cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.6998627.v1
title: aspectj_commit_to_bug_fixed_source

description: This CSV contains: bug_id, commit, source file fixed for aspectj project.
DOI: 10.6084/m9.figshare.24008271.v1
title: Supplementary Material for: Induction of vesicular trafficking and JNK-mediated apoptotic signaling in mononuclear leukocytes marks the immuno-proteostasis response to uremic proteins.

description: Introduction: Uremic retention solutes have been alleged to induce cell death in different cell types, including peripheral blood mononuclear leukocytes (PBL), which may contribute to uremic leukopenia and immune dysfunction. Methods: The molecular effects of these solutes were investigated in uremic PBL (u-PBL) and mononuclear cell lines (THP-1 and K562) exposed to the high-molecular-weight fraction of uremic plasma (u-HMW; prepared 50 kDa microconcentrator ultrafiltration). Results: u-PBL show reduced cell viability and increased apoptotic death compared to healthy control PBL (c-PBL). u-HMW induce apoptosis both in u-PBL and c-PBL, as well as in mononuclear cell lines, also stimulating cellular H2O2 formation and secretion, IRE1-α-mediated endoplasmic reticulum stress signaling and JNK/cJun pathway activation. Also, u-HMW induce autophagy in THP-1 monocytes. u-PBL were characterized by the presence in their cellular proteome of the main proteins and carbonylation targets of u-HMW, namely albumin, transferrin and fibrinogen, and by the increased expression of RAGE, a scavenger receptor with promiscuous ligand binding properties involved in leukocyte activation and endocytosis. Conclusions: In conclusion, large uremic solutes induce abnormal endocytosis and terminal alteration of cellular proteostasis mechanisms in PBL, including UPR/ERSR and autophagy. These are potent triggers of JNK-mediated apoptotic signaling. The findings in this study describe at the molecular level the suicidal role of immune cells in facing the uremic disturbances of systemic proteostasis, a process that we define as the immuno-proteostasis response of uremia.
DOI: 10.6084/m9.figshare.25523641.v1
title: Source data and Data structure for "A primary sensory cortical interareal feedforward inhibitory circuit for tacto-visual integration"

description: Tactile sensation and vision are often both utilized for the exploration of objects that are within reach though it is not known whether or how these two distinct sensory systems might combine such information. Here in mice we find that stimulation of the contralateral whisker array suppresses visually evoked activity in a subarea of primary visual cortex (VISp) whose visual space covers the whisker search space. This is mediated by local fast spiking interneurons that receive a direct cortico-cortical input predominantly from layer 6 of the primary somatosensory barrel cortex (SSp-bfd). These data demonstrate functional convergence within and between two primary sensory cortical areas for multisensory object detection and recognition.Source data file for this research + Matlab data structure containing electrophysiological raw data, see also: https://github.com/simonweiler/cross_modal_SSp_VISp
DOI: 10.6084/m9.figshare.4928693.v1
title: Global Ocean Surface Diffusivities derived from Altimetry

description: The final realistic results are in the file `K_mix_uncorrected.nc`.<br>This file should be used for analysis purposes.<br>All other files are needed to reproduce results and plots using the analysis code (https://github.com/jbusecke/busecke_abernathey_2019_sciadv).<br>Permanently archived code from publication date can be found at https://zenodo.org/record/1472889.<br><br><br><br>
DOI: 10.6084/m9.figshare.7420388.v1
title: Pathology of dogs in Campo Grande, MS, Brazil naturally co-infected with Leishmania infantum and Ehrlichia canis

