cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.24541147.v4
title: <b>Chloroplast genome evolution of </b><b><i>Berberis </i></b><b>(Berberidaceae): implications for phylogeny and metabarcoding</b>

description: <i>Berberis</i> species play a crucial role in the formulation of Chinese patent medicine, Berberidis Radix, employed to address a range of ailments. These species have similar morphology, but different chemicals, potentially leading to misidentifications that can impact the medicine's efficacy. Therefore, it is imperative to develop suitable molecular markers to identify medicinal species. Furthermore, discrepancies exist in the taxonomy of the <i>Berberis</i> genus. In the current study, we <i>de novo</i> assembled the chloroplast genome of those six <i>Berberis</i> species (<i>B. </i><i>julianae</i>, <i>B. tsienii</i>, <i>B. pruinose</i>, <i>B. thunbergii</i>, <i>B. poiretii</i>, and <i>B. wilsoniae</i>) that commonly constitute Berberidis Radix, and compared them with other reported genomes. Our comparative analysis revealed similarities in genome structure, relative synonymous codon usage, amino acid frequency, repeats, and substitutions. Inverted repeats expansion and contraction affected the rate of mutations and found link to the phylogenetic classification of <i>Berberis</i>. We identified the <i>ndhD-ccsA</i> region as the most polymorphic region and applied it to the metabarcoding of Berberidis Radix medicine. The metabarcoding provided insight into their biological composition and confirmed six <i>Berberis </i>species commonly constitute Berberidis Radix. However, we also identified other <i>Berberis </i>species with lower read abundance. Our phylogenetic analysis supports the division of <i>Berberis</i> into four genera, which corroborates previous studies involving extensive sampling. In conclusion, this study offers comprehensive insights into the molecular evolution of the chloroplast genome and the phylogeny of the <i>Berberis</i> genus. Concurrently, through metabarcoding, we confirm the biological origin of Berberidis Radix, thus shedding light on its composition.
DOI: 10.15131/shef.data.12523217.v1
title: Data for Highly nonlinear trion-polaritons in a monolayer semiconductor

description: Experimental data supporting figures shown in the main text and supplementary materials of the paper "Highly nonlinear trion-polaritons in a monolayer semiconductor".
DOI: 10.17632/4by7d9mpmr
title: Triage Dermoscopic Images 

description: Diagnostic performance of medical providers in differentiating between malignant melanoma and benign nevi using the MClass-D test set from the International Skin Imaging Collaboration.
DOI: 10.17632/87d9rf4chw
title: Genome-wide association study for milk yield, frame, and udder conformation traits of Gir dairy cattle -- Supplemental files

description: These are the supplemental files for the article published in the Journal of Dairy Science, identified by the DOI:https://doi.org/10.3168/jds.2024-24648

Table S1. The number of animals genotyped, number of SNPs by chip.

Table S2. Gene identification and percentage of genetic variance explained by windows associated with milk yield and body conformation traits related to the udder and frame in Gir dairy cattle.

Figure S1. Linkage disequilibrium decay calculated as the r2 mean.

Figure S2. Rectangular Manhattan plot of the -log10 (P-value) for milk yield (a), hip height (b), hearth girth (c), and rum angle (d) in Gir dairy cattle. The dashed line indicates the Bonferroni threshold (0.05 divided by the number of SNPs)

Figure S3. Rectangular Manhattan plot of the -log10 (P-value) for rear udder width (a), udder depth (b), teat length (c), and teat diameter (d) in Gir dairy cattle. The dashed line indicates the Bonferroni threshold (0.05 divided by the number of windows)

Figure S4. Rectangular Manhattan plot of proportion of additive genetic variance (%) explained by 0.11-megabase window for milk yield (a), hip height (b), hearth girth (c) and rum angle (d) in Gir dairy cattle.

