cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.8287664.v2
title: Population genetic polymorphism and mutation analysis of 19 autosomal STR loci in Jiangsu Han individuals in Eastern China

description: <b>Aim:</b> Genetic polymorphisms and the mutation ratio of 19 autosomal short tandem repeat (STR) loci were analysed in 10,000 individuals and 7755 families from Jiangsu Province in Eastern China. <b>Subjects and methods:</b> Nineteen STR loci were amplified by a multiplex amplification system and genotyped on the ABI 3130 Genetic Analyser. Allele frequencies, forensic parameters and mutations for the 19 autosomal STR loci were statistically analysed. <b>Results:</b> In total, 344 genotypes were discovered. No significant deviation from Hardy-Weinberg equilibrium was observed. The combined power of discrimination reached 0.9999999999999999984341, and the combined probability of paternity exclusion was 0.999999989. The pairwise genetic distance and <i>p</i>-values between the Jiangsu and 17 published populations depended on the F<sub>ST</sub> value calculation and are shown by the neighbour-joining evolutionary tree. No statistically significant differences were found, except for the Xinjiang Altay Han (<i>p</i> = 0.01802) population. The average mutation rate of the Jiangsu population across all 19 loci was 1.4 × 10<sup>−3</sup>. The average mutation rate of the 13 core CODIS STR loci remained below 2 × 10<sup>−3</sup> and there was no difference and relatively high consistency (<i>p</i> <b>Conclusions:</b> Allelic genetic polymorphisms and mutation data were obtained from a large number of samples, which indicated that the amplification kit is suitable for forensic application and that the Jiangsu population has its own genetic characteristics that are different from those of other ethnic populations.
DOI: 10.6084/m9.figshare.8287664.v1
title: Population genetic polymorphism and mutation analysis of 19 autosomal STR loci in Jiangsu Han individuals in Eastern China

description: <b>Aim</b>: Genetic polymorphisms and the mutation ratio of 19 autosomal short tandem repeat (STR) loci were analysed in 10,000 individuals and 7,755 families from Jiangsu Province in Eastern China. <b>Subjects and methods</b>: Nineteen STR loci were amplified by a multiplex amplification system and genotyped on the ABI 3130 Genetic Analyzer. Allele frequencies, forensic parameters and mutation for the 19 autosomal STR loci were statistically analysed. <b>Results</b>: In total, 344 genotypes were discovered. No significant deviation from Hardy-Weinberg equilibrium was observed. The combined power of discrimination reached 0.9999999999999999984341, and the combined probability of paternity exclusion was 0.999999989. The pairwise genetic distance and P values between the Jiangsu and 17 published populations depended on the F<sub>ST</sub> value calculation and are shown by the neighbour-joining evolutionary tree. No statistically significant differences were found, except for the Xinjiang Altay Han (P = 0.01802) population. The average mutation rate of the Jiangsu population across all 19 loci was 1.4 × 10<sup>−3</sup>. The average mutation rate of the 13 core CODIS STR loci remained below 2 × 10<sup>−3</sup>, and there was no difference and relatively high consistency (<i>P</i> <b>Conclusions</b>: We obtained allelic genetic polymorphisms and mutation data from a large number of samples, which indicated that the amplification kit is suitable for forensic application and that the Jiangsu population has its own genetic characteristics that are different from those of other ethnic populations.
DOI: 10.6084/m9.figshare.8287628
title: DNA barcoding of the rodent genus <i>Oligoryzomys</i> (Cricetidae: Sigmodontinae): mitogenomic-anchored database and identification of nuclear mitochondrial translocations (Numts)

