cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.8230874.v1
title: Supplementary Material for: Environmental Factors and the Risk of Brain Tumours in Young People: A Systematic Review

description: <b><i>Background:</i></b> Brain tumours (BT) are one of the most frequent tumour types in young people, although little is known about their risk factors. <b><i>Objective:</i></b> The objective of the current work was to review and summarize the scientific literature concerning exposure to environmental factors and BT risk in young people (&lt;25 years old). <b><i>Methods:</i></b> PUBMED, Embase, Cochrane Library, Scopus, IME-Biomedina (bibliographic database of Consejo Superior de Investigaciones Científicas) and Web of science databases were searched. A score to assess the quality of the methodological information was created. <b><i>Results:</i></b> Some possible associations between BT risk in young people were reported for cadmium, consumption of well water, presence of nitrate or nitrate-nitrogen in tap water, mother’s passive smoking, air pollution, parental handling of pesticides at home and/or professional pesticide treatment within houses, living on a farm and/or with farm animals, some parental occupations and high amount of meat consumption. <b><i>Conclusions:</i></b> Although many of the studies reviewed suggest associations between the environmental exposures and BT in children and young adults, at present no reliable conclusion can be drawn as most results are based on small number of cases and exposure assessment is limited. Large-scale studies with better exposure assessment are needed to shed light on these possible associations, especially on exposure to heavy metals, tab water consumption, pesticides and parental smoking.
DOI: 10.6084/m9.figshare.8230787.v1
title: Magmatic sulphides in high-K calc-alkaline to shoshonitic and alkaline rocks

description: The uploaded supplementary material corresponds to the following data: Table S1: major element whole rock XRF analysis, Table S2: trace element whole rock XRF analysis,Table S3: trace element LA-ICP-MS analysis,<br>Table S4: Microprobe-EPMA sulphide analysis and Table S5: Reconstructed sulphide area % bulk composition.<br>
DOI: 10.6084/m9.figshare.8230766
title: TestData

description: Data of wind speed and temperature in Dublin is provided.
DOI: 10.6084/m9.figshare.8230766.v1
title: TestData

description: Data of wind speed and temperature in Dublin is provided.
DOI: 10.6084/m9.figshare.8230655
title: Lopes et al., A refinement to the formalin test in mice - Extended data

description: The spreadsheets refer to the Figures in the manuscript.
DOI: 10.6084/m9.figshare.8230685
title: HDX Workbench Export Data

description: Data export files from the HDX software HDX Workbench in support of the publication "<b>HDX-MS reveals structural determinants for RORγ hyperactivation by synthetic agonists"</b>
DOI: 10.6084/m9.figshare.8230655.v1
title: Lopes et al., A refinement to the formalin test in mice - Extended data

description: The spreadsheets refer to the Figures in the manuscript.
DOI: 10.6084/m9.figshare.8230655.v3
title: Lopes et al., A refinement to the formalin test in mice - Extended data

description: The spreadsheets refer to the Figures in the manuscript.
DOI: 10.6084/m9.figshare.8230547
title: Supplementary Material for: Comparison of Skin Structural and Functional Parameters in Well-Nourished and Moderately Undernourished Infants

description: <b><i>Background:</i></b> Little is known about the impact of nutrition on the development of skin structure and function in infants. <b><i>Methods:</i></b> We investigated epidermal, dermal, and subcutis parameters of aged-matched well-nourished and moderately undernourished infants in this single-center, cross-sectional, noninterventional study using noninvasive methods (skin caliper, 20-MHz sonography, transepidermal water loss, skin pH, and corneometry). Plasma fatty acids were determined as an indicator of nutritional differences. 310 infants from different age groups, i.e., 1 week, 4 weeks, and 6, 9, 12, 24, and 36 months were included. Approximately half of each age group was well-nourished (WHO reference values weight-for-height/length <i>Z</i>score: –0.75 ≤ <i>Z</i> ≤ 0.75) and the other half was moderately undernourished (–3 ≤ <i>Z</i> &lt; –2). <b><i>Results:</i></b> Structural maturational differences in the deeper dermis and subcutis regions of the skin and subtle functional changes in the epidermis were observed in moderately undernourished infants without notable clinical symptoms. Reduced skin barrier function or skin hydration were not observed in the undernourished infants, and skin pH shifted to more acidic values in this group. <b><i>Conclusion:</i></b> These findings reveal a greater impact of moderate undernutrition on the development of the dermis and subcutis and suggest that critical epidermal functions such as skin barrier and pH are mostly maintained.
DOI: 10.6084/m9.figshare.8230655.v2
title: Lopes et al., A refinement to the formalin test in mice - Extended data

