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opencc-zeroMay 2024View details →

The non-mitotic role of HMMR in regulating the localization of TPX2 and the dynamics of microtubules in neurons

A functional nervous system is built upon the proper morphogenesis of neurons to establish the intricate connection between them. The microtubule cytoskeleton is known to play various essential roles in this morphogenetic process. While many microtubule-associated proteins (MAPs) have been demonstrated to participate in neuronal morphogenesis, the function of many more remains to be determined. This study focuses on a MAP called HMMR in mice, which was originally identified as a hyaluronan binding protein and later found to possess microtubule and centrosome binding capacity. HMMR exhibits high abundance on neuronal microtubules and altering the level of HMMR significantly affects the morphology of neurons. Instead of confining to the centrosome(s) like cells in mitosis, HMMR localizes to microtubules along axons and dendrites. Furthermore, transiently expressing HMMR enhances the stability of neuronal microtubules and increases the formation frequency of growing microtubules along the neurites. HMMR regulates the microtubule localization of a non-centrosomal microtubule nucleator TPX2 along the neurite, offering an explanation for how HMMR contributes to the promotion of growing microtubules. This study sheds light on how progenitor cells utilize proteins involved in mitosis for non-mitotic functions.

opencc-by-4.0May 2024View details →

Data, code and supplementary material - Gone but not forgotten: dynamics of sperm storage and potential ejaculate digestion in the black soldier fly Hermetia illucens

Open the record for dataset details and reuse information.

opencc-by-4.0May 2024View details →

Data set for study "Thermal Dynamic Models for Predicting the Indoor Temperature of Multi-Zone Buildings"

Input data for the study "Thermal Dynamic Models for Predicting the Indoor Temperature of Multi-Zone Buildings"

opencc-zeroJun 2024View details →

Data from: Density matters: How population dynamics of house mice (Mus musculus) inform the epidemiology of Leptospira

Rodents are maintenance hosts of numerous pathogens, and both their density and the pathogen prevalence determine the risk they pose to other animals or humans. However, density is often overlooked. We investigated a capture-mark-recapture-sampling strategy to study introduced mice (Mus musculus) and Leptospira as a model and demonstrate the advantages of a combined approach. We estimated population density and Leptospira prevalence in mice in a replicated longitudinal survey conducted between 2016 and 2018. Capture-mark-recapture sessions were undertaken at two sites in Spring and Autumn and blood and kidney samples were collected at the end of each session. Mouse density and areas of activity were estimated using spatially explicit capture-recapture (SECR) models and both were compared between Leptospira positive and negative mice. Leptospira exposure and shedding status were estimated using Microscopic Agglutination Test, and a combination of culture and lipL32 PCR on kidneys. Leptospira prevalence was higher in spring (83% to 86%) than in autumn (31% to 37%) and mouse densities simultaneously varied from 3.6 to 55.9/ha. However, despite these variations in prevalence and density, the density of infected animals remained relatively constant over time (3 to 8/ha). Shedding or being seropositive was also associated with the activity of mice. Shedding or seropositive mice had a larger activity area, and seropositive mice were trapped on average one day earlier than seronegative mice. Synthesis and applications. Our results show how understanding the population dynamics of pathogen-carrying rodents is critical in epidemiology. The wider movement patterns and easier encounters of positive mice highlight the possibility of biases in classical prevalence surveys and have implications for disease transmission within and between species. Importantly, and quite counter-intuitively, Leptospira prevalence was negatively associated with mouse density, resulting in a constant density of shedders that contradicts the conventional view of higher exposure risk at high rodent density. More broadly, such hybrid sampling designs can improve animal and disease control policies and better inform modelling studies by providing more parameter estimates than classical prevalence surveys.

Data: Characterizing the sediment dynamics through in-situ measurements in the abyssal Manila Trench, northeast South China Sea

Along the Manila Trench, a total of four moorings were deployed in <a name="OLE_LINK5"></a>September 2019 and recovered in August 2020. The field measurements in velocity and turbidity were resampled to create hourly dataset.

