cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5281/zenodo.4899969
title: The heavy chain 4F2hc modulates the substrate affinity and specificity of the light chains LAT1 and LAT2

description: Data to Kantipudi S., Jeckelmann J.-M., Ucurum Z., Bosshart P.D. and Fotiadis D. <em>Int. J. Mol. Sci. </em>(2020) <strong>21</strong>, 7573.
DOI: 10.5281/zenodo.4899968
title: The heavy chain 4F2hc modulates the substrate affinity and specificity of the light chains LAT1 and LAT2

description: Data to Kantipudi S., Jeckelmann J.-M., Ucurum Z., Bosshart P.D. and Fotiadis D. <em>Int. J. Mol. Sci. </em>(2020) <strong>21</strong>, 7573.
DOI: 10.17632/6ymh4jrxvb.1
title: Biochemical characterization of protease activity of Nsp3 from SARS-CoV-2 and its inhibition by nanobodies

description: Of the 16 non-structural proteins (Nsps) encoded by SARS CoV-2, Nsp3 is the largest and plays important roles in the viral life cycle. Being a large, multidomain, transmembrane protein, Nsp3 has been the most challenging Nsp to characterize. Encoded within Nsp3 is the papain-like protease domain (PLpro) that cleaves not only the viral polypeptide but also K48-linked polyubiquitin and the ubiquitin-like modifier, ISG15, from host cell proteins. We here compare the interactors of PLpro and Nsp3 and find a largely overlapping interactome. Intriguingly, we find that near full length Nsp3 is a more active protease compared to the minimal catalytic domain of PLpro. Using a MALDI-TOF based assay, we screen 1971 approved clinical compounds and identify five compounds that inhibit PLpro with IC50s in the low micromolar range but showed cross reactivity with other human deubiquitinases and had no significant antiviral activity in cellular SARS-CoV-2 infection assays. We therefore looked for alternative methods to block PLpro activity and engineered competitive nanobodies that bind to PLpro at the substrate binding site with nanomolar affinity thus inhibiting the enzyme. Our work highlights the importance of studying Nsp3 and provides tools and valuable insights to investigate Nsp3 biology during the viral infection cycle.
DOI: 10.17632/hjhx8bj45c.1
title: Betaboltz: A Monte-Carlo simulation tool for gas scattering processes

description: We present an open-source code for the simulation of electron and ion transport for user-defined gas mixtures with static uniform electric and magnetic fields. The program provides microscopic interaction simulation and is interfaced with cross-section tables published by LXCat[1]. The framework was validated against drift velocity tables available in literature obtaining an acceptable match for atomic and non-polar molecular gases with spherical symmetry. The code is written in C++17 and is available as a shared library for easy integration into other simulation applications.
DOI: 10.5281/zenodo.4899964
title: Yeast cell-based transport assay for the functional characterization of human 4F2hc-LAT1 and ‐LAT2, and LAT1 and LAT2 substrates and inhibitors

description: Data to Kantipudi & Fotiadis (2021), <em>Front. Mol. Biosci. </em>(2021) <strong>8</strong>, 676854.
DOI: 10.5281/zenodo.4899963
title: Yeast cell-based transport assay for the functional characterization of human 4F2hc-LAT1 and ‐LAT2, and LAT1 and LAT2 substrates and inhibitors

description: Data to Kantipudi & Fotiadis (2021), <em>Front. Mol. Biosci. </em>(2021) <strong>8</strong>, 676854.
DOI: 10.17632/9vn4c2c7vy.1
title: umap_on_bulk_transcriptomic_analysis

description: This code enables the projection of bulk-transcriptome profiles from one dataset into the UMAP embedding coordinates.
DOI: 10.17632/86w6j7w6r5.1
title: transcriptomic_analysis_DGE_and_GSEA

description: Differential gene expression and gene set enrichment analysis; This file consists of loading the bulk transcriptomic data and differential gene expression (DGE) analysis.
DOI: 10.25573/data.14270720.v1
title: Mercury's crustal thickness and contractional strain

