cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.11847081.v1
title: Varenicline: mode of action, efficacy, safety and accumulated experience salient for clinical populations

description: <b>Objective:</b> Varenicline, a selective partial agonist of the α4β2 nicotinic acetylcholine receptor, is a smoking cessation pharmacotherapy that more than doubles the chance of quitting smoking at 6 months compared with placebo. This article reviews salient knowledge of the discovery, pharmacological characteristics, and the efficacy and safety of varenicline in general and in specific populations of smokers and provides recommendations to support use in clinical practice. <b>Methods</b>: Literature searches for varenicline were conducted using PubMed, with date limitations of 2000–2018 inclusive, using search terms covering the discovery, mechanism of action, pharmacokinetics, efficacy and safety in different populations of smokers, alternative quit approaches and combination therapy. Selection of safety and efficacy data was limited to clinical trials, meta-analyses and observational studies. <b>Results:</b> Standard administration of varenicline is efficacious in helping smokers to quit, including smokers with cardiovascular disease and chronic obstructive pulmonary disease. Furthermore, varenicline efficacy may be improved with pre-loading, a gradual quitting approach for smokers unwilling or unable to quit abruptly, and extended treatment in smokers who have recently quit to help maintain abstinence. Initial concerns regarding the association of varenicline with increased risk of neuropsychiatric and cardiovascular adverse events have been disproven after extensive clinical evaluations, and the benefit-risk profile of varenicline is considered favorable. <b>Conclusions:</b> Varenicline is efficacious and safe for all adult smokers with a range of clinical characteristics. Evidence suggests that approaches offering greater flexibility in timing and duration of treatment may further extend treatment efficacy and clinical reach.
DOI: 10.6084/m9.figshare.11847054
title: Supplementary Material for: Tips for Dealing with Common Beginner’s Mistakes Made during Endoscopic Ultrasound-Guided Gallbladder Drainage

description: Endoscopic ultrasound-guided gallbladder drainage (EUS-GBD) has been performed as an alternative to percutaneous drainage in surgically high-risk patients. Technical failures of EUS-GBD made by beginners are often attributed to failure of over-the-wire insertion of a fistula-dilating device or stent delivery system into the gallbladder, or stent misplacement in the final technical step. We herein report technical tips to prevent the failure of fistula dilation and provide tricks to avoid inward or outward stent misplacement.
DOI: 10.6084/m9.figshare.11847054.v1
title: Supplementary Material for: Tips for Dealing with Common Beginner’s Mistakes Made during Endoscopic Ultrasound-Guided Gallbladder Drainage

description: Endoscopic ultrasound-guided gallbladder drainage (EUS-GBD) has been performed as an alternative to percutaneous drainage in surgically high-risk patients. Technical failures of EUS-GBD made by beginners are often attributed to failure of over-the-wire insertion of a fistula-dilating device or stent delivery system into the gallbladder, or stent misplacement in the final technical step. We herein report technical tips to prevent the failure of fistula dilation and provide tricks to avoid inward or outward stent misplacement.
DOI: 10.6084/m9.figshare.11847045
title: Table 1.docx

description: Table 1 Calibrated micro-parameters for Jinping T<sub>2b</sub> marble model<b></b>
DOI: 10.6084/m9.figshare.11847045.v1
title: Table 1.docx

description: Table 1 Calibrated micro-parameters for Jinping T<sub>2b</sub> marble model<b></b>
DOI: 10.6084/m9.figshare.11847033
title: Auxiliary domains of the HrpB bacterial DExH-box helicase shape its RNA preferences

description: RNA helicases are fundamental players in RNA metabolism: they remodel RNA secondary structures and arrange ribonucleoprotein complexes. While DExH-box RNA helicases function in ribosome biogenesis and splicing in eukaryotes, information is scarce about bacterial homologs. HrpB is the only bacterial DExH-box protein whose structure is solved. Besides the catalytic core, HrpB possesses three accessory domains, conserved in all DExH-box helicases, plus a unique C-terminal extension (CTE). The function of these auxiliary domains remains unknown. Here, we characterize genetically and biochemically <i>Pseudomonas aeruginosa</i> HrpB homolog. We reveal that the auxiliary domains shape HrpB RNA preferences, affecting RNA species recognition and catalytic activity. We show that, among several types of RNAs, the single-stranded poly(A) and the highly structured MS2 RNA strongly stimulate HrpB ATPase activity. In addition, deleting the CTE affects only stimulation by structured RNAs like MS2 and rRNAs, while deletion of accessory domains results in gain of poly(U)-dependent activity. Finally, using hydrogen-deuterium exchange, we dissect the molecular details of HrpB interaction with poly(A) and MS2 RNAs. The catalytic core interacts with both RNAs, triggering a conformational change that reorients HrpB. Regions within the accessory domains and CTE are, instead, specifically responsive to MS2. Altogether, we demonstrate that in bacteria, like in eukaryotes, DExH-box helicase auxiliary domains are indispensable for RNA handling.
DOI: 10.6084/m9.figshare.11847033.v1
title: Auxiliary domains of the HrpB bacterial DExH-box helicase shape its RNA preferences

