cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.19317323.v1
title: Supplementary: Non-invasive genetic sampling reveals a habitat use adaptation of Chrysocyon brachyurus and Leopardus guttulus inside a protected area of Southeastern Brazil

description: Anthropogenic activities have modified landscapes leading to environmental damages and to a threatened biodiversity. As a result, protected areas have become the last refuge for many species. Protected areas surrounded by a highly modified landscape may accumulate species, especially large mammals, which may alter their habitual habitat use. Here we used non-invasive DNA analysis, molecular species identification, and landscape analyses to assess the habitat use of medium-sized carnivore species in an isolated protected area, Itatiaia National Park (PNI). Two species were by far the most sampled within PNI, <i>Chrysocyon brachyurus</i> and <i>Leopardus guttulus</i>. The spatial distribution of each species was assessed to the following landscape variables: digital elevation model; land use and land cover; slope and Euclidean distances from water and from urban buildings. The habitat use of <i>C. brachyurus</i> and <i>L. guttulus</i> was related to altitude, land use, and land coverage. We tested whether there were differences in the environmental indicators considering both species, which showed that higher altitudes, forest and/or grassland formation were indeed associated with them. We highlighted the unprecedented presence of both species at altitudes up to 2,631 meters. Our results indicated habitual habitat use adaptation for both species that could be a consequence of the highly modified landscape where PNI is inserted. Therefore, the results can be helpful for better understanding the species dynamics and their conservation in the face of landscape changes. Further, this study may be of help for management and conservation policies of this emblematic protected area.
DOI: 10.6084/m9.figshare.19317419.v1
title: 16S rRNA Abundance

description: According to the manufacturer’s detailed instructions, we used the Mobio Powersoil DNA Isolation Kit to extract genomic DNA from urine samples. We amplified the V3 and V4 regions of the 16S rRNA genes by the primers (F-primer:5′-ACTCCTACGGGAGGCAGCA-3′ and R-primer:5′- GGACTACHVGGGTWTCTAAT-3′). After the polymerase chain reaction products were purified using ampoule XP magnetic beads, we analyzed the samples using a paired-end sequencing strategy to use the Illumina HiSeq platform.The original paired-end reads were modified by filtration using Trimmomatic software 0.33[11]. Then Cutadapt is used to identify and remove the merging primer sequences. Next, the reads were further combined by FLASH software 1.2.11[12] and removed the chimeric sequences using UCHIME version 8.1[13]. After the obtained high-quality sequence were used for subsequent analysis. We classified sequences with a similarity level of 97% as an operational taxonomic unit (OTU) using USEARCH software 10.0[14]. Based on the Silva database[15], the taxonomic information was annotated and we further set OTUs to different phylogenetic levels (phylum, class, order, family, genus and species). We used QIME2 (https://qiime2.org/) to analyze the alpha diversity.
DOI: 10.6084/m9.figshare.15156834
title: Vertical offsets of normal fault scarps at the Paka and Silali volcanoes, Northern Kenya Rift, derived from the TanDEM-X science DEM. GIS dataset.

description: This dataset contains a shapefile with a point dataset of all vertical offsets that have been extracted along normal fault scarps at the Paka and Silali volcanoes, Kenya, using the TanDEM-X science DEM and a scarp-height-extraction tool.The tool is available at: 10.6084/m9.figshare.15156954<i><br></i><i>This is a companion dataset to the following publication, which we kindly ask you to cite if you use this dataset:<br>Riedl, S., Melnick, D., Njue, L., Sudo, M., & Strecker, M. R. (2022). Mid-Pleistocene to recent crustal extension in the inner graben of the Northern Kenya Rift. Geochemistry, Geophysics, Geosystems, 23, e2021GC010123.</i><br><b>Contents:</b><br><i>readme.md </i>- Detailed description of files and shapefile attributes<br><i>tandemx_scarpheights_pt.*</i> - Point Shapefile<br><i>scarp-height-profiles.pdf</i> - Data visualization: Figures of <i>scarp length vs vertical offset</i> for each analyzed fault scarp<br>
DOI: 10.6084/m9.figshare.15156834.v1
title: Vertical offsets of normal fault scarps at the Paka and Silali volcanoes, Northern Kenya Rift, derived from the TanDEM-X science DEM. GIS dataset.

