cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.8874428.v2
title: Supplementary Material for: Does Body Mass Index Impact the Outcomes of Ultrasound-Guided Percutaneous Nephrolithotomy?

description: <b><i>Background and Purpose:</i></b> To evaluate whether body mass index (BMI) has an impact on the outcomes of ultrasound-guided percutaneous nephrolithotomy (PCNL). <b><i>Materials and Methods:</i></b> The data of 359 patients who required PCNL at ShengJing hospital between June 2013 and July 2015 were reviewed, with the patients divided into 4 groups based on different ranges of BMI: &lt;25, 25–29.9, 30–34.9, and ≥35 kg/m<sup>2</sup>. Baseline characteristics and outcomes were compared between the groups. Multivariable logistic regressions were used to evaluate the independent contribution of BMI as a predictor of outcomes. The Modified Clavien classification system was used for reporting complications. Results were compared between the groups using the chi-square and multivariate logistic regression tests. <b><i>Results:</i></b> No significant differences were noted in the demographic data between the 4 groups. Ultrasound screening time, total operative time, and hospital stay all increased with increasing BMI. No difference was found in the complication rate, stone free rate, or need for auxiliary procedures. <b><i>Conclusion:</i></b> Obesity does not increase the incidence of complications in ultrasound-guided PCNL, and the efficacy of the technique for obese patients is similar to that for normal weight patients. The lateral decubitus position was preferred in patients with higher BMI.
DOI: 10.6084/m9.figshare.8874428.v1
title: Supplementary Material for: Does Body Mass Index Impact the Outcomes of Ultrasound-Guided Percutaneous Nephrolithotomy?

description: <b><i>Background and Purpose:</i></b> To evaluate whether body mass index (BMI) has an impact on the outcomes of ultrasound-guided percutaneous nephrolithotomy (PCNL). <b><i>Materials and Methods:</i></b> The data of 359 patients who required PCNL at ShengJing hospital between June 2013 and July 2015 were reviewed, with the patients divided into 4 groups based on different ranges of BMI: &lt;25, 25–29.9, 30–34.9, and ≥35 kg/m<sup>2</sup>. Baseline characteristics and outcomes were compared between the groups. Multivariable logistic regressions were used to evaluate the independent contribution of BMI as a predictor of outcomes. The Modified Clavien classification system was used for reporting complications. Results were compared between the groups using the chi-square and multivariate logistic regression tests. <b><i>Results:</i></b> No significant differences were noted in the demographic data between the 4 groups. Ultrasound screening time, total operative time, and hospital stay all increased with increasing BMI. No difference was found in the complication rate, stone free rate, or need for auxiliary procedures. <b><i>Conclusion:</i></b> Obesity does not increase the incidence of complications in ultrasound-guided PCNL, and the efficacy of the technique for obese patients is similar to that for normal weight patients. The lateral decubitus position was preferred in patients with higher BMI.
DOI: 10.6084/m9.figshare.8874377
title: supplementary table 1_Statistics of Abr MTCC strains replicons

description: Statistics for replicons of <i>Azospirillum brasiliense</i> MTCC strains
DOI: 10.6084/m9.figshare.8874377.v1
title: supplementary table 1_Statistics of Abr MTCC strains replicons

description: Statistics for replicons of <i>Azospirillum brasiliense</i> MTCC strains
DOI: 10.6084/m9.figshare.8874371
title: grid.266190.a

description: Network Graphs for institution grid.266190.a for "What Does a University Look Like?" poster
DOI: 10.6084/m9.figshare.8874371.v1
title: grid.266190.a

description: Network Graphs for institution grid.266190.a for "What Does a University Look Like?" poster
DOI: 10.6084/m9.figshare.8873864
title: Additional file 2: of Assessing cell-specific effects of genetic variations using tRNA microarrays

