Find research datasets worth reusing

Data Analysis for: Coupling Cell Size Regulation and Proliferation Dynamics for C. glutamicum Reveals Cell Division Based on Surface Area

<div>Data and methods of Data Analysis of: Coupling Cell Size Regulation and Proliferation Dynamics of</div> <div>C. glutamicum Reveals Cell Division Based on Surface Area</div> <div> </div> <div>Authors: Cesar Nieto and Zahra Vahdat at University of Delaware (2023)</div> <div>Correspondence: cnieto@udel.edu.</div> <div> </div> <div> </div>

Seamount subduction and accretion dynamics of the Franciscan complex

Dataset for "Seamount subduction and accretion dynamics of the Franciscan complex" by Bonnet et al. - D1: Sample location, description and mineralogy - D2 : Bulk rock analyses - D3 : EPMA data - D4 : Synthesis of temperatures from Raman Spectroscopy of Carbonaceous Material - D5 : Titanite U-Pb-trace element data - D6 : Zircon U-Pb-trace element data

opencc-zeroJan 2024View details →

Demographic mechanisms and anthropogenic drivers of contrasting population dynamics of hummingbirds

Conserving species requires knowledge of demographic rates (survival, recruitment) that govern population dynamics to allow the allocation of limited resources to the most vulnerable stages of target species' life cycles. Additionally, quantifying drivers of demographic change facilitates the enactment of specific remediation strategies. However, knowledge gaps persist in how similar environmental changes lead to contrasting population dynamics through demographic rates. For sympatric hummingbird species, the population of urban-associated partial-migrant Anna's hummigbird (Calypte anna) has increased, yet the populations of Neotropical migrants including rufous, calliope, and black-chinned hummingbirds have decreased. Here, we developed an integrated population model to jointly analyze 25 years of mark-recapture data and population survey data for these four species. We examined the contributions of demographic rates on population growth and evaluated the effects of anthropogenic stressors including human population density and crop cover on demographic change in relation to species' life histories. While recruitment appeared to drive the population increase of urban-associated Anna's hummingbirds, decreases in juvenile survival contributed most strongly to population declines of Neotropical migrants and highlight a potentially vulnerable phase in their life-history. Moreover, rufous hummingbird adult and juvenile survival rates were negatively impacted by human population density. Mitigating threats associated with intensively modified anthropogenic environments is a promising avenue for slowing further hummingbird population loss. Overall, our model grants critical insight into how anthropogenic modification of habitat affects the population dynamics of species of conservation concern.

Targeted micro-fiber arrays for measuring and manipulating localized multi-scale neural dynamics over large, deep brain volumes during behavior: resources and main figure data

