cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.2074270
title: The association between a novel polymorphism (rs1062577) in ESR1 and breast cancer susceptibility in the Han Chinese women

description: <i>Objective</i>: The aim of the present study was to analyze the genetic association between the three estrogen receptor 1 (ESR1) single nucleotide polymorphisms (SNPs; rs1062577, rs2881766, and rs9479118) and breast cancer risk in Han Chinese women. <i>Methods/materials</i>: To investigate the possible association of genetic polymorphisms of any of the three ESR1 SNPs in breast cancer patients (<i>n</i> = 198) and healthy controls (<i>n</i> = 218) collected from the college hospital, peripheral blood mononuclear cells samples were analyzed by high-resolution melt-polymerase chain reaction. Odds ratios and 95% confidence intervals were used to evaluate the association between the ESR1 SNPs and breast cancer. <i>Results</i>: Patients genotyped AA for ESR1 rs1062577 showed increased breast cancer risk (<i>p</i> = 0.005). In the menarche at ≤ 13-year-old group, there were significant differences in alleles A versus T at rs1062577 and alleles G versus T at rs2881766 between the breast cancer group and the control group. In the &gt; 13-year-old group, the AA genotype at rs1062577, the GG genotype at rs2881766, and the CC genotype at rs9479118 increased breast cancer susceptibility. <i>Conclusions</i>: These results showed that the ESR1 rs1062577 polymorphism increased breast cancer risk in Han Chinese women, which might be used as a new SNP marker.
DOI: 10.6084/m9.figshare.2074270.v1
title: The association between a novel polymorphism (rs1062577) in ESR1 and breast cancer susceptibility in the Han Chinese women

description: <i>Objective</i>: The aim of the present study was to analyze the genetic association between the three estrogen receptor 1 (ESR1) single nucleotide polymorphisms (SNPs; rs1062577, rs2881766, and rs9479118) and breast cancer risk in Han Chinese women. <i>Methods/materials</i>: To investigate the possible association of genetic polymorphisms of any of the three ESR1 SNPs in breast cancer patients (<i>n</i> = 198) and healthy controls (<i>n</i> = 218) collected from the college hospital, peripheral blood mononuclear cells samples were analyzed by high-resolution melt-polymerase chain reaction. Odds ratios and 95% confidence intervals were used to evaluate the association between the ESR1 SNPs and breast cancer. <i>Results</i>: Patients genotyped AA for ESR1 rs1062577 showed increased breast cancer risk (<i>p</i> = 0.005). In the menarche at ≤ 13-year-old group, there were significant differences in alleles A versus T at rs1062577 and alleles G versus T at rs2881766 between the breast cancer group and the control group. In the &gt; 13-year-old group, the AA genotype at rs1062577, the GG genotype at rs2881766, and the CC genotype at rs9479118 increased breast cancer susceptibility. <i>Conclusions</i>: These results showed that the ESR1 rs1062577 polymorphism increased breast cancer risk in Han Chinese women, which might be used as a new SNP marker.
DOI: 10.5281/zenodo.10866004
title: Macroramphosus_scolopax_zanfona_1.fasta.gz

description: .
DOI: 10.5281/zenodo.10866005
title: Macroramphosus_scolopax_zanfona_1.fasta.gz

description: .
DOI: 10.6084/m9.figshare.2075308
title: Cambrian granitic gneiss within the central Qiangtang terrane, Tibetan Plateau: implications for the early Palaeozoic tectonic evolution of the Gondwanan margin

description: The Tibetan Plateau is located in the eastern Himalayan–Alpine orogen, an area where previous research has focused on ophiolites and a high-pressure metamorphic belt, whereas comparatively little research has been undertaken on the Tibetan basement. Cambrian granitic gneiss crops out in the Duguer area of the South Qiangtang terrane in northern Tibet and yields zircon laser ablation inductively coupled plasma mass spectrometry (LA-ICP-MS) U–Pb ages of 502–492 Ma, providing insight into the possible existence of basement rocks within the South Qiangtang terrane. The granitic gneisses are geochemically similar to high-K, calc-alkaline S-type granites, and Hf isotopic analysis of zircons within the gneisses yields negative <i>ε</i>Hf(<i>t</i>) values (–7.4 to – 1.1) and old zircon Hf model ages (T<sub>DM</sub><sup>C</sup> = 1757–1406 Ma). These granitic gneisses were generated by partial melting of ancient pelitic rocks, and the resulting melts were contaminated by a small amount of mantle-derived material. Combining our new data with previous research, we conclude that these Cambrian granitic gneisses developed in a post-collisional tectonic setting after Pan-African tectonism. This suggests that the South Qiangtang terrane might have the same early Palaeozoic crystalline basement as the Lhasa, Himalaya, Baoshan, Gongshan, and Tengchong terranes.
DOI: 10.6084/m9.figshare.2075308.v1
title: Cambrian granitic gneiss within the central Qiangtang terrane, Tibetan Plateau: implications for the early Palaeozoic tectonic evolution of the Gondwanan margin

