cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.6970277
title: Supplemental Material for Garcia, Zoller and Anisimova, 2018

description: <b>Figure S1</b> Average relative frameshifted sequence length, l, across within relative gene length. Averages of the length of the frameshifted sequence after a slippery site are computed for 20 bins of equal width. Bins span the entire gene.<br><br><b>Figure S2</b> Frequency distribution of relative position of slippery sites l/L for all genes with -1 PRF signals in the PRFdb dataset. The mean of the distribution, as well as its 95% confidence intervals, are smaller than 0.5 -the expectation under randomly distributed slippery site locations.<br><br><b>Figure S3 </b>Testing the cost of -1 PRF mechanism maintenance. A) Number of slippery sites per gene and per nucleotide across protein expression levels (in molecules per cell) for genes from the integrated PaxDB data set. The red dotted line is the average number of slippery sites per gene. The blue line is a regression line through the data set. The text in the panels gives i) the Spearman correlation coefficient r and the p-value for the null-hypothesis that the correlation is zero and ii) the slope of the line and the p-value of the t-test for a non-zero slope value. B) The frequency distribution of the within-gene positions of the slippery sites, relative to the length of the gene, l/L. To ensure comparability, only genes from the von der Haar data set are considered. The mean of the distribution, as well as its 95% confidence intervals, are smaller than 0.5 -the expectation in the absence of selective pressure. C) Slippery site positions relative to gene length across protein expression levels in the von der Haar data set. The red line is the average slippery site position (computed across 20 bins of equal width in logarithmic scale) and the widgets are the uncertainty ( 1.96 standard error of the mean) around the average estimate. Averages with large uncertainties are in violet. Analogously to A), a regression line with the corresponding correlation coefficient r (with p-value) and slope (with p-value) are added.<br><br><b>Figure S4 </b>Codon Adaptation Index (CAI) frequency distributions of genes without -1 PRF signals (CAI of ORF) and with such signals (CAI of -1 PRF mRNA). The p-value given in the figure is for the two-sample Kolmogorov-Smirnov test for the two distributions.<br><br><b>Figure S5</b> Spearman rank correlation values between corrections of CAI to -1 PRF presence ( ˆIc, Ia) to protein expression levels P von der Haar (2008) for different -1 PRF efficiencies.<br><br>
DOI: 10.6084/m9.figshare.6970313.v1
title: Digital elevation model for the Tona Watershed

description: Digital elevation model of the Tona watershed to be used as an input for ArcSWAT.Raster resolution: 12.5x12.5 metersSpatial Reference: MAGNA COLOMBIA BOGOTA<br>
DOI: 10.6084/m9.figshare.6970211
title: GitHub Repo: ProspectiveAgeData

description: GitHub repository for calculation and dataset of prospective age and adjusted ageing measures following Sanderson & Scherbov 2008.<br>Automatically synced with new releases. <br><br>
DOI: 10.6084/m9.figshare.6970277.v1
title: Supplemental Material for Garcia, Zoller and Anisimova, 2018

description: <b>Figure S1</b> Average relative frameshifted sequence length, l, across within relative gene length. Averages of the length of the frameshifted sequence after a slippery site are computed for 20 bins of equal width. Bins span the entire gene.<br><br><b>Figure S2</b> Frequency distribution of relative position of slippery sites l/L for all genes with -1 PRF signals in the PRFdb dataset. The mean of the distribution, as well as its 95% confidence intervals, are smaller than 0.5 -the expectation under randomly distributed slippery site locations.<br><br><b>Figure S3 </b>Testing the cost of -1 PRF mechanism maintenance. A) Number of slippery sites per gene and per nucleotide across protein expression levels (in molecules per cell) for genes from the integrated PaxDB data set. The red dotted line is the average number of slippery sites per gene. The blue line is a regression line through the data set. The text in the panels gives i) the Spearman correlation coefficient r and the p-value for the null-hypothesis that the correlation is zero and ii) the slope of the line and the p-value of the t-test for a non-zero slope value. B) The frequency distribution of the within-gene positions of the slippery sites, relative to the length of the gene, l/L. To ensure comparability, only genes from the von der Haar data set are considered. The mean of the distribution, as well as its 95% confidence intervals, are smaller than 0.5 -the expectation in the absence of selective pressure. C) Slippery site positions relative to gene length across protein expression levels in the von der Haar data set. The red line is the average slippery site position (computed across 20 bins of equal width in logarithmic scale) and the widgets are the uncertainty ( 1.96 standard error of the mean) around the average estimate. Averages with large uncertainties are in violet. Analogously to A), a regression line with the corresponding correlation coefficient r (with p-value) and slope (with p-value) are added.<br><br><b>Figure S4 </b>Codon Adaptation Index (CAI) frequency distributions of genes without -1 PRF signals (CAI of ORF) and with such signals (CAI of -1 PRF mRNA). The p-value given in the figure is for the two-sample Kolmogorov-Smirnov test for the two distributions.<br><br><b>Figure S5</b> Spearman rank correlation values between corrections of CAI to -1 PRF presence ( ˆIc, Ia) to protein expression levels P von der Haar (2008) for different -1 PRF efficiencies.<br><br>
DOI: 10.6084/m9.figshare.6970121
title: Supplementary Material for: Association between Atopic Dermatitis and the Metabolic Syndrome: A Systematic Review

