Find research datasets worth reusing

opencc-by-4.0Aug 2023View details →

Mapping the interaction surface between CaVβ and actin and its role in calcium channel clearance

HADDOCK protein-protein docking data for the CaVβ/F-actin complex models reported in "Mapping the interaction surface between CaVβ and actin and its role in calcium channel clearance".   The dataset is divided in four different folders: <ol> <li>Cavbeta2: data for the docking between dimeric actin (PDB 5OOE) and CaVβ2 (PDB 5V2P) using XL-MS-derived distance restraints </li> <li>Cavbeta4: data for the docking between dimeric actin (PDB 5OOE) and CaVβ4 (PDB 1VYV) using XL-MS-derived distance restraints </li> <li>Monomer: data for the control docking between monomeric actin (PDB 5OOE) and CaVβ2 (PDB 5V2P) using XL-MS-derived distance restraints </li> <li>Ab_initio: data for the control dockings between dimeric actin (PDB 5OOE) and CaVβ2 (PDB 5V2P) without XL-MS-derived distance restraints and using the ab initio options available in HADDOCK 2.4</li> </ol>   Each of the Cavbeta folders (1-2) and the Monomer folder (3) contain: - Inputs:  <ul> <li>HADDOCK run parameter file (job_params.json)</li> <li>XL/MS-derived unambiguous distance restraints (unambig.tbl)</li> <li>Bioinformatics-derived (CPORT and NACCESS) ambiguous distance restraints (ambig.tbl)</li> </ul> - Outputs: <ul> <li>Top 4 models of the selected HADDOCK cluster (cluster1_1.pdb, ..., cluster1_4.pdb)</li> <li>Source data for the docking analyses presented in the Supplementary Information (Supplementary Figures 4, 6, 9, 13 and 14 and Supplementary Table 4)</li> </ul>   The Ab_initio folder (4) contains: - Input:  <ul> <li>HADDOCK run parameter files for each of the six control simulations presented in Supplementary Table 6 (job_params.json)</li> </ul> - Outputs: <ul> <li>Source data for the docking analyses presented in Supplementary Table 6</li> <li>Model from control simulation 1 shown in Supplementary Figure 5</li> </ul>

opencc-zeroNov 2021View details →

Simultaneous two-photon voltage or calcium imaging and multi-channel LFP recordings in barrel cortex of awake and anesthetized mice

Neuronal population activity, both spontaneous and sensory-evoked, generates propagating waves in cortex. However, high spatiotemporal-resolution mapping of these waves is difficult as calcium imaging, the work horse of current imaging, does not reveal subthreshold activity. Here, we present a platform combining voltage or calcium two-photon imaging with multi-channel local field potential (LFP) recordings in different layers of the barrel cortex from anesthetized and awake head-restrained mice. A chronic cranial window with access port allows injecting a viral vector expressing GCaMP6f or the voltage-sensitive dye (VSD) ANNINE-6plus, as well as entering the brain with a multi-channel neural probe. We present both average spontaneous activity and average evoked signals in response to multi-whisker air-puff stimulations. Time domain analysis shows the dependence of the evoked responses on the cortical layer and on the state of the animal, here separated into anesthetized, awake but resting, and running. The simultaneous data acquisition allows to compare the average membrane depolarization measured with ANNINE-6plus with the amplitude and shape of the LFP recordings. The calcium imaging data connects these data sets to the large existing database of this important second messenger. Interestingly, in the calcium imaging data, we found a few cells which showed a decrease in calcium concentration in response to vibrissa stimulation in awake mice. This system offers a multimodal technique to study the spatiotemporal dynamics of neuronal signals through a 3D architecture in vivo. It will provide novel insights on sensory coding, closing the gap between electrical and optical recordings.