description: Different parasites that commonly occur concomitantly can influence one another, sometimes with unpredictable effects. We evaluated pathological aspects of dogs naturally co-infected with Leishmania infantum and Ehrlichia canis. The health status of the dogs was investigated based on histopathological, hematological and biochemical analyses of 21 animals infected solely with L. infantum and 22 dogs co- infected with L. infantum and E. canis. The skin of both groups showed chronic, predominantly lymphohistioplasmacytic inflammatory reaction. The plasmacytosis in the lymphoid tissues was likely related with the hypergammaglobulinemia detected in all the dogs. The disorganization of extracellular matrix found in the reticular dermis of the inguinal region and ear, characterized by the substitution of thick collagen fibers for thin fibers, was attributed to the degree of inflammatory reaction, irrespective of the presence of parasites. In addition, the histopathological analysis revealed that twice as many dogs in the co-infected group presented Leishmania amastigotes in the ear skin than those infected solely with Leishmania, increasing the possibility of becoming infected through sand fly vectors. Our findings highlight the fact that the health of dogs infected concomitantly with L. infantum and E. canis is severely compromised due to their high levels of total plasma protein, globulins, alkaline phosphatase and creatine kinase, and severe anemia.
DOI: 10.6084/m9.figshare.14419715.v1
title: Supplementary Material for: Prestenting Versus Nonprestenting on the Outcomes of Flexible Ureteroscopy for Large Upper Urinary Stones: A Systematic Review and Meta-Analysis

description: <b><i>Introduction:</i></b> The purpose of this article is to evaluate the efficacy and safety of prestenting (PS) versus non-PS (NPS) of flexible ureteroscopy (fURS) to treat large upper urinary stones. <b><i>Methods:</i></b> We conducted a systematic literature research of PubMed, Ovid, Scopus (up to August 2019), and citation lists to identify eligible studies. All studies comparing PS versus NPS of fURS were included. Data were analyzed using the Cochrane Collaboration’s Review Manager (RevMan) 5.3 software. <b><i>Results:</i></b> Overall, 7 studies including 3,145 patients (PS 1,408; NPS 1,737) were included in this article. PS group was associated with older age (weighted mean difference [WMD] 0.91 year; <i>p</i> &lt; 0.001) and more male patients (odds ratio [OR] 1.34; <i>p</i> &lt; 0.001). There were no statistical differences between PS and NPS in BMI (WMD 0.34 kg/m<sup>2</sup>; <i>p</i> = 0.13), stone size (WMD 0.13 mm; <i>p</i> = 0.77), and operative time (WMD 0.44 min; <i>p</i> = 0.86). Compared with NPS, PS showed better initial success rate (OR 4.04; <i>p</i> &lt; 0.001) and higher SFR (OR 1.64; <i>p</i> &lt; 0.001). There were no statistical differences for complications (OR 0.84; <i>p</i> = 0.42) and Clavien-Dindo score ≥3 complications (OR 1.04; <i>p</i> = 0.93). <b><i>Conclusion:</i></b> PS could improve initial success rate and avoid secondary general anesthesia for first ureteral access sheath failed patients. PS could provide better SFR than NPS in the treatment of large upper urinary stones with fURS.
DOI: 10.6084/m9.figshare.25429396.v2
title: super resolution of historical Landsat images

description: The dataset provides annual images of Beijing, Shanghai, Wuhan, and Urumuqi from 1985 to 2015 at a resolution of 10 meters, created by enhancing the resolution of historical Landsat satellite images. It represents the first consistent high-resolution remote sensing archive spanning 30 years. This dataset offers a unique opportunity for researchers to observe and analyze the changes in these cities over this period. It is of significant importance for studies in urban planning, land use, environmental monitoring, and related fields.
DOI: 10.6084/m9.figshare.28606802.v1
title: MFPT.zip

description: MFPT Dataset: This dataset consists of 23 categories. The basic group includes three sets of normal data and three sets of outer race fault data, collected under a load of 270 lbs, a shaft speed of 25 Hz, and a sampling rate of 97656 kHz. The extended group contains two variable-load subsets: seven sets of outer race fault data (collected at loads ranging from 25 to 300 lbs with a sampling rate of 48828 kHz) and seven sets of inner race fault data (collected at loads ranging from 0 to 300 lbs with with a sampling rate of 48828 kHz).
DOI: 10.15468/dl.qrq8t4
title: Occurrence Download

