cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.13153517.v1
title: Supplementary Material for: Surveillance for Hepatocellular Carcinoma Also Improves Survival of Incidentally Detected Intrahepatic Cholangiocarcinoma Arisen in Liver Cirrhosis

description: <b><i>Background:</i></b> Due to its poor survival, intrahepatic cholangiocarcinoma (ICC) is held to be a much more aggressive cancer than hepatocellular carcinoma (HCC). In most published series, patients were diagnosed when symptomatic. However, ICC is now increasingly being discovered during the surveillance for HCC in cirrhosis. Whether this earlier detection of ICC is associated with an equally dismal prognosis or not is unknown. <b><i>Methods:</i></b> This is amulticenter retrospective study of consecutive ICC patients. Patients were stratified into subgroups according to the absence/presence of cirrhosis. A propensity score matching was performed to reduce the potential biases. Cirrhotic patients were further stratified according to their surveillance status. The lead-time bias and its potential effects were also estimated. <b><i>Results:</i></b> We gathered 184 patients. Eighty-five patients (46.2%) were cirrhotic. Liver cirrhosis was not related to a worse overall survival (33.0 vs. 32.0 months, <i>p</i> = 0.800) even after the propensity score analysis (43.0 in vs. 44.0 months in 54 pairs of patients, <i>p</i> = 0.878). Among the cirrhotic population, 47 (55.3%) patients had received a diagnosis of ICC during a surveillance programme. The 2 subgroups differed in maximum tumour dimensions (30 vs. 48 mm in surveyed and non-surveyed patients, respectively). Surveyed patients were more likely to receive surgical treatments (59.8 vs. 28.9%, <i>p</i> = 0.003). Overall survival was higher in surveyed patients (51.0 vs. 21.0 months, <i>p</i> &lt; 0.001). These benefits were confirmed after correcting for the lead-time bias. <b><i>Conclusions:</i></b> Cirrhotic patients have different clinical presentation and outcomes of ICC according to their surveillance status. In our series, ICC in cirrhosis was not associated with worse OS. Cirrhosis itself should not discourage either surgical or non-surgical treatments.
DOI: 10.6084/m9.figshare.19086020.v1
title: Supplemental file 2. Liver-specific DE mRNAs-down

description: Supplemental file 2. Liver-specific DE mRNAs-down
DOI: 10.6084/m9.figshare.26104951.v1
title: Supplementary Material for: Clinical, genetic and pathological studies in two brothers with Stress-Induced Childhood-Onset Neurodegeneration with Variable Ataxia and Seizures (CONDSIAS) – Case report

description: Introduction: Stress-induced childhood-onset neurodegeneration with variable ataxia and seizures (CONDSIAS) is an autosomal recessive disorder caused by biallelic pathogenic variants in the ADPRS gene. Since its first description in 2018, less than fifty cases have been reported world-wide, but thus far, without histopathology of the nervous system. 
Case presentation: We summarize the clinical, paraclinical and genetic characteristics of the disease in the proband, and the pathological work up in his older brother who passed away more than a decade ago. The characteristics of CONDSIAS in the two brothers overlapped with those of Friedreich ataxia. A final clarification of the diagnosis was made possible by whole exome sequencing (WES) that identified the homozygous pathogenic variants in the ADPRS gene. 
Conclusion: CONDSIAS is a rare disorder with highly variable presentation. Based on solely clinical and even pathological work up, establishing a definite diagnosis may be challenging. In the two brothers, we observed clinical and histopathological features of the disease suggesting, though not completely fulfilling the diagnosis of Friedreich ataxia. WES allowed us to rapidly identify the underlying genetic abnormality and to make a shortcut to the right diagnosis amongst recessive ataxias. As of today, no specific treatment for CONDSIAS is available. Repurposing of certain approved modalities that also target the affected pathway in CONDSIAS recently arose, though as yet without proven success. Knowing the biological relevance of the affected gene product offers potential targets for the development of disease modifying drugs for this highly disabling disease in the near future.
DOI: 10.6084/m9.figshare.16627873.v5
title: Road-river Structures and Rivers Datasets - Wales