Data and scripts for Journal of Geophysical Research – Earth Surface publication: Identification of debris-flow channels using high-resolution topographic data: A case study in the Quebrada del Toro, NW Argentina

This data source contains scripts and data associated with the JGR Earth Surface publication “Identification of debris-flow channels using high-resolution topographic data: A case study in the Quebrada del Toro, NW Argentina” by A. Mueting, B. Bookhagen, and M. R. Strecker. The Digital Elevation Model (DEM) of the lower part of the Quebrada del Toro and Río Capilla catchment in the NW Argentinian Andes was generated from SPOT-7 tri-stereo images using Ames Stereo Pipeline. The final dataset has a spatial resolution of 3 m. A full description of the DEM generation process and accuracy assessment can be found in the associated paper. The scripts are also available at https://github.com/UP-RS-ESP/DEM_ConnectedComponents.

opencc-by-4.0Jul 2021View details →

Supraglacial lakes and channels in West Antarctica and Antarctic Peninsula during January 2017

The maximum extent of supraglacial lakes and channels in West Antarctica and the Antarctic Peninsula in January 2017 was produced by a Dual-NDWI (Normalised Difference Water Index) approach with thresholds. >2000 individual scenes were captured by Sentinel-2 (S2, filename: TNNXXX_YYYYMMDD) and Landsat-8 (L8, filename: LC08_L1GT_NNNNNN_YYYYMMDD_YYYYMMDD_01_T2) satellite sensors during the entire month of January 2017. To obtain maximum coverage on the cloudy Antarctic Peninsula, the time period is extended to February 10, 2017 over this region. This dataset consists of the maximum extent of supraglacial hydrological activity during January 2017 and detailed 10,478 supraglacial features (10,223 lakes and 255 channels), with cumulative area 119.4 square km in total on the West Antarctic ice sheet and Antarctic Peninsula. In addition to the final product, the supraglacial hydrological features from both sensors (23,389 polygons for S2 and 17,571 polygons for L8) overlapping the final map are included in supplementary datasets. The supraglacial lake and channel polygons are available as digital GIS, Geographic Information System, shapefiles (.shp) and GeoJSON files as well as Google Earth format (.kmz). The code used to produce the lake and channel dataset for each sensor (S2 and L8) is implemented using Python, and can be accessed on Zenodo (<a href="https://eur02.safelinks.protection.outlook.com/?url=https%3A%2F%2Fdoi.org%2F10.5281%2Fzenodo.4906097&amp;data=04%7C01%7Ccorrd%40live.lancs.ac.uk%7Ce16045ed14e34f2cb4f108d92b70565e%7C9c9bcd11977a4e9ca9a0bc734090164a%7C0%7C0%7C637588586902880130%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C2000&amp;sdata=JPsWDkSk9wqxEcoxMGWzbNgleTFB1NoIFn7t0WlDg3Q%3D&amp;reserved=0">https://eur02.safelinks.protection.outlook.com/?url=https%3A%2F%2Fdoi.org%2F10.5281%2Fzenodo.4906097&amp;data=04%7C01%7Ccorrd%40live.lancs.ac.uk%7Ce16045ed14e34f2cb4f108d92b70565e%7C9c9bcd11977a4e9ca9a0bc734090164a%7C0%7C0%7C637588586902880130%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C2000&amp;sdata=JPsWDkSk9wqxEcoxMGWzbNgleTFB1NoIFn7t0WlDg3Q%3D&amp;reserved=0</a>) . Landsat-8 and Sentinel-2 imagery are freely available at  (<a href="https://eur02.safelinks.protection.outlook.com/?url=https%3A%2F%2Fearthexplorer.usgs.gov%2F&amp;data=04%7C01%7Ccorrd%40live.lancs.ac.uk%7Ce16045ed14e34f2cb4f108d92b70565e%7C9c9bcd11977a4e9ca9a0bc734090164a%7C0%7C0%7C637588586902880130%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C2000&amp;sdata=RidpbAMFz28isbZM6vNZWPMTdl3bl5OxO3SVWvBu6MQ%3D&amp;reserved=0">https://eur02.safelinks.protection.outlook.com/?url=https%3A%2F%2Fearthexplorer.usgs.gov%2F&amp;data=04%7C01%7Ccorrd%40live.lancs.ac.uk%7Ce16045ed14e34f2cb4f108d92b70565e%7C9c9bcd11977a4e9ca9a0bc734090164a%7C0%7C0%7C637588586902880130%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C2000&amp;sdata=RidpbAMFz28isbZM6vNZWPMTdl3bl5OxO3SVWvBu6MQ%3D&amp;reserved=0</a>) and (<a href="https://eur02.safelinks.protection.outlook.com/?url=https%3A%2F%2Fscihub.copernicus.eu%2F&amp;data=04%7C01%7Ccorrd%40live.lancs.ac.uk%7Ce16045ed14e34f2cb4f108d92b70565e%7C9c9bcd11977a4e9ca9a0bc734090164a%7C0%7C0%7C637588586902880130%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C2000&amp;sdata=lZINlehD3i%2BN%2BPSVZgSJnZa%2FruFq2vGHoEnkQGMmq%2Fg%3D&amp;reserved=0">https://eur02.safelinks.protection.outlook.com/?url=https%3A%2F%2Fscihub.copernicus.eu%2F&amp;data=04%7C01%7Ccorrd%40live.lancs.ac.uk%7Ce16045ed14e34f2cb4f108d92b70565e%7C9c9bcd11977a4e9ca9a0bc734090164a%7C0%7C0%7C637588586902880130%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C2000&amp;sdata=lZINlehD3i%2BN%2BPSVZgSJnZa%2FruFq2vGHoEnkQGMmq%2Fg%3D&amp;reserved=0</a>), respectively. The products provide a scientific benchmark to monitor the development of these features in a warming climate, and thus enhancing our capability to predict the calving and collapse of any ice shelves in the future. The results provide a baseline for future monitoring of supraglacial hydrology and can be particularly useful to train supervised machine learning algorithms. The lake and channel dataset will be valuable as training data for pixel-based or object-based approaches to map large-scale features automatically using machine learning. This dataset can also provide an a-priori lake distribution for studies incorporating synthetic-aperture radar, SAR and other sensors and platforms.

