cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.17185923.v1
title: An interpretation of the genetic polymorphism and population genetic background of Ankang Han population via a novel InDel panel

description: In this research, genotyping data of 43 InDel loci in 311 Han individuals in Ankang city, Shaanxi province, China were detected using a self-developed five-dye multiplex amplification panel. The allelic frequencies and forensic parameters of all InDel loci were calculated. The combined power of discrimination and probability of exclusion values were 0.999 999 999 999 999 998 827 39 and 0.999 887 424, respectively, which demonstrated that this 43-InDel panel was powerful for individual identifications in Ankang Han population. Moreover, genetic distances, pairwise <i>F<sub>ST</sub></i> values, principal component analyses, phylogenetic trees and STRUCTURE analyses were performed to investigate the genetic affinities between Ankang Han and reference groups. Population genetic investigations indicated that Ankang Han population had a close genetic relationship with Southern Han population compared with other reference groups.
DOI: 10.6084/m9.figshare.12991688.v1
title: Additional file 2 of Hair follicle regional specificity in different parts of bay Mongolian horse by histology and transcriptional profiling

description: Additional file 2. Gene differential expression results. Significant gene differential expression results between every two different parts.
DOI: 10.6084/m9.figshare.13515622
title: Additional file 7 of Transcriptome profiling reveals the effects of drought tolerance in Giant Juncao

description: Additional file 7. Degree and log2(FoldChange) value of hub genes under different treatments in the four modules.
DOI: 10.6084/m9.figshare.24001776.v1
title: Supervised Principal Component Regression for Functional Responses with High Dimensional Predictors

description: We propose a supervised principal component regression method for relating functional responses with high dimensional predictors. Unlike the conventional principal component analysis, the proposed method builds on a newly defined expected integrated residual sum of squares, which directly makes use of the association between the functional response and the predictors. Minimizing the integrated residual sum of squares gives the supervised principal components, which is equivalent to solving a sequence of nonconvex generalized Rayleigh quotient optimization problems. We reformulate the nonconvex optimization problems into a simultaneous linear regression with a sparse penalty to deal with high dimensional predictors. Theoretically, we show that the reformulated regression problem can recover the same supervised principal subspace under certain conditions. Statistically, we establish non-asymptotic error bounds for the proposed estimators when the covariate covariance is bandable. We demonstrate the advantages of the proposed method through numerical experiments and an application to the Human Connectome Project fMRI data.
DOI: 10.6084/m9.figshare.13515622.v1
title: Additional file 7 of Transcriptome profiling reveals the effects of drought tolerance in Giant Juncao

description: Additional file 7. Degree and log2(FoldChange) value of hub genes under different treatments in the four modules.
DOI: 10.6084/m9.figshare.17185923
title: An interpretation of the genetic polymorphism and population genetic background of Ankang Han population via a novel InDel panel

description: In this research, genotyping data of 43 InDel loci in 311 Han individuals in Ankang City, Shaanxi Province, China were detected using a self-developed five-dye multiplex amplification panel. The allelic frequencies and forensic parameters of all InDel loci were calculated. The combined power of discrimination and probability of exclusion values were 0.999 999 999 999 999 998 827 39 and 0.999 887 424, respectively, which demonstrated that this 43-InDel panel was powerful for individual identifications in Ankang Han population. Moreover, genetic distances, pairwise <i>F<sub>ST</sub></i> values, principal component analyses, phylogenetic trees and STRUCTURE analyses were performed to investigate the genetic affinities between Ankang Han and reference groups. Population genetic investigations indicated that Ankang Han population had a close genetic relationship with Southern Han population compared with other reference groups.
DOI: 10.6084/m9.figshare.24001776
title: Supervised Principal Component Regression for Functional Responses with High Dimensional Predictors

