cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.6694943
title: Additional file 1: of Engineering Geobacillus thermodenitrificans to introduce cellulolytic activity; expression of native and heterologous cellulase genes

description: Table S1. Codon harmonization of celS from C. thermocellum. An overview of the codon harmonization method used to adapt the C. thermocellum derived exoglucanase encoding gene celS for expression in G. thermodenitrificans. (XLSX 78 kb)
DOI: 10.6084/m9.figshare.6694943.v1
title: Additional file 1: of Engineering Geobacillus thermodenitrificans to introduce cellulolytic activity; expression of native and heterologous cellulase genes

description: Table S1. Codon harmonization of celS from C. thermocellum. An overview of the codon harmonization method used to adapt the C. thermocellum derived exoglucanase encoding gene celS for expression in G. thermodenitrificans. (XLSX 78 kb)
DOI: 10.6084/m9.figshare.6694928
title: Additional file 1 of CpG island composition differences are a source of gene expression noise indicative of promoter responsiveness

description: Supplementary Table 1. CSV file describing genomic data sources and acquisition dates. (CSV 1 kb)
DOI: 10.6084/m9.figshare.6694928.v1
title: Additional file 1 of CpG island composition differences are a source of gene expression noise indicative of promoter responsiveness

description: Supplementary Table 1. CSV file describing genomic data sources and acquisition dates. (CSV 1 kb)
DOI: 10.6084/m9.figshare.6694925
title: Additional file 10: of Identification of sonic hedgehog-regulated genes and biological processes in the cranial neural crest mesenchyme by comparative transcriptomics

description: Table of RT-PCR primer sequences. (XLS 37 kb)
DOI: 10.6084/m9.figshare.6694925.v1
title: Additional file 10: of Identification of sonic hedgehog-regulated genes and biological processes in the cranial neural crest mesenchyme by comparative transcriptomics

description: Table of RT-PCR primer sequences. (XLS 37 kb)
DOI: 10.6084/m9.figshare.6694904
title: MOESM1 of Microscopic species make the diversity: a checklist of marine flora and fauna around the Island of Sylt in the North Sea

description: Additional file 1. Marine flora and fauna around the Island of Sylt in the North Sea. Table S1. Microplankton; Table S2. Zooplankton; Table S3. Nekton; Table S4. Benthic microflora; Table S5. Benthic macroflora; Table S6. Benthic micro- and meiofauna; Table S7. Benthic macrofauna; Table S8. Birds and mammals; Table S9. Neobiota; Table S10. Number of species per table; Table S11. Taxonomic species composition around Sylt; Table S12. Comparison of species composition around Sylt with European waters and the world oceans.
DOI: 10.6084/m9.figshare.6694904.v1
title: MOESM1 of Microscopic species make the diversity: a checklist of marine flora and fauna around the Island of Sylt in the North Sea

description: Additional file 1. Marine flora and fauna around the Island of Sylt in the North Sea. Table S1. Microplankton; Table S2. Zooplankton; Table S3. Nekton; Table S4. Benthic microflora; Table S5. Benthic macroflora; Table S6. Benthic micro- and meiofauna; Table S7. Benthic macrofauna; Table S8. Birds and mammals; Table S9. Neobiota; Table S10. Number of species per table; Table S11. Taxonomic species composition around Sylt; Table S12. Comparison of species composition around Sylt with European waters and the world oceans.
DOI: 10.6084/m9.figshare.6694862
title: Additional file 1: of Acetylcholinesterase inhibitor insecticides related acute poisoning, availability and sales: trends during the post-insecticide-ban period of Anuradhapura, Sri Lanka

description: Admissions, availability, and sales related to acute AChEII poisoning, AChEII study, Anuradhapura, 2017. This provides the data of the entire survey and the results of chi-square for goodness of fit. (XLS 50 kb)
DOI: 10.6084/m9.figshare.6694862.v1
title: Additional file 1: of Acetylcholinesterase inhibitor insecticides related acute poisoning, availability and sales: trends during the post-insecticide-ban period of Anuradhapura, Sri Lanka