description: Road-river Structures Dataset - Wales (.csv file) contains structure locations determined by intersecting Ordnance Survey (OS) Open Rivers and Roads spatial datasets (used and adapted under the United Kingdom's Open Government License), types (culvert, bridge, ford), and associated river segment gradient and Strahler stream order. The X,Y coordinates in the .csv file are in the projected British National Grid.<br><br>The Rivers Dataset - Wales (shapefile in .zip) is a cleaned, value added, version of Ordnance Survey (OS) Open Rivers segments for Welsh catchments only (i.e., they don't flow into England before entering the sea). The river segments in this dataset were cleaned, and Strahler stream order generated, using Rivex 10.35. <br><br>The Rivers Dataset - Wales contains public sector information licensed under the United Kingdom's Open Government Licence v3.0.
DOI: 10.6084/m9.figshare.19561216.v12
title: Supplementary data

description: <em><strong>Supplementary datas of elemene liposome injection for the prevention and treatment of colorectal adenoma carcinogenesis based on network pharmacological analysis and experimental verification. Supplementary information: S1-S9 and Supplementary information legends (including supplementary Figures).</strong></em>
DOI: 10.6084/m9.figshare.26013553.v1
title: Supplementary Material for: Pressure-Induced Stromal Keratopathy After Surface Ablation Surgery

description: The purpose of this clinical report is to describe an unprecedented case of bilateral pressure-induced stromal keratopathy (PISK) following corneal photorefractive keratectomy (PRK), associated with presumed herpetic keratitis, and to present tomographic and biomechanical findings before and after appropriate treatment. A 33-year-old male patient was referred to our clinic with suspected delayed corneal epithelial healing three weeks after an uncomplicated PRK. A central layer of corneal opacity with a presumed fluid-filled interface area was observed upon slit-lamp biomicroscopy. Scheimpflug images from the Pentacam® revealed a hyperreflective area beneath the central cornea. Scheimpflug-based corneal tomography, biomechanical assessment using the Pentacam® AXL Wave, and the Corvis ST® were conducted. Goldmann applanation tonometry measured 23/13 mmHg, while non-contact tonometry intraocular pressure measured with the Corvis ST® (Corvis ST IOPnct) was 40.5/43.5 mmHg. Treatment with oral valacyclovir, combined with ocular hypotensive therapy, led to a significant reduction in IOP and improved corneal deformation parameters after one month. Surgeons should be aware of the inaccuracy of Goldmann applanation tonometry in pressure-induced stromal keratopathy, which can occur after LASIK or surface ablation.
DOI: 10.6084/m9.figshare.20399070.v1
title: SMISES data July 2022.dta

description: To create this dataset, sexual minority adolescents (n=186) were asked about the level of support and relevant information they received in their sex education classes.
DOI: 10.6084/m9.figshare.25816579.v1
title: Dataset_for_causal_reasoning_project.xlsx

description: Anonymized dataset for a research project.
DOI: 10.6084/m9.figshare.4307750.v1
title: NEON Teaching Data: LiDAR Point Cloud (.las) Data

description: This .las file contains sample LiDAR point cloud data collected by National Ecological Observatory Network's Airborne Observation Platform. The .las file format is a commonly used file format to store LIDAR point cloud data.<br>This teaching data set is used for several tutorials on the NEON website (neonscience.org). The dataset is for educational purposes, data for research purposes can be obtained from the NEON Data Portal (data.neonscience.org).<br><br>
DOI: 10.6084/m9.figshare.7334372.v1
title: Supplementary Material for: Microarray Profiling of TGF-β1-Induced Long Non-Coding RNA Expression Patterns in Human Lung Bronchial Epithelial BEAS-2B Cells

description: <b><i>Background/Aims:</i></b> TGF-β1 mediated radiation-induced bystander effects (RIBE) have been linked with malignant transformation and tumorigenesis. However, the underlying mechanisms are not fully understood. <b><i>Methods:</i></b> To reveal new molecules of regulatory functions in this process, lncRNA microarray was performed to profile both lncRNA and mRNA expression patterns in human lung bronchial epithelial BEAS-2B cells treated with TGF-β1 at a concentration measured in the medium conditioned by directly irradiated BEAS-2B cells. The potential functions of the differentially expressed lncRNAs were predicted by GO and KEGG pathway analyses of their co-expressed mRNAs. Cis- and trans-regulation of the lncRNAs were analyzed and the interaction networks were constructed using Cytoscape. qRT-PCR was conducted to validate the results of microarray profiling. CCK-8 assay was employed for functional validation of 3 identified lncRNAs. <b><i>Results:</i></b> 224 lncRNAs were found to be dysregulated, among which 6 lncRNAs were chosen for expression validation by qRT-PCR assay. Pathway analyses showed that differentially expressed lncRNAs are highly correlated with cell proliferation, transformation, migration, <i>etc</i>. Trans-regulation analyses showed that the differentially expressed lncRNAs most likely participate in the pathways regulated by four transcriptional factors, FOS, STAT3, RAD21 and E2F1, which have been identified to be involved in the modulation of oncogenic transformation, cell cycle progression, genomic instability, <i>etc</i>. lnc-THEMIS-2 and lnc-ITGB6-4, predicted to be regulated by STAT3 and E2F1 respectively, were found to rescue the decrease of cell viability induced by TGF-β1 treatment. <b><i>Conclusion:</i></b> Our findings suggest that the differentially expressed lncRNAs induced by TGF-β1 play crucial roles in the oncogenic transformation and tumorigenesis, which provide a better understanding of the underlying mechanisms related to tumorigensis induced by LD/LDR radiations.
DOI: 10.6084/m9.figshare.9980672.v1
title: Testing of Mobile Applications in the Wild: A Large-Scale Empirical Study on Android Apps

