cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.25378/janelia.26813593.v1
title: X-ray volume (xray2) registered to FIB-SEM of P7 mouse heart (jrc_mus-heart-1)

description: <br><b>Description</b>: X-ray volume (xray2) registered to FIB-SEM of P7 mouse heart (jrc_mus-heart-1)<b>X-ray ID</b>: xray2<b>Protocol</b>: After re-embedding in Durcupan, a 3D micro-CT scan of the entire block was performed using an XRadia Versa 510 X-ray microscope (Zeiss Microscopy). The tomogram facilitated precise selection of Regions of Interest (ROIs) and defined tissue boundaries. Multiple scans were conducted using different settings, with 4× and 20× objective lenses for overview and ROI selection, respectively. The sample block was then re-mounted on a 1 mm copper post for improved charge dissipation and trimmed to the ROI using an ultramicrotome. After each trimming step, X-ray tomograms were collected. Finally, a thin conductive layer was applied, consisting of a 10 nm gold layer followed by a 100 nm carbon layer.<b>Contributions</b>: X-ray microCT scans and trimming were performed by Zhiyuan Lu (HHMI/Janelia/EMSR). The sample collection through block trimming was supervised by Zhiheng Yu (HHMI/Janelia/EMSR). Regions of interest were selected by Christopher Bleck (HHMI/Janelia/EMSR), Wei-Ping Li (HHMI/Janelia/EMSR), Zhiyuan Lu, and Aubrey Weigel (HHMI/Janelia/CellMap Project Team). Data curation was handled by Rebecca Vorimo (HHMI/Janelia/CellMap Project Team) and Yurii Zubov (HHMI/Janelia/CellMap Project Team). The rest of the CellMap Project Team contributed to the overall development and review of the project. Aubrey Weigel provided oversight for the general project development.<b>X-ray voxel size (nm)</b>:<b>X-ray data dimensions (µm)</b>:<b>Dataset URL</b>: s3://janelia-cosem-datasets/jrc_mus-heart-1/jrc_mus-heart-1.zarr/recon-1/xray/xray-2/<b>Resulting, registered FIB-SEM volume</b>: https://doi.org/10.25378/janelia.24020919<br><br><b>Visualization website</b>: https://openorganelle.janelia.org/datasets/jrc_mus-heart-1
DOI: 10.6084/m9.figshare.28602170.v2
title: Wikidata Reference

description: Dataset SummaryThe Triple-to-Text Alignment dataset aligns Knowledge Graph (KG) triples from Wikidata with diverse, real-world textual sources extracted from the web. Unlike previous datasets that rely primarily on Wikipedia text, this dataset provides a broader range of writing styles, tones, and structures by leveraging Wikidata references from various sources such as news articles, government reports, and scientific literature. Large language models (LLMs) were used to extract and validate text spans corresponding to KG triples, ensuring high-quality alignments. The dataset can be used for training and evaluating relation extraction (RE) and knowledge graph construction systems.Data FieldsEach row in the dataset consists of the following fields:<b>subject</b> (<i>str</i>): The subject entity of the knowledge graph triple.<b>rel</b> (<i>str</i>): The relation that connects the subject and object.<b>object</b> (<i>str</i>): The object entity of the knowledge graph triple.<b>text</b> (<i>str</i>): A natural language sentence that entails the given triple.<b>validation</b> (<i>str</i>): LLM-based validation results, including:Fluent Sentence(s): <code>TRUE</code>/<code>FALSE</code>Subject mentioned in Text: <code>TRUE</code>/<code>FALSE</code>Relation mentioned in Text: <code>TRUE</code>/<code>FALSE</code>Object mentioned in Text: <code>TRUE</code>/<code>FALSE</code>Fact Entailed By Text: <code>TRUE</code>/<code>FALSE</code>Final Answer: <code>TRUE</code>/<code>FALSE</code><b>reference_url</b> (<i>str</i>): URL of the web source from which the text was extracted.<b>subj_qid</b> (<i>str</i>): Wikidata QID for the subject entity.<b>rel_id</b> (<i>str</i>): Wikidata Property ID for the relation.<b>obj_qid</b> (<i>str</i>): Wikidata QID for the object entity.Dataset CreationThe dataset was created through the following process:1. Triple-Reference Sampling and ExtractionAll relations from Wikidata were extracted using SPARQL queries.A sample of KG triples with associated reference URLs was collected for each relation.2. Domain Analysis and Web ScrapingURLs were grouped by domain, and sampled pages were analyzed to determine their primary language.English-language web pages were scraped and processed to extract plaintext content.3. LLM-Based Text Span Selection and ValidationLLMs were used to identify text spans from web content that correspond to KG triples.A Chain-of-Thought (CoT) prompting method was applied to validate whether the extracted text entailed the triple.The validation process included checking for fluency, subject mention, relation mention, object mention, and final entailment.4. Final Dataset Statistics12.5K Wikidata relations were analyzed, leading to 3.3M triple-reference pairs.After filtering for English content, 458K triple-web content pairs were processed with LLMs.80.5K validated triple-text alignments were included in the final dataset.
DOI: 10.6084/m9.figshare.25835149.v1
title: Supplementary Material for: Loss of one X and the Y chromosome changes the configuration of the X inactivation center in the genus Tokudaia