description: Admissions, availability, and sales related to acute AChEII poisoning, AChEII study, Anuradhapura, 2017. This provides the data of the entire survey and the results of chi-square for goodness of fit. (XLS 50 kb)
DOI: 10.6084/m9.figshare.6694847
title: Additional file 1: of Pancreatic cancer as a sentinel for hereditary cancer predisposition

description: Table S1. contains the list of the genes used in the study, as well as indicators for which pathway they belong to in subsequent analyses. Table S2. is the list of rare variants with corresponding in silico scores. Table S3. contains the total counts that were used to create Fig. 2. (XLSX 73 kb)
DOI: 10.6084/m9.figshare.6694847.v1
title: Additional file 1: of Pancreatic cancer as a sentinel for hereditary cancer predisposition

description: Table S1. contains the list of the genes used in the study, as well as indicators for which pathway they belong to in subsequent analyses. Table S2. is the list of rare variants with corresponding in silico scores. Table S3. contains the total counts that were used to create Fig. 2. (XLSX 73 kb)
DOI: 10.6084/m9.figshare.6694772
title: Additional file 5: of Analysis of novel caudal hindbrain genes reveals different regulatory logic for gene expression in rhombomere 4 versus 5/6 in embryonic zebrafish

description: Table S2. Detailed analysis of WT and hoxb1b mutant RNA-seq data.Â 866 differentially expressed genes identified from the RNA-Seq experiment are listed in sheet 2. All GO terms associated with Biological Processes for both up-regulated and down-regulated genes are shown in sheets 3 and 4. Sheet 5 shows the subset of differentially expressed genes that is expressed in the hindbrain. In sheet 5, the genes in column A were derived from the ZFIN database (refer to sheet 3 in Additional file 2: Table S1). (XLSX 215 kb)
DOI: 10.6084/m9.figshare.6694772.v1
title: Additional file 5: of Analysis of novel caudal hindbrain genes reveals different regulatory logic for gene expression in rhombomere 4 versus 5/6 in embryonic zebrafish

description: Table S2. Detailed analysis of WT and hoxb1b mutant RNA-seq data.Â 866 differentially expressed genes identified from the RNA-Seq experiment are listed in sheet 2. All GO terms associated with Biological Processes for both up-regulated and down-regulated genes are shown in sheets 3 and 4. Sheet 5 shows the subset of differentially expressed genes that is expressed in the hindbrain. In sheet 5, the genes in column A were derived from the ZFIN database (refer to sheet 3 in Additional file 2: Table S1). (XLSX 215 kb)
DOI: 10.6084/m9.figshare.6694754
title: Additional file 3: of Genetic diversity analysis of cultivated and wild grapevine (Vitis vinifera L.) accessions around the Mediterranean basin and Central Asia

description: Table S3. Ancestry values (mean and standard deviation values over 20 iterations) for the genetic groups inferred by STRUCTURE analysis of 1378 sativa and sylvestris grapevine samples genotyped at 20 SSR loci. (XLSX 145 kb)
DOI: 10.6084/m9.figshare.6694754.v1
title: Additional file 3: of Genetic diversity analysis of cultivated and wild grapevine (Vitis vinifera L.) accessions around the Mediterranean basin and Central Asia

description: Table S3. Ancestry values (mean and standard deviation values over 20 iterations) for the genetic groups inferred by STRUCTURE analysis of 1378 sativa and sylvestris grapevine samples genotyped at 20 SSR loci. (XLSX 145 kb)
DOI: 10.6084/m9.figshare.6694733
title: Additional file 2: of Genetic diversity analysis of cultivated and wild grapevine (Vitis vinifera L.) accessions around the Mediterranean basin and Central Asia

