cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.13655534.v1
title: Supplementary Material for: Clinical Implementation of In-House Developed MR-Based Patient-Specific 3D Models of Liver Anatomy

description: Knowledge of patient-specific liver anatomy is key to patient safety during major hepatobiliary surgery. Three-dimensional (3D) models of patient-specific liver anatomy based on diagnostic MRI images can provide essential vascular and biliary anatomical insight during surgery. However, a method for generating these is not yet publicly available. This paper describes how these 3D models of the liver can be generated using open source software, and then subsequently integrated into a sterile surgical environment. The most common image quality aspects that degrade the quality of the 3D models as well possible ways of eliminating these are also discussed. Per patient, a single diagnostic multiphase MRI scan with hepatospecific contrast agent was used for automated segmentation of liver contour, arterial, portal, and venous anatomy, and the biliary tree. Subsequently, lesions were delineated manually. The resulting interactive 3D model could be accessed during surgery on a sterile covered tablet. Up to now, such models have been used in 335 surgical procedures. Their use simplified the surgical treatment of patients with a high number of liver metastases and contributed to the localization of vanished lesions in cases of a radiological complete response to neoadjuvant treatment. They facilitated perioperative verification of the relationship of tumors and the surrounding vascular and biliary anatomy, and eased decision-making before and during surgery.
DOI: 10.15468/dl.ajkrqj
title: Occurrence Download

description: A dataset containing 14 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is China",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is one of (Spergularia marina (L.) Besser, Ruppia maritima L.)",
 "Year 2000-2025"
 ]
}

 The dataset includes 14 records from 3 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0009575-250426092105405/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.5979877.v1
title: Inclusion and intellectual disability: special and common schools under the point of view of students themselves

description: ABSTRACT Considering that under the banner of inclusion school transfers between special and common schools have been taking place throughout national territory, it is necessary to investigate how the public students of these schools perceive this process, since the literature warns about the absence of student participation on the decisions about their schooling process. This work aimed to investigate the thoughts of students with intellectual disabilities (ID) on special and regular schools, taking their school transfers as a scenario, be this transfer from the special to the common school or vice versa. It is a descriptive research with multiple case design that involved the study of five cases of ID students who were transferred. The instruments used for data collection were the Drawing-and-Story procedure with the students and complementary interviews with family members. The analysis of the data allowed us to identify that the students assigned to the special school the role of reception and care, and to the common school a place of learning and knowledge, with awareness that these are two distinct forms of schooling, each with its pros and cons. The analysis of the results shows that the study reached its objectives and brought practical, political and scientific implications related to the schooling of the students with ID, especially when giving voice to the target of the school transfer.
DOI: 10.17608/k6.auckland.28603691.v1
title: Fibre orientations

description: <b>Fibre orientations</b><b>General information</b>The fibres were extracted from the micro-computed tomography data using structure tensors. They can be viewed with Cmgui using the .com files. The path for the <b>set dir</b> command in the .com files needs to be changed before visualising the fibres. The fibres were coloured based on the angle relative to the centreline of the uterine horns.<b>Contents</b>There is one folder for each stage of the estrus cycle which contains the fibres for one rat. The binary folder contains the .exnode and .exelem files that are used by Cmgui. The .com files contains the commands to visualise the fibres.
DOI: 10.6084/m9.figshare.28660652.v1
title: Supplementary Material from Genetic structure and demographic history of house mice in Western Europe inferred using whole-genome sequences

description: filtered_merged_autosomes.snp
DOI: 10.6084/m9.figshare.10084601.v1
title: hgcA-proteins

description: FASTA-formatted file of all identified hgcA proteins
DOI: 10.6084/m9.figshare.14865120.v1
title: Supplementary Material for: Time- and Stimulus-Dependent Characteristics of Innate Immune Cells in Organ-Cultured Human Corneal Tissue

