Top 10 Biorxiv Papers Today


3.06 Mikeys
#1. Functional cortico-subcortical reorganization after complete hemispheric disconnection for intractable epilepsy
Thomas Blauwblomme, Athena Demertzi, Jean-Marc Tacchela, Ludovic Fillon, Marie Bourgeois, Emma Lositto, Monika Eisermann, Daniele Marinazzo, Federico Raimondo, Sarael Alcauter, Frederik Van de Steen, Nigel Colenbier, Steven Laureys, Volodia Dangouloff-Ros, Lionel Naccache, Nathalie Boddaert, Rima Nabbout
Hemispherotomy is a treatment for drug-resistant epilepsy with the whole hemisphere involved in seizure onset. As recovery mechanisms are still debated, we characterize functional reorganization with multimodal MRI in two children operated on the right hemisphere (RH). We found that interhemispheric functional connectivity was abolished in both patients. The healthy left hemispheres (LH) displayed focal hyperperfusion in motor and limbic areas, and preserved network-level organization. The disconnected RHs were hypoperfused despite sustained network-level organization. Functional connectivity was increased in the left thalamo-cortical loop and between the cerebelli. The classification probability of the RH corresponding to a minimally conscious state was smaller than for the LH. We conclude that after hemispherotomy, neurological rehabilitation is sustained by cortical disinhibition and reinforcement of connectivity driven by subcortical structures in the remaining hemisphere. Our results highlight the effect of vascularization on...
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biorxiv_neursci: Functional cortico-subcortical reorganization after complete hemispheric disconnection for intractable epilepsy https://t.co/EsuSeZCRpY #biorxiv_neursci
biorxivpreprint: Functional cortico-subcortical reorganization after complete hemispheric disconnection for intractable epilepsy https://t.co/OEgL21WDsb #bioRxiv
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Sample Sizes : [11, 16, 9, 3, 11, 9, 11, 9, 11, 16, 9, 3]
Authors: 17
Total Words: 10916
Unqiue Words: 3316

2.636 Mikeys
#2. Identifying hetero-protein complexes in the nuclear envelope
Jared Hennen, Kwang-Ho Hur, John Kohler, Siddarth Reddy Karuka, Isaac Angert, GW Gant Luxton, Jochen Mueller
The nucleus is delineated by the nuclear envelope (NE), which is a double membrane barrier composed of the inner and outer nuclear membranes as well as a ~40 nm wide lumen. In addition to its barrier function, the NE acts as a critical signaling node for a variety of cellular processes which are mediated by protein complexes within this subcellular compartment. While fluorescence fluctuation spectroscopy (FFS) is a powerful tool for characterizing protein complexes in living cells, it was recently demonstrated that conventional FFS methods are not suitable for applications in the NE because of the presence of slow nuclear membrane undulations. We previously addressed this challenge by developing time-shifted mean-segmented Q (tsMSQ) analysis and applied it to successfully characterize protein homo-oligomerization in the NE. However, many NE complexes, such as the linker of the nucleoskeleton and cytoskeleton (LINC) complex, are formed by heterotypic interactions, which single-color tsMSQ is unable to characterize. Here, we...
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biorxivpreprint: Identifying hetero-protein complexes in the nuclear envelope https://t.co/g642zX0bat #bioRxiv
biorxiv_biophys: Identifying hetero-protein complexes in the nuclear envelope https://t.co/xdrodV4W8E #biorxiv_biophys
biophotonicat: Identifying hetero-protein complexes in the nuclear envelope (relevance: 64%) https://t.co/XFEh8Wt8c9 #biophotonics #biomedicaloptics
jmvarberg: RT @biorxivpreprint: Identifying hetero-protein complexes in the nuclear envelope https://t.co/g642zX0bat #bioRxiv
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Authors: 7
Total Words: 0
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2.373 Mikeys
#3. Power and pitfalls of computational methods for inferring clone phylogenies and mutation orders from bulk sequencing data
Sayaka Miura, Tracy Vu, Jiamin Deng, Tiffany Buturla, Jiyeong Choi, Sudhir Kumar
Background: Tumors harbor extensive genetic heterogeneity in the form of distinct clone genotypes that arise over time and across different tissues and regions of a cancer patient. Many computational methods produce clone phylogenies from population bulk sequencing data collected from multiple tumor samples. These clone phylogenies are used to infer mutation order and clone origin times during tumor progression, rendering the selection of the appropriate clonal deconvolution method quite critical. Surprisingly, absolute and relative accuracies of these methods in correctly inferring clone phylogenies have not been consistently assessed. Methods: We evaluated the performance of seven computational methods in producing clone phylogenies for simulated datasets in which clones were sampled from multiple sectors of a primary tumor (multi-region) or primary and metastatic tumors in a patient (multi-site). We assessed the accuracy of tested methods metrics in determining the order of mutations and the branching pattern within the...