description: Source data tRNA microarrays. (XLSX 18 kb)
DOI: 10.6084/m9.figshare.8873864.v1
title: Additional file 2: of Assessing cell-specific effects of genetic variations using tRNA microarrays

description: Source data tRNA microarrays. (XLSX 18 kb)
DOI: 10.6084/m9.figshare.8873792
title: Additional file 2: of Caffeine citrate enhanced cisplatin antitumor effects in osteosarcoma and fibrosarcoma in vitro and in vivo

description: Table S1. The information on quantitative changes. (XLSX 19 kb)
DOI: 10.6084/m9.figshare.8873792.v1
title: Additional file 2: of Caffeine citrate enhanced cisplatin antitumor effects in osteosarcoma and fibrosarcoma in vitro and in vivo

description: Table S1. The information on quantitative changes. (XLSX 19 kb)
DOI: 10.6084/m9.figshare.8873747
title: Additional file 2: of Association of Cytokeratin 5 and Claudin 3 expression with BRCA1 and BRCA2 germline mutations in women with early breast cancer

description: Data (XLSX 40 kb)
DOI: 10.6084/m9.figshare.8873747.v1
title: Additional file 2: of Association of Cytokeratin 5 and Claudin 3 expression with BRCA1 and BRCA2 germline mutations in women with early breast cancer

description: Data (XLSX 40 kb)
DOI: 10.6084/m9.figshare.8873708
title: Additional file 3: of Incidence of catastrophic expenditures linked to obstetric and neonatal care at 92 facilities in Lubumbashi, Democratic Republic of the Congo, 2015

description: Description of data. (XLSX 596â kb)
DOI: 10.6084/m9.figshare.8873708.v1
title: Additional file 3: of Incidence of catastrophic expenditures linked to obstetric and neonatal care at 92 facilities in Lubumbashi, Democratic Republic of the Congo, 2015

description: Description of data. (XLSX 596â kb)
DOI: 10.6084/m9.figshare.8873651
title: Additional file 6: of Tumor mutational burden quantification from targeted gene panels: major advancements and challenges

description: Table S6. Proposed recommendations for consistent TMB quantification and reporting. We report recommendations formulated by the TMB Harmonization Working Group ( https://www.focr.org/tmb ) as well as indications emerging from the studies reviewed in this work. (XLSX 24 kb)
DOI: 10.6084/m9.figshare.8873651.v1
title: Additional file 6: of Tumor mutational burden quantification from targeted gene panels: major advancements and challenges

description: Table S6. Proposed recommendations for consistent TMB quantification and reporting. We report recommendations formulated by the TMB Harmonization Working Group ( https://www.focr.org/tmb ) as well as indications emerging from the studies reviewed in this work. (XLSX 24 kb)
DOI: 10.6084/m9.figshare.8873645
title: Additional file 5: of Tumor mutational burden quantification from targeted gene panels: major advancements and challenges

description: Table S5. Empirical analysis of TMB association or predictive value for immunotherapy response. These analyses were performed on panel-based TMB values, directly calculated by panel sequencing. The table reports measures of TMB association with immunotherapy response (odds ratios, hazard ratios and corresponding p-values), differences in TMB distribution between responders and non-responders (Mann-Whitney U, unpaired Student’s t and Fisher’s test p values) and measures of TMB predictive value (AUC, specificity, sensitivity). We also specify how patients were stratified (“Comparison”), the method used to determine TMB cutoff, the cohort considered for the analysis (if different cohorts were analyzed in the study), the type of immunotherapy, cancer type and number of patients. (XLSX 19 kb)
DOI: 10.6084/m9.figshare.8873639
title: Additional file 4: of Tumor mutational burden quantification from targeted gene panels: major advancements and challenges