Summary: Neural population dynamics relevant for behavior vary over multiple spatial and temporal scales across 3-dimensional volumes. Current optical approaches lack the spatial coverage and resolution necessary to measure and manipulate naturally occurring patterns of large-scale, distributed dynamics within and across deep brain regions such as the striatum. We designed a new micro-fiber array approach capable of chronically measuring and optogenetically manipulating local dynamics across over 100 targeted locations simultaneously in head-fixed and freely moving mice. We developed a semi-automated micro-CT based strategy to precisely localize positions of each optical fiber. This highly-customizable approach enables investigation of multi-scale spatial and temporal patterns of cell-type and neurotransmitter specific signals over arbitrary 3-D volumes at a spatial resolution and coverage previously inaccessible. We applied this method to resolve rapid dopamine release dynamics across the striatum volume which revealed distinct, modality specific spatiotemporal patterns in response to salient sensory stimuli extending over millimeters of tissue. Targeted optogenetics through our fiber arrays enabled flexible control of neural signaling on multiple spatial scales, better matching endogenous signaling patterns, and spatial localization of behavioral function across large circuits.  Files included:  <ul> <li>Vu, M-A. et al. (2023) - Key Resources Table.xlsx -- key resources used in this study</li> <li>README_figure_data_and_analysis.txt --a description of the organization of the files within this repository</li> <li>README_preprocessing_code.txt -- details about the preprocessing pipeline (including registration and localization pipelines) and annotation of the preprocessed data structure</li> <li>preprocessing_code.zip -- contains all the preprocessing code</li> <li>Fig01.zip -- preprocessed data and analysis code for main Figure 1</li> <li>Fig03.zip -- preprocessed data and analysis code for main Figure 3</li> <li>Fig04.zip -- preprocessed data and analysis code for main Figure 4</li> <li>Fig05.zip -- preprocessed data and analysis code for main Figure 5</li> <li>Fig06.zip -- preprocessed data and analysis code for main Figure 6</li> <li>Fig07.zip -- preprocessed data and analysis code for main Figure 7</li> <li>SuppFig01.zip -- preprocessed data and analysis code for supplemental Figure 1</li> <li>SuppFig02.zip -- preprocessed data and analysis code for supplemental Figure 2</li> <li>SuppFig03.zip -- preprocessed data and analysis code for supplemental Figure 3</li> <li>SuppFig04.zip -- preprocessed data and analysis code for supplemental Figure 4</li> <li>SuppFig05.zip -- preprocessed data and analysis code for supplemental Figure 5</li> <li>SuppFig06.zip -- preprocessed data and analysis code for supplemental Figure 6</li> <li>SuppFig07.zip -- preprocessed data and analysis code for supplemental Figure 7</li> </ul> Each .zip file contains a folder corresponding to a figure.  Within each figure folder will be a folder corresponding to the letter (e.g., A, B, C) of the panel within the figure. In addition to the panel folders, when applicable, there may also be a folder containing general-use functions or scripts, or interim results .mat files, that are called by the scripts within the subfolders. In each subfolder there will be 3 things: <ol> <li>a folder of preprocessed data (see README_preprocessing_code.txt)</li> <li>a folder of the analysis scripts that analyzed the preprocessed data and generated the figure</li> <li>a README text file detailing the contents of both folders and the analysis workflow.</li> </ol>

openJan 2024View details →

Assessing microbiome population dynamics using wild-type isogenic standardized hybrid (WISH)-tags

Microbiomes feature recurrent compositional structures under given environmental conditions. However, these patterns may conceal diverse underlying population dynamics that require intra-strain resolution. Here, we developed a genomic tagging system, termed wild-type isogenic standardized hybrid (WISH)-tags, that can be combined with quantitative PCR and next-generation sequencing for microbial strain enumeration. We experimentally validated the performance of 62 tags and showed they can be differentiated with high precision. WISH-tags were introduced into model and non-model bacterial members of the mouse and plant microbiota. Intra-strain priority effects were tested using one species of isogenic barcoded bacteria in the murine gut and the Arabidopsis phyllosphere, both with and without microbiota context. We observed colonization resistance against late arriving strains of Salmonella typhimurium in the mouse gut, whereas the phyllosphere accommodated Sphingomonas latecomers in a proportional manner to their presence at the late inoculation timepoint. This demonstrates that WISH-tags are a resource for deciphering population dynamics underlying microbiome assembly across biological systems.

opencc-zeroJan 2024View details →

Data from: Molecular docking and dynamics studies to identify novel active compounds targeting potential breast cancer receptor proteins from an indigenous herb Euphorbia thymifolia Linn

Breast cancer has become most prevalent disease and their incidence has doubled in Indian scenario. Targeted therapy with the novel compounds derived from plants could be the promising approach for the development of drugs. Euphorbia thymifolia L is a widely growing tropical herb which has been reported for its various ethnopharmacological properties, including anticancer properties. The aim of the present study was to identify the active phytocompounds present in the methanolic extract using an In-silico approach. The methanolic extract of E. thymifolia (ME.ET) was subjected to GC-MS analysis and the identified compounds were docked with potential protein targets implicated in breast cancer such as ERK1, AKT, EGFR/HER2, ER, MELK, PLK1, PTK6. Compounds with good docking score were further subjected to dynamics study to understand the protein ligand binding stability, ligand pathway calculation, molecular mechanics energies combined with Poisson-Boltzmann (MM/PBSA) calculation using Schrodinger suite. Out of 219 unique phytocompounds subjected to docking, two compounds namely, 3,6,9,12-tetraoxatetradecane-1,14-diyl dibenzoate (TTDB) and succinic acid, 2-(dimethylamino)ethyl 4-isopropylphenyl ester (SADPE) showed good docking score. Molecular dynamics study showed high affinity and low binding energy for TTDB with HER2, ERK1 and SADPE with ER. Hence this is the first study to identify and report active compounds from E.thymifolia linn. Further invitro and invivo anticancer studies can be performed to confirm these results and understand the molecular mechanism by which TTDB and SADPE exhibit anticancer activity against breast cancer.

