cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.15153679.v2
title: Additional file 10 of Identification of Brassica napus small RNAs responsive to infection by a necrotrophic pathogen

description: Additional file 10: Supplementary Table 7. GO term enrichment analysis of 5918 transcripts possibly regulated by pha-siRNAs based on psRNA target analysis.
DOI: 10.6084/m9.figshare.15153682
title: Additional file 11 of Identification of Brassica napus small RNAs responsive to infection by a necrotrophic pathogen

description: Additional file 11: Supplementary Table 8. GO term enrichment analysis of psRNA target-predicted targets of 1601 targets of miR1885-triggered ta-siRNAs.
DOI: 10.6084/m9.figshare.15153682.v2
title: Additional file 11 of Identification of Brassica napus small RNAs responsive to infection by a necrotrophic pathogen

description: Additional file 11: Supplementary Table 8. GO term enrichment analysis of psRNA target-predicted targets of 1601 targets of miR1885-triggered ta-siRNAs.
DOI: 10.6084/m9.figshare.15153685
title: Additional file 12 of Identification of Brassica napus small RNAs responsive to infection by a necrotrophic pathogen

description: Additional file 12: Supplementary Table 9. Primers used in this study.
DOI: 10.6084/m9.figshare.15153685.v2
title: Additional file 12 of Identification of Brassica napus small RNAs responsive to infection by a necrotrophic pathogen

description: Additional file 12: Supplementary Table 9. Primers used in this study.
DOI: 10.6084/m9.figshare.15153688
title: Additional file 1 of Identification of Brassica napus small RNAs responsive to infection by a necrotrophic pathogen

description: Additional file 1: Supplementary File 1. Output of the software PHAS Tank showing candidate PHAS loci.
DOI: 10.6084/m9.figshare.15153679.v1
title: Additional file 10 of fIdentification of B. napus small RNAs responsive to infection by a necrotrophic pathogen

description: Additional file 10: Supplementary Table 7. GO term enrichment analysis of 5918 transcripts possibly regulated by pha-siRNAs based on psRNA target analysis.
DOI: 10.6084/m9.figshare.15153682.v1
title: Additional file 11 of fIdentification of B. napus small RNAs responsive to infection by a necrotrophic pathogen

description: Additional file 11: Supplementary Table 8. GO term enrichment analysis of psRNA target-predicted targets of 1601 targets of miR1885-triggered ta-siRNAs.
DOI: 10.6084/m9.figshare.15153685.v1
title: Additional file 12 of fIdentification of B. napus small RNAs responsive to infection by a necrotrophic pathogen

description: Additional file 12: Supplementary Table 9. Primers used in this study.
DOI: 10.6084/m9.figshare.15153688.v2
title: Additional file 1 of Identification of Brassica napus small RNAs responsive to infection by a necrotrophic pathogen

description: Additional file 1: Supplementary File 1. Output of the software PHAS Tank showing candidate PHAS loci.
DOI: 10.6084/m9.figshare.15153688.v1
title: Additional file 1 of fIdentification of B. napus small RNAs responsive to infection by a necrotrophic pathogen

description: Additional file 1: Supplementary File 1. Output of the software PHAS Tank showing candidate PHAS loci.
DOI: 10.6084/m9.figshare.15153700.v2
title: Additional file 5 of Identification of Brassica napus small RNAs responsive to infection by a necrotrophic pathogen

description: Additional file 5: Supplementary Table 2. Cleaved products of the 73 miRNA families. All targets identified using degradome sequencing in infected and mock samples are included.
DOI: 10.6084/m9.figshare.15153697
title: Additional file 4 of Identification of Brassica napus small RNAs responsive to infection by a necrotrophic pathogen

description: Additional file 4: Supplementary Table 1. All small RNA biogenesis loci identified using the program Sho:rtStack.
DOI: 10.6084/m9.figshare.15153697.v2
title: Additional file 4 of Identification of Brassica napus small RNAs responsive to infection by a necrotrophic pathogen

description: Additional file 4: Supplementary Table 1. All small RNA biogenesis loci identified using the program Sho:rtStack.
DOI: 10.6084/m9.figshare.15153700
title: Additional file 5 of Identification of Brassica napus small RNAs responsive to infection by a necrotrophic pathogen

description: Additional file 5: Supplementary Table 2. Cleaved products of the 73 miRNA families. All targets identified using degradome sequencing in infected and mock samples are included.
DOI: 10.6084/m9.figshare.15153703
title: Additional file 6 of Identification of Brassica napus small RNAs responsive to infection by a necrotrophic pathogen