Data supporting "Seasonal dynamics and punctuated carbon sink reduction suggest photosynthetic capacity of boreal silver birch is reduced by the accumulation of hexose"

Data supporting our New Phytologist publication: "Seasonal dynamics and punctuated carbon sink reduction suggest photosynthetic capacity of boreal silver birch is reduced by the accumulation of hexose". The file present the data produced during long-term (three consecutive years 2019-2021) field observations and short-term girdling manipulation of top-crown shoots in three mature Betula pendula trees as details of our manuscript. Values of leaf gas-exchange, environmental variables, leaf water and nitrogen status, and concentrations of sucrose, hexoses (glucose and fructose), starch, total sugar, and total non-structural carbohydrate in leaves are listed.

Molecular dynamics trajectories and portable binary run files for the self-assembly of heparin and amyloid-β(16-22) with the ProMPT forcefield

<h1>About this repository</h1> Self-assembly simulations of heparin and amyloid-β(16-22) were performed at various numbers of peptides (N_pep), number of heparin molecules (N_hep), degrees of polymerization of heparin (hep_dp) and rigidity factors (rig_f) for heparin. This repository contains one folder per system, characterized by a combination of four system variables: N_pep, N_hep, hep_dp and rig_f.  The simulations were performed on the GROMACS 2019.4 molecular dynamics engine, with the ProMPT forcefield for coarse-grained molecular dynamics. Four independent trials: trial_A, trial_B, trial_C and trial_D were performed per system, each with different starting velocities. Each trial was run for 3000 ns. <h1>Contents</h1> <h2><code>> heparin_abeta_trajectories.zip</code></h2> The repository contains the zip file <code>heparin_abeta_trajectories.zip</code> with 13 folders named according to the convention,<code> "{N_pep}pep_{N_hep}hep_dp{hep_dp}_{rig_f}xRigid"</code>. For example, data for the system consisting of 16 peptides (N_pep), 1 heparin (N_hep), 18 monosaccharides in length (hep_dp) with a rigidity factor of 100 (rig_f) would be stored in the directory <code>16pep_1hep_dp18_100xRigid/</code>. If the system did not contain heparin, N_hep, hep_dp and rig_f  were set to 0 by default. For example, data for the system consisting of 16 peptides (N_pep) and no heparin would be stored in the directory <code>16pep_0hep_dp0_0xRigid/</code>. A directory such as <code>16pep_1hep_dp18_100xRigid/</code> will have the following contents: <ul> <li><code>solute_only.ndx</code> Contains an index group for solute molecules (peptides and/or heparin) only.</li> <li><code>trial_A/</code> <ul> <li><code>md.tpr</code> Portable run file with which the current trajectory was generated. This file may be used to reproduce the trajectory as well.</li> <li><code>solute_only.cluster_center.xtc </code> A gromacs trajectory containing only the solute molecules (peptides and/or heparin), centered with the gromacs tool gmx trjconv</li> <li><code>solute_only.tpr </code> A gromacs portable binary input file containing data for the solute molecules (peptides and/or heparin) only, generated with the gmx convert-tpr tool. This file may be used during analysis of the solute_only.cluster_center.xtc trajectory.</li> </ul> </li> <li><code>trial_B/</code> contents same as <code>trial_A/</code></li> <li><code>trial_C/</code> contents same as <code>trial_A/</code></li> <li><code>trial_D/</code> contents same as <code>trial_A/</code></li> </ul> <h2><code>> psf_files_for_VMD_visualization.zip</code></h2> This zip file contains thirteen .psf files, one per system, that can be used in accord with <code>solute_only.cluster_center.xtc </code>files to visualize trajectories on the Visual Molecular Dynamics (VMD) software. Please seek out the associated publication for essential context on these trajectories.  To access the source files with which these simulations were set-up, and a brief tutorial, see: <a href="https://github.com/suhasgotla/heparin_amyloid_self-assembly">https://github.com/suhasgotla/heparin_amyloid_self-assembly</a>

