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244 results for “Model Organisms”
The zebra mussel (Dreissena polymorpha) as a model organism for ecotoxicological studies: a prior 1H NMR spectrum interpretation of a whole body extract for metabolism monitoring.
<p>NMR data of the zebra mussel <em>Dreissena polymorpha</em> whole body polar extract metabolome</p> <p>- 1D <sup>1</sup>H annotated spectrum - 600 MHz</p> <p>- 2D <sup>1</sup>H-<sup>1</sup>H JRES spectrum - 600 MHz</p> <p>- 2D<sup>1</sup>H-<sup>1</sup>H COSY spectrum - 600 MHz</p> <p>- 2D<sup>1</sup>H-<sup>1</sup>H TOCSY spectrum - 600 MHz</p> <p>- 2D<sup>1</sup>H-<sup>13</sup>C HSQC spectrum - 600 MHz</p> <p>- 2D<sup>1</sup>H-<sup>13</sup>C HSQC spectrum - 800 MHz</p> <p>- 2D<sup>1</sup>H-<sup>31</sup>P HSQC spectrum - 800 MHz</p> <p>- <sup>1</sup>H annotated spectrum description tables (.xlsx)</p> <p>- Instructions for data visualization in Topspin</p>
Evaluation of the administrative management model in a municipality in Peru, incorporating the Intelligent Organization Theory
<p><strong>Background:</strong> This study begins with the analysis of the current management models and their degree of effectiveness in municipal administration. Its aim is to design an administrative management model that enables effective administration in the District Municipality of Nueva Cajamarca, Peru, based on the theory of intelligent organizations.</p><p><strong>Method: </strong>The research type employed in this study is diagnostic-propositional, utilizing both deductive and inductive methods, in alignment with a mixed-method approach and a non-experimental nature of the study. Data was collected from three distinct populations, including the 189 municipal employees engaged in administrative roles, who were subjected to a 50-question survey. This survey aimed to assess their perceptions regarding the current management model and its relationship with administrative effectiveness. Additionally, interviews were conducted with three experts to gain deeper insights into the behavior of the variables under investigation.</p><p><strong>Results: </strong>Finally, documentary information about the management models currently in use was collected. This facilitated the triangulation of data collection, processing, analysis, and inferences from three sources of information. The results reveal a positive, direct, and significant correlation between the management model and administrative effectiveness. It becomes evident that the current management model is deficient, resulting in a low level of administrative effectiveness</p><p><strong>Conclusion: </strong></p><p>The management model based on the theory of intelligent organizations was validated using a rubric by experts in effective management. The main pillars of this model include transformational leadership, structural change, and cultural change.</p>
Knowledge Discovery from Porous Organic Cages Literature Using a Large Language Model
<p>This article presents a GPT-4-based literature reading method that incorporates multi-label text classification and a follow-up information extraction, in which the potential of GPT-4 can be fully exploited to rapidly extract valid information from the literature. In the process of multi-label text classification, the prompt-engineered GPT-4 demonstrated the ability to label text with proper recall rates according to the type of information contained in text, including authors, affiliations, synthetic procedures, surface area, and the CCDC number of corresponding cages. Additionally, GPT-4 demonstrated proficiency in information extraction, effectively transforming labeled text into concise tabulated data. Furthermore, we built a chatbot based on this database, allowing for quick and comprehensive searching across the entire database and responding for cage-related questions.</p>
Supplementary Material for "Model-Free Analysis of Experimental Residual Diploar Couplings in Small Organic Compounds"
<p>NMR Spectra (CLIP-HSQC, perfectCLIP-HSQC, TSE-PSYCHEDELIC) of isopinocampheol in six alignment conditions.</p> <p>Simulation input (experimental RDC data in six alignment media, input geometries, keywords) and output files (simulation / geometry trajectories, alignment data, SECONDA analysis) for isopinocampheol runs with the TITANIA software.</p>
Model simulations using a parameterization of convective organization effects
