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1,154 results for “Pooling”
Fig. 2 in Pools and rapids as spawning and nursery areas for fish in a river stretch without floodplains
Fig. 2. Light trap used to capture the ichthyoplankton.
Recovery and analysis of transcriptome subsets from pooled single-cell RNA-seq libraries
<p>Processed data files for manuscript: "Recovery and analysis of transcriptome subsets from pooled single-cell RNA-seq libraries" <a href="https://doi.org/10.1093/nar/gky1204">https://doi.org/10.1093/nar/gky1204</a> . Scripts for generating figures are found here: https://github.com/rnabioco/scrna-subsets</p>
A Deep Dive into Bitcoin Mining Pools
<p>Dataset retrieved and used with the code hosted <a href="https://github.com/MatteoRomiti/Deep_Dive_BTC_Mining_Pools">here</a> for this <a href="https://arxiv.org/abs/1905.05999">paper</a> published at <a href="https://weis2019.econinfosec.org/">WEIS 2019</a></p> <p>Abstract</p> <p>Miners play a key role in cryptocurrencies such as Bitcoin: they invest substantial computational resources in processing transactions and minting new currency units. It is well known that an attacker controlling more than half of the network’s mining power could manipulate the state of the system at will. While the influence of large mining pools appears evenly split, the actual distribution of mining power within these pools and their economic relationships with other actors remain undisclosed. To this end, we conduct the first in-depth analysis of mining reward distribution within three of the four largest Bitcoin mining pools and examine their cross-pool economic relationships. Our results suggest that individual miners are simultaneously operating across all three pools and that in each analyzed pool a small number of actors (≤ 20) receives over 50% of all BTC payouts. While the extent of an operator’s control over the resources of a mining pool remains an open debate, our findings are in line with previous research, pointing out centralization tendencies in large mining pools and cryptocurrencies in general</p> <p> </p>
Gaze-Stabilizing Central Vestibular Neurons Project Asymmetrically to Extraocular Motoneuron Pools
<p><strong>ABSTRACT </strong>Within reflex circuits, specific anatomical projections allow central neurons to relay sensations to effectors that generate movements. A major challenge is to relate anatomical features of central neural populations, such as asymmetric connectivity, to the computations the populations perform. To address this problem, we mapped the anatomy, modeled the function, and discovered a new behavioral role for a genetically defined population of central vestibular neurons in rhombomeres 5–7 of larval zebrafish. First, we found that neurons within this central population project preferentially to motoneurons that move the eyes downward. Concordantly, when the entire population of asymmetrically projecting neurons was stimulated collectively, only downward eye rotations were observed, demonstrating a functional correlate of the anatomical bias. When these neurons are ablated, fish failed to rotate their eyes following either nose-up or nose-down body tilts. This asymmetrically projecting central population thus participates in both upward and downward gaze stabilization. In addition to projecting to motoneurons, central vestibular neurons also receive direct sensory input from peripheral afferents. To infer whether asymmetric projections can facilitate sensory encoding or motor output, we modeled differentially projecting sets of central vestibular neurons. Whereas motor command strength was independent of projection allocation, asymmetric projections enabled more accurate representation of nose-up stimuli. The model shows how asymmetric connectivity could enhance the representation of imbalance during nose-up postures while preserving gaze stabilization performance. Finally, we found that central vestibular neurons were necessary for a vital behavior requiring maintenance of a nose-up posture: swim bladder inflation. These observations suggest that asymmetric connectivity in the vestibular system facilitates representation of ethologically relevant stimuli without compromising reflexive behavior.</p> <p><strong>SIGNIFICANCE STATEMENT</strong> Interneuron populations use specific anatomical projections to transform sensations into reflexive actions. Here we examined how the anatomical composition of a genetically defined population of balance interneurons in the larval zebrafish relates to the computations it performs. First, we found that the population of interneurons that stabilize gaze preferentially project to motoneurons that move the eyes downward. Next, we discovered through modeling that such projection patterns can enhance the encoding of nose-up sensations without compromising gaze stabilization. Finally, we found that loss of these interneurons impairs a vital behavior, swim bladder inflation, that relies on maintaining a nose-up posture. These observations suggest that anatomical specialization permits neural circuits to represent relevant features of the environment without compromising behavior.</p>
Ab initio design of microbial communities from large-scale seed pools using deep learning and rapid ptimization
