cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.6713597.v1
title: Tuboperitoneal fistula, ectopic pregnancy, and remnants of fallopian tube: a confocal microtomography analysis and 3D reconstruction of human fallopian tube pathologies

description: <b>Objective:</b> The aim of this study was to provide a three-dimensional (3D) microscopic reconstruction of morphological modifications of the fallopian tube (FT) following surgical sterilization (including tuboperitoneal fistula) and ectopic pregnancy (EP) using confocal microtomography (micro-CT). <b>Methods:</b> Six specimens of FT from elective and emergency surgeries were selected: three remnants of the FT (RFT) from surgical sterilization, including one presenting tuboperitoneal fistula, and three FTs with EP. The specimens were fixed in formalin and stained with Lugol solution. Micro-CT studies were conducted on the specimens using protocols adapted from biological studies. <b>Results:</b> Three RFTs from surgical sterilization and three FTs affected by EPs were successfully scanned using micro-CT. There was good contrast impregnation, allowing tissue segmentation and analysis of different sections of the FTs. Three FT specimens from EP exhibited considerable distortion of the tubal anatomy, mainly from the blood clot in the tubal abortion. Three RFT specimens exhibited some features observed in traditional microscopy, such as tubal distension and loss of normal anatomical characteristics of a normal FT, and indicated the presence of a tuboperitoneal fistula in one of the three specimens. <b>Conclusion:</b> Micro-CT can identify morphological characteristics of FT pathologies previously described in a microscopic scale, with tissue contrast and the possibility of 3D reconstruction. Micro-CT is also useful in guiding traditional sectioning of specimens for histopathological studies.
DOI: 10.6084/m9.figshare.6713549
title: Prenatal diagnosis of suprarenal mass by magnetic resonance imaging: a case series

description: <b>Objective:</b> The aim of this study was to evaluate the perinatal outcomes and postnatal follow-up of prenatally diagnosed suprarenal masses (SRMs) evaluated by magnetic resonance imaging (MRI). <b>Methods:</b> Thirteen fetuses with SRMs detected during routine prenatal ultrasound screening were evaluated by MRI between February 2007 and May 2015. The prenatal characteristics of the masses, complications of the pregnancies, and related malformations were collected as the postnatal clinical, radiological, and pathological data. <b>Results:</b> The median gestational age at MRI was 30 weeks (18–41), and birth weight was 3285 (1700–3750) g. The mean follow-up period was 6 years (1.3–10). We observed 69.2% of the masses, which were predominantly cystic (69.2%), located on the left side. Associated malformations were found in 23% of the fetuses, with congenital heart defects being more prevalent. During the pregnancy, 15.4% of the fetuses had involution of the SRM, and one fetus had surgical treatment and different ultrasound and MRI diagnoses. Of the 69.2% of the cases, spontaneous resolution occurred in 30.7% during the first year of life and 38.4% the masses presented without modifications or signs of regression since the neonatal period. <b>Conclusions:</b> Prenatal SRMs were associated with congenital heart defects. Spontaneous regression and absence of modifications in the masses were commonly observed in the long-term follow-up of the SRMs.
DOI: 10.6084/m9.figshare.6713549.v1
title: Prenatal diagnosis of suprarenal mass by magnetic resonance imaging: a case series

description: <b>Objective:</b> The aim of this study was to evaluate the perinatal outcomes and postnatal follow-up of prenatally diagnosed suprarenal masses (SRMs) evaluated by magnetic resonance imaging (MRI). <b>Methods:</b> Thirteen fetuses with SRMs detected during routine prenatal ultrasound screening were evaluated by MRI between February 2007 and May 2015. The prenatal characteristics of the masses, complications of the pregnancies, and related malformations were collected as the postnatal clinical, radiological, and pathological data. <b>Results:</b> The median gestational age at MRI was 30 weeks (18–41), and birth weight was 3285 (1700–3750) g. The mean follow-up period was 6 years (1.3–10). We observed 69.2% of the masses, which were predominantly cystic (69.2%), located on the left side. Associated malformations were found in 23% of the fetuses, with congenital heart defects being more prevalent. During the pregnancy, 15.4% of the fetuses had involution of the SRM, and one fetus had surgical treatment and different ultrasound and MRI diagnoses. Of the 69.2% of the cases, spontaneous resolution occurred in 30.7% during the first year of life and 38.4% the masses presented without modifications or signs of regression since the neonatal period. <b>Conclusions:</b> Prenatal SRMs were associated with congenital heart defects. Spontaneous regression and absence of modifications in the masses were commonly observed in the long-term follow-up of the SRMs.
DOI: 10.6084/m9.figshare.6713543
title: Additional file 9: of Post-translational buffering leads to convergent protein expression levels between primates

