cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.10001114.v1
title: MOESM1 of Genetic and environmental variation impact the cuticular hydrocarbon metabolome on the stigmatic surfaces of maize

description: Additional file 1: Table S1. Abundances of all hydrocarbon constituents for silk samples from inbred lines grown in 2009 and 2010. Individual metabolite abundances (Îźmol/g dry weight) are provided for each silk extract in this study, which includes emerged and husk-encased silk extracts from 32 inbred lines evaluated at either or both 3-days and 6-days post-silk emergence in either or both the 2009 and 2010 growing seasons. A key to column headings is provided in the file.
DOI: 10.6084/m9.figshare.10001072
title: Additional file 1: of Repertoire-wide gene structure analyses: a case study comparing automatically predicted and manually annotated gene models

description: Table ST1. Data sources and used files: list of publications, download sources, and used files of all seven species; Table ST2. Auto vs. manual: counts of gene models that were subjected to manual annotation including non-coding models, as well as of OGS, MAN-ADD, MAN-SUB, AUTO, and AUTO-SUB; Table ST3. Tests: results of Bonferroni-corrected two-sample Kolmogorov-Smirnov tests and two-sample Wilcoxon tests of all combinations of the five (sub)sets given for each species and each gene structural property; Table ST4. Correlation coefficients: lists for each species and each set (AUTO, OGS, AUTO-SUB, MAN-SUB, MAN-ADD, and resampled samples 1–1000) the Spearman’s rank correlation coefficient of each of the four comparisons; Table ST5. Cuticle proteins — all v1.1: list of cuticle protein genes manually added or manually annotated in Oncopeltus fasciatus; Table ST6. Chemoreceptors — all v1.1: list of chemoreceptor genes manually added or manually annotated in Oncopeltus fasciatus; Table ST7. CP and CR KS-tests: results of (Bonferroni-corrected) two-sample Kolmogorov-Smirnov tests comparing cuticle protein (CP) and chemoreceptor (CR) gene model structure properties to OGS, MAN-ADD and each other. (XLSX 933 kb)
DOI: 10.6084/m9.figshare.10001072.v1
title: Additional file 1: of Repertoire-wide gene structure analyses: a case study comparing automatically predicted and manually annotated gene models

description: Table ST1. Data sources and used files: list of publications, download sources, and used files of all seven species; Table ST2. Auto vs. manual: counts of gene models that were subjected to manual annotation including non-coding models, as well as of OGS, MAN-ADD, MAN-SUB, AUTO, and AUTO-SUB; Table ST3. Tests: results of Bonferroni-corrected two-sample Kolmogorov-Smirnov tests and two-sample Wilcoxon tests of all combinations of the five (sub)sets given for each species and each gene structural property; Table ST4. Correlation coefficients: lists for each species and each set (AUTO, OGS, AUTO-SUB, MAN-SUB, MAN-ADD, and resampled samples 1–1000) the Spearman’s rank correlation coefficient of each of the four comparisons; Table ST5. Cuticle proteins — all v1.1: list of cuticle protein genes manually added or manually annotated in Oncopeltus fasciatus; Table ST6. Chemoreceptors — all v1.1: list of chemoreceptor genes manually added or manually annotated in Oncopeltus fasciatus; Table ST7. CP and CR KS-tests: results of (Bonferroni-corrected) two-sample Kolmogorov-Smirnov tests comparing cuticle protein (CP) and chemoreceptor (CR) gene model structure properties to OGS, MAN-ADD and each other. (XLSX 933 kb)
DOI: 10.6084/m9.figshare.10000877
title: MOESM3 of Mapping of resistance to corn borers in a MAGIC population of maize

description: Additional file 3: Table S1. A SNPs significantly associated with silking (days from sowing to silking). The significance of the association, and the variance explained by each SNP are included in the table. B SNPs significantly associated with grain yield (g plant− 1). The significance of the association, and the variance explained by each SNP are included in the table. C SNPs significantly associated with plant height (cm). The significance of the association, and the variance explained by each SNP are included in the table.
DOI: 10.6084/m9.figshare.10000877.v1
title: MOESM3 of Mapping of resistance to corn borers in a MAGIC population of maize

description: Additional file 3: Table S1. A SNPs significantly associated with silking (days from sowing to silking). The significance of the association, and the variance explained by each SNP are included in the table. B SNPs significantly associated with grain yield (g plant− 1). The significance of the association, and the variance explained by each SNP are included in the table. C SNPs significantly associated with plant height (cm). The significance of the association, and the variance explained by each SNP are included in the table.
DOI: 10.6084/m9.figshare.10000826
title: MOESM1 of Anti-inflammatory and vasculogenic conditioning of peripheral blood mononuclear cells reinforces their therapeutic potential for radiation-injured salivary glands