description: Table S2. Determination of flower phenotype and genotype. The APT3 gene marker distinguished females (F) from males (M) or hermaphrodites (H). SSR marker VVIb23 is tightly linked to the flower sex locus and the unique allele 282 is linked to hermaphrodism. (XLSX 57 kb)
DOI: 10.6084/m9.figshare.6694733.v1
title: Additional file 2: of Genetic diversity analysis of cultivated and wild grapevine (Vitis vinifera L.) accessions around the Mediterranean basin and Central Asia

description: Table S2. Determination of flower phenotype and genotype. The APT3 gene marker distinguished females (F) from males (M) or hermaphrodites (H). SSR marker VVIb23 is tightly linked to the flower sex locus and the unique allele 282 is linked to hermaphrodism. (XLSX 57 kb)
DOI: 10.6084/m9.figshare.6694718
title: Additional file 2: of Analysis of novel caudal hindbrain genes reveals different regulatory logic for gene expression in rhombomere 4 versus 5/6 in embryonic zebrafish

description: Table S1. Identification of additional r4, r5 and r6 genes. This file represents the data downloaded from ZFIN and how it was parsed to generate a list of 107 rhombomere-restricted genes expressed in r4, r5 and r6. Sheet 1 lists 1820 genes that are expressed in the hindbrain, rhombomeres 4, 5 and 6. Sheet 2 represents 1194 genes that are expressed in the hindbrain, rhombomeres 4, 5 and 6 during the first 24Â h development. Sheet 4 has the list of 107 genes that re restricted to rhombomeres 4, 5 and 6. Sheets 5, 6 and 7 represent the genes sorted according to their expression location and additional information associated to these genes are also listed in the last three sheets. (XLSX 112 kb)
DOI: 10.6084/m9.figshare.6694718.v1
title: Additional file 2: of Analysis of novel caudal hindbrain genes reveals different regulatory logic for gene expression in rhombomere 4 versus 5/6 in embryonic zebrafish

description: Table S1. Identification of additional r4, r5 and r6 genes. This file represents the data downloaded from ZFIN and how it was parsed to generate a list of 107 rhombomere-restricted genes expressed in r4, r5 and r6. Sheet 1 lists 1820 genes that are expressed in the hindbrain, rhombomeres 4, 5 and 6. Sheet 2 represents 1194 genes that are expressed in the hindbrain, rhombomeres 4, 5 and 6 during the first 24Â h development. Sheet 4 has the list of 107 genes that re restricted to rhombomeres 4, 5 and 6. Sheets 5, 6 and 7 represent the genes sorted according to their expression location and additional information associated to these genes are also listed in the last three sheets. (XLSX 112 kb)
DOI: 10.6084/m9.figshare.6694712
title: Additional file 1: of Genetic diversity analysis of cultivated and wild grapevine (Vitis vinifera L.) accessions around the Mediterranean basin and Central Asia

description: Table S1. SSR allelic profile of 1378 sativa and sylvestris grapevine samples genotyped at 20 SSR molecular markers. (XLSX 643 kb)
DOI: 10.6084/m9.figshare.6694712.v1
title: Additional file 1: of Genetic diversity analysis of cultivated and wild grapevine (Vitis vinifera L.) accessions around the Mediterranean basin and Central Asia

description: Table S1. SSR allelic profile of 1378 sativa and sylvestris grapevine samples genotyped at 20 SSR molecular markers. (XLSX 643 kb)
DOI: 10.6084/m9.figshare.6694685
title: Additional file 12: of Analysis of novel caudal hindbrain genes reveals different regulatory logic for gene expression in rhombomere 4 versus 5/6 in embryonic zebrafish

description: Table S3. Detailed analysis of WT and gas6 mutants RNA-seq data.Â 1590 differentially expressed genes were identified from the RNA-Seq experiment and is shown in sheet 2. All the GO terms associated with Biological Processes for both up-regulated and down-regulated genes are listed in sheets 3 and 4. Sheet 5 shows the subset of differentially expressed genes that are expressed in the hindbrain. (XLSX 889 kb)
DOI: 10.6084/m9.figshare.6694685.v1
title: Additional file 12: of Analysis of novel caudal hindbrain genes reveals different regulatory logic for gene expression in rhombomere 4 versus 5/6 in embryonic zebrafish