description: Table S4. In silico analysis of TMB association or predictive value for immunotherapy response. These analyses were performed on panel-based TMB values simulated in silico using a subset of WES which only contains genes targeted by the panel. The table reports measures of TMB association with immunotherapy response (odds ratios, hazard ratios and corresponding p-values), differences in TMB distribution between responders and non-responders (Mann-Whitney U and Fisherâ s p values) and measures of TMB predictive value (AUC, specificity, sensitivity). (XLSX 9 kb)
DOI: 10.6084/m9.figshare.8873645.v1
title: Additional file 5: of Tumor mutational burden quantification from targeted gene panels: major advancements and challenges

description: Table S5. Empirical analysis of TMB association or predictive value for immunotherapy response. These analyses were performed on panel-based TMB values, directly calculated by panel sequencing. The table reports measures of TMB association with immunotherapy response (odds ratios, hazard ratios and corresponding p-values), differences in TMB distribution between responders and non-responders (Mann-Whitney U, unpaired Student’s t and Fisher’s test p values) and measures of TMB predictive value (AUC, specificity, sensitivity). We also specify how patients were stratified (“Comparison”), the method used to determine TMB cutoff, the cohort considered for the analysis (if different cohorts were analyzed in the study), the type of immunotherapy, cancer type and number of patients. (XLSX 19 kb)
DOI: 10.6084/m9.figshare.8873636
title: Additional file 3: of Tumor mutational burden quantification from targeted gene panels: major advancements and challenges

description: Table S3. Empirical analysis of the correlation between panel-based and WES-based TMB. Correlation between panel-based and WES-based TMB, considered the gold standard value, is used to estimate the accuracy of panel-based TMB quantification. Correlation analysis is performed on TMB values calculated for samples with matched panel and whole exome sequencing. (XLSX 6 kb)
DOI: 10.6084/m9.figshare.8873639.v1
title: Additional file 4: of Tumor mutational burden quantification from targeted gene panels: major advancements and challenges

description: Table S4. In silico analysis of TMB association or predictive value for immunotherapy response. These analyses were performed on panel-based TMB values simulated in silico using a subset of WES which only contains genes targeted by the panel. The table reports measures of TMB association with immunotherapy response (odds ratios, hazard ratios and corresponding p-values), differences in TMB distribution between responders and non-responders (Mann-Whitney U and Fisherâ s p values) and measures of TMB predictive value (AUC, specificity, sensitivity). (XLSX 9 kb)
DOI: 10.6084/m9.figshare.8873627
title: Additional file 1: of Tumor mutational burden quantification from targeted gene panels: major advancements and challenges

description: Table S1. Technical specifications of gene panels used or proposed for TMB quantification. For each gene panel, it is reported the type of cancer and sample for which it was designed, the enrichment method, the targeted sequencing size (Genomic space) and the number of targeted genes (# genes). (XLSX 6 kb)
DOI: 10.6084/m9.figshare.8873633
title: Additional file 2: of Tumor mutational burden quantification from targeted gene panels: major advancements and challenges

description: Table S2. In silico analysis of the correlation between panel-based and WES-based TMB. Correlation between panel-based and WES-based TMB, considered the gold standard value, is used to estimate the accuracy of panel-based TMB quantification. Panel-based TMB quantification was simulated in silico using a subset of WES which only contains genes targeted by the panel. (XLSX 11 kb)
DOI: 10.6084/m9.figshare.8873636.v1
title: Additional file 3: of Tumor mutational burden quantification from targeted gene panels: major advancements and challenges

description: Table S3. Empirical analysis of the correlation between panel-based and WES-based TMB. Correlation between panel-based and WES-based TMB, considered the gold standard value, is used to estimate the accuracy of panel-based TMB quantification. Correlation analysis is performed on TMB values calculated for samples with matched panel and whole exome sequencing. (XLSX 6 kb)
DOI: 10.6084/m9.figshare.8873627.v1
title: Additional file 1: of Tumor mutational burden quantification from targeted gene panels: major advancements and challenges

