cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.17632/fgjy2s3nk7
title: Concrete Cracks Image Dataset (CCID)

description: The dataset is collected from the Faculty of Engineering and Natural Sciences, Gumushane, Turkey. Two smartphones with an Android operating system were used in the image shooting. These devices are Samsung Galaxy M31 and Samsung Galaxy A50. The total number of images was 2126, produced from smartphone cameras. The dataset has two categories: “No Cracks” and “Cracks.” Images have different pixel resolutions such as 1860x4032 and 1504x3264 are in jpg format.
DOI: 10.17632/nxbbhbwnm3
title: Expanding the Landscape of Drug Targets for 112 Chronic Diseases Using a Machine Learning-Assisted Genetic Priority Score

description: Identifying genetic drivers of chronic diseases is crucial for drug discovery. We developed a Machine Learning-assisted Genetic Priority Score (ML-GPS) that incorporates genetic associations with predicted disease phenotypes to enhance target discovery.

Dependencies:
- Python 3.11.6
- scikit-learn 1.4.1
- LightGBM 4.0.0
- scipy 1.12.0
- statsmodels 0.14.1

Jupyter notebooks:
1. Phecode diagnosis prediction models - code to train phecode diagnosis prediction models among UK Biobank participants.
2. ML-GPS models - code to train ML-GPS in Open Targets and externally test it in SIDER. Cleaned Open Targets and SIDER datasets are in the "Datasets" folder. Models take approximately 10 minutes to train on 24 threads.
DOI: 10.6084/m9.figshare.22196950.v1
title: Countermapping SDG 5 to address violence against women and girls in the favelas of Maré, Rio de Janeiro, Brazil

description: Violence Against Women and Girls (VAWG) remains one of the most significant problems affecting women globally with its elimination being central to achieving SDG 5 on gender equality. While information on its prevalence is increasing globally, this is often at the national scale with limited local-level data. Responding to feminist critiques of SDG 5 and target 5.2 in terms of the importance of capturing more nuanced data on grassroots women’s experiences as agents rather than victims, this paper reflects on countermapping VAWG in the favelas of Maré in Rio de Janeiro, Brazil. Drawing on countermapping methodologies, it analyses a series of countermaps highlighting the prevalence of VAWG, but also the need to report and resist it locally. Only by revealing the complexity of VAWG and women’s practices to deal with it can such violence be truly eliminated in order to meet SDG 5 and target 5.2.
DOI: 10.6084/m9.figshare.4907162.v1
title: RNA-seq raw data of PS-N_1_1

description: File 1 of RNA-seq raw data of
N48-2 biological replicate 1 spikelets at pollen mother cell stage. Paired-end sequencing
strategy was applied on the Illumina HiSeq 4000 sequencing platform.
DOI: 10.17632/grk69zzskx
title: WeChat Functions Influence Participation of Leisure Travels in Shanghai

description: Because of the hitherto unknown impact of COVID-19's leisure travel industry in 2020, the radius of leisure activities has also been shrinking. At the same time, online activities not only occupy more leisure time, but also promote WeChat marketing as a new means of promotion. 2021 is about to enter the post epidemic era, so that the purpose of this study is to explore the impact of online participation of WeChat functions on offline participation behaviour of leisure tourism in Shanghai, so as to recovery the follow-up participation of leisure tourism.
DOI: 10.17632/kz7667g4pf
title: Coprecipitation of phosphate with calcite: Molecular-scale evidence for incorporation and inclusion mechanisms

description: Raw data for the manuscript to be published by Geochimica et Cosmochimica Acta as "Coprecipitation of phosphate with calcite: Molecular-scale evidence for incorporation and inclusion mechanisms".
DOI: 10.17632/z6pdk5pyg9
title: A new protein requirement system for dairy cows: supplementary material of the article https://doi.org/10.3168/jds.2022-22348

description: supplementary material of the article. Silva and Oliveira (2022). A new protein requirement system for dairy cows. Journal of Dairy Science.  https://doi.org/10.3168/jds.2022-22348
DOI: 10.6084/m9.figshare.1091449.v2
title: metaseq supplemental data (ChIP-seq bigWigs, Kc)

description: Supplementary data for the metaseq manuscript. This dataset is intended to be downloaded and unpacked automatically, along with the rest of the supplemental data files, using the <code>download-metaseq-supplemental.py</code> script found at http://figshare.com/download/file/1577683.
DOI: 10.6084/m9.figshare.14221991.v1
title: Antonson, Rivera et al NL