description: We propose a supervised principal component regression method for relating functional responses with high dimensional predictors. Unlike the conventional principal component analysis, the proposed method builds on a newly defined expected integrated residual sum of squares, which directly makes use of the association between the functional response and the predictors. Minimizing the integrated residual sum of squares gives the supervised principal components, which is equivalent to solving a sequence of nonconvex generalized Rayleigh quotient optimization problems. We reformulate the nonconvex optimization problems into a simultaneous linear regression with a sparse penalty to deal with high dimensional predictors. Theoretically, we show that the reformulated regression problem can recover the same supervised principal subspace under certain conditions. Statistically, we establish non-asymptotic error bounds for the proposed estimators when the covariate covariance is bandable. We demonstrate the advantages of the proposed method through numerical experiments and an application to the Human Connectome Project fMRI data.
DOI: 10.6084/m9.figshare.13515610.v1
title: Additional file 3 of Transcriptome profiling reveals the effects of drought tolerance in Giant Juncao

description: Additional file 3. KEGG enrichment in DEGs at different drought stress and rehydration conditions.
DOI: 10.6084/m9.figshare.13515616.v1
title: Additional file 5 of Transcriptome profiling reveals the effects of drought tolerance in Giant Juncao

description: Additional file 5. DEGs associated with plant hormone signal transduction pathway at different drought stress and rehydration condition.
DOI: 10.6084/m9.figshare.25273324
title: data sheet.csv

description: Bibliometrics data for meaningful work conducted in December 2023.
DOI: 10.6084/m9.figshare.25273324.v1
title: data sheet.csv

description: Bibliometrics data for meaningful work conducted in December 2023.
DOI: 10.6084/m9.figshare.12991756
title: Additional file 2 of Association between Neu5Gc carbohydrate and serum antibodies against it provides the molecular link to cancer: French NutriNet-Santé study

description: Additional file 2: Supplementary data file S1. National world meat and cancer.
DOI: 10.6084/m9.figshare.12991759
title: Additional file 3 of Association between Neu5Gc carbohydrate and serum antibodies against it provides the molecular link to cancer: French NutriNet-Santé study

description: Additional file 3: Supplementary data file S2. Glycan microarray.
DOI: 10.6084/m9.figshare.12991759.v1
title: Additional file 3 of Association between Neu5Gc carbohydrate and serum antibodies against it provides the molecular link to cancer: French NutriNet-Santé study

description: Additional file 3: Supplementary data file S2. Glycan microarray.
DOI: 10.6084/m9.figshare.12991756.v1
title: Additional file 2 of Association between Neu5Gc carbohydrate and serum antibodies against it provides the molecular link to cancer: French NutriNet-Santé study

description: Additional file 2: Supplementary data file S1. National world meat and cancer.
DOI: 10.6084/m9.figshare.16137537
title: figshare file 2

description: The binary matrix merging 149 sectors into 96 sectors.
DOI: 10.6084/m9.figshare.16137537.v1
title: figshare file 2

description: The binary matrix merging 149 sectors into 96 sectors.
DOI: 10.6084/m9.figshare.15088522.v1
title: Additional file 4 of The preoperative prognostic value of the radiomics nomogram based on CT combined with machine learning in patients with intrahepatic cholangiocarcinoma

description: Additional file 4: Supplement Figure 1 and 2. Radiomics feature selection using a parametric method, the LASSO logistic regression.
DOI: 10.6084/m9.figshare.15088522
title: Additional file 4 of The preoperative prognostic value of the radiomics nomogram based on CT combined with machine learning in patients with intrahepatic cholangiocarcinoma

description: Additional file 4: Supplement Figure 1 and 2. Radiomics feature selection using a parametric method, the LASSO logistic regression.
DOI: 10.6084/m9.figshare.24001941
title: <i>circFAM134B</i> is a key factor regulating reticulophagy-mediated ferroptosis in hepatocellular carcinoma