description: A dataset containing 482 species occurrences available in GBIF matching the query:
{
 "and" : [
 "HasGeospatialIssue is false",
 "HasCoordinate is true",
 "OccurrenceStatus is Present",
 {
 "not" : {
 "BasisOfRecord" : [
 "is one of (Observation, Human Observation, Machine Observation, Living Specimen)"
 ]
 }
 },
 "TaxonKey is Pherbina coryleti (Scopoli, 1763)"
 ]
}

 The dataset includes 482 records from 28 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0009608-250426092105405/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.6084/m9.figshare.14716830.v1
title: Wild boar detection-nondetection data

description: Detection-nondetection data (March 2019 - May 2020) derived from a camera trapping network in Wallonia (Belgium). The dataset consists of the binary variable 'obs', supplemented with metadata about the survey (site and survey information) as well as selected site-specific covariates of interest, extracted from the LifeWatch ecotope database. Data set in CSV-format. We refer to the README for a more detailed description.
DOI: 10.6084/m9.figshare.11406885.v1
title: Supplementary Material for: Machine Learning Prediction of Radiofrequency Thermal Ablation Efficacy: A New Option to Optimize Thyroid Nodule Selection

description: <b><i>Background:</i></b> Radiofrequency (RF) is a therapeutic modality for reducing the volume of large benign thyroid nodules. If thermal therapies are interpreted as an alternative strategy to surgery, critical issues in their use are represented by the extent of nodule reduction and by the durability of nodule reduction over a long period of time. <b><i>Objective:</i></b> To assess the ability of machine learning to discriminate nodules with volume reduction rate (VRR) &lt; or ≥50% at 12 months following RF treatment. <b><i>Methods:</i></b> A machine learning model was trained with a dataset of 402 cytologically benign thyroid nodules subjected to RF at six Italian Institutions. The model was trained with the following variables: baseline nodule volume, echostructure, macrocalcalcifications, vascularity, and 12-month VRR. <b><i>Results:</i></b> After training, the model could distinguish between nodules having VRR &lt;50% from those having VRR ≥50% in 85% of cases (accuracy: 0.85; 95% confidence interval [CI]: 0.80–0.90; sensitivity: 0.70; 95% CI: 0.62–0.75; specificity: 0.99; 95% CI: 0.98–1.0; positive predictive value: 0.95; 95% CI: 0.92–0.98; negative predictive value: 0.95; 95% CI: 0.92–0.98). <b><i>Conclusions:</i></b> This study demonstrates that a machine learning model can reliably identify those nodules that will have VRR &lt; or ≥50% at 12 months after one RF treatment session. Predicting which nodules will be poor or good responders represents valuable data that may help physicians and patients decide on the best treatment option between thermal ablation and surgery or in predicting if more than one session might be necessary to obtain a significant volume reduction.
DOI: 10.6084/m9.figshare.20368902.v1
title: Suppl_Table_1_HistoneMarks_peak_gene.ids.rpkm.mean.txt

description: Data sets for A quadruple transgenic reprogrammable mouse model containing SLC34a1-Cre, dTomato, rtTA, and OKMS is used to determine epigenetic memory in kidney proximal tubule cell derived induced Pluripotent Stem Cells. Authors: Gabriel Khelifi1,2*, Theresa Chow3,4*, Jennifer Whiteley3, Victoire Fort1,2, Benjamin D. Humphreys5, Samer Hussein1,2,#, and Ian M. Rogers3,4,6,7,#
DOI: 10.6084/m9.figshare.22877087.v1
title: PRJCA009490

description: functional annotation of two sandalwood genome
DOI: 10.6084/m9.figshare.25009556.v2
title: The miRNA sequences of animals and plants.

