cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5281/zenodo.2605120
title: RefleX: X-ray diffraction images dataset

description: Image dataset prepared for the RefleX study, described in <em>"Detecting anomalies in X-ray diffraction images using Convolutional Neural Networks"</em><em>.</em> The dataset contains 6311 X-ray diffraction images in 1024x1024 png format (reflex_img_1024_inter_nearest.zip). The repository also contains a file mapping each image to a set of labels (labels.csv) and files describing the assignment of each image to training, validation, and testing sets (labels_train.csv, labels_val.csv, labels_test.csv). The dataset can be used for multi-label classification. Each diffraction image can exhibit any combination of seven classes: Ice ring, Diffuse Scattering, Background Ring, Non-uniform Detector, Loop Scattering, Strong Background, and Artifact.
DOI: 10.5281/zenodo.4554474
title: CheckMyBlob web server ligand datasets

description: Ligand data set used to train and evaluate the CheckMyBlob web server, as described in <em>"</em>Recognizing and validating ligands with CheckMyBlob<em>"</em> by Brzezinski, D. <em>et al.</em>
DOI: 10.5281/zenodo.4554473
title: CheckMyBlob web server ligand datasets

description: Ligand data set used to train and evaluate the CheckMyBlob web server, as described in <em>"</em>Recognizing and validating ligands with CheckMyBlob<em>"</em> by Brzezinski, D. <em>et al.</em>
DOI: 10.6084/m9.figshare.1263932
title: Testing ecological theories with sequence similarity networks: marine ciliates exhibit similar geographic dispersal patterns as multicellular organisms (file : V4dataset.fna)

description: file : V4dataset.fna Testing ecological theories with sequence similarity networks: marine ciliates exhibit similar geographic dispersal patterns as multicellular organisms (file : readme_Forster_et_al_BMC) http://dx.doi.org/10.6084/m9.figshare.1264013 Background: High-throughput sequencing technologies are lifting major limitations to molecular-based ecological studies of eukaryotic microbial diversity, but in silico analyses of the resulting millions of short amplicons remain a major bottleneck for these approaches. Here, we introduced the analytical and statistical framework of sequence similarity networks, increasingly used in evolutionary studies and graph theory, into the field of ecology to analyze novel pyrosequenced V4 SSU-rDNA sequence data sets in the context of previous studies, including SSU-rDNA Sanger sequence data from cultured ciliates and from previous environmental diversity inventories.<br>Results: Our broadly applicable protocol quantified progress in the description of genetic diversity of ciliates by environmental rRNA amplicons studies, detected a fundamental historical bias, the tendency to recover already known groups, in these surveys, and revealed substantial amounts of hidden microbial diversity. Moreover, network measures demonstrated that ciliates are not globally dispersed, but present strong local patterns at intermediate geographical scale, as observed for bacteria, plants, and animals.<br>Conclusions: Although currently available ‘universal’ primers used for local in-depth sequencing surveys provide little hope to exhaust the significantly higher ciliate (and most likely microbial) diversity than previously thought, sequence similarity networks, since they identify groups of divergence sequences sharing distinctive similarities, offer a promising way to guide the design of novel primers and to further explore such a vast and structured microbial diversity.
DOI: 10.6084/m9.figshare.1264013
title: Testing ecological theories with sequence similarity networks: marine ciliates exhibit similar geographic dispersal patterns as multicellular organisms (file : readme_Forster_et_al_BMC)

