cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.22779355.v1
title: Accommodating time-varying heterogeneity in risk estimation under the Cox model: a transfer learning approach

description: Transfer learning has attracted increasing attention in recent years for adaptively borrowing information across different data cohorts in various settings. Cancer registries have been widely used in clinical research because of their easy accessibility and large sample size. Our method is motivated by the question of how to utilize cancer registry data as a complement to improve the estimation precision of individual risks of death for inflammatory breast cancer (IBC) patients at The University of Texas MD Anderson Cancer Center. When transferring information for risk estimation based on the cancer registries (i.e., source cohort) to a single cancer center (i.e., target cohort), time-varying population heterogeneity needs to be appropriately acknowledged. However, there is no literature on how to adaptively transfer knowledge on risk estimation with time-to-event data from the source cohort to the target cohort while adjusting for time-varying differences in event risks between the two sources. Our goal is to address this statistical challenge by developing a transfer learning approach under the Cox proportional hazards model. To allow data-adaptive levels of information borrowing, we impose Lasso penalties on the discrepancies in regression coefficients and baseline hazard functions between the two cohorts, which are jointly solved in the proposed transfer learning algorithm. As shown in the extensive simulation studies, the proposed method yields more precise individualized risk estimation than using the target cohort alone. Meanwhile, our method demonstrates satisfactory robustness against cohort differences compared with the method that directly combines the target and source data in the Cox model. We develop a more accurate risk estimation model for the MD Anderson IBC cohort given various treatment and baseline covariates, while adaptively borrowing information from the National Cancer Database to improve risk assessment.
DOI: 10.6084/m9.figshare.8099405
title: Additional file 6: of Transcript analyses reveal a comprehensive role of abscisic acid in modulating fruit ripening in Chinese jujube

description: DEGs related to hormone metabolism and signaling. (XLSX 21 kb)
DOI: 10.6084/m9.figshare.8099363
title: Additional file 11: of Transcript analyses reveal a comprehensive role of abscisic acid in modulating fruit ripening in Chinese jujube

description: Accession of clean reads submitted to sequence read archives (SRA) of NCBI. (XLSX 10 kb)
DOI: 10.6084/m9.figshare.8099369
title: Additional file 1: of Transcript analyses reveal a comprehensive role of abscisic acid in modulating fruit ripening in Chinese jujube

description: Statistic information of RNA-seq data. (XLSX 11 kb)
DOI: 10.6084/m9.figshare.8099405.v1
title: Additional file 6: of Transcript analyses reveal a comprehensive role of abscisic acid in modulating fruit ripening in Chinese jujube

description: DEGs related to hormone metabolism and signaling. (XLSX 21 kb)
DOI: 10.6084/m9.figshare.8099369.v1
title: Additional file 1: of Transcript analyses reveal a comprehensive role of abscisic acid in modulating fruit ripening in Chinese jujube

description: Statistic information of RNA-seq data. (XLSX 11 kb)
DOI: 10.6084/m9.figshare.7050707.v1
title: Effects of gluten and moisture content on water mobility during the drying process for Chinese dried noodles

description: To investigate the water mobility during a drying process, noodles were prepared with different gluten contents (10.0%, 12.5%, 15.0%, 17.5%, 20.0%, 22.5%, or 25.0%) and moisture contents (30%, 32%, or 34%), and dried on a food moisture analysis technology platform. Three types of water were deduced from relaxation signals measured by low-field nuclear magnetic resonance (LF-NMR) spectroscopy. Peak time <i>T</i><sub>22</sub> increased with gluten and moisture content but decreased with drying time from 4–6 to 1.0–1.7 ms after 1.5 h. Gluten content mainly affected the drying rate (DR) in the middle drying period, whereas initial moisture content had an influence in the middle drying period and final drying period.
DOI: 10.6084/m9.figshare.8099378
title: Additional file 2: of Transcript analyses reveal a comprehensive role of abscisic acid in modulating fruit ripening in Chinese jujube

