cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.10047941.v1
title: Additional file 8: Table S3. of Identification of the WRKY gene family and functional analysis of two genes in Caragana intermedia

description: Primers employed for qRT-PCR and the analysis of transgenic plant construction. (XLS 27Â kb)
DOI: 10.6084/m9.figshare.22622549
title: Additional file 2 of CRISPR screens identify gene targets at breast cancer risk loci

description: Additional file 2: Table S1. BC risk signals identified in GWAS and INQUSIT gene predictions. Signals from BC GWAS and INQUISIT gene prediction for these signals.
DOI: 10.6084/m9.figshare.22622552
title: Additional file 3 of CRISPR screens identify gene targets at breast cancer risk loci

description: Additional file 3: Table S2. sgRNA sequences. Sequences of sgRNAs used in various CRISPR screens in this study.
DOI: 10.6084/m9.figshare.20001026
title: Additional file 19 of Integrated proteogenomic characterization of urothelial carcinoma of the bladder

description: Additional file 19. Table S7: Differentially expressed among immune clusters. Related to Figure 7, Additional file 7: Fig. S7. A. Gene analysis by WGCNA. B. Pathways upregulated in modules. C. Genes were screened from the MEblue module. D. Genes upregulated in each histologic group. E. Pathways upregulated in each histologic group.
DOI: 10.6084/m9.figshare.22622549.v1
title: Additional file 2 of CRISPR screens identify gene targets at breast cancer risk loci

description: Additional file 2: Table S1. BC risk signals identified in GWAS and INQUSIT gene predictions. Signals from BC GWAS and INQUISIT gene prediction for these signals.
DOI: 10.6084/m9.figshare.20001014
title: Additional file 15 of Integrated proteogenomic characterization of urothelial carcinoma of the bladder

description: Additional file 15. Table S3: Differentially expressed mRNAs, proteins, and phosphoproteins between tumors and MNUs. Related to Figure 3, Additional file 3: Fig. S3. A. Lists of mRNAs, proteins, and phosphoproteins used for principal component analysis (PCA). B. Lists of differentially expressed mRNAs, proteins and phosphoproteins (Wilcoxon rank-sum test, FDR &lt; 0.01, Tumors/MNUs ratio &gt; 2 or &lt; 1/2) in tumors and MNUs. C. A list of genes with significant patient survival difference on both protein and mRNA level. D. A list of candidate target genes of UC.
DOI: 10.6084/m9.figshare.22622552.v1
title: Additional file 3 of CRISPR screens identify gene targets at breast cancer risk loci

description: Additional file 3: Table S2. sgRNA sequences. Sequences of sgRNAs used in various CRISPR screens in this study.
DOI: 10.6084/m9.figshare.22622555
title: Additional file 4 of CRISPR screens identify gene targets at breast cancer risk loci

description: Additional file 4: Table S3. Raw counts from different CRISPR screens. Raw sequencing reads from various CRISPR screens.
DOI: 10.6084/m9.figshare.20001020.v1
title: Additional file 17 of Integrated proteogenomic characterization of urothelial carcinoma of the bladder

description: Additional file 17. Table S5: Multi-omics characteristics of proteomic subtypes in 116 UC samples. Related to Figure 5, Additional file 5: Fig. S5. A. Information of immune clusters. B. Genes upregulated in each proteomic subtype. C. Lists of upregulated proteins in one of the three proteomic subtypes. D. Contributions of 30 COSMIC signatures in 113 UC patients. E. Genes of each Signatures used in this figure. F. Survival analysis of selected factors.
DOI: 10.6084/m9.figshare.20001153.v1
title: Additional file 1 of A genetic correlation scan identifies blood proteins associated with bone mineral density

description: Additional file 1: Supplementary Table 1. The basic characteristics of the participants included in per cohort and age strata.
DOI: 10.6084/m9.figshare.13187428.v2
title: Missing Data Imputation With Baseline Information in Longitudinal Clinical Trials