description: Additional file 1. a Flow cytometric analysis of M2 macrophages (CCR2-/Galectin3+) in the PI-/CD11b+ cell fraction of PBMNCs (Day 0) and E-MNCs (Day 5). CCR2-/Galectin3+ cells occupied approximately 50% of the CD11b positive cell fraction in E-MNCs. High levels of intracellular galectin 3 expression are considered essential for transcriptional activation towards M2 macrophages after M1. b Flow cytometric analysis of T helper cells (CD3+/CD4+) in the PI fraction of PBMNCs (Day 0) and E-MNCs (Day 5). CXCR4+/CXCR6− cells (Th2) were approximately 20% of the CD3- and CD4-positive T helper cell fraction of E-MNCs. Th1, CXCR3 positive cells in T helper cells; Th17, CXCR4 and CXCR6 positive cells in T helper cells. c Representative pictures of EPC-CFU (Scale bar: 100 μm) at 7 days of EPC-CFA (100×), and the right panel shows ILB4-conjugated FITC binding and AcLDL-DiI uptake of each EPC-CFU (Scale bar: 100 μm) (40×). d Percentage of endothelial stem/progenitor cell fraction (c-kit+/Sca-1+/lineage−) in PBMNCs and E-MNCs.
DOI: 10.6084/m9.figshare.10000817
title: MOESM4 of Quantitative nuclear histomorphometric features are predictive of Oncotype DX risk categories in ductal carcinoma in situ: preliminary findings

description: Additional file 4: Section S4. name list for all the extracted nuclear histomorphometric features.
DOI: 10.6084/m9.figshare.10000826.v2
title: MOESM1 of Anti-inflammatory and vasculogenic conditioning of peripheral blood mononuclear cells reinforces their therapeutic potential for radiation-injured salivary glands

description: Additional file 1. a Flow cytometric analysis of M2 macrophages (CCR2-/Galectin3+) in the PI-/CD11b+ cell fraction of PBMNCs (Day 0) and E-MNCs (Day 5). CCR2-/Galectin3+ cells occupied approximately 50% of the CD11b positive cell fraction in E-MNCs. High levels of intracellular galectin 3 expression are considered essential for transcriptional activation towards M2 macrophages after M1. b Flow cytometric analysis of T helper cells (CD3+/CD4+) in the PI fraction of PBMNCs (Day 0) and E-MNCs (Day 5). CXCR4+/CXCR6− cells (Th2) were approximately 20% of the CD3- and CD4-positive T helper cell fraction of E-MNCs. Th1, CXCR3 positive cells in T helper cells; Th17, CXCR4 and CXCR6 positive cells in T helper cells. c Representative pictures of EPC-CFU (Scale bar: 100 μm) at 7 days of EPC-CFA (100×), and the right panel shows ILB4-conjugated FITC binding and AcLDL-DiI uptake of each EPC-CFU (Scale bar: 100 μm) (40×). d Percentage of endothelial stem/progenitor cell fraction (c-kit+/Sca-1+/lineage−) in PBMNCs and E-MNCs.
DOI: 10.6084/m9.figshare.10000817.v1
title: MOESM4 of Quantitative nuclear histomorphometric features are predictive of Oncotype DX risk categories in ductal carcinoma in situ: preliminary findings

description: Additional file 4: Section S4. name list for all the extracted nuclear histomorphometric features.
DOI: 10.6084/m9.figshare.10000814
title: MOESM1 of The recombination-cold region as an epidemiological marker of recombinogenic opportunistic pathogen Mycobacterium avium

description: Additional file 1. Information of data sources used in this study.
DOI: 10.6084/m9.figshare.10000826.v1
title: MOESM1 of Anti-inflammatory and vasculogenic conditioning of peripheral blood mononuclear cells reinforces their therapeutic potential for radiation-injured salivary glands