description: Data for crustal thickness and dynamic pressure maps and spreadsheets for histograms.
DOI: 10.5281/zenodo.5031881
title: pGAN Synthetic Dataset: A Deep Learning Approach to Private Data Sharing of Medical Images Using Conditional GANs

description: Synthetic dataset for <strong>A Deep Learning Approach to Private Data Sharing of Medical Images Using Conditional GANs</strong> <strong> Dataset specification:</strong> MRI images of Vertebral Units labelled based on region Dataset is comprised of 10000 pairs of images and labels Image and label pair number k can be selected by: synthetic_dataset['images'][k] and synthetic_dataset['regions'][k] Images are 3D of size (9, 64, 64) Regions are stored as an integer. Mapping is 0: cervical, 1: thoracic, 2: lumbar Arxiv paper: https://arxiv.org/abs/2106.13199<br> Github code: https://github.com/tcoroller/pGAN/ Abstract: Sharing data from clinical studies can facilitate innovative data-driven research and ultimately lead to better public health. However, sharing biomedical data can put sensitive personal information at risk. This is usually solved by anonymization, which is a slow and expensive process. An alternative to anonymization is sharing a synthetic dataset that bears a behaviour similar to the real data but preserves privacy. As part of the collaboration between Novartis and the Oxford Big Data Institute, we generate a synthetic dataset based on COSENTYX Ankylosing Spondylitis (AS) clinical study. We apply an Auxiliary Classifier GAN (ac-GAN) to generate synthetic magnetic resonance images (MRIs) of vertebral units (VUs). The images are conditioned on the VU location (cervical, thoracic and lumbar). In this paper, we present a method for generating a synthetic dataset and conduct an in-depth analysis on its properties of along three key metrics: image fidelity, sample diversity and dataset privacy.
DOI: 10.5281/zenodo.5031880
title: pGAN Synthetic Dataset: A Deep Learning Approach to Private Data Sharing of Medical Images Using Conditional GANs

description: Synthetic dataset for <strong>A Deep Learning Approach to Private Data Sharing of Medical Images Using Conditional GANs</strong> <strong> Dataset specification:</strong> MRI images of Vertebral Units labelled based on region Dataset is comprised of 10000 pairs of images and labels Image and label pair number k can be selected by: synthetic_dataset['images'][k] and synthetic_dataset['regions'][k] Images are 3D of size (9, 64, 64) Regions are stored as an integer. Mapping is 0: cervical, 1: thoracic, 2: lumbar Arxiv paper: https://arxiv.org/abs/2106.13199<br> Github code: https://github.com/tcoroller/pGAN/ Abstract: Sharing data from clinical studies can facilitate innovative data-driven research and ultimately lead to better public health. However, sharing biomedical data can put sensitive personal information at risk. This is usually solved by anonymization, which is a slow and expensive process. An alternative to anonymization is sharing a synthetic dataset that bears a behaviour similar to the real data but preserves privacy. As part of the collaboration between Novartis and the Oxford Big Data Institute, we generate a synthetic dataset based on COSENTYX Ankylosing Spondylitis (AS) clinical study. We apply an Auxiliary Classifier GAN (ac-GAN) to generate synthetic magnetic resonance images (MRIs) of vertebral units (VUs). The images are conditioned on the VU location (cervical, thoracic and lumbar). In this paper, we present a method for generating a synthetic dataset and conduct an in-depth analysis on its properties of along three key metrics: image fidelity, sample diversity and dataset privacy.
DOI: 10.6073/pasta/5e27751f4a453aa7f57ffcb073740bbd
title: CME01 The Consumer Size Manipulation Experiment (ConSME) at Konza Prairie

description: Herbivores of varying size classes exist with the grassland biome (large mammals, small mammals, insects), however their independent and interactive effects on grassland plant species composition and function are understudied. Here we aim to tease apart the effects of three size classes of herbivores within the Konza Prairie system, and whether these effects vary across fire regimes.
DOI: 10.25573/data.14270720
title: Mercury's crustal thickness and contractional strain

description: Data for crustal thickness and dynamic pressure maps and spreadsheets for histograms.
DOI: 10.25573/data.14270720.v3
title: Mercury's crustal thickness and contractional strain

