cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.28023449
title: Supplementary Material for: Discrimination of T-stage using tumor weight and size - a potential approach to guide perioperative decision making in patients with bladder cancer

description: Introduction: 
To examine the value of tumor size, weight, and density in predicting pathological tumor stage in patients with suspected bladder cancer (BCa), minimize interobserver variability of estimated tumor size, and thus provide a more objective instrument to describe the extent of local tumor growth.

Methods: 
An institutional dataset of 588 consecutive patients undergoing TUR-BT for suspected BCa from 05/2016 - 09/2018 was used. Separate Mann-Whitney-U tests examined differences in each unit between non-muscle-invasive (NMIBC) and muscle-invasive BCa (MIBC) and between Ta/CIS and T1 NMIBC. Intraoperative tumor size, weight, and respective density were calculated. We then calculated multivariable logistic regression models to examine each unit's predictive value and distinguish between endpoints.

Results: 
Overall, 367 patients undergoing TUR-BT were diagnosed with BCa. In patients with MIBC (n=73), the median size (p&lt;0.001) and weight (p&lt;0.001) were higher compared to NMIBC. In contrast, tumor density (p&lt;0.001) was lower. On multivariable analysis, increasing size and weight were associated with higher odds of T1 (size: OR 2.50, 95%CI 1.87-3.35; weight: OR 1.65, 95%CI 1.26-2.15) and muscle-invasive disease (size: OR 1.51, 95%CI 1.29-1.78; weight: OR 1.09, 95%CI 1.03-1.15). Meanwhile, an increasing density was associated with lower odds of both outcomes (T1:OR 0.96, 95%CI 0.89-1.02; MIBC: OR 0.81, 95%CI 0.69-0.96). 

Conclusion: 
In patients diagnosed with BCa, tumor size, and weight showed similar predictive power concerning T1 NMIBC and MIBC. Tumor density failed to predict the local tumor stage sufficiently. These results may lay the foundation for improving objective measurement of the local tumor burden in patients with BCa and may help guide further immediate treatment decisions.
DOI: 10.6084/m9.figshare.c.3774230_d7.v1
title: MOESM4 of Estimation of single-year-of-age counts of live births, fetal losses, abortions, and pregnant women for counties of Texas

description: Additional file 4. This file contains single-year-of-age live births for the entire state of Texas.
DOI: 10.6084/m9.figshare.c.3774248_d4
title: Additional file 4: of Delta rhythmicity is a reliable EEG biomarker in Angelman syndrome: a parallel mouse and human analysis

description: Seizure and medication history for children with AS. This file is a table that provides the following information for each child with AS where it was available: (1) age at EEG, (2) gender, (3) molecular diagnosis, (4) history of seizures (yes/no), (5) age of onset of seizures, (6) seizures controlled at the time of EEG (yes/no), (7) types of seizures in the past, and (8) medications at the time of EEG. (XLS 36 kb)
DOI: 10.6084/m9.figshare.c.3774230_d7
title: MOESM4 of Estimation of single-year-of-age counts of live births, fetal losses, abortions, and pregnant women for counties of Texas

description: Additional file 4. This file contains single-year-of-age live births for the entire state of Texas.
DOI: 10.6084/m9.figshare.c.3774266_d1.v1
title: Additional file 10: Dataset S5. of No evidence for a bovine mastitis Escherichia coli pathotype

description: Predicted GIs and prophages of MAEC 1303. (XLSX 68 kb)
DOI: 10.6084/m9.figshare.c.3774230_d8.v1
title: MOESM5 of Estimation of single-year-of-age counts of live births, fetal losses, abortions, and pregnant women for counties of Texas

description: Additional file 5. This file contains our estimated single-year-of-age live births for the 254 counties of Texas for the year 2010.
DOI: 10.6084/m9.figshare.c.3774266_d2.v1
title: Additional file 11:Â Dataset S6. of No evidence for a bovine mastitis Escherichia coli pathotype