description: The Tibetan Plateau is located in the eastern Himalayan–Alpine orogen, an area where previous research has focused on ophiolites and a high-pressure metamorphic belt, whereas comparatively little research has been undertaken on the Tibetan basement. Cambrian granitic gneiss crops out in the Duguer area of the South Qiangtang terrane in northern Tibet and yields zircon laser ablation inductively coupled plasma mass spectrometry (LA-ICP-MS) U–Pb ages of 502–492 Ma, providing insight into the possible existence of basement rocks within the South Qiangtang terrane. The granitic gneisses are geochemically similar to high-K, calc-alkaline S-type granites, and Hf isotopic analysis of zircons within the gneisses yields negative <i>ε</i>Hf(<i>t</i>) values (–7.4 to – 1.1) and old zircon Hf model ages (T<sub>DM</sub><sup>C</sup> = 1757–1406 Ma). These granitic gneisses were generated by partial melting of ancient pelitic rocks, and the resulting melts were contaminated by a small amount of mantle-derived material. Combining our new data with previous research, we conclude that these Cambrian granitic gneisses developed in a post-collisional tectonic setting after Pan-African tectonism. This suggests that the South Qiangtang terrane might have the same early Palaeozoic crystalline basement as the Lhasa, Himalaya, Baoshan, Gongshan, and Tengchong terranes.
DOI: 10.6084/m9.figshare.2077489
title: Analysis of association between common variants in the <i>SLCO6A1</i> gene with schizophrenia, bipolar disorder and major depressive disorder in the Han Chinese population

description: <b>Objectives</b> The <i>SLCO6A1</i> gene belongs to a superfamily of genes which is known to be a solute carrier family of OATPs (SLCO). The <i>SLCO6A1</i> gene encodes OATP6A1 protein in humans. A previous genome-wide association study (GWAS) of schizophrenia conducted in the Swedish population demonstrated a significant association of rs6878284, which is located in the <i>SLCO6A1</i> gene, with schizophrenia. To further investigate whether this gene is also a risk locus for schizophrenia (SCZ), bipolar disorder (BPD) and major depressive disorder (MDD) in the Han Chinese population, a case–control study was designed. <b>Methods</b> In total 1,248 unrelated SCZ cases, 1,344 BPD cases, 1,056 unrelated MDD cases and 1,248 normal controls were analysed in this study. We genotyped five SNPs using the Sequenom MassARRAY platform. <b>Results</b> We found no association of rs6878284 with SCZ [Corrected <i>P</i><sub>allele </sub>= 0.969, Corrected <i>P</i><sub>genotype </sub>= 0.997]. Furthermore, we found a statistically significant association of the rs7734060 genotype with MDD after correction [rs7734060: Corrected <i>P</i><sub>allele</sub> = 0.114, Corrected <i>P</i><sub>genotype</sub> = 0.036] in the Han Chinese population. <b>Conclusions</b> This is the first study which reveals no association of rs6878284 with SCZ and also predicts that rs7734060 could be a risk locus for MDD in the Han Chinese population.
DOI: 10.6084/m9.figshare.2077489.v1
title: Analysis of association between common variants in the <i>SLCO6A1</i> gene with schizophrenia, bipolar disorder and major depressive disorder in the Han Chinese population