description: Nowadays, mobile applications (a.k.a., apps) are used by over two billion users for every type of need, including social and emergency connectivity. Their pervasiveness in today world has inspired the software testing research community in devising approaches to allow developers to better test their apps and improve the quality of the tests being developed. In spite of this research effort, we still notice a lack of empirical analyses aiming at assessing the actual quality of test cases manually developed by mobile developers: this perspective could provide evidence-based findings on the future research directions in the field as well as on the current status of testing in the wild. As such, we performed a large-scale empirical study targeting 1,780 open-source Android apps and aiming at assessing (1) the extent to which these apps are actually tested, (2) how well-designed are the available tests, and (3) what is their effectiveness. The key results of our study show that mobile developers still tend not to properly test their apps, possibly because of time to market requirements. Furthermore, we discovered that the test cases of the considered apps have a low (i) design quality, both in terms of test code metrics and test smells, and (ii) effectiveness when considering code coverage as well as assertion density.
DOI: 10.6084/m9.figshare.12881351.v1
title: CommsBio_19-1661A-Raw data.xlsx

description: Dataset is an Excel file composed of 27 compiled sets of raw data, which constitute the data for the article by Penco-Campillo et al to be published in Communications Biology in 2020.<br>
DOI: 10.6084/m9.figshare.28735973.v1
title: A near-complete telomere-to-telomere assembly and annotation of the Magnaporthe oryzae 70-15 reference genome

description: <i>Magnaporthe oryzae</i> is a devastating fungal pathogen that causes substantial yield losses in rice and other cereal crops worldwide. A high-quality genome assembly is critical for addressing challenges posed by this pathogen. However, the current widely used MG8 assembly of the <i>M. oryzae</i> strain 70-15 reference genome contains numerous gaps and unresolved repetitive regions. Here, we report a complete 44.82 Mb high-quality nuclear genome and a 35.95 kb circular mitochondrial genome for strain 70-15, generated using deep-coverage PacBio high-fidelity sequencing (HiFi) and high-resolution chromatin conformation capture (Hi-C) data. Notably, we successfully resolved one or both telomere sequences for all seven chromosomes and achieved telomere-to-telomere (T2T) assemblies for chromosomes 2, 3, 4, 6, and 7. Based on this T2T assembly, we predicted 12,100 protein-coding genes and 493 effectors. This high-quality T2T assembly represents a significant advancement in <i>M. oryzae</i> genomics and provides an enhanced reference for studies in genome biology, comparative genomics, and population genetics of this economically important plant pathogen.
DOI: 10.6084/m9.figshare.5829687.v8
title: Single-cell RNA-seq data from Smart-seq2 sequencing of FACS sorted cells (v2)