description: This is the data set used for the final statistical tests of Antonson, Rivera et al. for our in press at Neuroscience Letters.
DOI: 10.6084/m9.figshare.26968513.v1
title: Data from: Nestling plumage colour variation in a sexually dichromatic hole-nesting passerine bird: potential functions and mechanisms

description: Animal colouration is subject to various selection pressures, which often results in the phenomenon of sexual dichromatism and gradual colour development. Despite extensive knowledge about adult colouration, the significance of nestling or fledgling plumage colouration of birds remains understudied. Focusing on the collared flycatcher (Ficedula albicollis), this explorative study investigated colour variation in pre-fledging stage of nestlings. We collected reflectance spectra from the brown primary coverts and the yellow tip of these coverts of the nestlings from 71 nests, and applied DNA-based sex-determination. We revealed significant sex differences in offspring colour: females had brown coverts with higher brightness and lower UV chroma, and their yellow stripe had lower brightness, UV chroma, and saturation. We detected low but significant repeatability of colouration between nestlings within the same nests. Nestlings did not show phenotypic integration between the colour of coverts and their terminal stripe. The results also suggested that the colouration of the yellow plumage part was probably determined by white structural background and porphyrin pigmentation. Based on our results we offer future testable hypotheses on the potential adaptive functions of early-life sex-specific colouration patterns in birds in different contexts, including parent-offspring communication or hiding from predators.
DOI: 10.6084/m9.figshare.28519610.v1
title: Fault-driven exhumation in the southeastern margin of the Tibetan Plateau: Thermochronological insights into Cenozoic crustal deformation_Supporting Information

description: <b>Figure S</b><b>1</b><b>. </b>Apatite fission track radial plots. Both 1σ and 95% confidence uncertainties are given for both the calculated central age and the degree of dispersion. P(χ2) values above 0.05 suggest that the data can statistically be interpreted as a single population.
DOI: 10.6084/m9.figshare.28952606.v35
title: Logic innovation NEW

description: Logic innovation
DOI: 10.17632/2hkynzbbzj
title: Strengthening atmospheric greenhouse effect at the Arctic “North Slope of Alaska” site evidenced by long-term records of the downwelling longwave radiance spectrum

description: Arctic Amplification, the accelerated warming of the Arctic compared to lower latitude, remains poorly understood, particularly regarding the role of clouds. In this study, we analyze 26 years of Downwelling Longwave Radiation (DLR) measurements from an Extended-range Atmospheric Emitted Radiance Interferometer (E-AERI) at the U.S. Department of Energy's North Slope of Alaska site. Our analysis reveals a pan-spectral increase in DLR under all sky conditions, primarily driven by an enhanced greenhouse effect from thick/low clouds and greenhouse gases. We find that the observed DLR trends are primarily driven by radiance changes within individual sky conditions, rather than changes in cloud fraction, suggesting fundamental shifts in atmospheric emissivity and/or temperature. Comparative analysis between the Southern Great Plains (mid-latitude) and North Slope of Alaska (high-latitude) sites demonstrates that clouds impacts the longwave surface energy balance differently between the two locations. In the Arctic, the pan-spectral increase in DLR trend dampens out the radiative cooling of the warming surface, contributing significantly to Arctic Amplification. Consistent positive trends are found in the far-infrared, a spectral region sensitive to even small changes of the dry and cold Arctic’s atmosphere and of significant interest in the current warming context. Additionally, we observe a relatively weaker DLR trend in the ozone absorption band under every sky condition, indicating a tropospheric ozone radiative forcing in the Arctic climate.
DOI: 10.17632/y5yf2sp2zm
title: Network pharmacology combined with experimental validation to investigate the protective effect of Leontopodium leontopodioides on alcohol-induced liver injury

description: There are six folds. The folds named AST ALT, IL-IBETA, and MDA describe the original data of ELISA results; The fold named HE slice contains the original pics of H/E results of liver; The fold named heatmap contains the original data of heatmap of serum metabolites; The fold named immunohistochemical results contains the original pics of immunohistochemical experiments.
DOI: 10.6084/m9.figshare.13377335.v1
title: Kaplan-Meier Curves: R script