description: This dataset contains a shapefile with a point dataset of all vertical offsets that have been extracted along normal fault scarps at the Paka and Silali volcanoes, Kenya, using the TanDEM-X science DEM and a scarp-height-extraction tool.The tool is available at: 10.6084/m9.figshare.15156954<i><br></i><i>This is a companion dataset to the following publication, which we kindly ask you to cite if you use this dataset:<br>Riedl, S., Melnick, D., Njue, L., Sudo, M., & Strecker, M. R. (2022). Mid-Pleistocene to recent crustal extension in the inner graben of the Northern Kenya Rift. Geochemistry, Geophysics, Geosystems, 23, e2021GC010123.</i><br><b>Contents:</b><br><i>readme.md </i>- Detailed description of files and shapefile attributes<br><i>tandemx_scarpheights_pt.*</i> - Point Shapefile<br><i>scarp-height-profiles.pdf</i> - Data visualization: Figures of <i>scarp length vs vertical offset</i> for each analyzed fault scarp<br>
DOI: 10.5281/zenodo.4265559
title: Datasets for feature-specific class prediction, from readings in several cell-types.

description: The cell-types featured here are A549, H1ESC, HeLa, IMR90, K562, and MCF7. These happen to be the 6 cell-types out of 8 existing in our integrative database, GREG (https://doi.org/10.1093/database/baz162). The normalized read-coverages from features (variables) like DNA-Protein bindings, histone modifications; ChIP-Seq data, are mapped through genomic intervals of 2 Kbs, genome-wide. These genomic intervals (technically <em>bins</em>), are classified as <em><strong>Hubs</strong></em> or <strong><em>Non-Hubs</em></strong>. Hubs are those bins that are engaged in genomic crosstalk at a distance of 1Mb or Inf., and are Non-Hubs otherwise. Note that features are inconsistent across different cell-types, due to the availability of data. The BAM files have been sourced from ENCODE and NCBI repositories. Also, the users might want to use <em>unique() in R</em> or something similar to refine the datasets for non-redundant instances (if existing).<em> </em> The analysis following this data can be tracked at https://github.com/mora-lab/GREG-Hubs.
DOI: 10.5281/zenodo.4265558
title: Datasets for feature-specific class prediction, from readings in several cell-types.

description: The cell-types featured here are A549, H1ESC, HeLa, IMR90, K562, and MCF7. These happen to be the 6 cell-types out of 8 existing in our integrative database, GREG (https://doi.org/10.1093/database/baz162). The normalized read-coverages from features (variables) like DNA-Protein bindings, histone modifications; ChIP-Seq data, are mapped through genomic intervals of 2 Kbs, genome-wide. These genomic intervals (technically <em>bins</em>), are classified as <em><strong>Hubs</strong></em> or <strong><em>Non-Hubs</em></strong>. Hubs are those bins that are engaged in genomic crosstalk at a distance of 1Mb or Inf., and are Non-Hubs otherwise. Note that features are inconsistent across different cell-types, due to the availability of data. The BAM files have been sourced from ENCODE and NCBI repositories. Also, the users might want to use <em>unique() in R</em> or something similar to refine the datasets for non-redundant instances (if existing).<em> </em> The analysis following this data can be tracked at https://github.com/mora-lab/GREG-Hubs.
DOI: 10.6084/m9.figshare.19317494
title: Supplementary: Scats sampling reveals habitat use adaptation

description: Anthropogenic activities have modified landscapes leading to environmental damages and to a threatened biodiversity. As a result, protected areas have become the last refuge for many species. Protected areas surrounded by a highly modified landscape may accumulate species, especially large mammals, which may alter their habitual habitat use. Here we used non-invasive DNA analysis, molecular species identification, and landscape analyses to assess the habitat use of medium-sized carnivore species in an isolated protected area, Itatiaia National Park (PNI). Two species were by far the most sampled within PNI, <i>Chrysocyon brachyurus</i> and <i>Leopardus guttulus</i>. The spatial distribution of each species was assessed to the following landscape variables: digital elevation model; land use and land cover; slope and Euclidean distances from water and from urban buildings. The habitat use of <i>C. brachyurus</i> and <i>L. guttulus</i> was related to altitude, land use, and land coverage. We tested whether there were differences in the environmental indicators considering both species, which showed that higher altitudes, forest and/or grassland formation were indeed associated with them. We highlighted the unprecedented presence of both species at altitudes up to 2,631 meters. Our results indicated habitual habitat use adaptation for both species that could be a consequence of the highly modified landscape where PNI is inserted. Therefore, the results can be helpful for better understanding the species dynamics and their conservation in the face of landscape changes. Further, this study may be of help for management and conservation policies of this emblematic protected area
DOI: 10.6084/m9.figshare.19317494.v1
title: Supplementary: Scats sampling reveals habitat use adaptation

