-blocking agents and that the cytotoxicity of the G-quadruplex ligand pyridostatin involves trapping topoisomerase II on DNA. This map of the DNA damage response provides a rich resource to study this fundamental cellular system and has implications for the development and use of genotoxic agents in cancer therapy.

13: A comparison of neuronal population dynamics measured with calcium imaging and electrophysiology
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Posted to bioRxiv 15 Nov 2019

A comparison of neuronal population dynamics measured with calcium imaging and electrophysiology
2,224 downloads neuroscience

Ziqiang Wei, Bei-Jung Lin, Tsai-Wen Chen, Kayvon Daie, Karel Svoboda, Shaul Druckmann

Calcium imaging with fluorescent protein sensors is widely used to record activity in neuronal populations. The transform between neural activity and calcium-related fluorescence involves nonlinearities and a low-pass filter, but the effects of the transformation on analyses of neural populations are not well understood. We compared neuronal spikes and fluorescence in matched neural populations in behaving mice. We report multiple discrepancies between analyses performed on the two types of data, which were only partially resolved by spike inference algorithms applied to fluorescence. To model the relation between spiking and fluorescence we simultaneously recorded spikes and fluorescence from individual neurons. Using these recordings we developed a model transforming spike trains to synthetic-imaging data. The model recapitulated the differences in analyses. Our analysis highlights challenges in relating electrophysiology and imaging data, and suggests forward modeling as an effective way to understand differences between these data.

14: Long read sequencing of 1,817 Icelanders provides insight into the role of structural variants in human disease
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Posted to bioRxiv 20 Nov 2019

Long read sequencing of 1,817 Icelanders provides insight into the role of structural variants in human disease
2,216 downloads genetics

Doruk Beyter, Helga Ingimundardottir, Hannes Eggertsson, Eythor Bjornsson, Snaedis Kristmundsdottir, Svenja Mehringer, Hakon Jonsson, Marteinn T Hardarson, Droplaug N Magnusdottir, Ragnar P. Kristjansson, Sigurjon A Gudjonsson, Sverrir T Sverrisson, Guillaume Holley, Gudmundur Eyjolfsson, Isleifur Olafsson, Olof Sigurdardottir, Gisli Masson, Unnur Thorsteinsdottir, D.F. Gudbjartsson, Patrick Sulem, Olafur T Magnusson, Bjarni V. Halldorsson, K. Stefansson

Long-read sequencing (LRS) promises to improve characterization of structural variants (SVs), a major source of genetic diversity. We generated LRS data on 1,817 Icelanders using Oxford Nanopore Technologies, and identified a median of 23,111 autosomal structural variants per individual (a median of 11,506 insertions and 11,576 deletions), spanning cumulatively a median of 9.9 Mb. We found that rare SVs are larger in size than common ones and are more likely to impact protein function. We discovered an association with a rare deletion of the first exon of PCSK9 . Carriers of this deletion have 0.93 mmol/L (1.36 sd) lower LDL cholesterol levels than the population average (p-value = 2.4·10−22). We show that SVs can be accurately characterized at population scale using long read sequence data in a genomewide non-targeted fashion and how these variants impact disease.

15: Comprehensive integration of single cell data
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Posted to bioRxiv 02 Nov 2018

Comprehensive integration of single cell data
2,160 downloads genomics

Tim Stuart, Andrew Butler, Paul Hoffman, Christoph Hafemeister, Efthymia Papalexi, William M. Mauck, Marlon Stoeckius, Peter Smibert, Rahul Satija

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 develop a computational strategy to "anchor" diverse datasets together, enabling us to integrate and compare single cell measurements not only across scRNA-seq technologies, but different modalities as well. After demonstrating substantial improvement over existing methods for data integration, we anchor scRNA-seq experiments with scATAC-seq datasets to explore chromatin differences in closely related interneuron subsets, and project single cell protein measurements onto a human bone marrow atlas to annotate and characterize lymphocyte populations. Lastly, we demonstrate how anchoring can harmonize in-situ gene expression and scRNA-seq datasets, allowing for the transcriptome-wide imputation of spatial gene expression patterns, and the identification of spatial relationships between mapped cell types in the visual cortex. Our work presents a strategy for comprehensive integration of single cell data, including the assembly of harmonized references, and the transfer of information across datasets. Availability: Installation instructions, documentation, and tutorials are available at: https://www.satijalab.org/seurat