description: Atopic dermatitis (AD) may be associated with the metabolic syndrome and by that carry an increased risk of cardio­vascular disease. Our objective was to provide an update on current knowledge of the association between AD and metabolic syndrome, including each component of the metabolic syndrome. A systematic literature review was performed to identify studies investigating the association between metabolic syndrome and AD from PubMed, Embase, and the Cochrane Library in accordance with the Preferred Reporting Items for Systematic reviews and Meta-Analyses (PRISMA) guidelines. A total of 14 studies, investigating the association between AD and the metabolic syndrome or AD and components of metabolic syndrome fulfilled the inclusion criteria and were included. It seems unlikely that the association between AD and metabolic syndrome is causal. However, women with AD tended to have components of metabolic syndrome more often than women without AD. There was a positive association between AD and central obesity measured as waist circumference, and this association was stronger for women than men. Despite conflicting results regarding hypertension, the association between hypertension and AD also appeared stronger for women. On the other hand, the association between AD and hyperglycemia appears unlikely, and the association between AD and cholesterol levels was inconsistent. In conclusion, it remains unclear whether AD is a risk factor for metabolic syndrome and its components. However, data indicate that central obesity is associated with AD and that the association is stronger for women than men.
DOI: 10.6084/m9.figshare.6970211.v1
title: ProspectiveAgeData

description: Calculation and dataset of prospective age and adjusted ageing measures following Sanderson & Scherbov 2008
DOI: 10.6084/m9.figshare.6970121.v1
title: Supplementary Material for: Association between Atopic Dermatitis and the Metabolic Syndrome: A Systematic Review

description: Atopic dermatitis (AD) may be associated with the metabolic syndrome and by that carry an increased risk of cardio­vascular disease. Our objective was to provide an update on current knowledge of the association between AD and metabolic syndrome, including each component of the metabolic syndrome. A systematic literature review was performed to identify studies investigating the association between metabolic syndrome and AD from PubMed, Embase, and the Cochrane Library in accordance with the Preferred Reporting Items for Systematic reviews and Meta-Analyses (PRISMA) guidelines. A total of 14 studies, investigating the association between AD and the metabolic syndrome or AD and components of metabolic syndrome fulfilled the inclusion criteria and were included. It seems unlikely that the association between AD and metabolic syndrome is causal. However, women with AD tended to have components of metabolic syndrome more often than women without AD. There was a positive association between AD and central obesity measured as waist circumference, and this association was stronger for women than men. Despite conflicting results regarding hypertension, the association between hypertension and AD also appeared stronger for women. On the other hand, the association between AD and hyperglycemia appears unlikely, and the association between AD and cholesterol levels was inconsistent. In conclusion, it remains unclear whether AD is a risk factor for metabolic syndrome and its components. However, data indicate that central obesity is associated with AD and that the association is stronger for women than men.
DOI: 10.6084/m9.figshare.6970085
title: Supplementary Material for: Bronchial Thermoplasty-Induced Acute Airway Effects Assessed with Optical Coherence Tomography in Severe Asthma