opencc-by-4.0Jan 2024View details →

Data needed to reproduce analysis from "Frost matters: Incorporating late-spring frost in a dynamic vegetation model regulates regional productivity dynamics in European beech forests"

Data to reproduce analysis from "Frost matters: Incorporating late-spring frost in a dynamic vegetation model regulates regional productivity dynamics in European beech forests". This includes: <ol> <li>Tree ring data (meyer, bdn, principe, dittmar)</li> <li>LPJ-GUESS model output (frost_validation, frost_sensitivity, runs_22012024_revision)</li> <li>Data used for plotting</li> </ol>

opencc-zeroJan 2024View details →

Subregions specific dynamics of striatal dopamine

<div> <div> <div> Transient increases in dopamine within the striatum can encode reward prediction errors, critical signals for updating predictions of future rewards. However, it is unclear how this mechanism can provide suitable feedback for predictions across a wide range of time horizons: from seconds or less (if singing a song) to potentially hours or more (if hunting for food). Here we report that dopamine transients in distinct striatal subregions convey prediction errors over distinct time scales. Dopamine dynamics systematically accelerated from ventral to dorsal- medial to dorsal-lateral striatum, in the tempo of their spontaneous fluctuations, their temporal integration of prior rewards, and their discounting of future rewards. This spectrum of time scales for evaluative computations can help achieve efficient learning and adaptive motivation for a wide range of behaviors. </div> </div> </div>

opencc-zeroFeb 2024View details →

Data from: Disentangling the dynamics among climate, food availability, and reproduction in a pair-living, monogamous primate

We examined the hypothesis that pair-living, monogamous social systems evolved in environments with evenly distributed food resources, a homogenous distribution of females in space prevents males from monopolizing more than one female. Our study investigated the interplay between climatic variables (ambient temperature, rainfall), food availability (forest structure, phenology data), and infant production in a pair-living monogamous owl monkey population (322 births, 21 years, 22 groups) in the humid Chaco of Argentina. Associations between climatology and fruit availability ranged from -0.29 to 0.38, and some extreme events negatively impacted fruit availability. Variation in fruit availability was higher among years than territories, whereas infant production varied more among territories than it did across years. Our study makes specific contributions to examining the hypothetical "homogeneity" in the temporal and spatial distribution of food available to a pair-living monogamous primate and how such variation relates to infant production in the population.

opencc-by-4.0Feb 2024View details →

Ligand efficacy modulates conformational dynamics of the µ-opioid receptor

This dataset includes DEER data from: Zhao and Elgeti et al. (2024) doi: 10.1038/s41586-024-07295-2

opencc-by-4.0Feb 2024View details →

Learning Markovian Dynamics with Spectral Maps

Used in the following publications: <ul> <li> J. Rydzewski, T. Gökdemir Learning Markovian Dynamics with Spectral Maps J. Chem. Phys. 160, 091102 (2024) <a href="https://doi.org/10.1063/5.0189241">doi:10.1063/5.0189241</a> / <a href="https://arxiv.org/abs/2311.16411">arXiv:2311.16411</a> / <a href="https://zenodo.org/records/10678142">Zenodo:10678142</a> / <a href="https://www.plumed-nest.org/eggs/24/005/">plumID:24.005</a> </li> <li> J. Rydzewski Spectral Map: Embedding Slow Kinetics in Collective Variables J. Phys. Chem. Lett. 14, 5216 (2023) <a href="https://doi.org/10.1021/acs.jpclett.3c01101">DOI:10.1021/acs.jpclett.3c01101</a> / <a href="https://arxiv.org/abs/2404.01809">arXiv:2404.01809</a> </li> </ul>

opencc-by-4.0Jul 2023View details →

Collective dynamics and pair-distribution function of active Brownian ellipsoids

Supplemental data for the following manuscript: Stephan Bröker, Michael te Vrugt, Raphael Wittkowski, "Collective dynamics and pair-distribution function of active Brownian ellipsoids"