Data for "CryoDRGN-ET: Deep reconstructing generative networks for visualizing dynamic biomolecules inside cells"

Trained models weights, training parameters, sampled density maps, reconstructed density maps for featured classes, and plotting scripts are included for each of the following datasets and training runs: <ul> <li>M. pneumoniae ribosome, initial training run with all 18,466 particles, 1 tilt per particle</li> <li>M. pneumoniae ribosome, training run with 16,655 filtered particles and 10 tilts per particle</li> <li>M. pneumoniae ribosome, training run with 16,655 filtered particles and 41 tilts per particle</li> <li>S. cerevisiae ribosome, initial training run with all 119,031 particles, 10 tilts per particle</li> <li>S. cerevisiae ribosome, training run with 93,281 filtered particles, 10 tilts per particle</li> <li>S. cerevisiae ribosome, training run with 30,657 particles in the non-rotated state, 10 tilts per particle</li> <li>S. cerevisiae ribosome, training run with 62,624 particles in the rotated state, 10 tilts per particle</li> <li>S. cerevisiae fatty acid synthase, initial training run with all 33,492 particles, 10 tilts per particle</li> <li>S. cerevisiae fatty acid synthase, training run with all 5,239 filtered particles, 10 tilts per particle</li> </ul>

Improvements to the dynamic wake meandering model by incorporating the turbulent Schmidt number

Data to replicate the figures in Brugger, P., Markfort, C., and Porté-Agel, F.: Improvements to the Dynamic Wake Meandering Model by incorporating the turbulent Schmidt number, Wind Energ. Sci. Discuss. [preprint], https://doi.org/10.5194/wes-2023-150, 2023.

Parallel dynamics of bacterial genome reduction across independent transitions to endosymbiosis.

The establishment of symbiosis dramatically alters the evolution of the associated species, making symbiotic systems ideal models for studying the impact of lifestyle changes on genomes. Here, we focused on Enterobacterales, a large and ancient bacterial lineage that includes endosymbionts with diverse host associations, ranging from gut inhabitants to intracellular environments, and from horizontal to vertical transmission. Leveraging over two hundred genomes, along with cutting-edge single-copy gene concatenation and multi-copy gene family approaches, we inferred a robust phylogenetic framework that supports eleven independent transitions to endosymbiosis. Inferences on patterns of genome evolution confirm previous hypotheses about the processes underlying genome reduction: a substantial spike in gene loss always occurs simultaneously with the establishment of endosymbiosis, while a reduction in gene acquisition mechanisms is associated with the subsequent genome erosion. Furthermore, gene family loss frequencies were correlated across independent endosymbiotic clades; genes with more conserved functions and stronger constraints on sequence evolution are lost less frequently, suggesting that differences in gene essentiality and dispensability drive the observed parallelism. Our analyses contribute to the coming of age of the theory of genome evolution in symbiotic associations and provide novel insights into the importance of recombination as an opposing force against genome erosion.

Dataset from Mannerfelt et al., (2024): Dynamic LIA advances hastened the demise of small valley glaciers in central Svalbard

<h1>Data from Bolterdalen and Foxdalen, Svalbard</h1> This repository contains geospatial data from 1914 to 2019 of the valleys Bolterdalen and Foxdalen on Svalbard, associated with (and explained further in) Mannerfelt et al., (2024); <a href="https://cdnsciencepub.com/doi/10.1139/as-2024-0024">https://cdnsciencepub.com/doi/10.1139/as-2024-0024</a>. Its contents are: <ul> <li>Shapefiles of geomorphological features</li> <li>Glacier outlines</li> <li>DEMs of the glaciers and their forefields</li> <li>Orthomosaics of the glaciers and their forefields</li> <li>Interpreted GPR measurements; interpolated and as point data.</li> </ul> The 2009/2011 DEM has no associated orthomosaic in the repository. This is available as a WMTS service from the Norwegian Polar Institute: https://geodata.npolar.no/arcgis/rest/services/Basisdata/NP_Ortofoto_Svalbard_WMTS_25833/MapServer/WMTS/1.0.0/WMTSCapabilities.xml For more info (or there is an issue with the link), visit: <a href="https://geodata.npolar.no/">https://geodata.npolar.no/</a>   NOTE: One file is slightly misnamed; "Rieperbreen_forefield_ortho_2019.tif" was collected in the autumn of 2017. To cite the dataset, please cite the associated paper: Mannerfelt, E. S., Hodson, A. J., Håkansson, L., and Lovell, H. (2024). Dynamic LIA advances hastened the demise of small valley glaciers in central Svalbard. Arctic Science.