description: Statistic information of mapping data. (XLSX 11 kb)
DOI: 10.6084/m9.figshare.7050707
title: Effects of gluten and moisture content on water mobility during the drying process for Chinese dried noodles

description: To investigate the water mobility during a drying process, noodles were prepared with different gluten contents (10.0%, 12.5%, 15.0%, 17.5%, 20.0%, 22.5%, or 25.0%) and moisture contents (30%, 32%, or 34%), and dried on a food moisture analysis technology platform. Three types of water were deduced from relaxation signals measured by low-field nuclear magnetic resonance (LF-NMR) spectroscopy. Peak time <i>T</i><sub>22</sub> increased with gluten and moisture content but decreased with drying time from 4–6 to 1.0–1.7 ms after 1.5 h. Gluten content mainly affected the drying rate (DR) in the middle drying period, whereas initial moisture content had an influence in the middle drying period and final drying period.
DOI: 10.6084/m9.figshare.21206692
title: Additional file 10 of Selection and Validation of 48 KASP Markers for Variety Identification and Breeding Guidance in Conventional and Hybrid Rice (Oryza sativa L.)

description: Additional file 10: Table S10 The list of conventional japonica after deleting the possible redundant sib lines from the same breeding institutes.
DOI: 10.6084/m9.figshare.8099357
title: Additional file 10: of Transcript analyses reveal a comprehensive role of abscisic acid in modulating fruit ripening in Chinese jujube

description: Sequences for ABA pathway genes. (XLSX 124 kb)
DOI: 10.6084/m9.figshare.21206728
title: Additional file 7 of Selection and Validation of 48 KASP Markers for Variety Identification and Breeding Guidance in Conventional and Hybrid Rice (Oryza sativa L.)

description: Additional file 7: Table S7 The list of 518 varieties.
DOI: 10.6084/m9.figshare.21206728.v1
title: Additional file 7 of Selection and Validation of 48 KASP Markers for Variety Identification and Breeding Guidance in Conventional and Hybrid Rice (Oryza sativa L.)

description: Additional file 7: Table S7 The list of 518 varieties.
DOI: 10.6084/m9.figshare.8099363.v1
title: Additional file 11: of Transcript analyses reveal a comprehensive role of abscisic acid in modulating fruit ripening in Chinese jujube

description: Accession of clean reads submitted to sequence read archives (SRA) of NCBI. (XLSX 10 kb)
DOI: 10.6084/m9.figshare.21206704.v1
title: Additional file 14 of Selection and Validation of 48 KASP Markers for Variety Identification and Breeding Guidance in Conventional and Hybrid Rice (Oryza sativa L.)

description: Additional file 14: Table S14 The result of Loglikelihood (LK) produced by Admixture.
DOI: 10.6084/m9.figshare.22779355
title: Accommodating time-varying heterogeneity in risk estimation under the Cox model: a transfer learning approach

description: Transfer learning has attracted increasing attention in recent years for adaptively borrowing information across different data cohorts in various settings. Cancer registries have been widely used in clinical research because of their easy accessibility and large sample size. Our method is motivated by the question of how to utilize cancer registry data as a complement to improve the estimation precision of individual risks of death for inflammatory breast cancer (IBC) patients at The University of Texas MD Anderson Cancer Center. When transferring information for risk estimation based on the cancer registries (i.e., source cohort) to a single cancer center (i.e., target cohort), time-varying population heterogeneity needs to be appropriately acknowledged. However, there is no literature on how to adaptively transfer knowledge on risk estimation with time-to-event data from the source cohort to the target cohort while adjusting for time-varying differences in event risks between the two sources. Our goal is to address this statistical challenge by developing a transfer learning approach under the Cox proportional hazards model. To allow data-adaptive levels of information borrowing, we impose Lasso penalties on the discrepancies in regression coefficients and baseline hazard functions between the two cohorts, which are jointly solved in the proposed transfer learning algorithm. As shown in the extensive simulation studies, the proposed method yields more precise individualized risk estimation than using the target cohort alone. Meanwhile, our method demonstrates satisfactory robustness against cohort differences compared with the method that directly combines the target and source data in the Cox model. We develop a more accurate risk estimation model for the MD Anderson IBC cohort given various treatment and baseline covariates, while adaptively borrowing information from the National Cancer Database to improve risk assessment.
DOI: 10.6084/m9.figshare.21206716.v1
title: Additional file 3 of Selection and Validation of 48 KASP Markers for Variety Identification and Breeding Guidance in Conventional and Hybrid Rice (Oryza sativa L.)