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biorxivpreprint: Power and pitfalls of computational methods for inferring clone phylogenies and mutation orders from bulk sequencing data https://t.co/8Lc4SaRUnf #bioRxiv
biorxiv_cancer: Power and pitfalls of computational methods for inferring clone phylogenies and mutation orders from bulk sequencing data https://t.co/9niUPA3n7X #biorxiv_cancer
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Repository: CloneFinderAPI
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Language: Python
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Forks: 1
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Authors: 6
Total Words: 11133
Unqiue Words: 3308

2.204 Mikeys
#4. A Computational Model of Normal and Impaired Lexical Decision: Graded Semantic Effects
Ya-Ning Chang, Steve Furber, Matthew Lambon Ralph, Stephen Welbourne
Lexical decision is an important paradigm in studies of visual word recognition yet the underlying mechanisms supporting the activity are not well understood. While most models of visual word recognition focus on orthographic processing as the primary locus of the lexical decision, a number of behavioural studies have suggested a flexible role for semantic processing regulated by the similarity of the nonword foil to real words. Here we developed a computational model that interactively combines visual-orthographic, phonological and semantic processing to perform lexical decisions. Importantly, the model was able to differentiate words from nonwords by dynamically integrating measures of polarity across the key processing layers. The model was more reliant on semantic information when nonword foils were pseudowords as opposed to consonant strings. Moreover, the model was able to capture a range of standard reading effects in lexical decision. Damage to the model also resulted in reading patterns observed in patients with pure...
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biorxiv_neursci: A Computational Model of Normal and Impaired Lexical Decision: Graded Semantic Effects https://t.co/YxC9yPVvk4 #biorxiv_neursci
biorxivpreprint: A Computational Model of Normal and Impaired Lexical Decision: Graded Semantic Effects https://t.co/vHLolm2RXn #bioRxiv
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Authors: 4
Total Words: 0
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2.198 Mikeys
#5. Pervasive introgression of MHC genes in newt hybrid zones
Katarzyna Dudek, Tomasz S Gaczorek, Piotr Zieliński, Wiesław Babik
Variation in the vertebrate major histocompatibility complex (MHC) genes is crucial for fighting pathogen assault. Because new alleles confer a selective advantage, MHC should readily introgress between species, even under limited hybridization. Using replicated transects through two hybrid zones between strongly reproductively isolated newts, we demonstrated recent and ongoing MHC introgression. Its extent correlated with the age of contact. In the older zone, MHC similarity between species within transects exceeded that of between transects within species, implying pervasive introgression — a massive exchange of MHC genes, not limited to specific variants. In simulations, the observed pattern emerged under the combined action of balancing selection and hybridization, but not when these processes acted separately. Thus, massive introgression at advanced stages of divergence can introduce novel and restore previously lost MHC variation, boosting the adaptive potential of hybridizing taxa. In consequence, MHC genes may be the last...
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biorxivpreprint: Pervasive introgression of MHC genes in newt hybrid zones https://t.co/7k3X8GJkuN #bioRxiv
biorxiv_evobio: Pervasive introgression of MHC genes in newt hybrid zones https://t.co/kCe8ZZL3ML #biorxiv_evobio
sbotlite: RT @biorxivpreprint: Pervasive introgression of MHC genes in newt hybrid zones https://t.co/7k3X8GJkuN #bioRxiv
Riberiusz: RT @biorxivpreprint: Pervasive introgression of MHC genes in newt hybrid zones https://t.co/7k3X8GJkuN #bioRxiv
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2.194 Mikeys
#6. Micro-probing enables high-resolution mapping of neuronal subpopulations using fMRI
Joana Carvalho, Azzurra Invernizzi, Khazar Ahmadi, Michael B. Hoffmann, Remco J. Renken, Frans W. Cornelissen
The characterization of receptive field (RF) properties is fundamental to understanding the neural basis of sensory and cognitive behaviour. The combination of non-invasive imaging, such as fMRI, with biologically inspired neural modeling has enabled the estimation of population RFs directly in humans. However, current approaches require making numerous a priori assumptions, so these cannot reveal unpredicted properties, such as fragmented RFs or subpopulations. This is a critical limitation in studies on adaptation, pathology or reorganization. Here, we introduce micro-probing (MP), a technique for fine-grained and assumption free characterisation of subpopulation RFs. Without specific stimuli or adapted models, MP mapped the bilateral RFs characteristic of observers with a congenital pathway disorder. Moreover, in healthy observers, MP revealed voxels that capture the activity of multiple neuronal subpopulations. Thus, MP provides a versatile framework to visualize, analyze and model, without restrictions, the diverse RFs of...
