cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.12408653.v2
title: Sequence Data

description: Over the years, several methods have been proposed for the computational PPI prediction with different performance evaluation strategies. While attempting to benchmark performance scores, most of these methods often suffer with ill-treated cross-validation strategies, adhoc selection of positive/negative samples etc. To address these issues, in our proposed multi-level feature based PPI prediction approach <i>JUPPI</i>, using sequence, domain and GO information as features, a refined evaluation strategy has been introduced. During the evaluation process, we first extract high quality negative data using three-stage filtering, and then introduce a pair-input based cross validation strategy with three difficulty levels for test-set predictions. Our proposed evaluation strategy reduces the component-level overlapping issue in test sets. Performance of <i>JUPPI</i> is compared with those of the <i>state-of-the-art</i> approaches in this domain and tested on six independent PPI datasets. In almost all the datasets, <i>JUPPI</i> outperforms the <i>state-of-the-art</i> not only at human proteome level for PPI prediction, but also for prediction of interactors for intrinsic disordered human proteins.
DOI: 10.6084/m9.figshare.12420968.v7
title: Benchmarking atlas-level data integration in single-cell genomics - integration task datasets

description: Pancreas, Lung atlas, human immune cell, and human and mouse immune cell integration RNA integration tasks, and all ATAC mouse brain integration tasks from the manuscript "Benchmarking atlas-level data integration in single-cell genomics". <br><br>These datasets were aggregated from public datasets, cell annotations were harmonized or reannotated, and the data was consistently preprocessed using scran pooling and log+1 transformation (for RNA tasks). In the immune cell datasets an erythrocyte development trajectory was also annotated. Details on dataset preprocessing can be found in the paper and in the accompanying Github at https://www.github.com/theislab/scib.<br><br>Please cite the paper and the papers the individual datasets were aggregated from when using this data.<br>
DOI: 10.6084/m9.figshare.16944808.v1
title: Supplementary data for black carbon in sediments from hadal trench regions

description: The concentration, 13C and 14C isotopes of black carbon in sediments from six trench regions<br>
DOI: 10.6084/m9.figshare.25013561.v1
title: MDS F1000

description: This dataset is uploaded as a part of manuscript titled "<b>Cytogenetic profile and risk of transformation to Acute Myeloid Leukemia (AML) in Indonesian patients with Myelodysplastic syndrome (MDS)</b><b> – </b><b>A </b><b>Pilot Study"</b>
DOI: 10.6084/m9.figshare.28430921.v1
title: Underlying data for Supplementary Figure S2 and Figure S6: Scanning Electron Microscopy - Electron Dispersive Spectroscopy elemental composition data for particles collected from the West Antarctic Peninsula in January 2020.

description: This is the underlying data for Figure S2 and S6 in the following study:Jones et al., (2025) <b>Antarctic glaciers export carbon-stabilised iron(II)-rich particles to the surface Southern Ocean</b>. <i>Nature Communications.</i>
DOI: 10.6084/m9.figshare.5899651.v12
title: BSDB Meeting Programs

description: These are the programs of historical meetings organised by the British Society for Developmental Biology (BSDB), starting from the inaugural meeting in 1964.<br>
DOI: 10.17605/osf.io/y9jfx
title: Effects of Interoperability among Public Administrations on Spanish Guaranteed Minimum Income

description: The aim of the study is a multi-method analysis of interoperability on conditonal GMI/IMV income in Spain, i.e. electronic data exchange among multilevel administrations and the repercussions for accreditation of requirements, in line with citizens' right not to provide information that is already kept by public administrations.
The investigation intensively describes the administrative burden in terms of compliance costs for applicants and also tests the effects of interoperable documents on approved income records.
DOI: 10.17632/n7tsnsm9d7
title: Ranchi Water demand future projections

description: Projections for future domestic water demand for Ranchi using WEAP tool, till the year 2037
DOI: 10.17632/ztxx2dhpsm
title: EU energy policy - official documents on natural gas market

description: The data consists of a sample of EU official documents on EU policies and measures for the natural gas sector in the last 30 years. These are directives, regulations, proposals of laws, complemented with decisions taken on specific issues and press releases and communications on opinions expressed by EU institutions. These sources make it possible to provide documentary evidence on (i) the interplay between the EU and Member States in energy policy and on jurisdiction overlaps; (ii) the EU focus on domestic market competition as compared to energy security of the imported supplies. 

