cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.3501857
title: 3dPrintedCenterpiecesRawFiles.zip

description: These are raw scan files to reproduce figures in the publication http://arxiv.org/abs/1602.07181 (PONE-D-16-09431) supporting the utility of 3D printed centerpieces in analytical ultracentrifugation<br>
DOI: 10.6084/m9.figshare.3501794
title: Data for Morales et al. Neutral and selective drivers of colour evolution in a widespread Australian passerine (unpublished, re-submitted to J. of Biogeography, August 2016)

description: Contents:Colour data: One "csv" file for each plumage patch containing: ID - Identifier for specimen Lon - Longitude Lat - Latitude Source - Museum (which) or field Patch - Plumage patch wl300-wl700 - raw spectral data Band - Specimen band, if present Sex alt and bio: Altitude and bioclimatic variables (www.worldclim.org/bioclim) x,y,z - summarised spectral data VS - Very Short cone S - Short cone M - Medium cone L - Long cone PC1.65 - PCAxyz axis 1 PC2.65 - PCAxyz axis 2 PC3.65 - PCAxyz axis 3 year - year of collection Vegetation_MVG_PAST_4.1 - vegetation density score sPCA_scores_pred - Kriging prediction of sPCA sPCA_scores_var - Kriging prediction (variance) of sPCA sPCA_scores_stdev - Kriging prediction (standard deviation) of sPCA DistCoast - Distance to coast<br>Genetic data: all the genetic data needed to replicate the analysis. Raw sequencing reads can be found in SRA accession: SRP079228<br>Hybrid_capture_probes.fasta - capture probe design in fasta formatRANDOM_SNP_STRUCTURE_MAF0.05_MissingData_10.str - SNPs in STRUCTURE format containing only one SNP per capture probe (not used in this paper, but useful)SampleInfo - ID, Code, Latitude and Longitude for each sample in the SNP datasetSNP_ACGT_MAF0.05_MissingData_10.txt - SNPs in 012 formatSNP_STRUCTURE_MAF0.05_MissingData_10.str - SNPs in STRUCTURE format (can be read in adegent for sPCA)NEUTRAL_SNPs_MAF0.05_MissingData_10.str - SNP file after outlier and Z-linked loci filteringRANDOM_NEUTRAL_SNP_MAF0.05_MissingData_10.str - SNP file after outlier and Z-linked loci filtering containing only one SNP per capture probe (not used in this paper, but useful for analysis that required unlinked loci)
DOI: 10.6084/m9.figshare.3501794.v1
title: Data for Morales et al. Neutral and selective drivers of colour evolution in a widespread Australian passerine

description: Contents:Colour data: One "csv" file for each plumage patch containing: ID - Identifier for specimen Lon - Longitude Lat - Latitude Source - Museum (which) or field Patch - Plumage patch wl300-wl700 - raw spectral data Band - Specimen band, if present Sex alt and bio: Altitude and bioclimatic variables (www.worldclim.org/bioclim) x,y,z - summarised spectral data VS - Very Short cone S - Short cone M - Medium cone L - Long cone PC1.65 - PCAxyz axis 1 PC2.65 - PCAxyz axis 2 PC3.65 - PCAxyz axis 3 year - year of collection Vegetation_MVG_PAST_4.1 - vegetation density score sPCA_scores_pred - Kriging prediction of sPCA sPCA_scores_var - Kriging prediction (variance) of sPCA sPCA_scores_stdev - Kriging prediction (standard deviation) of sPCA DistCoast - Distance to coast<br>Genetic data: all the genetic data needed to replicate the analysis. Raw sequencing reads can be found in SRA accession: SRP079228<br>Hybrid_capture_probes.fasta - capture probe design in fasta formatRANDOM_SNP_STRUCTURE_MAF0.05_MissingData_10.str - SNPs in STRUCTURE format containing only one SNP per capture probe (not used in this paper, but useful)SampleInfo - ID, Code, Latitude and Longitude for each sample in the SNP datasetSNP_ACGT_MAF0.05_MissingData_10.txt - SNPs in 012 formatSNP_STRUCTURE_MAF0.05_MissingData_10.str - SNPs in STRUCTURE format (can be read in adegent for sPCA)
DOI: 10.6084/m9.figshare.3501794.v2
title: Data for Morales et al. Neutral and selective drivers of colour evolution in a widespread Australian passerine

