Rxivist logo

Rxivist.org combines preprints from bioRxiv.org with data from Twitter to help you find the papers being discussed in your field.
Currently indexing 67,284 bioRxiv papers from 296,196 authors.

Most tweeted bioRxiv papers, last 7 days

Results 541 through 560 out of 738

 

541: Action representation in the mouse parieto-frontal network

Tuce Tombaz, Benjamin A. Dunn et al.

1 tweets (posted 24 May 2019) neuroscience

The posterior parietal cortex (PPC), along with anatomically linked frontal areas, form a cortical network which mediates several functions that support goal-directed behavior, including sensorimotor transformations and decision making. In primates, this network also links performed and observed actions via mirror neurons, which fire both when an individual performs an action and when they observe the same action performed by a conspecific. Mirror neurons are thought to be important for social learning and imitation, but it is not known whether mirror-like neurons occur in similar networks in other species that can learn socially, such as rodents. We therefore imaged Ca2+ responses in large neural ensembles in PPC and secondary motor cortex (M2) while mice performed and observed several actions in pellet reaching and wheel running tasks. In all animals, we found spatially overlapping neural ensembles in PPC and M2 that robustly encoded a variety of naturalistic behaviors, and that subsets of cells could stably encode multiple actions. However, neural responses to the same set of observed actions were absent in both brain areas, and across animals. Statistical modeling analyses also showed that performed actions, especially those that were task-specific, outperformed observed actions in predicting neural responses. Overall, these findings show that performed and observed actions do not drive the same cells in the parieto-frontal network in mice, and suggest that sensorimotor mirroring in the mammalian cortex may have evolved more recently, and only in certain species.

https://rxivist.org/papers/51553
https://doi.org/10.1101/646414

542: Can we assume the gene expression profile as a proxy for signaling network activity?

Mehran Piran, Reza Karbalaei et al.

1 tweets (posted 21 May 2019) systems biology

Studying relationships among gene-products by gene expression profile analysis is a common approach in systems biology. Many studies have generalized the outcomes to the different levels of central dogma information flow and assumed correlation of transcript and protein expression levels. All these efforts partook in the current understanding of signaling network models and expanded the signaling databases. In fact, due to the unavailability or high-cost of the experiments, most of the studies do not usually look for di...

https://rxivist.org/papers/51233
https://doi.org/10.1101/643866

543: A spiking neural-network model of goal-directed behaviour

Ruggero Basanisi, Andrea Brovelli et al.

1 tweets (posted 06 Dec 2019) animal behavior and cognition

In mammals, goal-directed and planning processes support flexible behaviour usable to face new situations or changed conditions that cannot be tackled through more efficient but rigid habitual behaviours. Within the Bayesian modelling approach of brain and behaviour, probabilistic models have been proposed to perform planning as a probabilistic inference. Recently, some models have started to face the important challenge met by this approach: grounding such processes on the computations implemented by brain spiking netw...

https://rxivist.org/papers/68218
https://doi.org/10.1101/867366

544: RePAIR: a power solution to animal experimentation

Valeria Bonapersona, Herbert Hoijtink et al.

1 tweets (posted 05 Dec 2019) animal behavior and cognition

Low statistical power challenges the reliability of animal research; yet, increasing sample sizes to the required level raises important ethical and practical issues. We present an alternative solution, RePAIR, which capitalizes on the observation that control groups in general are expected to be similar to each other. As shown in a simulation study, including information of previous control experiments in the statistical analysis using RePAIR reduced the required sample size by 49% or increased power up to 100%. We val...

https://rxivist.org/papers/68053
https://doi.org/10.1101/864652

545: easyCLIP Quantifies RNA-Protein Interactions and Characterizes Recurrent PCBP1 Mutations in Cancer

Douglas F. Porter, Paul A. Khavari

1 tweets (posted 17 May 2019) molecular biology

RNA-protein interactions mediate a host of cellular processes, underscoring the need for methods to quantify their occurrence in living cells. RNA interaction frequencies for the average cellular protein are undefined, however, and there is no quantitative threshold to define a protein as an RNA-binding protein (RBP). Ultraviolet (UV) cross-linking immunoprecipitation (CLIP)-sequencing, an effective and widely used means of characterizing RNA-protein interactions, would particularly benefit from the capacity to quantita...

https://rxivist.org/papers/50979
https://doi.org/10.1101/635888

546: Set1/COMPASS repels heterochromatin invasion at euchromatic sites by disrupting Suv39/Clr4 activity and nucleosome stability

R.A. Greenstein, Ramon R Barrales et al.

1 tweets (posted 08 May 2019) genetics

Protection of euchromatin from invasion by gene-repressive heterochromatin is critical for cellular health and viability. In addition to constitutive loci such as pericentromeres and subtelomeres, heterochromatin can be found interspersed in gene-rich euchromatin, where it regulates gene expression pertinent to cell fate. While hetero- and euchromatin are globally poised for mutual antagonism, the mechanisms underlying precise spatial encoding of heterochromatin containment within euchromatic sites remain opaque. We inv...

https://rxivist.org/papers/50249
https://doi.org/10.1101/630970

547: A megaplasmid family responsible for dissemination of multidrug resistance in Pseudomonas

Adrian Cazares, Matthew P. Moore et al.