description: RNA helicases are fundamental players in RNA metabolism: they remodel RNA secondary structures and arrange ribonucleoprotein complexes. While DExH-box RNA helicases function in ribosome biogenesis and splicing in eukaryotes, information is scarce about bacterial homologs. HrpB is the only bacterial DExH-box protein whose structure is solved. Besides the catalytic core, HrpB possesses three accessory domains, conserved in all DExH-box helicases, plus a unique C-terminal extension (CTE). The function of these auxiliary domains remains unknown. Here, we characterize genetically and biochemically <i>Pseudomonas aeruginosa</i> HrpB homolog. We reveal that the auxiliary domains shape HrpB RNA preferences, affecting RNA species recognition and catalytic activity. We show that, among several types of RNAs, the single-stranded poly(A) and the highly structured MS2 RNA strongly stimulate HrpB ATPase activity. In addition, deleting the CTE affects only stimulation by structured RNAs like MS2 and rRNAs, while deletion of accessory domains results in gain of poly(U)-dependent activity. Finally, using hydrogen-deuterium exchange, we dissect the molecular details of HrpB interaction with poly(A) and MS2 RNAs. The catalytic core interacts with both RNAs, triggering a conformational change that reorients HrpB. Regions within the accessory domains and CTE are, instead, specifically responsive to MS2. Altogether, we demonstrate that in bacteria, like in eukaryotes, DExH-box helicase auxiliary domains are indispensable for RNA handling.
DOI: 10.6084/m9.figshare.11846904
title: Corymbia hamersleyana genotype sheet

description: Genalex formatted genotype table for Corymbia hamersleyana
DOI: 10.6084/m9.figshare.11846904.v1
title: Corymbia hamersleyana genotype sheet

description: Genalex formatted genotype table for Corymbia hamersleyana
DOI: 10.6084/m9.figshare.11846826
title: Additional file 7 of Assembly of hundreds of novel bacterial genomes from the chicken caecum

description: Additional file 7: Dataset S6. CAZymes which were identified as being significantly more abundant by DESeq2 between diets and lines.
DOI: 10.6084/m9.figshare.11846823
title: Additional file 6 of Assembly of hundreds of novel bacterial genomes from the chicken caecum

description: Additional file 6: Dataset S5. MAGs which were identified as being significantly more abundant by DESeq2 between diets and lines.
DOI: 10.6084/m9.figshare.11846826.v1
title: Additional file 7 of Assembly of hundreds of novel bacterial genomes from the chicken caecum

description: Additional file 7: Dataset S6. CAZymes which were identified as being significantly more abundant by DESeq2 between diets and lines.
DOI: 10.6084/m9.figshare.11846823.v1
title: Additional file 6 of Assembly of hundreds of novel bacterial genomes from the chicken caecum

description: Additional file 6: Dataset S5. MAGs which were identified as being significantly more abundant by DESeq2 between diets and lines.
DOI: 10.6084/m9.figshare.11846811
title: Additional file 4 of Assembly of hundreds of novel bacterial genomes from the chicken caecum

description: Additional file 4: Dataset S3. Taxonomy assigned by MAGpy to MAGs.
DOI: 10.6084/m9.figshare.11846814
title: Additional file 5 of Assembly of hundreds of novel bacterial genomes from the chicken caecum

description: Additional file 5: Dataset S4. Clustering of samples at 60% AAI to form genus clusters. Novel genera were defined as clusters of MAGs at 60% AAI which were not assigned a genus by GTDB-Tk.
DOI: 10.6084/m9.figshare.11846811.v1
title: Additional file 4 of Assembly of hundreds of novel bacterial genomes from the chicken caecum

description: Additional file 4: Dataset S3. Taxonomy assigned by MAGpy to MAGs.
DOI: 10.6084/m9.figshare.11846814.v1
title: Additional file 5 of Assembly of hundreds of novel bacterial genomes from the chicken caecum