description: This is the code for the Kaplan-Meier curves and corresponding statistical analysis for Agnew et al. 2020
DOI: 10.6084/m9.figshare.19501274.v1
title: Dataset of Article Positive and Negative Politeness Strategies Used by the Characters <i>Every Waking Breath<i> Movie</i></i>

description: This data repository is for an article entitled Positive and Negative Politeness Strategies Used by the Characters <em>Every Waking Breath Movie</em>. If you use the data and figures in this repository for your research, please cite this work as follows: <br> Aspitasari, F; Budiarsa, I.M; Rajeg, G.P.W (2022): Dataset of Article for Positive and Negative Politeness Strategies Used by the Characters Every Waking Breath Movie. figshare. Dataset. [Available on] https://doi.org/10.6084/m9.figshare.19501274. <br> <br>
DOI: 10.6084/m9.figshare.28529279.v1
title: Data from the results of "Evaluation of the effectiveness of regulatory measures for the use of natural ecological space based on the remote sensing-driven PLUS-InVEST model: A case study from the Central Mountainous Area of Hainan Island"

description: In this study, the remote sensing data-driven PLUS-InVEST coupled model was used to evaluate and forecast the habitat quality and degree of degradation in the central mountainous region of Hainan Island, a global biodiversity hotspot. By setting natural ecological space use control measures, namely ecological protection redlines, the spatiotemporal variations in land use/cover and habitat quality were investigated under two regulatory scenarios: natural development (ND) and ecology priority (EP).
DOI: 10.15468/dl.p9p4y4
title: Occurrence Download

description: A dataset containing 0 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Sagamichthys schnakenbecki (Krefft, 1953)",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "BasisOfRecord is one of (Specimen, Living Specimen, Observation, Human Observation, Machine Observation, Material sample, Literature Occurrence, Material citation, Occurrence evidence)",
 "Geometry POLYGON ((45.6579 11.3446,44.9648 11.0757,44.9648 10.8496,51.6539 10.8496,51.6211 10.9131,51.7357 12.0497,51.4872 12.2937,50.7681 12.4846,50.3292 12.3424,50.0295 12.0332,49.0651 11.773,47.2785 11.6543,46.4751 11.2145,45.6579 11.3446))"
 ]
}

 The dataset includes 0 records from 0 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0013208-250525065834625/datasets/export for details.
DOI: 10.17608/k6.auckland.5664661.v1
title: INFORMAS Protocol: Food Promotion Module - TV Advertising: Annex 2 (TV Coding Tool)

description: Data Coding Sheets
DOI: 10.17632/7v2z7k7bt9
title: Data for: Network Pharmacology-based Identification of the Key Mechanism of Qinghuo Rougan Formula Acting on Uveitis.

description: We identified 259 major candidate targets of QHRGF and successfully constructed a ‘QHRGF-compound-target-uveitis’ network. Gene enrichment analysis revealed that targets in the cell cycle, autoimmune disease and related signalling pathways were relevant.
DOI: 10.17632/krz6ck7pym
title: Data for: Six1 and Irx1 have reciprocal interactions during cranial placode and otic vesicle formation

description: Six1-Irx1 reciprocal interactions in cranial placode development
DOI: 10.6084/m9.figshare.5241844.v1
title: Erratum: Minor Elevation in C-Reactive Protein Levels Predicts Incidence of Erythropoiesis-Stimulating Agent Hyporesponsiveness among Hemodialysis Patients