<h4>This repository contains the full results of our paper: <strong><em>Ab initio</em> design of microbial communities from large-scale seed pools using deep learning and rapid ptimization.</strong></h4> <p>Authors: Xiaoqing Jiang#, Jiaheng Hou#, Haoyu Zhang#, Jinyuan Guo, Shaohua Gu, Yulin Liao, Xinrun Yang, Peter X. Geng, Yiyan Zhou, Qian Guo, Chunhui Wang, Mo Li, Alexandre Jousset, Zhong Wei*, and Huaiqiu Zhu*</p> <p>The results including:</p> <p><strong>(1)</strong> <strong>GEM.tar.gz</strong>: The eBiota-GEM dataset, containing 21,514 Genome-Scale Metabolic Models (GEMs) constructed using CarveMe based on RefSeq complete genomes.</p> <p><strong>(2) Baterial_evaluation.tar.gz</strong>: The evaluation of the ability to uptake substrates and secret productions for all 21,514 GEMs.</p> <p><strong>(3) Community_results.tar.gz</strong>: The results calculated from eBiota-GEM includes various combinations for two-bacterial consortia, covering strain IDs, substrates, products, yields, dual-bacterial growth, single-bacterial growth, co-occurrence predictions, interactions and total production.</p> <p><strong>(4) DeepCooc_files.tar.gz</strong>: The parameter files of DeepCooc, required by eBiota platform.</p>
Source pool diversity and proximity shape the compositional uniqueness of insular mammal assemblages worldwide
<p>Islands have been the test bed of several theories in community ecology, biogeography, and evolutionary biology. Progress within these disciplines has given a more comprehensive and mechanistic understanding of the processes governing variation in species richness among islands. However, it remains unclear whether these same processes also explain variation in species and phylogenetic composition among islands. Integrating theory from ecology and biogeography, we infer the roles of dispersal, selection, and stochasticity on the composition of insular assemblages within archipelagos. We further assess the influence of source pool diversity and connectivity on the compositional uniqueness of insular assemblages. Island systems worldwide. We compiled data on species composition of non-volant mammals on ∼200 islands in nine archipelagos distributed worldwide from the literature. We used variation partitioning to quantify the relative influence of the environment (selection) and geographic distance (dispersal) relative to a null model (stochasticity, randomness) on taxonomic and phylogenetic compositional turnover within archipelagos. We then used a linear mixed model to gain further insight into the underlying mechanisms shaping variation in assemblage composition among islands at a global scale. Specifically, we assessed the influence of source pool diversity, isolation from the source pool, and island characteristics on compositional uniqueness. Our results suggest that within-archipelago variation in the composition of insular mammal assemblages is associated with stochastic or unmeasured processes rather than abiotic selection or dispersal limitation. The diversity and proximity of the source pool, as well as some island characteristics, explained variation in phylogenetic, but not taxonomic, compositional uniqueness globally. Within archipelagos, the largely unexplained variation in compositional turnover points to the overwhelming influence of extinction mediated by ecological drift or other stochastic processes, which obscures or overrides the signature of selection and/or dispersal. Globally, isolated islands associated with highly diverse source pools exhibit high phylogenetic uniqueness whereas well-connected islands associated with small source pools show the opposite trend. Phylogenetically unique assemblages also tend to occur on islands with a small elevational span and low annual temperature variation. Taken together, our results suggest that source pool diversity, along with the potential for colonization from those pools, plays an important role in shaping the composition of insular mammal assemblages worldwide. </p>
Improving the efficiency of single cell genome sequencing based on overlapping pooling strategy
Single cell genome sequencing has become a useful tool in medicine and biology studies. However, an independent library is required for each cell in single cell genome sequencing, so that the cost grows in step with the number of cells. In this study, we report a study on efficient single-cell copy number variation (CNV) analysis based on overlapping pooling strategy together with branch and bound (B&B) algorithm. Single cells are overlapped pooled before sequencing, and later are assorted into specific types by estimating their CNV patterns by B&B algorithm. Instead of constructing libraries for each cell, a library is required only for each pool. As long as the number of pools is smaller than the cells, fewer libraries are needed, and a lower cost is spent. Through computer simulations, we overlapping pooled 80 cells into 40 and 27 pools and classified them into cell types based on CNV pattern. The results showed that 84% cells in 40 pools and 76.5% cells in 27 pools were correctly classified on average, while only half or one-third of the sequencing libraries are required. Combining with traditional approaches, our method is expected to significantly improve the efficiency of single cell genome sequencing.