description: DNA barcoding has become a standard method for species identification in taxonomically complex groups. An important step of the barcoding process is the construction of a library of voucher-based material that was properly identified by independent methods, free of inaccurate identification, and paralogs. We provide here a <i>cytochrome oxidase I</i> (<i>mt-Co1</i>) DNA barcode database for species of the genus <i>Oligoryzomys</i>, based on type material and karyotyped specimens, and anchored on the mitochondrial genome of one species of <i>Oligoryzomys</i>, <i>O. stramineus</i>. To evaluate the taxonomic determination of new COI sequences, we assessed species intra/interspecific genetic distances (barcode gap), performed the General Mixed Yule Coalescent method (GMYC) for lineages’ delimitation, and identified diagnostic nucleotides for each species of <i>Oligoryzomys</i>. Phylogenetic analyses of <i>Oligoryzomys</i> were performed on 2 datasets including 14 of the 23 recognized species of this genus: a <i>mt-Co1</i> only matrix, and a concatenated matrix including <i>mt-Co1</i>, <i>cytochrome b</i> (<i>mt-Cytb</i>), and <i>intron 7 of the nuclear fibrinogen beta chain gene</i> (<i>i7Fgb</i>). We recovered nuclear-mitochondrial translocated (Numts) pseudogenes on our samples and identified several published sequences that are cases of Numts. We analyzed the rate of non-synonymous and synonymous substitution, which were higher in Numts in comparison to mtDNA sequences. GMYC delimitations and DNA barcode gap results highlight the need for further work that integrate molecular, karyotypic, and morphological analyses, as well as additional sampling, to tackle persistent problems in the taxonomy of <i>Oligoryzomys</i>.
DOI: 10.6084/m9.figshare.8287628.v2
title: DNA barcoding of the rodent genus <i>Oligoryzomys</i> (Cricetidae: Sigmodontinae): mitogenomic-anchored database and identification of nuclear mitochondrial translocations (Numts)

description: DNA barcoding has become a standard method for species identification in taxonomically complex groups. An important step of the barcoding process is the construction of a library of voucher-based material that was properly identified by independent methods, free of inaccurate identification, and paralogs. We provide here a <i>cytochrome oxidase I</i> (<i>mt-Co1</i>) DNA barcode database for species of the genus <i>Oligoryzomys</i>, based on type material and karyotyped specimens, and anchored on the mitochondrial genome of one species of <i>Oligoryzomys</i>, <i>O. stramineus</i>. To evaluate the taxonomic determination of new COI sequences, we assessed species intra/interspecific genetic distances (barcode gap), performed the General Mixed Yule Coalescent method (GMYC) for lineages’ delimitation, and identified diagnostic nucleotides for each species of <i>Oligoryzomys</i>. Phylogenetic analyses of <i>Oligoryzomys</i> were performed on 2 datasets including 14 of the 23 recognized species of this genus: a <i>mt-Co1</i> only matrix, and a concatenated matrix including <i>mt-Co1</i>, <i>cytochrome b</i> (<i>mt-Cytb</i>), and <i>intron 7 of the nuclear fibrinogen beta chain gene</i> (<i>i7Fgb</i>). We recovered nuclear-mitochondrial translocated (Numts) pseudogenes on our samples and identified several published sequences that are cases of Numts. We analyzed the rate of non-synonymous and synonymous substitution, which were higher in Numts in comparison to mtDNA sequences. GMYC delimitations and DNA barcode gap results highlight the need for further work that integrate molecular, karyotypic, and morphological analyses, as well as additional sampling, to tackle persistent problems in the taxonomy of <i>Oligoryzomys</i>.
DOI: 10.6084/m9.figshare.8287628.v1
title: DNA barcoding of the rodent genus <i>Oligoryzomys</i> (Cricetidae: Sigmodontinae): mitogenomic-anchored database and identification of nuclear mitochondrial translocations (Numts)

