cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.6999710.v1
title: Additional file 1: of Forward and reverse mutations in stages of cancer development

description: Table S1. Information on 103 samples analyzed by AluScan. (XLSX 13Â kb)
DOI: 10.6084/m9.figshare.7523990.v1
title: Additional file 1: of Recommendation for the definition of postoperative radiotherapy target volume based on a pooled analysis of patterns of failure after radical surgery among patients with thoracic esophageal squamous cell carcinoma

description: Table S1. Eligible studies list. Table S2. Study list that containing patients number receiving postoperative radiation therapy. Table S3. Recurrence pattern summary using recurrence rate based on studies with no PORT or just doing the PORT in not more than 10% of patients. Table S4. Recurrence pattern summary using recurrence ratio based on the studies with no PORT or just doing the PORT in not more than 10% of patients. Figure S1. Recurrence pattern summary using recurrence ratio based on the studies with no PORT or just doing the PORT in not more than 10% of patients. (ZIP 143 kb)
DOI: 10.6084/m9.figshare.7523834.v1
title: Additional file 1: of Interactive effects of multiple vernalization (Vrn-1)- and photoperiod (Ppd-1)-related genes on the growth habit of bread wheat and their association with heading and flowering time

description: Table S2. The genotypes of Ppd-1 and their effects on heading and flowering dates. (XLS 25 kb)
DOI: 10.6084/m9.figshare.7524014
title: MOESM2 of Genomics and biochemistry investigation on the metabolic pathway of milled wood and alkali lignin-derived aromatic metabolites of Comamonas serinivorans SP-35

description: Additional file 2. Genome annotation of Comamonas serinivorans SP-35.
DOI: 10.6084/m9.figshare.7524014.v1
title: MOESM2 of Genomics and biochemistry investigation on the metabolic pathway of milled wood and alkali lignin-derived aromatic metabolites of Comamonas serinivorans SP-35

description: Additional file 2. Genome annotation of Comamonas serinivorans SP-35.
DOI: 10.6084/m9.figshare.6999737
title: Additional file 2: of Forward and reverse mutations in stages of cancer development

description: Table S2. Tumor purities of B-N-P-T tetra and B-N-T trio samples estimated by absCN-seq. (XLSX 10Â kb)
DOI: 10.6084/m9.figshare.6999776
title: Additional file 2: of bioSyntax: syntax highlighting for computational biology

description: Table S1. Biological class definitions and colour definitions for the default bioSyntax theme in hexadecimal (gedit, sublime, VSCode, and gvim), cterm (vim), and 8-bit ANSI escape character (less) colours. (XLS 186 kb)
DOI: 10.17028/rd.lboro.14339624.v1
title: Supplementary information files for Concurrent measurement of nitrate and ammonium in water and soil samples using ion‐selective electrodes: tackling sensitivity and precision issues

description: Supplementary files for article Concurrent measurement of nitrate and ammonium in water and soil samples using ion‐selective electrodes: tackling sensitivity and precision issues. In this paper, we demonstrate the suitability, sensitivity, and precision of low‐cost and easy‐to‐use ion‐selective electrodes (ISEs) for concurrent detection of NH<sub>4</sub><sup>+</sup> and NO<sub>3</sub><sup>‐</sup> in soil and water by technical and non‐technical end‐users to enable efficient soil and water management exposed to chronic reactive nitrogen loading. We developed a simplified methodology for sample preparation followed by the demonstration of an analytical methodology resulting in improvements of sensitivity and precision of ISEs. Herein, we compared and contrasted ISEs with traditional laboratory‐based technique such as Flow Injection Analysis (FIA) and portable colorimetric assay followed by comparisons of linear regression and Bayesian nonlinear calibration approaches applied on both direct potentiometry and standard addition modes of analysis in terms of in‐field applications and improvement of sensitivity and precision. The ISEs were validated for sensing on a range of ambient soil and water samples representing a range of NH<sub>4</sub><sup>+</sup> and NO<sub>3</sub><sup>‐</sup> concentrations from pristine to excessive saturation conditions. Herein developed methodology showed excellent agreement with lab‐based and portable analytical techniques while demonstrating improvements in precision and sensitivity analysis illustrated by a decrease in confidence intervals by 50‐60%. We also demonstrated the utilization of the entire ISE response curve thus removing the biases originating from linear approximation which is often currently employed. Therefore, we show that ISEs are robust yet low cost and an easy to use technology that can enable high‐frequency measurement of mineral N and help to improve our understanding of N transformation processes as influenced by soil management, fertilization, land use, and climate change.
DOI: 10.6084/m9.figshare.6999782.v1
title: Additional file 6: of Forward and reverse mutations in stages of cancer development

