cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.8058923
title: Mapping a keystone shrub species, huckleberry (<i>Vaccinium membranaceum</i>), using seasonal colour change in the Rocky Mountains

description: Black huckleberries (<i>Vaccinium membranaceum</i>) provide a critical food resource to many wildlife species, including apex omnivores such as the grizzly bear (<i>Ursus arctos</i>), and play an important socioeconomic role for many communities in western North America, especially indigenous peoples. Remote sensing imagery offers the potential for accurate landscape-level mapping of huckleberries because the shrub changes colour seasonally. We developed two methods, for local and regional scales, to map a shrub species using leaf seasonal colour change from remote sensing imagery. We assessed accuracy with ground-based vegetation surveys. The high-resolution supervised random forest classification from one-meter resolution National Agricultural Imagery Program (NAIP) imagery achieved an overall accuracy of 75.31% (kappa = 0.26). The approach using multi-temporal 30-meter Landsat imagery similarly had an overall accuracy of 79.19% (kappa = .31). We found underprediction error was related to higher forest cover and a lack of visible colour change on the ground in some plots. Where forest cover was low, both models performed better. In areas with &lt;10% forest cover, the high-resolution classification achieved an accuracy of 80.73% (kappa = 0.48), while the Landsat model had an accuracy of 82.55% (kappa = 0.47). Based on the fine-scale predictions, we found that 94% of huckleberry shrubs identified in our study area of Glacier National Park, Montana, USA are over 100 meters from human recreation trails. This information could be combined with productivity and phenology information to estimate the timing and availability of food resources for wildlife and to provide managers with a tool to identify and manage huckleberries. The development of the multi-temporal Landsat models sets the stage for assessment of impacts of disturbance at regional scales on this ecologically, culturally, and economically important shrub species. Our approach to map huckleberries is straightforward, efficient and accessible to wildlife and environmental managers and researchers in diverse fields.
DOI: 10.6084/m9.figshare.8058887.v2
title: Measuring the structural impact of mutations on cytochrome P450 21A2, the major steroid 21-hydroxylase related to congenital adrenal hyperplasia

description: Congenital adrenal hyperplasia is an inherited autosomal recessive disorder related to deficient cortisol synthesis. The deficiency of steroid 21-hydroxylase (cytochrome P450 21A2), an enzyme involved in cortisol synthesis, is responsible for ∼95% of cases of congenital adrenal hyperplasia. This metabolic disease exhibits three clinical forms: salt-wasting, simple virilizing, and non-classical form, which are divided according to the degree of severity. In the present study, structural and mutational analyses were performed in order to identify the structural impact of mutations on cytochrome P450 21A2 and correlate them with patient clinical severity. The following mutations were selected: arginine-356 to tryptophan (R356W), proline-30 to leucine (P30L), isoleucine-172 to asparagine (I172N), valine-281 to leucine (V281L), and the null mutation glutamine-318 (Q318X). Our computational approach mapped the location of residues on P450 and identified their implications on enzyme electrostatic potential mapping to progesterone and heme binding pockets. Using molecular dynamics simulations, we analyzed the structural stability of ligand binding and protein structure, as well as possible conformational changes at the catalytic pocket that leads to impairment of enzymatic activity. Our study sheds light on the impact structural mutations have over steroid 21-hydroxylase structure-function in the cell. Communicated by Ramaswamy H. Sarma
DOI: 10.6084/m9.figshare.8058923.v1
title: Mapping a keystone shrub species, huckleberry (<i>Vaccinium membranaceum</i>), using seasonal colour change in the Rocky Mountains