description: DNA barcoding has become a standard method for species identification in taxonomically complex groups. An important step of the barcoding process is the construction of a library of voucher-based material that was properly identified by independent methods, free of inaccurate identification, and paralogs. We provide here a <i>cytochrome oxidase I</i> (<i>mt-Co1</i>) DNA barcode database for species of the genus <i>Oligoryzomys</i>, based on type material and karyotyped specimens, and anchored on the mitochondrial genome of one species of <i>Oligoryzomys</i>, <i>O. stramineus</i>. To evaluate the taxonomic determination of new COI sequences, we assessed species intra/interspecific genetic distances (barcode gap), performed the General Mixed Yule Coalescent method (GMYC) for lineages’ delimitation, and identified diagnostic nucleotides for each species of <i>Oligoryzomys</i>. Phylogenetic analyses of <i>Oligoryzomys</i> were performed on 2 datasets including 14 of the 23 recognized species of this genus: a <i>mt-Co1</i> only matrix, and a concatenated matrix including <i>mt-Co1</i>, <i>cytochrome b</i> (<i>mt-Cytb</i>), and <i>intron 7 of the nuclear fibrinogen beta chain gene</i> (<i>i7Fgb</i>). We recovered nuclear-mitochondrial translocated (Numts) pseudogenes on our samples and identified several published sequences that are cases of Numts. We analyzed the rate of non-synonymous and synonymous substitution, which were higher in Numts in comparison to mtDNA sequences. GMYC delimitations and DNA barcode gap results highlight the need for further work that integrate molecular, karyotypic, and morphological analyses, as well as additional sampling, to tackle persistent problems in the taxonomy of <i>Oligoryzomys</i>.
DOI: 10.6084/m9.figshare.8287433
title: Additional file 1: of Improved outcomes in patients with positive metal sensitivity following revision total knee arthroplasty

description: Figure S1. Metal allergens panel. (XLSX 10 kb)
DOI: 10.6084/m9.figshare.8287433.v1
title: Additional file 1: of Improved outcomes in patients with positive metal sensitivity following revision total knee arthroplasty

description: Figure S1. Metal allergens panel. (XLSX 10 kb)
DOI: 10.6084/m9.figshare.8287334
title: Additional file 1: of Refinement of breast cancer molecular classification by miRNA expression profiles

description: Table S1. Summary of differentially expressed microRNAs. The selected cutoff for significance was FDR 0.01. (XLSX 2878 kb)
DOI: 10.6084/m9.figshare.8287328
title: MOESM2 of Transcriptome-based molecular systematics: Rhodnius montenegrensis (Triatominae) and its position within the Rhodnius prolixus–Rhodnius robustus cryptic–species complex

description: Additional file 2: Alignment S1. Cytb sequences. Alignment S2. ITS2 sequences. Alignment S3. D2-28S sequences.
DOI: 10.6084/m9.figshare.8287334.v1
title: Additional file 1: of Refinement of breast cancer molecular classification by miRNA expression profiles

description: Table S1. Summary of differentially expressed microRNAs. The selected cutoff for significance was FDR 0.01. (XLSX 2878 kb)
DOI: 10.6084/m9.figshare.8287325
title: MOESM1 of Transcriptome-based molecular systematics: Rhodnius montenegrensis (Triatominae) and its position within the Rhodnius prolixus–Rhodnius robustus cryptic–species complex

description: Additional file 1: Table S1. Details on transcriptome-read queries. Table S2. ITS2 sequences generated in this study.
DOI: 10.6084/m9.figshare.8287328.v1
title: MOESM2 of Transcriptome-based molecular systematics: Rhodnius montenegrensis (Triatominae) and its position within the Rhodnius prolixus–Rhodnius robustus cryptic–species complex

description: Additional file 2: Alignment S1. Cytb sequences. Alignment S2. ITS2 sequences. Alignment S3. D2-28S sequences.
DOI: 10.6084/m9.figshare.8287325.v1
title: MOESM1 of Transcriptome-based molecular systematics: Rhodnius montenegrensis (Triatominae) and its position within the Rhodnius prolixus–Rhodnius robustus cryptic–species complex

description: Additional file 1: Table S1. Details on transcriptome-read queries. Table S2. ITS2 sequences generated in this study.
DOI: 10.6084/m9.figshare.8287304
title: Additional file 3: of A simplified transposon mutagenesis method to perform phenotypic forward genetic screens in cultured cells

description: Table S1. Results from vemurafenib resistance screen in A375 cells. (XLSX 14 kb)
DOI: 10.6084/m9.figshare.8287304.v1
title: Additional file 3: of A simplified transposon mutagenesis method to perform phenotypic forward genetic screens in cultured cells