The dataset supports one of the preliminary hypotheses that the EU policy paradigm and policy narratives for decades have been dominated by the goal of market competition in the sphere of the EU domestic market, while only recently and particularly during the energy crisis energy security started to receive more attention. This hypothesis is supported also by recent measures addressing energy security and the energy crisis, which show how these are tackled with perspectives and policy tools anchored to the domestic dimension of the EU market, while little or no space is left for strategies of energy diplomacy that consider the bigger picture of a fast-changing global energy market. 

Data is collected by following the Relevance Sampling method (Krippendorff, 2004), which is not a probabilistic method but one whose main sampling criterion concerns the relevance of data for the research question. In this paper, the selection of EU official documents was conducted by consulting EUR-Lex, the EU official database containing all EU laws and official documents. The research was done by using the following keywords: “natural gas”, “energy infrastructure”, “energy market competition”, “energy security”. 

The selected sample is composed of 20 documents, in a population of around 120 documents resulting from the searches. The main criterion for the selection was the relevance of the content of each document for the core topics of the paper, namely competition policies, energy security and prices, and infrastructure. Several documents were discarded because they address aspects that are not relevant for the research question. 

The database is innovative because it classifies EU official documents based on two main criteria: namely, whether the policy targets (i) the domestic or the import market; (ii) market competition or energy security. The database also provides a brief summary of each policy/measure to enrich the scope of the data collected and add important details that in some cases signal important evolutions in EU energy policy and trends (for example the latest responses to the energy crisis).
DOI: 10.6084/m9.figshare.25331812.v1
title: Point cloud from UAV

description: Point cloud extracted from UAV mission.
DOI: 10.6084/m9.figshare.25348090.v1
title: Supplementary Material for: An Improvement of exertional dyspnea by the re-introduction of anti-EGFR antibody in patients with metastatic rectal cancer who developed cancerous lymphangiopathy: A case report

description: Introduction: Re-exposure to anti-EGFR antibodies, such as re-introduction or re-challenge with anti-EGFR antibodies, has attracted much attention in metastatic colorectal cancer. Re-introduction of anti-EGFR antibodies often shows good therapeutic outcomes, as most patients eligible for re-introduction discontinued treatment due to adverse events despite a good treatment response at front-line treatment. We herein report a case of improvement in exertional dyspnea by re-introduction of anti-EGFR antibody in a patient with metastatic rectal cancer who developed cancerous lymphangiopathy. Case presentation: A 68-year-old man who underwent curative surgery for stage IIIB rectal cancer was diagnosed with multiple lung metastases. During late-line treatment, respiratory failure developed due to multiple lung metastases and cancerous lymphangiopathy. Two months after the initiation of irinotecan+cetuximab, which had been discontinued due to acneiform eruptions despite a good treatment response at first-line treatment, his dyspnea and performance status were dramatically improved. Conclusion: This case indicates that re-introduction of anti-EGFR antibody to patients who have discontinued anti-EGFR antibody due to skin toxicity despite a good treatment response is a very useful treatment option for metastatic colorectal cancer.
DOI: 10.6084/m9.figshare.7695977.v1
title: Inferring the size of the causal universe: features and fusion of causal attribution networks

description: Data on causal attribution networks used in the study "Inferring the size of the causal universe: features and fusion of causal attribution networks" by Berenberg & Bagrow (preprint: https://arxiv.org/abs/1812.06038)<br>The data are a CSV file with columns "causes", "effects" and "origin". The latter describes which of the three causal attribution networks was the source of each cause-effect link.
DOI: 10.17632/xbp7h6jkh6
title: Album Photographs dataset

description: 50 years old album photographs image dataset with so many degradations like blurring, colour bleed, discoloration, scratches, fungus etc
DOI: 10.6084/m9.figshare.3528398.v1
title: Appendix A. Effects of intraguild predation on the intraguild prey and shared prey in unstructured vs. structured habitats and in habitats categorized according to structure.