description: Anthropogenic activities have modified landscapes leading to environmental damages and to a threatened biodiversity. As a result, protected areas have become the last refuge for many species. Protected areas surrounded by a highly modified landscape may accumulate species, especially large mammals, which may alter their habitual habitat use. Here we used non-invasive DNA analysis, molecular species identification, and landscape analyses to assess the habitat use of medium-sized carnivore species in an isolated protected area, Itatiaia National Park (PNI). Two species were by far the most sampled within PNI, <i>Chrysocyon brachyurus</i> and <i>Leopardus guttulus</i>. The spatial distribution of each species was assessed to the following landscape variables: digital elevation model; land use and land cover; slope and Euclidean distances from water and from urban buildings. The habitat use of <i>C. brachyurus</i> and <i>L. guttulus</i> was related to altitude, land use, and land coverage. We tested whether there were differences in the environmental indicators considering both species, which showed that higher altitudes, forest and/or grassland formation were indeed associated with them. We highlighted the unprecedented presence of both species at altitudes up to 2,631 meters. Our results indicated habitual habitat use adaptation for both species that could be a consequence of the highly modified landscape where PNI is inserted. Therefore, the results can be helpful for better understanding the species dynamics and their conservation in the face of landscape changes. Further, this study may be of help for management and conservation policies of this emblematic protected area
DOI: 10.5517/ccdc.csd.cc23hs2h
title: CCDC 1951576: Experimental Crystal Structure Determination

description: Related Article: Hong Zeng|2022|CSD Communication|||
DOI: 10.6084/m9.figshare.13252388
title: Widespread nociceptive maps in the human neonatal somatosensory cortex - RAW DATA

description: Brain activity (fNIRS) was recorded following a clinically-required heel lance procedure or innocuous mechanical stimulation of the limbs (heel and hand) at the bedside in the neonatal unit at University College London Hospitals. <br>Files are in .nirs format for use with Homer2 open access software. <br>Note: Accidental triggers during recording have been removed. To revert file to original state in Homer2 would reintroduce these triggers as well as remove trigger labels. <br>Triggers currently 'excluded' (dashed lines) during heel or hand touches, denote those during which movement of the baby was observed.<br><br>
DOI: 10.6084/m9.figshare.13252388.v2
title: Widespread nociceptive maps in the human neonatal somatosensory cortex - RAW DATA

description: Brain activity (fNIRS) was recorded following a clinically-required heel lance procedure or innocuous mechanical stimulation of the limbs (heel and hand) at the bedside in the neonatal unit at University College London Hospitals. <br>Files are in .nirs format for use with Homer2 open access software. <br>Note: all triggers during movement of the baby or accidental triggering have been removed. To revert file to original state in Homer2 would reintroduce these triggers as well as remove trigger labels. <br>
DOI: 10.25934/pr00005843.2
title: Available IPD datapackage for study 'Randomised, Double-blind, Parallel-group, Placebo-controlled, Duloxetine-referenced, Fixed Dose Study Comparing the Efficacy and Safety of [Vortioxetine] Lu AA21004 in Acute Treatment of Major Depressive Disorder in Elderly Patients'

description: To assess the efficacy of Vortioxetine (5 mg daily) versus placebo in the acute treatment of depression by means of the change from baseline in the 24-item Hamilton Depression Scale (HAM-D24) total score after 8 weeks of double-blind treatment in elderly patients.
DOI: 10.5281/zenodo.6334826
title: Standardization of Methodology of Light-to-Heat Conversion Efficiency Determination for Colloidal Nanoheaters

description: Localized photothermal therapy (PTT) has been demonstrated to be a promising method of combating cancer, that additionally synergistically enhances other treatment modalities such as photodynamic therapy or chemotherapy. PTT exploits nanoparticles (called nanoheaters), that upon proper biofunctionalization may target cancerous tissues, and under light stimulation may convert the energy of photons to heat, leading to local overheating and treatment of cancerous cells. Despite extensive work, there is, however, no agreement on how to accurately and quantitatively compare light-to-heat conversion efficiency (ηQ) and rank the nanoheating performances of various groups of nanomaterials. This disagreement is highly problematic because the obtained ηQ values, measured with various methods, differ significantly for similar nanomaterials. In this work, we experimentally review existing optical setups, methods, and physical models used to evaluate ηQ. In order to draw a binding conclusion, we cross-check and critically evaluate the same Au@SiO2 sample in various experimental conditions. This critical study let us additionally compare and understand the influence of the other experimental factors, such as stirring, data recording and analysis, and assumptions on the effective mass of the system, in order to determine ηQ in a most straightforward and reproducible way. Our goal is therefore to contribute to the understanding, standardization, and reliable evaluation of ηQ measurements, aiming to accurately rank various nanoheater platforms.
DOI: 10.5281/zenodo.6334825
title: Standardization of Methodology of Light-to-Heat Conversion Efficiency Determination for Colloidal Nanoheaters

