cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.3501626.v1
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.
DOI: 10.6084/m9.figshare.3498641
title: Pachycephalosauridae

description: Phylogenetic data matrix for analysis of Pachycephalosauridae. Based on data matrix of Longrich et al. (2010), with the addition of <i>Acrotholus</i>, <i>Amtocephale</i>, the Sandy Site Pachycephalosaurine and RBCM.EH.2006.019.
DOI: 10.6084/m9.figshare.3498641.v1
title: Pachycephalosauridae

description: Phylogenetic data matrix for analysis of Pachycephalosauridae. Based on data matrix of Longrich et al. (2010), with the addition of <i>Acrotholus</i>, <i>Amtocephale</i>, the Sandy Site Pachycephalosaurine and RBCM.EH.2006.019.
DOI: 10.6084/m9.figshare.3498524
title: The Concept of Gravitorotational Acceleration and its Consequences for Compact Stellar Objects and Sun

description: In a previous series of papers relating to the Combined Gravitational Action (CGA), we have exclusively studied orbital motion without spin. In the present paper we apply CGA to any self<i>-</i>rotating material body, <i>i.e</i>., an axially spinning massive object, which itself may be locally seen as a gravitorotational source because it is capable of generating the gravitorotational (field) acceleration, which seems to be unknown to previously existing theories of gravity. The consequences of such an acceleration are very interesting, particularly for Compact Stellar Objects and Sun.
DOI: 10.6084/m9.figshare.3498524.v1
title: The Concept of Gravitorotational Acceleration and its Consequences for Compact Stellar Objects and Sun

description: In a previous series of papers relating to the Combined Gravitational Action (CGA), we have exclusively studied orbital motion without spin. In the present paper we apply CGA to any self<i>-</i>rotating material body, <i>i.e</i>., an axially spinning massive object, which itself may be locally seen as a gravitorotational source because it is capable of generating the gravitorotational (field) acceleration, which seems to be unknown to previously existing theories of gravity. The consequences of such an acceleration are very interesting, particularly for Compact Stellar Objects and Sun.
DOI: 10.6084/m9.figshare.3498488
title: Combustion Properties of Birch (<i>Betula pendula</i>) Black Liquors From Sulfur-Free Pulping

description: Sulfur-free pulping has an environmental advantage over the traditional kraft process. This article describes the combustion properties of the black liquors produced from silver birch (<i>Betula pendula</i>) sawdust using three different cooking processes: two sulfur-free cooks (soda-anthraquinone and oxygen-alkali), and one reference kraft cook. It also considers the corresponding black liquors from an integrated forest biorefinery, in which a hot-water pretreatment of feedstock was performed prior to pulping. With the same cooking time, the total burning times for the sulfur-free black liquors were higher (15–55%) than those for the conventional kraft black liquors. However, no significant differences were noted between the total burning times for black liquors from pretreated feedstock and those from untreated feedstock. Especially in the case of untreated feedstock, the results showed that the kraft black liquors typically swelled more (25–45%) than the sulfur-free black liquors. It was further observed that the kraft and soda-anthraquinone black liquors from the untreated feedstock swelled more than those from the pretreated feedstock, while the oxygen-alkali black liquors swelled less.
DOI: 10.6084/m9.figshare.3498488.v1
title: Combustion Properties of Birch (<i>Betula pendula</i>) Black Liquors From Sulfur-Free Pulping

description: Sulfur-free pulping has an environmental advantage over the traditional kraft process. This article describes the combustion properties of the black liquors produced from silver birch (<i>Betula pendula</i>) sawdust using three different cooking processes: two sulfur-free cooks (soda-anthraquinone and oxygen-alkali), and one reference kraft cook. It also considers the corresponding black liquors from an integrated forest biorefinery, in which a hot-water pretreatment of feedstock was performed prior to pulping. With the same cooking time, the total burning times for the sulfur-free black liquors were higher (15–55%) than those for the conventional kraft black liquors. However, no significant differences were noted between the total burning times for black liquors from pretreated feedstock and those from untreated feedstock. Especially in the case of untreated feedstock, the results showed that the kraft black liquors typically swelled more (25–45%) than the sulfur-free black liquors. It was further observed that the kraft and soda-anthraquinone black liquors from the untreated feedstock swelled more than those from the pretreated feedstock, while the oxygen-alkali black liquors swelled less.
DOI: 10.6084/m9.figshare.3498485
title: <i>CB5C</i> affects the glucosinolate profile in <i>Arabidopsis thaliana</i>

