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50 results for “Enhanced sampling”
Improving the Efficiency of Variationally Enhanced Sampling with Wavelet-Based Bias Potentials
<p>Archive with data supporting the paper "Improving the Efficiency of Variationally Enhanced Sampling with Wavelet-Based Bias Potentials" and the related PhD thesis by B. Pampel</p>
Diverse Title Generation for Stack Overflow Posts with Multiple Sampling Enhanced Transformer
<p>Dataset for our paper "Diverse Title Generation for Stack Overflow Posts with Multiple Sampling Enhanced Transformer"</p> <p>(<a href="https://github.com/zfj1998/M3NSCT5">zfj1998/M3NSCT5: the code base for our paper "Diverse Title Generation for Stack Overflow Posts with Multiple Sampling Enhanced Transformer" (github.com)</a>)</p> <p>Including three files representing the train/val/test datasets. Each file contains all the collected data covering eight programming languages.</p>
BRAIN Journal-An Enhancement over Texture Feature Based Multiclass Image Classification under Unknown Noise-Figure 1. Sample Images of sixteen categories
<p>An image is often corrupted by noise in its acquisition or transmission. Noise is any<br> undesired information that degrades the image and appears in images from a variety of sources.</p> <p>Basically, there are three standard noise models [17], which model the types of noise<br> encountered in most images; they are additive noise, multiplicative noise and impulse noise. In this<br> work we have considered the occurrence of additive noise. An image function is given by f (x, y)<br> where (x, y) is spatial coordinate and f is intensity at point(x, y). Let f (x, y) be the original image,<br> g(x, y) be the noisy version and η(x, y) be the noise function, which returns random values coming<br> from an arbitrary distribution.</p>
Jumping the green wall: the use of PNA-DNA clamps to enhance microbiome sampling depth in wildlife microbiome research
As microbiome research moves away from model organisms to wildlife, new challenges for microbiome high throughput sequencing arise caused by the variety of wildlife diets. High levels of contamination are commonly observed emanating from the host (mitochondria) or diet (chloroplast). Such high contamination levels affect the overall sequencing depth of wildlife samples thus decreasing statistical power and leading to poor performance in downstream analysis. We developed an amplification protocol utilizing PNA-DNA clamps to maximize the use of resources and to increase the sampling depth of true microbiome sequences in samples with high levels of plastid contamination. We chose two study organisms, a bat (Leptonyteris yerbabuenae) and a bird (Mimus parvulus), both relying on heavy plant-based diets that sometimes lead to traces of plant-based faecal material producing high contamination signals from chloroplasts and mitochondria. On average, our protocol yielded a 13-fold increase in bacterial sequence amplification compared with the standard protocol (Earth Microbiome Protocol) used in wildlife research. For both focal species, we were able significantly to increase the percentage of sequences available for downstream analyses after the filtering of plastids and mitochondria. Our study presents the first results obtained by using PNA-DNA clamps to block the PCR amplification of chloroplast and mitochondrial DNA from the diet in the gut microbiome of wildlife. The method involves a cost-effective molecular technique instead of the filtering out of unwanted sequencing reads. As 33% and 26% of birds and bats, respectively, have a plant-based diet, the tool that we present here will optimize the sequencing and analysis of wild microbiomes.
Jumping the green wall: the use of PNA-DNA clamps to enhance microbiome sampling depth in wildlife microbiome research
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Enhancing comparative T-cell receptor repertoire analysis in small biological samples through pooling homologous cell samples from multiple mice
<p>All data files used to generate the figures in the paper are shared in this project.</p> <p>Scripts are available on <a href="https://github.com/i3-unit/CRM_24" target="_blank" rel="noopener">GitHub</a>.</p>
Leech-derived iDNA complements traditional surveying methods, enhancing species detections for rapid biodiversity sampling in the tropics
<p>Deforestation, exploitation, and other drivers of biodiversity loss in Madagascar leave its highly endangered and predominantly endemic wildlife at risk of extinction. Decreasing biodiversity threatens to compromise ecosystem functions and vital services provided to people. New, economical, and diverse methods of biodiversity monitoring can help to establish reliable baseline and long-term records of species richness. Metabarcoding with invertebrate-derived DNA (iDNA) has emerged as a promising new biosurveillance tool. An unexpected wet forest fragment tucked in the dry cliffs of Madagascar's southcentral plateau, the Ivohibory Protected Area (IPA), hosts a unique mosaic of species diversity, featuring both dry and wet forest species. Recently elevated to protected status, the IPA has been surveyed for flora and fauna with a range of inventory methods over three years and six expeditions (2016, 2017, & 2019). We collected 1,451 leeches over 12 days from the IPA to supplement known species richness and to compare results against current records. With iDNA, we pooled tissues, and isolated, and amplified bloodmeal DNA with five sets of primers. We detected 20 species of which four are species of frogs previously undetected and three of which are previously unknown to exist in this region. iDNA surveys can provide complementary data to traditional surveying methods like camera traps, line transects, and bioacoustic methods.</p>
Does Hamiltonian Replica Exchange via lambda-hopping enhance the sampling in alchemical binding free energy calculations?