description: Predicted GIs and prophages of MAEC ECC-1470. (XLSX 46 kb)
DOI: 10.6084/m9.figshare.c.3774230_d8
title: MOESM5 of Estimation of single-year-of-age counts of live births, fetal losses, abortions, and pregnant women for counties of Texas

description: Additional file 5. This file contains our estimated single-year-of-age live births for the 254 counties of Texas for the year 2010.
DOI: 10.6084/m9.figshare.c.3774266_d1
title: Additional file 10: Dataset S5. of No evidence for a bovine mastitis Escherichia coli pathotype

description: Predicted GIs and prophages of MAEC 1303. (XLSX 68 kb)
DOI: 10.15468/dl.ra568b
title: Occurrence Download

description: A dataset containing 14316 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Arabidopsis lyrata (L.) O'Kane & Al-Shehbaz"
 ]
}

 The dataset includes 14316 records from 319 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0038682-241126133413365/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.jmgksq
title: Occurrence Download

description: A dataset containing 1969 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Polygala tenuifolia Willd."
 ]
}

 The dataset includes 1969 records from 67 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0038683-241126133413365/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.6084/m9.figshare.c.3774266_d7
title: Additional file 16: Dataset S8. of No evidence for a bovine mastitis Escherichia coli pathotype

description: This file includes virulence-associated genes with significant Fisherâ  s exact test p-values (and Bonferroni correction), which tested the association of VFs with either pathotype (MAEC or commensal strains). Additionally, the pathotype-enriched virulence-associated genes (MAEC or commensal isolates) with a 70% inclusion and 30% exclusion cutoff and their potential association with phylogroup-enriched categories or soft core genomes are listed. It also specifies the pathotype group soft core VF set and virulence-associated genes classified as underrepresented and unspecific. (XLSX 29 kb)
DOI: 10.6084/m9.figshare.c.3774266_d8
title: Additional file 17: Dataset S9. of No evidence for a bovine mastitis Escherichia coli pathotype

description: Significant virulence associated genes (with and without Bonferroni correction) with phylogroup A versus B1 according to Fisherâ  s exact test. Moreover, phylogroup-enriched virulence-associated genes (A, B1, B2, or E), phylogroup group soft core VF set, underrepresented, and unspecific virulence-associated genes are specified. (XLSX 46 kb)
DOI: 10.6084/m9.figshare.c.3774266_d9.v1
title: Additional file 18: Dataset S10. of No evidence for a bovine mastitis Escherichia coli pathotype

description: BLASTP+ hit results for the pga and paa gene regions and binary presence/absence matrix in the 25 bovine-associated E. coli genomes. The spreadsheet file includes also Fisherâ  s exact test p-values for significant associated genes to either pathotype or phylogroup. (XLSX 40 kb)
DOI: 10.6084/m9.figshare.c.3774293_d1.v1
title: Additional file 1: of Healthcare professionals’ and parents’ experiences of the confirmatory testing period: a qualitative study of the UK expanded newborn screening pilot

description: Semi-structured interview schedule - Parents. (ODT 19 kb)
DOI: 10.6084/m9.figshare.c.3774266_d9
title: Additional file 18: Dataset S10. of No evidence for a bovine mastitis Escherichia coli pathotype

description: BLASTP+ hit results for the pga and paa gene regions and binary presence/absence matrix in the 25 bovine-associated E. coli genomes. The spreadsheet file includes also Fisherâ  s exact test p-values for significant associated genes to either pathotype or phylogroup. (XLSX 40 kb)
DOI: 10.6084/m9.figshare.c.3774293_d1
title: Additional file 1: of Healthcare professionals’ and parents’ experiences of the confirmatory testing period: a qualitative study of the UK expanded newborn screening pilot

description: Semi-structured interview schedule - Parents. (ODT 19 kb)
DOI: 10.6084/m9.figshare.c.3774296_d1.v1
title: Additional file 1: of The epidemiology of drowning in low- and middle-income countries: a systematic review