description: The spreadsheets refer to the Figures in the manuscript.
DOI: 10.6084/m9.figshare.8230547.v1
title: Supplementary Material for: Comparison of Skin Structural and Functional Parameters in Well-Nourished and Moderately Undernourished Infants

description: <b><i>Background:</i></b> Little is known about the impact of nutrition on the development of skin structure and function in infants. <b><i>Methods:</i></b> We investigated epidermal, dermal, and subcutis parameters of aged-matched well-nourished and moderately undernourished infants in this single-center, cross-sectional, noninterventional study using noninvasive methods (skin caliper, 20-MHz sonography, transepidermal water loss, skin pH, and corneometry). Plasma fatty acids were determined as an indicator of nutritional differences. 310 infants from different age groups, i.e., 1 week, 4 weeks, and 6, 9, 12, 24, and 36 months were included. Approximately half of each age group was well-nourished (WHO reference values weight-for-height/length <i>Z</i>score: –0.75 ≤ <i>Z</i> ≤ 0.75) and the other half was moderately undernourished (–3 ≤ <i>Z</i> &lt; –2). <b><i>Results:</i></b> Structural maturational differences in the deeper dermis and subcutis regions of the skin and subtle functional changes in the epidermis were observed in moderately undernourished infants without notable clinical symptoms. Reduced skin barrier function or skin hydration were not observed in the undernourished infants, and skin pH shifted to more acidic values in this group. <b><i>Conclusion:</i></b> These findings reveal a greater impact of moderate undernutrition on the development of the dermis and subcutis and suggest that critical epidermal functions such as skin barrier and pH are mostly maintained.
DOI: 10.6084/m9.figshare.8230535
title: Supplementary Material for: Developing and Testing Electronic Health Record-Derived Caries Indices

description: Caries indices, the basis of epidemiologic caries measures, are not easily obtained in clinical settings. This study’s objective was to design, test, and validate an automated program (Valid Electronic Health Record Dental Caries Indices Calculator Tool [VERDICT]) to calculate caries indices from an electronic health record (EHR). Synthetic use case scenarios and actual patient cases of primary, mixed, and permanent dentition, including decayed, missing, and filled teeth (DMFT/dmft) and tooth surfaces (DMFS/dmfs) were entered into the EHR. VERDICT measures were compared to a previously validated clinical electronic data capture (EDC) system and statistical program to calculate caries indices. Four university clinician-researchers abstracted EHR caries exam data for 45 synthetic use cases into the EDC and post-processed with SAS software creating a gold standard to compare the ­VERDICT-derived caries indices. Then, 2 senior researchers abstracted EHR caries exam data and calculated caries indices for 24 patients, allowing further comparisons to VERDICT indices. Agreement statistics were computed among abstractors, and discrepancies were resolved by consensus. Agreement statistics between the 2 final-phase abstractors and the VERDICT measures showed extremely high concordance: Lin’s concordance coefficients (LCCs) &gt;0.99 for dmfs, dmft, DS, ds, DT, dt, ms, mt, FS, fs, FT, and ft; LCCs &gt;0.95 for DMFS and DMFT; and LCCs of 0.92–0.93 for MS and MT. Caries indices, essential to developing primary health outcome measures for research, can be reliably derived from an EHR using VERDICT. Using these indices will enable population oral health management approaches and inform quality improvement efforts.
DOI: 10.6084/m9.figshare.8230541
title: Draft genomes of female and male turbot (Scophthalmus maximus)

description: Turbot (<i>Scophthalmus maximus</i>) is a commercially important species and is among the most produced flatfish in aquaculture. It has a drastic sexual dimorphism where females are larger. We sequenced and de novo assembled female and male genomes in the present study. Female_evm.gff3 is the annotation gff3 file of the female turbot’s assembled genome. turbot_Orthogroups.tsv is a list of the gene families generated in your analysis. turbot_TE.denovo.gff and turbot_TE.homo.gffare the repeat annotations.
DOI: 10.6084/m9.figshare.8230532
title: Supplementary Material for: Fast Feedback Inhibition of Adrenocorticotropic Hormone Secretion by Endogenous Cortisol in Humans