description: Introduction: X chromosome inactivation (XCI) is an essential mechanism for dosage compensation between females and males in mammals. In females, XCI is controlled by a complex, conserved locus termed the X inactivation center (Xic), in which the lncRNA Xist is the key regulator. However, little is known about the Xic in species with unusual sex chromosomes. The genus Tokudaia includes three rodent species endemic to Japan. Tokudaia osimensis (TOS) and Tokudaia tokunoshimensis (TTO) lost the Y chromosome (XO/XO), while Tokudaia muenninki (TMU) acquired a neo-X region by fusion of the X chromosome and an autosome (XX/XY). We compared the gene location and structure in the Xic among Tokudaia species. Methods: Gene structure of nine genes in Xic were predicted, and the gene location and genome sequences of Xic were compared between mouse and Tokudaia species. The expression level of gene was confirmed by TPM calculation using RNA-seq data. Results: Compared to mouse, the Xic gene order and location were conserved in Tokudaia species. However, remarkable structure changes were observed in lncRNA genes, Xist and Tsix, in the XO/XO species. In Xist, important functional repeats, B-, C-, D-, and E-repeats, were partially or completely lost due to deletions in these species. RNA-seq data showed that female-specific expression patterns of Xist and Tsix were confirmed in TMU, however not in the XO/XO species. Additionally, three deletions and one inversion were confirmed in the intergenic region between Jpx and Ftx in the XO/XO species. Conclusion: Our findings indicate that even if the Xist and Tsix lncRNAs are expressed, they are incapable of producing a successful and lasting XCI in the XO/XO species. We hypothesized that the significant structure change in intergenic region of Jpx-Ftx resulted in the inability to perform the X chromosome inactivation, and, as a result, a lack of Xist expression. Our results collectively suggest that structural changes in the Xic occurred in the ancestral lineage of XO/XO species, likely due to the loss of one X chromosome and the Y chromosome and a consequence of the degradation of XCI system.
DOI: 10.6084/m9.figshare.23993688.v1
title: Boulder Clay Glacier: Merging GPR data

description: Data associated with the paper: G. Roncoroni, E. Forte, I. Santin, M. Pipan, (2023), <b>Deep Learning based multi-frequency GPR data merging</b>, Geophysics, DOI: Data are associated to code presented in https://github.com/Giacomo-Roncoroni/merging_GPR/
DOI: 10.6084/m9.figshare.26085265.v2
title: A Dataset of Distribution and Characterization of Underground Wastewater Treatment Plants in China

description: Underground wastewater treatment plants (U-WWTPs) have emerged as a novel paradigm for urban wastewater pollutants management, offering benefits such as alleviating the Not-in-my-backyard (NIMBY) effect and utilizing land resources efficiently. China stands at the forefront, witnessing swift advancements in U-WWTP technology and deployment. However, the absence of a thorough understanding of their geographical distribution and operational characteristics could lead to misaligned planning and construction, resulting in inefficient resource allocation and treatment capacities for urban wastewater treatment. This dataset provides an up-to-date overview of the spatial distribution, processes selection, and discharge standards for all U-WWTPs in China (with total number of 201) constructed since 1995. To enhance comparative analysis, the dataset has been supplemented with information on conventional aboveground wastewater treatment plants (A-WWTPs), comprising a total of 2464 records, which enriching a more comprehensive evaluation of different wastewater treatment approaches. Utilizing this dataset can provide essential data supports for the strategic management of urban wastewater systems and serve as a valuable reference for the paradigmatic renovation of existing wastewater treatment plants (WWTPs).
DOI: 10.6084/m9.figshare.28334438.v1
title: Datasets