description: Articles Selected for Inclusion and Demographics of Drowning Deaths. (XLSX 20 kb)
DOI: 10.6084/m9.figshare.c.3774293_d2.v1
title: Additional file 2: of Healthcare professionals’ and parents’ experiences of the confirmatory testing period: a qualitative study of the UK expanded newborn screening pilot

description: Semi-structured interview schedule - Healthcare Professionals. (ODT 16 kb)
DOI: 10.6084/m9.figshare.c.3774266_d10
title: Additional file 19: Dataset S11. of No evidence for a bovine mastitis Escherichia coli pathotype

description: Pathotype group soft core and unspecific categorisation of the fec, paa, and pga gene regions in the 13 phylogroup A bovine-associated E. coli genomes. (XLSX 8 kb)
DOI: 10.6084/m9.figshare.c.3774266_d10.v1
title: Additional file 19: Dataset S11. of No evidence for a bovine mastitis Escherichia coli pathotype

description: Pathotype group soft core and unspecific categorisation of the fec, paa, and pga gene regions in the 13 phylogroup A bovine-associated E. coli genomes. (XLSX 8 kb)
DOI: 10.6084/m9.figshare.c.3774296_d1
title: Additional file 1: of The epidemiology of drowning in low- and middle-income countries: a systematic review

description: Articles Selected for Inclusion and Demographics of Drowning Deaths. (XLSX 20 kb)
DOI: 10.6084/m9.figshare.c.3774266_d14
title: Additional file 22:Â Dataset S13. of No evidence for a bovine mastitis Escherichia coli pathotype

description: This zip archive contains the GENBANK files with the reannotations of five of the eleven reference bovine-associated E. coli genomes. Included are E. coli strains AA86, D6-113.11, D6-117.07, D6-117.29, and ECA-727. (ZIP 15 Mb)
DOI: 10.6084/m9.figshare.c.3774266_d15.v1
title: Additional file 23:Â Dataset S14. of No evidence for a bovine mastitis Escherichia coli pathotype

description: This zip archive contains the GENBANK files with the reannotations of six of the eleven reference bovine-associated E. coli genomes. Included are E. coli strains ECA-O157, ECC-Z, O32:H37 P4, P4-NR, O157:H43Â T22, and W26. (ZIP 18 Mb)
DOI: 10.5904/wgms-glambie-2024-07
title: Glacier Mass Balance Intercomparison Exercise (GlaMBIE)

description: This dataset contains the input data and results of GlaMBIE. The input data represents the original data submitted to GlaMBIE, edited to fit the monthly grid and format of GlaMBIE. The results contain the final combined estimates amongst observation methods (DEM differencing & glaciological method, altimetry, gravimetry) and the results for each observation method individually. The datasets' time resolution is annual. Results exist for the hydrological year as well as for the calendar year. Within GlaMBIE, the solutions per observation method are combined into one regional solution and then converted to calendar years for global aggregation. GlaMBIE (2024, Nature) provides more information about the approach and results.
DOI: 10.6084/m9.figshare.c.3774266_d15
title: Additional file 23:Â Dataset S14. of No evidence for a bovine mastitis Escherichia coli pathotype

description: This zip archive contains the GENBANK files with the reannotations of six of the eleven reference bovine-associated E. coli genomes. Included are E. coli strains ECA-O157, ECC-Z, O32:H37 P4, P4-NR, O157:H43Â T22, and W26. (ZIP 18 Mb)
DOI: 10.6084/m9.figshare.c.3774266_d16.v1
title: Additional file 2: Table S2. of No evidence for a bovine mastitis Escherichia coli pathotype

description: MLST allele profiles, ST and CC numbers for the 64 E. coli and four Shigella spp. strains. (XLSX 10 kb)
DOI: 10.6084/m9.figshare.c.3774266_d16
title: Additional file 2: Table S2. of No evidence for a bovine mastitis Escherichia coli pathotype