description: <b><i>Background:</i></b> Bronchial thermoplasty (BT) is an endoscopic treatment for severe asthma targeting airway smooth muscle (ASM) with radiofrequent energy. Although implemented worldwide, the effect of BT treatment on the airways is unclear. Optical coherence tomography (OCT) is a novel imaging technique, based on near-infrared light, that generates high-resolution cross-sectional airway wall images. <b><i>Objective:</i></b> To assess the safety and feasibility of OCT in severe asthma patients and determine acute airway effects of BT by OCT and compare these to the untreated right middle lobe (RML). <b><i>Methods:</i></b> Severe asthma patients were treated with BT (TASMA trial). During the third BT procedure, OCT imaging was performed immediately following BT in the airways of the upper lobes, the right lower lobe treated 6 weeks prior, and the untreated RML. <b><i>Results:</i></b> 57 airways were imaged in 15 patients. No adverse events occurred. Three distinct OCT patterns were discriminated: low-intensity scattering pattern of (1) bronchial and (2) peribronchial edema and (3) high-intensity scattering pattern of epithelial sloughing. (Peri)bronchial edema was seen in all BT-treated airways, and less pronounced in only 1/3 of the RML airways. These effects extended beyond the ASM layer and more distal than the directly BT-treated areas and were reduced, but not resolved, after 6 weeks. Epithelial sloughing occurred in 11/14 of the BT-treated airways and was absent in untreated RML airways. <b><i>Conclusions:</i></b> Acute BT effects can be safely assessed with OCT and 3 distinct patterns were identified. The acute effects extended beyond the targeted ASM layer and distal of directly BT-treated airway areas, suggesting that BT might also target smaller distal airways.
DOI: 10.6084/m9.figshare.6970085.v1
title: Supplementary Material for: Bronchial Thermoplasty-Induced Acute Airway Effects Assessed with Optical Coherence Tomography in Severe Asthma

description: <b><i>Background:</i></b> Bronchial thermoplasty (BT) is an endoscopic treatment for severe asthma targeting airway smooth muscle (ASM) with radiofrequent energy. Although implemented worldwide, the effect of BT treatment on the airways is unclear. Optical coherence tomography (OCT) is a novel imaging technique, based on near-infrared light, that generates high-resolution cross-sectional airway wall images. <b><i>Objective:</i></b> To assess the safety and feasibility of OCT in severe asthma patients and determine acute airway effects of BT by OCT and compare these to the untreated right middle lobe (RML). <b><i>Methods:</i></b> Severe asthma patients were treated with BT (TASMA trial). During the third BT procedure, OCT imaging was performed immediately following BT in the airways of the upper lobes, the right lower lobe treated 6 weeks prior, and the untreated RML. <b><i>Results:</i></b> 57 airways were imaged in 15 patients. No adverse events occurred. Three distinct OCT patterns were discriminated: low-intensity scattering pattern of (1) bronchial and (2) peribronchial edema and (3) high-intensity scattering pattern of epithelial sloughing. (Peri)bronchial edema was seen in all BT-treated airways, and less pronounced in only 1/3 of the RML airways. These effects extended beyond the ASM layer and more distal than the directly BT-treated areas and were reduced, but not resolved, after 6 weeks. Epithelial sloughing occurred in 11/14 of the BT-treated airways and was absent in untreated RML airways. <b><i>Conclusions:</i></b> Acute BT effects can be safely assessed with OCT and 3 distinct patterns were identified. The acute effects extended beyond the targeted ASM layer and distal of directly BT-treated airway areas, suggesting that BT might also target smaller distal airways.
DOI: 10.6084/m9.figshare.6970211.v2
title: GitHub Repo: ProspectiveAgeData

description: GitHub repository for calculation and dataset of prospective age and adjusted ageing measures following Sanderson & Scherbov 2008.<br>Automatically synced with new releases. <br><br>
DOI: 10.6084/m9.figshare.6970040
title: Supplementary Material for: Characterization and Outcomes of Disease Progression in 52 Patients Treated with <b><i>BRAF</i></b>-V600 + MEK Inhibitors for Advanced Melanoma