description: <b><i>Background:</i></b> Using high-frequency blood sampling, we demonstrate glucocorticoid fast feedback (FF) mediated by endogenous cortisol in 6 normal humans. <b><i>Methods:</i></b> We stimulated adrenocorticotropic hormone (ACTH) secretion by ovine corticotropin-releasing hormone (oCRH) with the experimental paradigm in which a high-frequency blood sampling was designed for plasma ACTH and cortisol determinations. <b><i>Results:</i></b> We saw previously unrecognized variability in the timing of key events such as onsets of ACTH and cortisol secretion, onset and offset of FF, and in FF duration. This variability mandated analyses referenced to case-wise event times rather than referenced simply to time since oCRH administration. The mean time of FF onset was 4.0 min (range 0–9; median 3) after cortisol secretion began, and the mean FF duration was 7.5 min (range 3–18; median 6.0). The FF effect was rate-sensitive and does not reflect level-sensitive cortisol feedback. In agreement with previous estimates using hydrocortisone infusions, the rate of rise of cortisol that triggered FF was approximately 44 nmol/L/min or 1.6 µg/dL/min. FF onset followed the trigger cortisol slope with an average lag of 1 min (range 0–3; median 0). Unexpectedly, this trigger cortisol slope quickly declined within the FF period. <b><i>Conclusions:</i></b> This experimental design may enable new physiological studies of human FF that is mediated by endogenous cortisol, including mechanisms, reproducibility, and generalizability to other activating stimuli.
DOI: 10.6084/m9.figshare.8230541.v2
title: Draft genomes of female and male turbot (Scophthalmus maximus)

description: Turbot (<i>Scophthalmus maximus</i>) is a commercially important species and is among the most produced flatfish in aquaculture. It has a drastic sexual dimorphism where females are larger. We sequenced and de novo assembled female and male genomes in the present study. Female_evm.gff3 is the annotation gff3 file of the female turbot’s assembled genome. turbot_Orthogroups.tsv is a list of the gene families generated in your analysis. turbot_TE.denovo.gff and turbot_TE.homo.gffare the repeat annotations.
DOI: 10.6084/m9.figshare.8230529
title: Supplementary Material for: Lobar Quantification by Ventilation/Perfusion SPECT/CT in Patients with Severe Emphysema Undergoing Lung Volume Reduction with Endobronchial Valves

description: <b><i>Background:</i></b> Endoscopic lung volume reduction (ELVR) therapy using one-way valves is used to treat chronic obstructive pulmonary disease patients with severe heterogeneous emphysema. A successful treatment results in atelectasis of the treated pulmonary lobe with subsequent reduction of ventilation (V) and perfusion (Q). <b><i>Objective:</i></b> We evaluated the effects of ELVR on the targeted lobe using a new 3-dimensional ventilation and perfusion (V/Q) single-photon emission computed tomography (SPECT)/computed tomography (CT) analysis, which allows for simultaneous semi-automatic lobar pulmonary quantification of volume, ventilation and perfusion, on the first consecutive patients treated with ELVR at Rigshospitalet, Denmark. V/Q planar scintigraphy and V/Q SPECT/CT and lung function measurements were performed before and 6 months after intervention. <b><i>Results:</i></b> We included 24 subjects (60 years, range 46–74 years; 37.5% men) with a baseline FEV<sub>1</sub> of 25% predicted and RV of 257% predicted. V/Q SPECT/CT-assessed volume of the targeted lobe decreased by a mean of –395 mL and a relative mean of –26.8%, whilst ventilation and perfusion decreased by a relative mean of –37.1 and –25.7%. There was a significant increase in the same parameters of the non-targeted lobe(s) on the ipsilateral side. None of these changes were found in the analysis of planar V/Q imaging. The total lung volume decreased on average by –420 mL. Six months after ELVR, FEV<sub>1</sub> had increased by 22%. Significant correlations were found between changes in FEV<sub>1</sub> and changes in the volume of the treated lobe (SPECT/CT). <b><i>Conclusion:</i></b> Semi-automatic SPECT/CT analysis can quantify volume, ventilation and perfusion changes in pulmonary lobes and may be used in the assessment of patient eligibility for ELVR, identifying target lobes, and evaluation of the regional effects of treatment.
DOI: 10.6084/m9.figshare.8230532.v1
title: Supplementary Material for: Fast Feedback Inhibition of Adrenocorticotropic Hormone Secretion by Endogenous Cortisol in Humans