description: Table S5. Summary of CNV mutations in B-N-P-T tetra samples. (XLSX 11Â kb)
DOI: 10.6084/m9.figshare.6999833
title: Additional file 2: of MetaBinG2: a fast and accurate metagenomic sequence classification system for samples with many unknown organisms

description: Sequence classification results ofÂ MetaSUBÂ data from Boston. (XLSX 71Â kb)
DOI: 10.6084/m9.figshare.6999860.v1
title: Additional file 4: of MetaBinG2: a fast and accurate metagenomic sequence classification system for samples with many unknown organisms

description: Sequence classification results of MetaSUB data from Sacramento. (XLSX 16Â kb)
DOI: 10.6084/m9.figshare.7523843.v1
title: Additional file 2: of Interactive effects of multiple vernalization (Vrn-1)- and photoperiod (Ppd-1)-related genes on the growth habit of bread wheat and their association with heading and flowering time

description: Table S1. Primers used in this study. (XLS 71 kb)
DOI: 10.6084/m9.figshare.7524092
title: MOESM16 of Copy number variation in the MSRB3 gene enlarges porcine ear size through a mechanism involving miR-584-5p

description: Additional file 16: Table S8. Predicted target genes of miR-584-5p in silico.
DOI: 10.6084/m9.figshare.7524092.v1
title: MOESM16 of Copy number variation in the MSRB3 gene enlarges porcine ear size through a mechanism involving miR-584-5p

description: Additional file 16: Table S8. Predicted target genes of miR-584-5p in silico.
DOI: 10.6084/m9.figshare.7524164
title: Additional file 1: of Genome-wide analysis and stress-responsive expression of CCCH zinc finger family genes in Brassica rapa

description: Detailed information of CCCH gene family in B.rapa. Sequences and information of CCCH genes and proteins came from http://brassicadb.org/brad / (XLSX 51 kb)
DOI: 10.6084/m9.figshare.6999908
title: Additional file 8: of Construction of a high-density genetic map and fine QTL mapping for growth and nutritional traits of Crassostrea gigas

description: Summary of the sex-specific maps. (XLS 35 kb)
DOI: 10.6084/m9.figshare.7524170
title: Additional file 2: of Genome-wide analysis and stress-responsive expression of CCCH zinc finger family genes in Brassica rapa

description: CCCH duplicated genes of B. rapa. Syntenic analysis between Arabidopsis and B. rapa was detected at http://brassicadb.org/brad/searchSyntenytPCK.php ; Ka and Ks were calculated by DnaSP 6.0; Cover of CDS and Identify of protein was checked by NCBI. (XLSX 15 kb)
DOI: 10.6084/m9.figshare.7524224
title: Additional file 9: of Genome-wide analysis and stress-responsive expression of CCCH zinc finger family genes in Brassica rapa

description: Primers list of subfamily- IX in B. rapa. (XLSX 12 kb)
DOI: 10.6084/m9.figshare.6999818.v1
title: Additional file 1: of Construction of a high-density genetic map and fine QTL mapping for growth and nutritional traits of Crassostrea gigas

description: Adaptors and primers used in this study. (XLS 34 kb)
DOI: 10.6084/m9.figshare.7524173.v1
title: Additional file 3: of Genome-wide analysis and stress-responsive expression of CCCH zinc finger family genes in Brassica rapa