description: file : readme_Forster_et_al_BMC Background: High-throughput sequencing technologies are lifting major limitations to molecular-based ecological studies of eukaryotic microbial diversity, but in silico analyses of the resulting millions of short amplicons remain a major bottleneck for these approaches. Here, we introduced the analytical and statistical framework of sequence similarity networks, increasingly used in evolutionary studies and graph theory, into the field of ecology to analyze novel pyrosequenced V4 SSU-rDNA sequence data sets in the context of previous studies, including SSU-rDNA Sanger sequence data from cultured ciliates and from previous environmental diversity inventories. Results: Our broadly applicable protocol quantified progress in the description of genetic diversity of ciliates by environmental rRNA amplicons studies, detected a fundamental historical bias, the tendency to recover already known groups, in these surveys, and revealed substantial amounts of hidden microbial diversity. Moreover, network measures demonstrated that ciliates are not globally dispersed, but present strong local patterns at intermediate geographical scale, as observed for bacteria, plants, and animals.<br>Conclusions: Although currently available ‘universal’ primers used for local in-depth sequencing surveys provide little hope to exhaust the significantly higher ciliate (and most likely microbial) diversity than previously thought, sequence similarity networks, since they identify groups of divergence sequences sharing distinctive similarities, offer a promising way to guide the design of novel primers and to further explore such a vast and structured microbial diversity.
DOI: 10.6084/m9.figshare.1266266
title: Testing ecological theories with sequence similarity networks: marine ciliates exhibit similar geographic dispersal patterns as multicellular organisms (file : Novel_diversity_V4_BIOM_cDNA.fasta)

description: file : Novel_diversity_V4_BIOM_cDNA.fasta see details in Testing ecological theories with sequence similarity networks: marine ciliates exhibit similar geographic dispersal patterns as multicellular organisms (file : readme_Forster_et_al_BMC) http://dx.doi.org/10.6084/m9.figshare.1264013 Background: High-throughput sequencing technologies are lifting major limitations to molecular-based ecological studies of eukaryotic microbial diversity, but in silico analyses of the resulting millions of short amplicons remain a major bottleneck for these approaches. Here, we introduced the analytical and statistical framework of sequence similarity networks, increasingly used in evolutionary studies and graph theory, into the field of ecology to analyze novel pyrosequenced V4 SSU-rDNA sequence data sets in the context of previous studies, including SSU-rDNA Sanger sequence data from cultured ciliates and from previous environmental diversity inventories.<br>Results: Our broadly applicable protocol quantified progress in the description of genetic diversity of ciliates by environmental rRNA amplicons studies, detected a fundamental historical bias, the tendency to recover already known groups, in these surveys, and revealed substantial amounts of hidden microbial diversity. Moreover, network measures demonstrated that ciliates are not globally dispersed, but present strong local patterns at intermediate geographical scale, as observed for bacteria, plants, and animals.<br>Conclusions: Although currently available ‘universal’ primers used for local in-depth sequencing surveys provide little hope to exhaust the significantly higher ciliate (and most likely microbial) diversity than previously thought, sequence similarity networks, since they identify groups of divergence sequences sharing distinctive similarities, offer a promising way to guide the design of novel primers and to further explore such a vast and structured microbial diversity.
DOI: 10.6084/m9.figshare.5400778
title: A python notebook summarizing the analysis of usALEX-smFRET for the formation of figure 2

description: The following Python notebook summarizes the analysis performed by the FRETBursts software to form figure 2
DOI: 10.6084/m9.figshare.5400916
title: A python notebook summarizing the analysis of usALEX-smFRET for the formation of figure S4

description: The following Python notebook summarizes the analysis performed by the FRETBursts software to form figure S3
DOI: 10.6084/m9.figshare.5400802
title: A python notebook summarizing the analysis of usALEX-smFRET for the formation of figure S2

description: The following Python notebook summarizes the analysis performed by the FRETBursts software to form figure S2
DOI: 10.15131/shef.data.10049825
title: Data and figures related to publication: Improved ambient stability of thermally annealed Zinc Nitride thin films