description: In longitudinal clinical trials, missing data are inevitable despite every effort made to retain patients in the trial. Missing data cause difficulty in the estimation and interpretation of the treatment effect. When the primary objective is to assess the treatment effect in a realistic setting, it is necessary to take into consideration the impact of noncompliance to the treatment regimen. For estimation following the intention-to-treat principle, a return-to-baseline (RTB) approach may be used for continuous endpoints in some longitudinal clinical trials. The RTB approach is based on the assumption that the unobserved outcomes at the end of the trial represent a return to the baseline value, that is, any change observed while on treatment can be expected to wash out after patients drop out. This article describes a statistical approach for RTB analyses. The method for calculating the sample size using RTB approach is presented. A detailed illustration using this RTB approach based on publicly available longitudinal antidepressant clinical trial data is provided. Extensive simulations are presented to evaluate the performance of this RTB approach under various missing data mechanisms. Important limitations regarding the appropriateness of the underlying assumptions of RTB are discussed.
DOI: 10.6084/m9.figshare.22622564.v1
title: Additional file 7 of CRISPR screens identify gene targets at breast cancer risk loci

description: Additional file 7: Table S6. Results from CRISPRqtl screen in B80-T5 cells. The Sceptre algorithm was used to identify gene expression changes following CRISPRi mediated targeting of 16 loci associated with increased BC risk.
DOI: 10.6084/m9.figshare.22622558.v1
title: Additional file 5 of CRISPR screens identify gene targets at breast cancer risk loci

description: Additional file 5: Table S4. MAGeCK analysis from CRISPR screens. MAGeCK analysis for identification of enriched and depleted genes in CRISPR screens.
DOI: 10.6084/m9.figshare.22622561
title: Additional file 6 of CRISPR screens identify gene targets at breast cancer risk loci

description: Additional file 6: Table S5. HiChIP interactions in K5+/K19+ and B80-T5 cells. Chromatin interactions between BC risk signals and genes at a 2Mb window.
DOI: 10.6084/m9.figshare.22622558
title: Additional file 5 of CRISPR screens identify gene targets at breast cancer risk loci

description: Additional file 5: Table S4. MAGeCK analysis from CRISPR screens. MAGeCK analysis for identification of enriched and depleted genes in CRISPR screens.
DOI: 10.6084/m9.figshare.22622591.v1
title: Additional file 4 of Analysis of serum reproductive hormones and ovarian genes in pubertal female goats

description: Additional file 4: Table S3. GO analysis of DEGs.
DOI: 10.6084/m9.figshare.22622561.v1
title: Additional file 6 of CRISPR screens identify gene targets at breast cancer risk loci

description: Additional file 6: Table S5. HiChIP interactions in K5+/K19+ and B80-T5 cells. Chromatin interactions between BC risk signals and genes at a 2Mb window.
DOI: 10.6084/m9.figshare.25188116
title: Reconfigurable spin current transmission and magnon–magnon coupling in hybrid ferrimagnetic insulators.xlsx

description: This is the repository for the paper "<b>Reconfigurable spin current transmission and magnon–magnon coupling in hybrid ferrimagnetic insulators</b>". It includes the source data that support the findings of this study.
DOI: 10.6084/m9.figshare.7420304.v1
title: Forage sorghum-legumes intercropping: effect on growth, yields, nutritional quality and economic returns

description: ABSTRACT Cereal-legumes intercropping is among the most economical and effective agronomic strategies to boost forage biomass production, nutritional quality and monetary returns. This review synthesizes the research findings on how intercropping affects productivity, quality, competitiveness and economic viability of sorghum-legumes mixed, row and strip intercropping systems under varied pedo-climatic conditions. Though component crops show yield reductions in row (additive and row-replacement series), mixed (seed blended crops) and strip intercropping systems, in general overall productivity per unit land area increases to a great extent. The significantly higher resource capturing with better utilization efficacy by intercrops in temporal and spatial dimensions helps explain their greater productivity. In addition, forage intercrops result in improved nutritional quality as legumes contain protein in double quantity than cereals. Cereal-legumes intercropping systems yield higher quantities of lush green forage with improved quality traits, which ultimately increase monetary benefits. Furthermore, legumes inclusion as an intercrop with cereals has the potential to serve as a nitrogen-saving strategy due to the biological nitrogen fixation (BNF) process. Moreover, cereal-legume intercropping systems are effective in reducing weed infestations and soil erosion by providing extended soil cover, as well as in increasing water use efficiency and improving soil fertility. However, despite a significant increase in overall productivity, component crops suffer yield losses in intercropping systems owing to competition for the finite divisible pool of growth resources. Thus, there is a dire need to optimize spatial and temporal arrangements in sorghum-legumes intercropping systems to achieve maximum productivity and economic returns.
DOI: 10.6084/m9.figshare.22622585
title: Additional file 2 of Analysis of serum reproductive hormones and ovarian genes in pubertal female goats