description: Table S1. Technical specifications of gene panels used or proposed for TMB quantification. For each gene panel, it is reported the type of cancer and sample for which it was designed, the enrichment method, the targeted sequencing size (Genomic space) and the number of targeted genes (# genes). (XLSX 6 kb)
DOI: 10.6084/m9.figshare.8873633.v1
title: Additional file 2: of Tumor mutational burden quantification from targeted gene panels: major advancements and challenges

description: Table S2. In silico analysis of the correlation between panel-based and WES-based TMB. Correlation between panel-based and WES-based TMB, considered the gold standard value, is used to estimate the accuracy of panel-based TMB quantification. Panel-based TMB quantification was simulated in silico using a subset of WES which only contains genes targeted by the panel. (XLSX 11 kb)
DOI: 10.6084/m9.figshare.8873600
title: of Role of PRY-1/Axin in heterochronic miRNA-mediated seam cell development

description: of Role of PRY-1/Axin in heterochronic miRNA-mediated seam cell development
DOI: 10.6084/m9.figshare.8873600.v2
title: of Role of PRY-1/Axin in heterochronic miRNA-mediated seam cell development

description: of Role of PRY-1/Axin in heterochronic miRNA-mediated seam cell development
DOI: 10.6084/m9.figshare.8873600.v1
title: Additional file 6: of Role of PRY-1/Axin in heterochronic miRNA-mediated seam cell development

description: Figure S3. Adult stage qRT-PCR analysis of heterochronic miRNAs in C. elegans and C. briggsae pry-1 mutants. (A) pry-1(mu38) adults show differences in the pattern of miRNA expression compared to the L1 stage. All miRNAs, except lin-4 and miR-48, are downregulated. (B) Cbr-pry-1(sy5353) adults show altered expression of miR-246, miR-48 and miR-84. Each data point represents the mean of two replicates and error bar represents the SEM, *p
DOI: 10.6084/m9.figshare.8873585
title: Additional file 4: of Role of PRY-1/Axin in heterochronic miRNA-mediated seam cell development

description: Table S3. A list of novel miRNAs in C. elegans. The IDs of miRNAs are based on the sequential numbering of unique reads in our analysis. For each novel miRNA, the table lists the miRDeep score, read count, chromosomal location, and the sequence. (XLSX 380 kb)
DOI: 10.6084/m9.figshare.8873588
title: Additional file 3: of What makes a bad egg? Egg transcriptome reveals dysregulation of translational machinery and novel fertility genes important for fertilization

description: List of differentially expressed genes (DEGs) in bad quality eggs as compared to good quality eggs that were the most modified among the 66 DEGs found by microarray analysis. (XLSX 10 kb)
DOI: 10.6084/m9.figshare.8873582
title: Additional file 2: of What makes a bad egg? Egg transcriptome reveals dysregulation of translational machinery and novel fertility genes important for fertilization

description: Sequences of the primer pairs that were used in this study. (XLSX 13 kb)
DOI: 10.6084/m9.figshare.8873588.v1
title: Additional file 3: of What makes a bad egg? Egg transcriptome reveals dysregulation of translational machinery and novel fertility genes important for fertilization

description: List of differentially expressed genes (DEGs) in bad quality eggs as compared to good quality eggs that were the most modified among the 66 DEGs found by microarray analysis. (XLSX 10 kb)
DOI: 10.5519/qd.d0t7q657
title: Query on the Natural History Museum Data Portal (data.nhm.ac.uk) (42 records)
DOI: 10.6084/m9.figshare.8873582.v1
title: Additional file 2: of What makes a bad egg? Egg transcriptome reveals dysregulation of translational machinery and novel fertility genes important for fertilization

description: Sequences of the primer pairs that were used in this study. (XLSX 13 kb)
DOI: 10.6084/m9.figshare.8873585.v2
title: Additional file 4: of Role of PRY-1/Axin in heterochronic miRNA-mediated seam cell development

