cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.10653857
title: Article Data for 18 mixtures.zip

description: The data include the experimental VLE data of mixtures and the predicted results of models. For the mixture densities, experimental data and corresponding predictions are also listed in the Excel.
DOI: 10.6084/m9.figshare.10653830
title: Supplementary Material for: Development of a Novel Inflammation-Based Index for Hepatocellular Carcinoma

description: <b><i>Background:</i></b> The aim of current study was to (1) construct and validate a novel hepatocellular carcinoma (HCC)-specific inflammatory index; (2) compare the performances of the Integrated Liver Inflammatory Score (ILIS) to existing 4 inflammatory indices in HCC; (3) explore the association between the inflammatory indices and systemic/intratumoral inflammatory markers. <b><i>Methods:</i></b> Two cohorts from Hong Kong (HK; <i>n</i> = 1,315) and Newcastle (<i>n</i> = 574) were studied. A novel index was constructed from the HK training set (<i>n</i> = 627). The index was constructed from the training set by combing independent prognostic circulating parameters, followed by validating in the validation set of HK cohort (<i>n</i> = 688) and the Newcastle cohort. Its prognostic performance was compared to 4 inflammatory indices, namely, the neutrophil to lymphocyte ratio, platelet-to-lymphocyte ratio, prognostic nutrition index, and systemic immune-inflammation index, were compared in the HK cohort. Circulating cytokines and intratumoral gene expression were analyzed in a subset of patients with available samples and correlated with the inflammatory indices. <b><i>Results:</i></b> In the training set of the HK cohort, the ILIS, was generated: –0.057 × albumin (g/L) + 0.978 × log (Bilirubin, µmol/L) + 1.341 × log (alkaline phosphatase, IU/L) + 0.086 × Neutrophil (10<sup>9</sup>/L) + 0.301 × log (alpha-fetoprotein, µg/L). With cutoff of 2.60 and 3.87, the ILIS could categorize patients into 3 risk groups in the both validation cohorts. ILIS outperforms other inflammatory indices and remains an independent prognosticator for overall survival after adjustment with Barcelona Clinic Liver Cancer (hazard ratio 31.90, <i>p</i> &lt; 0.001). The ILIS had the best prognostic performances as compared to other inflammatory indices. In exploratory analyses, the ILIS correlated with circulating inflammatory cytokines (e.g., IL-8) but not with any intratumoral inflammatory gene expression. <b><i>Conclusions:</i></b> ILIS is an HCC-specific prognostic index built on 5 readily available blood parameters. Its versatility is validated both Eastern and Western population of HCC. The score is correlated with levels of circulating cytokines.
DOI: 10.17632/6ngrrxcsv8.1
title: SATIN - Sains dan Teknologi Informasi

description: SATIN - Sains dan Teknologi Informasi adalah Jurnal Lembaga Penelitian dan Pengabdian kepada Masyarakat (LPPM) STMIK-AMIK Riau.
DOI: 10.6084/m9.figshare.10648976
title: Supplementary Material for: Age-Related Serum Thyroid-Stimulating Hormone Reference Range in Older Patients Treated with Levothyroxine: A Randomized Controlled Feasibility Trial (SORTED 1)

description: <b><i>Introduction:</i></b> Serum thyroid-stimulating hormone (TSH) increases with age but target TSH is similar in younger and older hypothyroid patients on treatment. It is unknown if quality of life (QoL), hypothyroid symptoms and cardiovascular risk factors change in older hypothyroid patients treated to an age-appropriate reference range. <b><i>Objective:</i></b> To assess if a higher target serum TSH of 4.01–8.0 mU/L is feasible in, and acceptable to, older treated hypothyroid patients. <b><i>Methods:</i></b> A single-blind (participant) randomised controlled feasibility trial involving 48 hypothyroid patients aged ≥80 years on established and stable levothyroxine (LT4) therapy with serum TSH levels within the standard reference range (0.4–4.0 mU/L) was conducted. Standard (0.4–4.0 mU/L) or higher (4.1–8.0 mU/L) TSH target (standard TSH [ST] or higher TSH [HT] groups) LT4 for 24 weeks was administered. The outcome measures evaluated were thyroid function tests, QoL, hypothyroid symptoms, cardiovascular risk factors and serum marker of bone resorption in participants that completed the trial (<i>n</i> = 21/24 ST group, <i>n</i> = 19/24 HT group). <b><i>Results:</i></b> At 24 weeks, in the ST and HT groups, respectively, median (interquartile range) serum TSH was 1.25 (0.76–1.72) and 5.50 (4.05–9.12) mU/L, mean (± SD) free thyroxine (FT4) was 19.4 ± 3.5 and 15.9 ± 2.4 pmol/L, and daily LT4 dose was 82.1 ± 26.4 and 59.2 ± 23.9 µg. There was no suggestion of adverse impact of a higher serum TSH in the HT group with regard to any of the outcomes assessed. <b><i>Conclusions:</i></b> In hypothyroid patients aged ≥80 years on LT4 therapy for 24 weeks, there was no evidence that a higher target serum TSH was associated with an adverse impact on patient reported outcomes, cardiovascular risk factors or bone resorption marker over 24 weeks. Longer-term trials assessing morbidity and mortality outcomes and health-utility in this age group are feasible and should be performed.
DOI: 10.6084/m9.figshare.10646693
title: Downregulation of miR-193a-3p is involved in the pathogenesis of hepatocellular carcinoma by targeting CCND1 Peer J #40214