description: Contents:Colour data: One "csv" file for each plumage patch containing: ID - Identifier for specimen Lon - Longitude Lat - Latitude Source - Museum (which) or field Patch - Plumage patch wl300-wl700 - raw spectral data Band - Specimen band, if present Sex alt and bio: Altitude and bioclimatic variables (www.worldclim.org/bioclim) x,y,z - summarised spectral data VS - Very Short cone S - Short cone M - Medium cone L - Long cone PC1.65 - PCAxyz axis 1 PC2.65 - PCAxyz axis 2 PC3.65 - PCAxyz axis 3 year - year of collection Vegetation_MVG_PAST_4.1 - vegetation density score sPCA_scores_pred - Kriging prediction of sPCA sPCA_scores_var - Kriging prediction (variance) of sPCA sPCA_scores_stdev - Kriging prediction (standard deviation) of sPCA DistCoast - Distance to coast<br>Genetic data: all the genetic data needed to replicate the analysis. Raw sequencing reads can be found in SRA accession: SRP079228<br>Hybrid_capture_probes.fasta - capture probe design in fasta formatRANDOM_SNP_STRUCTURE_MAF0.05_MissingData_10.str - SNPs in STRUCTURE format containing only one SNP per capture probe (not used in this paper, but useful)SampleInfo - ID, Code, Latitude and Longitude for each sample in the SNP datasetSNP_ACGT_MAF0.05_MissingData_10.txt - SNPs in 012 formatSNP_STRUCTURE_MAF0.05_MissingData_10.str - SNPs in STRUCTURE format (can be read in adegent for sPCA)NEUTRAL_SNPs_MAF0.05_MissingData_10.str - SNP file after outlier and Z-linked loci filteringRANDOM_NEUTRAL_SNP_MAF0.05_MissingData_10.str - SNP file after outlier and Z-linked loci filtering containing only one SNP per capture probe (not used in this paper, but useful for analysis that required unlinked loci)
DOI: 10.6084/m9.figshare.3501794.v3
title: Data for Morales et al. Neutral and selective drivers of colour evolution in a widespread Australian passerine (unpublished, re-submitted to J. of Biogeography, August 2016)

description: Contents:Colour data: One "csv" file for each plumage patch containing: ID - Identifier for specimen Lon - Longitude Lat - Latitude Source - Museum (which) or field Patch - Plumage patch wl300-wl700 - raw spectral data Band - Specimen band, if present Sex alt and bio: Altitude and bioclimatic variables (www.worldclim.org/bioclim) x,y,z - summarised spectral data VS - Very Short cone S - Short cone M - Medium cone L - Long cone PC1.65 - PCAxyz axis 1 PC2.65 - PCAxyz axis 2 PC3.65 - PCAxyz axis 3 year - year of collection Vegetation_MVG_PAST_4.1 - vegetation density score sPCA_scores_pred - Kriging prediction of sPCA sPCA_scores_var - Kriging prediction (variance) of sPCA sPCA_scores_stdev - Kriging prediction (standard deviation) of sPCA DistCoast - Distance to coast<br>Genetic data: all the genetic data needed to replicate the analysis. Raw sequencing reads can be found in SRA accession: SRP079228<br>Hybrid_capture_probes.fasta - capture probe design in fasta formatRANDOM_SNP_STRUCTURE_MAF0.05_MissingData_10.str - SNPs in STRUCTURE format containing only one SNP per capture probe (not used in this paper, but useful)SampleInfo - ID, Code, Latitude and Longitude for each sample in the SNP datasetSNP_ACGT_MAF0.05_MissingData_10.txt - SNPs in 012 formatSNP_STRUCTURE_MAF0.05_MissingData_10.str - SNPs in STRUCTURE format (can be read in adegent for sPCA)NEUTRAL_SNPs_MAF0.05_MissingData_10.str - SNP file after outlier and Z-linked loci filteringRANDOM_NEUTRAL_SNP_MAF0.05_MissingData_10.str - SNP file after outlier and Z-linked loci filtering containing only one SNP per capture probe (not used in this paper, but useful for analysis that required unlinked loci)
DOI: 10.6084/m9.figshare.3501761
title: North African Berber dataset