description: Zinc nitride films are known to readily oxidize in an ambient atmosphere, forming a ZnO/Zn(OH)2 medium. We report that post-growth thermal annealing significantly improves the stability of zinc nitride with a three-order magnitude increase in degradation time from a few days in un-annealed films to several years after annealing. A degradation study was performed on samples annealed under a flow of nitrogen at 200–400 °C, which showed that the stability of the films depends strongly on the annealing temperature. We propose a mechanism for this improvement, which involves a stabilization of the native oxide layer that forms on the surface of zinc nitride films after exposure to ambient conditions. The result holds significant promise for the use of zinc nitride in devices where operational stability is a critical factor in applications.<br><br>The study reported in this paper was funded by the EPSRC (Fund code EP/M507611/1) and Johson Matthey PLC. The financial support by these parties is highly appreciated.<br><br>The data required to reproduce each figure panel is provided in different text files. Columns are separated by a space character. The first line in each column describes the dataset. The complete figures are also included as .tif files.<br><br>With the added context of the paper, it should be easy to reproduce the figures.<br><br><b>Figure 1:</b> Transmittance spectra of (a) an as-deposited and (b) an annealed 700 nm Zn<sub>3</sub>N<sub>2</sub> film for up to 18 weeks. (c) Scanning Electron Microscopy image of a partially oxidised Zn<sub>3</sub>N<sub>2</sub> film.<br><b><br>Figure 2:</b> (a) Refractive index, n, and (b) extinction coefficient, k, of the Zn<sub>3</sub>n<sub>2</sub> layer obtained by spectroscopic ellipsometry for different annealing temperatures.<br><br><b>Figure 3:</b> Thickness of (a) the Zn<sub>3</sub>N<sub>2</sub> layer and (b) oxide layers over several months for annealed samples. (c) Lifetime of the Zn<sub>3</sub>N<sub>2</sub> layer as a function of annealing temperature. The data points marked with * were extrapolated based on the oxidation rates measured in this study.<br><br><b>Figure 4:</b> X-ray diffraction scans of the (400) peak for Zn<sub>3</sub>N<sub>2</sub> samples annealed at different temperatures. The dashed line shows the expected position of the (400) peak based on crystallographic data.<br><br><br>
DOI: 10.17632/g666hxgrty.1
title: Numerical data for "Force distribution within a barchan dune"

description: This dataset contains information from numerical simulations on the distribution of forces within a subaqueous barchan dune. The files contain information of the contact forces between two particles (in contact force 0.5 s folder), and the resultant force acting on each particle (in total force 1.5 s folder) forming a barchan dune under the action of a turbulent water flow.
DOI: 10.21227/nqp1-sp19
title: Re-curated Breast Imaging Subset DDSM Dataset (RBIS-DDSM)

description: Re-curated Breast Imaging Subset DDSM Dataset (RBIS-DDSM) is a curated version of 849 images from the CBIS-DDSM dataset available online with a permissive copyright license (CC-BY-SA 3.0). The  CBIS-DDSM dataset is an improved version of the DDSM dataset. The authors of the CBIS-DDSM dataset attempted to improve the ground truth by applying simple image processing based methods to enhance the edges without any manual intervention from medical experts in order to segment and annotate masses. However, these annotations (segmentation maps) are inaccurate in most of the images. RBIS-DDSM provides more accurate annotations marked manually under the supervision of an experienced senior Radiologist. These annotations can be used for localisation tasks and to evaluate the inter-rater agreement when used with annotations provided in the CBIS-DDSM dataset. The ROI was manually marked for the images using an in-house Matlab GUI tool.  Note: The local annotations for mass and micro-calcifications were marked as ellipses around the pathologies and are not an exact semantic segmentation. This dataset should not be used to evaluate models/algorithms designed for semantic segmentation tasks.
DOI: 10.22003/xfel.eu-data-002804-00
title: Spin states of FeS and FeHx at and beyond telluric core-mantle boundary conditions by simultaneous x-ray emission and x-ray diffraction
DOI: 10.22003/xfel.eu-data-003478-00
title: HED startup days CW31 and 32
DOI: 10.34808/bsk4-eg58
title: Multi-parameter dataset on limnological variables and modern sedimentation at Lake Żabińskie, northeast Poland, 2012-2021

description: The dataset presents the results of a decade-long investigations of limnological processes and sedimentation at Lake Żabińskie located in northeast Poland. We collected a wide range of information on the lake water physical and chemical characteristics, modern sedimentation dynamics, and hydrochemistry of incoming streams and outflow from the lake. The overall monitoring program was designed to capture a pattern of relationships between meteorological conditions, limnological processes, and modern sedimentation and to answer the question if meteorological and limnological phenomena can be precisely tracked with varves.
DOI: 10.5281/zenodo.1217129
title: Data For: "Simulation Of Uranium Plasma Plume Dynamics In Atmospheric Oxygen Produced Via Femtosecond Laser Ablation"

description: Data generated by 2D reactive, compressible, multi-species fluid model of uranium femtosecond laser ablation in an atmospheric oxygen environment. The dataset consists of a series of plain text tabular data files recorded at several time points during the simulation run. The data files are numbered according to the simulation time in nanoseconds (FFF-0100.txt is the data at 100 ns) and are given at intervals of 50 ns for the first 500 ns of simulation time, and every 100 ns thereafter, up to the total simulation time of 10000 ns. The initial conditions are provided in the first data file (FFF-0000.txt). Each data file contains spatially-resolved values of the fluid moments along with the molar concentrations of each species considered in the model (total of 30 species), given in a column format delimited by spaces.