description: Additional file 1. a Flow cytometric analysis of M2 macrophages (CCR2-/Galectin3+) in the PI-/CD11b+ cell fraction of PBMNCs (Day 0) and E-MNCs (Day 5). CCR2-/Galectin3+ cells occupied approximately 50% of the CD11b positive cell fraction in E-MNCs. High levels of intracellular galectin 3 expression are considered essential for transcriptional activation towards M2 macrophages after M1. b Flow cytometric analysis of T helper cells (CD3+/CD4+) in the PI fraction of PBMNCs (Day 0) and E-MNCs (Day 5). CXCR4+/CXCR6− cells (Th2) were approximately 20% of the CD3- and CD4-positive T helper cell fraction of E-MNCs. Th1, CXCR3 positive cells in T helper cells; Th17, CXCR4 and CXCR6 positive cells in T helper cells. c Representative pictures of EPC-CFU (Scale bar: 100 μm) at 7 days of EPC-CFA (100×), and the right panel shows ILB4-conjugated FITC binding and AcLDL-DiI uptake of each EPC-CFU (Scale bar: 100 μm) (40×). d Percentage of endothelial stem/progenitor cell fraction (c-kit+/Sca-1+/lineage−) in PBMNCs and E-MNCs.
DOI: 10.6084/m9.figshare.10000814.v1
title: MOESM1 of The recombination-cold region as an epidemiological marker of recombinogenic opportunistic pathogen Mycobacterium avium

description: Additional file 1. Information of data sources used in this study.
DOI: 10.6084/m9.figshare.10000799
title: MOESM1 of Quantitative nuclear histomorphometric features are predictive of Oncotype DX risk categories in ductal carcinoma in situ: preliminary findings

description: Additional file 1: Section S1. Continuous ODx DCIS risk scores for each individual patients involved in D1.
DOI: 10.6084/m9.figshare.10000790
title: MOESM2 of Risk factors for Blastocystis infection in HIV/AIDS patients with highly active antiretroviral therapy in Southwest China

description: Additional file 2. The sequence of Blastocystis in this study.
DOI: 10.6084/m9.figshare.10000778
title: Binding of cloned Cel enzymes on clay minerals related to the pI of the enzymes and database survey of cellulases of soil bacteria for pI

description: The <i>Cel</i> genes from <i>Bacillus licheniformis</i> MSB03 were cloned and expressed to investigate binding ability on clay minerals and sea sand at pH ranging 3 to 9. FTIR analysis has been done to characterize bound enzymes on clay minerals. Subsequent, surveying of NCBI database for extracellular enzymes of soil bacteria was carried out. Among the five cloned Cel enzymes assayed for binding to clay minerals, only Cel5H enzyme had the binding ability. Enzyme Cel5H exhibited highest binding to montmorillonite followed by kaolinite and sea sand. Interestingly, Cel5H had higher pI value of 9.24 than other proteins (5.2–5.7). Cel5H binding to montmorillonite was shown to be negatively affected below pH 3 and above pH 9. Infrared absorption spectra of the Cel5H-montmorillonite complexes showed distinct peaks for clay minerals and bound proteins. Furthermore, database survey of soil bacterial extracellular enzymes revealed that <i>Bacillus</i> species enzymes had higher pI than other soil bacterial enzymes. Binding of Cel5H enzyme on clay minerals.
DOI: 10.6084/m9.figshare.10000790.v1
title: MOESM2 of Risk factors for Blastocystis infection in HIV/AIDS patients with highly active antiretroviral therapy in Southwest China

description: Additional file 2. The sequence of Blastocystis in this study.
DOI: 10.6084/m9.figshare.10000799.v1
title: MOESM1 of Quantitative nuclear histomorphometric features are predictive of Oncotype DX risk categories in ductal carcinoma in situ: preliminary findings

description: Additional file 1: Section S1. Continuous ODx DCIS risk scores for each individual patients involved in D1.
DOI: 10.6084/m9.figshare.10000778.v1
title: Binding of cloned Cel enzymes on clay minerals related to the pI of the enzymes and database survey of cellulases of soil bacteria for pI

description: The <i>Cel</i> genes from <i>Bacillus licheniformis</i> MSB03 were cloned and expressed to investigate binding ability on clay minerals and sea sand at pH ranging 3 to 9. FTIR analysis has been done to characterize bound enzymes on clay minerals. Subsequent, surveying of NCBI database for extracellular enzymes of soil bacteria was carried out. Among the five cloned Cel enzymes assayed for binding to clay minerals, only Cel5H enzyme had the binding ability. Enzyme Cel5H exhibited highest binding to montmorillonite followed by kaolinite and sea sand. Interestingly, Cel5H had higher pI value of 9.24 than other proteins (5.2–5.7). Cel5H binding to montmorillonite was shown to be negatively affected below pH 3 and above pH 9. Infrared absorption spectra of the Cel5H-montmorillonite complexes showed distinct peaks for clay minerals and bound proteins. Furthermore, database survey of soil bacterial extracellular enzymes revealed that <i>Bacillus</i> species enzymes had higher pI than other soil bacterial enzymes. Binding of Cel5H enzyme on clay minerals.
DOI: 10.6084/m9.figshare.10000619
title: Experiment Data Bx Demonstrator