description: North African Berbers dataset<br>
DOI: 10.6084/m9.figshare.3501728
title: Introduction to robust estimation of ERP data

description: This data package contains the slides, Matlab m files and a dataset for an ERP workshop I gave in Washington DC, Glasgow, Fribourg, Frankfurt & Berlin. The goal of the workshop is to use hands-on exercises to introduce the basic principles and the Matlab implementation of robust estimation, using resampling methods (bootstrap & permutation) in conjunction with robust estimators. The workshop covers why classic t-tests and ANOVAs on means are not necessarily the best options, and how robust approaches can help. In particular, it demonstrates techniques to compare entire distributions, how to build confidence intervals about any quantity using the bootstrap, and how to effectively control for multiple comparisons. The methods are applied to single-subject and group analyses, and examples are provided to integrate both levels into informative figures.
DOI: 10.6084/m9.figshare.3501689
title: Perylene molecule penetrating in a zeolite channel

description: Supporting movie for the article "One-Dimensional Self-Assembly of Perylene-Diimide Dyes by Unidirectional Transit of Zeolite Channel Openings" published in:<i><strong>Chem. Commun.</strong></i>, 2016<strong>DOI: </strong>10.1039/C6CC05303C<br>The movie features a dye molecule (perylene-diimide, cyan) passing through the narrow channel opening of a porous material (zeolite L, grey). The motions of the molecule and of the porous host are cooperative, and allow the entrance and encapsulation of the dye. The interactions of the carbonyl oxygens of the dye (red) with the zeolite potassium cations (purple) play a key role in the process.<br>Popular summary of this article: https://goo.gl/T5bSL4Blog post on this paper: see the 3rd link below
DOI: 10.6084/m9.figshare.3501689.v3
title: Perylene molecule penetrating in a zeolite channel

description: Supporting movie for the article "One-Dimensional Self-Assembly of Perylene-Diimide Dyes by Unidirectional Transit of Zeolite Channel Openings" published in:<i><strong>Chem. Commun.</strong></i>, 2016<strong>DOI: </strong>10.1039/C6CC05303C<br>The movie features a dye molecule (perylene-diimide, cyan) passing through the narrow channel opening of a porous material (zeolite L, grey). The motions of the molecule and of the porous host are cooperative, and allow the entrance and encapsulation of the dye. The interactions of the carbonyl oxygens of the dye (red) with the zeolite potassium cations (purple) play a key role in the process.<br>Popular summary of this article: https://goo.gl/T5bSL4Blog post on this paper: see the 3rd link below
DOI: 10.6084/m9.figshare.3501674
title: Supplementary Material for: Induction of Genes Expressed in Endothelial Cells of the Corpus Callosum in the Chronic Cerebral Hypoperfusion Rat Model