<p>We propose a parameterization scheme of convective organization effects based on a moisture-distribution approach. We implement it into a regional climate model and evaluate its performance against a convection-permitting model simulation. The related model simulations are included in this dataset.</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>
Data from: Microplastic exposure is associated with epigenomic effects in the model organism Pimephales promelas (fathead minnow)
<p>Microplastics have evolutionary and ecological impacts across species, affecting organisms' development, reproduction, and behavior along with contributing to genotoxicity and stress. As plastic pollution is increasing and ubiquitous, gaining a better understanding of organismal responses to microplastics is necessary. Gene methylation is a heritable form of molecular regulation that is influenced by environmental conditions, including exposure to pollutants, therefore determining epigenetic responses to microplastics will reveal potential chronic consequences of this pollutant. We performed an experiment across two generations of fathead minnows (<em>Pimephales promelas</em>) to elucidate transgenerational effects of microplastic exposure. We exposed the first generation of fish to four different treatments of microplastics: two concentrations of each of pre-consumer polyethylene (PE) and PE collected from Lake Ontario. We then raised the second generation from these parents with no microplastic exposure. We used reduced-representation methylation sequencing on adult liver tissue and homogenized larvae to evaluate DNA methylation differences among treatments, sexes, and generations. Our findings show the origin of the plastic had a larger effect in female minnows whereas the effect of concentration was stronger in the males. We also observed transgenerational effects, highlighting a mechanism in which parents can pass on the effects of microplastic exposure to their offspring. Many of the differentially methylated genes found in our analyses are known to interact with estrogenic chemicals associated with plastic and are related to metabolism. This study highlights the persistent and potentially serious impacts of microplastic pollution on gene regulation in freshwater systems.</p>
Data for publication "A unified surface tension model for multi-component salt, organic and surfactant solutions"
<p>This repository contains the data of the publication:</p> <p>Title: "A unified surface tension model for multi-component<br>salt, organic and surfactant solutions"<br>Authors: Judith Kleinheins, Claudia Marcolli, Cari Dutcher, Nadia Shardt<br>Date: 2024</p>
Supplementary materials for "Effects of mesozooplankton growth and reproduction on plankton and organic carbon dynamics in a marine biogeochemical model"
<h2>Overview</h2> <p>This folder contains supplementary materials corresponding to the analysis conducted for "Effects of mesozooplankton growth and reproduction on plankton and organic carbon dynamics in a marine biogeochemical model". The folder is structured into two .zip files. <a href="../api/records/10720907/draft/files/ZENODO_PISCES_MLC.zip/content" target="_blank" rel="noopener noreferrer">ZENODO_PISCES_MLC.zip</a> contains the analysis presented in the paper. BDM-MAREDAT-ZENODO.zip contains the outputs from the Biomass Distribution Models pipeline developped by Nielja Knecht (<a href="../doi/10.5281/zenodo.7888451">10.5281/zenodo.7888451</a>) applied to the MAREDAT mesozooplankton product. </p> <h2>ZENODO_PISCES_MLC Folder Structure</h2> <h3>BDM</h3> <ul> <li><strong>MAREDAT_TUNED_SDM.csv</strong>: This file contains the BDM mesozooplankton biomass monthly climatology from MAREDAT data.</li> </ul> <h3>CODE</h3> <p>This directory contains Jupyter Notebook files (<code>.ipynb</code>) and related Python scripts used for data analysis and visualization. Below is a list of the files:</p> <ul> <li><strong>Code_Fig3_FigA8_FigA17.ipynb</strong>: Jupyter Notebook for generating figures 3, A8, and A17.</li> <li><strong>Code_Fig4.ipynb</strong>: Jupyter Notebook for generating figure 4.</li> <li><strong>Code_Fig5_FigA12_FigA13.ipynb</strong>: Jupyter Notebook for generating figures 5, A12, and A13.</li> <li><strong>Code_Fig6.ipynb</strong>: Jupyter Notebook for generating figure 6.