description: Additional file 6: Supplementary Table 3. Targets of conserved microRNAs based on degradome sequencing data from the infected sample. Table includes genes targeted by multiple miRNAs and multiple genes targeted by the same miRNA. Targets only found in the infected sample are included.
DOI: 10.6084/m9.figshare.15153697.v1
title: Additional file 4 of fIdentification of B. napus small RNAs responsive to infection by a necrotrophic pathogen

description: Additional file 4: Supplementary Table 1. All small RNA biogenesis loci identified using the program Sho:rtStack.
DOI: 10.6084/m9.figshare.15153700.v1
title: Additional file 5 of fIdentification of B. napus small RNAs responsive to infection by a necrotrophic pathogen

description: Additional file 5: Supplementary Table 2. Cleaved products of the 73 miRNA families. All targets identified using degradome sequencing in infected and mock samples are included.
DOI: 10.6084/m9.figshare.15153706
title: Additional file 7 of Identification of Brassica napus small RNAs responsive to infection by a necrotrophic pathogen

description: Additional file 7: Supplementary Table 4. Genes targeted by conserved miRNAs only in the infected sample.
DOI: 10.6084/m9.figshare.15153703.v2
title: Additional file 6 of Identification of Brassica napus small RNAs responsive to infection by a necrotrophic pathogen

description: Additional file 6: Supplementary Table 3. Targets of conserved microRNAs based on degradome sequencing data from the infected sample. Table includes genes targeted by multiple miRNAs and multiple genes targeted by the same miRNA. Targets only found in the infected sample are included.
DOI: 10.6084/m9.figshare.15153706.v2
title: Additional file 7 of Identification of Brassica napus small RNAs responsive to infection by a necrotrophic pathogen

description: Additional file 7: Supplementary Table 4. Genes targeted by conserved miRNAs only in the infected sample.
DOI: 10.6084/m9.figshare.15153712
title: Additional file 9 of Identification of Brassica napus small RNAs responsive to infection by a necrotrophic pathogen

description: Additional file 9: Supplementary Table 6. Known and novel miRNAs identified in this study.
DOI: 10.6084/m9.figshare.15153709
title: Additional file 8 of Identification of Brassica napus small RNAs responsive to infection by a necrotrophic pathogen

description: Additional file 8: Supplementary Table 5. Conserved micro RNA sequences with evidence of differential expression during infection.
DOI: 10.6084/m9.figshare.15153709.v2
title: Additional file 8 of Identification of Brassica napus small RNAs responsive to infection by a necrotrophic pathogen

description: Additional file 8: Supplementary Table 5. Conserved micro RNA sequences with evidence of differential expression during infection.
DOI: 10.6084/m9.figshare.15153712.v2
title: Additional file 9 of Identification of Brassica napus small RNAs responsive to infection by a necrotrophic pathogen

description: Additional file 9: Supplementary Table 6. Known and novel miRNAs identified in this study.
DOI: 10.6084/m9.figshare.15153706.v1
title: Additional file 7 of fIdentification of B. napus small RNAs responsive to infection by a necrotrophic pathogen

description: Additional file 7: Supplementary Table 4. Genes targeted by conserved miRNAs only in the infected sample.
DOI: 10.6084/m9.figshare.15153703.v1
title: Additional file 6 of fIdentification of B. napus small RNAs responsive to infection by a necrotrophic pathogen

description: Additional file 6: Supplementary Table 3. Targets of conserved microRNAs based on degradome sequencing data from the infected sample. Table includes genes targeted by multiple miRNAs and multiple genes targeted by the same miRNA. Targets only found in the infected sample are included.
DOI: 10.6084/m9.figshare.15153712.v1
title: Additional file 9 of fIdentification of B. napus small RNAs responsive to infection by a necrotrophic pathogen

description: Additional file 9: Supplementary Table 6. Known and novel miRNAs identified in this study.
DOI: 10.6084/m9.figshare.15153709.v1
title: Additional file 8 of fIdentification of B. napus small RNAs responsive to infection by a necrotrophic pathogen

description: Additional file 8: Supplementary Table 5. Conserved micro RNA sequences with evidence of differential expression during infection.
DOI: 10.6084/m9.figshare.16456401
title: Additional file 2 of Accessory enzymes of hypercellulolytic Penicillium funiculosum facilitate complete saccharification of sugarcane bagasse