description: <i>Background:</i> Cerebrovascular white matter lesions (WMLs) are associated with cognitive impairment in patients with subcortical vascular dementia. We performed a comprehensive gene expression analysis to elucidate genes associated with WML development in a chronic cerebral hypoperfusion rat model. <i>Methods:</i> Brains of rats with bilateral carotid ligation (2VO, n = 10) and sham-operated rats (n = 5-10/group) were removed on days 1, 7, or 28 after surgery. Total RNA isolated from the corpus callosum was evaluated by microarray analysis and quantitative reverse transcription-polymerase chain reaction. <i>Results:</i> On days 7 and 28, WMLs exhibited histologic changes. On day 7, 16 genes were differentially expressed between groups. mRNA levels of Ptprb, Kcnj8, Crispld2, Bcl6b, and Gja5 were differentially expressed in 2VO rats on day 7, but then returned to normal, whereas mRNA levels of Vwf and Trappc6a were upregulated after day 7. Immunohistochemistry showed that GJA5 and vWF were detected in endothelial cells, KCNJ8 in endothelial cells and astrocytes, CRISPLD2 in neurons and astrocytes, and TRAPPC6A in neurons. <i>Conclusion:</i> Our findings indicate novel genes that may be associated with WML development in the chronic cerebral hypoperfusion rat model, and suggest an important role of neurovascular dysfunction in the pathophysiology.
DOI: 10.6084/m9.figshare.3501674.v1
title: Supplementary Material for: Induction of Genes Expressed in Endothelial Cells of the Corpus Callosum in the Chronic Cerebral Hypoperfusion Rat Model

description: <i>Background:</i> Cerebrovascular white matter lesions (WMLs) are associated with cognitive impairment in patients with subcortical vascular dementia. We performed a comprehensive gene expression analysis to elucidate genes associated with WML development in a chronic cerebral hypoperfusion rat model. <i>Methods:</i> Brains of rats with bilateral carotid ligation (2VO, n = 10) and sham-operated rats (n = 5-10/group) were removed on days 1, 7, or 28 after surgery. Total RNA isolated from the corpus callosum was evaluated by microarray analysis and quantitative reverse transcription-polymerase chain reaction. <i>Results:</i> On days 7 and 28, WMLs exhibited histologic changes. On day 7, 16 genes were differentially expressed between groups. mRNA levels of Ptprb, Kcnj8, Crispld2, Bcl6b, and Gja5 were differentially expressed in 2VO rats on day 7, but then returned to normal, whereas mRNA levels of Vwf and Trappc6a were upregulated after day 7. Immunohistochemistry showed that GJA5 and vWF were detected in endothelial cells, KCNJ8 in endothelial cells and astrocytes, CRISPLD2 in neurons and astrocytes, and TRAPPC6A in neurons. <i>Conclusion:</i> Our findings indicate novel genes that may be associated with WML development in the chronic cerebral hypoperfusion rat model, and suggest an important role of neurovascular dysfunction in the pathophysiology.
DOI: 10.6084/m9.figshare.3501635
title: PowerPoint Slides for: Structured Exercise in Obese Diabetic Patients with Chronic Kidney Disease: A Randomized Controlled Trial

description: <i>Background:</i> Patients with type 2 diabetes mellitus (DM), obesity, and chronic kidney disease (CKD) are generally physically inactive and may benefit from exercise. Our objective was to determine the effects of structured exercise on physical fitness, kidney function, endothelial function, inflammation, and body composition in such patients. <i>Methods:</i> In this randomized, controlled trial, 36 male patients (age 49-81) were randomly assigned to exercise + diet management (n = 18) or diet alone (n = 18). Participants were eligible if they had type 2 DM, body mass index &gt;30 kg/m2, CKD stages 2-4, and persistent proteinuria (&gt;200 mg/g creatinine for &gt;3 months). The exercise intervention was a 12-week (3 days per week) program of aerobic and resistance training followed by 40 weeks of home exercise. The primary outcome measure was change from baseline in urine protein to creatinine ratio (UPCR) at 12 and 52 weeks. <i>Results:</i> Thirty-two participants completed the study (14 exercise + diet, 18 diet-alone group). The change from baseline in UPCR was slightly greater in the diet-alone group at 12 weeks but not at 52 weeks. Changes in both symptom-limited and constant-workrate treadmill times were significantly higher in the exercise + diet group at 12 weeks but not at 52 weeks. There were no significant differences in urine albumin to creatinine ratio, estimated glomerular filtration rate, endothelial function, inflammation, or body composition between the groups.<i>Conclusions:</i> In obese diabetic subjects with CKD, structured exercise improved exercise capacity but not body composition or renal function. This is a work of the US Government and is not subject to copyright protection in the USA. Foreign copyrights may apply.
DOI: 10.6084/m9.figshare.3501635.v1
title: PowerPoint Slides for: Structured Exercise in Obese Diabetic Patients with Chronic Kidney Disease: A Randomized Controlled Trial