description: Additional file 5: Dataset S4. Clustering of samples at 60% AAI to form genus clusters. Novel genera were defined as clusters of MAGs at 60% AAI which were not assigned a genus by GTDB-Tk.
DOI: 10.6084/m9.figshare.11846799
title: Additional file 2 of Assembly of hundreds of novel bacterial genomes from the chicken caecum

description: Additional file 2: Dataset 1. Average coverage of MAGs in all samples. Coverage was calculated by mapping MAG scaffolds to the adaptor trimmed Illumina reads for each sample. The average coverage of the scaffolds from a MAG within a sample were taken as the average abundance of that MAG in the sample.
DOI: 10.6084/m9.figshare.11846805
title: Additional file 3 of Assembly of hundreds of novel bacterial genomes from the chicken caecum

description: Additional file 3: Dataset S2. Description of each chicken MAG (metagenome-assembled genome), including novelty of species or strain, NCBI_name, GTDB-Tk taxonomy, CheckM completeness and contamination, assembly size (mb), N50, number of contigs, the longest contig length (bp) and the GC content.
DOI: 10.6084/m9.figshare.11846799.v1
title: Additional file 2 of Assembly of hundreds of novel bacterial genomes from the chicken caecum

description: Additional file 2: Dataset 1. Average coverage of MAGs in all samples. Coverage was calculated by mapping MAG scaffolds to the adaptor trimmed Illumina reads for each sample. The average coverage of the scaffolds from a MAG within a sample were taken as the average abundance of that MAG in the sample.
DOI: 10.6084/m9.figshare.11846805.v1
title: Additional file 3 of Assembly of hundreds of novel bacterial genomes from the chicken caecum

description: Additional file 3: Dataset S2. Description of each chicken MAG (metagenome-assembled genome), including novelty of species or strain, NCBI_name, GTDB-Tk taxonomy, CheckM completeness and contamination, assembly size (mb), N50, number of contigs, the longest contig length (bp) and the GC content.
DOI: 10.6084/m9.figshare.11846790
title: Additional file 1 of Beyond large-effect loci: large-scale GWAS reveals a mixed large-effect and polygenic architecture for age at maturity of Atlantic salmon

description: Additional file 1: Table S1. Mean discordance between imputed and actual genotypes per chromosome. Table S2. List of the 120 candidate genes tagged by the 116 significant SNPs identified with conditional and joint analysis. The P-value indicates significance of the association test performed in BOLT-LMM using a non-infinitesimal model. P-value (COJO) indicates the significance of the SNP after conditional and joint analysis. Beta and its corresponding standard error (Beta_SE) were estimated using BOLT-LMM and indicate the effect size of the minor allele. The odds ratio (OR) and its corresponding transformed standard error (SE_T) were calculated using LMOR. Table S3. List of all 512,397 SNPs in the final dataset. Output statistics from BOLT-LMM (p-value, Beta & Beta_SE) and LMOR (OR, log(OR) & SE_T) are listed. The p-value indicates significance of the association test performed in BOLT-LMM using a non-infinitesimal model. Beta and its corresponding standard error (Beta_SE) were estimated using BOLT-LMM and indicate the effect size of the minor allele. The odds ratio (OR) and its corresponding transformed standard error (SE_T) were calculated using LMOR. Table S4. Estimated heritabilities from GCTA using the 50K array dataset. Estimates are given on the observed quantitative scale and when transformed on the liability scale assuming population prevalences of 1%, 2.5% and 5%.
DOI: 10.6084/m9.figshare.11846790.v1
title: Additional file 1 of Beyond large-effect loci: large-scale GWAS reveals a mixed large-effect and polygenic architecture for age at maturity of Atlantic salmon

description: Additional file 1: Table S1. Mean discordance between imputed and actual genotypes per chromosome. Table S2. List of the 120 candidate genes tagged by the 116 significant SNPs identified with conditional and joint analysis. The P-value indicates significance of the association test performed in BOLT-LMM using a non-infinitesimal model. P-value (COJO) indicates the significance of the SNP after conditional and joint analysis. Beta and its corresponding standard error (Beta_SE) were estimated using BOLT-LMM and indicate the effect size of the minor allele. The odds ratio (OR) and its corresponding transformed standard error (SE_T) were calculated using LMOR. Table S3. List of all 512,397 SNPs in the final dataset. Output statistics from BOLT-LMM (p-value, Beta & Beta_SE) and LMOR (OR, log(OR) & SE_T) are listed. The p-value indicates significance of the association test performed in BOLT-LMM using a non-infinitesimal model. Beta and its corresponding standard error (Beta_SE) were estimated using BOLT-LMM and indicate the effect size of the minor allele. The odds ratio (OR) and its corresponding transformed standard error (SE_T) were calculated using LMOR. Table S4. Estimated heritabilities from GCTA using the 50K array dataset. Estimates are given on the observed quantitative scale and when transformed on the liability scale assuming population prevalences of 1%, 2.5% and 5%.
DOI: 10.6084/m9.figshare.11846787
title: Additional file 1 of Health and the built environment in United States cities: measuring associations using Google Street View-derived indicators of the built environment