description: Data for crustal thickness and dynamic pressure maps and spreadsheets for histograms.
DOI: 10.25790/bml0cm.71
title: Google
DOI: 10.5519/qd.ykw5tdyv
title: Query on the Natural History Museum Data Portal (data.nhm.ac.uk) (641 records)
DOI: 10.5281/zenodo.5032380
title: Example dataset of stLFR linked reads to run Aquila_stLFR

description: We provide this small chromosome (chr21) example dataset to run Aquila_stLFR. Aquila_stLFR: https://github.com/maiziex/Aquila_stLFR
description: add the test_freebayes.vcf file
DOI: 10.5281/zenodo.4905002
title: Example dataset of stLFR linked reads to run Aquila_stLFR

description: We provide this small chromosome (chr21) example dataset to run Aquila_stLFR. Aquila_stLFR: https://github.com/maiziex/Aquila_stLFR
description: add the test_freebayes.vcf file
DOI: 10.5519/qd.392ehedj
title: Query on the Natural History Museum Data Portal (data.nhm.ac.uk) (1 records)
DOI: 10.15129/9b946240-b42b-4a3b-8606-7cc87e2254de
title: Data for "Towards Designing Mobile Apps for Independent Travel: Exploring Current Barriers and Opportunities for Supporting Young Adults with Down’s Syndrome"

description: Sketches of user interfaces for smartphone apps to support young adults with Down's Syndrome. This study aimed to investigate barriers to independent travel and to reveal the possibility of overcoming these barriers for people living with DS. The study explored the current uses of smart devices and technologies by young adults with DS and their parents. Also, gathered the design requirements to design a smartphone app to support barriers to independent travel for young adults living with DS and their caregivers.
DOI: 10.6084/m9.figshare.14847585
title: Superior Railroad Prairie 1983

description: Species list of Superior Railroad Prairie generated by the 1983 Plant taxonomy class<br>Includes map of location<br>
DOI: 10.6084/m9.figshare.14847585.v1
title: Superior Railroad Prairie 1983

description: Species list of Superior Railroad Prairie generated by the 1983 Plant taxonomy class<br>Includes map of location<br>
DOI: 10.6084/m9.figshare.14847579
title: Ultrasine Data.xlsx

description: Raw data collected from patients who were scanned via an ultrasound-guided automated spinal landmark identification program to assist anesthetists on spinal needle insertion point with a graphical user interface
DOI: 10.6084/m9.figshare.14847579.v1
title: Ultrasine Data.xlsx

description: Raw data collected from patients who were scanned via an ultrasound-guided automated spinal landmark identification program to assist anesthetists on spinal needle insertion point with a graphical user interface
DOI: 10.6084/m9.figshare.14724828
title: DATA from: Chloroplastic and nuclear diversity of endemic Prunus armeniaca L. species in the oasis agroecosystems

description: Genotype of the 33 accessions for each of the 24 microsatellite loci.FASTA alignment of chloroplast sequences
DOI: 10.6084/m9.figshare.14724828.v3
title: DATA from: Chloroplastic and nuclear diversity of endemic Prunus armeniaca L. species in the oasis agroecosystems

description: Genotype of the 33 accessions for each of the 24 microsatellite loci.FASTA alignment of chloroplast sequences
DOI: 10.25345/c5j83c
title: MassIVE MSV000087703 - Proteomic analysis of single tears from healthy human subjects
title: 23 volunteers were recruited for this study. Tears were collected using microcapillary tubes (MCT). For each volunteer, a single tear sample was taken from one eye. For two of these volunteers, the procedure was performed in the morning (9-10 AM) and in the afternoon (5-6 PM) on the same day, once a week for 3 consecutive weeks. Proteins were purified from 5 uL of tear sample using the methanol-chloroform precipitation protocol. The lyophilized proteins were resuspended in ammonium bicarbonate 50 mM, pH 8. An in-solution trypsin digestion was performed. For each run, 1 ug of peptides was injected and each sample was injected twice. Analyses were performed by LC-MS/MS using an Orbitrap Fusion mass spectrometer coupled to an EASY-nLC 1000 nanoflow high-pressure liquid chromatography. Peptides were separated on a commercial analytical nanocolumn. MS scans were performed using the Orbitrap (OT) analyzer with a resolution of 120 000. Precursor ions were selected for higher collisional dissociation (HCD) and the collision energy was set to 30%. Dynamic exclusion was set at 45 s, with a repeat count of 1.
DOI: 10.6073/pasta/c241a69eb9c0f6c7f534e70e0476943a
title: History and Dynamics of American Beech in Coastal New England 1620-2006