</li> <li><strong>Code_Fig7.ipynb</strong>: Jupyter Notebook for generating figure 7.</li> <li><strong>Code_FigA10.ipynb</strong>: Jupyter Notebook for generating figure A10.</li> <li><strong>Code_FigA11.ipynb</strong>: Jupyter Notebook for generating figure A11.</li> <li><strong>Code_FigA14.ipynb</strong>: Jupyter Notebook for generating figure A14.</li> <li><strong>Code_FigA15.ipynb</strong>: Jupyter Notebook for generating figure A15.</li> <li><strong>Code_FigA16.ipynb</strong>: Jupyter Notebook for generating figure A16.</li> <li><strong>Code_FigA1.ipynb</strong>: Jupyter Notebook for generating figure A1.</li> <li><strong>Code_FigA2.ipynb</strong>: Jupyter Notebook for generating figure A2.</li> <li><strong>Code_FigA6_FigA7.ipynb</strong>: Jupyter Notebook for generating figures A6 and A7.</li> <li><strong>Code_FigA9.ipynb</strong>: Jupyter Notebook for generating figure A9.</li> <li><strong>Code_POC_metrics_not_in_the_paper.ipynb</strong>: Jupyter Notebook containing metrics related to particulate organic carbon (POC) not included in the paper.</li> <li><strong>Code_Table3.ipynb</strong>: Jupyter Notebook for generating table 3.</li> <li><strong>Code_Table4.ipynb</strong>: Jupyter Notebook for generating table 4.</li> <li><strong>Code_Table5.ipynb</strong>: Jupyter Notebook for generating table 5.</li> <li><strong>GlobalEstimatesAbstract.ipynb</strong>: Jupyter Notebook containing global estimates abstract.</li> <li><strong>mlctools</strong>: Python package containing utility functions for the analysis.</li> </ul> <h3>OBS</h3> <p>This directory contains observed data used in the analysis:</p> <ul> <li><strong>BATS_zooplankton.csv</strong>: Zooplankton data from the Bermuda Atlantic Time-series Study (BATS).</li> <li><strong>CHL2.nc</strong>: Chlorophyll data in NetCDF format.</li> <li><strong>climatology_n_0_5.nc</strong>: Climatological data in NetCDF format.</li> <li><strong>HOTS_zooplankton.csv</strong>: Zooplankton data from the Hawaii Ocean Time-series (HOTS).</li> </ul> <h3>OUTPUT</h3> <p>This directory contains output files from PISCES simulations (yearly, monthly and 5-day-average outputs). </p> <ul> <li><strong>0class</strong>: Output files for the '0class' classification corresponding to PISCES-v2.</li> <li><strong>0classregrid</strong>: Regridded output files for the '0class' classification corresponding to PISCES-v2.</li> <li><strong>10classes</strong>: Output files for the '10classes' classification corresponding to PISCES-MOG.</li> <li><strong>10classesregrid</strong>: Regridded output files from PISCES-MOG.</li> <li><strong>2classes</strong>: Output files from PISCES-MOG-2LS.</li> <li><strong>2classesregrid</strong>: Regridded output files from PISCES-MOG-2LS.</li> <li><strong>NOALLOregrid</strong>: Regridded output files from PISCES-MOG-NA.</li> </ul> <h3>PLOT</h3> <p>This directory contains plots generated during the analysis:</p> <h3>TEMP</h3> <p>This directory contains temporary files used during the analysis, including data files and matrices.</p> <h2>BDM-MAREDAT-ZENODO Folder </h2> <p>BDM-MAREDAT-ZENODO.zip contains the outputs from the Biomass Distribution Models pipeline developped by Nielja Knecht (<a href="../doi/10.5281/zenodo.7888451">10.5281/zenodo.7888451</a>) applied to the MAREDAT mesozooplankton product. </p> <p>For any inquiries or data access requests, please contact corentin.clerc -at- usys.ethz.ch</p>
Replication data for "Gekko gecko as a model organism for understanding aspects of laryngeal vocal evolution"
<p>This dataset contains raw data and analysis code used in the preparation of the manuscript “<em>Gekko gecko</em> as a model organism for understanding aspects of laryngeal vocal evolution”.</p>
New parameter estimates for exogenous organic materials including biochar for the Rothamsted carbon model
<p><span>This parameter set has been established within the EJP Soil project Carboseq and is fully explained in the corresponding report (Leifeld, J., Hardy, B., Budai, A., Elsgaard, L., Keel, S.G., Levavasseur, F., Liang, Z., Mondini, C., Plaza, C., Rodrigues, L. 2024. Soil organic carbon sequestration potential of agricultural soils in Europe. Final report EJP Soil CarboSeq work package 3 – Biochar and other organic amendments).</span></p>
Genetics of Cardiac Aging Implicate Organ-Specific Variation - GWAS Summary Stats and Model Weights
Open the record for dataset details and reuse information.