16: High throughput, error corrected Nanopore single cell transcriptome sequencing
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Posted to bioRxiv 05 Nov 2019

High throughput, error corrected Nanopore single cell transcriptome sequencing
2,128 downloads genomics

Kevin Lebrigand, Virginie Magnone, Pascal Barbry, Rainer Waldmann

Droplet-based high throughput single cell isolation techniques tremendously boosted the throughput of single cell transcriptome profiling experiments. However, those approaches only allow analysis of one extremity of the transcript after short read sequencing. We introduce an approach that combines Oxford Nanopore sequencing with unique molecular identifiers to obtain error corrected full length sequence information with the 10xGenomics single cell isolation system. This allows to examine differential RNA splicing and RNA editing at a single cell level.

17: Multiversal SpaceTime (MSpaceTime) Not Neural Network as Source of Intelligence in Generalized Quantum Mechanics, Extended General Relativity, Darwin Dynamics for Artificial Super Intelligence Synthesis
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Posted to bioRxiv 29 Nov 2019

Multiversal SpaceTime (MSpaceTime) Not Neural Network as Source of Intelligence in Generalized Quantum Mechanics, Extended General Relativity, Darwin Dynamics for Artificial Super Intelligence Synthesis
2,112 downloads neuroscience

Yang Zhang

This article has been withdrawn by bioRxiv owing to a screening error.

18: 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
2,106 downloads physiology

Anna Wiik, Tommy R Lundberg, Eric Rullman, Daniel P Andersson, Mats Holmberg, Mirko Mandic, Torkel B Brismar, Olof Dahlqvist Leinhard, Setareh Chanpen, John Flanagan, Stefan Arver, Thomas 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.

19: Deep generative model embedding of single-cell RNA-Seq profiles on hyperspheres and hyperbolic spaces
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Posted to bioRxiv 25 Nov 2019

Deep generative model embedding of single-cell RNA-Seq profiles on hyperspheres and hyperbolic spaces
2,069 downloads bioinformatics

Jiarui Ding, Aviv Regev

Single-cell RNA-Seq (scRNA-seq) has become an invaluable tool for studying biological systems in health and diseases. While dimensionality reduction is a crucial step in interpreting the relation between cells based on scRNA-seq, current methods often are hampered by "crowding" of cells in the center of the latent space, biased by batch effects, or inadequately capture developmental relationships. Here, we introduced scPhere, a scalable deep generative model to embed cells into low-dimensional hyperspherical or hyperbolic spaces, as a more accurate representation of the data. ScPhere resolves cell crowding, corrects multiple, complex batch factors, facilitates interactive visualization of large datasets, and gracefully uncovers pseudotemporal trajectories. We demonstrate scPhere on six large datasets in complex tissue from human patients or animal development, demonstrating how it controls for both technical and biological factors and highlights complex cellular relations and biological insights.

20: A simple method for spray-on gene editing in planta
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Posted to bioRxiv 25 Oct 2019

A simple method for spray-on gene editing in planta
2,068 downloads plant biology

Cara Doyle, Katie Higginbottom, Thomas A. Swift, Mark Winfield, Christopher Bellas, David Benito-Alifonso, Taryn Fletcher, M. Carmen Galan, Keith Edwards, Heather M. Whitney

Potential innovation in Plant research using gene-edited and genetically modified plants is currently being hindered by inefficient and costly plant transformation. We show that carbon dots formed from natural materials (quasi-spherical, <10nm nanoparticles) can act as a fast vehicle for carrying plasmids into mature plant cells, resulting in transient plant transformation in a number of important crop species with no negative impacts on photosynthesis or growth. We further show that GFP, Cas9, and gRNA introduced into wheat via foliar application (spraying on) of plasmid coated carbon dots are expressed and, in the case of Cas9, make genome edits in SPO11 genes. Therefore, we present a protocol for spray-on gene editing that is simple, inexpensive, fast, transforms in planta , and is applicable to multiple crop species. We believe this technique creates many opportunities for the future of plant transformation in research and shows great promise for plant protein production systems.

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