description: MLST allele profiles, ST and CC numbers for the 64 E. coli and four Shigella spp. strains. (XLSX 10 kb)
DOI: 10.6084/m9.figshare.c.3774266_d19.v1
title: Additional file 5: Table S3. of No evidence for a bovine mastitis Escherichia coli pathotype

description: This file includes the SRA study accession numbers for the Illumina and 454 raw reads of the 14 E. coli genomes of this study. Additionally it lists the assembly statistics for all 23 bovine-associated E. coli draft genomes. (XLSX 8 kb)
DOI: 10.6084/m9.figshare.c.3774266_d18
title: Additional file 4: Dataset S1. of No evidence for a bovine mastitis Escherichia coli pathotype

description: This zip archive contains the binary presence/absence matrix of 13,481 OGs in the 25 bovine-associated E. coli genomes and the R script for the Fisherâ  s exact tests to test the associations of OGs/VFs with either pathotype or phylogroup (A/B1). The R script includes also code to create the Manhattan plots in Additional file 3: Figure S3. The binary presence/absence matrix of virulence-associated genes needed as second input for the R script is enclosed in Additional file 14: Dataset S7. (ZIP 16 kb)
DOI: 10.6084/m9.figshare.c.3774266_d20.v1
title: Additional file 6: Dataset S2. of No evidence for a bovine mastitis Escherichia coli pathotype

description: Singleton OGs in the 25 bovine-associated E. coli genomes. (XLSX 248 kb)
DOI: 10.6084/m9.figshare.c.3774266_d19
title: Additional file 5: Table S3. of No evidence for a bovine mastitis Escherichia coli pathotype

description: This file includes the SRA study accession numbers for the Illumina and 454 raw reads of the 14 E. coli genomes of this study. Additionally it lists the assembly statistics for all 23 bovine-associated E. coli draft genomes. (XLSX 8 kb)
DOI: 10.6084/m9.figshare.c.3774266_d21.v1
title: Additional file 7: Dataset S3. of No evidence for a bovine mastitis Escherichia coli pathotype

description: This file includes the pathotype-enriched OGs (MAEC or commensal isolates) with a 70% inclusion and 30% exclusion cutoff and their potential association with phylogroup-enriched categories or soft core genomes. OGs significantly associated according to Fisherâ  s exact test and with a Bonferroni correction are indicated. It also specifies the pathotype group soft core genome and OGs classified as underrepresented and unspecific. For each OG the locus tag and annotation of one representative protein from one E. coli genome of the group is shown (or in the case of paralogs several representative proteins). (XLSX 523 kb)
DOI: 10.6084/m9.figshare.c.3774266_d23.v1
title: Additional file 9: Table S4. of No evidence for a bovine mastitis Escherichia coli pathotype

description: All-strain soft core genome with 70% inclusion cutoff. (XLSX 185 kb)
DOI: 10.6084/m9.figshare.c.3774266_d20
title: Additional file 6: Dataset S2. of No evidence for a bovine mastitis Escherichia coli pathotype

description: Singleton OGs in the 25 bovine-associated E. coli genomes. (XLSX 248 kb)
DOI: 10.6084/m9.figshare.c.3774266_d22.v1
title: Additional file 8: Dataset S4. of No evidence for a bovine mastitis Escherichia coli pathotype

description: Phylogroup-enriched OGs (A, B1, B2, or E) with Fisher exact test p-values (and Bonferroni correction) for phylogroup A versus B1 associations and vice versa. Furthermore the file includes the phylogroup group soft core, underrepresented, and unspecific OGs. (XLSX 541 kb)
DOI: 10.6084/m9.figshare.c.3774266_d21
title: Additional file 7: Dataset S3. of No evidence for a bovine mastitis Escherichia coli pathotype