description: Variation in forest response to hurricane disturbance in coastal New England Research on disturbance in forest ecosystems has generally focused on either catastrophic disturbances generating stand-replacing successional sequences, or small-scale disturbances (e.g. individual tree-fall gaps) resulting in tree-by-tree replacement. The role of moderate disturbances in forest development, in contrast, is poorly understood. While the most severe hurricanes can cause catastrophic disturbance, the vast majority of hurricanes that affect forests from the Caribbean to the northeastern United States are moderate in intensity. In this study we examine both individual and population level responses of beech (Fagus grandifolia) and oak species (Quercus spp.) to hurricanes of varying intensity in coastal Massachusetts. We characterize growth response to disturbance using a novel approach that explicitly compares the range of growth responses observed following known disturbances to the range of growth responses in non-event years. The tree species exhibited a wide range of growth and regeneration responses to hurricanes; however, only a single storm caused dramatic increases in growth and new establishment for beech. The results of this study highlight the importance of wind disturbance in the establishment and persistence of beech, and suggest that while some moderate disturbances have little or no effect on species growth and regeneration dynamics, individual storms may have substantial impacts. Forest response to wind storms of varying, but moderate intensities, depended on local site conditions, including environmental, meteorological, topographical, historical and biological factors. Beech dominance in a coastal New England forest Monodominant forests occur in a wide range of tropical and temperate ecosystems, but the mechanisms enabling their development are not well understood. This study examines the history and dynamics of beech-dominated forests in coastal New England in order to identify factors that facilitate beech dominance. We also characterize beech structural variation with respect to edaphic and environmental conditions, and describe ‘dwarf beech forests’ which have not been documented in the literature. The development of beech dominance in the study area, Naushon Island, Massachusetts, was influenced by numerous factors - selective oak harvesting in the early historical period, infrequent fire, frequent and occasionally intense hurricanes, intense deer herbivory, minimal anthropogenic disturbance over the past 150 years, and geographic isolation – and facilitated by beech’s ability to persist in the understory and reproduce vegetatively. This study highlights the importance of both disturbance history and species-specific traits in the development of monodominant forests, and suggests that these stands can persist for long periods of time in the absence of pest, pathogen, or other disturbances.
DOI: 10.6084/m9.figshare.14182445
title: Data from: Insulin sensitivity across the menstrual cycle

description: Title: Relationship between insulin sensitivity and menstrual cycle phase is modified by BMI, fitness and physical activity: results from NHANES.Data csv file.
DOI: 10.17632/gtfrr4j5cx.2
title: Data_S1

description: Dimensionality reduction by UMAP reinforces sample heterogeneity analysis in bulk transcriptomic data - Supplementary Data S1
DOI: 10.17632/7pkd3tkg8m.1
title: PLY and MDSCs

description: Our data indicated that the mitigation of EAE with pseudolycorine chloride comes from its ability to target a range of anti-inflammatory pathways, including inhibition of the differentiation of M-MDSCs and proliferation of MDSCs both in vitro and in vivo, decrease in inflammatory infiltration and demyelination in the spinal cord, and preventing the migration of MDSCs and related Th17 cells to the CNS.
DOI: 10.15482/usda.adc/1522649
title: Data from: Annual Compensation for Floral Herbivory by an Iterocarpic Thistle
DOI: 10.17632/7pkd3tkg8m.2
title: PLY and MDSCs