description: Additional file 2: Total number of proteins detected in the proteome of PfMig188 modulated with varying concentrations of sugarcane bagasse and their abundance ratio.
DOI: 10.6084/m9.figshare.16456401.v1
title: Additional file 2 of Accessory enzymes of hypercellulolytic Penicillium funiculosum facilitate complete saccharification of sugarcane bagasse

description: Additional file 2: Total number of proteins detected in the proteome of PfMig188 modulated with varying concentrations of sugarcane bagasse and their abundance ratio.
DOI: 10.6084/m9.figshare.16456446
title: Additional file 1 of Method for reconstructing mortality by educational groups

description: Additional file 1. Estimated life tables by country, sex and educational attainment.
DOI: 10.6084/m9.figshare.16456446.v1
title: Additional file 1 of Method for reconstructing mortality by educational groups

description: Additional file 1. Estimated life tables by country, sex and educational attainment.
DOI: 10.6084/m9.figshare.16456449
title: Additional file 5 of Expression profiles and functional prediction of long non-coding RNAs LINC01133, ZEB1-AS1 and ABHD11-AS1 in the luminal subtype of breast cancer

description: Additional file 5. File S1. The list of 420 luminal samples obtained from UCSC Xena Browser and the Genomic Data Commons (GDC) database.
DOI: 10.6084/m9.figshare.16456449.v1
title: Additional file 5 of Expression profiles and functional prediction of long non-coding RNAs LINC01133, ZEB1-AS1 and ABHD11-AS1 in the luminal subtype of breast cancer

description: Additional file 5. File S1. The list of 420 luminal samples obtained from UCSC Xena Browser and the Genomic Data Commons (GDC) database.
DOI: 10.6084/m9.figshare.16456452
title: Additional file 6 of Expression profiles and functional prediction of long non-coding RNAs LINC01133, ZEB1-AS1 and ABHD11-AS1 in the luminal subtype of breast cancer

description: Additional file 6. File S2. The list of co-expressed genes with LINC01133, ZEB1-AS1 and ABHD11-AS1 across the selected luminal A and B BC samples.
DOI: 10.6084/m9.figshare.16456452.v1
title: Additional file 6 of Expression profiles and functional prediction of long non-coding RNAs LINC01133, ZEB1-AS1 and ABHD11-AS1 in the luminal subtype of breast cancer

description: Additional file 6. File S2. The list of co-expressed genes with LINC01133, ZEB1-AS1 and ABHD11-AS1 across the selected luminal A and B BC samples.
DOI: 10.6084/m9.figshare.16456461
title: Additional file 7 of Expression profiles and functional prediction of long non-coding RNAs LINC01133, ZEB1-AS1 and ABHD11-AS1 in the luminal subtype of breast cancer

description: Additional file 7. File S3. The list of biological process (BP), cellular component (CC), and molecular function (MF) categories, retrieved from DAVID database.
DOI: 10.6084/m9.figshare.16456461.v1
title: Additional file 7 of Expression profiles and functional prediction of long non-coding RNAs LINC01133, ZEB1-AS1 and ABHD11-AS1 in the luminal subtype of breast cancer

description: Additional file 7. File S3. The list of biological process (BP), cellular component (CC), and molecular function (MF) categories, retrieved from DAVID database.
DOI: 10.6084/m9.figshare.19901931
title: Elemental Chalcogen (Se, S) in PEG-400 to the Synthesis of Seleno- and Thioflavones from 2-Chlorophenyl Ethynyl Ketone and Nucleophilic Species of Chalcogen

description: An alternative green method was developed for the synthesis of thio-and selenoflavones by the ring closure of 2-chlorophenyl ethynyl ketone with NaHY (Y = S, Se). These nucleophilic chalcogen species were generated in situ using NaBH4 to reduce the elemental chalcogen in the presence of polyethylene glycol-400 (PEG-400). The efficiency of this reaction is strongly dependent on the PEG-400 solvent, acting like a crown ether, complexing with the sodium atom of NaHY species, making the chalcogen nucleophile more active. The synthetic protocol proceeded efficiently at 100 °C under argon, using a range of 2-chlorophenyl ethynyl ketone containing alkyl, aryl, or vinyl groups and the sulfur and selenium chalcogen. By this efficient and simple approach, 18 chalcogenoflavones were obtained in good to excellent yields after 2 h.
DOI: 10.6084/m9.figshare.19901931.v1
title: Elemental Chalcogen (Se, S) in PEG-400 to the Synthesis of Seleno- and Thioflavones from 2-Chlorophenyl Ethynyl Ketone and Nucleophilic Species of Chalcogen