Replication data for: Spatial and temporal origins of the La Perouse low oxygen pool: A combined Lagrangian statistical approach
<p>This dataset contains:</p> <p>a) <strong>NEP36 </strong>daily Model (NEMO) Output from 20130228 till 20131005 in NetCDF format,</p> <p>b) Moving Vessel Profiler (<strong>MVP</strong>) Survey data gathered onboard the R/V Falkor during August 2013 in ASCII .mat files,</p> <p>c) Files required to initialize and run Lagrangian Particle tracking model <strong>ARIANE </strong>i.e. one mesh_mask file in netCDF format and one text file containing initial positions based on the Eulerian grid of the sliced NEP36 model</p> <p>d) the output files from running the particle tracking model ARIANE in NetCDF format</p>
Data for the Eastern African power pool's energy systems model, developed in OSeMOSYS
<p>This repository consists of the following datasets</p> <p>1. EAPP_reference scenario_datafile.DD- This dataset is a model file that needs to be used with the code available in this <a href="https://github.com/KTH-dESA/OSeMOSYS/blob/master/OSeMOSYS_GNU_MathProg/osemosys_short.txt">GitHub</a> link. This data file (in concurrence with the OSeMOSYS code) can be used to create a linear programming file (LP file) to be solved using any mathematical optimisation solver like GLPSOL/C-PLEX/GUROBI/CBC.</p> <p>2. Main article_EAPP_data for figures.xlsx- This excel file contains the base data used to illustrate the figures in the main article.</p> <p>3. Supplementary article_EAPP_data for figures.xlsx- This excel file contains the base data used to illustrate the figures in the supplementary article.</p>
GDS file for Pool-Seq object -- DEST + VA data
<p>See https://github.com/Jcbnunez/Cville-Seasonality-2016-2019</p>
Pooling robustness in distance sampling: Avoiding bias when there is unmodelled heterogeneity
<p>Data from a two-visit line transect survey of four songbird species gathered in spring 2004. Study area size was 33.2 ha of woodland and parkland on the Montrave Estate near Leven in Fife, Scotland.</p>
Optimal Catastrophe Risk Pooling
<p>This repository contains the code to reproduce the analysis in the paper: "Increasing countries’ financial resilience through global catastrophe risk pooling" from Ciullo et al..</p>
A genome-wide optical pooled screen reveals regulators of antiviral responses
<p>Supplementary Datasets for "A genome-wide optical pooled screen reveals regulators of antiviral responses"</p> <p><strong>Supplementary Dataset 1. </strong>Mean per-gene extracted features for all channels of genome-wide screen</p> <p><strong>Supplementary Dataset 2. </strong>Features from single cells in secondary antibody screen</p> <p><strong>Supplementary Dataset 3. </strong>Features from single cells in secondary reporter screen</p> <p><strong>Supplementary Dataset 4. </strong>IRF3 translocation scores from primary and secondary IRF3 antibody and IRF3 reporter screens (the latter upon both Sendai virus and VSV infection) and SeV intensity scores from secondary antibody screen.</p> <p><strong>Supplementary Dataset 5. </strong>Peroxisome and Sendai virus feature scores from genome-wide screen</p>
Data for: SNPs detected in pool-seq data from resistant and susceptible Cimex lectularius populations
<p>In the last few years, the bed bug <em>Cimex lectularius</em> has been an increasing problem world-wide, mainly due to the development of insecticide resistance to pyrethroids. The characterization of resistance alleles is a prerequisite to improve surveillance and resistance management. To identify genomic variants associated with pyrethroid resistance in <em>Cimex lectularius</em>, we compared the genetic composition of two recent and resistant populations with that of two ancientsusceptible strains using a genome-wide pool-seq design. We identified a large 6 Mb "superlocus" showing particularly high genetic differentiation and association with the resistance phenotype. This superlocus contained several clustered resistance genes, andwas also characterized by a high density of structural variants (inversions, duplications). The possibility that this superlocus constitute a resistance "supergene" that evolved after the clustering of alleles adapted to insecticide and after reduction in recombination is discussed.</p>
Data from: Pooled genome-wide CRISPR activation screening for rapamycin resistance genes in Drosophila cells