description: Localized photothermal therapy (PTT) has been demonstrated to be a promising method of combating cancer, that additionally synergistically enhances other treatment modalities such as photodynamic therapy or chemotherapy. PTT exploits nanoparticles (called nanoheaters), that upon proper biofunctionalization may target cancerous tissues, and under light stimulation may convert the energy of photons to heat, leading to local overheating and treatment of cancerous cells. Despite extensive work, there is, however, no agreement on how to accurately and quantitatively compare light-to-heat conversion efficiency (ηQ) and rank the nanoheating performances of various groups of nanomaterials. This disagreement is highly problematic because the obtained ηQ values, measured with various methods, differ significantly for similar nanomaterials. In this work, we experimentally review existing optical setups, methods, and physical models used to evaluate ηQ. In order to draw a binding conclusion, we cross-check and critically evaluate the same Au@SiO2 sample in various experimental conditions. This critical study let us additionally compare and understand the influence of the other experimental factors, such as stirring, data recording and analysis, and assumptions on the effective mass of the system, in order to determine ηQ in a most straightforward and reproducible way. Our goal is therefore to contribute to the understanding, standardization, and reliable evaluation of ηQ measurements, aiming to accurately rank various nanoheater platforms.
DOI: 10.25934/pr00005844.2
title: Available IPD datapackage for study 'A Randomised, Double-blind, Parallel-group, Placebo-controlled, Duloxetine-referenced, Fixed-dose Study Evaluating the Efficacy and Safety of Lu AA21004 (15 and 20 mg/Day) in the Acute Treatment of Adult Patients With Major Depressive Disorder'

description: The purpose of the study is to evaluate the efficacy, tolerability and the safety of two fixed doses of vortioxetine in the treatment of major depressive disorder.
DOI: 10.5281/zenodo.6334837
title: Sowing storms: how model timestep can control tropical cyclone frequency in a GCM

description: Supplementary dataset to JAMES article "Sowing storms: how model timestep can control tropical cyclone frequency in a GCM" DOI:10.1029/2021MS002791
description: {"references": ["Zarzycki, Colin, Sowing storms: how model timestep can control tropical cyclone frequency in a GCM, DOI:10.1029/2021MS002791"]}
DOI: 10.5281/zenodo.6334836
title: Sowing storms: how model timestep can control tropical cyclone frequency in a GCM

description: Supplementary dataset to JAMES article "Sowing storms: how model timestep can control tropical cyclone frequency in a GCM" DOI:10.1029/2021MS002791
description: {"references": ["Zarzycki, Colin, Sowing storms: how model timestep can control tropical cyclone frequency in a GCM, DOI:10.1029/2021MS002791"]}
DOI: 10.25934/pr00005846.2
title: Available IPD datapackage for study 'Randomised, Double-blind, Parallel-group, Active-comparator (Venlafaxine Extended Release), Fixed-dose Study of [Vortioxetine] Lu AA21004 in Major Depressive Disorder in Asian Countries'

description: This study will be conducted with the aim of investigating the efficacy, safety and tolerability of 10 mg/day Vortioxetine in Asian patients compared to an approved active comparator (venlafaxine extended release 150 mg/day).
DOI: 10.3886/e132762v2-111380
title: Data and Code for: The Effects of Parental and Sibling Incarceration: Evidence from Ohio

description: Every year, millions of Americans experience the incarceration of a family member. Using 30 years of administrative data from Ohio and exploiting differing incarceration propensities of randomly assigned judges, this paper provides the first quasi-experimental estimates of the effects of parental and sibling incarceration in the US. Contrary to conventional wisdom, parental incarceration has a net positive effect on some important outcomes for children, reducing their likelihood of incarceration by 4.9 percentage points and improving their adult neighborhood quality. While estimates on academic performance and teen parenthood are imprecise, we reject large positive or negative effects. Sibling incarceration leads to similar reductions in criminal activity.
description: Children of incarcerated parents in Cuyahoga County, Franklin County, and Hamilton County .
DOI: 10.6084/m9.figshare.19317536
title: Appendix to BEH 3751