description: Table S3. Detailed analysis of WT and gas6 mutants RNA-seq data.Â 1590 differentially expressed genes were identified from the RNA-Seq experiment and is shown in sheet 2. All the GO terms associated with Biological Processes for both up-regulated and down-regulated genes are listed in sheets 3 and 4. Sheet 5 shows the subset of differentially expressed genes that are expressed in the hindbrain. (XLSX 889 kb)
DOI: 10.6084/m9.figshare.3761562.v1588
title: Online Labour Index: Measuring the Online Gig Economy for Policy and Research

description: Data repository for the data underlying the Online Labour Index. See http://ilabour.oii.ox.ac.uk online-labour-index/ for details.
DOI: 10.6084/m9.figshare.6693488
title: Sunflower Atlas

description: Sunflower parts.
DOI: 10.6084/m9.figshare.6693485
title: Durasphere® EXP: a non-biodegradable agent for treatment of primary Vesico-Ureteral reflux in children

description: ABSTRACT Introduction: Durasphere® EXP (DEXP) is a compound of biocompatible and non--biodegradable particles of zirconium oxide covered with pyrolytic carbon. The aim of this study is to evaluate the durability of off-label use of DEXP in the treatment of primary vesicoureteral reflux in children. Materials and Methods: Patients who underwent subureteric injection of DEXP for the correction of primary VUR were retrospectively reviewed. Patients aged &gt;18 years as well as those who had grade-I or -V VUR, anatomic abnormalities (duplicated system, hutch diverticulum), neurogenic bladder or treatment refractory voiding dysfunction were excluded. Radiologic success was defined as the resolution of VUR at the 3rd month control. Success was radiographically evaluated at the end of the first year. Results: Thirty-eight patients (9 boys, 29 girls; mean age, 6.3±2.7 years) formed the study cohort. Forty-six renal units received DEXP (grade II: 22; grade III: 18; grade IV: 6). Mean volume per ureteric orifice to obtain the mound was 0.70±0.16mL. First con- trol VCUG was done after 3 months in all patients. After the first VCUG, 6 patients had VUR recurrence. Short-term radiologic success of DEXP was 84.2%. Rate of radiologic success at the end of the first year was 69.4% (25/32). Lower age (p:0.006) and lower amount of injected material (p:0.05) were associated with higher success rates at the end of 1 year. Conclusion: This is the first study to assess the outcomes of DEXP for treatment of primary VUR in children. After 1 year of follow-up, DEXP had a 69.4% success rate.
DOI: 10.6084/m9.figshare.6693485.v1
title: Durasphere® EXP: a non-biodegradable agent for treatment of primary Vesico-Ureteral reflux in children

description: ABSTRACT Introduction: Durasphere® EXP (DEXP) is a compound of biocompatible and non--biodegradable particles of zirconium oxide covered with pyrolytic carbon. The aim of this study is to evaluate the durability of off-label use of DEXP in the treatment of primary vesicoureteral reflux in children. Materials and Methods: Patients who underwent subureteric injection of DEXP for the correction of primary VUR were retrospectively reviewed. Patients aged &gt;18 years as well as those who had grade-I or -V VUR, anatomic abnormalities (duplicated system, hutch diverticulum), neurogenic bladder or treatment refractory voiding dysfunction were excluded. Radiologic success was defined as the resolution of VUR at the 3rd month control. Success was radiographically evaluated at the end of the first year. Results: Thirty-eight patients (9 boys, 29 girls; mean age, 6.3±2.7 years) formed the study cohort. Forty-six renal units received DEXP (grade II: 22; grade III: 18; grade IV: 6). Mean volume per ureteric orifice to obtain the mound was 0.70±0.16mL. First con- trol VCUG was done after 3 months in all patients. After the first VCUG, 6 patients had VUR recurrence. Short-term radiologic success of DEXP was 84.2%. Rate of radiologic success at the end of the first year was 69.4% (25/32). Lower age (p:0.006) and lower amount of injected material (p:0.05) were associated with higher success rates at the end of 1 year. Conclusion: This is the first study to assess the outcomes of DEXP for treatment of primary VUR in children. After 1 year of follow-up, DEXP had a 69.4% success rate.
DOI: 10.6084/m9.figshare.6693482
title: Antibodies anti-trypanosomatides in domestic cats in Paraná: who is at highest risk of infection?