description: <i>Background:</i> Patients with type 2 diabetes mellitus (DM), obesity, and chronic kidney disease (CKD) are generally physically inactive and may benefit from exercise. Our objective was to determine the effects of structured exercise on physical fitness, kidney function, endothelial function, inflammation, and body composition in such patients. <i>Methods:</i> In this randomized, controlled trial, 36 male patients (age 49-81) were randomly assigned to exercise + diet management (n = 18) or diet alone (n = 18). Participants were eligible if they had type 2 DM, body mass index &gt;30 kg/m2, CKD stages 2-4, and persistent proteinuria (&gt;200 mg/g creatinine for &gt;3 months). The exercise intervention was a 12-week (3 days per week) program of aerobic and resistance training followed by 40 weeks of home exercise. The primary outcome measure was change from baseline in urine protein to creatinine ratio (UPCR) at 12 and 52 weeks. <i>Results:</i> Thirty-two participants completed the study (14 exercise + diet, 18 diet-alone group). The change from baseline in UPCR was slightly greater in the diet-alone group at 12 weeks but not at 52 weeks. Changes in both symptom-limited and constant-workrate treadmill times were significantly higher in the exercise + diet group at 12 weeks but not at 52 weeks. There were no significant differences in urine albumin to creatinine ratio, estimated glomerular filtration rate, endothelial function, inflammation, or body composition between the groups.<i>Conclusions:</i> In obese diabetic subjects with CKD, structured exercise improved exercise capacity but not body composition or renal function. This is a work of the US Government and is not subject to copyright protection in the USA. Foreign copyrights may apply.
DOI: 10.6084/m9.figshare.3501632
title: PowerPoint Slides for: Genetic Features of Chinese Patients with Gitelman Syndrome: Sixteen Novel SLC12A3 Mutations Identified in a New Cohort

description: <i>Background:</i> Gitelman syndrome (GS) is an autosomal recessive renal tubulopathy caused by inactivating mutations in the <i>SLC12A3</i> gene. Although hundreds of different mutations across the <i>SLC12A3</i> gene have been reported worldwide, data from mainland China are limited. We investigated the clinical manifestations and genetic features of Chinese patients with GS. <i>Methods:</i> Fifty-four unrelated Chinese patients with clinically diagnosed GS were included. Clinical manifestations and biochemical parameters were collected and analyzed. All exons and flanking regions of the <i>SLC12A3</i> and <i>CLCNKB</i> genes were screened by direct sequencing. <i>Results:</i>Weakness was the most commonly reported symptom in this cohort of patients with GS. In gender-based analyses, higher systolic blood pressure and urine protein excretion were observed in male patients. For genetic screening, 2 pathogenic<i>SLC12A3</i> mutations were identified in 38 patients (70.4%), 1 mutation in 11 patients (20.4%) and no mutation in 5 patients (9.3%). In total, 42 distinct pathogenic mutations throughout <i>SLC12A3</i> were identified; 16 were novel, including 9 missense, 1 deletion, 1 insertion, 3 splice site and 2 nonsense mutations. Eleven mutations were recurrently found in different patients. Among them, T60M and D486N were identified in 11 individuals. No <i>CLCNKB</i> mutations were found. <i>Conclusion:</i> Sixteen novel <i>SLC12A3</i> pathogenic mutations were identified in a cohort of Chinese patients with GS. T60M and D486N were most frequent and appear to be important candidate alleles in Chinese patients with GS.
DOI: 10.6084/m9.figshare.3501632.v1
title: PowerPoint Slides for: Genetic Features of Chinese Patients with Gitelman Syndrome: Sixteen Novel SLC12A3 Mutations Identified in a New Cohort