description: Translational gene expression buffering. A .csv file listing results from testing for translational gene expression buffering between species for genes that are quantifiable in all three species across all three data types. Column names follow the same convention as AdditionalÂ fileÂ 5. (CSV 600Â kb)
DOI: 10.6084/m9.figshare.6713543.v1
title: Additional file 9: of Post-translational buffering leads to convergent protein expression levels between primates

description: Translational gene expression buffering. A .csv file listing results from testing for translational gene expression buffering between species for genes that are quantifiable in all three species across all three data types. Column names follow the same convention as AdditionalÂ fileÂ 5. (CSV 600Â kb)
DOI: 10.6084/m9.figshare.6713540
title: Additional file 8: of Post-translational buffering leads to convergent protein expression levels between primates

description: Inter-species divergence in translation efficiency. A .csv file listing results from testing for differences in translation efficiency between species for genes that are quantifiable in all three species across all three data types. Column names follow the same convention as AdditionalÂ fileÂ 5. (CSV 606Â kb)
DOI: 10.6084/m9.figshare.6713540.v1
title: Additional file 8: of Post-translational buffering leads to convergent protein expression levels between primates

description: Inter-species divergence in translation efficiency. A .csv file listing results from testing for differences in translation efficiency between species for genes that are quantifiable in all three species across all three data types. Column names follow the same convention as AdditionalÂ fileÂ 5. (CSV 606Â kb)
DOI: 10.6084/m9.figshare.6713531
title: Additional file 7: of Post-translational buffering leads to convergent protein expression levels between primates

description: Transformed ribosome profiling, RNA-seq, and quantitative mass spectrometry data for genes that are quantifiable in all three species across all three data types. A total of six R objects are included in this .RData file. Ribo.expressed.data: TMM normalized log2RPKM values of ribosome profiling data, ribo.expressed.weights: corresponding voom weights for ribosome profiling data, ribo.expressed.ref: TMM normalized log2RPKM values of ribosome profiling data for the reference cell line (GM19238), RNA.expressed.data: TMM normalized log2RPKM values of RNA-seq data, RNA.expressed.weights: corresponding voom weights for RNA-seq data, RNA.expressed.ref: TMM normalized log2RPKM values of RNA-seq data for the reference cell line (GM19238), protein.expressed.data: trimmed mean centered SILAC ratios for quantitative mass spectrometry data. (RDATAÂ 1942Â kb)
DOI: 10.6084/m9.figshare.6713531.v1
title: Additional file 7: of Post-translational buffering leads to convergent protein expression levels between primates

description: Transformed ribosome profiling, RNA-seq, and quantitative mass spectrometry data for genes that are quantifiable in all three species across all three data types. A total of six R objects are included in this .RData file. Ribo.expressed.data: TMM normalized log2RPKM values of ribosome profiling data, ribo.expressed.weights: corresponding voom weights for ribosome profiling data, ribo.expressed.ref: TMM normalized log2RPKM values of ribosome profiling data for the reference cell line (GM19238), RNA.expressed.data: TMM normalized log2RPKM values of RNA-seq data, RNA.expressed.weights: corresponding voom weights for RNA-seq data, RNA.expressed.ref: TMM normalized log2RPKM values of RNA-seq data for the reference cell line (GM19238), protein.expressed.data: trimmed mean centered SILAC ratios for quantitative mass spectrometry data. (RDATAÂ 1942Â kb)
DOI: 10.6084/m9.figshare.6713522
title: Additional file 6: of Post-translational buffering leads to convergent protein expression levels between primates

description: Species-specific protein translation. A .csv table of raw ribosome profiling counts listing genes that are quantifiable in at least one species (see details on criteria in â Methodsâ ). Columns of Boolean labels indicate whether or not a gene is expressed in a species and whether a gene is only expressed in that species. (CSV 103Â kb)
DOI: 10.6084/m9.figshare.6713522.v1
title: Additional file 6: of Post-translational buffering leads to convergent protein expression levels between primates