description: Abstract The aim of this study were to detect antibodies anti-Leishmania spp. and anti-Trypanosoma cruzi in two different populations of domestic cats (Felis catus domesticus) from North Paraná referred for surgical castration and to determine which characteristics of the animals studied may be associated with seropositivity. Serum samples from 679 cats were analyzed using enzyme-linked immunosorbent assay (ELISA) and indirect immunofluorescence antibody test (IFAT) in series. Associations between age, sex, race, year of care and animal group were verified using the simple logistic regression. Percentage of 8.5% (58/679) of cats were positive for Leishmania spp. and 7.6% (51/673) for T. cruzi by the tests ELISA and IFAT. Animals collected by non-governmental animal protection organizations presented more seropositivity for Leishmania spp. (p&lt;0.0001). Results shown that Leishmania spp. and T. cruzi are present in domestic cats in the northern part of the state of Paraná, as well as, owners of non-governmental animal protection organizations may be more exposed to leishmaniasis when compared to other animal owners evaluated in the present study.
DOI: 10.6084/m9.figshare.6693482.v1
title: Antibodies anti-trypanosomatides in domestic cats in Paraná: who is at highest risk of infection?

description: Abstract The aim of this study were to detect antibodies anti-Leishmania spp. and anti-Trypanosoma cruzi in two different populations of domestic cats (Felis catus domesticus) from North Paraná referred for surgical castration and to determine which characteristics of the animals studied may be associated with seropositivity. Serum samples from 679 cats were analyzed using enzyme-linked immunosorbent assay (ELISA) and indirect immunofluorescence antibody test (IFAT) in series. Associations between age, sex, race, year of care and animal group were verified using the simple logistic regression. Percentage of 8.5% (58/679) of cats were positive for Leishmania spp. and 7.6% (51/673) for T. cruzi by the tests ELISA and IFAT. Animals collected by non-governmental animal protection organizations presented more seropositivity for Leishmania spp. (p&lt;0.0001). Results shown that Leishmania spp. and T. cruzi are present in domestic cats in the northern part of the state of Paraná, as well as, owners of non-governmental animal protection organizations may be more exposed to leishmaniasis when compared to other animal owners evaluated in the present study.
DOI: 10.6084/m9.figshare.6693476
title: COX-2 gene expression and methylation profile in Sapajus apella as an experimental model for gastric adenocarcinoma

description: Abstract Gastric cancer (GC) remains one of the main causes of cancer-related death worldwide. There are two distinct histological types of GC: diffuse and intestinal. The latter is characterized by the presence of pre-neoplastic lesions. One of the most frequently altered enzymes in intestinal GC is COX-2, an important lesion marker. This work aimed to study COX-2 methylation and expression in N-methyl-N-Nitrosurea (MNU)-induced intestinal GC in six Sapajus apella animals. The partial promoter sequence of S. apella COX-2 gene was obtained and used to identify transcription factors and cis-regulatory element binding sites. The COX-2 methylation pattern was assessed using Methylation-Specific PCR (MSP), and expression was analyzed by immunohistochemistry (IHQ). A total of 20 samples were obtained. A 675 bp fragment of the S. apella COX-2 promoter region was obtained, and it was 99.2% and 68.2% similar to H. sapiens and S. boliviensis, respectively. Similar to humans, several transcription factors and cis-regulatory element binding sites were identified in the S. apella sequence. MSP revealed that all samples were methylated. However, IHQ results demonstrated positive COX-2 expression in all pre-neoplastic and tumoral samples. The results suggest that the analyzed fragment is not crucial in COX-2 regulation of GC in S. apella.
DOI: 10.6084/m9.figshare.6693476.v1
title: COX-2 gene expression and methylation profile in Sapajus apella as an experimental model for gastric adenocarcinoma