description: 1.The detail results of dual luciferase reporter experiments.txt2.The details of KEGG and GO analyses.xlsx3. Expression levels of miR-193a-3p and CCND1 in TCGA database and qRT-PCR in house
DOI: 10.17632/zxb5vhjrf5.1
title: Proteomic datasets of milk extracellular vesicles obtained from bovine leukemia virus-infected cattle

description: These datasets contain the identified proteins in milk extracellular vesicles from bovine leukemia virus-infected cattle by using a comprehensive proteomic analysis nanoLC-MS/MS method.
DOI: 10.6084/m9.figshare.10646693.v1
title: Downregulation of miR-193a-3p is involved in the pathogenesis of hepatocellular carcinoma by targeting CCND1

description: 1.The detail results of dual luciferase reporter experiments.txt2.The details of KEGG and GO analyses.xlsx3. Expression levels of miR-193a-3p and CCND1 in TCGA database and qRT-PCR in house
DOI: 10.17632/xv3kdy7r6k.4
title: PHND: Pashtu Handwritten Numerals Dataset

description: We introduce a real Pashtu handwritten numerals dataset (PHND) having 50, 000 scanned images and make publically available for research and scientific use. Although more than fifty million people in the world use this language for written and oral communication, no significant efforts are devoted to the Pashtu Optical Character Recognition (POCR). We present a database which will help in devolopement of POCR.
DOI: 10.6084/m9.figshare.10636556
title: LDS2.vcf

description: VCF file derived from project.NIST.hc.snps.indels.NIST7035.vcf.A disease-associated mutation in the TGFBR2 gene (see Patient 4 in PMID:30101859) was spiked into the VCF file. The file is intended to be used to test gene prioritization software.<br>
DOI: 10.6084/m9.figshare.10636784
title: shared data for 2019 RSV article

description: Code and important intermediary results.<br>
DOI: 10.6084/m9.figshare.10636784.v1
title: shared data for 2019 RSV article

description: Code and important intermediary results.<br>
DOI: 10.6084/m9.figshare.10634699
title: Supplementary Material for: Local Surgery Improves Survival in Patients with Primary Metastatic Breast Cancer: A Population-Based Study

description: The clinical value of local surgery in the breast cancer patients with distant metastasis is still unclear. A total of 8,922 primary metastatic breast cancer patients from the Surveillance, Epidemiology, and End Results (SEER) database were analyzed in the current study. Primary outcome variables included breast cancer-specific survival (BCSS) and overall survival (OS). Among the patients, 1,724 (19.3%) who underwent surgical treatment (ST) of primary breast tumor had increased OS (<i>p</i> &lt; 0.001) and BCSS (<i>p</i> &lt; 0.001) compared with those in the nonsurgical treatment (NST) group. Multivariate analysis revealed that surgery improved survival and was an independent prognostic factor for OS (hazard ratio [HR] = 0.617; 95% confidence interval [CI], 0.562–0.676, <i>p</i> &lt; 0.001) and BCSS (HR = 0.623; 95% CI, 0.565–0.686, <i>p</i> &lt; 0.001). Further result showed that ST tended to prolong the survival of patients with 1 or 2 distant metastatic sites (<i>p</i> &lt; 0.05 for OS, <i>p</i> &lt; 0.05 for BCSS). However, no differences were found in prognostic outcomes between different surgical procedure groups (<i>p</i> = 0.886 for OS, <i>p</i> = 0.943 for BCSS). In conclusion,<b><i></i></b>our study suggested that local surgery appeared to confer a survival benefit, which may provide new understanding of treatment for these patients.
DOI: 10.6084/m9.figshare.10634699.v1
title: Supplementary Material for: Local Surgery Improves Survival in Patients with Primary Metastatic Breast Cancer: A Population-Based Study