opencc-by-4.0Dec 2021View details →

Mechanism of Praziquantel action at a parasitic flatworm ion channel

Data supporting Park et al. [Mechanism of praziquantel action at a parasitic flatworm ion channel]

Spectrum and Temperature Evolution of Lightning Channel and Dependence on Discharge Feature

Temperature is one of the crucial parameters reflecting the energy and current transfer characteristics in the lightning discharge channel. According to the spectra of eight return strokes recorded simultaneously by two high-speed slitless spectrographs with different time resolutions, the spectral-structure and temperature evolution of the return stroke channels over time was quantitatively analyzed. Different from the previous report, one of the spectrographs has recorded the ionic lines in the spectra within approximately 200 microseconds during the return stroke. The ionic line intensity decayed rapidly with time as the current declined, while the atomic line intensity decreased more slowly. The spectral-structure evolution characteristics indicate that the ionic lines in the spectra existed throughout the discharge current process (including the continuing current (CC) stage). Additionally, it further suggests that the ionic line intensities are associated with the discharge currents and that their radiation mechanism is closely related to the collision excitation under the action of strong currents. The temperature calculated using the ionic lines can reflect the thermodynamic properties of the current-carrying channel. The temperature calculated using atomic lines is significantly lower than that calculated using the ionic lines in the same spectrum. The radiation mechanism of the atomic lines differs from that of the ionic lines. Compared with the decay of the ionic-line intensity, the decline of the channel temperature is slower, and there is even a slight increase in the CC stage. This property reflects the effect of the current action integral.

Spectrum and Temperature Evolution of Lightning Channel and Dependence on Discharge Feature

Supplementary Table S1 (raw data) of "Filtration extraction method using microfluidic channel for measuring environmental DNA "

Supplementary Table S1 (all raw data) of "Filtration extraction method using microfluidic channel for measuring environmental DNA ". Each data of the validation experiment; Experiment 1-4 was located in different sheets..

opencc-by-4.0Sep 2021View details →

Exploring Kv1.2 channel inactivation through MD simulations and network analysis

MD equilibration trajectories of Kv1.2 WT and mutants in dcd format can be visualized using visualization tools such as VMD or PyMol after uploading the topology file (.prmtop).

opencc-by-4.0Jan 2022View details →

Contemporary Wooden Watercraft of the Zanzibar Channel, Tanzania: Type and Technology, Continuity, and Innovation. Photogrammetry Files.