description: Table S3. A list of novel miRNAs in C. elegans. The IDs of miRNAs are based on the sequential numbering of unique reads in our analysis. For each novel miRNA, the table lists the miRDeep score, read count, chromosomal location, and the sequence. (XLSX 380 kb)
DOI: 10.6084/m9.figshare.8873585.v1
title: Additional file 4: of Role of PRY-1/Axin in heterochronic miRNA-mediated seam cell development

description: Table S3. A list of novel miRNAs in C. elegans. The IDs of miRNAs are based on the sequential numbering of unique reads in our analysis. For each novel miRNA, the table lists the miRDeep score, read count, chromosomal location, and the sequence. (XLSX 25 kb)
DOI: 10.6084/m9.figshare.8873573
title: Additional file 1: of What makes a bad egg? Egg transcriptome reveals dysregulation of translational machinery and novel fertility genes important for fertilization

description: The complete list of the 66 DEGs including the gene description, Ensembl annotation, corrected p-value, and fold change. Analysis was performed with the GeneSpring GX program. (XLSX 13 kb)
DOI: 10.6084/m9.figshare.8873573.v1
title: Additional file 1: of What makes a bad egg? Egg transcriptome reveals dysregulation of translational machinery and novel fertility genes important for fertilization

description: The complete list of the 66 DEGs including the gene description, Ensembl annotation, corrected p-value, and fold change. Analysis was performed with the GeneSpring GX program. (XLSX 13 kb)
DOI: 10.6084/m9.figshare.8873525
title: MOESM2 of Impact of inflammation on brain subcellular energetics in anesthetized rats

description: Additional file 2. Table S1: All statistically significant up and down-regulated genes identified by RNA sequencing.
DOI: 10.6084/m9.figshare.8873525.v1
title: MOESM2 of Impact of inflammation on brain subcellular energetics in anesthetized rats

description: Additional file 2. Table S1: All statistically significant up and down-regulated genes identified by RNA sequencing.
DOI: 10.6084/m9.figshare.8873465
title: MOESM3 of Genetic homogeneity of Anopheles maculatus in Indonesia and origin of a novel species present in Central Java

description: Additional file 3: Table S2. Pairwise genetic distance of cox1 sequences. Genetic distances were calculated with the Kimura 2 parameters using Mega X.
DOI: 10.6084/m9.figshare.8873465.v1
title: MOESM3 of Genetic homogeneity of Anopheles maculatus in Indonesia and origin of a novel species present in Central Java

description: Additional file 3: Table S2. Pairwise genetic distance of cox1 sequences. Genetic distances were calculated with the Kimura 2 parameters using Mega X.
DOI: 10.6084/m9.figshare.8873450
title: MOESM1 of Genetic homogeneity of Anopheles maculatus in Indonesia and origin of a novel species present in Central Java

description: Additional file 1: Table S1. Pairwise genetic distance of ITS2 sequences. Genetic distances were calculated with the Kimura 2 parameters using Mega X.
DOI: 10.6084/m9.figshare.8873450.v1
title: MOESM1 of Genetic homogeneity of Anopheles maculatus in Indonesia and origin of a novel species present in Central Java

description: Additional file 1: Table S1. Pairwise genetic distance of ITS2 sequences. Genetic distances were calculated with the Kimura 2 parameters using Mega X.
DOI: 10.6084/m9.figshare.8873429
title: Additional file 1: of Postoperative acute exacerbation of interstitial pneumonia in pulmonary and non-pulmonary surgery: a retrospective study

description: Characteristics of patients with developing acute exacerbation of interstitial pneumonia. (XLSX 11 kb)
DOI: 10.6084/m9.figshare.8873429.v1
title: Additional file 1: of Postoperative acute exacerbation of interstitial pneumonia in pulmonary and non-pulmonary surgery: a retrospective study

description: Characteristics of patients with developing acute exacerbation of interstitial pneumonia. (XLSX 11 kb)
DOI: 10.6084/m9.figshare.8873321
title: Additional file 1: of PhenPath: a tool for characterizing biological functions underlying different phenotypes