description: Black huckleberries (<i>Vaccinium membranaceum</i>) provide a critical food resource to many wildlife species, including apex omnivores such as the grizzly bear (<i>Ursus arctos</i>), and play an important socioeconomic role for many communities in western North America, especially indigenous peoples. Remote sensing imagery offers the potential for accurate landscape-level mapping of huckleberries because the shrub changes colour seasonally. We developed two methods, for local and regional scales, to map a shrub species using leaf seasonal colour change from remote sensing imagery. We assessed accuracy with ground-based vegetation surveys. The high-resolution supervised random forest classification from one-meter resolution National Agricultural Imagery Program (NAIP) imagery achieved an overall accuracy of 75.31% (kappa = 0.26). The approach using multi-temporal 30-meter Landsat imagery similarly had an overall accuracy of 79.19% (kappa = .31). We found underprediction error was related to higher forest cover and a lack of visible colour change on the ground in some plots. Where forest cover was low, both models performed better. In areas with &lt;10% forest cover, the high-resolution classification achieved an accuracy of 80.73% (kappa = 0.48), while the Landsat model had an accuracy of 82.55% (kappa = 0.47). Based on the fine-scale predictions, we found that 94% of huckleberry shrubs identified in our study area of Glacier National Park, Montana, USA are over 100 meters from human recreation trails. This information could be combined with productivity and phenology information to estimate the timing and availability of food resources for wildlife and to provide managers with a tool to identify and manage huckleberries. The development of the multi-temporal Landsat models sets the stage for assessment of impacts of disturbance at regional scales on this ecologically, culturally, and economically important shrub species. Our approach to map huckleberries is straightforward, efficient and accessible to wildlife and environmental managers and researchers in diverse fields.
DOI: 10.6084/m9.figshare.8058887.v1
title: Measuring the structural impact of mutations on cytochrome P450 21A2, the major steroid 21-hydroxylase related to congenital adrenal hyperplasia

description: Congenital adrenal hyperplasia is an inherited autosomal recessive disorder related to deficient cortisol synthesis. The deficiency of steroid 21-hydroxylase (cytochrome P450 21A2), an enzyme involved in cortisol synthesis, is responsible for ∼95% of cases of congenital adrenal hyperplasia. This metabolic disease exhibits three clinical forms: salt-wasting, simple virilizing, and non-classical form, which are divided according to the degree of severity. In the present study, structural and mutational analyses were performed in order to identify the structural impact of mutations on cytochrome P450 21A2 and correlate them with patient clinical severity. The following mutations were selected: arginine-356 to tryptophan (R356W), proline-30 to leucine (P30L), isoleucine-172 to asparagine (I172N), valine-281 to leucine (V281L), and the null mutation glutamine-318 (Q318X). Our computational approach mapped the location of residues on P450 and identified their implications on enzyme electrostatic potential mapping to progesterone and heme binding pockets. Using molecular dynamics simulations, we analyzed the structural stability of ligand binding and protein structure, as well as possible conformational changes at the catalytic pocket that leads to impairment of enzymatic activity. Our study sheds light on the impact structural mutations have over steroid 21-hydroxylase structure-function in the cell. Communicated by Ramaswamy H. Sarma
DOI: 10.6084/m9.figshare.8058902.v1
title: Reconstructing Draft Genomes Using Genome-Resolved Meta- genomics to Decipher Fresh Water Lake Microbial Characteristics

description: We have taken water sample during winter and rainy season from Rabindra sarovar lake located at south kolkata and did metagenomic analysis. For metagenome analysis we followed genome resolved metagenomics approach. In this method samples are assembled after sequencing, then assembled samples are binned using binning tool to recover genome bins(n=18). Here in this repository we have uploaded recovered genome bins (.fasta) and their respective protein sequences (.faa). In-addition we have also uploaded prokka annotation files (.tsv)<br>
DOI: 10.6084/m9.figshare.8058818
title: Dataset 1.2: Yeast amino-acids raw data

description: Supplementary Dataset from the work "Rules of amino acid composition by which disordered regions adjust to high expression".<br>This table contains amino-acid level information of yeast proteins.<br><br>The compressed file contains the same table with the full proteome data, not excluding the missing information and including the membrane proteins.
DOI: 10.6084/m9.figshare.8058902.v2
title: Reconstructing Draft Genomes Using Genome-Resolved Meta- genomics to Decipher Fresh Water Lake Microbial Characteristics