description: Additional file 2: Table S1. Reads filter and comparison.
DOI: 10.6084/m9.figshare.10047968
title: Additional file 1: of Targeted next-generation sequencing identification of mutations in patients with disorders of sex development

description: Genes associated with disorders of sex development (DSD). (XLSX 25 kb)
DOI: 10.6084/m9.figshare.10047968.v1
title: Additional file 1: of Targeted next-generation sequencing identification of mutations in patients with disorders of sex development

description: Genes associated with disorders of sex development (DSD). (XLSX 25 kb)
DOI: 10.6084/m9.figshare.10047974
title: Additional file 3: of Targeted next-generation sequencing identification of mutations in patients with disorders of sex development

description: SNV validation of the YH sample. (XLSX 12.8 kb)
DOI: 10.6084/m9.figshare.10047974.v1
title: Additional file 3: of Targeted next-generation sequencing identification of mutations in patients with disorders of sex development

description: SNV validation of the YH sample. (XLSX 12.8 kb)
DOI: 10.6084/m9.figshare.10047977
title: Additional file 4: of Targeted next-generation sequencing identification of mutations in patients with disorders of sex development

description: Sequencing quality statistics of all samples. (XLSX 14.4 kb)
DOI: 10.6084/m9.figshare.10047977.v1
title: Additional file 4: of Targeted next-generation sequencing identification of mutations in patients with disorders of sex development

description: Sequencing quality statistics of all samples. (XLSX 14.4 kb)
DOI: 10.6084/m9.figshare.10047980
title: Additional file 5: of Targeted next-generation sequencing identification of mutations in patients with disorders of sex development

description: Sex chromosome dosage analysis. (XLSX 14.1 kb)
DOI: 10.6084/m9.figshare.10047980.v1
title: Additional file 5: of Targeted next-generation sequencing identification of mutations in patients with disorders of sex development

description: Sex chromosome dosage analysis. (XLSX 14.1 kb)
DOI: 10.6084/m9.figshare.10047983
title: Additional file 6: of Targeted next-generation sequencing identification of mutations in patients with disorders of sex development

description: Primers used for candidate variant validation. (XLSX 17.1 kb)
DOI: 10.6084/m9.figshare.10047983.v1
title: Additional file 6: of Targeted next-generation sequencing identification of mutations in patients with disorders of sex development

description: Primers used for candidate variant validation. (XLSX 17.1 kb)
DOI: 10.6084/m9.figshare.10047989
title: Additional file 8: of Targeted next-generation sequencing identification of mutations in patients with disorders of sex development

description: Number of candidate variants in 23 patients after filtering. (XLSX 13.9 kb)
DOI: 10.6084/m9.figshare.10047989.v1
title: Additional file 8: of Targeted next-generation sequencing identification of mutations in patients with disorders of sex development

description: Number of candidate variants in 23 patients after filtering. (XLSX 13.9 kb)
DOI: 10.6084/m9.figshare.22622585.v1
title: Additional file 2 of Analysis of serum reproductive hormones and ovarian genes in pubertal female goats

description: Additional file 2: Table S1. Reads filter and comparison.
DOI: 10.6084/m9.figshare.22622588
title: Additional file 3 of Analysis of serum reproductive hormones and ovarian genes in pubertal female goats

description: Additional file 3: Table S2. Details of DEGs.
DOI: 10.6084/m9.figshare.22622594.v1
title: Additional file 5 of Analysis of serum reproductive hormones and ovarian genes in pubertal female goats

description: Additional file 5: Table S4. KEGG analysis of DEGs.
DOI: 10.6084/m9.figshare.7950881.v1
title: Additional file 4: of De novo transcriptome and phytochemical analyses reveal differentially expressed genes and characteristic secondary metabolites in the original oolong tea (Camellia sinensis) cultivar ‘Tieguanyin’ compared with cultivar ‘Benshan’

description: Table S3. Read count data in transcriptome dataset. (XLSX 4399 kb)
DOI: 10.6084/m9.figshare.17912441
title: The attributes of ECG records