description: External dataset used for PhenPath evaluation. We estimate the performance of PhenPathTOOL in retrieving relevant associations between groups of co-occurring phenotypes and possible causative genes, collecting from Orphanet [37] a blind set consisting of 87 diseases, not included in OMIM nor, consequently, used to build PhenPathDB (see Methods section 5.3 for further details on the dataset). (TSV 23 kb)
DOI: 10.6084/m9.figshare.8873321.v1
title: Additional file 1: of PhenPath: a tool for characterizing biological functions underlying different phenotypes

description: External dataset used for PhenPath evaluation. We estimate the performance of PhenPathTOOL in retrieving relevant associations between groups of co-occurring phenotypes and possible causative genes, collecting from Orphanet [37] a blind set consisting of 87 diseases, not included in OMIM nor, consequently, used to build PhenPathDB (see Methods section 5.3 for further details on the dataset). (TSV 23 kb)
DOI: 10.6084/m9.figshare.8873270
title: Additional file 8: of Transcriptional responses of Xanthomonas oryzae pv. oryzae to type III secretion system inhibitor ortho-coumaric acid

description: Table S3. Signaling pathway and transcriptional regulators which were common regulated at all four of time points by OCA. (XLSX 11 kb)
DOI: 10.6084/m9.figshare.8873273
title: Additional file 9: of Transcriptional responses of Xanthomonas oryzae pv. oryzae to type III secretion system inhibitor ortho-coumaric acid

description: Table S4. Iron metabolism related genes which were regulated by OCA at each time point. (XLSX 12 kb)
DOI: 10.6084/m9.figshare.8873270.v1
title: Additional file 8: of Transcriptional responses of Xanthomonas oryzae pv. oryzae to type III secretion system inhibitor ortho-coumaric acid

description: Table S3. Signaling pathway and transcriptional regulators which were common regulated at all four of time points by OCA. (XLSX 11 kb)
DOI: 10.6084/m9.figshare.8873273.v1
title: Additional file 9: of Transcriptional responses of Xanthomonas oryzae pv. oryzae to type III secretion system inhibitor ortho-coumaric acid

description: Table S4. Iron metabolism related genes which were regulated by OCA at each time point. (XLSX 12 kb)
DOI: 10.6084/m9.figshare.8873243
title: Additional file 5: of Transcriptional responses of Xanthomonas oryzae pv. oryzae to type III secretion system inhibitor ortho-coumaric acid

description: Table S2. Common DEGs at all four of time points associated with electron carrier activity. (XLSX 9 kb)
DOI: 10.6084/m9.figshare.8873243.v1
title: Additional file 5: of Transcriptional responses of Xanthomonas oryzae pv. oryzae to type III secretion system inhibitor ortho-coumaric acid

description: Table S2. Common DEGs at all four of time points associated with electron carrier activity. (XLSX 9 kb)
DOI: 10.6084/m9.figshare.8873228
title: Additional file 3: of Transcriptional responses of Xanthomonas oryzae pv. oryzae to type III secretion system inhibitor ortho-coumaric acid

description: Table S1. Common DEGs at all four of time points. (XLSX 47 kb)
DOI: 10.6084/m9.figshare.8873228.v1
title: Additional file 3: of Transcriptional responses of Xanthomonas oryzae pv. oryzae to type III secretion system inhibitor ortho-coumaric acid

description: Table S1. Common DEGs at all four of time points. (XLSX 47 kb)
DOI: 10.6084/m9.figshare.8872790
title: grid.26009.3d

description: Network Graphs for institution grid.26009.3d created for "What Does a University Look Like?" poster
DOI: 10.6084/m9.figshare.8872787
title: DLBCL of Waldeyer's ring_DATA_2019.6.24.sav

description: DATA_Patients with early stage DLBCL of Waldeyer's ring