description: The clinical value of local surgery in the breast cancer patients with distant metastasis is still unclear. A total of 8,922 primary metastatic breast cancer patients from the Surveillance, Epidemiology, and End Results (SEER) database were analyzed in the current study. Primary outcome variables included breast cancer-specific survival (BCSS) and overall survival (OS). Among the patients, 1,724 (19.3%) who underwent surgical treatment (ST) of primary breast tumor had increased OS (<i>p</i> &lt; 0.001) and BCSS (<i>p</i> &lt; 0.001) compared with those in the nonsurgical treatment (NST) group. Multivariate analysis revealed that surgery improved survival and was an independent prognostic factor for OS (hazard ratio [HR] = 0.617; 95% confidence interval [CI], 0.562–0.676, <i>p</i> &lt; 0.001) and BCSS (HR = 0.623; 95% CI, 0.565–0.686, <i>p</i> &lt; 0.001). Further result showed that ST tended to prolong the survival of patients with 1 or 2 distant metastatic sites (<i>p</i> &lt; 0.05 for OS, <i>p</i> &lt; 0.05 for BCSS). However, no differences were found in prognostic outcomes between different surgical procedure groups (<i>p</i> = 0.886 for OS, <i>p</i> = 0.943 for BCSS). In conclusion,<b><i></i></b>our study suggested that local surgery appeared to confer a survival benefit, which may provide new understanding of treatment for these patients.
DOI: 10.6084/m9.figshare.10630139
title: The impact of sample processing on inflammatory markers in serum: Lessons learned

description: <b>Objectives:</b> To investigate the effect of sample handling on inflammatory cytokines in serum and highlight challenges with using samples pre-collected from biobanks for biomarker research. <b>Methods:</b> Cytokine concentrations (IL-1β, IL-2, IL-6, IL-8, IL-10, TNFα, and IFNγ) were measured in serum samples of 205 patients with bipoldar disorder (BD) from the Mayo Clinic Bipolar Disorder Biobank and 205 non-psychiatric controls from the Mayo Clinic Biobank. As cytokine concentrations varied by recruitment site, <i>post-hoc</i> models were used to test the effect of clinical variables and pre-processing time on cytokines. To evaluate the effect of pre-processing time experimentally, cytokines were assayed in serum and plasma from 6 healthy volunteers processed at different time points. <b>Results:</b> Cytokine levels were significantly higher in the BD group. However, both cytokine levels and pre-processing times differed by recruitment site, and <i>post-hoc</i> analyses revealed that pre-processing time was significantly associated with several cytokines. An experiment using samples from healthy volunteers confirmed that concentrations for most cytokines increased with longer pre-processing times. <b>Conclusions:</b> Delays in processing influence cytokine concentrations in blood samples. Given the increasing use of biobanks in research, this study highlights the need to carefully evaluate sample collection and handling methods when designing biomarker studies.
DOI: 10.6084/m9.figshare.10630139.v1
title: The impact of sample processing on inflammatory markers in serum: Lessons learned

description: <b>Objectives:</b> To investigate the effect of sample handling on inflammatory cytokines in serum and highlight challenges with using samples pre-collected from biobanks for biomarker research. <b>Methods:</b> Cytokine concentrations (IL-1β, IL-2, IL-6, IL-8, IL-10, TNFα, and IFNγ) were measured in serum samples of 205 patients with bipoldar disorder (BD) from the Mayo Clinic Bipolar Disorder Biobank and 205 non-psychiatric controls from the Mayo Clinic Biobank. As cytokine concentrations varied by recruitment site, <i>post-hoc</i> models were used to test the effect of clinical variables and pre-processing time on cytokines. To evaluate the effect of pre-processing time experimentally, cytokines were assayed in serum and plasma from 6 healthy volunteers processed at different time points. <b>Results:</b> Cytokine levels were significantly higher in the BD group. However, both cytokine levels and pre-processing times differed by recruitment site, and <i>post-hoc</i> analyses revealed that pre-processing time was significantly associated with several cytokines. An experiment using samples from healthy volunteers confirmed that concentrations for most cytokines increased with longer pre-processing times. <b>Conclusions:</b> Delays in processing influence cytokine concentrations in blood samples. Given the increasing use of biobanks in research, this study highlights the need to carefully evaluate sample collection and handling methods when designing biomarker studies.
DOI: 10.6084/m9.figshare.10619747
title: Metadata record for: CE-QUAL-W2 model of dam outflow elevation impact on temperature, dissolved oxygen and nutrients in a reservoir