1 tweets (posted 08 May 2019) microbiology

Multidrug resistance (MDR) represents a global threat to health. Although plasmids can play an important role in the dissemination of MDR, they have not been commonly linked to the emergence of antimicrobial resistance in the pathogen Pseudomonas aeruginosa. We used whole genome sequencing to characterize a collection of P. aeruginosa clinical isolates from a hospital in Thailand. Using long-read sequence data we obtained complete sequences of two closely related megaplasmids (>420 kb) carrying large arrays of antibioti...

https://rxivist.org/papers/50236
https://doi.org/10.1101/630780

548: The memory of hyperosmotic stress response in yeast is modulated by gene-positioning

Zacchari Ben Meriem, Yasmine Khalil et al.

1 tweets (posted 02 May 2019) genetics

Cellular memory is a critical ability displayed by microorganisms in order to adapt to potentially detrimental environmental fluctuations. In the unicellular eukaryote S. cerevisiae cellular memory can take the form of a faster or a decreased response following repeated stresses in cell population. Using microfluidics and fluorescence time-lapse microscopy, we studied how yeasts respond to short-pulsed hyperosmotic stresses at the single-cell level by analyzing the dynamical behavior of the stress responsive STL1 promot...

https://rxivist.org/papers/49803
https://doi.org/10.1101/625756

549: Golgi outposts locally regulate microtubule orientation in neurons but are not required for the overall polarity of the dendritic cytoskeleton

Sihui Z Yang, Jill Wildonger

1 tweets (posted 05 Dec 2019) cell biology

Microtubule-organizing centers (MTOCs) often play a central role in organizing the cellular microtubule networks that underlie cell function. In neurons, microtubules in axons and dendrites have distinct polarities. Dendrite-specific Golgi outposts, in particular multi-compartment outposts, have emerged as regulators of acentrosomal microtubule growth, raising the question of whether outposts contribute to establishing the overall polarity of the dendritic microtubule cytoskeleton. The cis-Golgi matrix protein GM130 has...

https://rxivist.org/papers/68060
https://doi.org/10.1101/866574

550: Trajectory-based differential expression analysis for single-cell sequencing data

Koen Van den Berge, Hector Roux de Bezieux et al.

1 tweets (posted 02 May 2019) bioinformatics

Trajectory inference has radically enhanced single-cell RNA-seq research by enabling the study of dynamic changes in gene expression levels during biological processes such as the cell cycle, cell type differentiation, and cellular activation. Downstream of trajectory inference, it is vital to discover genes that are associated with the lineages in the trajectory to illuminate the underlying biological processes. Furthermore, genes that are differentially expressed between developmental/activational lineages might be hi...

https://rxivist.org/papers/49744
https://doi.org/10.1101/623397

551: Plant community functional composition and diversity drive fine-scale variability in carbon cycling in the tundra

Konsta Happonen, Anna-Maria Virkkala et al.

1 tweets (posted 05 Dec 2019) ecology

We investigated how plant functional traits influence fine-scale patterns of tundra carbon cycling, and how carbon cycling responds to climate warming. We built a hierarchical model that included abiotic conditions (summer air and winter soil temperatures, and soil resources), plant community functional composition and diversity (plant size and leaf economics), and carbon cycling (above-ground and soil organic carbon stocks, and photosynthetic and respiratory fluxes). We also simulated warming effects on the peak-season...

https://rxivist.org/papers/68070
https://doi.org/10.1101/865899

552: Neo-sex chromosomes, genetic diversity and demographic history in the Critically Endangered Raso lark

Elisa Dierickx, Simon Sin et al.

1 tweets (posted 24 Apr 2019) genomics

Small effective population sizes could expose island species to inbreeding and loss of genetic variation. Here we investigate factors shaping genetic diversity in the Raso lark, which has been restricted to a single islet for ~500 years, with a population size of a few hundred. We assembled a reference genome for the related Eurasian skylark and then assessed diversity and demographic history using RAD-seq data (75 samples from Raso larks and two related mainland species). We first identify broad tracts of suppressed re...

https://rxivist.org/papers/49164
https://doi.org/10.1101/617563

553: Clustering by phenotype and genome-wide association study in autism

Akira Narita, Masato Nagai et al.

1 tweets (posted 22 Apr 2019) neuroscience

Autism spectrum disorder (ASD) has phenotypically and genetically heterogeneous characteristics. Here, we show a two-step genome-wide association study (GWAS). We used two datasets: one genotyped with the Illumina Human Omni2.5 (Omni2.5) in the discovery stage, and the other genotyped with the Illumina BeadChip 1Mv3 (1Mv3) in the replication stage. In the first step in the discovery stage, we observed no significant associations in a GWAS of 597 probands and 370 controls. In the second step in the discovery stage, we co...

https://rxivist.org/papers/49031
https://doi.org/10.1101/614958

554: Systemic Treatment with Nicotinamide Riboside is Protective in Three Mouse Models of Retinal Degeneration

Xian Zhang, Nathaniel F Henneman et al.