description: Gene-count tables for FACS sorted cells sequenced with Smart-Seq2 from 20 organs of 7 mice. Cells are grouped by tissue of origin.<br><br>Includes data for 53,760 cells, 44,879 of which passed a QC cutoff of at least 500 genes and 50,000 reads.<br>Cell annotations using the Cell Ontology [1] controlled vocabulary are in a separate csv.<br>This differs from v1 by renaming "Brain_Neurons" --&gt; "Brain_Non-microglia" to be consistent with the manuscript.<br><br>Update 2018-09-20: Updated annotations to latest manuscript version<br>Update 2018-02-16: Separated Diaphragm cells from Muscle cells, and Aorta cells from Heart cells.<br>Update 2018-02-20: Aorta and Heart erroneously contained Diaphragm and Muscle data, and have now been corrected.<br>Update 2018-03-09: Renamed tissues for nomenclature standards: "Colon" --&gt; "Large_Intestine" "Muscle" --&gt; "Limb_Muscle" "Mammary" --&gt; "Mammary_Gland" "Brain_Microglia" --&gt; "Brain_Myeloid" "Brain_Non-microglia" --&gt; "Brain_Non-Myeloid"Update 2018-03-22: Renamed subtissues:<br>- tissue: Heart, subtissue: ? --&gt; tissue: Heart, subtissue: Unknown- tissue: Skin, subtissue: NA --&gt; tissue: Skin, subtissue: Telogen<br>Update 2018-03-23: Removed row numbers in first column of metadata_FACS.csv<br>Update 2018-03-27: Added tissue tSNEs and cluster ids<br><br>[1] http://purl.obolibrary.org/obo/cl.owl<br>
DOI: 10.6084/m9.figshare.14258387.v3
title: Norfish 05 Irish Herring Fishery 1520-1790

description: The Irish herring fisheries were highly productive at the beginning of the sixteenth century and were one of the largest industries in Ireland at that time (Hayes, 2021). The fishery suffered a decline towards the end of the sixteenth century due to a mixture of persistent warfare, environmental change and shifts in market conditions. The fishery recovered in the seventeenth century but was severely disrupted during the 1641 Rebellion and Confederate period in Ireland. Large scale herring fishing again resumed in the later seventeenth century and continued to fluctuate over the next century, before briefly becoming one of the most productive herring fisheries in Europe in the later eighteenth century.
DOI: 10.6084/m9.figshare.21821253.v4
title: Source data file

description: This source data includes dynamics of community composition, detected metabolites in metabolomics, differentially expressed genes in transcriptomic data, abundances of different genotypes in co-culture and concentrations of AAs.
DOI: 10.6084/m9.figshare.11459931.v1
title: The impact of improving feelings of relatedness on motivation and engagement for tertiary students

description: First-year undergraduates may be particularly prone to experiencing difficulties with facilitating feelings of relatedness, due to the recent shift in educational environments (i.e. from high school to university), which may be unfamiliar. Therefore, the current study aimed to determine whether the implementation of a single pedagogical strategy, centred within the self-determination theory framework, could effectively address students’ innate need for relatedness. Specifically, informal verbal feedback was utilized to enhance teacher–student communication, where the teacher spoke with each undergraduate student individually at the start of every lesson for 1–2 minutes. A total of 243 Advanced Science undergraduates enrolled in the first-year course at the University of New South Wales, Sydney, were included in the study. Seventy-one undergraduates were enrolled in 2016, whereas 172 undergraduates were enrolled in 2017. A mixed research methodology was employed to best leverage the utility of both qualitative and quantitative data. Interestingly, the use of informal verbal feedback as a pedagogical strategy significantly improved the student’ perceptions of receiving helpful feedback to aid their learning. These findings are important as they emphasize the utility and effectiveness of implementing one new pedagogical strategy to facilitate student’ motivation, by enhancing feelings of relatedness.
DOI: 10.6084/m9.figshare.23276357.v1
title: Data for J. Appl. Phys. 133, 000000 (2023); doi: 10.1063/5.0151207

description: This repository lists data for J. Appl. Phys. 133, 000000 (2023); doi: 10.1063/5.0151207
DOI: 10.60893/figshare.adv.26940157.v1
title: Supplementary Material

description: Detailed equations
DOI: 10.6084/m9.figshare.3528719.v1
title: Appendix D. Sensitivity to increasing variability vs. longevity in randomly constructed life histories.

description: Sensitivity to increasing variability vs. longevity in randomly constructed life histories.
DOI: 10.6084/m9.figshare.1136060.v1
title: Graphml file of the parasite-parasite network (no aggregation of node names)

description: One version of the network produced by Vincent Labatut's R code.
DOI: 10.6084/m9.figshare.12200906.v1
title: Cost-utility Analysis of Screening for Diabetic Retinopathy in Japan: A Probabilistic Markov Modeling Study