description: Detailed information of CCCH gene family in Arabidopsis, rice, B. oleracea and B. nigra. Information came from Wang et al. [23]. (XLS 238 kb)
DOI: 10.6084/m9.figshare.7524086
title: MOESM15 of Copy number variation in the MSRB3 gene enlarges porcine ear size through a mechanism involving miR-584-5p

description: Additional file 15: Table S7. CNV distribution in 59 Landrace pigs used for eQTL mapping of miR-584-5p.
DOI: 10.6084/m9.figshare.7524119.v1
title: MOESM3 of Copy number variation in the MSRB3 gene enlarges porcine ear size through a mechanism involving miR-584-5p

description: Additional file 3: Table S2. Primers for CNV genotyping.
DOI: 10.6084/m9.figshare.6999812.v1
title: Additional file 8: of Forward and reverse mutations in stages of cancer development

description: Table S7. The exact residue-by-residue SNV mutations in each sample of the B-N-T trio sample cases. (XLSX 3018Â kb)
DOI: 10.6084/m9.figshare.7524101.v1
title: MOESM17 of Copy number variation in the MSRB3 gene enlarges porcine ear size through a mechanism involving miR-584-5p

description: Additional file 17: Table S9. Differentially expressed genes identified in ear tissue between CNV/CNV and wild-type animals.
DOI: 10.6084/m9.figshare.6999842
title: Additional file 3: of Construction of a high-density genetic map and fine QTL mapping for growth and nutritional traits of Crassostrea gigas

description: Phenotype values and variance. Full names for the abbreviation are shown in Additional file 2. (XLS 112 kb)
DOI: 10.6084/m9.figshare.7524119
title: MOESM3 of Copy number variation in the MSRB3 gene enlarges porcine ear size through a mechanism involving miR-584-5p

description: Additional file 3: Table S2. Primers for CNV genotyping.
DOI: 10.6084/m9.figshare.6999659
title: Additional file 15: of Forward and reverse mutations in stages of cancer development

description: Table S11. The exact window-by-window CNV mutations in each sample of the B-N-P-T tetra sample cases. (XLSX 783Â kb)
DOI: 10.6084/m9.figshare.6999848.v1
title: Additional file 3: of MetaBinG2: a fast and accurate metagenomic sequence classification system for samples with many unknown organisms

description: Sequence classification results ofÂ  MetaSUB data from New York. (XLSX 2515Â kb)
DOI: 10.6084/m9.figshare.21155387.v1
title: A scalable system for the fast production of RNA with homogeneous terminal ends

description: In vitro transcription (IVT) using T7 RNA polymerase has become the most common method to synthesize RNAs for use in basic research and pharmaceutical applications. To solve the heterogeneity issue associated with the system, cis-acting ribozymes have been exploited to direct co-transcriptional processing to yield target RNAs with precisely defined ends. However, traditionally used ribozymes have many limitations, such as low efficiency and special sequence requirements of target RNAs. In addition, the introduction of ribozymes in IVT complicates the downstream purification of target RNAs. Here we describe a new cassette of engineered ribozymes (HHV-Kt and Twister-Kt) that can work in concert to produce RNA with defined 5’ and 3’ ends. The pair of ribozymes displayed reliably high activity when working with RNA of various lengths and structures. The engineered ribozymes also carry a K-turn RNA motif that enables fast post-IVT clearance of cleaved ribozymes and uncleaved precursors using K-turn affinity resins. Finally, we demonstrated the scalability of our system for the rapid production of large quantities of homogeneous RNA samples.
DOI: 10.6084/m9.figshare.7524164.v1
title: Additional file 1: of Genome-wide analysis and stress-responsive expression of CCCH zinc finger family genes in Brassica rapa

description: Detailed information of CCCH gene family in B.rapa. Sequences and information of CCCH genes and proteins came from http://brassicadb.org/brad / (XLSX 51 kb)
DOI: 10.6084/m9.figshare.7524170.v1
title: Additional file 2: of Genome-wide analysis and stress-responsive expression of CCCH zinc finger family genes in Brassica rapa