Dynamic shifts in the Southern Benguela Upwelling System since the latest Miocene

The dataset consists of planktic foraminiferal abundance data and stable oxygen and carbon isotope records of shallow and deep-dwelling planktic foraminifera.

opencc-zeroMar 2024View details →

Data from: Seasonal host community dynamics constrain the risk of parasite transmission between migrant and resident species

Seasonal migration shapes the community dynamics that influence pathogen transmission between migrants and resident species. While theoretical and empirical evidence has accumulated, whether migration increases or decreases the risk of cross-species infection remains inconclusive. We studied how the seasonal arrival and departure of a single avian migrant species change the composition of local communities in breeding areas affecting the haemosporidian infection dynamics. The seasonal reordering of resident species abundances induced by migrants, minimizes the opportunities for contact between highly infected hosts and susceptible species, either migrants or residents, thereby limiting the transmission of parasites to occasional spillover events. The occurrence of spillover dynamics during the seasonal sympatry between migrants and residents provides a plausible explanation that reconciles empirical inconsistencies in the intersection of animal migration and infection risk at the host community level. Our findings underscore the critical role played by seasonality in shaping infection dynamics in migratory systems.

Comparative Pore Structure and Dynamics for Bacterial Microcompartment Shell Protein Assemblies in Sheets or Shells

<blockquote> Input structures for a manuscript, along with selected output data and structures. This directory structure contains a cut-down copy of the directories used to generate the simulation data and the analysis. In order to make this fit into the 50GB Zenodo limit, it was constructed with the following tar commands: For <a href="../api/records/10800570/draft/files/bmc_shell_vs_sheet.tar.gz/content" target="_blank" rel="noopener noreferrer">bmc_shell_vs_sheet.tar.gz:</a> <code>tar -zcvf bmc_shell_vs_sheet.tar.gz --exclude="*BAK" --exclude="*#" --exclude="*log" --exclude="*xsc" --exclude="*coor" --exclude="*vel" --exclude="*[0-9].out" --exclude="*old" --exclude="*dcd" --exclude="*tmp" --exclude="*ppm" --exclude="*png" --exclude="*pdf"  --exclude="*catchy*" --exclude="*svg" --exclude="*restart*" --exclude="*history" --exclude="core.*" --exclude="FFTW_NAMD*" --exclude="*avi" --exclude="*mp4" --exclude="*pcad*" --exclude="*pcaa*" --exclude="*ammn*" --exclude="*amnp*" --exclude="*amsa*" --exclude="*dtnt*" --exclude="*mthl*" --exclude="*ntrt*" --exclude="*.inp" --exclude="*.sph"   --exclude="structures" --exclude="test-sim" --exclude="test-sim-flatten-constantarea" --exclude="*.dx"</code> For <a href="../api/records/10800570/draft/files/bmcflattenmdff.tar.gz/content" target="_blank" rel="noopener noreferrer">bmcflattenmdff.tar.gz</a>: <code>tar --exclude="emdensitymap" --exclude="emstructures" --exclude="forSaad" --exclude="*dcd" --exclude="*ppm" --exclude="*mp4" --exclude="*png" --exclude="*old" --exclude="*BAK" --exclude="*txt" --exclude="animations" --exclude="apbs*" -zcvf bmcflattenmdff.tar.gz</code> The bmc_shell_vs_sheet has the folder test-sim-curved for shell simulation while test-sim-flatten-noconstantratio for sheet simulation. Pore analysis for shell can be found in hole2 and for sheet in hole-flatten Analysis has been done with various *py *sh and *tcl files For visualizing trajectories in VMD  "load*.tcl" scripts were used. The bmcflattenmdff contains all the scripts needed for converting the shell topology to sheet. </blockquote>

Data from: Dynamics of IGF signalling during the ovulatory peak in women undergoing ovarian stimulation.