Development of an imaging toolbox to assess the therapeutic potential and biodistribution of macrophages in a mouse model of multiple organ dysfunction
<p>Data set to accompany manuscript entitled "Development of an imaging toolbox to assess the therapeutic potential and biodistribution of regenerative therapies in a mouse model of multiple organ dysfunction " which can be found on BioRxiv.</p>
Three-point contact data for "Multi-contact statistics distinguish models of chromosome organization"
<p>Three-point contact data for the publication "Multi-contact statistics distinguish models of chromosome organization".</p>
Supplementary Material for "TITANIA Model-Free Interpretation of Residual Dipolar Couplings in the Context of Organic Compounds"
<p>Simulation input (RDC data, input geometries, keywords) and output files (simulation / geometry trajectories, alignment data, SECONDA analysis) for isopinocampheol, tubocurarine and strychnine runs with the TITANIA software.</p>
Target enrichment of long open reading frames and ultraconserved elements to link microevolution and macroevolution in non-model organisms
<p>Despite the increasing accessibility of high-throughput sequencing, obtaining high-quality genomic data on non-model organisms without proximate well-assembled and annotated genomes remains challenging. Here we describe a workflow that takes advantage of distant genomic resources and ingroup transcriptomes to select and jointly enrich long open reading frames (ORFs) and ultraconserved elements (UCEs) from genomic samples for integrative studies of microevolutionary and macroevolutionary dynamics. This workflow is applied to samples of the African unionid bivalve tribe Coelaturini (Parreysiinae) at basin and continent-wide scales. Our results indicate that ORFs are efficiently captured without prior identification of intron-exon boundaries. The enrichment of UCEs was less successful but nevertheless produced substantial datasets. Exploratory continent-wide phylogenetic analyses with ORF supercontigs (> 515,000 parsimony informative sites) resulted in a fully resolved phylogeny, the backbone of which was also retrieved with UCEs (> 11,000 informative sites). Variant calling on ORFs and UCEs of Coelaturini from the Malawi Basin produced ~2,000 SNPs per population pair. Estimates of nucleotide diversity and population differentiation were similar for ORFs and UCEs. They were low compared to previous estimates in mollusks, but comparable to those in recently diversifying Malawi cichlids and other taxa at an early stage of speciation. Skimming off-target sequence data from the same enriched libraries of Coelaturini from the Malawi Basin, we reconstructed the maternally-inherited mitogenome, which displays the gene order inferred for the most recent common ancestor of Unionidae. Overall, our workflow and results provide exciting perspectives for integrative genomic studies of microevolutionary and macroevolutionary dynamics in non-model organisms.</p>
Can short-term data accurately model long-term environmental exposures? Investigating the multigenerational adaptation potential of Daphnia magna to environmental concentrations of organic ultraviolet filters
<p>Organic ultraviolet filters (UVFs) are contaminants of concern, ubiquitously found in many aquatic environments due to their use in personal care products to protect against ultraviolet radiation. Research regarding the toxicity of UVFs such as avobenzone, octocrylene and oxybenzone indicates that these chemicals may pose a threat to invertebrate species; however, minimal long-term studies have been conducted to determine how these UVFs may affect continuously exposed populations. The present study modeled the effects of a 5-generation exposure of <em>Daphnia</em> <em>magna</em> to these UVFs at environmental concentrations. Avobenzone and octocrylene resulted in minor, transient decreases in reproduction and wet mass. Oxybenzone exposure resulted in > 40% mortality, 46% decreased reproduction and 4-fold greater reproductive failure over the F0 and F1 generations; however, normal function was largely regained by the F2 generation. These results indicate that <em>Daphnia</em> are able to acclimate over long-term exposures to concentrations of 6.59 μg/L avobenzone, ~0.6 μg/L octocrylene or 16.5 μg/L oxybenzone. This suggests that short-term studies indicating high toxicity may not accurately represent long-term outcomes in wild populations, adding additional complexity to risk assessment practices at a time when many regions are considering or implementing UVF bans in order to protect these most sensitive invertebrate species.</p>
Modelling knowledge organization systems and structures