For details on the model implementation and simulation conditions, please refer to the associated manuscript.
DOI: 10.5281/zenodo.3701957
title: Prediction of plasma etching yields by machine learning to reveal the complexity of underlying physics

description: tables
DOI: 10.5439/1052226
title: Solar Resource & Meteorological Assessment Project (SOLRMAP): Observed Atmospheric and Solar Information System (OASIS); Tucson, Arizona (Data)

description: The U.S. Department of Energy's National Renewable Energy Laboratory collaborates with the solar industry to establish high quality solar and meteorological measurements. This Solar Resource and Meteorological Assessment Project (SOLRMAP) provides high quality measurements to support deployment of power projects in the United States. The no-funds-exchanged collaboration brings NREL solar resource assessment expertise together with industry needs for measurements. The end result is high quality data sets to support the financing, design, and monitoring of large scale solar power projects for industry in addition to research-quality data for NREL model development. NREL provides consultation for instrumentation and station deployment, along with instrument calibrations, data acquisition, quality assessment, data distribution, and summary reports. Industry participants provide equipment, infrastructure, and station maintenance.
DOI: 10.6084/m9.figshare.21929859
title: Supplementary Material for: The epidemiology of moderate and severe traumatic brain injury in Central Norway

description: Introduction: Few studies account for prehospital deaths when estimating incidence and mortality rates of moderate and severe traumatic brain injury (msTBI). In a population-based study, covering both urban and rural areas, including also prehospital deaths, the aim was to estimate incidence and mortality rates of msTBI. Further, we studied the 30-day and 6-month case-fatality proportion of severe TBI in relation to age. Methods: All patients aged ≥17 years who sustained a msTBI in Central Norway were identified by three sources: 1) the regional trauma center, 2) the general hospitals, and 3) the Norwegian Cause of Death Registry. Incidence and mortality rates were standardized according to the World Health Organization’s world standard population. Case-fatality proportions were calculated by the number of deaths from severe TBI at 30 days and 6 months, divided by all patients with severe TBI. Results: The overall incidence rates of moderate and severe TBI were 4.9 and 6.7 per 100,000 person-years, respectively, increasing from age 70 years. The overall mortality rate was 3.4 per 100,000 person-years, also increasing from age 70 years. Incidence and mortality rates were highest in men. The case-fatality proportion in people with severe TBI was 49% in people aged 60-69 years and 81% in people aged 70-79 years. Discussion/Conclusion: The overall incidence and mortality rate for msTBI in Central Norway was low but increased from age 70, and among those ≥80 years of age with severe TBI, nearly all died. Overall estimates are strongly influenced by high incidence and mortality rates in the elderly, and studies should therefore report age-specific estimates, for better comparison of incidence and mortality rates.
DOI: 10.6084/m9.figshare.21931383.v2
title: Responses of dental students to ageism scale: India

description: This dataset contains consent of the participants. It contains demographic data such as gender, age, year of study, months of clinical experience, attending gerodontology course, presence of elderly member in the family and area of residence. It also depicts the responses of dental students to each of the 27 items in the ageism scale. <br>
DOI: 10.6084/m9.figshare.21975515
title: Supplementary Material for: Piceatannol protects against high glucose-induced injury of renal tubular epithelial cells via regulating carbonic anhydrase 2