description: An alternative green method was developed for the synthesis of thio-and selenoflavones by the ring closure of 2-chlorophenyl ethynyl ketone with NaHY (Y = S, Se). These nucleophilic chalcogen species were generated in situ using NaBH4 to reduce the elemental chalcogen in the presence of polyethylene glycol-400 (PEG-400). The efficiency of this reaction is strongly dependent on the PEG-400 solvent, acting like a crown ether, complexing with the sodium atom of NaHY species, making the chalcogen nucleophile more active. The synthetic protocol proceeded efficiently at 100 °C under argon, using a range of 2-chlorophenyl ethynyl ketone containing alkyl, aryl, or vinyl groups and the sulfur and selenium chalcogen. By this efficient and simple approach, 18 chalcogenoflavones were obtained in good to excellent yields after 2 h.
DOI: 10.6084/m9.figshare.19901945
title: Stability Analyses by HPLC-MS of Guanitoxin Isolated from Sphaerospermopsis torques-reginae

description: Guanitoxin (GNT) is a natural organophosphate produced by some species of freshwater cyanobacteria, which inhibits the active site of acetylcholinesterase, preventing the hydrolysis of cholinesterases and consequently causing serious disturbances in the neuromuscular system. Despite having a chemical structure like synthetic organophosphates, there is still no analytical standard available for environmental and freshwater monitoring. Therefore, this study investigated the stability of GNT under different storage conditions, pH, and temperature. The toxin is produced by the cyanobacterium Sphaerospermopsis torques-reginae and monitored by liquid chromatography coupled to mass spectrometry (LC-MS) and LC-MS/MS for the identification and verification of its stability. The main degradation product formed is the hydroxy-amino-guanidinic derivative of the toxin. The results also indicate that GNT is stable in acidic medium (pH = 3.0), but can gradually degrade at room temperature (&gt; 23 ºC) over a period of 96 h. Lyophilized biomass of S. torques-reginae containing GNT remained stable when stored in a refrigerator below 4 ºC. In addition, the extraction yield is higher when prepared from fresh S. torques-reginae cells than from lyophilized material. Thus, the results shown here contribute with valuable information for studies that aim at the isolation, identification, and monitoring of GNT in samples of raw water and cyanobacterial blooms.
DOI: 10.6084/m9.figshare.19901945.v1
title: Stability Analyses by HPLC-MS of Guanitoxin Isolated from Sphaerospermopsis torques-reginae

description: Guanitoxin (GNT) is a natural organophosphate produced by some species of freshwater cyanobacteria, which inhibits the active site of acetylcholinesterase, preventing the hydrolysis of cholinesterases and consequently causing serious disturbances in the neuromuscular system. Despite having a chemical structure like synthetic organophosphates, there is still no analytical standard available for environmental and freshwater monitoring. Therefore, this study investigated the stability of GNT under different storage conditions, pH, and temperature. The toxin is produced by the cyanobacterium Sphaerospermopsis torques-reginae and monitored by liquid chromatography coupled to mass spectrometry (LC-MS) and LC-MS/MS for the identification and verification of its stability. The main degradation product formed is the hydroxy-amino-guanidinic derivative of the toxin. The results also indicate that GNT is stable in acidic medium (pH = 3.0), but can gradually degrade at room temperature (&gt; 23 ºC) over a period of 96 h. Lyophilized biomass of S. torques-reginae containing GNT remained stable when stored in a refrigerator below 4 ºC. In addition, the extraction yield is higher when prepared from fresh S. torques-reginae cells than from lyophilized material. Thus, the results shown here contribute with valuable information for studies that aim at the isolation, identification, and monitoring of GNT in samples of raw water and cyanobacterial blooms.
DOI: 10.6084/m9.figshare.12950856
title: Growth patterns and cardiovascular abnormalities in SGA fetuses: 2. Normal growth and progressive growth restriction