<p>Loss-of-function and gain-of-function genetic perturbations provide valuable insights into gene function. In <em>Drosophila</em> cells, while genome-wide loss-of-function screens have been extensively used to reveal mechanisms of a variety of biological processes, approaches for performing genome-wide gain-of-function screens are still lacking. Here, we describe a pooled CRISPR activation (CRISPRa) screening platform in <em>Drosophila</em> cells and apply this method to both focused and genome-wide screens to identify rapamycin resistance genes. The screens identified three genes as novel rapamycin resistance genes: a member of SLC16 family of monocarboxylate transporters (<em>CG8468)</em>, a member of the lipocalin protein family (<em>CG5399</em>), and a zinc finger C2H2 transcription factor (<em>CG9932</em>). Mechanistically, we demonstrate that <em>CG5399</em> overexpression activates the RTK-Akt-mTOR signaling pathway and that activation of insulin receptor (InR) by <em>CG5399</em> requires cholesterol and clathrin-coated pits at the cell membrane. This study establishes a novel platform for functional genetic studies in <em>Drosophila</em> cells.</p>
Large-scale saliva pooling as a screening strategy to control transmission_raw data
<p>This dataset include the raw data of our experience after building a bespoke laboratory to control critical areas by pooling samples of saliva. From August 2020 to February 2022; 928,528 individual self-samples of saliva were processed in 52,580 pools, 4,935 of which were positive and helped us detect 5,806 nonsymptomatic individuals. </p> <p>The dataset was collected directly from the laboratory information system and was processed to delete the columns with sensitive information.</p> <p>The Dataset was charged as XLSX file and only need a compatible software.</p> <p>To facilitate the understanding of the data set, which uses the Galician language and an internal nomenclature of our laboratory, we include a sheet named "description" and a README file in which it defines the terms used and their equivalence with those used in the article.</p>
Methods of species pool determination as predictors of survival in seeding and transplanting experiments
<ol> <li><span>Community composition is limited by a species' ability to reach, establish, and survive on a site. Establishment and survival are constrained by both abiotic conditions and biotic interactions that operate together on local scales. They decide which species from the pool will form the community. For this reason, it is very important to clearly define the species pool, against which the community composition is compared. </span></li> <li><span>The effect of biotic and abiotic factors can be assessed experimentally, and the species pool by using estimation methods based on broad-scale observational data. We compared success of five species pool estimation methods in predicting establishment and survival in a seed/transplant addition experiment. </span></li> <li> <span>In four different locations, we added resident and non-resident species to plots with and without competition and</span><span> tested the ability of the species to thrive in both competition-free gaps (constrained mainly by abiotic conditions) and in intact vegetation (complete community filter). In these treatments, we studied the seedling recruitment and survival, and the establishment and survival of pre-grown transplants. The ability of species pool assessment methods to predict species performance in individual treatments was compared. The comparison of results from individual treatments indicates the importance of individual components of the community filter. </span> </li> <li><span>Species pool assessment methods, based on species co-occurrence patterns (Beals index, Favourability, and Unconstrained ordination), were the best predictors of species performance in the intact vegetation but were less successful in the competition-free environment. Methods based on co-occurrence patterns were the most effective for predicting seedling establishment, while seed germination alone and transplant survival were poorly predictable. </span></li> <li><span>The biotic filter was the principal factor defining our community composition, especially for the process of seedling establishment. The roles of biotic and abiotic filters are very difficult to distinguish without an experimental approach and the ratio of their importance changes during plant ontogenesis.</span></li> </ol>