description: <b><i>Background:</i></b> Hemodialysis (HD) patients occasionally experience minor asymptomatic elevation in C-reactive protein (CRP) levels, which may be associated with difficulty in managing renal anemia using erythropoiesis-stimulating agents (ESAs). Here, we assessed whether elevation of CRP predicts future incidences of ESA hyporesponsiveness. <b><i>Methods:</i></b> A total of 2,956 HD patients lacking ESA hyporesponsiveness and infectious diseases were enrolled, and the association between CRP levels and incidence of ESA hyporesponsiveness was assessed. CRP levels were divided into 4 categories (normal [&lt;1.0 mg/l], mild [1.0≤ CRP &lt;3.0 mg/l], moderate [3.0≤ CRP &lt;10.0 mg/l] and high [≥10.0 mg/l]). The primary outcome was the cumulative incidence of ESA hyporesponsiveness, defined as a failure to achieve hemoglobin level ≥10 g/dl despite receiving high doses of ESAs (≥9,000 U/week recombinant human epoetin [rHuEPO]-α or rHuEPO-β and ≥60 μg/week darbepoetin-α) during 12 months of follow-up. <b><i>Results:</i></b> The cumulative incidence of ESA hyporesponsiveness was 134 (4.8%) occurrences over 4 months and 300 (12.4%) over 12 months. The elevated CRP groups had significantly higher incidence of ESA hyporesponsiveness over 4 months of follow-up than the normal reference group (adjusted relative risk [RR] 1.6, 95% CI 1.0-2.6 for moderate; adjusted RR 2.5, 95% CI 1.5-4.1 for high). Furthermore, the association remained consistent even over 12 months (adjusted RR 1.4, 95% CI 1.0-1.8 for moderate; adjusted RR 1.6, 95% CI 1.1-2.4 for high). <b><i>Conclusions:</i></b> Elevated CRP levels were associated with future incidence of ESA hyporesponsiveness from low-grade inflammation (3.0≤ CRP &lt;10.0 mg/l).
DOI: 10.17632/gb83sywsjc
title: A single-cell atlas of the tumor and immune ecosystem of human breast cancer. Wagner et al.

description: Breast cancer is a heterogeneous disease. Tumor cells and associated healthy cells form ecosystems that determine disease progression and response to therapy. To characterize features of breast cancer ecosystems and their associations with clinical data, we analyzed 144 human breast tumor and 50 non-tumor tissue samples using mass cytometry. The expression of 73 proteins in 26 million cells was evaluated using tumor and immune cell-centric antibody panels. Tumors displayed individuality in tumor cell composition, including phenotypic abnormalities and phenotype dominance. Relationship analyses between tumor and immune cells revealed characteristics of ecosystems related to immunosuppression and poor prognosis. High frequencies of PD-L1+ tumor-associated macrophages and exhausted T cells were found in high-grade ER+ and ER− tumors. This large-scale, single-cell atlas deepens our understanding of breast tumor ecosystems and suggests that ecosystem-based patient classification will facilitate identification of individuals for precision medicine approaches targeting the tumor and its immunoenvironment.
DOI: 10.17632/gjcyvs5nfx
title: Dataset for a Study titled "Drug Utilization Pattern and Adverse Drug Reactions of Chemotherapy in Pediatric Patients" at Muhimbili National Hospital Data

description: Cancer is a non-communicable disease (NCDs) that reduces the quality of life. It is a group of diseases that involves abnormal cell growth that invades or spreads to other parts of the body. The study that generated this dataset aimed to assess the utilisation pattern and adverse drug reactions (ADRs) of chemotherapy in paediatric patients at Muhimbili National Hospital (MNH), Dar es Salaam, Tanzania. 

A descriptive cross-sectional study was conducted for three months from February to April 2021 in paediatric cancer patients undergoing chemotherapy at MNH. A total of 123 Children diagnosed with cancer and on chemotherapy during the study period were enrolled. Patients’ socio-demographics, clinical information, chemotherapy status, prescribed medications and prevalence of ADRs were collected from patient files.

Presented are underlining data (in Microsoft Excel format) containing the data from the extraction of data from patient files. The first sheet contains paediatric.xlsx contains raw data before analysis in two sheets. One sheet called patients having demographic information about the patients. The second sheet contains information about the medications used by a patient. The two sheets are linked by patient_ID. R statistical software was used to combine the files to form a combined dataset called combined.xlsx which has information about patients and the medications they use. Along with the datasets there is an R script (analysis.R) that was used for data analysis which can be used to reproduce the whole analysis. The data collection tool has also been added as a word document.
DOI: 10.17632/x5fkgwtmhz
title: Optimorph Simulation Dataset

description: This dataset provides detailed urban building energy modeling (UBEM) simulation data for various urban block configurations in Tehran, Iran. The data was generated using a parametric modeling workflow in Grasshopper, incorporating multiple urban morphological parameters.
DOI: 10.6084/m9.figshare.22300354.v1
title: Paper 3 Combined Full Transcripts All.docx

description: Qualitative insights into the efficacy and impact of an educational scholarship scheme designed to engage communities in incentivizing high school students of developing African countries in order to optimise test scores and expedite SDG-4 actualisation.
DOI: 10.6084/m9.figshare.29133269.v1
title: Warm-wet climate reshapes arid lake microbes: Diversity increases despite stability loss with functional compensation