description: Effects of intraguild predation on the intraguild prey and shared prey in unstructured vs. structured habitats and in habitats categorized according to structure.
DOI: 10.6084/m9.figshare.12016983.v9
title: samples

description: <b>tblASVsamples.csv: The day of collection of 12,546 stool microbiome samples for 1,870 patients and the stool consistency</b>SampleID: stool sample identifierPatientID: deidentified identifier of a patientTimepoint: deidentified day of sample collectionConsistency: stool consistencyAccession: the NCBI SRA accession number for the amplicon sequencing data corresponding to this sampleBioProject: project-level SRA identifierDayRelativeToNearestHCT: day of sample collection relative to nearest day of bone marrow transplantAccessionShotgun: the NCBI SRA accession number for the shotgun sequencing data corresponding to this samplePool: pool labelRun: run labelShotgunBatchID: iGO project number
DOI: 10.6084/m9.figshare.12904499.v1
title: Gene database of Sulfolobus islandicus M.16.4

description: <i>Sulfolobus islandicus</i> is an archaeal thermoacidophile that thrives at low pH and high temperature environments. Encapsulated with a proteinaceous S-layer, the microbe is thought to be of importance in our understanding of the evolution of eukaryotic life. This work sought to provide fundamental information about the genetic repertoire of <i>S. islandicus</i> M.16.4 by parsing its annotated genome sequence downloaded from Genbank. Comprising gene name, gene function, and gene sequence, the resource should find use in functional genomics studies seeking to understand functions of less-often-encountered genes different from those of bacteria.
DOI: 10.6084/m9.figshare.21513366.v3
title: Data and reproducible R code from the Resistance Diversity Experiment

description: All data and reproducible R code from the Resistance Diversity Experiment
DOI: 10.6084/m9.figshare.23789844.v1
title: Cell type annotaion for human PBMC scRNA-seq–based aging clocks

description: The cell type annotation of the data which were used in the Science Advances paper titled "Human PBMC scRNA-seq–based aging clocks reveal ribosome to inflammation balance as a single-cell aging hallmark and super longevity" (DOI: 10.1126/sciadv.abq7599).
DOI: 10.6084/m9.figshare.26965213.v1
title: RE-YOLO Dataset

description: This dataset is the dataset used for the training of the RE-YOLO apple picking detection algorithm.
DOI: 10.6084/m9.figshare.28279832.v1
title: Supplementary Material for: New features in a rare monogenic obesity: CPE DEFICIENCY

description: Introduction: CarboxypeptidaseE (CPE) is an enzyme involved in the neuropepetides/hormones processing. Its deficiency is associated with endocrinopathies comparable to those caused by proprotein convertase1/3(PC1/3) deficiency. In this case report we expand the clinical features of CPE deficiency by examining the index case’s clinical/laboratory results, which are also indicative of PC1/3 deficiency.
Case presentation: The index case, 13.5 years old, had obesity, central hypothyroidism, developmental delay, hypogonadotropic hypogonadism, enuresis. A four-hour oral-glucose-tolerance-test revealed glucose intolerance with a partial insulin deficiency and postprandial hypoglycemia. Proinsulin level was high. Partial central diabetes insipidus was verified with a water-deprivation-test. Administration of desmopressin successfully alleviated the symptoms of polyuria-polydipsia and enuresis. Brain-derived-neurotrophic-factor level, which might be linked to ID, was low. The eight-month-old sibling had central hypothyroidism and hypotonicity,but has not yet developed obesity. 
Conclusion: Patients with CPE deficiency should undergo evaluation not only for hypothyroidism and hypogonadism but also for glucose and water metabolism disorders. The presentation of new cases may lead to the discovery of novel findings, and the identification of other pituitary hormone deficiencies.
DOI: 10.6084/m9.figshare.29136005.v1
title: Data.xlsx

description: This is the data used in the article titled 'Hometown, Culture, and Philanthropy'.
DOI: 10.6084/m9.figshare.923494.v1
title: Anthropogenic Mechanisms in Bio- Morphological Evolution A case study of Öset & Rynningeviken Evolutionary Biology

description: The paper is a study of micro and macro biological changes of wetland ecology,<br>a region once used for both agricultural and industrial purposes. It is now<br>under wetland restoration. The study area has been used both as a waste<br>dump, fossil fuel deport and extensive cultivation around lake Hjälmaren on<br>the Eastern side of Örebro City
DOI: 10.6084/m9.figshare.22309195.v4
title: Genome assembly of the Korean intertidal mud-creeper <em>Batillaria attramentaria</em>