description: Abstract Gastric cancer (GC) remains one of the main causes of cancer-related death worldwide. There are two distinct histological types of GC: diffuse and intestinal. The latter is characterized by the presence of pre-neoplastic lesions. One of the most frequently altered enzymes in intestinal GC is COX-2, an important lesion marker. This work aimed to study COX-2 methylation and expression in N-methyl-N-Nitrosurea (MNU)-induced intestinal GC in six Sapajus apella animals. The partial promoter sequence of S. apella COX-2 gene was obtained and used to identify transcription factors and cis-regulatory element binding sites. The COX-2 methylation pattern was assessed using Methylation-Specific PCR (MSP), and expression was analyzed by immunohistochemistry (IHQ). A total of 20 samples were obtained. A 675 bp fragment of the S. apella COX-2 promoter region was obtained, and it was 99.2% and 68.2% similar to H. sapiens and S. boliviensis, respectively. Similar to humans, several transcription factors and cis-regulatory element binding sites were identified in the S. apella sequence. MSP revealed that all samples were methylated. However, IHQ results demonstrated positive COX-2 expression in all pre-neoplastic and tumoral samples. The results suggest that the analyzed fragment is not crucial in COX-2 regulation of GC in S. apella.
DOI: 10.6084/m9.figshare.6693473
title: Whole genome sequence of Mycobacterium kansasii isolates of the genotype 1 from Brazilian patients with pulmonary disease demonstrates considerable heterogeneity

description: Mycobacterium kansasii is an opportunistic pathogen and one of the most commonly encountered species in individuals with lung disease. We here report the complete genome sequence of 12 clinical isolates of M. kansasii from patients with pulmonary disease in Brazil.
DOI: 10.6084/m9.figshare.6693473.v1
title: Whole genome sequence of Mycobacterium kansasii isolates of the genotype 1 from Brazilian patients with pulmonary disease demonstrates considerable heterogeneity

description: Mycobacterium kansasii is an opportunistic pathogen and one of the most commonly encountered species in individuals with lung disease. We here report the complete genome sequence of 12 clinical isolates of M. kansasii from patients with pulmonary disease in Brazil.
DOI: 10.6084/m9.figshare.6693470
title: Cryptosporidium occurrence in ruminants from the North Pioneer mesoregion of Paraná, Brazil

description: Abstract The aim of this study was to investigate the occurrence of Cryptosporidium in cattle and sheep from the North Pioneer mesoregion of the state of Paraná. For this, 317 stool samples were collected from cattle and sheep on 16 properties in six municipalities in the North Pioneer mesoregion of Paraná. For detection of Cryptosporidium species, molecular analysis was performed using nested-PCR techniques targeting the 18S rRNA gene. Of the 37 beef cows and 115 calves analyzed, four (10.8%) and 14 (12.2%), respectively, were positive for Cryptosporidium. Of the 12 cows and 52 calves, one (8.3%) and 14 (26.9%), respectively, were positive for Cryptosporidium; and of the 42 ewes and 59 lambs, six (14.3%) and 12 (20.3%), respectively were positive for Cryptosporidium. Cattle (15.3%) and sheep (17.8%) were both susceptible to infection. All the properties of the municipalities of Assaí, Ibaiti and, Leópolis presented infected animals. The study showed that Cryptosporidium occurs in most municipalities assessed, that dairy calves had a higher risk (Odds Ratio=2,66, p-value=0,018) for infection than beef calves, and that sheep are just as susceptible to infection as are cattle, and that further Cryptosporidium studies are developed.