This upload contains the photogrammetry files of 9 wooden vessels discussed in the paper 'Contemporary Wooden Watercraft of the Zanzibar Channel, Tanzania: Type and Technology, Continuity, and Innovation' published in the International Journal of Nautical Archaeology (IJNA).  The paper documents and presents the range of wooden fishing and cargo-carrying watercraft in use in the contemporary Zanzibar Channel, Tanzania. The work is based on surveys conducted in 2018 on Unguja, the principal island of the Zanzibar archipelago, and in 2019– 2020 in Bagamoyo, mainland Tanzania, and its immediate environs. The authors present a broad typology of the principal wooden vessel types in the form of 3D photogrammetric models, orthographic views, and photographs. The principal construction features and uses of each type are presented and the state of play of contemporary wooden-boat construction in this part of East Africa discussed.

opencc-by-4.0Jan 2022View details →

Metamorphic evolution of the Greater Himalayan Sequence, Bhagirathi Valley (India) through a combination of channel flow and in-sequence shearing

Dataset of a manuscript entitled "Metamorphic evolution of the Greater Himalayan Sequence, Bhagirathi Valley (India) through a combination of channel flow and in-sequence shearing " submitted in Tectonics (AGU)

opencc-by-4.0Jan 2022View details →

How Are Communication Channels on GitHub Presented to Their Intended Audience? – Dataset

This dataset includes the data used for the thematic analysis of the paper in the title. <ul> <li>all_projects.csv includes all large GitHub projects as described in the paper.</li> <li>analyzed_projects.csv includes the analyzed projects.</li> <li>checkRegex.py is the python script used to automatically find communication channels in markdown files.</li> <li>download_markdown_files.py is the python script used to download the markdown files.</li> </ul>

opencc-by-4.0Mar 2022View details →

Optimal Mowing Regime in Enhancing Biodiversity in Seasonal Floodplains along Engineered Channels, Survey data

This is the survey dataset used in the publication " Optimal Mowing Regime in Enhancing Biodiversity in Seasonal Floodplains along Engineered Channels".

opencc-by-4.0Apr 2022View details →

Temporal Evolution Feature on Spectrum and Temperature of Lightning return stroke Channel

Temperature is one of the crucial parameters reflecting the energy and current transfer characteristics in the lightning discharge channel. According to the spectra of eight lightning return strokes recorded simultaneously by two high-speed slitless spectrographs with different time resolutions, the spectral-structure and temperature evolution of the return stroke channels over time was quantitatively analyzed. Different from the previous report, one of the spectrographs have recorded the ionic lines in the spectra within approximately 200 microseconds during the return stroke. The ionic line intensity decayed rapidly with time as the current declined, while the atomic line intensity decreased more slowly. The spectral-structure evolution characteristics indicate that the ionic lines in the spectra existed throughout the discharge current process (including the continuing current (CC) stage). Additionally, it further suggests that the ionic line intensities are associated with the discharge currents and that their radiation mechanism is closely related to the collision excitation under the action of strong currents. The temperature calculated by the ionic lines can reflect the thermodynamic properties of the current-carrying channel. The temperature calculated using atomic lines is significantly lower than that calculated by the ionic lines in the same spectrum. The radiation mechanism of the atomic lines differs from that of the ionic lines. Compared with the decay of the ionic-line intensity, the decline of the channel temperature calculated by ionic lines is slower. The temperature calculated by atomic lines shown the similar feature, and it is even basically unchanged in the CC stage. This property reflects the persistent heating effect of the current.

opencc-by-4.0Apr 2022View details →

Modeled data related to the article "Diffusive Wave Models for Operational Forecasting of Channel Routing at Continental Scale"

The data holder contains modeled data on water level and discharge from some test cases.

opencc-by-4.0Apr 2022View details →

Chanalyzer: a computational geometry approach for the analysis of protein channel shape and dynamics

Dataset of molecular dynamics trajectories described in the "Chanalyzer: a computational geometry approach for the analysis of protein channel shape and dynamics" work. Trajectories of differently functionalized MscL channel forms.  The *_xyzr.tar.gz files contain the processed frames in the xyzr format, which is a compatible input for NanoShaper The conf.prm file is the parameter file that has been used for the NanoShaper tool

opencc-zeroMay 2022View details →

Effects of acute exposure to polystyrene nanoplastics on the channel catfish larvae: Insights from energy metabolism and transcriptomic analysis