Figure S5. Rectangular Manhattan plot of proportion of additive genetic variance (%) explained by 0.11-megabase window for (a) rear udder width, (b) udder depth, (c) teat length and (d) teat diameter in Gir dairy cattle.
DOI: 10.17632/t8wjfxm5cc
title: Roasting

description: NIR Spectra for different roasting times of coffee, using a temperature of 185 C.
DOI: 10.6084/m9.figshare.28356086.v1
title: Databases Scopus-WoS Meta-Analysis

description: Databases Scopus-WoS Meta-Analysis
DOI: 10.6084/m9.figshare.29086511.v1
title: Municípios tomados pelo movimento zapatista 1994

description: Mapa das cidades ocupadas pelo movimento zapatista em 1994.
DOI: 10.17632/8gh9rm9fmk
title: Nonlinear dynamics of cardiovascular autonomic regulation during the sustained weight test in patients with type 2 diabetes mellitus

description: Introduction: The analysis of non-linear dynamics of cardiovascular autonomic regulation based on heart rate variability has not been previously studied in patients with type 2 diabetes mellitus using the sustained weight test as an inducer of cardiovascular hyperreactivity.
Objective: To determine the variations in the non-linear dynamics of cardiovascular autonomic ­regulation during the sustained weight test in patients with type 2 diabetes mellitus.
Method: A quasi-experimental, before-after study with a control group, from June-August 2018, at the No. 1 School of Medicine in Santiago de Cuba. We worked with 15 patients suffering from type 2 diabetes mellitus without other associated disease and 15 healthy subjects, to whom the sustained weight test was applied.
Results: In patients with diabetes mellitus, when performing the sustained weight test, there was a significant increase in the hemodynamic parameters TAS, TAD, TAM and FC. In the sample entropy, a parameter that evaluates the adaptability of the systems, there is a significant decrease (2.28 ± 0.33 vs. 1.83 ± 0.47 ms; p = 0.003143). The value of the C statistic of the sample entropy at baseline was established at 0.973, being the variable with the highest predictive capacity.
Conclusions: In patients with type 2 diabetes mellitus during the sustained weight test, there was a decrease in the complexity of cardiovascular autonomic regulation, the basal sample entropy was the indicator of greater efficacy in the identification of cardiovascular autonomic alterations.
DOI: 10.17632/w54896dknh
title: Impact of vegetation cover on the hydraulic characteristics of rectangular and rounded broad-crested weirs

description: Open research data-jgr
DOI: 10.6084/m9.figshare.29067488.v1
title: Admission and Discharge Functional Status Scale Scores for Enrolled Patients

description: The table demonstrates admission and discharge functional status scale scores for patients enrolled and outcome categories. Outcome categories are defined as:- Favorable outcome: A change in functional status scale score (FSS) of less than 3 points from admission to discharge<br>- Unfavorable outcome: A change in functional status scale score (FSS) of greater than or equal to 3 points from admission to discharge<br>- Severe disability: A composite discharge FSS of greater than or equal to 16 points<br>- No severe disability: A composite discharge FSS of less than 16 points<br>- Death: Patient died during hospital admission<br>- Alive: Patient was alive at hospital discharge
DOI: 10.17632/7436r2hmjy
title: OR5K1 is the evolutionary conserved sensor for foodborne and semiochemical alkylpyrazines

description: These are the raw luminescence data (RLU, relative luminescence units, mock-substracted) underlying the EC50 values of all pyrazines and other compounds, to be published in a paper with the title "OR5K1 is the evolutionary conserved sensor for foodborne and semiochemical alkylpyrazines".
The data are in Excel files. Each Excel file contains the concentration-response relations of all compounds tested on a particular odorant receptor type or ortholog.
Some files contain the raw data of a single compound screen versus 616 odorant receptors, or a screen of 178 key food odorants versus a particular odorant receptor type.
DOI: 10.17632/rpzxg4zws5
title: Human injury-based safety decision of automated vehicles (Qingfan Wang, Qing Zhou, Miao Lin, Bingbing Nie1*)

description: The data and code accompany the paper titled "Human injury-based safety decision of automated vehicles".
DOI: 10.6084/m9.figshare.12642953.v6
title: Expanded dataset of mechanical properties and observed phases of multi-principal element alloys

description: This data article presents a compilation of mechanical properties of 630 multi-principal element alloys.Built upon recently published MPEA databases, this article includes updated records from previous reviews (with minor error corrections) along with new data from articles that were published since 2019.The extracted properties include composition, processing method, microstructure, density, hardness, yield strength, ultimate tensile strength, elongation, and Young’s modulus.Additionally, descriptors (e.g. grain size) not included in previous reviews were also extracted for articles that reported them.
DOI: 10.6084/m9.figshare.16985137.v1
title: antismash_2021_11_09.tar.gz

description: Biosynthetic gene clusters for Escovopsis and other hypocreaceae fungi
DOI: 10.6084/m9.figshare.22124222.v1
title: Validation of Flipped English Learning Readiness Questionnaire for Persian Students