description: Additional file 1. Built environment predictors of health-related behaviors and outcomes, with full regression results for demographic covariates.
DOI: 10.6084/m9.figshare.11846787.v1
title: Additional file 1 of Health and the built environment in United States cities: measuring associations using Google Street View-derived indicators of the built environment

description: Additional file 1. Built environment predictors of health-related behaviors and outcomes, with full regression results for demographic covariates.
DOI: 10.6084/m9.figshare.11846718
title: Additional file 1 of Proteomic analysis of synaptic protein turnover in the anterior cingulate cortex after nerve injury

description: Additional file 1: Table S1. The LPF profiles of synaptic proteins smaller than 90 kDa in the ACC and hippocampus of the sham and nerve-injured mice. Red indicates p
DOI: 10.6084/m9.figshare.11846718.v1
title: Additional file 1 of Proteomic analysis of synaptic protein turnover in the anterior cingulate cortex after nerve injury

description: Additional file 1: Table S1. The LPF profiles of synaptic proteins smaller than 90 kDa in the ACC and hippocampus of the sham and nerve-injured mice. Red indicates p
DOI: 10.6084/m9.figshare.11846688
title: Additional file 3 of Haemosporidioses in wild Eurasian blackbirds (Turdus merula) and song thrushes (T. philomelos): an in situ hybridization study with emphasis on exo-erythrocytic parasite burden

description: Additional file 3. Comparison of exo-erythrocytic parasite burdens of Plasmodium-infected Eurasian blackbirds (Turdus merula) and song thrushes (Turdus philomelos) collected during different months from May to March of the years 2002–2018.
DOI: 10.6084/m9.figshare.11846688.v1
title: Additional file 3 of Haemosporidioses in wild Eurasian blackbirds (Turdus merula) and song thrushes (T. philomelos): an in situ hybridization study with emphasis on exo-erythrocytic parasite burden

description: Additional file 3. Comparison of exo-erythrocytic parasite burdens of Plasmodium-infected Eurasian blackbirds (Turdus merula) and song thrushes (Turdus philomelos) collected during different months from May to March of the years 2002–2018.
DOI: 10.6084/m9.figshare.11846640
title: Additional file 2 of Genetic diversity and population structure analysis based on the high density SNP markers in Ethiopian durum wheat (Triticum turgidum ssp. durum)

description: Additional file 2 : Table S2. List of polymorphic SNPs, their alleles and chromosomes used for genetic diversity analysis in Ethiopian durum wheat accessions.
DOI: 10.6084/m9.figshare.11846631
title: Additional file 1 of Genetic diversity and population structure analysis based on the high density SNP markers in Ethiopian durum wheat (Triticum turgidum ssp. durum)

description: Additional file 1 : Table S1. Accession names and types, cultivated areas, seed sources and population structure of 192 Ethiopian durum wheat accessions used for the current study.
DOI: 10.6084/m9.figshare.11846640.v1
title: Additional file 2 of Genetic diversity and population structure analysis based on the high density SNP markers in Ethiopian durum wheat (Triticum turgidum ssp. durum)

description: Additional file 2 : Table S2. List of polymorphic SNPs, their alleles and chromosomes used for genetic diversity analysis in Ethiopian durum wheat accessions.
DOI: 10.6084/m9.figshare.11846631.v1
title: Additional file 1 of Genetic diversity and population structure analysis based on the high density SNP markers in Ethiopian durum wheat (Triticum turgidum ssp. durum)

description: Additional file 1 : Table S1. Accession names and types, cultivated areas, seed sources and population structure of 192 Ethiopian durum wheat accessions used for the current study.
DOI: 10.6084/m9.figshare.11846601
title: Additional file 6 of Pan-tissue transcriptome analysis of long noncoding RNAs in the American beaver Castor canadensis

description: Additional file 6: Table S2. Tissue-specific RPKM per contig. Columns are as follows: Contig, the contig’s identifier; type, the classification of the contig as “known” or “novel”; remaining columns are of the format “RPKM_TissueType”, where TissueType is one of the 16 tissues collected and profiled (see Methods Section “Sample Collection”). Values in these columns are the tissue-specific RPKM for the contig, calculated as described in the Methods Section “Tissue Atlas of lncRNAs”. Known lncRNA transcript contigs are listed first, followed by novel, with contigs listed in ascending numerical order within each category
DOI: 10.6084/m9.figshare.11846601.v1
title: Additional file 6 of Pan-tissue transcriptome analysis of long noncoding RNAs in the American beaver Castor canadensis