description: Ferroptosis is an important mode of regulated cell death (RCD). Its inhibition is closely related to therapeutic resistance and poor prognosis in hepatocellular carcinoma (HCC). Previous reports have demonstrated ferroptosis as a biological process highly dependent on selective autophagy, such as ferritinophagy, lipophagy, and clockophagy. Our study also revealed a role for ER-phagy-mediated ferroptosis in HCC cells treated with multi-targeted tyrosine kinase inhibitors (TKIs). In the current study, we found that the homologous circular RNA (circRNA) of the family with sequence similarity 134, member B (<i>FAM134B</i>), hsa_circ_0128505 (was abbreviated as <i>circFAM134B</i> in the present study), was identified to specifically target ER-phagy to promote lenvatinib (LV)-induced ferroptosis using reactive oxygen species (ROS), Fe<sup>2+</sup>, malondialdehyde (MDA), and western blot (WB) assays in HCC cells. RNA pull-down and mass spectrometry analyses suggested that <i>circFAM134B</i> and <i>FAM134B</i> mRNA were enriched with several common interacting proteins. Among them, poly (A) binding protein cytoplasmic 4 (PABPC4) was identified as the most enriched binding partner. It was proven to be a novel antagonist against the nonsense-mediated mRNA decay (NMD) mechanism. We then applied RNA immunoprecipitation (RIP), RNA pull-down, luciferase reporter, and NMD reporter gene assays to further explore the exact role and underlying mechanism of <i>circFAM134B-</i>PABPC4-FAM134B axis in HCC cells. <i>circFAM134B</i> was confirmed as a sponge that competitively interacted with PABPC4, thereby influencing <i>FAM134B</i> mRNA nonsense decay. Our results provide novel evidences and strategies for the comprehensive treatment of HCC.
DOI: 10.6084/m9.figshare.24001941.v1
title: <i>circFAM134B</i> is a key factor regulating reticulophagy-mediated ferroptosis in hepatocellular carcinoma

description: Ferroptosis is an important mode of regulated cell death (RCD). Its inhibition is closely related to therapeutic resistance and poor prognosis in hepatocellular carcinoma (HCC). Previous reports have demonstrated ferroptosis as a biological process highly dependent on selective autophagy, such as ferritinophagy, lipophagy, and clockophagy. Our study also revealed a role for ER-phagy-mediated ferroptosis in HCC cells treated with multi-targeted tyrosine kinase inhibitors (TKIs). In the current study, we found that the homologous circular RNA (circRNA) of the family with sequence similarity 134, member B (<i>FAM134B</i>), hsa_circ_0128505 (was abbreviated as <i>circFAM134B</i> in the present study), was identified to specifically target ER-phagy to promote lenvatinib (LV)-induced ferroptosis using reactive oxygen species (ROS), Fe<sup>2+</sup>, malondialdehyde (MDA), and western blot (WB) assays in HCC cells. RNA pull-down and mass spectrometry analyses suggested that <i>circFAM134B</i> and <i>FAM134B</i> mRNA were enriched with several common interacting proteins. Among them, poly (A) binding protein cytoplasmic 4 (PABPC4) was identified as the most enriched binding partner. It was proven to be a novel antagonist against the nonsense-mediated mRNA decay (NMD) mechanism. We then applied RNA immunoprecipitation (RIP), RNA pull-down, luciferase reporter, and NMD reporter gene assays to further explore the exact role and underlying mechanism of <i>circFAM134B-</i>PABPC4-FAM134B axis in HCC cells. <i>circFAM134B</i> was confirmed as a sponge that competitively interacted with PABPC4, thereby influencing <i>FAM134B</i> mRNA nonsense decay. Our results provide novel evidences and strategies for the comprehensive treatment of HCC.
DOI: 10.6084/m9.figshare.16137627
title: figshare file 3

description: The binary matrix merging 149 sectors into 45 sectors.
DOI: 10.6084/m9.figshare.16137627.v1
title: figshare file 3

description: The binary matrix merging 149 sectors into 45 sectors.
DOI: 10.6084/m9.figshare.21904837
title: Sea level changes and sequence stratigraphy of the Lower-Middle Jurassic Quse and Sewa formations in the Qiangtang Basin, central Tibet: Geochemical and palynological perspectives