description: This is the data spss file
DOI: 10.6084/m9.figshare.24678549.v1
title: Annotated single-cell RNA-seq dataset used in "A Retrospective View on Triple Negative Breast Cancer Microenvironment: Novel Markers, Interactions, and Mechanisms of Tumor-Associated Components using public Single-cell RNA Seq Datasets"

description: <b>Abstract</b><b>Purpose</b><b>:</b> Triple-negative breast cancer presents a significant clinical challenge due to its aggressive nature and limited treatment options. This subtype is notorious for a poorer prognosis compared to other breast cancer forms, primarily due to the lack of identifiable treatment targets.<b>Methods: </b>In our study, we delve deep into the molecular landscape of TNBC using public single-cell RNA sequencing datasets. Our integrative analysis aims to identify unique markers specific to TNBC, unravel the intricate gene mechanisms they are involved in, and explore new avenues for potential therapeutic interventions.<b>Results: </b>Employing three comprehensive datasets, our study offers a novel perspective on the tumor microenvironment of TNBC. Specifically, we found 12 marker genes, including DSC2 and CDKN2A, uniquely expressed in TNBC cells, marking an advancement in understanding this cancer subtype. A comparative analysis of these markers across various components of the tumor microenvironment, including both cancerous and normal cells, highlights a distinctive feature. A key discovery of our study is the interaction between DSC2 and DSG2 genes within TNBC cells, suggesting a novel pathway of intercellular communication exclusive to this cancer type.<b>Conclusion: </b>This finding not only corroborates previous hypotheses but also lays the foundation for a new structural understanding of triple-negative breast cancer, as revealed through our single-cell analysis workflow.
DOI: 10.17632/95vhrskbbd
title: Multimodal Phishing Detection on Social Networking Sites: A Systematic Review

description: This contains the results returned by IEEE Xplore, ACM Digital Library, Scopus, and Web of Science with the tailored queries mentioned in the paper with the same title, and the list of 32 articles selected for the study. The records and results are shared as a part of the systematic review study.
DOI: 10.6084/m9.figshare.19929965.v1
title: Supplementary Data 1 of Oh et al. (2022)

description: Supplementary Data 1 of Oh et al. (2022). : Site-level observations of wetland δ13C-CH4 from Holmes et al. (2015) and Sherwood et al. (2017).
DOI: 10.6084/m9.figshare.21893046.v1
title: Yellow warbler Galapagos data

description: Animals across diverse lineages use referential calls to warn of and respond to specific threats, though the ability to understand these calls may be dependent on experience with the threat being referenced. Yellow warblers (<em>Setophaga petechia</em>) produce referential ‘seet’ calls towards brood parasitic brown-headed cowbirds (<em>Molothrus ater</em>), which threaten the warblers’ reproductive success. Seet calls are produced frequently in populations sympatric with cowbirds, but rarely in allopatric populations, even when those populations are genetically similar, begging the question of the role of personal experience in anti-parasitic responsiveness in aggression and propensity to seet call towards brood parasites. Here we tested for seet call responses from a yellow warbler population on the Galapagos Islands (subspecies <em>aureola</em>), which has been geographically isolated from the mainland and brood parasites for ~300,000 years. We presented playbacks of brown-headed cowbird calls (allopatric brood parasite), seet calls (North American yellow warbler’s referential anti-parasitic call), chip calls (yellow warbler’s general alarm call), sympatric predator calls, and harmless allopatric and sympatric control songs to breeding yellow warblers, and compared behavioral and vocal responses between treatments. We found that in response to playbacks signaling brood parasitic risk (seet and cowbird calls), Galapagos yellow warblers showed aggression comparable to controls, and much lower compared to chip or predator playbacks. Galapagos yellow warblers never produced any seet calls in response to the playbacks. Our results suggest that in geographic isolation from cowbirds, Galapagos yellow warblers do not produce or respond to referential alarm calls indicating mainland brood parasitic nest threats.
DOI: 10.6084/m9.figshare.27789447.v1
title: Energy for tilt and twist grain boundaries in BCC Fe

description: This file contains the crystallographic parameters of grain boundaries and corresponding energies calculated for BCC Fe using molecular dynamics simulation.
DOI: 10.17632/x4mt4y7z7z
title: Spatial transcriptomics reveals differential inflammatory pathways in discoid lupus erythematosus and lichen planus