description: <b><i>Purpose:</i></b> The pattern of immune cells infiltrating the corneal stroma has been extensively studied in mice, but data on human tissue have been far less elaborate. To further characterize the number and differentiation state of resident immune cells in organ-cultured human corneal tissue, we employed a comprehensive bioinformatic deconvolution (xCell) of bulk RNA-sequencing (RNA-seq) data, immunohistochemistry (IHC), and flow cytometry (FC). <b><i>Methods:</i></b> A transcriptome-based analysis of immune cell types in human corneal samples was performed. The results were validated by IHC, focusing on the identification of pro-inflammatory (M1) and regulatory (M2) macrophages. A protocol was established to identify these 2 different macrophage populations in human corneal tissue by means of FC. Subsequently, corneal samples in organ culture were differentially stimulated by IL-10, IL-4 & IL-13, or LPS and macrophage populations were evaluated regarding their response to these stimuli. Furthermore, cell survival was analyzed in correlation with time in organ culture. <b><i>Results:</i></b> xCell-based mathematical deconvolution of bulk RNA-seq data revealed the presence of CD8 T cells, Th17 cells, dendritic cells, and macrophages as the predominant immune cell types in organ-cultured human corneal tissue. Furthermore, RNA-seq allowed the detection of different macrophage marker genes in corneal samples, including <i>PTPRC</i> (CD45), <i>ITGAM</i> (CD11b), <i>CD14</i>, and <i>CD74</i>. Our RNA-seq data showed no evidence of a relevant presence of monocytes in human corneal tissue. The presence of different macrophage subtypes was confirmed by IHC. The disintegration and subsequent FC analysis of human corneal samples showed the presence of both M1 (HLA-DR<sup>+</sup>, CD282<sup>+</sup>, CD86<sup>+</sup>, and CD284<sup>+</sup>) and M2 (CD163<sup>+</sup> and CD206<sup>+</sup>) macrophage subtypes. Furthermore, we found that the total number of macrophages in corneal samples decreased more than the total cell count with increasing tissue culture time. Treatment with IL-10 led to higher total cell counts per cornea and to an increased expression of the M2 marker CD163 (<i>p</i> &lt; 0.05) while expression levels of various M1 macrophage markers were not significantly reduced by interleukin treatment. <b><i>Conclusions:</i></b> Regarding different macrophage populations, untreated human corneas showed more M1 than M2 macrophages. With increasing organ culture time, these macrophages decreased. In terms of cell dynamics, adding interleukins to the organ culture medium influenced the phenotype of macrophages within the cornea as detected by FC. Modifying the immunomodulatory properties of human grafts appears a promising approach to further reduce the risk of graft rejection in patients. In this context, treatment with interleukins was more effective in upregulating M2 macrophages than in suppressing M1 macrophages in corneal tissue.
DOI: 10.6084/m9.figshare.28005653.v1
title: Alternating dominance of Westerlies and East Asian winter monsoon on dust activities across the NE Qinghai-Tibet Plateau since 18.5 ka

description: It contacts grain size data, element data, and OSL sensitivity data
DOI: 10.6084/m9.figshare.11857716.v1
title: genomes.txt

description: genomes.txt
DOI: 10.6084/m9.figshare.24612096.v1
title: Supplementary Material for: Transcription factor MITF inhibits the transcription of CPT1B to regulate fatty acid β-oxidation and thus affects stemness in lung adenocarcinoma cells

description: Introduction: Cancer stem cells (CSCs) play critical roles in lung adenocarcinoma (LUAD) progression, and fatty acid oxidation is key for CSC growth and survival. Therefore, investigating the molecular mechanisms regulating fatty acid β-oxidation in LUAD is important for its treatment. Methods: Bioinformatics analysis assessed CPT1B and MITF expression and their correlation in LUAD tissues, as well as the pathways enriched by CPT1B. qRT-PCR assessed expression of CPT1B and MITF, while CCK-8 and sphere-forming assays were used to measure cell viability and stemness, respectively. Dual staining detected lipid accumulation, while kits were used to measure fatty acid β-oxidation and glycerol content. qRT-PCR was used to assay expression of lipid oxidation genes. Western blot was used to examine expression of stem cell-related markers. Dual luciferase assay and ChIP assay were used to verify the binding relationship between MITF and CPT1B. Results: CPT1B was found to be highly expressed in LUAD and enriched in linoleic acid metabolism pathway and α-linolenic acid metabolism pathway. Functional experiments showed that CPT1B could promote stemness in LUAD cells by regulating fatty acid β-oxidation. Additionally, CPT1B was found to be regulated by the upstream transcription factor MITF, which was lowly expressed in LUAD and could downregulate CPT1B expression. Rescue experiments revealed that CPT1B/MITF axis could affect stemness in LUAD cells by regulating fatty acid β-oxidation. Conclusion: Transcription factor MITF inhibited transcription of CPT1B to regulate fatty acid β-oxidation, thereby suppressing stemness in LUAD cells. MITF and CPT1B may become new targets for LUAD.
DOI: 10.6084/m9.figshare.19114250.v1
title: Monthly SPI and SPEI raster dataset over China from 1979 to 2018