description: Integrating over six decades of environmental data, a decade of field surveys, and targeted mesocosm experiments in Lake Bosten, China, we reveal that a transition to a warm-wet climate significantly influences microbial community diversity, ecological network structure, and functional potential.
DOI: 10.6084/m9.figshare.14286926.v1
title: Transcriptome profile of highly osteoblastic/cementoblastic periodontal ligament cell clones

description: Abstract Heterogeneous cell populations of osteo/cementoblastic (O/C) or fibroblastic phenotypes constitute the periodontal dental ligament (PDL). A better understanding of these PDL cell subpopulations is essential to propose regenerative approaches based on a sound biological rationale. Objective Our study aimed to clarify the differential transcriptome profile of PDL cells poised to differentiate into the O/C cell lineage. Methodology To characterize periodontal-derived cells with distinct differentiation capacities, single-cell-derived clones were isolated from adult human PDL progenitor cells and their potential to differentiate into osteo/cementoblastic (O/C) phenotype (C-O clones) or fibroblastic phenotype (C-F clones) was assessed in vitro. The transcriptome profile of the clonal cell lines in standard medium cultivation was evaluated using next-generation sequencing technology (RNA-seq). Over 230 differentially expressed genes (DEG) were identified, in which C-O clones showed a higher number of upregulated genes (193) and 42 downregulated genes. Results The upregulated genes were associated with the Cadherin and Wnt signaling pathways as well as annotated biological processes, including “anatomical structure development” and “cell adhesion.” Both transcriptome and RT-qPCR showed up-regulation of WNT2, WNT16, and WIF1 in C-O clones. Conclusions This comprehensive transcriptomic assessment of human PDL progenitor cells revealed that expression of transcripts related to the biological process “anatomical structure development,” Cadherin signaling, and Wnt signaling can identify PDL cells with a higher potential to commit to the O/C phenotype. A better understanding of these pathways and their function in O/C differentiation will help to improve protocols for periodontal regenerative therapies.
DOI: 10.6084/m9.figshare.19386973.v1
title: Additional file 2 of Standards and quality of care for older persons in long term care facilities: a scoping review

description: Additional file 2.
DOI: 10.6084/m9.figshare.5505037.v1
title: Results Data from An empirical measure of nonlinear strain for soft tissue indentation

description: Data used to construct graphs and figures presented in results
DOI: 10.17632/9wgp6255hn
title: PySCF-NAO: An efficient and flexible implementation of linear response time-dependent density functional theory with numerical atomic orbitals

description: We present an algorithm and its implementation to calculate the properties of electronic excitations in molecules and clusters from first principles, using time-dependent density functional theory (TDDFT). The algorithm assumes the use of some localized functions as a basis set to represent the spatial degrees of freedom. It relies on an iterative computation of the induced density according to the Dyson-like equation for the linear response function. The current implementation is built upon so-called numerical atomic orbitals. It is suitable for a wide variety of density functional theory (DFT) software. In this work, we demonstrate TDDFT calculations starting from preceding DFT runs with SIESTA, GPAW and PySCF packages, while a coupling with the other DFT packages such as Fireball and OpenMX is planned. The mentioned packages are capable of performing ab initio molecular dynamics simulations, and the speed of our TDDFT implementation makes feasible to perform a configuration average of the optical absorption spectra. Our code is written mostly in Python language allowing for a quick and compact implementation of most numerical methods and data-managing tasks with the help of NumPy/SciPy libraries and Python intrinsic constructs. Part of the code is written in C and Fortran to achieve a competitive speed in particular sections of the algorithm. Many parts of the current algorithm and implementation are useful in other ab initio methods for electronic excited states, such as Hedin’s GW, Bethe–Salpeter equation and DFT with hybrid functionals. Corresponding proof-of-principles implementations are already part of the code.
DOI: 10.17632/bvwh9d6227
title: PMU-Frequency Data at 1-second Interval (December 2020- July 2024)

description: The dataset contains PMU-frequency data situated in the North-Eastern Regional Load Dispatch Centre (NERLDC), Grid-India, Meghalaya, India at 1-second intervals between December 2020 to June 2023.
DOI: 10.17632/znrzchc6wj
title: Passive acoustic measurement of bedload transport: towards a global calibration curve?
DOI: 10.6084/m9.figshare.22678534.v1
title: BacCam Sequencing Datasets

description: Raw datasets for the BacCam paper.