description: Here, we performed spatial transcriptomics using GeoMx® Digital Spatial Profiling, a highly multiplex method for detection of proteins and RNA in fixed tissue (Merritt et al., 2020) to broadly profile immune response pathways in keratinocytes and immune cells between patients with DLE and LP. Specifically, we used the Cancer Transcriptome Atlas (1868 genes) on archived biopsies from patients with DLE (n=9) and LP (n=10) and control skin (n=4). First, tissues were initially stained with morphological markers CD45 and pan-cytokeratin (Pan-CK) to identify regions of interest (ROIs) for subsequent analysis. Cell-masking was used to select mRNA in either keratinocytes (Pan-CK+) or CD45+ immune cells, but no other cells that may have been present in the geometric ROI. A total of 311 segments (CD45+ cells or PanCK+ cells) from 153 ROIs across 23 unique patient samples for a total of 95,823 cells were included in this analysis.
DOI: 10.17632/svmmkykdhd
title: Cyber-attacks on Public Key Cryptography 

description: Data records on scientific publication on Cyber-attacks on Public Key Cryptography
DOI: 10.17632/x2fr7sfm4f
title: Automatic Thoughts, Academic Competence, and Social Competence in Modelling Social Anxiety in Adolescents

description: Data set of "Automatic Thoughts, Academic Competence, and Social Competence in Modelling Social Anxiety in Adolescents" Hypotheses of Study
Automatic thoughts indirectly affect social competence through academic competence (Hypothesis 1). 
Academic competence indirectly affects social anxiety through social competence (Hypothesis 2). 
Automatic thoughts indirectly affect social anxiety through multiple mediations of academic and social competence (Hypothesis 3).

The Scales
Social Anxiety Scale for Adolescents; (SAS-A) was used to measure the level of social anxiety in adolescents (La Greca & Lopez, 1998). The scale consists of 22 items in three sub- dimensions: Fear of Negative Evaluation, Social Avoidance and Distress-New, and Social Avoidance and Distress General. 
Automatic Thoughts
The Automatic Thoughts Questionnaire (ATQ) developed by Hollon and Kendall (1980) was used to measure the automatic thoughts of the participants. The scale aims to measure the most common automatic thoughts associated with depression and negative self-evaluations. The scale consists of five factors: negative self-concept, confusion and escape fantasies, personal maladjustment and desire for change, loneliness/isolation, and giving up/helplessness. 
Academic and Social Competence
The academic and social competence of the participants were measured with the Perceived Competence Scale (PCS) developed by Özer et al. (2016). Consisting of 30 items, the scale has two sub-dimensions: academic competence and social competence. 
Description of variable
AC-P3 Academic competence Parcel 3, AC-P2 Academic competence Parcel 2, AC-P1 Academic competence Parcel 1, SC-P3 Social Competence Parcel 3, SC-P2 Social Competence Parcel 2, SC-P1 Social Competence Parcel 1, ATQ-G Automatic Thoughts Questionnaire Giving up/Helplessness, ATQ-L Automatic Thoughts-Loneliness/Isolation, ATQ-P Automatic Thoughts-Personal Maladjustment and Desire For Change, ATQ-C Automatic Thoughts-Confusion and Escape Fantasies, ATQ-N Automatic Thoughts-Negative Self-concept, SA-General Social Anxiety-Social Avoidance And General Anguish, SA-New Social Anxiety-Social Avoidance And Anguish In New Situations, SA-FNE Social Anxiety- Fear Of Negative Evaluation
DOI: 10.6084/m9.figshare.5100730.v3
title: Alnus viridis chorology

description: Distribution map of green alder (<i>Alnus viridis</i>)<br><br>These maps were produced by combining numerous and heterogeneous data collected from atlas monographs providing complete species distribution maps, from national to regional atlases, occurrence geo-databases, scientific and grey literature.<br>The maps were created using ESRI shapefiles (*.shp, *.shx, *.dbf, *.prj files) archived in the ZIP file. Species range is mapped with polygon features (name suffix "plg"), which define continuous areas of occupancy of the species, and with point features (name suffix "pnt"), which identify more fragmented and isolated populations. If synanthropic occurrences are reported outside the species natural range, additional point and/or polygon shapefiles are also present (suffix "syn"). <br>Polygon borders delimiting species ranges are generalized across the mainland and sea boundaries. This offers the possibility to mask sea areas or to clip and extract the terrestrial range parts using GIS data layers of the users' choice. An additional version of polygon ranges are clipped with a coastline (name suffix "clip"), which have been derived from Natural Earth dataset "Admin 0 - Countries" 1:50M version 4.1.0 (https://www.naturalearthdata.com). <br><br>Please cite as:<br>Caudullo, G., Welk, E., San-Miguel-Ayanz, J., 2017. Chorological maps for the main European woody species. Data in Brief 12, 662-666. DOI: doi.org/10.1016/j.dib.2017.05.007 <br><br>Additional information and used references are on 'supplementary materials' document:<br>https://doi.org/10.6084/m9.figshare.5091901<br><br>Chorological maps are part of the "European Atlas of Forest Tree Species" project:<br>https://w3id.org/mtv/FISE-Comm/v01
DOI: 10.6084/m9.figshare.19314413.v1
title: Data File