description: Additional file 3: Table S3 The 331 KASP genotype of 46 varieties.
DOI: 10.6084/m9.figshare.8099384.v1
title: Additional file 3: of Transcript analyses reveal a comprehensive role of abscisic acid in modulating fruit ripening in Chinese jujube

description: GO enrichment for DEGs at DAT1. (XLSX 17 kb)
DOI: 10.6084/m9.figshare.20099252.v1
title: Anonymized Imaging Data for 2-Minute MRI to 6-Minute Synthetic MRI project

description: Ground-truth 2-minute T2-weighted MRI scans, ground-truth 6-minute T2-weighted MRI scans, and generated synthetic 6-minute quality T2-weighted MRI scans (with and without N4 bias field correction) related to synthetic MRI project (https://www.frontiersin.org/journals/oncology/articles/10.3389/fonc.2022.975902/full) in DICOM format. Images correspond to 18 patients used in project test set.<br>DICOM RT Structure files for various head and neck organs at risk auto-segmented by an in-house ADMIRE deep learning algorithm were also included.<br><i>Note:</i> Training set images are expected to be included in large scale repository efforts in conjunction with The Cancer Imaging Archive in future.<br><br>
DOI: 10.6084/m9.figshare.20099252
title: Anonymized Imaging Data for 2-Minute MRI to 6-Minute Synthetic MRI project

description: Ground-truth 2-minute T2-weighted MRI scans, ground-truth 6-minute T2-weighted MRI scans, and generated synthetic 6-minute quality T2-weighted MRI scans (with and without N4 bias field correction) related to synthetic MRI project (https://www.frontiersin.org/journals/oncology/articles/10.3389/fonc.2022.975902/full) in DICOM format. Images correspond to 18 patients used in project test set.<br>DICOM RT Structure files for various head and neck organs at risk auto-segmented by an in-house ADMIRE deep learning algorithm were also included.<br><i>Note:</i> Training set images are expected to be included in large scale repository efforts in conjunction with The Cancer Imaging Archive in future.<br><br>
DOI: 10.6084/m9.figshare.21206722.v1
title: Additional file 5 of Selection and Validation of 48 KASP Markers for Variety Identification and Breeding Guidance in Conventional and Hybrid Rice (Oryza sativa L.)

description: Additional file 5: Table S5 The result of CV error produced by Admixture.
DOI: 10.6084/m9.figshare.7586408
title: Repeat annotation and Non-coding RNA annotation of Platysternon megacephalum

description: Repeat annotation and Non-coding RNA annotation of Platysternon megacephalum.
DOI: 10.6084/m9.figshare.21206692.v1
title: Additional file 10 of Selection and Validation of 48 KASP Markers for Variety Identification and Breeding Guidance in Conventional and Hybrid Rice (Oryza sativa L.)

description: Additional file 10: Table S10 The list of conventional japonica after deleting the possible redundant sib lines from the same breeding institutes.
DOI: 10.6084/m9.figshare.21206698
title: Additional file 12 of Selection and Validation of 48 KASP Markers for Variety Identification and Breeding Guidance in Conventional and Hybrid Rice (Oryza sativa L.)