description: <b><i>Background:</i></b> Using high-frequency blood sampling, we demonstrate glucocorticoid fast feedback (FF) mediated by endogenous cortisol in 6 normal humans. <b><i>Methods:</i></b> We stimulated adrenocorticotropic hormone (ACTH) secretion by ovine corticotropin-releasing hormone (oCRH) with the experimental paradigm in which a high-frequency blood sampling was designed for plasma ACTH and cortisol determinations. <b><i>Results:</i></b> We saw previously unrecognized variability in the timing of key events such as onsets of ACTH and cortisol secretion, onset and offset of FF, and in FF duration. This variability mandated analyses referenced to case-wise event times rather than referenced simply to time since oCRH administration. The mean time of FF onset was 4.0 min (range 0–9; median 3) after cortisol secretion began, and the mean FF duration was 7.5 min (range 3–18; median 6.0). The FF effect was rate-sensitive and does not reflect level-sensitive cortisol feedback. In agreement with previous estimates using hydrocortisone infusions, the rate of rise of cortisol that triggered FF was approximately 44 nmol/L/min or 1.6 µg/dL/min. FF onset followed the trigger cortisol slope with an average lag of 1 min (range 0–3; median 0). Unexpectedly, this trigger cortisol slope quickly declined within the FF period. <b><i>Conclusions:</i></b> This experimental design may enable new physiological studies of human FF that is mediated by endogenous cortisol, including mechanisms, reproducibility, and generalizability to other activating stimuli.
DOI: 10.6084/m9.figshare.8230541.v1
title: female_evm.gff3

description: Turbot (<i>Scophthalmus maximus</i>) is a commercially important species and is among the most produced flatfish in aquaculture. It has a drastic sexual dimorphism where females are larger. We sequenced and de novo assembled female and male genomes in the present study.
DOI: 10.6084/m9.figshare.8230526
title: Supplementary Material for: Sexual Dimorphism of a Genetic Risk Score for Obesity and Related Traits among Chinese Patients with Type 2 Diabetes

description: <b><i>Background:</i></b> Obesity is more prevalent in men than in women in China, especially within the middle-aged population. <b><i>Objectives:</i></b> The present study aims to determine the contribution of sexual dimorphisms to obesity and related traits in terms of the mechanisms involving the obesity-related genetic variants among patients of Chinese Han ancestry with type 2 diabetes. <b><i>Method:</i></b> In the Chinese National Diabetes and Metabolic Disorders Study, 2,555 out of 4,036 patients with type 2 diabetes were treatment naive, including 1,142 men and 1,413 women. Single-nucleotide polymorphisms (SNP) from 18 genomic loci previously found to be associated with obesity-related traits were successfully genotyped, and a genetic risk score (GRS) was constructed by summing the risk alleles for obesity. <b><i>Results:</i></b> Single SNP analysis showed that genetic variants in <i>SLC30A10,</i> <i>TMEM18, GNPDA2,</i> <i>PRL,</i> <i>TFAP2B,</i> <i>BDNF,</i> <i>MTCH2,</i> <i>FTO,</i> and <i>MC4R</i> were nominally associated with waist circumference (WC), BMI, and risk for abdominal or general obesity in the untreated patients with type 2 diabetes, as well as in the total group of patients with type 2 diabetes (untreated and treated) (<i>p</i> &lt; 0.05). Interactions between sex and SNP in <i>PRL,</i> <i>MTCH2,</i>and <i>FTO</i> were detected (<i>p</i> &lt; 0.05). In the untreated patients with diabetes, the GRS was nominally associated with WC (β = 0.0032, SE = 0.0011; <i>p</i> = 0.003), BMI (β = 0.0030, SE = 0.0013; <i>p</i> = 0.027), and increased risk for abdominal (OR = 1.08; 95% CI 1.02–1.13; <i>p</i> = 0.004) or general obesity (OR = 1.07; 95% CI 1.02–1.13; <i>p</i> = 0.011) in men but not in women. GRS-sex interactions were detected in the determinant of WC (<i>p</i> = 0.019) and abdominal obesity (<i>p</i> = 0.016). Among patients aged 30–60 years, GRS was found to be significantly associated with WC (β = 0.0050, SE = 0.0016; <i>p</i> = 0.002) and abdominal obesity (OR = 1.10; 95% CI 1.04–1.17; <i>p</i> = 0.001) and nominally associated with BMI (β = 0.0057, SE = 0.0020; <i>p</i> = 0.005) and general obesity (OR = 1.07; 95% CI 1.01–1.14; <i>p</i> = 0.027) in men, whereas in women none of the associations were detected. GRS-sex interactions were present in the determinant of WC (<i>p</i> = 0.015), BMI (<i>p</i> = 0.032), and abdominal obesity (<i>p</i> = 0.012). Among patients aged 60 years or older, neither an association of GRS with obesity-related traits nor GRS-sex interactions were detected. <b><i>Conclusions:</i></b> Genetic factors contribute to obesity-related traits in a sex-dependent pattern among middle-aged Chinese, and men tend to be more susceptible to the genetic risk of obesity.
DOI: 10.6084/m9.figshare.8230517
title: Supplementary Material for: Age-Related Oxidative Changes in Primary Porcine Fibroblasts Expressing Mutated Huntingtin