description: This dataset contains key characteristics about the data described in the Data Descriptor CE-QUAL-W2 model of dam outflow elevation impact on temperature, dissolved oxygen and nutrients in a reservoir. <br> Contents: <br> 1. human readable metadata summary table in CSV format 2. machine readable metadata file in JSON format <br> <br> Versioning Note:Version 2 was generated when the metadata format was updated from JSON to JSON-LD. This was an automatic process that changed only the format, not the contents, of the metadata.<br>
DOI: 10.6084/m9.figshare.10603835
title: The Hot and the Colorful: Understanding the Metabolism, Genetics and Evolution of Consumer Preferred Metabolic Traits in Pepper and Related Species

description: Recent advances in genomics and metabolomics have made the study of specialized metabolism far more tractable than it was previously. Here we evaluate specialized metabolite pathways of <i>Capsicum</i> spp. (peppers), focusing mainly on carotenoids, flavonoids, and capsaicinoids as examples of classes of secondary metabolites. To place these data in the context of the evolution of metabolic pathways, we compare the extent of genomic and chemical diversity in several species of the nightshades (Solanaceae), the family to which pepper belongs. We further discuss the genetic mechanisms known to underly metabolic diversity prior to carrying out a detailed genomic study of the enzymes active in the pathways influencing fruit color and pungency. Using large-scale comparative analyses across 25 sequenced plant genomes, we identify orthologs of structural metabolic genes and discuss the data in terms of variation of gene family size and its impact on the diversity of secondary metabolites. BCAA: branched-chain amino acid; K-Pg: Cretaceous-Paleogene; ROS: reactive oxygen species; TE: transposable element; WGD: whole genome duplication
DOI: 10.6084/m9.figshare.10604243
title: Helical and linear morphotypes of <i>Arthrospira</i> sp. PCC 8005 display genomic differences and respond differently to <sup>60</sup>Co gamma irradiation

description: <i>Arthrospira</i> are multicellular cyanobacteria that typically reside in alkaline lakes of (sub)tropical regions and are mass cultivated around the globe in a variety of outdoor facilities and photobioreactors for their high nutritional, pharmaceutical and clinical value. <i>Arthrospira</i> sp. strain PCC 8005 was selected by the European Space Agency as an oxygen producer and nutritional end-product in a bioregenerative life support system for long-haul missions. Being highly resistant to ionizing radiation, it is also an ideal candidate for other space applications such as <i>in situ</i> resource utilization and terraformation. During long-term strain maintenance involving continuous subculturing we noted an irreversible morphological change in PCC 8005 subcultures i.e. from only helical to only straight trichomes. These morphotypes displayed differences in growth rate, buoyancy and resistance to gamma radiation. We also found marked differences in antioxidant capacity, pigment content and trehalose concentration, while whole-genome comparison revealed a difference of 168 SNPs, 48 indels and four large insertions affecting, in total, 41 coding regions across both genomes. Although nine of these regions encoded proteins with a known function, no conclusive genotype-phenotype associations could be determined. Nonetheless, genomic changes within the <i>gvp</i>C gene (encoding a gas vesicle protein) and within the regulatory region of the <i>psb</i>D gene (encoding the D2 protein of PSII) provided some clues for the observed differences in buoyancy and growth.
DOI: 10.6084/m9.figshare.10607993
title: Supplementary Material for: Vascular White Matter Lesions in Young Adults: A Neurology Outpatient Clinic Registry

description: <b><i>Introduction:</i></b> Although frequently assumed to be age-related changes, vascular white matter lesions (WML) are sometimes found in young adults. Etiology is usually attributed to sporadic small vessel disease; nevertheless, genetic disorders may also be implicated. We aimed to characterize the population of young adults with vascular WML in Neurology outpatient clinics. <b><i>Methods:</i></b> Neurologists from 12 Portuguese hospitals were invited to include patients aged 18–55 years evaluated in consultation, with vascular WML on MRI, scoring II or III in the Fazekas scale. Central imaging validation was performed by 2 independent, blinded, Neuroradiologists. Demographic and clinical data were collected as well as results of investigations performed. <b><i>Results:</i></b> During 2 years, 77 patients were included (mean age 47.7 years). Vascular risk factors were present in 88.3% patients (hypertension in 53.2%) and previous history of stroke in 36.4%. Patients without history of stroke were younger (46.6 ± 7.2 vs. 49.6 ± 3.9 years, <i>p</i> = 0.045) and had fewer vascular risk factors (<i>p</i> &lt; 0.001). They were more frequently females (87.8 vs. 46.4%, <i>p</i> &lt; 0.001), and headache (30.6 vs. 3.6%, <i>p</i> = 0.007), contrary to focal symptoms (16.3 vs. 53.6%, <i>p</i> = 0.001), was the most frequent reason of referral. Etiological investigations performed differed between Neurologists. A genetic disorder was identified in 6 out of 58 patients (CADASIL <i>n</i> = 5; COL4A1 <i>n</i> = 1). <b><i>Conclusion:</i></b> Young adults with vascular WML evaluated in Neurology outpatient clinics concentrate in the oldest age groups. Vascular risk factors should be screened carefully in this population. Among patients without history of stroke, females largely outweigh males. Diagnostic investigations performed do not follow a standardized protocol.
DOI: 10.6084/m9.figshare.10603835.v1
title: The Hot and the Colorful: Understanding the Metabolism, Genetics and Evolution of Consumer Preferred Metabolic Traits in Pepper and Related Species