description: Cytochrome b<sub>5</sub> (CB5) proteins are small heme-binding proteins, that influence cytochrome P450 activity. While only one CB5 isoform is found in mammals, higher plants have several isoforms of these proteins. The roles of the many CB5 isoforms in plants remain unknown. We hypothesized that CB5 proteins support the cytochrome P450 enzymes of plant specialized metabolism and found <i>CB5C</i> from <i>Arabidopsis thaliana</i> to co-express with glucosinolate biosynthetic genes. We characterized the glucosinolate profiles of 2 T-DNA insertion mutants of <i>CB5C</i>, and found that long-chained aliphatic glucosinolates were reduced in one of the mutant lines – a phenotype that was exaggerated upon methyl-jasmonate treatment. These results support the hypothesis, that <i>CB5C</i> influences glucosinolate biosynthesis, however, the mode of action remains unknown. Furthermore, the mutants differed in their biomass response to methyl jasmonate treatment. Thereby, our results highlight the varying effects of T-DNA insertion sites, as the 2 analyzed alleles show different phenotypes.
DOI: 10.6084/m9.figshare.3498485.v1
title: <i>CB5C</i> affects the glucosinolate profile in <i>Arabidopsis thaliana</i>

description: Cytochrome b<sub>5</sub> (CB5) proteins are small heme-binding proteins, that influence cytochrome P450 activity. While only one CB5 isoform is found in mammals, higher plants have several isoforms of these proteins. The roles of the many CB5 isoforms in plants remain unknown. We hypothesized that CB5 proteins support the cytochrome P450 enzymes of plant specialized metabolism and found <i>CB5C</i> from <i>Arabidopsis thaliana</i> to co-express with glucosinolate biosynthetic genes. We characterized the glucosinolate profiles of 2 T-DNA insertion mutants of <i>CB5C</i>, and found that long-chained aliphatic glucosinolates were reduced in one of the mutant lines – a phenotype that was exaggerated upon methyl-jasmonate treatment. These results support the hypothesis, that <i>CB5C</i> influences glucosinolate biosynthesis, however, the mode of action remains unknown. Furthermore, the mutants differed in their biomass response to methyl jasmonate treatment. Thereby, our results highlight the varying effects of T-DNA insertion sites, as the 2 analyzed alleles show different phenotypes.
DOI: 10.6084/m9.figshare.3498479
title: Does the exclusion of meiofauna affect the estimation of biotic indices using stream invertebrates?

description: Biomonitoring of rivers is usually undertaken using information based on macroinvertebrate assemblages. However, exclusion of meiofauna (i.e. invertebrates less than 0.5 mm in size) when sorting benthic invertebrates can affect the estimation of densities and other biotic indices. In the present study, the effect of excluding the less than 0.5 mm fraction of invertebrates on estimation of benthic invertebrate indices was investigated in the Naro Moru River, Kenya. The Shannon–Wiener diversity index, Pielou’s evenness index, a multimetric index, Simpson’s diversity index, Margalef’s diversity index, mean invertebrate density, taxa richness, and Ephemeroptera, Plecoptera and Trichoptera (EPT) densities were determined. Only mean invertebrate and EPT densities differed significantly between the greater than 0.5 mm and total fractions. In conclusion, exclusion of meiofauna from invertebrate samples can affect the estimation of some stream invertebrate biotic indices.
DOI: 10.6084/m9.figshare.3498479.v1
title: Does the exclusion of meiofauna affect the estimation of biotic indices using stream invertebrates?