description: Experiment responses and results of the bx demonstrator experiment for the paper "What do Users Expect of Bidirectional Transformations?"<br>
DOI: 10.6084/m9.figshare.10000619.v1
title: Experiment Data Bx Demonstrator

description: Experiment responses and results of the bx demonstrator experiment for the paper "What do Users Expect of Bidirectional Transformations?"<br>
DOI: 10.6084/m9.figshare.10000571
title: Supplementary Material for: Trigonelline through the Attenuation of Oxidative Stress Exerts Antidepressant- and Anxiolytic-Like Effects in a Mouse Model of Maternal Separation Stress

description: Depression and anxiety are common psychiatric disorders accounting for social and economic burdens. Previous studies have shown that oxidative stress and oxidant/antioxidant imbalance are involved in the pathophysiology of psychiatric disorders. Experiencing early-life adversities (like maternal separation [MS] stress) provoked psychiatric disorders. Trigonelline (TRG) is a pyridine alkaloid that has various pharmacological effects including hypoglycemic, neuroprotective and memory-improving properties. To investigate the antidepressant- and anxiolytic-like effects of TRG focusing oxidative stress, we applied the MS paradigm to male mice at postnatal day (PND) 2–14 (3 h daily, 9–12 a.m.) and investigated the behaviors at PND 45–47. Using valid behavioral tests including a forced swimming test (FST), splash test, open field test (OFT) and elevated plus maze (EPM), we investigated behavioral modifications. Additionally, we examined the effects of MS and TRG treatment on the level of malondialdehyde (MDA), nitric oxide (NO) and also antioxidant capacity in the brain and serum. Our results showed that MS provoked depressive- and anxiety-like behaviors in the FST, OFT, EPM and splash test, which are associated with an increase in MDA and NO levels as well as a decrease in antioxidant capacity in the brain and serum samples. Findings determined that TRG significantly reversed the negative effects of MS on behavior that is accompanied by a decrease in MDA and NO as well as an increase in antioxidant capacity. Findings of the present study showed that beneficial effects of TRG may be, at least partially, mediated via the reduction of oxidative stress and an increase of antioxidant capacity.
DOI: 10.6084/m9.figshare.10000577
title: Supplementary Material for: A Meta-Analysis of the Impact of Obesity, Metabolic Syndrome, Insulin Resistance, and Microbiome on the Diagnosis of Barrett’s Esophagus

description: <b><i>Background and Aim:</i></b> The etiology and pathogenesis of Barrett’s esophagus (BE) have been widely studied during recent decades. However, the association between BE and possible risk factors, including abdominal obesity (AO), metabolic syndrome (MetS), insulin resistance (IR), and the microbiome has not reached a consensus and lacks a systematic assessment. The purpose of our study is to evaluate, quantify, and summarize the association between these factors and BE risk. <b><i>Methods:</i></b> A systematic search of Pubmed, Embase, and Cochrane Library databases was performed to identify relevant studies before September 2018. Studies were estimated with the OR, the weighted mean difference (WMD), and the 95% CI by using a random effects model. Subgroup analysis and publication bias were also performed. <b><i>Results:</i></b> A total of 46 citations were included in the analysis, and 119,273 subjects were analyzed (AO 13, MetS 15, IR 9, and microbiome: 9). The pooled results showed that AO (<i>p</i> &lt; 0.01, OR 1.30, 95% CI 1.11–1.52, <i>I</i><sup>2</sup> = 31.9%), MetS (<i>p</i> &lt; 0.01, OR 1.68, 95% CI 1.40–2.01, <i>I</i><sup>2</sup> = 87.6%), and IR (<i>p</i> &lt; 0.01, WMD 0.23, 95% CI 0.11–0.35, <i>I</i><sup>2</sup> = 55.8%) were all significantly associated with an increased risk of BE, but except for the microbiome (<i>p</i> &gt; 0.05, OR 1.27, 95% CI 0.66–2.43, <i>I</i><sup>2</sup> = 46.7%). In addition, subgroup analyses were stratified by waist-to-hip ratio, waist circumference, body mass index, diagnosis criteria, strain type, geographical region, and study design, respectively. Moreover, we observed no evidence of publication bias in Egger’s and Begg’s tests. <b><i>Conclusions:</i></b> Our study reveals that AO, MetS, and IR are significantly associated with BE risk, except for the microbiome. The mechanism of BE induced by 3 risk factors should be further explored.
DOI: 10.6084/m9.figshare.10000556
title: Value Judgment

description: This is the dataset based on the survey responses of the general population and patients in the Netherlands
DOI: 10.6084/m9.figshare.10000556.v1
title: Value Judgment