description: CCCH duplicated genes of B. rapa. Syntenic analysis between Arabidopsis and B. rapa was detected at http://brassicadb.org/brad/searchSyntenytPCK.php ; Ka and Ks were calculated by DnaSP 6.0; Cover of CDS and Identify of protein was checked by NCBI. (XLSX 15 kb)
DOI: 10.6084/m9.figshare.6999698
title: Additional file 17: of Forward and reverse mutations in stages of cancer development

description: Table S13. SNV mutations enriched pathways and genes in B-N-P-T tetra sample cases. (XLSX 109Â kb)
DOI: 10.6084/m9.figshare.6999899
title: Additional file 7: of Construction of a high-density genetic map and fine QTL mapping for growth and nutritional traits of Crassostrea gigas

description: Detailed information of 5024 haplotype markers used for genetic map construction. (XLS 1260 kb)
DOI: 10.6084/m9.figshare.6999899.v2
title: Additional file 7: of Construction of a high-density genetic map and fine QTL mapping for growth and nutritional traits of Crassostrea gigas

description: Detailed information of 5024 haplotype markers used for genetic map construction. (XLS 1260 kb)
DOI: 10.6084/m9.figshare.19582444
title: Additional file 15 of High activity and high functional connectivity are mutually exclusive in resting state zebrafish and human brains

description: Additional file 15. Table S1.
DOI: 10.6084/m9.figshare.6999659.v1
title: Additional file 15: of Forward and reverse mutations in stages of cancer development

description: Table S11. The exact window-by-window CNV mutations in each sample of the B-N-P-T tetra sample cases. (XLSX 783Â kb)
DOI: 10.6084/m9.figshare.6999698.v1
title: Additional file 17: of Forward and reverse mutations in stages of cancer development

description: Table S13. SNV mutations enriched pathways and genes in B-N-P-T tetra sample cases. (XLSX 109Â kb)
DOI: 10.6084/m9.figshare.7524200.v1
title: Additional file 6: of Genome-wide analysis and stress-responsive expression of CCCH zinc finger family genes in Brassica rapa

description: The number of different CCCH types in Plants. (XLSX 10 kb)
DOI: 10.6084/m9.figshare.7524101
title: MOESM17 of Copy number variation in the MSRB3 gene enlarges porcine ear size through a mechanism involving miR-584-5p

description: Additional file 17: Table S9. Differentially expressed genes identified in ear tissue between CNV/CNV and wild-type animals.
DOI: 10.6084/m9.figshare.6999848
title: Additional file 3: of MetaBinG2: a fast and accurate metagenomic sequence classification system for samples with many unknown organisms

description: Sequence classification results ofÂ  MetaSUB data from New York. (XLSX 2515Â kb)
DOI: 10.6084/m9.figshare.7523990
title: Additional file 1: of Recommendation for the definition of postoperative radiotherapy target volume based on a pooled analysis of patterns of failure after radical surgery among patients with thoracic esophageal squamous cell carcinoma

description: Table S1. Eligible studies list. Table S2. Study list that containing patients number receiving postoperative radiation therapy. Table S3. Recurrence pattern summary using recurrence rate based on studies with no PORT or just doing the PORT in not more than 10% of patients. Table S4. Recurrence pattern summary using recurrence ratio based on the studies with no PORT or just doing the PORT in not more than 10% of patients. Figure S1. Recurrence pattern summary using recurrence ratio based on the studies with no PORT or just doing the PORT in not more than 10% of patients. (ZIP 143 kb)
DOI: 10.6084/m9.figshare.6999800.v1
title: Additional file 7: of Forward and reverse mutations in stages of cancer development

description: Table S6. Summary of SNV mutations in B-N-T trio samples. (XLSX 14Â kb)
DOI: 10.6084/m9.figshare.13291147
title: Additional file 3 of Breastfeeding restored the gut microbiota in caesarean section infants and lowered the infection risk in early life

description: Additional file 3.
DOI: 10.6084/m9.figshare.7524458.v1
title: Additional file 1: of Comparative analysis of the mitochondrial genomes of oriental spittlebug trible Cosmoscartini: insights into the relationships among closely related taxa