description: Biomonitoring of rivers is usually undertaken using information based on macroinvertebrate assemblages. However, exclusion of meiofauna (i.e. invertebrates less than 0.5 mm in size) when sorting benthic invertebrates can affect the estimation of densities and other biotic indices. In the present study, the effect of excluding the less than 0.5 mm fraction of invertebrates on estimation of benthic invertebrate indices was investigated in the Naro Moru River, Kenya. The Shannon–Wiener diversity index, Pielou’s evenness index, a multimetric index, Simpson’s diversity index, Margalef’s diversity index, mean invertebrate density, taxa richness, and Ephemeroptera, Plecoptera and Trichoptera (EPT) densities were determined. Only mean invertebrate and EPT densities differed significantly between the greater than 0.5 mm and total fractions. In conclusion, exclusion of meiofauna from invertebrate samples can affect the estimation of some stream invertebrate biotic indices.
DOI: 10.6084/m9.figshare.3498473
title: goodModels.dat

description: These data are the population of parameter values for a single-compartment model neuron obtained by fitting the impedance amplitude and phase profile attributes to the biological PD neuron of the crab pyloric network.
DOI: 10.6084/m9.figshare.3498473.v2
title: goodModels.dat

description: These data are the population of parameter values for a single-compartment model neuron obtained by fitting the impedance amplitude and phase profile attributes to the biological PD neuron of the crab pyloric network.
DOI: 10.6084/m9.figshare.12917279
title: Aberrant Splicing of SDHC in Families With Unexplained Succinate Dehydrogenase- Deficient Paragangliomas - Supplementary Material

description: Supplemental data to accompany: Aberrant Splicing of SDHC in Families With Unexplained Succinate Dehydrogenase-Deficient ParagangliomasJ Endocrinol Soc 2020https://doi.org/10.1210/jendso/bvaa071
DOI: 10.6084/m9.figshare.3498473.v1
title: goodModels.dat

description: These data are the population of parameter values for a single-compartment model neuron obtained by fitting the impedance amplitude and phase profile attributes to the biological PD neuron of the crab pyloric network.
DOI: 10.6084/m9.figshare.3498446
title: HCP-MMP1.0 projected on fsaverage

description: Hi All!<br>Following instructions gathered via twitter and the HCP message board, I've projected the new HCP-MMP1.0 parcellation onto fsaverage. I have attached the annotation files here and detailed my process below:<br>1. Download the correct data from BALSA:https://balsa.wustl.edu/WN56<br>2. Download the correct spheres from the HCP github page:this is detailed here: https://www.mail-archive.com/hcp-users%40humanconnectome.org/msg02890.html<br>3. Using workbench, convert parcellation dabel.nii file label.gii file:<br>wb_command -cifti-separate Q1-Q6_RelatedParcellation210.L.CorticalAreas_dil_Colors.32k_fs_LR.dlabel.nii COLUMN -label CORTEX_LEFT Q1-Q6_RelatedParcellation210.L.CorticalAreas_dil_Colors.32k_fs_LR.label.gii<br>wb_command -cifti-separate Q1-Q6_RelatedParcellation210.R.CorticalAreas_dil_Colors.32k_fs_LR.dlabel.nii COLUMN -label CORTEX_RIGHT Q1-Q6_RelatedParcellation210.R.CorticalAreas_dil_Colors.32k_fs_LR.label.gii<br>4. Using workbench, convert label.gii file to fsaverage space:<br>wb_command -label-resample Q1-Q6_RelatedParcellation210.L.CorticalAreas_dil_Colors.32k_fs_LR.label.gii L.sphere.32k_fs_LR.surf.gii fs_L-to-fs_LR_fsaverage.L_LR.spherical_std.164k_fs_L.surf.gii BARYCENTRIC left.fsaverage164.label.gii<br>wb_command -label-resample Q1-Q6_RelatedParcellation210.R.CorticalAreas_dil_Colors.32k_fs_LR.label.gii R.sphere.32k_fs_LR.surf.gii fs_R-to-fs_LR_fsaverage.R_LR.spherical_std.164k_fs_R.surf.gii BARYCENTRIC right.fsaverage164.label.gii<br><br>5. Using freesurfer, convert files from gii to annot:<br>mris_convert --annot left.fsaverage164.label.gii fs_L-to-fs_LR_fsaverage.L_LR.spherical_std.164k_fs_L.surf.gii lh.HCP-MMP1.annot<br>mris_convert --annot right.fsaverage164.label.gii fs_R-to-fs_LR_fsaverage.R_LR.spherical_std.164k_fs_R.surf.gii rh.HCP-MMP1.annot<br>6. Rejoice and share!<br>
DOI: 10.6084/m9.figshare.3498323
title: A systematic evaluation for the potential translation of CD166-related expression as a cancer biomarker