description: One-hot coding sequences of plant and animal miRNAs
DOI: 10.6084/m9.figshare.12401549.v1
title: 4 and 6 coupled players

description: 4 and 6 coupled violin players with high coupling when increasing linearly the delay.Files with the number 24 are for 4 coupled players and files with the number 26 are for 6 coupled players*.aiff = raw sounds files of the experiment*. = raw data files of the parameters of the system during the experiment*.mat = analyzed data of one of the measurements showing the phase of each players<br>*.m = code file for analyzing the data and making the figure*.fig = the figure in the paper
DOI: 10.6084/m9.figshare.24104508.v1
title: DRS & EDS Dataset in Supporting Information Jiao JW et al., 2023.xlsx

description: The dataset set includes two worksheets in the EXCEL. The first worksheet documents the EDS data in the SEM observations and diffuse reflectance spectroscopy data. The second one documents the DRS data including the band intensity of goethite and hematite and the hematite/goethite ratio.
DOI: 10.6084/m9.figshare.5918617.v1
title: Supplementary Material for: Downregulation of the Cl<sup>-</sup>/HCO<sub>3</sub><sup>-</sup>Exchanger Pendrin in Kidneys of Mice with Cystic Fibrosis: Role in the Pathogenesis of Metabolic Alkalosis

description: <b><i>Background/Aims:</i></b> Patients with cystic fibrosis (CF) are prone to the development of metabolic alkalosis; however, the pathogenesis of this life threatening derangement remains unknown. We hypothesized that altered acid base transport machinery in the kidney collecting duct underlies the mechanism of impaired bicarbonate elimination in the CF kidney. <b><i>Methods:</i></b> Balance studies in metabolic cages were performed in WT and CFTR knockout (CF) mice with the intestinal rescue in response to bicarbonate loading or salt restriction, and the expression levels and cellular distribution of acid base and electrolyte transporters in the proximal tubule, collecting duct and small intestine were examined by western blots, northern blots and/or immunofluorescence labeling. <b><i>Results:</i></b> Baseline parameters, including acid-base and systemic vascular volume status were comparable in WT and CF mice, as determined by blood gas, kidney renin expression and urine chloride excretion. Compared with WT animals, CF mice demonstrated a significantly higher serum HCO<sub>3</sub><sup>-</sup> concentration (22.63 in WT vs. 26.83 mEq/l in CF mice; n=4, p=0.013) and serum pH (7.33 in WT vs. 7.42 in CF mice; n=4, p=0.00792) and exhibited impaired kidney HCO<sub>3</sub><sup>-</sup> excretion (urine pH 8.10 in WT vs. 7.35 in CF mice; n=7, p=0.00990) following a 3-day oral bicarbonate load. When subjected to salt restriction, CF mice developed a significantly higher serum HCO<sub>3</sub><sup>-</sup> concentration vs. WT animals (29.26 mEq/L in CF mice vs. 26.72 in WT; n=5, p=0.0291). Immunofluorescence labeling demonstrated a profound reduction in the apical expression of the Cl<sup>-</sup>/HCO<sub>3</sub><sup>-</sup> exchanger pendrin in cortical collecting duct cells and western and northern blots indicated diminished plasma membrane abundance and mRNA expression of pendrin in CF kidneys. <b><i>Conclusions:</i></b> We propose that patients with cystic fibrosis are prone to the development of metabolic alkalosis secondary to the inactivation of the bicarbonate secreting transporter pendrin, specifically during volume depletion, which is a common occurrence in CF patients.
DOI: 10.6084/m9.figshare.5126389.v1
title: Supplementary Material for: In vitro and in vivo Characterization of a New Organic Nitrate Hybrid Drug Covalently Bound to Pioglitazone