description: This file includes the pathotype-enriched OGs (MAEC or commensal isolates) with a 70% inclusion and 30% exclusion cutoff and their potential association with phylogroup-enriched categories or soft core genomes. OGs significantly associated according to Fisherâ  s exact test and with a Bonferroni correction are indicated. It also specifies the pathotype group soft core genome and OGs classified as underrepresented and unspecific. For each OG the locus tag and annotation of one representative protein from one E. coli genome of the group is shown (or in the case of paralogs several representative proteins). (XLSX 523 kb)
DOI: 10.6084/m9.figshare.c.3774266_d22
title: Additional file 8: Dataset S4. of No evidence for a bovine mastitis Escherichia coli pathotype

description: Phylogroup-enriched OGs (A, B1, B2, or E) with Fisher exact test p-values (and Bonferroni correction) for phylogroup A versus B1 associations and vice versa. Furthermore the file includes the phylogroup group soft core, underrepresented, and unspecific OGs. (XLSX 541 kb)
DOI: 10.6084/m9.figshare.c.3774266_d23
title: Additional file 9: Table S4. of No evidence for a bovine mastitis Escherichia coli pathotype

description: All-strain soft core genome with 70% inclusion cutoff. (XLSX 185 kb)
DOI: 10.6084/m9.figshare.c.3774314_d2.v1
title: Additional file 2: of Horizontal gene transfer is not a hallmark of the human genome

description: Protein sequences for Ensembl genes in Tables 1 and 2. (FA 24 kb)
DOI: 10.6084/m9.figshare.c.3775328_d1.v1
title: Additional file 10: Table S8. of The link between adjacent codon pairs and mRNA stability

description: Multivariate linear models. Shown are intercept and slope estimates. (XLSX 44Â kb)
DOI: 10.6084/m9.figshare.c.3775331_d1.v1
title: MOESM1 of Synthesis, crystallographic, spectroscopic studies and biological activity of new cobalt(II) complexes with bioactive mixed sulindac and nitrogen-donor ligands

description: Additional file 1: Table S1. Physical properties and yield of Cobalt(II) sulindac compounds.
DOI: 10.6084/m9.figshare.c.3775328_d2.v1
title: Additional file 11: Table S9. of The link between adjacent codon pairs and mRNA stability

description: Test for heteroscedasticity. Shown are P values from studentized Breusch-Pagan tests to assess heteroscedasticity of the residuals of the linear models. (XLSX 46Â kb)
DOI: 10.6084/m9.figshare.c.3775310_d7
title: Additional file 7: of Fitness, fatness and the reallocation of time between childrenâ  s daily movement behaviours: an analysis of compositional data

description: Study data. (XLSX 42Â kb)
DOI: 10.6084/m9.figshare.c.3775328_d5.v1
title: Additional file 3: Table S3. of The link between adjacent codon pairs and mRNA stability

description: Test for association of the inhibitory codon pairs with mRNA synthesis/decay rate, protein abundance per mRNA, ribosome occupancy, and protein decay rate. (A) Spearmanâ  s correlation and partial correlation coefficients to assess associations between the fraction of the inhibitory codon pairs and the gene expression variables. P values obtained according to Kim [16] and those based on permutation tests are shown. (B) Same as (A) but for Kendallâ  s correlation coefficients. (C) Same as (A) but for the presence/absence of the inhibitory codon pairs. (D) Same as (B) but for the presence/absence of the inhibitory codon pairs. (XLSX 54Â kb)
DOI: 10.6084/m9.figshare.c.3775328_d5
title: Additional file 3: Table S3. of The link between adjacent codon pairs and mRNA stability

description: Test for association of the inhibitory codon pairs with mRNA synthesis/decay rate, protein abundance per mRNA, ribosome occupancy, and protein decay rate. (A) Spearmanâ  s correlation and partial correlation coefficients to assess associations between the fraction of the inhibitory codon pairs and the gene expression variables. P values obtained according to Kim [16] and those based on permutation tests are shown. (B) Same as (A) but for Kendallâ  s correlation coefficients. (C) Same as (A) but for the presence/absence of the inhibitory codon pairs. (D) Same as (B) but for the presence/absence of the inhibitory codon pairs. (XLSX 54Â kb)
DOI: 10.6084/m9.figshare.c.3775328_d6
title: Additional file 4: Table S4. of The link between adjacent codon pairs and mRNA stability