description: This dataset contains the raw data used in the article “Novel field experiment on alkalinity enhancement in intertidal environments – a trailblazer for natural climate solutions” to be published in the Journal of Geophysical Research - Biogeoscience.The data is provided as “Fig*.csv or Tab*.csv” files, processed in Excel, and organised following the structure of the figures presented in the manuscript (e.g., Fig3.csv corresponds to data shown in Fig.3).
DOI: 10.4121/21399657.v2
title: I.AM. archive containing long range box-toss experiments with Box005 and Box006 for validation of impact models

description: I.AM. archive as part of the Impact-Aware Robotics Archives Collection. This archive contains recordings of experiments that are executed under the scenario of TOSS. In these recordings, Box005 and Box006 are manually tossed on a stationary and a running conveyor. The purpose of these experiments is to validate the box-conveyor impact modeling framework to assess how well it can predict the rest-pose of the box. This modeling framework is used within the H2020 I.AM. project (www.i-am-project.eu). The involved contact is between the object and the environment, which in these recordings are Box005 and Box006 and a conveyor (Conveyor002), respectively. All the recordings in the archive were performed at the Innovation Lab of Vanderlande, located within the TU/e campus. More information about the dataset, the objects, and the environments used, can be found on https://impact-aware-robotics-database.tue.nl/.
DOI: 10.6084/m9.figshare.20484390.v1
title: LK93 genome

description: The nuclear and mitochondrial genomes of <em>Bipolaris sorokiniana</em> strain LK93, a fungal pathogen causing wheat root rot
DOI: 10.6084/m9.figshare.1619698.v1
title: Files to reproduce rigid docking

description: This set of files contain the rigid beta-lactoglobulin receptor, all of the natural ligands, the configuration file for Autodock Vina as well as a script to batch execute docking of the ligands.
DOI: 10.6084/m9.figshare.20161733.v2
title: Manuscript submitted to WRR_Gao et al., 2022

description: The paper with this data is still in the submission stage.The data cannot be used by others unless the author agrees.
DOI: 10.6084/m9.figshare.27563214.v1
title: Training/Validation/Testing CIC-DDoS2019 dataset optimized by Ameur Salem ZAIDOUN

description: This is a optimized CIC-DDoS2019 dataset by Ameur Salem ZAIDOUN, it can be used for efficient Training/Validation/Testing models in relationship with SDN DDoS detection and classification.
DOI: 10.6084/m9.figshare.13238480.v2
title: CODIFICACIÓN ENTREVISTAS ESTRUCTURADAS Y GRUPOS DE DISCUSIÓN

description: Codificación de las entrevistas estructuradas realizadas a 45 jóvenes profesionales de la información y los dos grupos de discusión con participantes pertenecientes a la misma muestra, para la investigación titulada <i>Los nuevos periodistas ante las fake news. Construcción conceptual y representaciones sociales del fenómeno de la desinformación. </i>Investigador: David García-Marín (Universidad Carlos III de Madrid).<br>
DOI: 10.6084/m9.figshare.5318281.v1
title: Role of interoceptive accuracy in topographical changes in emotion-induced bodily sensations

description: This dataset is from a study "Role of interoceptive accuracy in topographical changes in emotion-induced bodily sensations". This dataset does not include individual sensation map because participants did not consent to have their sensation map made publicly available. The present study investigated whether or not interoceptive accuracy was associated with topographical changes in this map following emotion-induced bodily sensations. This study included 31 participants who observed short video clips containing emotional stimuli and then reported their sensations on the body map. Interoceptive accuracy was evaluated with a heartbeat detection task and the spatial patterns of bodily sensations to specific emotions, including anger, fear, disgust, happiness, sadness, and neutral, were visualized using Statistical Parametric Mapping (SPM) analyses. Distinct patterns of bodily sensations were identified for different emotional states. In addition, positive correlations were found between the magnitude of sensation in emotion-specific regions and interoceptive accuracy across individuals. A greater degree of interoceptive accuracy was associated with more specific topographical changes after emotional stimuli.
DOI: 10.6084/m9.figshare.25662924.v1
title: Supplementary Material for: Intrathecal anesthesia prevents ventricular arrhythmias in rats with myocardial ischemia/reperfusion