description: Introduction: We here evaluated the efficacy of piceatannol (PIC) in high glucose (HG)-induced injury of renal tubular epithelial cells HK-2. Methods: After the establishment of HG-induced cell injury model and the treatment with PIC at both high and low concentrations and/or Acetazolamide (ACZ, the inhibitor of carbonic anhydrase 2 (CA2)), MTT and flow cytometry assays were carried out to confirm the viability and apoptosis of HK-2 cells. The levels of oxidative stress markers lactate dehydrogenase (LDH), malondialdehyde (MDA), and reactive oxygen species (ROS), the ratio of glutathione/oxidized glutathione (GSH/GSSG), and the CA2 activity were determined. Both quantitative reverse-transcription polymerase chain reaction and Western blot were used to calculate the expressions of CA2 (the predicted target gene of PIC via intersecting the data from bioinformatic analyses), and AKT pathway- (Phosphatase and tensin homolog (PTEN), phosphorylated (p)-AKT, AKT) and apoptosis-related proteins (Bcl-2 and cleaved caspase-3). Results: HG suppressed cell viability and the levels of GSH/GSSG ratio, CA2, pThr308-AKT/AKT, pSer473-AKT/AKT, and Bcl-2, while promoting cell apoptosis, the levels of LDH, MDA, and ROS and the expressions of PTEN and cleaved caspase-3. All effects of HG were reversed by PIC at a high concentration. CA2 was predicted and identified as the target of PIC. In HG-treated HK-2 cells, additionally, ACZ reversed the effects of PIC on the viability, apoptosis, and the levels of both oxidative stress markers and AKT pathway- and apoptosis-related factors. Conclusion: PIC protects against HG-induced injury of HK-2 cells via regulating CA2.
DOI: 10.6084/m9.figshare.22109861
title: Supplementary Material for: Phenotypic Variation in 46,XX Disorders of Sex Development due to the 4th Zinc Finger Domain Variant of WT1 : A Familial Case Report

description: Introduction: The variants in the zinc finger (ZF) domains 1–3 in WT1 are one of the major causes of 46,XY disorders of sex development. Recently, the variants in fourth ZF (ZF4 variants) were reported to cause 46,XX DSD. However, all the nine patients reported were de novo, and no familial cases were identified. Case presentation and Results: The proband (16yrs social female), had 46,XX karyotype with dysplastic testes and moderate virilization in genitalia. A ZF4 variant, p.Arg495Gln in WT1 was identified in the proband, her brother and mother. The mother did not show any virilization with normal fertility, and the 46,XY brother developed normal puberty. Discussion/Conclusion: The phenotypic variations due to ZF4 variant are extremely broad in 46,XX cases.
DOI: 10.6084/m9.figshare.22346578
title: Supplementary Material for: X-Linked Hydrocephalus with New <b><i>L1CAM</i></b> Pathogenic Variants: Review of the Most Prevalent Molecular and Phenotypic Features

description: <b><i>Introduction:</i></b> The underlying molecular defects of congenital hydrocephalus are heterogeneous and many isolated forms of hydrocephalus remain unsolved at the molecular level. Congenital hydrocephalus in males associated with agenesis of the corpus callosum is a notable characteristic of <i>L1CAM</i> gene which is by far the most common genetic etiology of congenital hydrocephalus. <b><i>Methods and Results:</i></b> Sequencing of the <i>L1CAM</i> gene on 25 male patients/fetuses who had been presented with hydrocephalus revealed 6 patients and two fetuses with different hemizygous pathogenic variants. Our study identified 4 novel variants and 4 previously reported. The detection rate was 32%, and all the variants were shown to be maternally inherited. Nonsense variants were detected in 3 patients, while missense variants were detected in 2 patients. Frameshift, silent, and splicing variant, each was detected in 1 patient. The clinical manifestations of the patients are in line with those frequently observed including communicating hydrocephalus and agenesis of the corpus callosum. Moreover, rippled ventricles with subdural collection and asymmetry of ventricles after shunt operation were seen in 1 patient and 2 patients, respectively. In addition, abnormal basal ganglia were found in 4 patients which seems to be an additional distinct new finding. We also describe a patient with novel nonsense variant with the rare association of Hirschsprung’s disease. This patient displayed additionally multiple porencephalic cysts and encephalomalacia secondary to hemorrhage due to repeated infections after shunt operation. The patients with the missense variants showed long survival, while those with truncating variants showed poor prognosis. <b><i>Conclusion:</i></b> This report adds knowledge of novel pathogenic variants to the <i>L1CAM</i> variant database. Furthermore, we evaluated the clinical and imaging data of these patients.