description: The traditional monthly SPI/SPEI fitting by various probability distributions (Gamma, Gumbel, Logistic, Log-Logistic, and Normal for SPI and Log-Logistic, Generalized extreme value, Normal, and Pearson type III for SPEI) in 3-month scale with a spatial resolution of 0.1° × 0.1° developed based on the China Meteorological Forcing dataset. All data are in NetCDF format.
DOI: 10.6084/m9.figshare.24769470.v1
title: Conversational Skills in Language Learning Games: A Speech Recognition Technology Dataset

description: The "SpeechRec_LanguageLearning_ConversationalSkills" dataset is a collection of data generated in a game-based language learning environment, aiming to explore the impact of Speech Recognition Technology (SRT) on the development of conversational skills. The dataset encompasses speaking test results conducted within the context of language learning games utilizing SRT.
DOI: 10.25375/uct.14254394.v3
title: Data for "Intracellular mechanics and TBX3 expression jointly dictate the spreading mode of melanoma cells in 3D environments"

description: Quantitative data for Publication <br>G Higgins, F Higgins, DM Lang, T Abdalrahman, MH Zaman, S Prince, T Franz."Intracellular stiffness, mitochondrial activity and TBX3 expression jointly dictate the spreading mode of melanoma cells in 3D environments", bioRxiv, 2021<br><br>Three Excel files<br>File 1<br>File name: Microrheology Data<br>Data: Mitochondrial mean square displacement (MSD) and intracellular fluidity (α, Alpha)<br>Number of worksheets: 4<br>Worksheet name - Description of data<br>* D1 MSD - MSD data of isolated cells on Day 1<br>* D1 Alpha - Fluidity α of isolated cells on Day 1<br>* D7 MSD - MSD data of cell clusters on Day 7<br>* D7 Alpha - Fluidity α of cell clusters on Day 7<br><br>File 2<br>File name: Morphology Data<br>Data: Morphometric descriptors of cells, i.e. cell area, cell roundness<br>Number of worksheets: 1<br><br>File 3<br>File name: TBX3 Data<br>Data: Intracellular TBX3 expression levels<br>Number of worksheets: 1<br>
DOI: 10.6084/m9.figshare.1334229.v1
title: Highest Resolution in vivo Human Brain MRI Using Prospective Motion Correction: highest resolution GRE data

description: Full dataset (21 slices) of the highest<br>resolution T2* 2D GRE scan (shown in Fig. 6).
DOI: 10.6084/m9.figshare.12278402.v1
title: Genome-wide macroevolutionary signatures of key innovations in butterflies colonizing new host plants

description: This folder contains:Data 1 - Phylogenetic analyses PapilionidaeData 2 - Molecular dating PapilionidaeData 3 - Host-plants for PapilionidaeData 4 - Phylogenetic analyses AristolochiaceaeData 5 - Molecular dating of AristolochiaceaeData 6 - Geographic distributions and biogeographic analysesData 7 - Diversification analysesData 8 - Genomic dataset and analysesSupplementary Figures and Tables<br>Source data file to reproduce Figures 3a and Figures 4b-d of the main text<br>Supplementary data files to show large Excel tables for reuse<br><br><br>
DOI: 10.6084/m9.figshare.13238507.v2
title: Questionnaire-child developmental delay and pesticide

description: Questionnaire using for the study project of Chlorpyrifos and other pesticide exposure and suspected developmental delay in children aged 0-5 year: a case-control study in Phitsanulok, Thailand
DOI: 10.6084/m9.figshare.28795667.v1
title: Sentinel_2dataset.rar

description: The labelled dataset was generated for Mask R-CNN from Sentinel-2 data.
DOI: 10.6084/m9.figshare.28828238.v1
title: Figure 2 _ Pranevicius et al (2025)

description: Figure 2_ PER and TIM timecourses.
DOI: 10.6084/m9.figshare.21176320.v3
title: code and data for <em>A Classification Scheme for Static Origin–Destination Data Visualizations</em>

description: the python scripts implement functions in section 5, and the data is a matrix for Table 2 in this paper.
DOI: 10.6084/m9.figshare.811808.v1
title: Standard curve malachite green

description: Standard curve of inorganic phosphate (Pi) in malachite green assay was generated with a 0.02 mM KH2PO4 solution. A serial of standard solution containing different pmol of Pi were added to 950 µl of malachite green solution. Reactions were incubated for 20 min at room temperature. Absorbance at 620 nm was measured in a cuvette with the malachite green solution as a blank. Duplicates were set up for each standard concentration and the average value of the duplicates was used for plotting the standard curve.
DOI: 10.6084/m9.figshare.7000499.v1
title: Supplementary Material for: Peak Troponin I Levels Are Associated with Functional Outcome in Intracerebral Hemorrhage