description: We have taken water sample during winter and rainy season from Rabindra sarovar lake located at south kolkata and did metagenomic analysis. For metagenome analysis we followed genome resolved metagenomics approach. In this method samples are assembled after sequencing, then assembled samples are binned using binning tool to recover genome bins(n=27). Here in this repository we have uploaded recovered genome bins (.fna) and their respective protein sequences (.faa). In-addition we have also uploaded assembled data of both season(.fasta).<br>
DOI: 10.6084/m9.figshare.8058902.v3
title: Reconstructing Draft Genomes Using Genome-Resolved Meta- genomics to Decipher Fresh Water Lake Microbial Characteristics - Main Data

description: We have taken water sample during winter and rainy season from Rabindra sarovar lake located at south kolkata and did metagenomic analysis. For metagenome analysis we followed genome resolved metagenomics approach. In this method samples are assembled after sequencing, then assembled samples are binned using binning tool to recover genome bins(n=27). Here in this repository we have uploaded recovered genome bins (.fna) and their respective protein sequences (.faa). In-addition we have also uploaded assembled data of both season(.fasta).<br>
DOI: 10.6084/m9.figshare.8058902.v4
title: Reconstructing Draft Genomes Using Genome-Resolved Meta- genomics to Decipher Fresh Water Lake Microbial Characteristics - Main Data

description: We have taken water sample during winter and rainy season from Rabindra sarovar lake located at south kolkata and did metagenomic analysis. For metagenome analysis we followed genome resolved metagenomics approach. In this method samples are assembled after sequencing, then assembled samples are binned using binning tool to recover genome bins(n=27). Here in this repository we have uploaded recovered genome bins (.fna) and their respective 16S (.fa) as well as protein sequences (.faa) with annotation. In-addition we have also uploaded assembled data of both season(.fasta). <br>
DOI: 10.6084/m9.figshare.8058740.v1
title: Adipocyte abundances of CES1, CRYAB, ENO1 and GANAB are modified <i>in-vitro</i> by glucose restriction and are associated with cellular remodelling during weight regain

description: Long-term weight loss maintenance is a problem of overweight and obesity. Changes of gene expression during weight loss (WL) by calorie restriction (CR) are linked to the risk of weight regain (WR). However, detailed information on genes/proteins involved in the mechanism is still lacking. Therefore, we developed an <i>in-vitro</i> model system for glucose restriction (GR) and refeeding (RF) to uncover proteome differences between GR with RF vs normal feeding, of which we explored the relation with WR after WL. Human Simpson-Golabi-Behmel Syndrome cells were subjected to changing levels of glucose to mimic the condition of CR and RF. Proteome profiling was performed by liquid chromatography tandem mass spectrometry. This <i>in-vitro</i> model revealed 44 proteins differentially expressed after GR and RF versus feeding including proteins of the focal adhesions. Four proteins showed a persistent up- or down-regulation: liver carboxylesterase (CES1), mitochondrial superoxide dismutase [Mn] (SOD2), alpha-crystallin B-chain (CRYAB), alpha-enolase (ENO1). <i>In-vivo</i> weight loss-induced RNA expression changes linked CES1, CRYAB and ENO1 to WR. Moreover, of these 44 proteins, CES1 and glucosidase II alpha subunit (GANAB) during follow up correlated with WR. Correlation clustering of <i>in-vivo</i> protein expression data indicated an interaction of these proteins with structural components of the focal adhesions and cytoplasmic filaments in the adipocytes.
DOI: 10.6084/m9.figshare.8058818.v4
title: Dataset 1.2: Yeast amino-acids raw data

description: Supplementary Dataset from the work "Rules of amino acid composition by which disordered regions adjust to high expression".<br>This table contains amino-acid level information of yeast proteins.<br><br>The compressed file contains the same table with the full proteome data, not excluding the missing information and including the membrane proteins.
DOI: 10.6084/m9.figshare.8058818.v3
title: Dataset 1.2: Yeast amino-acids raw data

description: Supplementary Dataset from the work "Rules of amino acid composition by which disordered regions adjust to high expression".<br>This table contains amino-acid level information of yeast proteins.<br><br>The compressed file contains the same table with the full proteome data, not excluding the missing information and including the membrane proteins.
DOI: 10.6084/m9.figshare.8058515
title: Two-stage permutation tests for determining homogeneity within a spatial cluster