description: This is the dataset based on the survey responses of the general population and patients in the Netherlands
DOI: 10.6084/m9.figshare.10000493
title: Near Infrared Spectroscopy technology for prediction of chemical composition of natural fresh pastures

description: This study evaluates the potential of Fourier-Transform Near Infrared Spectroscopy (FT-NIRS) to estimate the chemical composition of fresh natural pastures of Tuscany without previous drying and grinding. Chemical composition of herbage samples is determined by applying usual chemistry. FT-NIRS calibration and cross-validation were developed applying spectra pre-treatment and two statistical models: partial least square regression and principal component regression. The results are evaluated in terms of coefficients of determination (R<sup>2</sup>), root mean square error (RMSE) and residual prediction deviation (RPD). Calibration results, using partial least square models, obtained a R<sup>2</sup> in calibration greater than 0.95 for dry matter and crude protein, intermediate values (&gt;0.75) for the fibre fraction and lower results for ash and crude fat (&lt;0.75). The chemometric analysis shows lower results using principal component regression than partial least square models, although dry matter and acid detergent fibre obtained relatively high R<sup>2</sup> in calibration (0.876 and 0.863, respectively). Cross-validation achieved both lower R<sup>2</sup> and higher errors than calibration. Despite the wide variability of the data set, the results suggest that coupling FT-NIRS with partial least squares analysis allows us to estimate some chemical parameters of natural pastures, while the use of principal component regression models needs further evaluation.
DOI: 10.6084/m9.figshare.10000391
title: Supplementary Material for: Adalimumab Dose Intensification in Recalcitrant Hidradenitis Suppurativa/Acne Inversa

description: <b><i>Background:</i></b> Adalimumab is the only approved compound for the treatment of adult patients with moderate-to-severe hidradenitis suppurativa (HS) who did not respond to a systemic classical treatment. Despite its significant short- and long-term efficacy, a percentage of patients do not respond sufficiently. Moreover, some primary responders experience a response loss with time. <b><i>Objective:</i></b> To analyse the effectiveness of adalimumab dose intensification in HS patients. <b><i>Methods:</i></b> A case series of adalimumab 80 mg/week subcutaneously (s.c.) compassionate use in patients with HS, who did not respond sufficiently or in primary responders with progressive response loss to the registered adalimumab dose of 40 mg/week s.c. Patients were collected and evaluated retrospectively. Patients’ data were extracted from medical records. <b><i>Results:</i></b> The 14 patients collected were Caucasian with HS of Hurley stage II–III and moderate or severe International HS Severity Score System (IHS4) stage. Adalimumab dose intensification significantly improved IHS4 score, Pain Index, HS-Physician Global Assessment, pain, and Cardiff Dermatology Life Quality Index. Two young female patients with HS and Crohn’s disease developed psoriatic lesions during the treatment with adalimumab 80 mg/week s.c. <b><i>Conclusion:</i></b> An enhanced level of effectiveness was assessed in the majority of the HS patients treated with adalimumab dose intensification (80 mg/week s.c.). Larger studies are required to evaluate this observation.
DOI: 10.6084/m9.figshare.10000493.v1
title: Near Infrared Spectroscopy technology for prediction of chemical composition of natural fresh pastures

description: This study evaluates the potential of Fourier-Transform Near Infrared Spectroscopy (FT-NIRS) to estimate the chemical composition of fresh natural pastures of Tuscany without previous drying and grinding. Chemical composition of herbage samples is determined by applying usual chemistry. FT-NIRS calibration and cross-validation were developed applying spectra pre-treatment and two statistical models: partial least square regression and principal component regression. The results are evaluated in terms of coefficients of determination (R<sup>2</sup>), root mean square error (RMSE) and residual prediction deviation (RPD). Calibration results, using partial least square models, obtained a R<sup>2</sup> in calibration greater than 0.95 for dry matter and crude protein, intermediate values (&gt;0.75) for the fibre fraction and lower results for ash and crude fat (&lt;0.75). The chemometric analysis shows lower results using principal component regression than partial least square models, although dry matter and acid detergent fibre obtained relatively high R<sup>2</sup> in calibration (0.876 and 0.863, respectively). Cross-validation achieved both lower R<sup>2</sup> and higher errors than calibration. Despite the wide variability of the data set, the results suggest that coupling FT-NIRS with partial least squares analysis allows us to estimate some chemical parameters of natural pastures, while the use of principal component regression models needs further evaluation.
DOI: 10.6084/m9.figshare.10000388
title: Raw data Bioassays.xlsx

description: The data provided are insecticide bioassays using a series of transgenic An. gambiae mosquitoes overexpressing a number of metabolic resistance genes