description: Table S1. Results from vemurafenib resistance screen in A375 cells. (XLSX 14 kb)
DOI: 10.6084/m9.figshare.8287229
title: Additional file 1: of Facility readiness in low and middle-income countries to address care of high risk/ small and sick newborns

description: Facility readiness data collection tool (level II newborn care). (XLSX 29 kb)
DOI: 10.6084/m9.figshare.8287229.v1
title: Additional file 1: of Facility readiness in low and middle-income countries to address care of high risk/ small and sick newborns

description: Facility readiness data collection tool (level II newborn care). (XLSX 29 kb)
DOI: 10.6084/m9.figshare.8287214
title: Additional file 1: of Incidence of cardiovascular disease and its associated risk factors in at-risk men and women in the United Arab Emirates: a 9-year retrospective cohort study

description: Dataset. Incidence of cardiovascular disease and associated risk factors in at-risk men and women in the United Arab Emirates: a 9-year retrospective cohort study. ID identification, DM diabetes mellitus, HTN hypertension, HDL-C high-density lipoprotein cholesterol, LDL-C low-density lipoprotein cholesterol, HbA1c glycosylated hemoglobin, eGFR estimated glomerular filtration rate, SBP systolic blood pressure, DBP diastolic blood pressure, BMI body mass index, CVD cardiovascular disease. (XLSX 126 kb)
DOI: 10.6084/m9.figshare.8287214.v1
title: Additional file 1: of Incidence of cardiovascular disease and its associated risk factors in at-risk men and women in the United Arab Emirates: a 9-year retrospective cohort study

description: Dataset. Incidence of cardiovascular disease and associated risk factors in at-risk men and women in the United Arab Emirates: a 9-year retrospective cohort study. ID identification, DM diabetes mellitus, HTN hypertension, HDL-C high-density lipoprotein cholesterol, LDL-C low-density lipoprotein cholesterol, HbA1c glycosylated hemoglobin, eGFR estimated glomerular filtration rate, SBP systolic blood pressure, DBP diastolic blood pressure, BMI body mass index, CVD cardiovascular disease. (XLSX 126 kb)
DOI: 10.6084/m9.figshare.8287193
title: Additional file 9: of A systematic analysis of genomics-based modeling approaches for prediction of drug response to cytotoxic chemotherapies

description: The file includes the MAD values for PCR models reported in results section A, B, C, and D. (XLSX 44 kb)
DOI: 10.6084/m9.figshare.8287196
title: Additional file 13: of Performance assessment of variant calling pipelines using human whole exome sequencing and simulated data

description: Table S8. Number of deletions and insertions with different base pair lengths detected by pipelines. (XLSX 59 kb)
DOI: 10.6084/m9.figshare.8287193.v1
title: Additional file 9: of A systematic analysis of genomics-based modeling approaches for prediction of drug response to cytotoxic chemotherapies

description: The file includes the MAD values for PCR models reported in results section A, B, C, and D. (XLSX 44 kb)
DOI: 10.6084/m9.figshare.8287196.v1
title: Additional file 13: of Performance assessment of variant calling pipelines using human whole exome sequencing and simulated data

description: Table S8. Number of deletions and insertions with different base pair lengths detected by pipelines. (XLSX 59 kb)
DOI: 10.6084/m9.figshare.8287184
title: Additional file 7: of A systematic analysis of genomics-based modeling approaches for prediction of drug response to cytotoxic chemotherapies

description: MAD for SVRLN models reported in Results section A. and B. (XLSX 18 kb)
DOI: 10.6084/m9.figshare.8287187
title: Additional file 8: of A systematic analysis of genomics-based modeling approaches for prediction of drug response to cytotoxic chemotherapies

description: The file includes the values of the Spearman correlation for PCR models corresponding to Figs.Â 3,Â 4, andÂ 5. (XLSX 86 kb)
DOI: 10.6084/m9.figshare.8287184.v1
title: Additional file 7: of A systematic analysis of genomics-based modeling approaches for prediction of drug response to cytotoxic chemotherapies