description: Species-specific protein translation. A .csv table of raw ribosome profiling counts listing genes that are quantifiable in at least one species (see details on criteria in â Methodsâ ). Columns of Boolean labels indicate whether or not a gene is expressed in a species and whether a gene is only expressed in that species. (CSV 103Â kb)
DOI: 10.6084/m9.figshare.6713513
title: Additional file 5: of Post-translational buffering leads to convergent protein expression levels between primates

description: Inter-species divergence in protein translation. A .csv file listing results from testing for differences in levels of protein translation between species for genes that are quantifiable in all three species. HvC.beta: coefficient estimated from a contrast comparing between human and chimpanzee (effectively log2 ratio of levels of protein translation between the two species). HvC.p.value: nominal p values derived from t tests. HvC.FDR: false discovery rate adjusted from nominal p value. HvC.FWER: family-wise error rate adjusted from nominal p value. (CSV 1507Â kb)
DOI: 10.6084/m9.figshare.6713513.v1
title: Additional file 5: of Post-translational buffering leads to convergent protein expression levels between primates

description: Inter-species divergence in protein translation. A .csv file listing results from testing for differences in levels of protein translation between species for genes that are quantifiable in all three species. HvC.beta: coefficient estimated from a contrast comparing between human and chimpanzee (effectively log2 ratio of levels of protein translation between the two species). HvC.p.value: nominal p values derived from t tests. HvC.FDR: false discovery rate adjusted from nominal p value. HvC.FWER: family-wise error rate adjusted from nominal p value. (CSV 1507Â kb)
DOI: 10.6084/m9.figshare.6713507
title: Additional file 4: of Post-translational buffering leads to convergent protein expression levels between primates

description: Ribosome profiling count Table. A .csv file listing raw ribosome profiling counts for genes that are quantifiable across all three species. (CSV 565Â kb)
DOI: 10.6084/m9.figshare.6713507.v1
title: Additional file 4: of Post-translational buffering leads to convergent protein expression levels between primates

description: Ribosome profiling count Table. A .csv file listing raw ribosome profiling counts for genes that are quantifiable across all three species. (CSV 565Â kb)
DOI: 10.6084/m9.figshare.6713498
title: Additional file 3: of Post-translational buffering leads to convergent protein expression levels between primates

description: Genome coordinates of primate orthologous exons. A .txt file listing genome coordinates for human (hg19), chimpanzee (Pantro3), and rhesus macaque (rheMac2) for orthologous exons used in this study. (TXT 20206Â kb)
DOI: 10.6084/m9.figshare.6713498.v1
title: Additional file 3: of Post-translational buffering leads to convergent protein expression levels between primates

description: Genome coordinates of primate orthologous exons. A .txt file listing genome coordinates for human (hg19), chimpanzee (Pantro3), and rhesus macaque (rheMac2) for orthologous exons used in this study. (TXT 20206Â kb)
DOI: 10.6084/m9.figshare.6713477
title: Additional file 7: of Therapy-induced stress response is associated with downregulation of pre-mRNA splicing in cancer cells

description: Proteins and their peptides identified by a proteome analysis of SKOV3 cells prior to and after Cisplatin treatment. (XLSX 8686 kb)
DOI: 10.6084/m9.figshare.6713477.v1
title: Additional file 7: of Therapy-induced stress response is associated with downregulation of pre-mRNA splicing in cancer cells

description: Proteins and their peptides identified by a proteome analysis of SKOV3 cells prior to and after Cisplatin treatment. (XLSX 8686 kb)
DOI: 10.6084/m9.figshare.6713474
title: Additional file 10: of Post-translational buffering leads to convergent protein expression levels between primates

description: Post-translational gene expression buffering. A .csv file listing results from testing for post-translational gene expression buffering between species for genes that are quantifiable in all three species across all three data types. Column names follow the same convention as AdditionalÂ fileÂ 5. (CSV 607Â kb)
DOI: 10.6084/m9.figshare.6713474.v1
title: Additional file 10: of Post-translational buffering leads to convergent protein expression levels between primates

description: Post-translational gene expression buffering. A .csv file listing results from testing for post-translational gene expression buffering between species for genes that are quantifiable in all three species across all three data types. Column names follow the same convention as AdditionalÂ fileÂ 5. (CSV 607Â kb)
DOI: 10.6084/m9.figshare.6713465
title: Additional file 6: of Therapy-induced stress response is associated with downregulation of pre-mRNA splicing in cancer cells