description: the historical meteorological data ((S1 Data File), hydrological data (S2 Data File), Four global climate model (GCMs) data (S3 Data File)
DOI: 10.6084/m9.figshare.24211983.v2
title: Evaluating the overlap of surface protected areas with different facets of groundwater biodiversity: Glass half empty or half full? - datasets and R code

description: The item contains multiple datasets (morphological database, distributional data, phylogeny and IUCN statuses) as well as spatial data (shapefiles) and R code to reproduce the analyses and results presented in the manuscript entitled "Evaluating the overlap of surface protected areas with different facets of groundwater biodiversity: glass hald empty or half full?". As some parts of the analyses take a considerable amount of time, the folder "prepared RDS files" contains several prepared files in RDS format for direct import in R for quicker run of the whole script.
DOI: 10.6084/m9.figshare.24764235.v1
title: All isolated heart data from 2 weeks of low calorie diet

description: <i>Effect of severe food restriction (sFR) on food and </i><i>water intake and body weight (BW) in male rats.</i><br><i>Effect of severe food restriction </i><i>(sFR) on isolated heart from male rats before </i><i>and after ischaemia–reperfusion (I/R).</i><i>Effect of severe food restriction (sFR) on incidence of arrhythmias in isolated heart from male rats during ischaemia.</i>
DOI: 10.6084/m9.figshare.4670506.v1
title: Qualitative Data Repository: Consensus Assessment Initiative Questionnaire for AWS

description: Self-assessment of Amazon Web Services for use as the primary server infrastructure for the Qualitative Data Repository (QDR)<br>
DOI: 10.6084/m9.figshare.5977552.v1
title: Extracellular vesicles mediate low dose ionizing radiation-induced immune and inflammatory responses in the blood

description: <b>Purpose:</b> Radiation-induced bystander effects (RIBE) imply the involvement of complex signaling mechanisms, which can be mediated by extracellular vesicles (EVs). Using an in vivo model, we investigated EV-transmitted RIBE in blood plasma and radiation effects on plasma EV miRNA profiles. <b>Materials and methods:</b> C57Bl/6 mice were total-body irradiated with 0.1 and 2 Gy, bone marrow-derived EVs were isolated, and injected systemically into naive, ‘bystander’ animals. Proteome profiler antibody array membranes were used to detect alterations in plasma, both in directly irradiated and bystander mice. MiRNA profile of plasma EVs was determined by PCR array. <b>Results:</b> M-CSF and pentraxin-3 levels were increased in the blood of directly irradiated and bystander mice both after low and high dose irradiations, CXCL16 and lipocalin-2 increased after 2 Gy in directly irradiated and bystander mice, CCL5 and CCL11 changed in bystander mice only. Substantial overlap was found in the cellular pathways regulated by those miRNAs whose level were altered in EVs isolated from the plasma of mice irradiated with 0.1 and 2 Gy. Several of these pathways have already been associated with bystander responses. <b>Conclusion:</b> Low and high dose effects overlapped both in EV-mediated alterations in signaling pathways leading to RIBE and in their systemic manifestations.
DOI: 10.6084/m9.figshare.7059317.v1
title: FileS4_UNCBreeding_PWKB6.xlsx

description: Results from breeding experiments assessing the late onset age of sterility in PWKB6 hybrids.
DOI: 10.17632/g788hgn5t2
title: Raw data on medicinal plant species for treatment of snakebites envenomation in Uganda

description: This data set describes the medicinal plant species used in the treatment of snakebites in Acholi, Teso and Karamoja sub regions of Uganda. It includes the how traditional medicinal practitioners (TMP) prepare and administer the medicinal plants, the parts used, type of snake envenomation treated and the frequency of citation. The data set also includes the biodata of the TMP.