description: <b><i>Background:</i></b> Combined treatment with <i>BRAF</i>-V600 and MEK inhibitors has significantly improved progression-free and overall survival of patients with <i>BRAF</i>-mutated melanoma. Pattern of disease progression and outcomes in patients have not been fully characterized. <b><i>Methods:</i></b> We conducted a single-center, retrospective, descriptive analysis of a cohort of 52 patients treated with <i>BRAF</i>-V600 + MEK inhibitors for advanced melanoma over a 12-month period. The aim of this study was to characterize disease progression, defined as metastatic pattern, disease kinetics, and response to subsequent therapies, in melanoma patients treated with <i>BRAF</i>-V600 + MEK inhibitors. <b><i>Results:</i></b> Disease progression was observed in 31/52 (59.6%) patients treated with <i>BRAF</i>-V600 + MEK inhibitors. Relapse of melanoma involved the CNS for 22/31 (70.9%) patients with disease progression, including 18/31 (58%) patients who had exclusive intracranial metastases. Sixteen patients died from disease progression. Among the 31 patients who had disease progression, the median time until a relapse was 8 months, and the median survival time after disease progression was 2 months. <b><i>Conclusion:</i></b> Our study shows that, for patients treated with <i>BRAF</i>-V600 + MEK inhibitors who lose response, disease progression was aggressive and had poor outcomes. Most patients had CNS metastases and low rates of therapeutic response to any subsequent therapy.
DOI: 10.6084/m9.figshare.6970040.v1
title: Supplementary Material for: Characterization and Outcomes of Disease Progression in 52 Patients Treated with <b><i>BRAF</i></b>-V600 + MEK Inhibitors for Advanced Melanoma

description: <b><i>Background:</i></b> Combined treatment with <i>BRAF</i>-V600 and MEK inhibitors has significantly improved progression-free and overall survival of patients with <i>BRAF</i>-mutated melanoma. Pattern of disease progression and outcomes in patients have not been fully characterized. <b><i>Methods:</i></b> We conducted a single-center, retrospective, descriptive analysis of a cohort of 52 patients treated with <i>BRAF</i>-V600 + MEK inhibitors for advanced melanoma over a 12-month period. The aim of this study was to characterize disease progression, defined as metastatic pattern, disease kinetics, and response to subsequent therapies, in melanoma patients treated with <i>BRAF</i>-V600 + MEK inhibitors. <b><i>Results:</i></b> Disease progression was observed in 31/52 (59.6%) patients treated with <i>BRAF</i>-V600 + MEK inhibitors. Relapse of melanoma involved the CNS for 22/31 (70.9%) patients with disease progression, including 18/31 (58%) patients who had exclusive intracranial metastases. Sixteen patients died from disease progression. Among the 31 patients who had disease progression, the median time until a relapse was 8 months, and the median survival time after disease progression was 2 months. <b><i>Conclusion:</i></b> Our study shows that, for patients treated with <i>BRAF</i>-V600 + MEK inhibitors who lose response, disease progression was aggressive and had poor outcomes. Most patients had CNS metastases and low rates of therapeutic response to any subsequent therapy.
DOI: 10.6084/m9.figshare.6969986
title: Miospores from the Brigantian stratotype section at Janny Wood, Cumbria

description: An Excel spreadsheet of biostratigraphical data
DOI: 10.6084/m9.figshare.6969986.v1
title: Miospores from the Brigantian stratotype section at Janny Wood, Cumbria

description: An Excel spreadsheet of biostratigraphical data
DOI: 10.6084/m9.figshare.6969980.v1
title: Annotation of high_quality_transcripts and unigenes of Anthurium andraeanum

description: Annotation of high_quality_transcripts and unigenes of Anthurium andraeanum
DOI: 10.6084/m9.figshare.6969929
title: Supplementary Material for: Evaluation of First-Trimester Physiological Midgut Herniation Using Three-Dimensional Ultrasound

description: <b><i>Introduction:</i></b> The aim of this study was to investigate the development of midgut herniation in vivo using three-dimensional (3D) ultrasonographic volume and distance measurements and to create reference data for physiological midgut herniation in ongoing pregnancies in a tertiary hospital population. <b><i>Materials and Methods:</i></b> The transvaginal 3D ultrasound volumes of 112 women, seen weekly during the first trimester of pregnancy, were obtained and subsequently analysed in a virtual reality environment. The width of the umbilical cord insertion, the maximum diameter of the umbilical cord, and the volume of midgut herniation were measured from 6 until 13 weeks gestational age (GA). <b><i>Results:</i></b> All parameters had a positive relation with GA, crown-rump length, and abdominal circumference. In approximately 1 of 10 volumes no midgut herniation could be observed at 9 and 10 weeks GA. In 5.0% of the fetuses the presence of midgut herniation could still be visualised at 12 weeks GA. <b><i>Conclusion:</i></b> Reference charts for several dimensions of physiological midgut herniation were created. In the future, our data might be used as a reference in the first trimester for comparison in case of a suspected pathological omphalocele.
DOI: 10.6084/m9.figshare.6969905
title: Mycobacterial Homology Database with 50% Identity Cutoff