Viral diversity and co-evolutionary dynamics across the ant phylogeny

This repository contains the alignment file and phylogeny of every viral clade assessed in this study. The viral phylogenies are in Newick format as well as a pdf and contain bootstrap values greater than 50. The alignment files are in PHYLIP format. Additionally, this repository contains nucleotide sequences of every viral sequence identified in this study and it is entitled:  "final_viruses_contigs.fasta" in fasta format.

opencc-zeroJun 2024View details →

Data from: Linking in vivo muscle dynamics to in situ force-length and force-velocity reveals that guinea fowl lateral gastrocnemius operates at shorter than optimal lengths

Force-length (F-L) and force-velocity (F-V) properties characterize skeletal muscle's intrinsic properties under controlled conditions, and it is thought that these properties can inform and predict in vivo muscle function. Here, we map dynamic in vivo operating range and mechanical function during walking and running, to the measured in situ F-L and F-V characteristics of guinea fowl (Numida meleagris) lateral gastrocnemius (LG), a primary ankle extensor. We use in vivo patterns of muscle (tendon) force, fascicle length, and activation to test the hypothesis that muscle fascicles operate at optimal lengths and velocities to maximize force or power production during walking and running. Our findings only partly support our hypothesis: in vivo LG velocities are consistent with optimizing power during work production, and economy of force at higher loads. However, LG does not operate at lengths on the force plateau (±5% Fmax) during force production. LG length was near L0 at the time of EMG onset but shortened rapidly such that force development during stance occurred almost entirely on the ascending limb of the F-L curve, at shorter than optimal lengths. These data suggest that muscle fascicles shorten across optimal lengths in late swing, to optimize the potential for rapid force development near the swing-stance transition. This may provide resistance against unexpected perturbations that require rapid force development at foot contact. We also found evidence of passive force rise (in absence of EMG activity) in late swing, at lengths where passive force is zero in situ, suggesting that history dependent and viscoelastic effects may contribute to in vivo force development. Direct comparison of in vivo work loops and physiological operating ranges to traditional measures of F-L and F-V properties suggests the need for new approaches to characterize dynamic muscle properties in controlled conditions that more closely resemble in vivo dynamics.

opencc-by-4.0Aug 2024View details →

Spatial dynamics of CD39⁺CD8⁺ exhausted T cells reveal tertiary lymphoid structures-mediated response to PD-1 blockade in esophageal cancer

Data related to the paper: "Spatial dynamics of CD39+CD8+ exhausted T cells reveal tertiary lymphoid structures-mediated response to PD-1 blockade in esophageal cancer,” Nature Communications (2024) The repository data consists of two main folders: IMC_dataset and MC_normalized_dataset. IMC_dataset includes: <ol> <li> IMC_denoised_dataset: This folder contains cell mask images and noise-reduced images for each sample. </li> <li> IMC_raw_dataset: This folder contains raw, unprocessed data. </li> <li> IMC_processed_data: This folder contains standardized single-cell information and spillover-corrected FCS files, along with the compensation matrix. </li> </ol> The MC_normalized dataset includes FCS files that have been sorted by barcode. Please note that in the IMC dataset, the following mass channels are blank: <ul> <li>Tumor-ROI: 80Ar, 127I, 131Xe, 145Nd, 146Nd, 149Sm, 160Gd, 171Yb, 174Yb, 176Yb, 190Os</li> <li>SLO-ROI: 80Ar, 127I, 131Xe, 145Nd, 146Nd, 149Sm, 160Gd, 176Yb, 190Os</li> </ul> The names attached to the file names are IDs.