Soil labile nitrogen pools for the Carbon action ACA experiment for year 2022 (4th year of experiment)
<p>This dataset describes labile nitrogen pools following four years of carbon farming experiments in the Carbon Action ACA dataset of 20 farms. The soils were sampled in July and analyzed for Total N, ISNT-N, Autoclave citrate protein -N, Water soluble organic N, inorganic N and potentially mineralizable N. </p> <p>The analysis is published open access in Soil Use And Management. https://doi.org/10.1111/sum.12930</p>
Dataset on flow dynamics in rivers with riffle-pool morphology: results from case studies and field experiments on the Tagliamento River, Italy
<p>Riffle-pool sequences in rivers, formed due to interactions between river flow, alluvium and vegetation, provide vital ecological services to aquatic organisms and therefore are considered as fundamental habitats in fluvial ecosystems. Nevertheless, the knowledge of associated riffle-pool hydrodynamics is limited because of a lack of high-resolution data collected in rivers and scaling effects present in laboratory studies. Here we present a dataset on turbulent flow structure in riffle-pool sequences of a natural river. Two case studies and two field-based experiments were carried out in a side branch of the braided gravel-bed Tagliamento River in Italy. Our case studies deliver detailed information about the there-dimensional structure of mean and turbulent flows in natural riffle-pool/run and pool-riffle/glide transitions. Field-based experiments completed with the in-stream flume models of a riffle-pool transition and a shallow jet model provide a methodological bridge for linking simplified hydrodynamic theories of shallow jets to complex flow structure documented by our case studies. Therefore, this dataset enables examination of scaling effects and can be widely used for validation of numerical models.</p> <p> </p>
Pooled datasets for scover manuscript
<p>These are scanpy objects of the pooled datasets associated with <a href="https://doi.org/10.1101/2020.11.26.400218">our recent work</a>. Please note the datasets are gzipped to save space. The original datasets were obtained through the following sources:</p> <ul> <li>Human kidney data: <a href="https://www.kidneycellatlas.org/">https://www.kidneycellatlas.org/</a></li> <li>Tabula Muris data: <a href="https://figshare.com/articles/dataset/Single-cell_RNA-seq_data_from_Smart-seq2_sequencing_of_FACS_sorted_cells_v2_/5829687/8">https://figshare.com/articles/dataset/Single-cell_RNA-seq_data_from_Smart-seq2_sequencing_of_FACS_sorted_cells_v2_/5829687/8</a> (CC BY 4.0)</li> <li>Human brain data: <a href="https://github.com/GreenleafLab/brainchromatin">https://github.com/GreenleafLab/brainchromatin</a> (data can also be found <a href="https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE162170">here</a>)</li> </ul> <p>Please find more information in our pre-print about how the datasets were created. For more information about the method, please see the <a href="https://github.com/jacobhepkema/scover">associated github</a>.</p>
ScienceDex guides
Understand access before you commit
These curated guides explain access requirements, typical timelines, costs, and reuse considerations for widely used research datasets.
Allen Brain Atlas
Allen Brain Atlas is an Allen Institute collection of brain map atlases, datasets, APIs, and analysis tools covering mouse, human, and non-human primate brain resources.
Annotated Behaviour and Observability Dataset (ABODe)
ABODe is a University of Edinburgh DataShare dataset for behavior classification in group-housed mice using home-cage video, identities, bounding boxes, ground-plate positions, and annotator labels.
DANDI Archive for NWB datasets
DANDI is a BRAIN Initiative archive for publishing and sharing neurophysiology data, including electrophysiology, optophysiology, and behavioral data packaged as NWB and related standards.
International Brain Laboratory public data
The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.
OpenNeuro
OpenNeuro is a free, open platform for sharing neuroimaging datasets, with public search, dataset pages, and download paths for web, S3, DataLad, and the OpenNeuro CLI.