description: The discovery of spatial clusters formed by proximal spatial units with similar non-spatial attribute values plays an important role in spatial data analysis. Although several spatial contiguity-constrained clustering methods are currently available, almost all of them discover clusters in a geographical dataset, even though the dataset has no natural clustering structure. Statistically evaluating the significance of the degree of homogeneity within a single spatial cluster is difficult. To overcome this limitation, this study develops a permutation test approach Specifically, the homogeneity of a spatial cluster is measured based on the local variance and cluster member permutation, and two-stage permutation tests are developed to determine the significance of the degree of homogeneity within each spatial cluster. The proposed permutation tests can be integrated into the existing spatial clustering algorithms to detect homogeneous spatial clusters. The proposed tests are compared with four existing tests (i.e., Park’s test, the contiguity-constrained nonparametric analysis of variance (COCOPAN) method, spatial scan statistic, and <i>q</i>-statistic) using two simulated and two meteorological datasets. The comparison shows that the proposed two-stage permutation tests are more effective to identify homogeneous spatial clusters and to determine homogeneous clustering structures in practical applications.
DOI: 10.6084/m9.figshare.8058515.v1
title: Two-stage permutation tests for determining homogeneity within a spatial cluster

description: The discovery of spatial clusters formed by proximal spatial units with similar non-spatial attribute values plays an important role in spatial data analysis. Although several spatial contiguity-constrained clustering methods are currently available, almost all of them discover clusters in a geographical dataset, even though the dataset has no natural clustering structure. Statistically evaluating the significance of the degree of homogeneity within a single spatial cluster is difficult. To overcome this limitation, this study develops a permutation test approach Specifically, the homogeneity of a spatial cluster is measured based on the local variance and cluster member permutation, and two-stage permutation tests are developed to determine the significance of the degree of homogeneity within each spatial cluster. The proposed permutation tests can be integrated into the existing spatial clustering algorithms to detect homogeneous spatial clusters. The proposed tests are compared with four existing tests (i.e., Park’s test, the contiguity-constrained nonparametric analysis of variance (COCOPAN) method, spatial scan statistic, and <i>q</i>-statistic) using two simulated and two meteorological datasets. The comparison shows that the proposed two-stage permutation tests are more effective to identify homogeneous spatial clusters and to determine homogeneous clustering structures in practical applications.
DOI: 10.6084/m9.figshare.8058497
title: Water40 10K

description: The Water40 10K Dataset<br>=====================================<br>The dataset contains 10K (H2O)40 water clusters from an MD simulation as detailed in: https://doi.org/10.1063/1.5020710<br>For each of the snapshots, the QM energy is calculated at the PBEh-3c level of theory.<br>The DOI for this dataset is: 10.6084/m9.figshare.8058497<br>Structures are saved in .xyz format in units of Ångstrøm, and energies are saved in the .txt file in units of Hartree. <br>
DOI: 10.6084/m9.figshare.8058497.v1
title: Water40 10K

description: The Water40 10K Dataset<br>=====================================<br>The dataset contains 10K (H2O)40 water clusters from an MD simulation as detailed in: https://doi.org/10.1063/1.5020710<br>For each of the snapshots, the QM energy is calculated at the PBEh-3c level of theory.<br>The DOI for this dataset is: 10.6084/m9.figshare.8058497<br>Structures are saved in .xyz format in units of Ångstrøm, and energies are saved in the .txt file in units of Hartree. <br>
DOI: 10.21227/dwyc-v151
title: Industrial overfeed refrigeration system

description: Dataset of the signals monitored in a typical overfeed refrigeration system. The system is composed of two compressors in parallel, four evaporative condensers and various evaporators distributed in the different spaces to refrigerate. The dataset contains variables from all the main components of the refrigeration system such as the compressors, the condensers and the evaporators, with additional information about the outdoor temperature, the temperature of the refrigerated spaces and all the set points. The dataset contains more than 2 years of operaton of data acquired every minute, from 2018/01/01 to 2020/05/08.
DOI: 10.6084/m9.figshare.8058302
title: Data from Extending Janzen’s hypothesis to temperate regions: a test using subterranean ecosystems