description: Batillaridae is a common gastropod family that occurs abundantly in the shallow coastal zone of the intertidal mudflats of the northwest Pacific Ocean, Australasia, and North America. In this family, <em>Batillaria attramentaria</em> is known for its biological invasion and colonization in estuarine and intertidal zones. It can endure and adapt the harsh intertidal conditions such as frequent temperature alteration, salinity, and air exposure. Therefore, we sequenced and assembled this Korean batillariid genome to get insight into its intertidal adaptive features. Approximately 53 Gb of DNA sequences were generated, and 863 scaffolds were assembled into a draft genome of 0.715 Gb with 97.1% BUSCO completeness value. A total of 40,596 genes were predicted. We estimated that <em>Batillaria attramentaria</em> and <em>Conus consors</em> diverged about 230 million years ago (MYA) based on the phylogenetic analysis of closely related gastropod species. This genome study sets the stage for genomics studies among native and introduced <em>Batillaria</em> populations and among the Batillaridae family members.
DOI: 10.6084/m9.figshare.24449446.v1
title: Prospects of Free Senior High School Education Policy in Ghana Surveys.xlsx

description: The data is from a research that reviews the prospects of Ghana's free High School Education policy that was implemented 7 years ago. Data was collected from students, parents and school management in all the regions in Ghana.
DOI: 10.6084/m9.figshare.29104991.v1
title: [<sup>18</sup>F]fluorocholine ([<sup>18</sup>F]FCH)

description: Time List and Cassette Layout for the synthesis of Fluorine-18 fluorocholine (FCH)
DOI: 10.17632/bxtrrv4f79
title: R-YSQ-Parenting Data

description: YSQ & Parenting Attitudes Istanbul Study
DOI: 10.17632/hkv2cjp47n
title: WB health data for classification

description: The WorldBank health data set has been compiled by the authors using Health data from the World Bank DataBank (https://data.worldbank.org, accessed May, 2023.) Among others, the DataBank offers country data for a variety of health indicators. We have filtered all health indicators for the Health Nutrition and Population Statistics database, for the year 2021, for all countries. We have eliminated all indicators that have missing values for more than 75% of the countries. The rest of the missing values in the data were replaced with the average value of their Region. Each year, countries are classified by the World Bank into four income categories: High Income, Upper-middle Income, Lower-middle Income, Low Income, and Not classified. Based on this information, we proposed two classes: lower-income countries (46 countries) and upper-income classes (140 countries).
DOI: 10.6084/m9.figshare.20424132.v1
title: Supplementary Material for: Mapping the pattern of essential neuroendocrine cells related to puberty and VA opsin expression provides further insight in the photoreceptive regulation of the BPG axis in Atlantic salmon (Salmo salar)

description: In Atlantic salmon (Salmo salar) seasonal photoperiod is shown to regulate the onset of sexual maturation, yet which brain region(s) are involved and how light information impacts the neuroendocrine system are still not fully understood in teleosts. Detailed knowledge about the photoperiodic regulation of maturation in fish is still missing. In birds, it is shown that gonadotrophin releasing hormone (GNRH) is located in the same neurons as vertebrate ancient (VA) opsin suggesting a direct photoreceptive regulation for onset of sexual maturity. This study presents a comprehensive topographic mapping of gnrh2, gnrh3, kisspeptin 2 (kiss2) gonadotrophin inhibiting hormone (gnih) and VA opsin using in situ hybridization on mature Atlantic salmon brains. Neurons positive for gnrh3 are expressed in the olfactory bulb and ventral telencephalon while gnrh2 positive neurons are located dorsally in midbrain tegmentum. Gnih expressing cell bodies are present in the ventral thalamus and extend caudally to the hypothalamus with kiss2 expressing cells appearing in a lateral position. VA opsin positive cells are present in the telencephalon, the rostro-dorsal ring of left habenula, the ventral thalamus and the midbrain tegmentum. The results show no similar co-location as found in birds, hypothesizing that the photoreceptive modulation of Gnrh in salmon may interact through neuronal networks. The topography analyses of the essential neuroendocrine cells related to sexual maturation in Atlantic salmon brain show that diencephalic (thalamus, hypothalamus) and midbrain (tegmentum) regions seem central for controlling sexual maturation.
DOI: 10.6084/m9.figshare.3085426.v1
title: Consensus signatures for LINCS L1000 perturbations