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biorxiv_neursci: Micro-probing enables high-resolution mapping of neuronal subpopulations using fMRI https://t.co/1vEfebWZKs #biorxiv_neursci
biorxivpreprint: Micro-probing enables high-resolution mapping of neuronal subpopulations using fMRI https://t.co/lQQ6qHr7H9 #bioRxiv
zuxfoucault: RT @biorxiv_neursci: Micro-probing enables high-resolution mapping of neuronal subpopulations using fMRI https://t.co/1vEfebWZKs #biorxiv_…
jospark09: RT @biorxiv_neursci: Micro-probing enables high-resolution mapping of neuronal subpopulations using fMRI https://t.co/1vEfebWZKs #biorxiv_…
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Authors: 6
Total Words: 13304
Unqiue Words: 3657

2.181 Mikeys
#7. H3K4me3 is neither instructive for, nor informed by, transcription.
Struan C Murray, Philipp Lorenz, Francoise Howe, Meredith Wouters, Thomas Brown, Shidong Xi, Harry Fischl, Walaa Khushaim, Joseph Regish Rayappu, Andrew Angel, Jane Mellor
H3K4me3 is a near-universal histone modification found predominantly at the 5' region of genes, with a well-documented association with gene activity. H3K4me3 has been ascribed roles as both an instructor of gene expression and also a downstream consequence of expression, yet neither has been convincingly proven on a genome-wide scale. Here we test these relationships using a combination of bioinformatics, modelling and experimental data from budding yeast in which the levels of H3K4me3 have been massively ablated. We find that loss of H3K4me3 has no effect on the levels of nascent transcription or transcript in the population. Moreover, we observe no change in the rates of transcription initiation, elongation, mRNA export or turnover, or in protein levels, or cell-to-cell variation of mRNA. Loss of H3K4me3 also has no effect on the large changes in gene expression patterns that follow galactose induction. Conversely, loss of RNA polymerase from the nucleus has no effect on the pattern of H3K4me3 deposition and little effect on...
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THebertMcGill: RT @biorxivpreprint: H3K4me3 is neither instructive for, nor informed by, transcription. https://t.co/F0v5RwyphZ #bioRxiv
marcotrizzino: RT @biorxivpreprint: H3K4me3 is neither instructive for, nor informed by, transcription. https://t.co/F0v5RwyphZ #bioRxiv
BioGibberish: RT @biorxivpreprint: H3K4me3 is neither instructive for, nor informed by, transcription. https://t.co/F0v5RwyphZ #bioRxiv
EvolPaper: RT @biorxiv_genomic: H3K4me3 is neither instructive for, nor informed by, transcription. https://t.co/7nGmmmd48G #biorxiv_genomic
PrecursorCell: RT @biorxivpreprint: H3K4me3 is neither instructive for, nor informed by, transcription. https://t.co/F0v5RwyphZ #bioRxiv
jason_tanny: RT @biorxivpreprint: H3K4me3 is neither instructive for, nor informed by, transcription. https://t.co/F0v5RwyphZ #bioRxiv
leehenry1971: RT @biorxivpreprint: H3K4me3 is neither instructive for, nor informed by, transcription. https://t.co/F0v5RwyphZ #bioRxiv
LeungCal: RT @biorxivpreprint: H3K4me3 is neither instructive for, nor informed by, transcription. https://t.co/F0v5RwyphZ #bioRxiv
tito_tasks: RT @biorxivpreprint: H3K4me3 is neither instructive for, nor informed by, transcription. https://t.co/F0v5RwyphZ #bioRxiv
maahoek: RT @biorxivpreprint: H3K4me3 is neither instructive for, nor informed by, transcription. https://t.co/F0v5RwyphZ #bioRxiv
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Authors: 11
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2.163 Mikeys
#8. What can we learn from over 100,000 Escherichia coli genomes?
Kaleb Z. Zion Abram, Zulema Udaondo, Carissa Bleker, Visanu Wanchai, Trudy M Wassenaar, David W Ussery
The explosion of microbial genome sequences in public databases allows for large-scale population studies of model organisms, such as Escherichia coli . We have examined more than one hundred-thousand E. coli and Shigella genomes . After removing outliers, genomes were classified into two broad clusters based on a semi-automated Mash analysis, which distinguished 14 distinct phylotypes, graphically illustrated by Cytoscape. From a set of more than ten-thousand good quality E. coli and Shigella genomes from GenBank, we find roughly 2,700 gene families in the E. coli species core, and more than 135,000 gene families in the E. coli pan-genome. Based on a set of 2,613 single-copy core proteins taken from one representative genome per phylotype, we constructed a robust phylogenetic tree. This is the largest E. coli genome dataset analyzed to date, and provides valuable insight into the population structure of the species.