1 tweets (posted 06 Dec 2019) molecular biology

Purpose: The retina is highly metabolically active, suggesting that metabolic dysfunction could underlie many retinal degenerative diseases. Nicotinamide adenine dinucleotide (NAD+) is a cofactor and a co-substrate in several cellular energetic metabolic pathways. Maintaining NAD+ levels may be therapeutic in retinal disease since retinal NAD+ levels decline with age and during retinal damage or degeneration. The purpose of this study was to investigate whether systemic treatment with nicotinamide riboside (NR), a NAD+ ...

https://rxivist.org/papers/68074
https://doi.org/10.1101/866798

555: Quantification of translation uncovers the functions of the alternative transcriptome

Lorenzo Calviello, Antje Hirsekorn et al.

1 tweets (posted 14 Apr 2019) genomics

At the center of the gene expression cascade, translation is fundamental in defining the fate of much of the transcribed genome. RNA sequencing enables the quantification of complex transcript mixtures, often detecting several splice isoforms of unknown functions for one gene. We have developed ORFquant , a new approach to annotate and quantify translation at the single open reading frame (ORF) level, using information from Ribo-seq data. Relying on a novel approach for transcript filtering, we quantify translation on t...

https://rxivist.org/papers/48519
https://doi.org/10.1101/608794

556: Targeted Nanopore Sequencing with Cas9 for studies of methylation, structural variants and mutations

Timothy Gilpatrick, Isac Lee et al.

1 tweets (posted 11 Apr 2019) genomics

Nanopore sequencing technology can rapidly and directly interrogate native DNA molecules. Often we are interested only in interrogating specific areas at high depth, but conventional enrichment methods have thus far proved unsuitable for long reads1. Existing strategies are currently limited by high input DNA requirements, low yield, short (<5kb) reads, time-intensive protocols, and/or amplification or cloning (losing base modification information). In this paper, we describe a technique utilizing the ability of Cas9 to...

https://rxivist.org/papers/48251
https://doi.org/10.1101/604173

557: Genetic Associations with Mathematics Tracking and Persistence in Secondary School

K Paige Harden, Benjamin W Domingue et al.

1 tweets (posted 05 Apr 2019) genetics

Maximizing the flow of students through the science, technology, engineering, and math (STEM) pipeline is important to promoting human capital development and reducing economic inequality. A critical juncture in the STEM pipeline is the highly-cumulative sequence of secondary school math courses. Students from disadvantaged schools are less likely to complete advanced math courses, but debate continues about why. Here, we address this question using student polygenic scores, which are DNA-based indicators of propensity ...

https://rxivist.org/papers/47802
https://doi.org/10.1101/598532

558: Increased expression of schizophrenia-associated gene C4 leads to hypoconnectivity of prefrontal cortex and reduced social interaction

Ashley L Comer, Tushare Jinadasa et al.

1 tweets (posted 04 Apr 2019) neuroscience

Schizophrenia is a severe mental disorder with an unclear pathophysiology. Increased expression of the immune gene C4 has been linked to a greater risk of developing schizophrenia; however, it is unknown whether C4 plays a causative role in this brain disorder. Using confocal imaging and whole-cell electrophysiology, we demonstrate that overexpression of C4 in mouse prefrontal cortex neurons leads to perturbations in dendritic spine development and hypoconnectivity, which mirror neuropathologies found in schizophrenia. ...

https://rxivist.org/papers/47745
https://doi.org/10.1101/598342

559: A Mechanism-based Outbreak Projection Study of Pertussis (Whooping Cough): Combining Particle Filtering and Compartmental Models with Pre-vaccination Surveillance data

Xiaoyan Li, Nathaniel D. Osgood

1 tweets (posted 03 Apr 2019) epidemiology

Particle filtering is a contemporary Sequential Monte Carlo state inference and identification methodology that allows filtering of general non-Gaussian and non-linear models in light of time series of empirical observations. Several previous lines of research have demonstrated the capacity to effectively apply particle filtering to low-dimensional compartmental transmission models. We demonstrate here implementation and evaluation of particle filtering to more complex compartmental transmission models for pertussis – i...

https://rxivist.org/papers/47633
https://doi.org/10.1101/598490

560: The representational space of observed actions

Raffaele Tucciarelli, Moritz F. Wurm et al.

1 tweets (posted 29 Mar 2019) neuroscience

Categorizing and understanding other people's actions is a key human capability. Whereas there exists a growing literature regarding the organization of objects, the representational space underlying the organization of observed actions remain largely unexplored. Here we examined the organizing principles of a large set of actions and the corresponding neural representations. Using multiple-regression representational similarity analysis of fMRI data, in which we accounted for variability due to major action-related fea...

https://rxivist.org/papers/47293
https://doi.org/10.1101/592071