description: <b><i>Background/Aims:</i></b> Organic nitrates represent a group of nitrovasodilators that are clinically used for the treatment of ischemic heart disease. The new compound CLC-3000 is an aminoethyl nitrate (AEN) derivative of pioglitazone, a thiazolidinedione antidiabetic agent combining the peroxisome proliferator-activated receptor γ agonist activity of pioglitazone with the NO-donating activity of the nitrate moiety. <b><i>Methods:</i></b> In vitro and in vivo characterization was performed by isometric tension recording, platelet function, bleeding time and detection of oxidative stress. <b><i>Results:</i></b> In vitro, CLC-3000 displayed more potent vasodilation than pioglitazone alone or classical nitrates. In vitro, some effects on oxidative stress parameters were observed. Authentic AEN or the AEN-containing linker CLC-1275 displayed antiaggregatory effects. In vivo treatment with CLC-3000 for 7 days did neither induce endothelial dysfunction nor nitrate tolerance nor oxidative stress. Acute or chronic administration of AEN increased the tail vein bleeding time in mice. <b><i>Conclusion:</i></b> In summary, the results of these studies demonstrate that CLC-3000 contains a vasodilative and antithrombotic activity that is not evident with pioglitazone alone, and that 7 days of exposure in vivo showed no typical signs of nitrate tolerance, endothelial dysfunction or other safety concerns in Wistar rats.
DOI: 10.6084/m9.figshare.19719088.v1
title: Indian Court Decision Annotated Corpus.xlsx

description: Dataset contains 50 Supreme Court of India Court Decisions annotated for Named Entity Recognition in the case documents with three different encoding schemes viz., IOB, IOBES, BILOU. The dataset is created using the CoNLL-2003 format.
DOI: 10.6084/m9.figshare.25093178.v2
title: Metabolomic Profiling Reveals Key Metabolites Associated with Hypertension Progression

description: Introduction: Pre-hypertension is a prevalent condition among the adult population worldwide. It is characterized by asymptomatic elevations in blood pressure beyond normal levels but not yet reaching the threshold for hypertension. If left uncontrolled, pre-hypertension can progress to hypertension, thereby increasing the risk of serious complications such as heart disease, stroke, kidney damage, and others. Objective: The precise mechanisms driving the progression of hypertension remain unknown. Thus, identifying the metabolic changes associated with this condition can provide valuable insights into potential markers or pathways implicated in the development of hypertension. Methods: In this study, we utilized untargeted metabolomics profiling, which examines over 1,000 metabolites to identifynovel metabolites contributing to the progression from pre-hypertension to hypertension. Data were collected from 323 participants through Qatar Biobank. Results: By comparing metabolic profiles between pre-hypertensive, hypertensive and normotensive individuals, six metabolites including stearidonate, hexadecadienoate, N6-carbamoylthreonyladenosine, 9 and 13-S-hydroxyoctadecadienoic acid (HODE), 2,3-dihydroxy-5-methylthio- 4-pentenoate (DMTPA), and linolenate were found to be associated with increased risk of hypertension, in both discovery and validation cohorts. Moreover, these metabolites showed a significant diagnostic performance with area under curve &gt;0.7. Conclusion: These findings suggest possible biomarkers that can predict the risk of progression from pre-hypertension to hypertension. This will aid in early detection, diagnosis, and management of this disease as well as its associated complications.<br>
DOI: 10.6084/m9.figshare.22283875.v1
title: Supplementary Material for: Cryotherapy after topical interferon alpha 2b to treat conjunctival primary acquired melanosis