description: <b>Objectives</b> The <i>SLCO6A1</i> gene belongs to a superfamily of genes which is known to be a solute carrier family of OATPs (SLCO). The <i>SLCO6A1</i> gene encodes OATP6A1 protein in humans. A previous genome-wide association study (GWAS) of schizophrenia conducted in the Swedish population demonstrated a significant association of rs6878284, which is located in the <i>SLCO6A1</i> gene, with schizophrenia. To further investigate whether this gene is also a risk locus for schizophrenia (SCZ), bipolar disorder (BPD) and major depressive disorder (MDD) in the Han Chinese population, a case–control study was designed. <b>Methods</b> In total 1,248 unrelated SCZ cases, 1,344 BPD cases, 1,056 unrelated MDD cases and 1,248 normal controls were analysed in this study. We genotyped five SNPs using the Sequenom MassARRAY platform. <b>Results</b> We found no association of rs6878284 with SCZ [Corrected <i>P</i><sub>allele </sub>= 0.969, Corrected <i>P</i><sub>genotype </sub>= 0.997]. Furthermore, we found a statistically significant association of the rs7734060 genotype with MDD after correction [rs7734060: Corrected <i>P</i><sub>allele</sub> = 0.114, Corrected <i>P</i><sub>genotype</sub> = 0.036] in the Han Chinese population. <b>Conclusions</b> This is the first study which reveals no association of rs6878284 with SCZ and also predicts that rs7734060 could be a risk locus for MDD in the Han Chinese population.
DOI: 10.6084/m9.figshare.2082862
title: Elevated interleukin-1β in peripheral blood mononuclear cells contributes to the pathogenesis of autoimmune thyroid diseases, especially of Hashimoto thyroiditis

description: <b>Purpose of the study:</b> To explore the relationship between IL-1β expression and two common autoimmune thyroid diseases: Hashimoto thyroiditis (HT) and Graves’ disease (GD). <b>Materials and methods:</b> qRT-PCR, Quantiglo ELISA, and flow cytometry were used to evaluate the expression levels of IL-1β in serum, peripheral blood mononuclear cells (PBMCs), and thyroid tissue samples from patients with HT or GD. Local infiltration of monocytes was assessed by immunohistochemical study of patients’ thyroid tissue samples. <b>Results:</b> Although no significant differences in IL-1β levels were found between samples of serum from patients with HT or GD and normal controls, we found that IL-1β mRNA and protein levels in PBMCs of HT patients were significantly higher than those of patients with GD, which were in turn higher than the level in normal controls. In addition, IL-1β mRNA was also increased in thyroid gland tissue from patients with HT compared to those with GD, and this was accompanied by increased local infiltration of monocytes into thyroid tissues. Correlation analysis of the clinical samples validated the association of high IL-1β levels with the pathogenesis of HT. <b>Conclusion:</b> Our study suggests that IL-1β may be an active etiologic factor in the pathogenesis of HT and thus present a new target for novel diagnostics and treatment.
DOI: 10.6084/m9.figshare.2082862.v1
title: Elevated interleukin-1β in peripheral blood mononuclear cells contributes to the pathogenesis of autoimmune thyroid diseases, especially of Hashimoto thyroiditis

description: <b>Purpose of the study:</b> To explore the relationship between IL-1β expression and two common autoimmune thyroid diseases: Hashimoto thyroiditis (HT) and Graves’ disease (GD). <b>Materials and methods:</b> qRT-PCR, Quantiglo ELISA, and flow cytometry were used to evaluate the expression levels of IL-1β in serum, peripheral blood mononuclear cells (PBMCs), and thyroid tissue samples from patients with HT or GD. Local infiltration of monocytes was assessed by immunohistochemical study of patients’ thyroid tissue samples. <b>Results:</b> Although no significant differences in IL-1β levels were found between samples of serum from patients with HT or GD and normal controls, we found that IL-1β mRNA and protein levels in PBMCs of HT patients were significantly higher than those of patients with GD, which were in turn higher than the level in normal controls. In addition, IL-1β mRNA was also increased in thyroid gland tissue from patients with HT compared to those with GD, and this was accompanied by increased local infiltration of monocytes into thyroid tissues. Correlation analysis of the clinical samples validated the association of high IL-1β levels with the pathogenesis of HT. <b>Conclusion:</b> Our study suggests that IL-1β may be an active etiologic factor in the pathogenesis of HT and thus present a new target for novel diagnostics and treatment.
DOI: 10.6084/m9.figshare.2116978
title: Data-Driven Confidence Interval Estimation Incorporating Prior Information with an Adjustment for Skewed Data

description: Bayesian credible interval (CI) estimation is a statistical procedure that has been well addressed in both the theoretical and applied literature. Parametric assumptions regarding baseline data distributions are critical for the implementation of this method. We provide a nonparametric technique for incorporating prior information into the equal-tailed (ET) and highest posterior density (HPD) CI estimators in the Bayesian manner. We propose to use a data-driven likelihood function, replacing the parametric likelihood function to create a distribution-free posterior. Higher order asymptotic propositions are derived to show the efficiency and consistency of the proposed method. We demonstrate that the proposed approach may correct confidence regions with respect to skewness of the data distribution. An extensive Monte Carlo (MC) study confirms the proposed method significantly outperforms the classical CI estimation in a frequentist context. A real data example related to a study of myocardial infarction illustrates the excellent applicability of the proposed technique. Supplementary material, including the R code used to implement the developed method, is available online.
DOI: 10.6084/m9.figshare.2116978.v1
title: Data-Driven Confidence Interval Estimation Incorporating Prior Information with an Adjustment for Skewed Data