description: <b>Table A1.</b> Model selection for predictors of each acoustic parameter (call duration; mean entropy; maximum, mean, and minimum frequency) using deviance information criterion (DIC) ranks.<br><b>Table A2.</b> Summary output for models of all five acoustic parameters (call duration; mean entropy; maximum, mean, and minimum frequency). Results correspond to the model selected in this table (parentheses, categorical variable levels; NN, nearest neighbour; CI, credible interval).<br>
DOI: 10.6084/m9.figshare.19317536.v1
title: Appendix to BEH 3751

description: <b>Table A1.</b> Model selection for predictors of each acoustic parameter (call duration; mean entropy; maximum, mean, and minimum frequency) using deviance information criterion (DIC) ranks.<br><b>Table A2.</b> Summary output for models of all five acoustic parameters (call duration; mean entropy; maximum, mean, and minimum frequency). Results correspond to the model selected in this table (parentheses, categorical variable levels; NN, nearest neighbour; CI, credible interval).<br>
DOI: 10.21227/9bs5-3b76
title: Peak-Efficiency-Test

description: Efficiency Measurment
DOI: 10.5281/zenodo.6334815
title: Data for the manuscript "Direct visualization of colloid transport over natural heterogeneous and artificial smooth rock surfaces"

description: The files contain the data used to produce the figures in the manuscript "<strong>Direct visualization of colloid transport over natural heterogeneous and artificial smooth rock surfaces</strong>" by Borgman, Be'er, and Weisbrod. Included in the data set: ImageAnalysesAndPlots.m: A MATLAB script to generate the figures from the included images and data files. myCmap.mat: A custom set of colors for the images. LH_btc.csv, LH_b_btc.csv, HH_btc.csv, HH_b_btc.csv: Data for the breakthrough curves. LH_t=360min.czi, HH_t=300min.czi: Final images from the experiments, from which the residual surface fluorescence is calculated. LHSurfTopo.csv, HHSurfTopo.csv: Tables containing the profilometer scan data. LH, HH: Folders containing the images for the colloid displacement front Exp01-Exp04: Images for calculating the dispersion coefficient PlotVelocities2.m: A script for plotting the calculated velocity fields velocity_magnitude_HH_flux_boundary.txt/velocity_magnitude_LH_flux_boundary.txt: The data files for the velocity fields. For the .czi files, it's necessary to use the Bio-Formats for MATLAB package.
DOI: 10.5281/zenodo.5081120
title: Data for the manuscript "Direct visualization of colloid transport over natural heterogeneous and artificial smooth rock surfaces"

description: The files contain the data used to produce the figures in the manuscript "<strong>Direct visualization of colloid transport over natural heterogeneous and artificial smooth rock surfaces</strong>" by Borgman, Be'er, and Weisbrod. Included in the data set: ImageAnalysesAndPlots.m: A MATLAB script to generate the figures from the included images and data files. myCmap.mat: A custom set of colors for the images. LH_btc.csv, LH_b_btc.csv, HH_btc.csv, HH_b_btc.csv: Data for the breakthrough curves. LH_t=360min.czi, HH_t=300min.czi: Final images from the experiments, from which the residual surface fluorescence is calculated. LHSurfTopo.csv, HHSurfTopo.csv: Tables containing the profilometer scan data. LH, HH: Folders containing the images for the colloid displacement front Exp01-Exp04: Images for calculating the dispersion coefficient PlotVelocities2.m: A script for plotting the calculated velocity fields velocity_magnitude_HH_flux_boundary.txt/velocity_magnitude_LH_flux_boundary.txt: The data files for the velocity fields. For the .czi files, it's necessary to use the Bio-Formats for MATLAB package.
DOI: 10.5519/qd.km7wxxeo
title: Query on the Natural History Museum Data Portal (data.nhm.ac.uk) (4631 records)
DOI: 10.34740/kaggle/dsv/3266313
title: Mahanagar Yatayat Dataset
DOI: 10.6084/m9.figshare.14534088
title: Anemone nemorosa Norway data (NJB)

description: Dataset used for the manuscript 'Functional trait variation of <i>Anemone nemorosa</i> along macro- and microclimatic gradients close to the northern range edge', submitted to Nordic Journal of Botany