description: Sequence stratigraphy is a commonly used approach to understand basin-fill history and the occurrence of conventional reservoir and/or probable source rocks. Reconstructing a sequence stratigraphic framework in carbonates, marls, and organic-rich mudstones is challenging due to environmental, petrophysical, and sedimentological variations that can be subtle, whereas seismic data may be lacking or of limited use. For this reason, incorporation between palynological analysis and chemostratigraphic profiles is becoming increasingly common to facilitate sequence stratigraphic reconstruction. This study investigates the Quse (lower Toarcian) and Sewa formations (upper Bajocian-Bathonian) in the Bilong Co section from the Qiangtang Basin of central Tibet. Eighty-three rock samples were analysed for their whole-rock inorganic geochemical composition, of which 25 rock samples were tested for palynological and palynofacies analyses. The palynological composition defined two associations for the study section. The lower part of the Bilong Co section consisted is dominated by a moderate to high abundance of opaque phytoclasts versus low to moderate amorphous organic matter (AOM) content with a high concentration of sphaeromorphs pollen grains, revealing deposition of this interval at times of low relative sea level in fluvio-deltaic settings. The middle to upper parts of the section comprised of significantly high AOM content versus low phytoclasts and high content of sphaeromorphs pollen grains, but with increasing the relative abundance of dinoflagellate cysts, indicating a phase of high sea level. Chemostratigraphic variations relevant to changes in relative sea level delineated the subdivision of the Quse and Sewa formations into two and three third-order transgressive-regressive sequences, respectively. The collision between the Lhasa and Qiangtang blocks during the Early-Middle Jurassic is suggested to control consequent subduction and sea level highstand, especially during deposition of the Sewa Formation. Geochemical proxies that relate to shelf carbonate production are calcium, strontium, whereas proxies that relate to siliciclastics include titanium, zirconium, manganese, aluminium, and silicon, other redox-sensitive proxy like uranium is also implemented. This indicates that chemostratigraphic proxies are a promising tool for the interpretation of sea level cyclicity in terms of systems tracts and bounding surfaces.
DOI: 10.6084/m9.figshare.21904837.v1
title: Sea level changes and sequence stratigraphy of the Lower-Middle Jurassic Quse and Sewa formations in the Qiangtang Basin, central Tibet: Geochemical and palynological perspectives

description: Sequence stratigraphy is a commonly used approach to understand basin-fill history and the occurrence of conventional reservoir and/or probable source rocks. Reconstructing a sequence stratigraphic framework in carbonates, marls, and organic-rich mudstones is challenging due to environmental, petrophysical, and sedimentological variations that can be subtle, whereas seismic data may be lacking or of limited use. For this reason, incorporation between palynological analysis and chemostratigraphic profiles is becoming increasingly common to facilitate sequence stratigraphic reconstruction. This study investigates the Quse (lower Toarcian) and Sewa formations (upper Bajocian-Bathonian) in the Bilong Co section from the Qiangtang Basin of central Tibet. Eighty-three rock samples were analysed for their whole-rock inorganic geochemical composition, of which 25 rock samples were tested for palynological and palynofacies analyses. The palynological composition defined two associations for the study section. The lower part of the Bilong Co section consisted is dominated by a moderate to high abundance of opaque phytoclasts versus low to moderate amorphous organic matter (AOM) content with a high concentration of sphaeromorphs pollen grains, revealing deposition of this interval at times of low relative sea level in fluvio-deltaic settings. The middle to upper parts of the section comprised of significantly high AOM content versus low phytoclasts and high content of sphaeromorphs pollen grains, but with increasing the relative abundance of dinoflagellate cysts, indicating a phase of high sea level. Chemostratigraphic variations relevant to changes in relative sea level delineated the subdivision of the Quse and Sewa formations into two and three third-order transgressive-regressive sequences, respectively. The collision between the Lhasa and Qiangtang blocks during the Early-Middle Jurassic is suggested to control consequent subduction and sea level highstand, especially during deposition of the Sewa Formation. Geochemical proxies that relate to shelf carbonate production are calcium, strontium, whereas proxies that relate to siliciclastics include titanium, zirconium, manganese, aluminium, and silicon, other redox-sensitive proxy like uranium is also implemented. This indicates that chemostratigraphic proxies are a promising tool for the interpretation of sea level cyclicity in terms of systems tracts and bounding surfaces.
DOI: 10.6084/m9.figshare.12991984
title: Additional file 10 of Transcriptomic characterization and innovative molecular classification of clear cell renal cell carcinoma in the Chinese population

description: Additional file 10: Table S4. a: this table gives the estimated tumor mutational burden (eTMB, the number of somatic mutations) and cell fractions from bulk expression matrix for 11 paired CccRCC samples. b: this table summarizes the pairwise correlation between eTMB and the corresponding cell fraction values from a.
DOI: 10.6084/m9.figshare.12991987.v1
title: Additional file 11 of Transcriptomic characterization and innovative molecular classification of clear cell renal cell carcinoma in the Chinese population