description: <i>Background:</i> Gitelman syndrome (GS) is an autosomal recessive renal tubulopathy caused by inactivating mutations in the <i>SLC12A3</i> gene. Although hundreds of different mutations across the <i>SLC12A3</i> gene have been reported worldwide, data from mainland China are limited. We investigated the clinical manifestations and genetic features of Chinese patients with GS. <i>Methods:</i> Fifty-four unrelated Chinese patients with clinically diagnosed GS were included. Clinical manifestations and biochemical parameters were collected and analyzed. All exons and flanking regions of the <i>SLC12A3</i> and <i>CLCNKB</i> genes were screened by direct sequencing. <i>Results:</i>Weakness was the most commonly reported symptom in this cohort of patients with GS. In gender-based analyses, higher systolic blood pressure and urine protein excretion were observed in male patients. For genetic screening, 2 pathogenic<i>SLC12A3</i> mutations were identified in 38 patients (70.4%), 1 mutation in 11 patients (20.4%) and no mutation in 5 patients (9.3%). In total, 42 distinct pathogenic mutations throughout <i>SLC12A3</i> were identified; 16 were novel, including 9 missense, 1 deletion, 1 insertion, 3 splice site and 2 nonsense mutations. Eleven mutations were recurrently found in different patients. Among them, T60M and D486N were identified in 11 individuals. No <i>CLCNKB</i> mutations were found. <i>Conclusion:</i> Sixteen novel <i>SLC12A3</i> pathogenic mutations were identified in a cohort of Chinese patients with GS. T60M and D486N were most frequent and appear to be important candidate alleles in Chinese patients with GS.
DOI: 10.6084/m9.figshare.3501626
title: PowerPoint Slides for: Cystatin C-Creatinine Based Glomerular Filtration Rate Equation in Obese Chronic Kidney Disease Patients: Impact of Deindexation and Gender

description: <i>Background:</i> Cystatin C is considered an alternative to creatinine to estimate glomerular filtration rate (GFR). However, studies have reported that increased adiposity is associated with a higher level of circulating cystatin C questioning the performance of estimation of GFR using cystatin C in obese subjects. <i>Methods:</i> We prospectively included 166 obese stages 1-5 chronic kidney disease (CKD) patients between 2013 and 2015. GFR was measured with a reference method without (measured GFR [mGFR]) and with adjustment to body surface area (mGFRr) and estimated (eGFR) or de-indexed eGFR using the Chronic Kidney Disease and Epidemiology (CKD-EPI) equation using creatinine (CKD-EPIcreat), cystatin (CKD-EPIcyst) and the combination of cystatin and creatinine (CKD-EPIcyst-creat). <i>Results:</i> The biases between mGFR and de-indexed CKD-EPIcyst-creat were significantly lower than de-indexed CKD-EPIcreat (p = 0.001). Accuracies were significantly better with de-indexed CKD-EPIcyst-creat compared to CKD-EPIcreat and CKD-EPIcyst, respectively (p = 0.04 and 0.03). Bland and Altman plot showed a great dispersion of all formulae when patients had a GFR &gt;60 ml/min. Interestingly, there is a gender difference; biases, precisions and accuracies of de-indexed CKD-EPIcyst-creat were significantly lower in obese women. These results may be related to a difference in the change of body composition during obesity in men versus women and in fact only waist circumference (WC) was positively and significantly correlated with cystatin C (p &lt; 0.0001) whereas body mass index (BMI; p = 0.3) was not; bias for CKD-EPIcyst-creat was related with WC. <i>Conclusion:</i> Cystatin C-creatinine-based GFR equations outperform creatinine-based formula in obese CKD patients especially those with BMI ≥35 and in obese women.