description: Our data indicated that the mitigation of EAE with pseudolycorine chloride comes from its ability to target a range of anti-inflammatory pathways, including inhibition of the differentiation of M-MDSCs and proliferation of MDSCs both in vitro and in vivo, decrease in inflammatory infiltration and demyelination in the spinal cord, and preventing the migration of MDSCs and related Th17 cells to the CNS.
DOI: 10.17632/sf4tmcg6d2.1
title: Supplementary data for "Automated Probabilistic Analysis and Parametric Modelling of the Seasonal-Diurnal Wind Vector"

description: Additional materials including supplementary figures, analysis scripts in R, fitted model parameters and model equations that accompany the open-access paper "Automated Probabilistic Analysis and Parametric Modelling of the Seasonal-Diurnal Wind Vector" in Journal of Energy and Power Technology, 2021, 2, jept.2102027.
DOI: 10.17632/ydfddjztrj.1
title: Determination of mitochondrial functions and damage in kidney in female LeeSung minipigs with a high-fat diet-induced obesity

description: We successfully established a DIO-related kidney injury in LeeSung minipigs. In addition, an ATP deficit and oxidative stress were observed in the renal cortex of DIO pigs. Our results provided additional evidences for the involvement of mitochondrial dysfunctions (biogenesis and dynamics) in DIO-related nephropathy.
DOI: 10.17632/ydfddjztrj.2
title: Determination of mitochondrial functions and damage in kidney in female LeeSung minipigs with a high-fat diet-induced obesity

description: We successfully established a DIO-related kidney injury in LeeSung minipigs. In addition, an ATP deficit and oxidative stress were observed in the renal cortex of DIO pigs. Our results provided additional evidences for the involvement of mitochondrial dysfunctions (biogenesis and dynamics) in DIO-related nephropathy.
DOI: 10.17632/674vgm3jtx.1
title: imported_fruits

description: imported fruits - Vietnam
DOI: 10.17632/krn357zs6r.1
title: Supplemental Figure SF1. Description of data preparation steps for a retrospective descriptive study of Environment, nutrition, and management practices for far-off, close-up, and fresh cows on 78 Canadian dairy farms.

description: Description of data preparation steps for a retrospective descriptive study of Environment, nutrition, and management practices for far-off, close-up, and fresh cows on 78 Canadian dairy farms.
DOI: 10.17632/ypx74nmfs8.3
title: Modules in Human Electrophysiological Connectomes of Phase-Synchronization

description: This dataset contains results from a study to identify modules in human connectomes of inter-regional phase-synchronization, from intra-cerebral stereo-EEG (Electroencephalographic) data. 'Module_assignments.xlsx' contains module assignments, separately for left and right hemispheres, for frequencies from 3 Hz to 320 Hz. Module assignments are provided for different spatial scales, as specified by the 'gamma' parameter of the Louvain community detection method, which we used to identify modules. 'NeurosynthTerms_ConsensusModules.xlsx' contains module assignments for 'consensus modules', i.e. sets of regions consistently assigned to the same module across frequencies and spatial scales. Further, it provides sets of terms related to perceptual, cognitive and motor processing, that are selectively associated to each of the consensus modules.
DOI: 10.17632/skxgmkc64k.1
title: Measured weather and power dataset for management of an island and grid-connected microgrid

description: This dataset presents the weather and power data files from renewable sources used to solve the economic dispatch problem of a microgrid that operates in the isolated and grid-connected modes. Methodology is used in the research article “Management of an island and grid-connected microgrid using hybrid economic model predictive control with weather data”. Automatic stations located in the Brazil's south and northeast furnished the weather data (irradiance, temperature, and wind speed). A script generates files containing weather forecasts from one-day ahead using the geographical coordinates of the weather stations. A microgrid management algorithm uses these forecasts to solve the optimal economic dispatch problem. There are five data files for each weather station: i) Weather database downloaded from the website of the National Meteorological Institute, ii) Weather research and forecasting (WRF) database derived from the raw data generated by the weather research and forecasting model, iii) Weather database that joins the forecasted data with the measured data in a single file, iv) Files containing only the temperature, irradiance, and wind speed data, v) Files containing the measured and forecasted wind and solar power.