description: <b><i>Background:</i></b> Troponin I is a widely used and reliable marker of myocardial damage and its levels are routinely measured in acute stroke care. So far, the influence of troponin I elevations during hospital stay on functional outcome in patients with atraumatic intracerebral hemorrhage (ICH) is unknown. <b><i>Methods:</i></b> Observational single-center study including conservatively treated ICH patients over a 9-year period. Patients were categorized according to peak troponin I level during hospital stay (≤0.040, 0.041–0.500, &gt; 0.500 ng/mL) and compared regarding baseline and hematoma characteristics. Multivariable analyses were performed to investigate independent associations of troponin levels during hospital stay with functional outcome – assessed using the modified Rankin Scale (mRS; favorable 0–3/unfavorable 4–6) – and mortality after 3 and 12 months. To account for possible confounding propensity score (PS)-matching (1: 1; caliper 0.1) was performed accounting for imbalances in baseline characteristics to investigate the impact of troponin I values on outcome. <b><i>Results:</i></b> Troponin elevations (&gt; 0.040 ng/mL) during hospital stay were observed in 308 out of 745 (41.3%) patients and associated with poorer status on admission (Glasgow Coma Scale/National Institute of Health Stroke Scale). Multivariable analysis revealed troponin I levels during hospital stay to be independently associated with unfavorable outcome after 12 months (risk ratio [95% CI]: 1.030 [1.009–1.051] per increment of 1.0 ng/mL; <i>p</i> = 0.005), but not with mortality. After PS-matching, patients with troponin I elevation (≥0.040 ng/mL) versus those without had a significant higher rate of ­unfavorable outcome after 3 and 12 months (mRS 4–6 at 3 months: &lt; 0.04 ng/mL: 159/265 [60.0%] versus ≥0.04 ng/mL: 199/266 [74.8%]; <i>p</i> &lt; 0.001; at 12 months: &lt; 0.04 ng/mL: 141/248 [56.9%] versus ≥0.04 ng/mL: 179/251 [71.3%]; <i>p</i> = 0.001). <b><i>Conclusions:</i></b> Troponin I elevations during hospital stay occur frequently in ICH patients and are independently associated with functional outcome after 3 and 12 months but not with mortality.
DOI: 10.6084/m9.figshare.24442654.v1
title: Supplementary Material for: Rapid and effective elimination of myoglobin with CytoSorb® hemoadsorber in patients with severe rhabdomyolysis

description: Introduction: Rhabdomyolysis is characterized by destruction of muscle fibres by various causes, diagnosed by increased creatin kinase concentrations in the blood. Myoglobin released into the blood may cause acute kidney injury. In this randomized controlled study, we hypothesized that myoglobin elimination would be faster when a hemoadsorber is added to a continuous venovenous hemodialysis. Methods: Four patients in the control group received CVVHD with a high cut-off hemofilter using high blood and dialysate flows for 48 hours. Four patients in the CytoSorb group received the same treatment, but in addition, the hemoadsorber CytoSorb® was inserted in front of the hemofilter and replaced once after 24 hours. Blood samples were drawn simultaneously before (pre) and after (post) the hemofilter or else the hemoadsorber, after 5 and 30 min, as well as after 2, 4, 8 and 24 hours. All measurements were repeated the next day after the hemoadsorber had been renewed in the CytoSorb group. Primary outcome was the area under the curve of the relative myoglobin concentrations as percent of baseline (AUC). To evaluate the efficacy of myoglobin removal, relative reductions in myoglobin concentrations during one passage through of each device at each time point were calculated. Results: Patients in the CytoSorb group had a significantly lower AUC during the first 24 hours (42±10% versus 63±6%, P = 0.029) as well as during the observation period of 48 hours (26±7% versus 51±12%, P = 0.029). The relative reductions for myoglobin were considerably higher in the CytoSorb compared to the control group during the first 8 hours. Conclusion: Myoglobin concentrations declined considerably faster when CytoSorb was added to a CVVHD. When compared to a high cut-off hemofilter, efficacy of CytoSorb in myoglobin elimination was much better. Because of saturation after 8 to 12 hours an exchange may be necessary.
DOI: 10.6084/m9.figshare.27060430.v1
title: Supplementary Material for: The impact of radiation dose and tumour burden on outcomes in hepatocellular carcinoma: 11-year experience in a 413-patient cohort treated with yttrium-90 resin microsphere radioembolisation