<p>t-REM HREM lamba-hopping/FEP+ tests on the APA molecule with ORAC<br> (www.chim.unifi.it/orac) </p> <p>The untarred archive contains the following directories: </p> <p>t-rem -> contains input for gas-phase tests<br> st-hrem -> contains input for solvated APA with solute tempering<br> lam-hop -> contains input for solvated APA with lambda-hopping<br> bin -> scripts for REM analysis <br> lib -> APA starting conf and potential parameters for the runs </p> <p>see also README files inside each dir for further details </p>
Cloud computing is one of the most popular and sophisticated technologies adopted by organizations worldwide. Some world-leading organizations enhance their efficiency and effectiveness by using cloud computing technology. Working from home (WFH) has been a popular trend among organizations during the coronavirus (COVID-19) pandemic. The COVID-19 saw a breakthrough in work cultures and environments where working from home was a remarkable success in remote working environments, despite being a rare phenomenon in Sri Lanka. Yet, it is argued that the deployment of work from home has not been effective among Sri Lankan business organizations due to a lack of IT infrastructure, facilities, and knowledge. The purpose of the study is to investigate the impact of cloud computing, embracing the service models (Infrastructure as a Service, Platform as a Service, and Software as a Service) as theoretical lenses and testing the COVID-19 as the moderator. The study has been conducted based on a deductive approach and adopted a stratified random sampling method. The sample consisted of 384 IT employees among those who had experienced working from home. The study utilized multiple regression and found that cloud computing service models significantly impact work from home with the moderating effect of COVID-19.
<p>Cloud computing is one of the most popular and sophisticated technologies adopted by organizations worldwide. Some world-leading organizations enhance their efficiency and effectiveness by using cloud computing technology. Working from home (WFH) has been a popular trend among organizations during the coronavirus (COVID-19) pandemic. The COVID-19 saw a breakthrough in work cultures and environments where working from home was a remarkable success in remote working environments, despite being a rare phenomenon in Sri Lanka. Yet, it is argued that the deployment of work from home has not been effective among Sri Lankan business organizations due to a lack of IT infrastructure, facilities, and knowledge. The purpose of the study is to investigate the impact of cloud computing, embracing the service models (Infrastructure as a Service, Platform as a Service, and Software as a Service) as theoretical lenses and testing the COVID-19 as the moderator. The study has been conducted based on a deductive approach and adopted a stratified random sampling method. The sample consisted of 384 IT employees among those who had experienced working from home. The study utilized multiple regression and found that cloud computing service models significantly impact work from home with the moderating effect of COVID-19.</p>
Molecular basis for the increased affinity of an RNA recognition motif with re-engineered specificity: A molecular dynamics and enhanced sampling simulations study.
<p>This repository contains the representative structures of the 20 clusters obtained, which constitute the “MD-adapted structure ensemble”: i.e., sets of atomic coordinates that capture the flexibility and the pre-miR20b (<a href="https://zenodo.org/api/files/ee12021f-4398-465a-9ff6-ddb7be32765f/ensemble_MD_2n7x.pdb?versionId=310a80f6-aa64-445d-8641-45faf9f1ac03">ensemble_MD_2n7x.pdb</a>) and Rbfox/pre-miR20b (<a href="https://zenodo.org/api/files/ee12021f-4398-465a-9ff6-ddb7be32765f/ensemble_MD_2n82.pdb?versionId=82d7afcb-8a92-4daa-8150-789dbd7b2474">ensemble_MD_2n82.pdb</a>) conformers suggested by MD simulations while still retaining the highest possible level of agreement with the primary NMR data.</p>
Molecular basis for the increased affinity of an RNA recognition motif with re-engineered specificity: A molecular dynamics and enhanced sampling simulations study.-PART 8
<p>Simulations of the miR20b RNA with the Case vdW modification to amber force field and OPC water molecules.</p>
MD simulations files for: Enhanced Sampling of Biomolecular Slow Conformational Transitions Using Adaptive Sampling and Machine Learning
<div>Colvar files and related python scripts of Ala2 and Ala10 simulations.</div>
Reviving diversity: cryoprotectants and culturing methods enhance recovery of mammalian gut microbes from field samples
<p>Welcome!</p> <p>Here you will find the codes used in the analysis we ran for our manuscript titled "Reviving diversity: cryoprotectants and culturing methods enhance recovery of mammalian gut microbes from field samples". We would be happy to help in way we can, so please do not hesitate to reach out if you have questions or suggestions.</p> <p>In summary, we developed this study in response to challenges encountered in our own field research. Recent advancements in culturomics and microbiology are enabling us to further explore the realm of microbiome science. We aspire for this study to serve as a foundational step toward identifying preservation methods that can help protect the microbial communities of wild animals.</p> <p>Our study aims are:</p> <ol> <li>The primary objective of this study was to evaluate the effectiveness of various preservation solutions in maintaining microbial integrity of gut samples during collection and for a short duration, simulating transportation conditions, prior to long-term storage at -80°C. We cultivated the samples in three distinct culture media to maximize the recovery of microbial diversity.