description: This file contains the ECG ID, the patient ID, the AHA codes, the age and sex, the record length, and the acquisition date of ECG records.
DOI: 10.6084/m9.figshare.17912444
title: ECG records

description: The dataset contains 25770 12-lead ECG records in the HDF5 format.
DOI: 10.6084/m9.figshare.17912444.v1
title: ECG records

description: The dataset contains 25770 12-lead ECG records in the HDF5 format.
DOI: 10.6084/m9.figshare.17912468
title: Food Wanting is Mediated by Transient Activation of Dopaminergic Signaling in the Honeybee Brain

description: Behavioral analysis of waggle dances and individual 
appetitive responses; hplc quantification of biogenic amines in the bee 
brain and pharmacolgical manipulation of these levels
DOI: 10.6084/m9.figshare.10048184
title: Thoracic endovascular aortic repair versus open chest surgical repair for patients with type B aortic dissection: a systematic review and meta-analysis

description: <b>Aim:</b> This meta-analysis study aimed to compare the efficacy and safety of TEVAR versus OCSR for TBAD patients. <b>Methods:</b> We systematically searched PubMed, EmBase, and the Cochrane library to identify studies compared the effectiveness of TEVAR and OCSR in TBAD patients from the inception up to July 2019. The summary results were calculated using a random-effects model. <b>Results:</b> The electronic search identified 1,894 studies, and 18 studies with 9,664 TBAD patients were included. We noted patients received TEVAR were associated with a reduced risk of in-hospital mortality, acute renal failure, respiratory failure, and bleeding as compared with OCSR, whereas no significant differences between groups for the risk of stroke, myocardial infarction, paraplegia, mesenteric ischaemia/infarction, reinterventions, sepsis, and spinal cord ischaemia. <b>Conclusions:</b> The findings of this meta-analysis study suggested that TEVAR resulted in more short-term survival benefits. Moreover, the reduced risk of acute renal failure, respiratory failure and bleeding was detected in TEVAR group. The treatment effects of TEVAR versus OCSR on specific complications should be further verified by a study with high-level of evidence.Key messageComprehensive collected studies investigated the treatment effectiveness between TEVAR and OCSR for TBAD patientsTEVAR resulted in more survival benefits, in addition to lower risk of acute renal failure, respiratory failure and bleedingThe results of stratified analyses according to patients’ characteristics were conducted Comprehensive collected studies investigated the treatment effectiveness between TEVAR and OCSR for TBAD patients TEVAR resulted in more survival benefits, in addition to lower risk of acute renal failure, respiratory failure and bleeding The results of stratified analyses according to patients’ characteristics were conducted
DOI: 10.6084/m9.figshare.10048184.v1
title: Thoracic endovascular aortic repair versus open chest surgical repair for patients with type B aortic dissection: a systematic review and meta-analysis

description: <b>Aim:</b> This meta-analysis study aimed to compare the efficacy and safety of TEVAR versus OCSR for TBAD patients. <b>Methods:</b> We systematically searched PubMed, EmBase, and the Cochrane library to identify studies compared the effectiveness of TEVAR and OCSR in TBAD patients from the inception up to July 2019. The summary results were calculated using a random-effects model. <b>Results:</b> The electronic search identified 1,894 studies, and 18 studies with 9,664 TBAD patients were included. We noted patients received TEVAR were associated with a reduced risk of in-hospital mortality, acute renal failure, respiratory failure, and bleeding as compared with OCSR, whereas no significant differences between groups for the risk of stroke, myocardial infarction, paraplegia, mesenteric ischaemia/infarction, reinterventions, sepsis, and spinal cord ischaemia. <b>Conclusions:</b> The findings of this meta-analysis study suggested that TEVAR resulted in more short-term survival benefits. Moreover, the reduced risk of acute renal failure, respiratory failure and bleeding was detected in TEVAR group. The treatment effects of TEVAR versus OCSR on specific complications should be further verified by a study with high-level of evidence.Key messageComprehensive collected studies investigated the treatment effectiveness between TEVAR and OCSR for TBAD patientsTEVAR resulted in more survival benefits, in addition to lower risk of acute renal failure, respiratory failure and bleedingThe results of stratified analyses according to patients’ characteristics were conducted Comprehensive collected studies investigated the treatment effectiveness between TEVAR and OCSR for TBAD patients TEVAR resulted in more survival benefits, in addition to lower risk of acute renal failure, respiratory failure and bleeding The results of stratified analyses according to patients’ characteristics were conducted
DOI: 10.6084/m9.figshare.17912507
title: diagnostic statement dictionary