description: This is a table of results from comparison of the annotated proteins from nine different mycobacterial species. The goal of its creation was to suggest which proteins are likely to have identical functions between species. This table reports only those protein comparisons with greater than 50% amino acid identity. Each row is a different gene used to search for close matches, each column is the genome used for searching. In parentheses next to the name of each match is the percent identity between the sequences (query vs each match).
DOI: 10.6084/m9.figshare.6969929.v1
title: Supplementary Material for: Evaluation of First-Trimester Physiological Midgut Herniation Using Three-Dimensional Ultrasound

description: <b><i>Introduction:</i></b> The aim of this study was to investigate the development of midgut herniation in vivo using three-dimensional (3D) ultrasonographic volume and distance measurements and to create reference data for physiological midgut herniation in ongoing pregnancies in a tertiary hospital population. <b><i>Materials and Methods:</i></b> The transvaginal 3D ultrasound volumes of 112 women, seen weekly during the first trimester of pregnancy, were obtained and subsequently analysed in a virtual reality environment. The width of the umbilical cord insertion, the maximum diameter of the umbilical cord, and the volume of midgut herniation were measured from 6 until 13 weeks gestational age (GA). <b><i>Results:</i></b> All parameters had a positive relation with GA, crown-rump length, and abdominal circumference. In approximately 1 of 10 volumes no midgut herniation could be observed at 9 and 10 weeks GA. In 5.0% of the fetuses the presence of midgut herniation could still be visualised at 12 weeks GA. <b><i>Conclusion:</i></b> Reference charts for several dimensions of physiological midgut herniation were created. In the future, our data might be used as a reference in the first trimester for comparison in case of a suspected pathological omphalocele.
DOI: 10.6084/m9.figshare.6969902
title: Mycobacterial Homology Database with 90% Identity Cutoff

description: This is a table of results from comparison of the annotated proteins from nine different mycobacterial species. The goal of its creation was to suggest which proteins are likely to have identical functions between species. This table reports only those protein comparisons with greater than 90% amino acid identity. Each row is a different gene used to search for close matches, each column is the genome used for searching. In parentheses next to the name of each match is the percent identity between the sequences (query vs each match).
DOI: 10.6084/m9.figshare.6969902.v1
title: Mycobacterial Homology Database with 90% Identity Cutoff

description: This is a table of results from comparison of the annotated proteins from nine different mycobacterial species. The goal of its creation was to suggest which proteins are likely to have identical functions between species. This table reports only those protein comparisons with greater than 90% amino acid identity. Each row is a different gene used to search for close matches, each column is the genome used for searching. In parentheses next to the name of each match is the percent identity between the sequences (query vs each match).
DOI: 10.6084/m9.figshare.6969899
title: Mycobacterial Homology Database with 75% Identity Cutoff

description: This is a table of results from comparison of the annotated proteins from nine different mycobacterial species. The goal of its creation was to suggest which proteins are likely to have identical functions between species. This table reports only those protein comparisons with greater than 75% amino acid identity. Each row is a different gene used to search for close matches, each column is the genome used for searching. In parentheses next to the name of each match is the percent identity between the sequences (query vs each match).
DOI: 10.6084/m9.figshare.6969896
title: Gene Ontology Annotations for MAC109 Genome

description: This reports the Gene Onotology (GO) annotations output by PANNZER2 for the MAC109 annotated proteins.
DOI: 10.6084/m9.figshare.6969899.v1
title: Mycobacterial Homology Database with 75% Identity Cutoff

description: This is a table of results from comparison of the annotated proteins from nine different mycobacterial species. The goal of its creation was to suggest which proteins are likely to have identical functions between species. This table reports only those protein comparisons with greater than 75% amino acid identity. Each row is a different gene used to search for close matches, each column is the genome used for searching. In parentheses next to the name of each match is the percent identity between the sequences (query vs each match).
DOI: 10.6084/m9.figshare.6969896.v1
title: Gene Ontology Annotations for MAC109 Genome

description: This reports the Gene Onotology (GO) annotations output by PANNZER2 for the MAC109 annotated proteins.