<p>In the last few decades, knowledge organization systems (KOS), especially thesauri,<br> classification schemes and lists of subject headings, have largely followed or conformed<br> with the established data models defined by standards, recommendations or best practices.<br> This long list contains some widely used models, such as ISO5964 Part 1, ISO2788, Z39.19,<br> BS 5723 and BS 6723, (Dextre Clarke, 2008) IFLA Principles Underlying Subject Heading<br> Languages (SHLs), and MARC 21 Format for Classification Data.<br> The FRSAD (Functional Requirements for Subject Authority Data) conceptual model is<br> the third member of the FRBR family, developed under the auspices of IFLA. The report<br> was approved in 2010 and will be published in 2011. FRSAD is a general conceptual model<br> that focuses on the subject relationship and therefore provides a theoretical framework for<br> all KOS and their data models. In addition, it also assists in the assessment of the potential<br> for international sharing and (re)use of subject authority data both within the library sector<br> and beyond.<br> In this paper FRSAD is compared to SKOS and SKOS XL as data models (with implementa-<br> tion examples).</p>
Dynamic Vegetation Model Dynamic Organic Soil Terrestrial Ecosystem Model (DVM-DOS-TEM) simulations focused on Eight Mile Lake, Alaska and Imnavait Creek, Alaska [2000-2015]
<p>This set of files store model simulations using the biosphere model Dynamic Vegetation Model Dynamic Organic Soil Terrestrial Ecosystem Model (DVM-DOS-TEM), developed to simulate biophysical and biogeochemical interactions between the soil, vegetation and atmosphere. To improve predictions of net carbon releases from thawing permafrost, we tested the sensitivity of a suite of model parameters. We analyzed the responses of ecosystem carbon balances to permafrost thaw by running site-level simulations at two long-term tundra ecological monitoring sites in Alaska: Eight Mile Lake (EML) and Imnavait Creek watershed (IMN). These sites are characterized by similar tussock tundra vegetation but differing soil drainage conditions and climate, IMN consists of well-drained soils, and EML has historically well-drained soils, however permafrost thaw has altered drainage conditions to wetter soils. Simulations were conducted at a 1km resolution, over a 1,000 km2 area (10x10 km square) centered on two long term ecological research sites in Alaska: Eight Mile Lake located in Interior Alaska (63.8900° N, 149.2535° W), and Imnavait creek watershed located on the northern foothills of the Brooks range (68°37′ N, 149°18′ W).</p> <p>Historical simulations are spanning the 2000 to 2015, and forced using climate simulations from the Climate Research Unit, time series 4.0. We ran 1,000 site level simulations for each model variable. The variables that are produced are gross primary productivity (GPP, in gC.m-2.m-1), net ecosystem exchange (NEE, gC.m-2.m-1), ecosystem respiration (RECO, gC/m2/m-1), active layer thickness (ALT, m), soil temperature (TLAYER,°C) at 5, 10, 40 cm depths, soil moisture (LWCLAYER, m-3/m-3) at 5, 10 cm depths, and snow depth (SNOWDEPTH, m), evapotransipiration(EET, mm/m2/time), potential evapotransipiration (PET, mm/m2/time), leaf area index (LAI, m2/m2), organic layer thickness (OLT, m). The data are stored as compiled csv files, with time as the index, and each model sample output stored in the columns. In addition, there is a postprocessing python script to demonstrate the step and workflow used to generate the individual csv files post processed from the raw model outputs stored as netcdfs.</p>
Alphafold predicted structures of VPS13 proteins from model organisms
<p>This upload contains AlphaFold-predicted structures of VPS13 proteins from a variety of organisms. Given the large size of these proteins, only partial sequences were predicted with AlphaFold(1) and the resulting structures were aligned in PyMOL(2). A summary of the structures uploaded here is presented as a collection of domain cartoons in the "VPS13 domain organization across eukaryotic evolution.pdf" file. </p> <p>The structures were generated with AlphaFold v2.029 on the Yale High Performance Cluster. Each *.zip file contains the best ranked predictions (out of five) for each sequence (*.pdb files) and the PyMOL assembled full structure (*.pse file). In a few cases, where a good alignment was not possible due to long disordered regions in the C-terminal portions (mostly in proteins from <em>D. discoideum</em> and <em>A. thaliana</em>), the full structures were aligned manually in PyMOL based on the continuity of the lipid transfer groove. The structures in PyMOL can be colour-coded by the confidence value of AlphaFold predictions using the following prompt:</p> <p>set_color n0, [0.051, 0.341, 0.827]<br> set_color n1, [0.416, 0.796, 0.945]<br> set_color n2, [0.996, 0.851, 0.212]<br> set_color n3, [0.992, 0.490, 0.302]<br> color n0, b < 100; color n1, b < 90<br> color n2, b < 70; color n3, b < 50</p> <p>Considering that full length structures were assembled by aligning different protein fragments and in view of the presence of flexible loops with low prediction confidence scores, the relative positions of different folded domains are not necessarily correct.</p> <p> </p> <p><strong>References</strong></p> <p>1. J. Jumper, <em>et al.</em>, Highly accurate protein structure prediction with AlphaFold. <em>Nature</em> 596, 583–589 (2021).</p> <p>2. The PyMOL Molecular Graphics System, Version 2.0. Schrödinger LLC.</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.