description: LINCS L1000 measures the transcriptional response to perturbations. However, a single perturbagen is often assessed at several conditions, such as dosages, timepoints, or cell lines. A consensus signature meta-analyzes several input signatures and condenses them into a single output signature.<br>We've computed consensus signatures for:<br>+ 1,170 DrugBank compounds+ 4,326 gene knockdowns+ 2,413 gene overexpressions+ 38,327 L1000 perturbations<br>Each signature contains dysregulation z-scores for 7,467 genes (978 measured and 6,489 inferred, see `genes.tsv`). The `consensi-{type}.tsv.bz2` files contain the perturbagen × gene matrix of z-scores. The `dysreg-{type}.tsv` files contain significantly dysregulated genes. The `dysreg-{type}-summary.tsv` files provide the counts of significantly up/down-regulated genes per perturbagen.<br>Our methods are available [on Thinklab](https://doi.org/10.15363/thinklab.d43#7). The [project GitHub repository](https://github.com/dhimmel/lincs) contains all of the datasets here besides `consensi-pert_id.tsv.bz2` due to its large file size.<br>If using these datasets, please attribute this figshare deposition and the LINCS L1000 project. Also please abide by the data release policy for the [NIH LINCS Program](http://www.lincsproject.org/data/data-release-policy/).<br>This is not an official LINCS L1000 repository. Users are warned that our modifications may have introduced errors or removed signal that was present the original data. We thank the L1000 team for posting their data and providing support including online office hours.
DOI: 10.6084/m9.figshare.5388310.v1
title: Mapping functional and anatomical connections within the human auditory pathway with ultra-high field MRI

description: Presentation and poster prepared for International Conference on Auditory Cortex (ICAC) 2017, Banf, Canada.
DOI: 10.17632/96d7kh5hwp
title: Asthma NIV

description: Non invasive ventilation in NIV data set
DOI: 10.17632/ffbkzd6yb8
title: Are scandium sulfate complexes an effective means of scandium mobilization?

description: Data for the manuscript titled "Are scandium sulfate complexes an effective means of scandium mobilization?” by Zhang, Xue-Ni; Williams-Jones, Anthony.E.; Yuan, Shun-Da; Wang, Jiaxin (2024). Table 1 shows the conditions for the AIMD simulation of the geometry of Sc-sulfate complexes at 175 - 250 oC and vapor-saturated water pressure. Table 2 shows the conditions for and results of experiments investigating the speciation of Sc in sulfate-bearing aqueous solutions. Table 3 shows bond lengths and configurations predicted by AIMD simulations for Sc-SO4 complexes. Table 4 shows the formation constants (log β) at temperatures from 175 to 250 oC for the scandium species identified in this study. Table 5 shows the Ryzhenko–Bryzgalin (MRB) model parameters for Sc(SO4)2-. Table 6 shows the equilibrium constants (log k) and their associated uncertainty (2σ) for the Sc2O3 dissolution reaction. Table 7 show the published formation constants for Sc3+sulfate complexes at ambient temperature. Supplementary files show the X-Ray diffractogram (XRD) for Sc2O3 after completion of experiments.
DOI: 10.6084/m9.figshare.1008899.v1
title: list of 374 UK Primary Care Database Studies metadata and scores for transparency of clinical coding

description: A large component of total EMR research is made up by primary care database (PCD) studies and UK PCDs are among the most researched in the world. As one of the largest and most<br>important resources for EMR-based research, it seems reasonable to expect reporting of code lists in UK PCD-based studies to be at least as comprehensive as in other EMR studies. To<br>evaluate levels of transparency in the reporting of clinical code lists, we took a representative sample of UK PCD studies and assessed each study on its extent of reporting of the clinical codes used. We took a sample of 450 papers from the original 1359 identified from a PubMed search. Of these, 374 (83\%) had both the full text accessible to the University of Manchester library and were examples of primary PCD research. Only 5\% (19 of 392) studies published the entire set of clinical codes needed to reproduce the study (usually in an online<br>appendix), while only an additional 9\% (32 of 392) stated explicitly that the clinical codes were available upon request. In a subset of<br>articles published since 2008, 6.9\% (16 of 231) published the entire set of codes and 10.4\% (24 of 231 )stated that clinical codes were available upon request. See https://github.com/rOpenHealth/ClinicalCodes/tree/master/paper