description: Table S1. Gene content of our nine sequenced specimens and other published Cercopidae mitogenomes. (XLSX 24 kb)
DOI: 10.6084/m9.figshare.6999764.v1
title: Additional file 4: of Forward and reverse mutations in stages of cancer development

description: Table S4. The exact residue-by-residue SNV mutations in each sample of the B-N-P-T tetra sample cases. (XLSX 652Â kb)
DOI: 10.6084/m9.figshare.7524470
title: Additional file 3: of Comparative analysis of the mitochondrial genomes of oriental spittlebug trible Cosmoscartini: insights into the relationships among closely related taxa

description: Table S3. Start and stop codons of 13 protein-coding genes of nine Cosmoscatini species. (XLSX 10 kb)
DOI: 10.6084/m9.figshare.7524554.v1
title: Additional file 1: of Analysis of repeated leukocyte DNA methylation assessments reveals persistent epigenetic alterations after an incident myocardial infarction

description: Supplemental methods, Table S1. CpGs from KORA EWAS. Those CpGs with a false discovery rate P &lt; 0.15 in an epigenome-wide association study in KORA using the difference in methylation between the baseline and follow-up exams as the outcome (after adjustment for technical factors) and the occurrence of an MI as the predictor while adjusting for clinical covariates (at both baseline and follow-up) in a generalized estimating equations model. Table S2. The 174 CpGs which were retained from the initial elastic net model performed in KORA. Table S3. Epigenetic loci with non-zero coefficients from the NAS elastic net model. Table S4. AUC for the model fit with the loci with non-zero betas from the NAS elastic net in KORA, NAS, and InCHIANTI. Table S5. Medication usage in KORA at baseline and follow-up. We divide out the medication usage in KORA at (a) baseline and (b) follow-up for those individuals who did not develop and incident MI during the observation time (MI free) vs those that did (MI cases). Table S6. Association between 11 epigenetic fingerprint loci and medications. Associations were performed relative to both starting and stopping six classes of medications: diuretic, beta-blockers, anti-platelet, calcium channel blocker, statins, ACE-inhibitor, and angiotensin inhibitor. Table S7. Count of the genes within 1 Mb of each epigenetic fingerprint loci. Table S8. Integration of methylation, gene expression, and metabolomics for the suggestive (P &lt; 0.001) gene expression-metabolite associations. Figure S1. Post hoc power estimations for the observed effects at our FDR cutoff of 0.15 for the initial screening EWAS. (ZIP 196 kb)
DOI: 10.6084/m9.figshare.7524587
title: Additional file 5: of DNA methylation age is not affected in psoriatic skin tissue

description: Table S4. CpGs associated with age (FDRâ &lt;â 0.05) in paired PN and PP samples. (XLSX 90Â kb)
DOI: 10.6084/m9.figshare.7524605
title: Additional file 8: of DNA methylation age is not affected in psoriatic skin tissue

description: Table S7. Eight hundred and eighty-one candidates Ps-dependent age-associated CpGs contrasted by NN and PP using a loose cut-off (Pâ &lt;â 0.01). (XLSX 208Â kb)
DOI: 10.6084/m9.figshare.6999776.v1
title: Additional file 2: of bioSyntax: syntax highlighting for computational biology

description: Table S1. Biological class definitions and colour definitions for the default bioSyntax theme in hexadecimal (gedit, sublime, VSCode, and gvim), cterm (vim), and 8-bit ANSI escape character (less) colours. (XLS 186 kb)
DOI: 10.6084/m9.figshare.6999836
title: Additional file 9: of Forward and reverse mutations in stages of cancer development

description: Table S8. Summary of SNV mutations in N-T-M trio samples. (A) AluScan, (B) WES-Non-Lung, (C) WES-NSCLC-L, (D) WES-NSCLC-H, and (E) WGS-Liver-M. (XLSX 48Â kb)
DOI: 10.6084/m9.figshare.6999860
title: Additional file 4: of MetaBinG2: a fast and accurate metagenomic sequence classification system for samples with many unknown organisms