description: Recent advances in genomics and metabolomics have made the study of specialized metabolism far more tractable than it was previously. Here we evaluate specialized metabolite pathways of <i>Capsicum</i> spp. (peppers), focusing mainly on carotenoids, flavonoids, and capsaicinoids as examples of classes of secondary metabolites. To place these data in the context of the evolution of metabolic pathways, we compare the extent of genomic and chemical diversity in several species of the nightshades (Solanaceae), the family to which pepper belongs. We further discuss the genetic mechanisms known to underly metabolic diversity prior to carrying out a detailed genomic study of the enzymes active in the pathways influencing fruit color and pungency. Using large-scale comparative analyses across 25 sequenced plant genomes, we identify orthologs of structural metabolic genes and discuss the data in terms of variation of gene family size and its impact on the diversity of secondary metabolites. BCAA: branched-chain amino acid; K-Pg: Cretaceous-Paleogene; ROS: reactive oxygen species; TE: transposable element; WGD: whole genome duplication
DOI: 10.6084/m9.figshare.10607993.v1
title: Supplementary Material for: Vascular White Matter Lesions in Young Adults: A Neurology Outpatient Clinic Registry

description: <b><i>Introduction:</i></b> Although frequently assumed to be age-related changes, vascular white matter lesions (WML) are sometimes found in young adults. Etiology is usually attributed to sporadic small vessel disease; nevertheless, genetic disorders may also be implicated. We aimed to characterize the population of young adults with vascular WML in Neurology outpatient clinics. <b><i>Methods:</i></b> Neurologists from 12 Portuguese hospitals were invited to include patients aged 18–55 years evaluated in consultation, with vascular WML on MRI, scoring II or III in the Fazekas scale. Central imaging validation was performed by 2 independent, blinded, Neuroradiologists. Demographic and clinical data were collected as well as results of investigations performed. <b><i>Results:</i></b> During 2 years, 77 patients were included (mean age 47.7 years). Vascular risk factors were present in 88.3% patients (hypertension in 53.2%) and previous history of stroke in 36.4%. Patients without history of stroke were younger (46.6 ± 7.2 vs. 49.6 ± 3.9 years, <i>p</i> = 0.045) and had fewer vascular risk factors (<i>p</i> &lt; 0.001). They were more frequently females (87.8 vs. 46.4%, <i>p</i> &lt; 0.001), and headache (30.6 vs. 3.6%, <i>p</i> = 0.007), contrary to focal symptoms (16.3 vs. 53.6%, <i>p</i> = 0.001), was the most frequent reason of referral. Etiological investigations performed differed between Neurologists. A genetic disorder was identified in 6 out of 58 patients (CADASIL <i>n</i> = 5; COL4A1 <i>n</i> = 1). <b><i>Conclusion:</i></b> Young adults with vascular WML evaluated in Neurology outpatient clinics concentrate in the oldest age groups. Vascular risk factors should be screened carefully in this population. Among patients without history of stroke, females largely outweigh males. Diagnostic investigations performed do not follow a standardized protocol.
DOI: 10.6084/m9.figshare.10596530
title: DATASET Lithospheric contraction on Mars: A 3D model of the Amenthes thrust fault system.

description: Data files associated with the research article "Lithospheric contraction on Mars: A 3D model of the Amenthes thrust fault system", published in the journal JGR Planets.
DOI: 10.6084/m9.figshare.10596530.v1
title: DATASET Lithospheric contraction on Mars: A 3D model of the Amenthes thrust fault system.

description: Data files associated with the research article "Lithospheric contraction on Mars: A 3D model of the Amenthes thrust fault system", published in the journal JGR Planets.