description: Additional file 12: Table S12 The result of PCA of 325 conventional varieties using 48 KASP markers.
DOI: 10.6084/m9.figshare.8099357.v1
title: Additional file 10: of Transcript analyses reveal a comprehensive role of abscisic acid in modulating fruit ripening in Chinese jujube

description: Sequences for ABA pathway genes. (XLSX 124 kb)
DOI: 10.6084/m9.figshare.21206704
title: Additional file 14 of Selection and Validation of 48 KASP Markers for Variety Identification and Breeding Guidance in Conventional and Hybrid Rice (Oryza sativa L.)

description: Additional file 14: Table S14 The result of Loglikelihood (LK) produced by Admixture.
DOI: 10.6084/m9.figshare.8099414.v1
title: Additional file 7: of Transcript analyses reveal a comprehensive role of abscisic acid in modulating fruit ripening in Chinese jujube

description: DEGs related to transcription factors involved in ripening regulation. (XLSX 27 kb)
DOI: 10.6084/m9.figshare.8099393
title: Additional file 4: of Transcript analyses reveal a comprehensive role of abscisic acid in modulating fruit ripening in Chinese jujube

description: KEGG pathway enrichment for DEGs (Level3) at DAT1. (XLSX 27 kb)
DOI: 10.6084/m9.figshare.21206695.v1
title: Additional file 11 of Selection and Validation of 48 KASP Markers for Variety Identification and Breeding Guidance in Conventional and Hybrid Rice (Oryza sativa L.)

description: Additional file 11: Table S11 The result of CV error produced by Admixture.
DOI: 10.6084/m9.figshare.21206731
title: Additional file 8 of Selection and Validation of 48 KASP Markers for Variety Identification and Breeding Guidance in Conventional and Hybrid Rice (Oryza sativa L.)

description: Additional file 8: Table S8 The 48 KASP genotype of 325 conventional varieties.
DOI: 10.6084/m9.figshare.17023774
title: Value of glycogen synthase 2 in intrahepatic cholangiocarcinoma prognosis assessment and its influence on the activity of cancer cells

description: Intrahepatic cholangiocarcinoma (ICC) is the second most common primary liver tumor with increasing incidence worldwide. Metabolic reprogramming caused by metabolic related gene disorders is a prominent hallmark of tumors, among which Glycogen Synthase 2 (GYS2) is the key gene responsible for regulating cellular energy metabolism, and its expression disorders are closely related to various tumors and glycometabolic diseases. However, we still know nothing about its role in ICC. This study is intended to reveal the functional role of GYS2 in the ICC progress and explore the underlying mechanism. Based on the integrated pan-cancer analysis of GYS2 in the GEPIA database, the expression of GYS2 in paired ICC and adjacent non tumor tissues was detected by qPCR. It was found that the expression of GYS2 was significantly down-regulated in ICC. Further analysis showed that its low expression was not only associated with the degree of pathological differentiation, tumor size, microvascular invasion and lymph node metastasis, but also an independent risk factor for unfavorable prognosis. Functional studies have shown that GYS2 overexpression can significantly impair the proliferation, replication, cloning, migration and invasion of cholangiocarcinoma cells, while the silencing GYS2 dramatically promotes the development of the aforementioned phenotypes, the underlying mechanism may be that GYS2 activates the P53 pathway. In conclusions,low GYS2 expression in ICC predicted unfavorable patient outcomes; GYS2 overexpression could significantly impair the proliferation, migration and invasion of cholangiocarcinoma cells via activating the P53 pathway and GYS2 was expected to become a potential therapeutic target for such patients.
DOI: 10.6084/m9.figshare.21206701
title: Additional file 13 of Selection and Validation of 48 KASP Markers for Variety Identification and Breeding Guidance in Conventional and Hybrid Rice (Oryza sativa L.)