description: Introduction
Transarterial radioembolisation (RE) using yttrium-90 (Y-90) microspheres is a widely used locoregional therapy for a broad spectrum of HCC given its favourable safety profile. We evaluated the real-world outcomes of unresectable HCC treated with resin Y-90 RE and the relationship between tumour absorbed dose and subsequent curative therapy with survival.
Methods 
Included were consecutive patients treated with Y-90 resin microspheres RE for unresectable HCC between January 2008 and May 2019 at the National Cancer Centre Singapore /Singapore General Hospital. The outcomes were stratified by tumour burden, distribution, presence of portal vein invasion (PVI) and liver function to improve prognostication. 
Results 
The median overall survival (OS) evaluated on 413 included patients was 20.9 months (95% CI 18.2 – 24.0). More than half of the patients (214/413, 51.8%) had HCC beyond up-to-seven criteria, and 37.3% had portal vein invasion (154/413, 37.3%). Majority (71.7%) had dosimetry calculated based on the partition model. Patients who received ≥150 Gy to tumour had significantly better outcomes (OS 32.2 months, 95% CI 18.3 – 46.4) than those who did not (OS 17.5 months, 95% CI 13.7 – 22.7, p &lt; 0.001). Seventy patients (17%) received curative therapies after tumour was downstaged by Y-90 RE and had better OS of 79.7 months (95% CI 40.4 – NE) compared to those who did not receive curative therapies (OS 17.1 months; 95% CI 13.5 – 20.4, p &lt; 0.001). Radioembolisation-induced liver injury was observed in 5.08% of the patients while 3.2% of the patients had possible radiation pneumonitis but none developed Grade 3-4 toxicity. For HCC without PVI, overall survival differed significantly with performance status, ALBI grade, tumour distribution, and radiation dose; for HCC with PVI, Child-Pugh class and AFP were significant predictors of survival. 
Conclusions 
Treatment outcomes for unresectable HCC using Y-90 RE were favourable. Incorporating tumour burden and distribution improved prognostication. Patients who received tumour absorbed dose above 150 Gy had better OS. Patients who subsequently received curative therapies after being downstaged by Y-90 RE had remarkable clinical outcomes.
DOI: 10.6084/m9.figshare.26726252.v1
title: Additional file 3 of Integrating uterine microbiome and metabolome to advance the understanding of the uterine environment in dairy cows with metritis

description: Supplementary Material 3
DOI: 10.6084/m9.figshare.902845_d1
title: Dengue_Occurrence_12122013.xlsx

description: A global geographic database of human dengue virus occurrence. The database comprises occurrence data linked to point or polygon locations, derived from peer-reviewed literature and case reports as well as informal online sources. Entries date from 1960 to 2012.
OCCURRENCE_ID: Unique identifier for each occurrence in the database after temporal and locational standardisation.
SOURCE_TYPE: Manual entry vs. HealthMap
LOCATION_TYPE: Whether the record represents a point or a polygon location
ADMIN_LEVEL: The administrative level which the record represents when the location type is a polygon. Values are 0 (national), 1 (state or province), 2 (district), and -999 when the location type is a point.
GAUL_AD0: The country-level global administrative unit layer (GAUL) code (see http://www.fao.org/geonetwork) which identifies the Admin-0 level occurrences as well as the Admin-0 polygon within which any smaller polygons and points lie.
GAUL_AD1: The first-level GAUL code which identifies the Admin-1 level occurrences as well as the Admin-1 polygon within which any smaller polygons and points lie. Values of -999 are assigned when the polygon was Admin-0 level.
GAUL_AD2: The second-level GAUL code which identifies the Admin-2 level occurrences as well as the Admin-2 polygon within which any points lie. Values of -999 are assigned when the polygon was Admin-0 or Admin-1 level.
POINT_ID: The unique identifier which was assigned to points falling within the same 5km x 5km pixel.
UNIQUE_LOCATION: A unique identifier created for all locations (both points and polygons) based upon the point IDs and the GAUL codes.
X: The longitudinal coordinate of the point or polygon centroid (WGS1984 Datum).
Y: The latitudinal coordinate of the point or polygon centroid (WGS1984 Datum).
YEAR: The year of the occurrence.
COUNTRY: The name of the country within which the occurrence lies.
REGION: The region within which the occurrence lies – values are Asia, Oceania (includes Australia), Africa (includes the Arabian peninsula), and Americas.