description: <i>Purpose</i>: To evaluate the cost-effectiveness for a screening interval longer than 1 year detecting diabetic retinopathy (DR) through the estimation of incremental costs per quality-adjusted life year (QALY) based on the best available clinical data in Japan. <i>Methods</i>: A Markov model with a probabilistic cohort analysis was framed to calculate incremental costs per QALY gained by implementing a screening program detecting DR in Japan. A 1-year cycle length and population size of 50,000 with a 50-year time horizon (age 40–90 years) was used. Best available clinical data from publications and national surveillance data was used, and a model was designed including current diagnosis and management of DR with corresponding visual outcomes. One-way and probabilistic sensitivity analyses were performed considering uncertainties in the parameters. <i>Results</i>: In the base-case analysis, the strategy with a screening program resulted in an incremental cost of 5,147 Japanese yen (¥; US$64.6) and incremental effectiveness of 0.0054 QALYs per person screened. The incremental cost-effectiveness ratio was ¥944,981 (US$11,857) per QALY. The simulation suggested that screening would result in a significant reduction in blindness in people aged 40 years or over (−16%). Sensitivity analyses suggested that in order to achieve both reductions in blindness and cost-effectiveness in Japan, the screening program should screen those aged 53–84 years, at intervals of 3 years or less. <i>Conclusions</i>: An eye screening program in Japan would be cost-effective in detecting DR and preventing blindness from DR, even allowing for the uncertainties in estimates of costs, utility, and current management of DR.
DOI: 10.6084/m9.figshare.25608321.v1
title: Mapping and quantification quality Based on the GRCH38 reference genome and gene annotation

description: In all plots, colors represent different sequencing batches. (A) Proportion of clean reads successfully mapped to the Grch38 human reference genome. (B) Percentage of mapped reads to multiple regions (two or more) on the reference genome. (C) Proportion of reads quantified as specific transcripts based on Ensembl gene annotation. (D) Number of reads successfully quantified across entire samples.
DOI: 10.6084/m9.figshare.5129914.v1
title: Supplementary Material for: Proliferation and Migration of Peripheral Retinal Pigment Epithelial Cells Are Associated with the Upregulation of Wingless-Related Integration and Bone Morphogenetic Protein Signaling in Dark Agouti Rats

description: <b><i>Objective:</i></b> The aim of this study was to investigate the possible migration of proliferating peripheral retinal pigment epithelial (RPE) cells and their association with differential gene expressions. <b><i>Materials and Methods:</i></b> The RPE layer was obtained from the inner aspect of the eyeball of dark agouti rats (12-13 weeks old) and was mounted on glass slides. The peripheral RPE cell proliferation was evaluated using bromodeoxyuridine immunohistochemistry (n = 10). The cell migration was examined using the Dil tracer technique (n = 40) at the end of weeks 6, 10, 14 and 18. Affymetrix microarray analysis was used to investigate differential gene expressions in peripheral and central RPE cells, which was authenticated by RT-PCR using 4 RPE-specific genes (n = 10). <b><i>Results:</i></b> In this study, peripheral RPE cells divided and appeared in clusters, but equatorial and central RPE cells rarely divided. The peripheral RPE cells migrated to the central RPE region in a time-dependent manner up to the end of week 14, but not later. The microarray analysis showed the expression of 9,645 out of a total of 35,220 genes studied. Among the 9,645 genes, 573 were differentially expressed (438 were upregulated and 135 were downregulated) in peripheral RPE cells as compared to central RPE cells. Of these 573 genes, 56 were associated with signaling pathways related to the regulation of cell proliferation, including Pax6, TGFβ, BMP and Wnt, and 404 were associated with pathways of cell migration. <b><i>Conclusions:</i></b> In this study,<b> </b>peripheral RPE cells divided and migrated to the central region. This process was associated with differential gene expressions in these cells.
DOI: 10.6084/m9.figshare.5576479.v1
title: Interaction mechanism of insulin with ZnO nanoparticles by replica exchange molecular dynamics simulation

description: The interaction of ZnO nanoparticles with biological molecules such as proteins is one of the most important and challenging problems in molecular biology. Molecular dynamics (MD) simulations are useful technique for understating the mechanism of various interactions of proteins and nanoparticles. In the present work, the interaction mechanism of insulin with ZnO nanoparticles was studied. Simulation methods including MD and replica exchange molecular dynamics (REMD) and their conditions were surveyed. According to the results obtained by REMD simulation, it was found that insulin interacts with ZnO nanoparticle surface via its polar and charged amino acids. Unfolding insulin at ZnO nanoparticle surface, the terminal parts of its chains play the main role. Due to the linkage between chain of insulin and chain of disulfide bonds, opposite directional movements of N terminal part of chain A (toward nanoparticle surface) and N termini of chain B (toward solution) make insulin unfolding. In unfolding of insulin at this condition, its helix structures convert to random coils at terminal parts chains.