description: Data associated with this study:<br>Mammola, S., Piano, E., Malard, F., Vernon, P. & Isaia, M. (2019). Extending Janzen's hypothesis to temperate regions: a test using subterranean ecosystems. Functional Ecology doi:10.1111/1365-2435.13382<br><br>Dataset:<br>1) Thermal_tolerance_test.txt – Results of the physiological experiments.<br><br>2) Morphological_measures.txt – Traits measured on adult female spiders.<br>3) Species_range.txt – Altitudinal range extent and thermal niche breadth of the spider species considered in the analyses.
DOI: 10.6084/m9.figshare.8058275
title: Fluoxetine-induced plasticity in the visual cortex outlasts the duration of the naturally occurring critical period

description: Heightened neuronal plasticity expressed during early postnatal life has been thought to permanently decline once critical periods have ended. For example, monocular deprivation is able to shift ocular dominance in the mouse visual cortex during the first months of life, but this effect is lost later in life. However, various treatments, such as the antidepressant fluoxetine, can reactivate a critical period-like plasticity in the adult brain. When monocular deprivation is supplemented with chronic fluoxetine administration, a major shift in ocular dominance is produced after the critical period has ended. In the current study, we characterized the temporal patterns of fluoxetine-induced plasticity in the adult mouse visual cortex, using <i>in vivo</i>optical imaging. We found that artificially-induced plasticity in ocular dominance extended beyond the duration of the naturally occurringcritical period, and continued as long as fluoxetine was administered. However, this fluoxetine-induced plasticity period ended as soon as the drug was not given. These features of antidepressant-induced plasticity may be useful when designing treatment strategies involving long-term antidepressant treatment in humans.
DOI: 10.6084/m9.figshare.8058275.v2
title: Fluoxetine-induced plasticity in the visual cortex outlasts the duration of the naturally occurring critical period

description: Heightened neuronal plasticity expressed during early postnatal life has been thought to permanently decline once critical periods have ended. For example, monocular deprivation is able to shift ocular dominance in the mouse visual cortex during the first months of life, but this effect is lost later in life. However, various treatments, such as the antidepressant fluoxetine, can reactivate a critical period-like plasticity in the adult brain. When monocular deprivation is supplemented with chronic fluoxetine administration, a major shift in ocular dominance is produced after the critical period has ended. In the current study, we characterized the temporal patterns of fluoxetine-induced plasticity in the adult mouse visual cortex, using <i>in vivo</i>optical imaging. We found that artificially-induced plasticity in ocular dominance extended beyond the duration of the naturally occurringcritical period, and continued as long as fluoxetine was administered. However, this fluoxetine-induced plasticity period ended as soon as the drug was not given. These features of antidepressant-induced plasticity may be useful when designing treatment strategies involving long-term antidepressant treatment in humans.
DOI: 10.6084/m9.figshare.8058212
title: Spatial variability of <sup>2</sup>H and <sup>18</sup>O composition of meteoric freshwater lakes in Scotland

description: Coastal regions, and in particular islands where precipitation from clouds formed out at sea occurs for the first time, are prime candidates for regions where <sup>2</sup>H and <sup>18</sup>O composition of precipitation will deviate significantly from the global mean geographic and physiographic trends of vapour-transport patterns. The results reported here are the outcome of a study that aimed to test this hypothesis by ‘isotopographically’ mapping the characteristic <i>δ</i><sup>2</sup>H and <i>δ</i><sup>18</sup>O signatures of Scottish freshwaters. The resulting isotope abundance landscapes or ‘isoscapes’ will underpin studies aiming to authenticate origin of Scottish produce but may also offer a baseline against which environmental changes could be assessed. Between April 2011 and May 2012 freshwater samples were collected from 127 different freshwater lochs and reservoirs across Scotland, and analysis results were compared to precipitation data provided by the British Geological Survey. Here we present the results of the <sup>2</sup>H and <sup>18</sup>O analyses of these water samples as well as the first detailed Scotland freshwater isoscapes with a grid resolution of about 5 × 5 km (0.05 degrees).