description: Description of gene clusters identified by the time clusterization analysis. (XLSX 415 kb)
DOI: 10.6084/m9.figshare.6713465.v1
title: Additional file 6: of Therapy-induced stress response is associated with downregulation of pre-mRNA splicing in cancer cells

description: Description of gene clusters identified by the time clusterization analysis. (XLSX 415 kb)
DOI: 10.6084/m9.figshare.6713453
title: Additional file 5: of Therapy-induced stress response is associated with downregulation of pre-mRNA splicing in cancer cells

description: Results of the enrichment analysis of genes that were differentially expressed in response to different stress factors. (XLSX 171 kb)
DOI: 10.6084/m9.figshare.6713453.v1
title: Additional file 5: of Therapy-induced stress response is associated with downregulation of pre-mRNA splicing in cancer cells

description: Results of the enrichment analysis of genes that were differentially expressed in response to different stress factors. (XLSX 171 kb)
DOI: 10.6084/m9.figshare.6713435
title: MOESM1 of The illusion of rarity in an epibenthic jellyfish: facts and artefacts in the distribution of Tesserogastria musculosa (Hydrozoa, Ptychogastriidae)

description: Additional file 1. Validated records of Tesserogastria musculosa Beyer, 1958. List of all the records of Tesserogastria musculosa Beyer, 1958 validated for this study and used to generate Fig.Â 4.
DOI: 10.6084/m9.figshare.6713435.v1
title: MOESM1 of The illusion of rarity in an epibenthic jellyfish: facts and artefacts in the distribution of Tesserogastria musculosa (Hydrozoa, Ptychogastriidae)

description: Additional file 1. Validated records of Tesserogastria musculosa Beyer, 1958. List of all the records of Tesserogastria musculosa Beyer, 1958 validated for this study and used to generate Fig.Â 4.
DOI: 10.6084/m9.figshare.6713408
title: Additional file 3: of Therapy-induced stress response is associated with downregulation of pre-mRNA splicing in cancer cells

description: (A) Description of all alternative splicing events in cancer cell lines after therapy. (B) Identification of stop codons in transcripts with retained introns, which were detected in at least half of cancer cell lines before and after chemotherapy. (C) Description of all alternative splicing events in PDX tumors after different types of therapy. (D) Identification of stop codons in transcripts with retained introns, which were detected in PDX tumors before and after chemotherapy. (E) Description of alternative splicing events in spliceosomal genes in PDX tumors after different types of therapy. (F) Description of insertions which were detected in 7 cell lines (A375, A549, H3122, N87, PC9, RT112, H358) used in our analysis of alternative splicing changes. (XLSX 716 kb)
DOI: 10.6084/m9.figshare.6713408.v1
title: Additional file 3: of Therapy-induced stress response is associated with downregulation of pre-mRNA splicing in cancer cells

description: (A) Description of all alternative splicing events in cancer cell lines after therapy. (B) Identification of stop codons in transcripts with retained introns, which were detected in at least half of cancer cell lines before and after chemotherapy. (C) Description of all alternative splicing events in PDX tumors after different types of therapy. (D) Identification of stop codons in transcripts with retained introns, which were detected in PDX tumors before and after chemotherapy. (E) Description of alternative splicing events in spliceosomal genes in PDX tumors after different types of therapy. (F) Description of insertions which were detected in 7 cell lines (A375, A549, H3122, N87, PC9, RT112, H358) used in our analysis of alternative splicing changes. (XLSX 716 kb)
DOI: 10.6084/m9.figshare.6713402
title: Additional file 2: of Disease-specific regulation of gene expression in a comparative analysis of juvenile idiopathic arthritis and inflammatory bowel disease

description: Table S1. List of genes included in transcriptional risk scores. Table S2. List of differentially expressed genes. Table S3. BTM across disease sub-types. Table S4. List of disease-by-eQTL interactions. Table S5. Colocalization analysis. (XLSX 329 kb)
DOI: 10.6084/m9.figshare.6713402.v1
title: Additional file 2: of Disease-specific regulation of gene expression in a comparative analysis of juvenile idiopathic arthritis and inflammatory bowel disease