</li> <li>The second objective was to compare the inventory of the preserved and cultured microbial community to that of the original uncultured samples, aiming to determine whether the preservation solutions retained unique taxa absent in the frozen original samples.</li> </ol> <p>Notes to keep in mind:</p> <ol> <li>We chose preservation solutions that have already been described for microbial culturing.</li> <li>We chose culture media that have already been described for microbial culturing, especially gut microbiome samples.</li> </ol> <p><em>As you go through the Rmd document included here, please make sure all documents have been properly downloaded. Additionally, please make sure to change the names of the alpha diversity metric files in the Rmd to that of the files here as they were modified for proper uploading methods here. </em></p>
Sample programs of an eco-redox model for the article: Microbial redox cycling enhances ecosystem thermodynamic efficiency and productivity
<p><span>Microbial life in low-energy ecosystems relies on individual energy conservation, optimizing </span><span>energy use in response to interspecific competition, and mutualistic interspecific syntrophy. Our study proposes a novel community-level strategy for increasing energy use efficiency. By</span> <span>utilizing a</span><span>n</span> <span>oxidation-reduction (redox) reaction network model that represents microbial redox metabolic interactions, we </span><span>investigated multiple species-level competition and cooperation within the network</span><span>. Our results suggest that microbial functional diversity allows for metabolic handoffs</span><span>, which in turn lead to increased energy use efficiency. Furthermore, the mutualistic division of labor and the resulting </span><span>complexity of redox pathways actively </span><span>drive material cycling, further promoting energy exploitation. Our findings reveal the potential of self-organized ecological interactions to develop efficient energy utilization strategies, with important implications for microbial ecosystem functioning and </span><span>co-</span><span>evolution of life and Earth.</span></p>
Sample programs of an eco-redox model for the article: Microbial redox cycling enhances ecosystem thermodynamic efficiency and productivity
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Leech-derived iDNA complements traditional surveying methods, enhancing species detections for rapid biodiversity sampling in the tropics
Open the record for dataset details and reuse information.
Data from: Longer amplicon metabarcoding primers enhance fish taxonomic resolution in eDNA samples
Open the record for dataset details and reuse information.
Multiple Parameter Replica Exchange Gaussian Accelerated Molecular Dynamics for Enhanced Sampling and Free Energy Calculation of Biomolecular Systems
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Supplementary material 3 from: Swenson SJ, Eichler L, Hörren T, Kolter A, Köthe S, Lehmann GUC, Meinel G, Mühlethaler R, Sorg M, Gemeinholzer B (2022) The potential of metabarcoding plant components of Malaise trap samples to enhance knowledge of plant-insect interactions. Metabarcoding and Metagenomics 6: e85213. https://doi.org/10.3897/mbmg.6.85213
Supplementary material 3 from: Swenson SJ, Eichler L, Hörren T, Kolter A, Köthe S, Lehmann GUC, Meinel G, Mühlethaler R, Sorg M, Gemeinholzer B (2022) The potential of metabarcoding plant components of Malaise trap samples to enhance knowledge of plant-insect interactions. Metabarcoding and Metagenomics 6: e85213. https://doi.org/10.3897/mbmg.6.85213
Software artifacts corresponding to the paper "Pragmatic Random Sampling of the Linux Kernel: Enhancing the Randomness and Correctness of the conf Tool"
<div><strong>Software artifacts corresponding to the paper "Pragmatic Random Sampling of the Linux Kernel: Enhancing the Randomness and Correctness of the conf Tool"</strong></div> <div> </div> <div> <div> <div>This repository is organized in two main folders:</div> <br> <div>1. <strong>randconfig+</strong> includes the source code of our tool randconfig+, which improves the randomness and correctness of the conf tool (a built-in Linux kernel tool for generating random samples of kernel configurations). It has two subfolders:</div> - <strong>source</strong>: includes the source code of randconfig+. <div> - <strong>bin</strong>: includes the compiled version of randconfig+.</div> <br> <div>2. <strong>experimental_validation</strong> includes the experimental validation of randconfig+ reported in the paper.</div> - <strong>systems</strong>: includes the 10 Linux Kernel versions analyzed in the paper. <div> - <strong>scripts_for_sample_generation</strong>: Bash shell scripts to generate the data.</div> <div> - <strong>data</strong>: includes the following data generated by the experimental validation:</div> <div> + Generated samples (subfolder configuration_samples). The samples are available in two formats: CSV and <a href="https://r4ds.hadley.nz/arrow">Apache Arrow</a>.</div> <div> + Entropies and number of distinct values per configuration option.</div> <div> + Data regarding the correctness of the samples and the time spent to generate them (subfolder correctness_and_runtime).</div> <div> - <strong>statistical_analysis</strong>: R scripts to perform the statistical analysis of the data (subfolder statistical_analysis).</div> <div> - <strong>plots</strong>: graphs produced from the data statistical analysis.</div> </div> </div>
ScienceDex guides
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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.