description: Additional file 13: Table S13 The reference allele frequency.
DOI: 10.6084/m9.figshare.21206695
title: Additional file 11 of Selection and Validation of 48 KASP Markers for Variety Identification and Breeding Guidance in Conventional and Hybrid Rice (Oryza sativa L.)

description: Additional file 11: Table S11 The result of CV error produced by Admixture.
DOI: 10.6084/m9.figshare.21206734
title: Additional file 9 of Selection and Validation of 48 KASP Markers for Variety Identification and Breeding Guidance in Conventional and Hybrid Rice (Oryza sativa L.)

description: Additional file 9: Table S9 The 48 KASP genotype of 193 hybrid varieties.
DOI: 10.6084/m9.figshare.21206698.v1
title: Additional file 12 of Selection and Validation of 48 KASP Markers for Variety Identification and Breeding Guidance in Conventional and Hybrid Rice (Oryza sativa L.)

description: Additional file 12: Table S12 The result of PCA of 325 conventional varieties using 48 KASP markers.
DOI: 10.6084/m9.figshare.22266814
title: Training dataset and model weight

description: The CT slices with labeled images used for training.
The model weight of Swin Transformer which was trained with patch size 672<sup>2 </sup>and hybrid loss
DOI: 10.6084/m9.figshare.6013907.v1
title: RAS-related GTPases <i>DIRAS1</i> and <i>DIRAS2</i> induce autophagic cancer cell death and are required for autophagy in murine ovarian cancer cells

description: Among the 3 GTPases in the DIRAS family, <i>DIRAS3/ARHI</i> is the best characterized. <i>DIRAS3</i> is an imprinted tumor suppressor gene that encodes a 26-kDa GTPase that shares 60% homology to RAS and RAP. DIRAS3 is downregulated in many tumor types, including ovarian cancer, where re-expression inhibits cancer cell growth, reduces motility, promotes tumor dormancy and induces macroautophagy/autophagy. Previously, we demonstrated that DIRAS3 is required for autophagy in human cells. <i>Diras3</i> has been lost from the mouse genome during evolutionary re-arrangement, but murine cells can still undergo autophagy. We have tested whether DIRAS1 and DIRAS2, which are homologs found in both human and murine cells, could serve as surrogates to DIRAS3 in the murine genome affecting autophagy and cancer cell growth. Similar to DIRAS3, these 2 GTPases share 40–50% homology to RAS and RAP, but differ from DIRAS3 primarily in the lengths of their N-terminal extensions. We found that DIRAS1 and DIRAS2 are downregulated in ovarian cancer and are associated with decreased disease-free and overall survival. Re-expression of these genes suppressed growth of human and murine ovarian cancer cells by inducing autophagy-mediated cell death. Mechanistically, DIRAS1 and DIRAS2 induce and regulate autophagy by inhibition of the AKT1-MTOR and RAS-MAPK signaling pathways and modulating nuclear localization of the autophagy-related transcription factors FOXO3/FOXO3A and TFEB. Taken together, these data suggest that DIRAS1 and DIRAS2 likely serve as surrogates in the murine genome for DIRAS3, and may function as a backup system to fine-tune autophagy in humans.
DOI: 10.6084/m9.figshare.25219169
title: Association between hypothyroidism and sperm quality parameter dataset

description: Subclinical hypothyroidism (SCH) has been recognized as a common endocrine disorder with potential impacts on reproductive health.
DOI: 10.6084/m9.figshare.25219169.v1
title: Association between hypothyroidism and sperm quality parameter dataset

description: Subclinical hypothyroidism (SCH) has been recognized as a common endocrine disorder with potential impacts on reproductive health.
DOI: 10.6084/m9.figshare.21206707
title: Additional file 15 of Selection and Validation of 48 KASP Markers for Variety Identification and Breeding Guidance in Conventional and Hybrid Rice (Oryza sativa L.)