description: <b>Introduction</b>: Many basic studies have provided some evidences for the correlations of CD166 to cancer. However, along with the growing studies on the clinical values of CD166 in cancer areas, some controversial and inconclusive results were obtained. <b>Areas covered</b>: An appropriate query and collection of the published articles was conducted through search in PubMed and EMBASE database. A subsequent systematical and quantitative summary of CD166 related expression and cancer was conducted with meta-analysis to clarify its clinical significance for potential translation as cancer biomarkers. <b>Expert commentary</b>: The overall results suggested total CD166 correlated to cancer risk, membrane CD166 correlated to nodal metastasis and cytoplasmic CD166 correlated to TNM stage, and disease-free survival. The membrane CD166, cytoplasmic CD166 and soluble CD166 showed great potential to be used as a panel of markers for predicting cancer overall survival. We might conclude that CD166 functions as a risk factor for cancers, and the alterations of its different functional isoforms were observed to correlate with specific or interplayed clinical outcomes.
DOI: 10.6084/m9.figshare.3498323.v1
title: A systematic evaluation for the potential translation of CD166-related expression as a cancer biomarker

description: <b>Introduction</b>: Many basic studies have provided some evidences for the correlations of CD166 to cancer. However, along with the growing studies on the clinical values of CD166 in cancer areas, some controversial and inconclusive results were obtained. <b>Areas covered</b>: An appropriate query and collection of the published articles was conducted through search in PubMed and EMBASE database. A subsequent systematical and quantitative summary of CD166 related expression and cancer was conducted with meta-analysis to clarify its clinical significance for potential translation as cancer biomarkers. <b>Expert commentary</b>: The overall results suggested total CD166 correlated to cancer risk, membrane CD166 correlated to nodal metastasis and cytoplasmic CD166 correlated to TNM stage, and disease-free survival. The membrane CD166, cytoplasmic CD166 and soluble CD166 showed great potential to be used as a panel of markers for predicting cancer overall survival. We might conclude that CD166 functions as a risk factor for cancers, and the alterations of its different functional isoforms were observed to correlate with specific or interplayed clinical outcomes.
DOI: 10.6084/m9.figshare.3498308
title: Morning Glory Predicted proteins

description: Predicted proteins from transcriptome assembly of Morning Glory Ipomoea Imperati. Illumina Hiseq reads assembled with Trinity, were clustered into highly similar<br>From Data report "Transcriptome dataset of halophyte beach morning glory, a close wild relative of sweet potato"
DOI: 10.6084/m9.figshare.3498308.v1
title: Morning Glory Predicted proteins

description: Predicted proteins from transcriptome assembly of Morning Glory Ipomoea Imperati. Illumina Hiseq reads assembled with Trinity, were clustered into highly similar<br>From Data report "Transcriptome dataset of halophyte beach morning glory, a close wild relative of sweet potato"
DOI: 10.6084/m9.figshare.3498263
title: CDHIT Cluster of assemblies

description: CDHIT cluster of Morning Glory Ipomoea Imperati. Illumina Hiseq reads assembled with Trinity, followed by clustering of highly similar sequences.<br>From Data report "Transcriptome dataset of halophyte beach morning glory, a close wild relative of sweet potato"
DOI: 10.6084/m9.figshare.3498263.v1
title: CDHIT Cluster of assemblies

description: CDHIT cluster of Morning Glory Ipomoea Imperati. Illumina Hiseq reads assembled with Trinity, followed by clustering of highly similar sequences.<br>From Data report "Transcriptome dataset of halophyte beach morning glory, a close wild relative of sweet potato"
DOI: 10.6084/m9.figshare.3498239
title: Morning Glory Transcriptome assembly

description: Transcriptome assembly of Morning Glory Ipomoea Imperati. Illumina Hiseq reads assembled with Trinity.<br>From Data report "Transcriptome dataset of halophyte beach morning glory, a close wild relative of sweet potato"
DOI: 10.6084/m9.figshare.3498239.v1
title: Morning Glory Transcriptome assembly