description: Additional file 6: Table S2. Tissue-specific RPKM per contig. Columns are as follows: Contig, the contig’s identifier; type, the classification of the contig as “known” or “novel”; remaining columns are of the format “RPKM_TissueType”, where TissueType is one of the 16 tissues collected and profiled (see Methods Section “Sample Collection”). Values in these columns are the tissue-specific RPKM for the contig, calculated as described in the Methods Section “Tissue Atlas of lncRNAs”. Known lncRNA transcript contigs are listed first, followed by novel, with contigs listed in ascending numerical order within each category
DOI: 10.24431/rw1k46u
title: Spatial response of northeast Pacific groundfish to anomalous warming in 2015

description: This dataset consists of two types of observations collected during NOAA's Oscar Dyson cruise DY-15-06, 11 June to 16 August 2015 in the Gulf of Alaska. The data types are as follows: (1) vertical CTD profiles of water temperature and salinity. Some CTD casts were conducted with a Sea-Bird 911plus CTD on a rosette. These went from the surface to within a few meters of the sea bottom. Other CTD casts were conducted with a Teledyne RDI Citadel NV CTD attached to a midwater fisheries trawl net that fished in the depth range where walleye pollock (gadus chalcogrammus) were detected from the ship's fish finder, and (2) shipboard underway time series measurements of ship behavior (position, heading, course over ground, speed over ground), atmospheric (long- and short-wave solar irradiance, atmospheric pressure, temperature, humidity, wind speed and direction at 17 m) and oceanic (water depth, temperature, salinity, chlorophyll a and turbidity at 2.5 m) parameters. Underway variables are averaged over 1 minute from samples every 5 seconds. The data files are in the following formats: digital graphs in gif, underway times series in CSV and CTD profiles in NetCDF.
DOI: 10.6084/m9.figshare.11846592
title: Additional file 5 of Pan-tissue transcriptome analysis of long noncoding RNAs in the American beaver Castor canadensis

description: Additional file 5: Table S1. Manual curation of the 40 known lncRNAs. Columns are as follows: Contig, the query contig’s identifier; Category, the classification of the contig (“probable lncRNA” or “possible lncRNA”, as per Methods Sec. “BLASTn-based classification of noncoding transcript contigs”); Matching Sequence (subject), the subject sequence identifier(s) as per BLASTn; Species, the species of the subject from the previous column; Description, the BLASTn descriptor of the subject sequence; E-value, BLASTn provided E-value for the query-subject pair; %ID, BLASTn provided percent identity between the contig and matching query sequence; length of match, BLASTn provided length, in nucleotides, of query-subject alignment. Only those subject-query pairs that were retained after steps 1 and 2 of curation, as described in the Methods Section, “BLASTn-based classification of noncoding transcript contigs”, are included in the table. Contigs are listed in ascending numerical order
DOI: 10.6084/m9.figshare.11846592.v1
title: Additional file 5 of Pan-tissue transcriptome analysis of long noncoding RNAs in the American beaver Castor canadensis

description: Additional file 5: Table S1. Manual curation of the 40 known lncRNAs. Columns are as follows: Contig, the query contig’s identifier; Category, the classification of the contig (“probable lncRNA” or “possible lncRNA”, as per Methods Sec. “BLASTn-based classification of noncoding transcript contigs”); Matching Sequence (subject), the subject sequence identifier(s) as per BLASTn; Species, the species of the subject from the previous column; Description, the BLASTn descriptor of the subject sequence; E-value, BLASTn provided E-value for the query-subject pair; %ID, BLASTn provided percent identity between the contig and matching query sequence; length of match, BLASTn provided length, in nucleotides, of query-subject alignment. Only those subject-query pairs that were retained after steps 1 and 2 of curation, as described in the Methods Section, “BLASTn-based classification of noncoding transcript contigs”, are included in the table. Contigs are listed in ascending numerical order
DOI: 10.6084/m9.figshare.11846586
title: Additional file 4 of Pan-tissue transcriptome analysis of long noncoding RNAs in the American beaver Castor canadensis

description: Additional file 4: Supplementary Data 2. [SuppData2.txt] Text file of 187 known and novel lncRNA transcript contigs, in FASTA format. The 147 novel contigs have no known orthologs (by BLASTn), very low coding potential scores (CPAT q