description: MAD for SVRLN models reported in Results section A. and B. (XLSX 18 kb)
DOI: 10.6084/m9.figshare.8287187.v1
title: Additional file 8: of A systematic analysis of genomics-based modeling approaches for prediction of drug response to cytotoxic chemotherapies

description: The file includes the values of the Spearman correlation for PCR models corresponding to Figs.Â 3,Â 4, andÂ 5. (XLSX 86 kb)
DOI: 10.6084/m9.figshare.8287172
title: Additional file 5: of A systematic analysis of genomics-based modeling approaches for prediction of drug response to cytotoxic chemotherapies

description: MAD for ANN models reported in Results section A. and B. (XLSX 18 kb)
DOI: 10.6084/m9.figshare.8287175
title: Additional file 6: of A systematic analysis of genomics-based modeling approaches for prediction of drug response to cytotoxic chemotherapies

description: Spearman correlations for SVRLN models reported in Results section A. and B and illustrated in Fig.Â 3. (XLSX 24 kb)
DOI: 10.6084/m9.figshare.8287169
title: Additional file 4: of A systematic analysis of genomics-based modeling approaches for prediction of drug response to cytotoxic chemotherapies

description: Spearman correlations for ANN models reported in Results section A. and B and illustrated in Fig.Â 3. (XLSX 26 kb)
DOI: 10.6084/m9.figshare.8287172.v1
title: Additional file 5: of A systematic analysis of genomics-based modeling approaches for prediction of drug response to cytotoxic chemotherapies

description: MAD for ANN models reported in Results section A. and B. (XLSX 18 kb)
DOI: 10.6084/m9.figshare.8287175.v1
title: Additional file 6: of A systematic analysis of genomics-based modeling approaches for prediction of drug response to cytotoxic chemotherapies

description: Spearman correlations for SVRLN models reported in Results section A. and B and illustrated in Fig.Â 3. (XLSX 24 kb)
DOI: 10.6084/m9.figshare.8287163
title: Additional file 3: of A systematic analysis of genomics-based modeling approaches for prediction of drug response to cytotoxic chemotherapies

description: P values for information entropy reported in Figure 4e.Â (XLSX 28 kb)
DOI: 10.6084/m9.figshare.8287169.v1
title: Additional file 4: of A systematic analysis of genomics-based modeling approaches for prediction of drug response to cytotoxic chemotherapies

description: Spearman correlations for ANN models reported in Results section A. and B and illustrated in Fig.Â 3. (XLSX 26 kb)
DOI: 10.6084/m9.figshare.8287163.v1
title: Additional file 3: of A systematic analysis of genomics-based modeling approaches for prediction of drug response to cytotoxic chemotherapies

description: P values for information entropy reported in Figure 4e.Â (XLSX 28 kb)
DOI: 10.6084/m9.figshare.8287148
title: Additional file 24: of A systematic analysis of genomics-based modeling approaches for prediction of drug response to cytotoxic chemotherapies

description: The number of cell lines from each histotype for each drug each drug. (CSV 3 kb)
DOI: 10.6084/m9.figshare.8287151
title: Additional file 25: of A systematic analysis of genomics-based modeling approaches for prediction of drug response to cytotoxic chemotherapies

description: Spearman correlations and MAD values for 5 fold nested cross validation for NLSVR models discussed in the supplementary materials. (XLSX 78 kb)
DOI: 10.6084/m9.figshare.8287154
title: Additional file 26: of A systematic analysis of genomics-based modeling approaches for prediction of drug response to cytotoxic chemotherapies

description: Spearman correlations and MAD scores using comparing tissue stratified and non-stratified models for a subset of the data as discussed in supplementary materials. (XLSX 68 kb)
DOI: 10.6084/m9.figshare.8287154.v1
title: Additional file 26: of A systematic analysis of genomics-based modeling approaches for prediction of drug response to cytotoxic chemotherapies