Dataset to reproduce the figures of article "Information dynamics of in silico EEG Brain Waves"

Data and code to reproduce results figures.

Dataset for "On the dynamics of ozone depletion events at Villum Research Station in the High Arctic" Pernov et al.

*************************************************************************************************************************************** Please contact Henrik Skov (hsk@envs.au.dk) and Jakob Boyd Pernov (jakob.pernov@gmail.com) before using any of these data.  *************************************************************************************************************************************** Please check (https://ebas.nilu.no/) for ozone, DMI (https://www.dmi.dk/publikationer) for meteorological data, and ERDA (https://erda.au.dk/) for meteorological data before downloading these data. These repositories are the original data sources.  This repo contains two files "All_Data_for_Pernov_et_al.csv" and "Only_Data_for_ML_Pernov_et_al.csv" Both datasets contain the following variables ozone mixing ratios (ppbv), ODE flags (0 is Non-ODE and 1 is ODE), wind direction (degrees), wind speed (m s-1), temperature (°C), RH (%), Pressure (hPa), percent of the time air masses spent below the mixed layer and over sea ice (SeaIce, %) and snow (Snow %) as well as the percent of the time air masses spent above the mixed layer (AML, %).  "All_Data_for_Pernov_et_al.csv" contains NaNs where data was unavailable when ozone data was available. The first column is the date and time (DD/MM/YYYY HH:mm).  "Only_Data_for_ML_Pernov_et_al.csv" contains no NaNs since data was imputed and radiation was gap-filled as outlined in the article and supplement. The first column is the index.

opencc-by-4.0Feb 2024View details →

All-atom molecular dynamics simulations of iRFP713/C15S/V254C/N136R

The trajectories of all-atom MD simulations of monomeric and dimeric iRFP713/C15S/V254C/N136R with PCB (phycocyanobilin) and BV (biliverdin).   Simulations have been performed using the CHARMM36 force field, running with the GROMACS 2022 package.

Data from: Investigating the Association of Seasonal Dynamics in GEDI Canopy Cover Profiles and Sentinel-1 Backscatter in Temperate Forests

This dataset supports the analysis about Investigating the Association of Seasonal Dynamics in GEDI Canopy Cover Profiles and Sentinel-1 Backscatter in Temperate Forests

opencc-zeroJun 2024View details →

Russian olive distribution and invasion dynamics along the Powder River, Montana and Wyoming, USA

The invasive shrub, Russian olive (Elaeagnus augustifolia), is widely established within riparian areas across the western United States (U.S.). Limited information on its distribution and invasion dynamics in northern regions has hampered understanding and management efforts. Given this lack of spatial and ecological information we worked with local stakeholders and developed two main objectives: 1) map the distribution of Russian olive along the Powder River (Montana and Wyoming, U.S.) with field data and remote sensing; and 2) relate that distribution to environmental variables to understand its habitat suitability and community/invasion dynamics. In the study watershed, field data showed Russian olive has reached near equal canopy cover (18.3%) to native plains cottonwood (Populus deltoides; 19.1%), with higher cover closer to the channel and over a broader range of elevations. At the basin scale, we modeled Russian olive distribution using field surveys, ocular sampling of aerial imagery, and spectral variables from Sentinel-2 MultiSpectral Instrument using a random forest model. A statistical model linking the resulting Russian olive percent cover detection map (RMSE = 15.42, R2 = 0.64) to environmental variables for the entire watershed indicated Russian olive cover increased with flow accumulation and groundwater depth, decreased with elevation, and was associated with poorer soil types. We attribute the success of Russian olive to its broad habitat suitability combined with changing hydrologic conditions favoring it over natives. This study provides a repeatable Russian olive detection methodology due to the use of Sentinel-2 imagery that is available worldwide, and provides insight into its ecological relationships and success with relevance for management across areas with similar environmental conditions.