description: Sequence classification results of MetaSUB data from Sacramento. (XLSX 16Â kb)
DOI: 10.6084/m9.figshare.5951815
title: Analysis of LncRNA expression in cell differentiation

description: Lineage-specific cell differentiation is a precise and coordinated biological process. To explore the roles of long noncoding RNA (lncRNA) in this process, the expression of polyA-minus RNAs was comparatively studied during the course of myocyte and adipocyte differentiation. In addition to identifying thousands of novel lncRNAs, distinct lncRNA profiles were revealed during lineage-specific differentiation, showing their active involvement in this process. This study further found that lncRNAs were organized in clusters and are co-regulated, constituting transcription open domains (TODs). In myocyte differentiation of C2C12 cells, loss-of-function screening identified three myogenic lncRNAs. Knockdown of their expression compromised not only the differentiation process, but also the essential signaling pathway. In addition to showing that lncRNAs are actively involved in cell differentiation, our results start to reveal a comprehensive signaling pathway, involving both protein and lncRNA factors.
DOI: 10.6084/m9.figshare.6999836.v1
title: Additional file 9: of Forward and reverse mutations in stages of cancer development

description: Table S8. Summary of SNV mutations in N-T-M trio samples. (A) AluScan, (B) WES-Non-Lung, (C) WES-NSCLC-L, (D) WES-NSCLC-H, and (E) WGS-Liver-M. (XLSX 48Â kb)
DOI: 10.6084/m9.figshare.7524125
title: MOESM4 of Copy number variation in the MSRB3 gene enlarges porcine ear size through a mechanism involving miR-584-5p

description: Additional file 4: Table S3. Primers for gene expression analysis.
DOI: 10.6084/m9.figshare.7524086.v1
title: MOESM15 of Copy number variation in the MSRB3 gene enlarges porcine ear size through a mechanism involving miR-584-5p

description: Additional file 15: Table S7. CNV distribution in 59 Landrace pigs used for eQTL mapping of miR-584-5p.
DOI: 10.6084/m9.figshare.21151223.v1
title: Additional file 3 of Atlas of regulated target genes of transcription factors (ART-TF) in human ES cells

description: Additional file 3: Surrogate ChIP-seq data for finding indirect regulated targets of transcription factors.
DOI: 10.6084/m9.figshare.21680513
title: Dataset1.zip

description: Additional projected images from simulations and experiments
DOI: 10.6084/m9.figshare.6999812
title: Additional file 8: of Forward and reverse mutations in stages of cancer development

description: Table S7. The exact residue-by-residue SNV mutations in each sample of the B-N-T trio sample cases. (XLSX 3018Â kb)
DOI: 10.6084/m9.figshare.7524578.v1
title: Additional file 3: of DNA methylation age is not affected in psoriatic skin tissue

description: Table S3. Eight thousand and thirty-two CpGs significantly associated with age in PP. (XLSX 534Â kb)
DOI: 10.6084/m9.figshare.7524587.v1
title: Additional file 5: of DNA methylation age is not affected in psoriatic skin tissue

description: Table S4. CpGs associated with age (FDRâ &lt;â 0.05) in paired PN and PP samples. (XLSX 90Â kb)
DOI: 10.6084/m9.figshare.6999899.v1
title: Additional file 7: of Construction of a high-density genetic map and fine QTL mapping for growth and nutritional traits of Crassostrea gigas

description: Detailed information of 5024 haplotype markers used for genetic map construction. (XLS 12914 kb)
DOI: 10.6084/m9.figshare.7524200
title: Additional file 6: of Genome-wide analysis and stress-responsive expression of CCCH zinc finger family genes in Brassica rapa

description: The number of different CCCH types in Plants. (XLSX 10 kb)
DOI: 10.6084/m9.figshare.7524464.v1
title: Additional file 2: of Comparative analysis of the mitochondrial genomes of oriental spittlebug trible Cosmoscartini: insights into the relationships among closely related taxa

description: Table S2. Codons usage for the 13 protein-coding genes of nine Cosmoscatini species. (XLSX 24 kb)