description: <b><i>Background:</i></b> Huntington’s disease (HD) is a devastating neurodegenerative disorder caused by CAG triplet expansions in the huntingtin gene. Oxidative stress is linked to HD pathology, although it is not clear whether this is an effect or a mediator of disease. The transgenic (TgHD) minipig expresses the N-terminal part of human-mutated huntingtin and represents a unique model to investigate therapeutic strategies towards HD. A more detailed characterization of this model is needed to fully utilize its potential. <b><i>Methods:</i></b> In this study, we focused on the molecular and cellular features of fibroblasts isolated from TgHD minipigs and the wild-type (WT) siblings at different ages, pre-symptomatic at the age of 24–36 months and with the onset of behavioural symptoms at the age of 48 months. We measured oxidative stress, the expression of oxidative stress-related genes, proliferation capacity along with the expression of cyclin B1 and D1 proteins, cellular permeability, and the integrity of the nuclear DNA (nDNA) and mitochondrial DNA in these cells. <b><i>Results:</i></b> TgHD fibroblasts isolated from 48-month-old animals showed increased oxidative stress, which correlated with the overexpression of <i>SOD2</i> encoding mitochondrial superoxide dismutase 2, and the <i>NEIL3</i> gene encoding DNA glycosylase involved in replication-associated repair of oxidized DNA. TgHD cells displayed an abnormal proliferation capacity and permeability. We further demonstrated increased nDNA damage in pre-symptomatic TgHD fibroblasts (isolated from animals aged 24–36 months). <b><i>Conclusions:</i></b> Our results unravel phenotypic alterations in primary fibroblasts isolated from the TgHD minipig model at the age of 48 months. Importantly, nDNA damage appears to precede these phenotypic alterations. Our results highlight the impact of fibroblasts from TgHD minipigs in studying the molecular mechanisms of HD pathophysiology that gradually occur with age.
DOI: 10.6084/m9.figshare.8230520
title: Supplementary Material for: Low Platelet Counts at Diagnosis Predict Better Survival for Patients with Intermediate-Risk Acute Myeloid Leukemia

description: <b><i>Background:</i></b> Aggressive growth of primitive and immature cells in the bone marrow results in reductions in megakaryocyte and platelet (PLT) counts, leading to thrombocytopenia in acute myeloid leukemia (AML). However, not all AML patients show thrombocytopenia at the time of diagnosis, and the association of PLT count with patient survival is largely unknown. <b><i>Methods:</i></b> A retrospective study was performed to determine PLT counts at diagnosis in the peripheral blood in 291 newly diagnosed AML patients and assess the association of PLT counts with the overall survival (OS) and disease-free survival (DFS) of these patients. <b><i>Results:</i></b> Low PLT counts (≤40 × 10<sup>9</sup>/L) were associated with better outcomes for the whole cohort (5-year OS, 55.1 ± 3.8 vs. 35.3 ± 3.5%, <i>p</i> &lt; 0.001; 5-year DFS, 49.1 ± 3.8 vs. 25.7 ± 4.0%, <i>p</i> &lt; 0.001) and intermediate-risk patients (5-year OS, 64.5 ± 5.4 vs. 41.0 ± 4.8%, <i>p</i> &lt; 0.001; 5-year DFS, 60.8 ± 5.6 vs. 28.6 ± 5.6%, <i>p</i> &lt; 0.001). Moreover, low PLT counts were related to deeper molecular remission. Low PLT counts correlated with better survival of intermediate-risk AML patients treated with chemotherapy only. Allogeneic hematopoietic stem cell transplantation attenuated the negative impact of high PLT counts on the survival of intermediate-risk patients. Furthermore, univariate and multivariate analyses demonstrated that PLT count at diagnosis was an independent prognostic factor for intermediate-risk AML. <b><i>Conclusion:</i></b> PLT count at diagnosis predicts survival for patients with intermediate-risk AML.