description: Bayesian credible interval (CI) estimation is a statistical procedure that has been well addressed in both the theoretical and applied literature. Parametric assumptions regarding baseline data distributions are critical for the implementation of this method. We provide a nonparametric technique for incorporating prior information into the equal-tailed (ET) and highest posterior density (HPD) CI estimators in the Bayesian manner. We propose to use a data-driven likelihood function, replacing the parametric likelihood function to create a distribution-free posterior. Higher order asymptotic propositions are derived to show the efficiency and consistency of the proposed method. We demonstrate that the proposed approach may correct confidence regions with respect to skewness of the data distribution. An extensive Monte Carlo (MC) study confirms the proposed method significantly outperforms the classical CI estimation in a frequentist context. A real data example related to a study of myocardial infarction illustrates the excellent applicability of the proposed technique. Supplementary material, including the R code used to implement the developed method, is available online.
DOI: 10.6084/m9.figshare.2151271
title: Prospective Study of Optimal Obesity Index Cut-Off Values for Predicting Incidence of Hypertension in 18–65-Year-Old Chinese Adults

description: The manuscript entitled "Prospective
Study of Optimal Obesity Index Cut-Off Values for Predicting Incidence of
Hypertension in 18–65-Year-Old Chinese Adults" was accepted by journal
"PLoS ONE", with a doi of "10.1371/journal.pone.0148140".
The file "k2" was the primary dataset of the manuscript.
DOI: 10.6084/m9.figshare.2151271.v1
title: k2.xlsx

description: The manuscript entitled "Prospective
Study of Optimal Obesity Index Cut-Off Values for Predicting Incidence of
Hypertension in 18–65-Year-Old Chinese Adults" was accepted by journal
"PLoS ONE", with a doi of "10.1371/journal.pone.0148140".
The file "k2" was the primary dataset of the manuscript.
DOI: 10.6084/m9.figshare.2151271.v2
title: Prospective Study of Optimal Obesity Index Cut-Off Values for Predicting Incidence of Hypertension in 18–65-Year-Old Chinese Adults

description: The manuscript entitled "Prospective
Study of Optimal Obesity Index Cut-Off Values for Predicting Incidence of
Hypertension in 18–65-Year-Old Chinese Adults" was accepted by journal
"PLoS ONE", with a doi of "10.1371/journal.pone.0148140".
The file "k2" was the primary dataset of the manuscript.
DOI: 10.6084/m9.figshare.2289280
title: Analytical method for fast screening and confirmation of multi-class veterinary drug residues in fish and shrimp by LC-MS/MS

description: A multi-class, multi-residue analytical method based on LC-MS/MS detection was developed for the screening and confirmation of 28 veterinary drug and metabolite residues in flatfish, shrimp and eel. The chosen veterinary drugs are prohibited or unauthorised compounds in Korea, which were categorised into various chemical classes including nitroimidazoles, benzimidazoles, sulfones, quinolones, macrolides, phenothiazines, pyrethroids and others. To achieve fast and simultaneous extraction of various analytes, a simple and generic liquid extraction procedure using EDTA-ammonium acetate buffer and acetonitrile, without further clean-up steps, was applied to sample preparation. The final extracts were analysed by ultra-high-performance liquid chromatography coupled with tandem mass spectrometry (UHPLC-MS/MS). The method was validated for each compound in each matrix at three different concentrations (5, 10 and 20 ng g<sup>–1</sup>) in accordance with Codex guidelines (CAC/GL 71-2009). For most compounds, the recoveries were in the range of 60–110%, and precision, expressed as the relative standard deviation (RSD), was in the range of 5–15%. The detection capabilities (CCβs) were below or equal to 5 ng g<sup>–1</sup>, which indicates that the developed method is sufficient to detect illegal fishery products containing the target compounds above the residue limit (10 ng g<sup>–1</sup>) of the new regulatory system (Positive List System – PLS).
DOI: 10.6084/m9.figshare.2289280.v1
title: Analytical method for fast screening and confirmation of multi-class veterinary drug residues in fish and shrimp by LC-MS/MS