description: To characterize growth processes and their associated cardiovascular abnormalities in SGA fetuses with normal growth and progressive growth restriction patterns as defined by Individualized Growth Assessment (IGA). A SGA cohort (EFW and BW &lt; 10th percentile) was derived from the PORTO study that included 47 fetuses with normal growth outcome (SGA Normal) and 34 fetuses with progressive growth restriction (SGA Growth Restricted, Pattern 1). Composite fetal size parameters were used to quantify growth pathology at individual third trimester time points (individual composite Prenatal Growth Assessment Score {icPGAS}) and calculated cumulatively during the third trimester (Fetal Growth Pathology Score 1{FGPS1}). Paired Doppler evaluations of the umbilical artery (UA), middle cerebral artery (MCA), ductus venosus (DV) and myocardial performance index (MPI) were used to detect cardiovascular anomalies. Outcome variables were birth age and birth weight. Ranking fetuses with respect to the severity of the 3rd trimester growth pathology (–FGPS1) revealed three subgroups in each of these two groups. In SGA Normal, no (51%), minimal (19%) or minor (30%) growth abnormalities were present. Although vascular flow abnormalities occurred without growth abnormalities (UA: 38%; MCA: 35%), they increased with minor growth disturbances (UA: 64%; MCA: 50%). All fetuses delivered at term and in only 7 cases (minor growth abnormalities subgroup) were the neonates abnormally small based on IGA criteria. In SGA Growth Restricted, Pattern 1, the progression of growth restriction was slow (47%), moderate (21%) and rapid (32%). Corresponding median –FGPS1 values were −1.34%, −2.67% and −4.88%, respectively. The median age of onset was 33.6, 29.7 and 29.7 weeks in these three subgroups. UA abnormalities occurred infrequently in the first two subgroups but were found in all cases of rapidly progressing pathology. Similar results were found for the MCA and DV + MPI Doppler parameters (rapid progression: MCA = 50%; DV + MPI = 50%). Premature delivery occurred less frequently with slow progression but was nearly 100% in the moderately and rapidly progressive subgroups. Negative FGPS1 growth restriction patterns can be used to classify SGA fetuses. Subgroups, based on ranked –FGPS1 values in both SGA Normal and SGA Growth Restricted Pattern 1 groups had marked differences in cardiovascular abnormalities and neonatal outcomes. The characteristics of these two groups are consistent with small, normally growing fetuses and fetuses with “early” growth restriction, respectively.
DOI: 10.6084/m9.figshare.12950856.v1
title: Growth patterns and cardiovascular abnormalities in SGA fetuses: 2. Normal growth and progressive growth restriction

description: To characterize growth processes and their associated cardiovascular abnormalities in SGA fetuses with normal growth and progressive growth restriction patterns as defined by Individualized Growth Assessment (IGA). A SGA cohort (EFW and BW &lt; 10th percentile) was derived from the PORTO study that included 47 fetuses with normal growth outcome (SGA Normal) and 34 fetuses with progressive growth restriction (SGA Growth Restricted, Pattern 1). Composite fetal size parameters were used to quantify growth pathology at individual third trimester time points (individual composite Prenatal Growth Assessment Score {icPGAS}) and calculated cumulatively during the third trimester (Fetal Growth Pathology Score 1{FGPS1}). Paired Doppler evaluations of the umbilical artery (UA), middle cerebral artery (MCA), ductus venosus (DV) and myocardial performance index (MPI) were used to detect cardiovascular anomalies. Outcome variables were birth age and birth weight. Ranking fetuses with respect to the severity of the 3rd trimester growth pathology (–FGPS1) revealed three subgroups in each of these two groups. In SGA Normal, no (51%), minimal (19%) or minor (30%) growth abnormalities were present. Although vascular flow abnormalities occurred without growth abnormalities (UA: 38%; MCA: 35%), they increased with minor growth disturbances (UA: 64%; MCA: 50%). All fetuses delivered at term and in only 7 cases (minor growth abnormalities subgroup) were the neonates abnormally small based on IGA criteria. In SGA Growth Restricted, Pattern 1, the progression of growth restriction was slow (47%), moderate (21%) and rapid (32%). Corresponding median –FGPS1 values were −1.34%, −2.67% and −4.88%, respectively. The median age of onset was 33.6, 29.7 and 29.7 weeks in these three subgroups. UA abnormalities occurred infrequently in the first two subgroups but were found in all cases of rapidly progressing pathology. Similar results were found for the MCA and DV + MPI Doppler parameters (rapid progression: MCA = 50%; DV + MPI = 50%). Premature delivery occurred less frequently with slow progression but was nearly 100% in the moderately and rapidly progressive subgroups. Negative FGPS1 growth restriction patterns can be used to classify SGA fetuses. Subgroups, based on ranked –FGPS1 values in both SGA Normal and SGA Growth Restricted Pattern 1 groups had marked differences in cardiovascular abnormalities and neonatal outcomes. The characteristics of these two groups are consistent with small, normally growing fetuses and fetuses with “early” growth restriction, respectively.