description: When primary acquired melanosis (PAM) with atypia affects the tarsal conjunctiva, a radical surgery can be mutilating, requiring reconstructive surgery of the eyelid. Topical Chemoteraphy associated to local crioteraphy may be an alternative. A 64-year-old Caucasian female presented with diffuse PAM of the right eye involving the inferior tarsal conjunctiva, fornix, and inferotemporal bulbar conjunctiva. Histological study showed a PAM with atypia (C-MIN 5). Given the extent of the lesion and its location, a wide mutilating excision was ruled out. Topical Interferon alpha 2b (IFN-α2b) treatment (1,000,000 IU/mL, 4 times a day) was administered during 10 weeks. However the regression was very slow. Then local cryotherapy was proposed (8s at –80ºC per aplication) to the entire pigmented lesion. This afforded progressive depigmentation, which was complete 2 months later. No recurrence of the lesion has been noted during 3 years of follow-up. The combination of the two procedures reduces IFN-α2b eyedrop administration time, enhancing patient compliance. The combination eradicated the tumour without compromising ocular cosmesis.
DOI: 10.6084/m9.figshare.3558585.v1
title: Supplement 1. Data files for abundance-weighted leaf traits, soil nutrient data for defining community composition, and reciprocal transplant experiment data, along with data from the test of switch drivers for the greenhouse experiment and the field experiment.

description: File List Abundance_weighted_leaf_traits.csv (MD5: f50ceaec03154c095a8fb713ff08bf13) Soil_nutrients.csv (MD5: 5fac67a5472ede6c7fd1c104783088a2) Samples_for_defining_communities.csv (MD5: 39d61c28a43b9f3851884019fb6dc0d5) Reciprocal_transplant_experiment.csv (MD5: 21785f772bd940c4b834e62e62725cb4) Drivers_greenhouse_experiment.csv ( MD5: 35cd6194bfa27147b99395efeca8b23b) Drivers_field_experiment.csv (MD5: 48ab4c8fba5e19acfe1e1a71c060a42d) Description "Abundance_weighted_leaf_traits" – the leaf trait data. "Soil_nutrients" – the soil data. "Samples_for_defining_communities" –data used to define the two communities. "Reciprocal_transplant_experiment" – species frequency data from the reciprocal transplant experiment. "Drivers_greenhouse_experiment" – the biomass data for each community for the test of drivers: greenhouse experiment. "Drivers_field_experiment" – The data from the test of drivers: field experiment.
DOI: 10.6084/m9.figshare.8152922.v2
title: Soil fungal communities Gutianshan (GTS)

description: Sequence information (18S for AMF and ITS1 for fungi) from soil samples collected in Gutianshan FDP (GTS).<br>This is the data repository for the soil fungal communities in Gutuansan (GTS) project.<br>-----------------File description------------------ sampled_tree_INFO.csv --&gt; Metadata associated with each sample including sample code,species code, tree tag, tree coordinates and dbh(cm).<br>- OTU_table_and_representative_OTU_sequences for ITS1.csv --&gt; OTU tables and representative OTU sequences for ITS1 based fungal community.<br>- OTU_table_and_representative_OTU_sequences for 18S.csv --&gt; OTU tables and representative OTU sequences for 18S based AM fungal community.
DOI: 10.6084/m9.figshare.28696835.v1
title: Soil description and nutrient chemistry data from the subarctic River Tana catchment (Finmark, Norway) collected as part of the project QUANTOM

description: Dataset is original data from an investigation of riparian soils in the subarctic River Tana, N Norway, as part of the project QUANTOM (QUANTification of dissolved Organic Matter and the metabolic balance in river networks; 2021-24) improving understanding of DOM sources and delivery along the River Tana and in-river transformations leading to carbon dioxide (CO<sub>2</sub>) emissions; project lead NIVA, Oslo). Soils in four subcatchments were sampled during October 2022 across the riparian zones (hillslope base to stream side) to determine biogeochemical properties relating to the cycling of C, N and P. The data here show the soil descriptions and analytical data of physical and chemical properties per horizon, according to soil, landscape position and site (subcatchment). The data accompany a science journal paper in preparation at date of doi creation and that will show full sampling and analytical methods. Data in the form of an Excel file are accompanied by column metadata and the data formatted to correct levels (d.p.) of analytical precision. Data are also provided as a .csv file.
DOI: 10.6084/m9.figshare.24151953.v2
title: experiment data.zip

description: It is the data for the free-fall experiment. It can be checked using software DHDAS.