description: Transcriptome assembly of Morning Glory Ipomoea Imperati. Illumina Hiseq reads assembled with Trinity.<br>From Data report "Transcriptome dataset of halophyte beach morning glory, a close wild relative of sweet potato"
DOI: 10.6084/m9.figshare.3498209
title: Scoring multiple features to predict drug disease associations using information fusion and aggregation

description: Prediction of drug–disease associations is one of the current fields in drug repositioning that has turned into a challenging topic in pharmaceutical science. Several available computational methods use network-based and machine learning approaches to reposition old drugs for new indications. However, they often ignore features of drugs and diseases as well as the priority and importance of each feature, relation, or interactions between features and the degree of uncertainty. When predicting unknown drug–disease interactions there are diverse data sources and multiple features available that can provide more accurate and reliable results. This information can be collectively mined using data fusion methods and aggregation operators. Therefore, we can use the feature fusion method to make high-level features. We have proposed a computational method named scored mean kernel fusion (SMKF), which uses a new method to score the average aggregation operator called scored mean. To predict novel drug indications, this method systematically combines multiple features related to drugs or diseases at two levels: the drug–drug level and the drug–disease level. The purpose of this study was to investigate the effect of drug and disease features as well as data fusion to predict drug–disease interactions. The method was validated against a well-established drug–disease gold-standard dataset. When compared with the available methods, our proposed method outperformed them and competed well in performance with area under cover (AUC) of 0.91, F-measure of 84.9% and Matthews correlation coefficient of 70.31%.
DOI: 10.6084/m9.figshare.3498209.v1
title: Scoring multiple features to predict drug disease associations using information fusion and aggregation

description: Prediction of drug–disease associations is one of the current fields in drug repositioning that has turned into a challenging topic in pharmaceutical science. Several available computational methods use network-based and machine learning approaches to reposition old drugs for new indications. However, they often ignore features of drugs and diseases as well as the priority and importance of each feature, relation, or interactions between features and the degree of uncertainty. When predicting unknown drug–disease interactions there are diverse data sources and multiple features available that can provide more accurate and reliable results. This information can be collectively mined using data fusion methods and aggregation operators. Therefore, we can use the feature fusion method to make high-level features. We have proposed a computational method named scored mean kernel fusion (SMKF), which uses a new method to score the average aggregation operator called scored mean. To predict novel drug indications, this method systematically combines multiple features related to drugs or diseases at two levels: the drug–drug level and the drug–disease level. The purpose of this study was to investigate the effect of drug and disease features as well as data fusion to predict drug–disease interactions. The method was validated against a well-established drug–disease gold-standard dataset. When compared with the available methods, our proposed method outperformed them and competed well in performance with area under cover (AUC) of 0.91, F-measure of 84.9% and Matthews correlation coefficient of 70.31%.
DOI: 10.6084/m9.figshare.3498206
title: ATM keypad QIIME analysis

description: This fileset contains QIIME commands and outputs used to carry out the analysis in the manuscript entitled <b>"Microbial community patterns associated with Automated Teller Machine (ATM) keypads in New York City" </b>(Bik et. al, submitted)<br>Microbial swab samples from Automated Teller Machine (ATM) keypads in New York City were subjected to environmental marker gene sequencing for the 16S rRNA gene (targeting bacteria/archaea) and 18S rRNA gene (targeting eukaryotes).<br><br>
DOI: 10.6084/m9.figshare.3498122
title: Data_randtag.xlsx

description: Data containing ERP values used in the article : <b>D</b><b>ecoding the locus of covert visuospatial attention from EEG signals.</b>
DOI: 10.6084/m9.figshare.3498122.v1
title: Data_randtag.xlsx

description: Data containing ERP values used in the article : <b>D</b><b>ecoding the locus of covert visuospatial attention from EEG signals.</b>
DOI: 10.6084/m9.figshare.3498119
title: A systematic review of outcomes in postoperative pain studies in pediatric and adolescent patients: Toward development of a core outcome set. 12/2015-7/2016

description: This is both the data extracted from each clinical trial in our study and the matrix used to make the social network analysis