description: Table S1. List of genes included in transcriptional risk scores. Table S2. List of differentially expressed genes. Table S3. BTM across disease sub-types. Table S4. List of disease-by-eQTL interactions. Table S5. Colocalization analysis. (XLSX 329 kb)
DOI: 10.6084/m9.figshare.6713399
title: Additional file 1: of Headline indicators for monitoring the performance of health systems: findings from the european Health Systems_Indicator (euHS_I) survey

description: List of excluded rather country-specific indicators. (XLSX 26 kb)
DOI: 10.6084/m9.figshare.6713399.v1
title: Additional file 1: of Headline indicators for monitoring the performance of health systems: findings from the european Health Systems_Indicator (euHS_I) survey

description: List of excluded rather country-specific indicators. (XLSX 26 kb)
DOI: 10.6084/m9.figshare.6713381
title: Additional file 1: of Comparison of village dog and wolf genomes highlights the role of the neural crest in dog domestication

description: Table S1. Description and accession numbers for canine genomes processed in this study. Indications for whether or not a sample was used in the ADMIXTURE analysis, selection scans (FST, XP-CLR, or VST) are provided. Table S2. Coordinates and annotations of outlier FST loci identified through the empirical approach, including intersecting Axelsson, Cagan and Blass, and Freedman loci [5, 8, 29]. Table S3. Parameters incorporated into demographic model for neutral evolution in village dog and wolf populations. Table S4. Coordinates and annotations of outlier FST loci identified through the simulation informed (non-empirical) approach, including genes as well as intersecting Axelsson, Cagan and Blass, and Freedman loci [5, 8, 29]. Table S5. Coordinates and annotations of outlier XP-CLR candidate domestication regions identified through simulation approach, including intersecting genes as well as intersecting Axelsson, Cagan and Blass, and Freedman loci [5, 8, 29]. Table S6. Predicted SNP effects (per variant effect predictor [42]) for sites in XP-CLR candidate domestication regions. Table S7. Coordinates of VST copy number outliers on autosomes and chromosome X. Table S8. Gene enrichment results for XP-CLR candidate domestication regions following p value adjustment (BLAST2GO). Table S9. Gene enrichment for XP-CLR candidate domestication regions following p value adjustment (EMBL-EBI). Table S10. Gene enrichment results for VST copy number outliers following p value adjustment. Table S11. Coordinates of VST copy number outliers on chromosome unknown (chrUn). Table S12. ddPCR results from 30 village, 3 New Guinea singing, and 5 breed dog samples of AMY2B segmental duplications. Table S13. ddPCR results from 48 breed dog samples of AMY2B segmental duplications. (XLSX 328Â kb)
DOI: 10.6084/m9.figshare.6713381.v1
title: Additional file 1: of Comparison of village dog and wolf genomes highlights the role of the neural crest in dog domestication

description: Table S1. Description and accession numbers for canine genomes processed in this study. Indications for whether or not a sample was used in the ADMIXTURE analysis, selection scans (FST, XP-CLR, or VST) are provided. Table S2. Coordinates and annotations of outlier FST loci identified through the empirical approach, including intersecting Axelsson, Cagan and Blass, and Freedman loci [5, 8, 29]. Table S3. Parameters incorporated into demographic model for neutral evolution in village dog and wolf populations. Table S4. Coordinates and annotations of outlier FST loci identified through the simulation informed (non-empirical) approach, including genes as well as intersecting Axelsson, Cagan and Blass, and Freedman loci [5, 8, 29]. Table S5. Coordinates and annotations of outlier XP-CLR candidate domestication regions identified through simulation approach, including intersecting genes as well as intersecting Axelsson, Cagan and Blass, and Freedman loci [5, 8, 29]. Table S6. Predicted SNP effects (per variant effect predictor [42]) for sites in XP-CLR candidate domestication regions. Table S7. Coordinates of VST copy number outliers on autosomes and chromosome X. Table S8. Gene enrichment results for XP-CLR candidate domestication regions following p value adjustment (BLAST2GO). Table S9. Gene enrichment for XP-CLR candidate domestication regions following p value adjustment (EMBL-EBI). Table S10. Gene enrichment results for VST copy number outliers following p value adjustment. Table S11. Coordinates of VST copy number outliers on chromosome unknown (chrUn). Table S12. ddPCR results from 30 village, 3 New Guinea singing, and 5 breed dog samples of AMY2B segmental duplications. Table S13. ddPCR results from 48 breed dog samples of AMY2B segmental duplications. (XLSX 328Â kb)