description: Introduction: Ventricular arrhythmia is commonly provoked by acute cardiac ischemia through sympathetic exaggeration and is often resistant to antiarrhythmic therapies. Thoracic epidural anesthesia has been reported to terminate fatal ventricular arrhythmia; however, its underlying mechanism is unknown. 
Methods: Rats were randomly divided into four groups: sham, sham plus bupivacaine, ischemia/reperfusion (IR), and IR plus bupivacaine groups. Bupivacaine (1 mg/mL, 0.05 mL/100 g body weight) was injected intrathecally into the L5-L6 intervertebral space prior to establishing a myocardial ischemia/reperfusion rat model. Thereafter, cardiac arrhythmia, cardiac function, myocardial injury, and electrical activities of the heart and spinal cord were evaluated.
Results: Intrathecal bupivacaine inhibited spinal neural activity, improved heart rate variability, reduced ventricular arrhythmia score, and ameliorated cardiac dysfunction in IR rats. Furthermore, intrathecal bupivacaine attenuated cardiac injury and myocardial apoptosis and regulated cardiomyocyte autophagy and connexin-43 distribution during myocardial IR.
Conclusion: Our results indicate that intrathecal bupivacaine blunts spinal neural activity to prevent cardiac arrhythmia and dysfunction induced by IR and that this antiarrhythmic activity may be associated with regulation of autonomic balance, myocardial apoptosis and autophagy, and cardiac gap junction function.
DOI: 10.6084/m9.figshare.12897032.v1
title: Max-Betweenness and Total-Betweenness Approaches of Path Betweenness Estimation

description: We provide the data gains from both path max-betweenness and total-betweenness approaches.
DOI: 10.6084/m9.figshare.3568419.v1
title: Appendix C. Rarefaction and extrapolation for species richness (incidence data).

description: Rarefaction and extrapolation for species richness (incidence data).
DOI: 10.6084/m9.figshare.27221217.v1
title: Homemaker output - Courtyard

description: This is an example output of the Homemaker Evolutionary design software for review.The project consists of eleven courtyard-style houses.
DOI: 10.6084/m9.figshare.7985195.v1
title: When and where plant-soil feedback may promote plant coexistence: A meta-analysis; Supplementary Table 1. File containing raw data and citations for the meta-analysis

description: File containing data used in a meta-analysis of pairwise plant-soil feedback. The dataset includes citations for published papers from which data were collected, plant species identity, plant species origin (native/non-native), phylogenetic distance between species pairs, mycorrhizal status of the plant species, N-fixing status of the plant species, ecosystem the study took place in, absolute latitude of the study, mean annual precipitation of the study, type of inoculant used in the experiment, fraction of inoculum used in the experiment, testing environment (field/greenhouse), soil training environment (field/greenhouse), testing community (individual/population/community), performance of the plant species (generally biomass), calculated plant-soil feedback and variance used in the meta-analysis.
DOI: 10.6084/m9.figshare.28448168.v2
title: The first chromosomal-level genome assembly of an allotetraploid oyster

description: We provide the details for genome annotation of allotetraploid oyster, including gene locations (.gff3), protein models (.pep), CDS (.cds) and exon (.exon) sequences.
DOI: 10.6084/m9.figshare.10294832.v1
title: Skeletal Muscle Transcriptional Networks Linked to Type I Myofiber Grouping in Parkinson’s Disease • Supplementary Materials

description: Table S1: Characteristics of WGCNA modules generated from skeletal muscle biopsiesTable S2: LightCyan Module Members (n=834)Table S3: SkyBlue Module Members (n=691)Table S4: LightCyan Module HubsTable S5: Genes associated with Percent Type I fibers in groups using single-gene analysis (DESeq2, n = 1911 transcripts)Table S6: SkyBlue Module HubsTable S7: Genes associated with mean type I myofiber group size using single-gene analysis (DESeq2, n = 1153 transcripts)
DOI: 10.6084/m9.figshare.19732255.v1
title: Supplementary Material for: Aurora Kinase A Is an Independent Predictor of Invasive Recurrence in Breast Ductal Carcinoma in situ

description: <b><i>Introduction:</i></b> Aurora Kinase A (AURKA/STK15) has a role in centrosome duplication and is a regulator of mitotic cell proliferation. It is over-expressed in breast cancer and other cancers, however; its role in ductal carcinoma in situ (DCIS) remains to be defined. This study aims to characterize AURKA protein expression in DCIS and evaluate its prognostic significance. <b><i>Methods:</i></b> AURKA was assessed immunohistochemically in a large well-characterized cohort of DCIS (<i>n</i> = 776 pure DCIS and 239 DCIS associated with invasive breast cancer [DCIS-mixed]) with long-term follow-up data (median = 105 months) and basic molecular characterization. <b><i>Results:</i></b> High AURKA expression was observed in 15% of DCIS cases and was associated with features of aggressiveness including larger tumour size, high nuclear grade, hormone receptor negativity, HER2 positivity, and high Ki67 proliferation index. AURKA expression was higher in DCIS associated with invasive breast cancer than in pure DCIS (<i>p</i> &lt; 0.0001). In the DCIS-mixed cohort, the invasive component showed higher AURKA expression than the DCIS component (<i>p</i> &lt; 0.0001). Outcome analysis revealed that AURKA was a predictor of invasive recurrence (<i>p</i> = 0.002). <b><i>Conclusion:</i></b> High AURKA expression is associated with poor prognosis in DCIS and might be a potential marker to predict DCIS progression to invasive disease.
DOI: 10.6084/m9.figshare.25982476.v1
title: Dataset and Code for "Geography for AI Sustainability and Sustainability for GeoAI"