description: This file describes the AHA statements and codes used in ECG records
DOI: 10.34740/kaggle/dsv/7588936
title: COVID Vaccination in World (updated daily)
DOI: 10.6084/m9.figshare.22624945
title: Additional file 5 of circMMD reduction following tumor treating fields inhibits glioblastoma progression through FUBP1/FIR/DVL1 and miR-15b-5p/FZD6 signaling

description: Additional file 5: Table S4. Differentially expressed genes between circMMD knockdown and NC groups.
DOI: 10.6084/m9.figshare.22624948
title: Additional file 6 of circMMD reduction following tumor treating fields inhibits glioblastoma progression through FUBP1/FIR/DVL1 and miR-15b-5p/FZD6 signaling

description: Additional file 6: Table S5. Candidate proteins extracted by circMMD sense probe.
DOI: 10.6084/m9.figshare.22624819
title: Additional file 1 of Genome-wide identification and expression analysis of DREB family genes in cotton

description: Additional file 1: Table S1. WGD or segmental and tandem gene pairs.
DOI: 10.5281/zenodo.10617483
title: A dataset to model Early Neolithic resource dependency in North-West Europe: draft and experimental code with dummy data

description: This code and the datasets are currently in preparation for the following paper (see below)

Here, we present a dummy code and data to replicate the analysis.

 

_____________

 

One major pillar of the Neolithisation process in Central Europe is the abundance of lithic resources for the production of high quality stone tools. Whether the raw material is sourced from local geological units or gets transported via large-scale communication networks is, however, not yet fully understood. To trace the distribution patterns of early Neolithic resource dispersal, this datasets presents a multicomponent network analysis and the first resource dependency model of Middle Eocene lithic records across Central-West Europe. The model builds on topographic landscape permeability and Bartonian silicite dispersal and estimates the chaîne opératoire from i) directly sourced raw material based on accumulative cost functions; ii) chronologically differentiated network models; iii) a probability model of potential site distributions based on a point process model. From these approaches, we resume that early Neolithic site locations were particularly targeted at connecting to the supraregional resource exchange network originating from the Paris Basin. Local resource mining predominated in the core region of Bartonian records whereas distant sites were located on or close to high-probability dissemination corridors. We conclude that major site distributions can be expected in close distance to the resource with satellite agglomerations in secondary centers in a star-shaped pattern across the study area.

 

Dataset to:

Kempf, M. & Denis, S. (2024): Resource dependency and communication networks in Early Neolithic North West Europe (under review)
DOI: 10.5281/zenodo.10617484
title: A dataset to model Early Neolithic resource dependency in North-West Europe: draft and experimental code with dummy data

description: This code and the datasets are currently in preparation for the following paper (see below)

Here, we present a dummy code and data to replicate the analysis.

 

_____________

 

One major pillar of the Neolithisation process in Central Europe is the abundance of lithic resources for the production of high quality stone tools. Whether the raw material is sourced from local geological units or gets transported via large-scale communication networks is, however, not yet fully understood. To trace the distribution patterns of early Neolithic resource dispersal, this datasets presents a multicomponent network analysis and the first resource dependency model of Middle Eocene lithic records across Central-West Europe. The model builds on topographic landscape permeability and Bartonian silicite dispersal and estimates the chaîne opératoire from i) directly sourced raw material based on accumulative cost functions; ii) chronologically differentiated network models; iii) a probability model of potential site distributions based on a point process model. From these approaches, we resume that early Neolithic site locations were particularly targeted at connecting to the supraregional resource exchange network originating from the Paris Basin. Local resource mining predominated in the core region of Bartonian records whereas distant sites were located on or close to high-probability dissemination corridors. We conclude that major site distributions can be expected in close distance to the resource with satellite agglomerations in secondary centers in a star-shaped pattern across the study area.

 

Dataset to:

Kempf, M. & Denis, S. (2024): Resource dependency and communication networks in Early Neolithic North West Europe (under review)