description: Spearman correlations and MAD scores using comparing tissue stratified and non-stratified models for a subset of the data as discussed in supplementary materials. (XLSX 68 kb)
DOI: 10.6084/m9.figshare.8287142
title: Additional file 23: of A systematic analysis of genomics-based modeling approaches for prediction of drug response to cytotoxic chemotherapies

description: This file includes MAD values corresponding to Figs. 3, 4, and 5. (XLSX 44 kb)
DOI: 10.6084/m9.figshare.8287148.v1
title: Additional file 24: of A systematic analysis of genomics-based modeling approaches for prediction of drug response to cytotoxic chemotherapies

description: The number of cell lines from each histotype for each drug each drug. (CSV 3 kb)
DOI: 10.6084/m9.figshare.8287151.v1
title: Additional file 25: of A systematic analysis of genomics-based modeling approaches for prediction of drug response to cytotoxic chemotherapies

description: Spearman correlations and MAD values for 5 fold nested cross validation for NLSVR models discussed in the supplementary materials. (XLSX 78 kb)
DOI: 10.6084/m9.figshare.8287136
title: Additional file 22: of A systematic analysis of genomics-based modeling approaches for prediction of drug response to cytotoxic chemotherapies

description: This file includes the values of the Spearman correlation for NLSVR models corresponding to Figs. 3, 4, and 5. (XLSX 67 kb)
DOI: 10.6084/m9.figshare.8287142.v1
title: Additional file 23: of A systematic analysis of genomics-based modeling approaches for prediction of drug response to cytotoxic chemotherapies

description: This file includes MAD values corresponding to Figs. 3, 4, and 5. (XLSX 44 kb)
DOI: 10.6084/m9.figshare.8287130
title: Additional file 21: of A systematic analysis of genomics-based modeling approaches for prediction of drug response to cytotoxic chemotherapies

description: MAD values for PCR CTR2 models discussed in section E. (XLSX 25 kb)
DOI: 10.6084/m9.figshare.8287136.v1
title: Additional file 22: of A systematic analysis of genomics-based modeling approaches for prediction of drug response to cytotoxic chemotherapies

description: This file includes the values of the Spearman correlation for NLSVR models corresponding to Figs. 3, 4, and 5. (XLSX 67 kb)
DOI: 10.6084/m9.figshare.8287124
title: Additional file 20: of A systematic analysis of genomics-based modeling approaches for prediction of drug response to cytotoxic chemotherapies

description: Spearman Correlations for PCR CTR2 models from 10 to 1000 genes presented in figure for section E and Fig.Â 6. (XLSX 38 kb)
DOI: 10.6084/m9.figshare.8287121
title: Additional file 1: of A systematic analysis of genomics-based modeling approaches for prediction of drug response to cytotoxic chemotherapies

description: Spearman correlations and MAD values of the 39 Drugs modeled in the NCI60. (XLSX 248 kb)
DOI: 10.6084/m9.figshare.8287130.v1
title: Additional file 21: of A systematic analysis of genomics-based modeling approaches for prediction of drug response to cytotoxic chemotherapies

description: MAD values for PCR CTR2 models discussed in section E. (XLSX 25 kb)
DOI: 10.6084/m9.figshare.8287121.v1
title: Additional file 1: of A systematic analysis of genomics-based modeling approaches for prediction of drug response to cytotoxic chemotherapies

description: Spearman correlations and MAD values of the 39 Drugs modeled in the NCI60. (XLSX 248 kb)
DOI: 10.6084/m9.figshare.8287124.v1
title: Additional file 20: of A systematic analysis of genomics-based modeling approaches for prediction of drug response to cytotoxic chemotherapies

description: Spearman Correlations for PCR CTR2 models from 10 to 1000 genes presented in figure for section E and Fig.Â 6. (XLSX 38 kb)
DOI: 10.6084/m9.figshare.8287115
title: Additional file 19: of A systematic analysis of genomics-based modeling approaches for prediction of drug response to cytotoxic chemotherapies

description: MAD values for NLSVR CTR2 models discussed in section E. (XLSX 26 kb)