description: Additional file 11: Table S5. a: this table provides whole transcriptome sequencing quality of 65 test samples in Chinese ccRCC dataset; b: this table summarizes the average depth of reads mapped to PBRM1 CDS region for Chinese ccRCC samples.
DOI: 10.6084/m9.figshare.12991984.v1
title: Additional file 10 of Transcriptomic characterization and innovative molecular classification of clear cell renal cell carcinoma in the Chinese population

description: Additional file 10: Table S4. a: this table gives the estimated tumor mutational burden (eTMB, the number of somatic mutations) and cell fractions from bulk expression matrix for 11 paired CccRCC samples. b: this table summarizes the pairwise correlation between eTMB and the corresponding cell fraction values from a.
DOI: 10.6084/m9.figshare.12991987
title: Additional file 11 of Transcriptomic characterization and innovative molecular classification of clear cell renal cell carcinoma in the Chinese population

description: Additional file 11: Table S5. a: this table provides whole transcriptome sequencing quality of 65 test samples in Chinese ccRCC dataset; b: this table summarizes the average depth of reads mapped to PBRM1 CDS region for Chinese ccRCC samples.
DOI: 10.6084/m9.figshare.12991996
title: Additional file 2 of Transcriptomic characterization and innovative molecular classification of clear cell renal cell carcinoma in the Chinese population

description: Additional file 2: Table S1. a: this table gives the detailed information for detected driver mutation in CccRCC dataset. b: this table gives RT-PCR and Sanger sequencing validation of computational predicted PBRM1 somatic mutations from RNA-Seq technology. Confirmed somatic mutation are highlighted in yellow.
DOI: 10.6084/m9.figshare.12991996.v1
title: Additional file 2 of Transcriptomic characterization and innovative molecular classification of clear cell renal cell carcinoma in the Chinese population

description: Additional file 2: Table S1. a: this table gives the detailed information for detected driver mutation in CccRCC dataset. b: this table gives RT-PCR and Sanger sequencing validation of computational predicted PBRM1 somatic mutations from RNA-Seq technology. Confirmed somatic mutation are highlighted in yellow.
DOI: 10.6084/m9.figshare.12991999
title: Additional file 3 of Transcriptomic characterization and innovative molecular classification of clear cell renal cell carcinoma in the Chinese population

description: Additional file 3: Table S2. This table contains detailed information on detected gene fusion events discovered in 55 CccRCC tumor samples.
DOI: 10.6084/m9.figshare.12991999.v1
title: Additional file 3 of Transcriptomic characterization and innovative molecular classification of clear cell renal cell carcinoma in the Chinese population

description: Additional file 3: Table S2. This table contains detailed information on detected gene fusion events discovered in 55 CccRCC tumor samples.
DOI: 10.6084/m9.figshare.12992014
title: Additional file 8 of Transcriptomic characterization and innovative molecular classification of clear cell renal cell carcinoma in the Chinese population

description: Additional file 8: Table S3. a: this table gives the top 300 differentially expressed genes between three classes defined by NMF clustering algorithm. b: this table contains top 20 significantly enriched Reactome pathways in the top 300 differentially expressed genes between three classes defined by NMF clustering algorithm. c: this table summarizes the molecular classification of ccRCC samples in both Chinese and TCGA datasets.
DOI: 10.6084/m9.figshare.12992014.v1
title: Additional file 8 of Transcriptomic characterization and innovative molecular classification of clear cell renal cell carcinoma in the Chinese population

description: Additional file 8: Table S3. a: this table gives the top 300 differentially expressed genes between three classes defined by NMF clustering algorithm. b: this table contains top 20 significantly enriched Reactome pathways in the top 300 differentially expressed genes between three classes defined by NMF clustering algorithm. c: this table summarizes the molecular classification of ccRCC samples in both Chinese and TCGA datasets.
DOI: 10.6084/m9.figshare.16137744
title: figshare file 4

description: The binary matrix merging 149 sectors into 91 sectors.
DOI: 10.6084/m9.figshare.16137744.v1
title: figshare file 4

description: The binary matrix merging 149 sectors into 91 sectors.