description: A multi-class, multi-residue analytical method based on LC-MS/MS detection was developed for the screening and confirmation of 28 veterinary drug and metabolite residues in flatfish, shrimp and eel. The chosen veterinary drugs are prohibited or unauthorised compounds in Korea, which were categorised into various chemical classes including nitroimidazoles, benzimidazoles, sulfones, quinolones, macrolides, phenothiazines, pyrethroids and others. To achieve fast and simultaneous extraction of various analytes, a simple and generic liquid extraction procedure using EDTA-ammonium acetate buffer and acetonitrile, without further clean-up steps, was applied to sample preparation. The final extracts were analysed by ultra-high-performance liquid chromatography coupled with tandem mass spectrometry (UHPLC-MS/MS). The method was validated for each compound in each matrix at three different concentrations (5, 10 and 20 ng g<sup>–1</sup>) in accordance with Codex guidelines (CAC/GL 71-2009). For most compounds, the recoveries were in the range of 60–110%, and precision, expressed as the relative standard deviation (RSD), was in the range of 5–15%. The detection capabilities (CCβs) were below or equal to 5 ng g<sup>–1</sup>, which indicates that the developed method is sufficient to detect illegal fishery products containing the target compounds above the residue limit (10 ng g<sup>–1</sup>) of the new regulatory system (Positive List System – PLS).
DOI: 10.6084/m9.figshare.2307169
title: Modeling of the Nup84 subcomplex of the Nuclear Pore Complex

description: These scripts demonstrate the use of IMP, MODELLER, and PMI in the modeling of the Nup84 complex using 286 DSS/EDC chemical cross-links and an electron microscopy (EM) 2D class average.

First, MODELLER is used to 
generate
initial structures for the individual components in the Nup84 complex. 
Then, IMP
is used to model these components using DSS/EDC crosslinks and the 
electron microscopy 2D class average for the entire Nup84 complex.
DOI: 10.6084/m9.figshare.2307169.v2
title: Modeling of the Nup84 subcomplex of the Nuclear Pore Complex

description: These scripts demonstrate the use of IMP, MODELLER, and PMI in the modeling of the Nup84 complex using 286 DSS/EDC chemical cross-links and an electron microscopy (EM) 2D class average.

First, MODELLER is used to 
generate
initial structures for the individual components in the Nup84 complex. 
Then, IMP
is used to model these components using DSS/EDC crosslinks and the 
electron microscopy 2D class average for the entire Nup84 complex.
DOI: 10.6084/m9.figshare.2352991
title: Pred-binding: large-scale protein–ligand binding affinity prediction

description: Drug target interactions (DTIs) are crucial in pharmacology and drug discovery. Presently, experimental determination of compound–protein interactions remains challenging because of funding investment and difficulties of purifying proteins. In this study, we proposed two <i>in silico</i> models based on support vector machine (SVM) and random forest (RF), using 1589 molecular descriptors and 1080 protein descriptors in 9948 ligand–protein pairs to predict DTIs that were quantified by <i>K</i><sub>i</sub> values. The cross-validation coefficient of determination of 0.6079 for SVM and 0.6267 for RF were obtained, respectively. In addition, the two-dimensional (2D) autocorrelation, topological charge indices and three-dimensional (3D)-MoRSE descriptors of compounds, the autocorrelation descriptors and the amphiphilic pseudo-amino acid composition of protein are found most important for <i>K</i><sub>i</sub> predictions. These models provide a new opportunity for the prediction of ligand–receptor interactions that will facilitate the target discovery and toxicity evaluation in drug development.
DOI: 10.6084/m9.figshare.2352991.v1
title: Pred-binding: large-scale protein–ligand binding affinity prediction

description: Drug target interactions (DTIs) are crucial in pharmacology and drug discovery. Presently, experimental determination of compound–protein interactions remains challenging because of funding investment and difficulties of purifying proteins. In this study, we proposed two <i>in silico</i> models based on support vector machine (SVM) and random forest (RF), using 1589 molecular descriptors and 1080 protein descriptors in 9948 ligand–protein pairs to predict DTIs that were quantified by <i>K</i><sub>i</sub> values. The cross-validation coefficient of determination of 0.6079 for SVM and 0.6267 for RF were obtained, respectively. In addition, the two-dimensional (2D) autocorrelation, topological charge indices and three-dimensional (3D)-MoRSE descriptors of compounds, the autocorrelation descriptors and the amphiphilic pseudo-amino acid composition of protein are found most important for <i>K</i><sub>i</sub> predictions. These models provide a new opportunity for the prediction of ligand–receptor interactions that will facilitate the target discovery and toxicity evaluation in drug development.