description: Test for association of the out-of-frame inhibitory codon pairs with mRNA decay rate, protein abundance per mRNA, and ribosome occupancy. (A) Spearmanâ  s correlation and partial correlation coefficients to assess associations between the fraction of the inhibitory codon pairs in the +1 frame and the gene expression variables. P values obtained according to Kim [16] and those based on permutation tests are shown. (B) Same as (A) but for Kendallâ  s correlation coefficients. (C) Same as (A) but for the presence/absence of the inhibitory codon pairs. (D) Same as (B) but for the presence/absence of the inhibitory codon pairs. (E) Same as (A) but for the +2 frame. (F) Same as (B) but for the +2 frame. (G) Same as (C) but for the +2 frame. (H) Same as (D) but for the +2 frame. (XLSX 57Â kb)
DOI: 10.6084/m9.figshare.c.3775337_d1.v1
title: Additional file 1: of Postnatal treatment using curcumin supplements to amend the damage in VPA-induced rodent models of autism

description: CAM curcumine data. (XLSX 50Â kb)
DOI: 10.6084/m9.figshare.c.3775328_d8.v1
title: Additional file 6: Table S6. of The link between adjacent codon pairs and mRNA stability

description: Test for association of codon optimality with mRNA decay rate, protein abundance per mRNA, and ribosome occupancy. (A) Spearman’s correlation and partial correlation coefficients to assess associations between codon optimality and the gene expression variables. P values obtained according to Kim [16] and those based on permutation tests are shown. (B) Same as (A) but for Kendall’s correlation coefficients. (XLSX 44 kb)
DOI: 10.6084/m9.figshare.c.3775328_d7
title: Additional file 5: Table S5. of The link between adjacent codon pairs and mRNA stability

description: Properties of 61 nonstop codons. Shown are corresponding amino acids, relative adaptiveness values for tAI [19, 24], classification of optimal (O) and nonoptimal (N) codons [20], and a binary variable to indicate whether the codon constitutes the inhibitory codon pairs [11]. (XLSX 42Â kb)
DOI: 10.6084/m9.figshare.c.3775337_d1
title: Additional file 1: of Postnatal treatment using curcumin supplements to amend the damage in VPA-induced rodent models of autism

description: CAM curcumine data. (XLSX 50Â kb)
DOI: 10.6084/m9.figshare.c.3775328_d8
title: Additional file 6: Table S6. of The link between adjacent codon pairs and mRNA stability

description: Test for association of codon optimality with mRNA decay rate, protein abundance per mRNA, and ribosome occupancy. (A) Spearman’s correlation and partial correlation coefficients to assess associations between codon optimality and the gene expression variables. P values obtained according to Kim [16] and those based on permutation tests are shown. (B) Same as (A) but for Kendall’s correlation coefficients. (XLSX 44 kb)
DOI: 10.6084/m9.figshare.c.3775349_d6.v1
title: MOESM6 of Comprehensive reconstruction and evaluation of Pichia pastoris genome-scale metabolic model that accounts for 1243 ORFs

description: Additional file 6. Essential genes and partially essential genes predicted by iRY1078.
DOI: 10.6084/m9.figshare.c.3775349_d6
title: MOESM6 of Comprehensive reconstruction and evaluation of Pichia pastoris genome-scale metabolic model that accounts for 1243 ORFs

description: Additional file 6. Essential genes and partially essential genes predicted by iRY1078.
DOI: 10.15468/dl.gd5qvk
title: Occurrence Download

description: A dataset containing 552 species occurrences available in GBIF matching the query:
{
 "and" : [
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "TaxonKey is Hyalomma dromedarii Koch, 1844"
 ]
}

 The dataset includes 552 records from 5 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0038685-241126133413365/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.