description: This is a dataset for "Geography for AI Sustainability and Sustainability for GeoAI". It includes the necessary data and code to reproduce the figures presented in the work.<br>The .csv file contains detailed information on the locations of data centers from three major cloud computing providers: Amazon Web Services, Microsoft Azure, and Google Cloud Platform. It includes the coordinates, launch time, and carbon intensity values (sourced from Electricity Map, as yearly average of 2023) for each data center.
DOI: 10.6084/m9.figshare.11704419.v1
title: Patient 7

description: Atrial Tachycardia patient #1Part 1 contains the raw ultrasound RF dataPart 2 contains the B-mode, multi-2D and 3D-rendered EWI activation timings
DOI: 10.6084/m9.figshare.28406078.v1
title: RAW data for Distinct autoregulatory roles of ELFN1 intracellular and extracellular domains on membrane trafficking, synaptic localization, and dimerization paper.

description: Synaptic adhesion molecules are essential components of the synapse, yet the diversity of these molecules and their associated functions remain to be fully characterized. Extracellular leucine rich repeat and fibronectin type III domain containing 1 (ELFN1) is a postsynaptic adhesion molecule in the brain that has been increasingly implicated in human neurological disease. ELFN1 is best known for trans-synaptically modulating group III metabotropic glutamate receptors (mGluRs). However, little is known about ELFN1 organization and regulation, which likely govern and precede its ultimate trans-synaptic engagement with group III mGluRs. Herein, we report that the intracellular ELFN1 domain controls membrane trafficking and post-synaptic localization of ELFN1. We pinpoint a ?30 amino acid juxtamembranous region required for membranetargeting and discover that ELFN1 exists as an obligate homodimer prior to its trafficking to the membrane. We determine that ELFN1 homodimerization is not appreciably affected by the intracellular region and instead utilizes the extracellular leucine rich repeats (LRR) domain. We find that a single membrane-targeting motif located in one protomer is sufficient for effective trafficking of the ELFN1 homodimer. We further demonstrate that the closest ELFN1 homolog, synaptic adhesion molecule ELFN2, exhibits similar properties and participates in heterodimerization with ELFN1. This establishes distinct autoregulatory roles of ELFN1 intracellular and extracellular domains on membrane trafficking, postsynaptic localization, and dimerization while indicating conservation of the mechanisms across the ELFN subfamily of cell adhesion molecules.
DOI: 10.6084/m9.figshare.1510946.v1
title: Ecoinformatics next 100 years - ESA 2015

description: Slides from talk in Friday morning session on BIEN Botanical Information and Ecological Network
DOI: 10.6084/m9.figshare.14403926.v1
title: Data from: Historical Indigenous Land-Use Explains Plant Functional Trait Diversity

description: Human land-use legacies have long-term effects on plant community composition and<br>ecosystem function. While ancient and historical land-use is known to affect biodiversity<br>patterns, it is unknown whether such legacies affect other plant community properties<br>such as the diversity of functional traits. Functional traits are a critical tool for<br>understanding ecological communities because they give insights into community<br>assembly processes as well as potential species interactions and other ecosystem<br>functions. Here, we present the first systematic study evaluating how plant functional trait<br>distributions and functional diversity are affected by ancient and historical Indigenous<br>forest management in the Pacific Northwest. We compare forest garden ecosystems —<br>managed perennial fruit and nut communities associated exclusively with archaeological<br>village sites — with surrounding periphery conifer forests. We find that forest gardens<br>have substantially greater plant and functional trait diversity than periphery forests even<br>more than 150 years after management ceased. Forests managed by Indigenous peoples<br>in the past now provide diverse resources and habitat for animals and pollinators and are<br>more productive than naturally forested ecosystems. Although ecological studies rarely<br>incorporate Indigenous land-use legacies, the positive effects of Indigenous land-use on<br>contemporary functional and taxonomic diversity that we observe provide some of the<br>strongest evidence yet that Indigenous management practices are tied to ecosystem health<br>and resilience.<br>