Supplementary table 1. Mean expression levels of genes in the IGF family and common proliferation markers across five time points before and up to 36 h after ovulation trigger. These supplementary data belong to the manuscript entitled "Dynamics of IGF signalling during the ovulatory peak in women undergoing ovarian stimulation" published in The Journal of Clinical Endocrinology & Metabolism (JCEM) (04 March 2024). This manuscript describes the expression of the insulin-like growth factor (IGF) system during the ovulatory peak in women and suggests that downregulation of IGF signalling is crucial for the sudden cessation in granulosa cell proliferation and onset of differentiation during this critical time course. This table shows data extracted from a microarray analysis of key IGF family members and common proliferation markers in granulosa cells collected from five different time-points (0 h (n =17), 12 h (n =7), 17 h (n =6), 32 h (n =9) and 36 h (n=44) after ovulation trigger), during the ovulatory peak from fifty women receiving fertility treatment at the Fertility Clinic, Department of Gynaecology and Obstetrics, Holbæk Hospital, Denmark. Differential expression with a false discovery rate (FDR)<0.01 combined with a gene expression fold change >2 was considered significant.  For further details please read the full manuscript published at JCEM following the DOI: https://doi.org/10.1210/clinem/dgae132.

Dataset for "Three-dimensional spin-wave dynamics, localization and interference in a synthetic antiferromagnet"

Data availability for the article titled "Three-dimensional spin-wave dynamics, localization and interference  in a synthetic antiferromagnet" by Girardi et al. published in Nature Communications. This data repository contains the following folders and files: •    TR Lamni Raw Data - Co: Files with extension .hdf5 are Time-Resolved Soft X-Ray Laminography Raw Data for all projections acquired to obtain the 3D reconstruction for the CoFeB layer. The projections’ data have been organized in sub-folders for the 7 frames acquired during the measurements. For each frame, a final folder “analysis” contains an aligned_projection.mat file with the angles of all measured projections and the sinogram information. •    TR Lamni Raw Data - Ni: Files with extension .hdf5 are Time-Resolved Soft X-Ray Laminography Raw Data for all projections acquired to obtain the 3D reconstruction for the NiFe layer. The projections’ data have been organized in sub-folders for the 7 frames acquired during the measurements. For each frame, a final folder “analysis” contains an aligned_projection.mat file with the angles of all measured projections and the sinogram information. •    Magnetic reconstruction – Ni edge: contains the .mat files of the 3D magnetic reconstruction obtained for Ni-edge for all 7 frames. In each file, the Mx, My and Mz components of the magnetization associated with the 3D reconstruction of the volume of the sample are present.  •    Magnetic reconstruction – Co edge: contains the .mat files of the 3D magnetic reconstruction obtained for Co-edge for all 7 frames. In each file, the Mx, My and Mz components of the magnetization associated with the 3D reconstruction of the volume of the sample are present.  •    vtk files: contains the post-processed files for all 7 frames in the .vtk format for the 3D visualization with the Paraview software. In each file, both vectorial and scalar data associated with the 3D reconstruction of the volume of the sample and analyzed in the paper are present. •    Mumax3 simulation dispersion relation: contains .ovf files (containing information about the Mx, My, Mz components of the magnetization as a function of the spatial position) obtained from the mumax3 simulation to study the spin wave dispersion relation of the sample investigated. The total simulation runtime is 10 ns, and each .ovf file corresponds to a frame saved every 0.01 ns. •    Mumax3 simulation 3D interference: contains the .ovf files (containing information about the Mx, My, Mz components of the magnetization as a function of the spatial position) for the static magnetization and 3 frames used to simulate the 3D interference pattern observed experimentally.

Integrated Modeling of Flow, Soil Erosion, and Nutrient Dynamics in a Regional Watershed: Assessing Natural and Human-Induced Impacts

Attached file is the verification data for the submitted manuscript "Integrated Modeling of Flow, Soil Erosion, and Nutrient Dynamics in a Regional Watershed: Assessing Natural and Human-Induced Impacts" .

Test data for MetIVA ( An XR-based Interactive Visualization Platform for Real-time Exploring Dynamic Earth Science Data)

Here,we presented the minimum demanded dataset to test the basic fuction of the software of MetIVA, which an XR-base interactive visualization platform for real-time exploring dynamic earth science data. The dynamic realtime data of traffic information (such as traffic volume, traffic spped, jam conditions) is directy obtained from the third-party supplier, such as Mapbox in the test version of MetIVA, the users can change it to other sources.  The users have their own accounts on the cloud computing platform to run the numerical models (such as WRF), the outputed results (in NetCDF format) can be sent to cloud storage and the link address need to be provided in the MetIVA.