description: Additional file 15: Table S15 The result of PCA of 193 hybrid varieties using 48 KASP markers.
DOI: 10.6084/m9.figshare.21206710
title: Additional file 1 of Selection and Validation of 48 KASP Markers for Variety Identification and Breeding Guidance in Conventional and Hybrid Rice (Oryza sativa L.)

description: Additional file 1: Table S1 The list of 378 KASP markers.
DOI: 10.6084/m9.figshare.21206701.v1
title: Additional file 13 of Selection and Validation of 48 KASP Markers for Variety Identification and Breeding Guidance in Conventional and Hybrid Rice (Oryza sativa L.)

description: Additional file 13: Table S13 The reference allele frequency.
DOI: 10.6084/m9.figshare.21206710.v1
title: Additional file 1 of Selection and Validation of 48 KASP Markers for Variety Identification and Breeding Guidance in Conventional and Hybrid Rice (Oryza sativa L.)

description: Additional file 1: Table S1 The list of 378 KASP markers.
DOI: 10.6084/m9.figshare.21206713
title: Additional file 2 of Selection and Validation of 48 KASP Markers for Variety Identification and Breeding Guidance in Conventional and Hybrid Rice (Oryza sativa L.)

description: Additional file 2: Table S2 The list of 46 varieties.
DOI: 10.6084/m9.figshare.18585353
title: The diagnostic value of serum YKL-40 in endometrial cancer: a meta-analysis

description: Serum YKL-40 is a promising non-invasive biomarker for the early diagnosis of endometrial cancer (EC), but its value is disputed. To investigate the serum YKL-40 in the early diagnostic value of EC. Databases were systematically searched again before April 2021 and 14 studies were finally included in this meta-analysis. Pooled sensitivity, specificity, negative likelihood ratio (NLR), positive likelihood ratio (PLR), diagnostic odds ratio (DOR), and summary receiver operating characteristic (SROC) curve analyses were assessed. This meta-analysis investigated the source of heterogeneity using sensitivity analysis, subgroup analysis, and meta-regression. Databases were systematically searched again before April 2021 and 14 studies were finally included in this meta-analysis. First, the SROC curve presented an area under the curve (AUC) of 0.853 (SE = 0.0213) for YKL-40 alone and an AUC of 0.946 (SE = 0.0268) for YKL-40 combined with other biomarkers. Second, diagnostic types might be related to the diagnostic accuracy and is a significant source of heterogeneity (<i>P</i> = 0.035). Serum YKL-40 helped diagnose EC, and its combination with other biomarkers was better than itself alone.
DOI: 10.6084/m9.figshare.21206716
title: Additional file 3 of Selection and Validation of 48 KASP Markers for Variety Identification and Breeding Guidance in Conventional and Hybrid Rice (Oryza sativa L.)

description: Additional file 3: Table S3 The 331 KASP genotype of 46 varieties.
DOI: 10.6084/m9.figshare.21206719
title: Additional file 4 of Selection and Validation of 48 KASP Markers for Variety Identification and Breeding Guidance in Conventional and Hybrid Rice (Oryza sativa L.)

description: Additional file 4: Table S4 The list of 50 KASP markers.
DOI: 10.6084/m9.figshare.21206722
title: Additional file 5 of Selection and Validation of 48 KASP Markers for Variety Identification and Breeding Guidance in Conventional and Hybrid Rice (Oryza sativa L.)

description: Additional file 5: Table S5 The result of CV error produced by Admixture.
DOI: 10.6084/m9.figshare.8099642
title: Additional file 5: of Mitochondrial genome and transcriptome analysis of five alloplasmic male-sterile lines in Brassica juncea

description: Table S4. Gene content of each mitochondrial genome and RNA editing number of each gene. (XLSX 13â kb)
DOI: 10.6084/m9.figshare.8099612.v1
title: Additional file 1: of Mitochondrial genome and transcriptome analysis of five alloplasmic male-sterile lines in Brassica juncea

description: Table S1. Sequencing and assembling statistical result of each mitochondrial genome. (XLSX 10â kb)