Microplastics (nanoplastics) pollution has been a major ecological issue threatening global aquatic ecosystems. However, knowledge of the adverse effects of nanoplastics and the effects on freshwater ecosystems is still limited. To understand the impacts of nanoplastics on freshwater ecosystems, it is essential to reveal the physiological changes caused by nanoplastics in freshwater organisms, especially at their early life-history stages. In the present study, the larval channel catfish Ietalurus punetaus were exposed to gradient concentrations (0, 5, 10, 25 and 50 mg/L) of 75-nm polystyrene nanoplastics (PS-NPs) for 24 h or 48 h, and changes in contents of energy metabolites, metabolic enzyme activities and transcriptome were assessed. The results showed glucose and triglyceride contents increased after 24 h of exposure to 10 or 25 mg/L of PS-NPs but decreased with increased concentrations or prolonged exposure duration. Activities of most metabolic enzymes analyzed decreased in the larvae after 48 h of exposure, especially in 25 or 50 mg/L of PS-NPs. These suggested that PS-NPs caused huge energy consumption and disturbed the energy metabolism in larval fish. Transcriptomic analysis showed that 48 h of exposure to 50 mg/L PS-NPs affected the expression of genes involved in protein digestion and induced response of proteasomes or heat shock proteins in the larval I. punetaus. The genes involved in peroxisome proliferator-activated receptors (PPAR) pathway and biosynthesis of amino acids were activated after the exposure. PS-NPs also depressed the expression of the genes involved in gonad development or muscle contraction in the larval I. punetaus. Overall, acute exposure to 75-nm PS-NPs disrupted the energy metabolism by consuming the energy reserves, and affected a series of molecular pathways which may further affect the development and survival of fish. This study provided the information about adverse effects of nanoplastics on the fish larvae and revealed the molecular pathways for the potential adverse outcomes.

opencc-zeroMay 2022View details →

Sequence conservation and structural features that are common within TRP channels

TRP proteins are a large family of cation-selective channels, surpassed in variety only by voltage-gated potassium channels. Detailed molecular mechanisms governing how membrane voltage, ligand binding, or temperature can induce conformational changes promoting the open state in TRP channels are still a matter of debate. Aiming to unveil distinctive structural features common to the transmembrane domains within the TRP family, we performed phylogenetic reconstruction, sequence statistics, and structural analysis over a large set of TRP channel genes. Here we report an exceptionally conserved set of residues. This fingerprint is composed of twelve residues localized at equivalent three-dimensional positions in TRP channels from the different subtypes. Moreover, these amino acids are arranged in three groups, connected by a set of aromatics located at the core of the transmembrane structure. We hypothesize that differences in the connectivity between these different groups of residues harbors the apparent differences in coupling strategies used by TRP subgroups.

opencc-zeroJul 2022View details →

Tyrosine phosphorylation tunes chemical and thermal sensitivity of TRPV2 ion channel

Transient receptor potential vanilloid 2 (TRPV2) is a multimodal ion channel implicated in diverse physiopathological processes. Its important involvement in immune responses has been suggested such as in the macrophages' phagocytosis process. However, the endogenous signaling cascades controlling the gating of TRPV2 remain to be understood. Here, we report that enhancing tyrosine phosphorylation remarkably alters the chemical and thermal sensitivities of TRPV2 endogenously expressed in rat bone marrow-derived macrophages. We identify that the protein tyrosine kinase JAK1 mediates TRPV2 phosphorylation at the molecular sites Tyr(335), Tyr(471), and Tyr(525). JAK1 phosphorylation is required for maintaining TRPV2 activity and the phagocytic ability of macrophages. We further show that TRPV2 phosphorylation is dynamically balanced by protein tyrosine phosphatase non-receptor type 1 (PTPN1). PTPN1 inhibition increases TRPV2 phosphorylation, further reducing the activation temperature threshold. Our data thus unveil an intrinsic mechanism where the phosphorylation/dephosphorylation dynamic balance sets the basal chemical and thermal sensitivity of TRPV2. Targeting this pathway will aid therapeutic interventions in physiopathological contexts.