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AstrobioMike: RT @biorxiv_genomic: What can we learn from over 100,000 Escherichia coli genomes? https://t.co/KFUajcwrhm #biorxiv_genomic
IFB_Bioinfo: RT @biorxiv_genomic: What can we learn from over 100,000 Escherichia coli genomes? https://t.co/KFUajcwrhm #biorxiv_genomic
prashbio: RT @biorxiv_genomic: What can we learn from over 100,000 Escherichia coli genomes? https://t.co/KFUajcwrhm #biorxiv_genomic
pierre_marijon: RT @biorxiv_genomic: What can we learn from over 100,000 Escherichia coli genomes? https://t.co/KFUajcwrhm #biorxiv_genomic
kofi_little_boy: RT @biorxiv_genomic: What can we learn from over 100,000 Escherichia coli genomes? https://t.co/KFUajcwrhm #biorxiv_genomic
ybazetag: RT @biorxiv_genomic: What can we learn from over 100,000 Escherichia coli genomes? https://t.co/KFUajcwrhm #biorxiv_genomic
HeleneChiapello: RT @biorxiv_genomic: What can we learn from over 100,000 Escherichia coli genomes? https://t.co/KFUajcwrhm #biorxiv_genomic
vallenet: RT @biorxivpreprint: What can we learn from over 100,000 Escherichia coli genomes? https://t.co/zfxBEB7jK9 #bioRxiv
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2.161 Mikeys
#9. Metabolic stress is a primary pathogenic event in transgenic Caenorhabditis elegans expressing neuronal human amyloid-β
Emelyne Teo, Sudharshan Ravi, Diogo Barardo, Hyung-Seok Kim, Sheng Fong, Amaury Cazenave-Gassiot, Tsze Yin Tan, Jianhong Ching, Jean-Paul Kovalik, Markus R Wenk, Rudiyanto Gunawan, Philip K Moore, Barry Halliwell, Nicholas Tolwinski, Jan Gruber
Alzheimer's disease (AD) is the most common neurodegenerative disease. Mitochondrial dysfunction is a key event in its etiology. We have previously modeled amyloid-beta (Aβ)-induced mitochondrial dysfunction in Caenorhabditis elegans by expressing human Aβ peptide specifically in neurons (GRU102). Here, we focus on deeper analysis of these metabolic changes associated with Aβ-induced mitochondrial dysfunction. Integrating metabolomics, transcriptomics, biochemical studies and computational modeling, we identify alterations in Krebs cycle metabolism following even low-level Aβ expression. In particular, GRU102 show reduced activity of a rate-limiting Krebs cycle enzyme, alpha-ketoglutarate dehydrogenase. These defects are associated with elevation of protein carbonyl content in mitochondria. Importantly, metabolic failure occurs before any significant increase in protein aggregates is detectable. Treatment with an anti-diabetes drug, Metformin, reverses metabolic defects, reduces protein aggregation and normalizes lifespan of...
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biorxiv_neursci: Metabolic stress is a primary pathogenic event in transgenic Caenorhabditis elegans expressing neuronal human amyloid-β https://t.co/VPliyYZLJ6 #biorxiv_neursci
biorxivpreprint: Metabolic stress is a primary pathogenic event in transgenic Caenorhabditis elegans expressing neuronal human amyloid-β https://t.co/a4PmksUu1L #bioRxiv
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Authors: 15
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2.157 Mikeys
#10. Prioritizing transcriptomic and epigenomic experiments by using an optimization strategy that leverages imputed data
Jacob Schreiber, Jeffrey Bilmes, William Stafford Noble
Successful science often involves not only performing experiments well, but also choosing well among many possible experiments. In a hypothesis generation setting, choosing an experiment well means choosing an experiment whose results are interesting or novel. In this work, we formalize this selection procedure in the context of genomics and epigenomics data generation. Specifically, we consider the task faced by a scientific consortium such as the National Institutes of Health ENCODE Consortium, whose goal is to characterize all of the functional elements in the human genome. Given a list of possible cell types or tissue types ("biosamples") and a list of possible high throughput sequencing assays, we ask "Which experiments should ENCODE perform next?" We demonstrate how to represent this task as an optimization problem, where the goal is to maximize the information gained in each successive experiment. Compared with previous work that has addressed a similar problem, our approach has the advantage that it can use imputed data to...
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biorxivpreprint: Prioritizing transcriptomic and epigenomic experiments by using an optimization strategy that leverages imputed data https://t.co/eYhydjuPGz #bioRxiv
biorxiv_genomic: Prioritizing transcriptomic and epigenomic experiments by using an optimization strategy that leverages imputed data https://t.co/os7dae1r3U #biorxiv_genomic
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Authors: 3
Total Words: 0
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