cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.7887128.v1
title: Supplementary Material for: Diversity of Nontuberculous Mycobacteria in Kuwait: Rapid Identification and Differentiation of <b><i>Mycobacterium</i></b> Species by Multiplex PCR, INNO-LiPA Mycobacteria v2 Assay and PCR Sequencing of rDNA

description: <b><i>Objective:</i></b> Nontuberculous mycobacteria (NTM) often cause disease that is clinically indistinguishable from tuberculosis. Specific identification is important as treatment varies according to <i>Mycobacterium</i> species causing the infection. This study used multiplex PCR (mPCR) assay for rapid differentiation of mycobacterial growth indicator tube 960 system (MGIT) cultures as <i>Mycobacterium tuberculosis</i> (MTB) or NTM together with INNO LiPA Mycobacteria v2 assay (LiPA) and/or PCR sequencing of rDNA for species-specific identification of selected MTB and all NTM isolates in Kuwait. <b><i>Materials and Methods:</i></b> DNA was extracted from MGIT cultures (<i>n</i> = 1,033) grown from 664 pulmonary and 369 extrapulmonary specimens from 1,033 suspected tuberculosis patients. mPCR was performed to differentiate MTB from NTM. LiPA was performed and results were interpreted according to kit instructions. rDNA was amplified and sequenced by using panmycobacterial primers. <b><i>Results:</i></b> mPCR identified 979 isolates as MTB, 53 as NTM and 1 isolate as mixed culture. LiPA and/or PCR sequencing confirmed 112 of 979 selected isolates as MTB. Mixed culture contained <i>M. tuberculosis</i> and <i>M. fortuitum</i>. LiPA yielded 12 patterns and identified 10 species/species complexes among 47 NTM, <i>M. kansasii</i> +<i> M. scrofulaceum</i> in one culture and 5 isolates only at genus level. PCR sequencing yielded more specific identification for 22 isolates at the species/subspecies level. <b><i>Conclusions:</i></b> mPCR rapidly differentiated MTB from NTM. LiPA identified 44 of 52 NTM isolates at the species/species complex level and 2 mixed cultures. PCR sequencing yielded more specific identification at the species/subspecies level. Rapid differentiation as MTB or NTM by mPCR, followed by species-specific NTM identification by LiPA/PCR sequencing is suitable for the proper management of mycobacterial infections in Kuwait.
DOI: 10.6084/m9.figshare.7887113
title: final article title

description: Test description of article
DOI: 10.6084/m9.figshare.7887110
title: MeFö i siffror 2018

description: Vanligt efterfrågade siffror från MeFö:s verksamnhet, bland annat antal nedladdade artiklar, antal sökningar i betalda databaser, mediabudget och utfall.<br>
DOI: 10.6084/m9.figshare.7887113.v1
title: final article title

description: Test description of article
DOI: 10.6084/m9.figshare.7887083
title: Postal recruitment for genetic studies of preterm birth: A feasibility study

description: Datasets and files pertaining to the study: Postal recruitment for genetic studies of preterm birth: A feasibility study
DOI: 10.6084/m9.figshare.7887032
title: Bayesian OpAL model

description: This is the output .Rdat file for a Bayesian OpAL model run on Parkinson's data from biorxiv McCoy et al. 2018 (Dopaminergic medication reduces striatal sensitivity to negative outcomes in Parkinson's disease<br>.
DOI: 10.6084/m9.figshare.7887083.v1
title: Data for OPPTIMUM genetics project

description: Datasets pertaining to the study: Postal recruitment for genetic studies of preterm birth: A feasibility studyFile 1. DNA extraction dataFile 2. OPPTIMUM trial dataFile 3. Questionnaire data
DOI: 10.6084/m9.figshare.7887083.v2
title: Postal recruitment for genetic studies of preterm birth.

description: Datasets pertaining to the study: Postal recruitment for genetic studies of preterm birth: A feasibility studyFile 1. DNA extraction dataFile 2. OPPTIMUM trial dataFile 3. Questionnaire data
DOI: 10.6084/m9.figshare.7887083.v4
title: Postal recruitment for genetic studies of preterm birth.

description: Datasets pertaining to the study: Postal recruitment for genetic studies of preterm birth: A feasibility studyFile 1. DNA extraction dataFile 2. OPPTIMUM trial dataFile 3. Questionnaire dataAppendix 1. Participant questionnaireAppendix 2. OPPTIMUM trial inclusion and exclusion criteriaAppendix 3. Recruitment pack contentsOPPTIMUM Genetics invitation lettersRecruitment pack lettersOPPTIMUM genetics patient information leafletsOPPTIMUM genetics consent formsSaliva sample collection instructions
DOI: 10.6084/m9.figshare.7887083.v5
title: Postal recruitment for genetic studies of preterm birth: A feasibility study

description: Datasets pertaining to the study: Postal recruitment for genetic studies of preterm birth: A feasibility studyFile 1. DNA extraction dataFile 2. OPPTIMUM trial dataFile 3. Questionnaire dataAppendix 1. Participant questionnaireAppendix 2. OPPTIMUM trial inclusion and exclusion criteriaAppendix 3. List of recruitment pack contentsOPPTIMUM Genetics invitation lettersRecruitment pack lettersOPPTIMUM genetics patient information leafletsOPPTIMUM genetics consent formsSaliva sample collection instructions
DOI: 10.6084/m9.figshare.7887083.v6
title: Postal recruitment for genetic studies of preterm birth: A feasibility study

description: Datasets pertaining to the study: Postal recruitment for genetic studies of preterm birth: A feasibility studyFile 1. DNA extraction dataFile 2. OPPTIMUM trial dataFile 3. Questionnaire dataFile 4. Comparison results of Y markers in baby samplesFile 5. Taqman, genotyping reportAppendix 1. Participant questionnaireAppendix 2. OPPTIMUM trial inclusion and exclusion criteriaAppendix 3. List of recruitment pack contentsOPPTIMUM Genetics invitation lettersRecruitment pack lettersOPPTIMUM genetics patient information leafletsOPPTIMUM genetics consent formsSaliva sample collection instructionsTaqman Genotyping reportComparison results of Y markers
DOI: 10.6084/m9.figshare.7886921
title: Pilot testing of a bioremediation system for water and soils contaminated with heavy metals: vegetable depuration module

description: We present a novel constructed wetland called a vegetable depuration module (VDM) as a pilot test of a bioremediation system (BS) for decontaminating water and soil polluted with heavy metals. The VDM consisted of a pool filled with stones of different granulometry and a substrate top layer composed of a mixture of soil and volcanic ash (50:50, v/v) supplemented with 350 ppm Zn. The BS of sunflower plants colonized by the arbuscular mycorrhizal fungus <i>Rhizophagus intraradices</i> was planted in the VDM. Initially, the substrate registered high concentrations of Zn, Cr, Mn, Cu, and Sr, and had Eh &gt; +500 mV and pH 8.4. Irrigation with a Cu solution by vertical flow was carried out. After 3 months, bioaccumulation factors ranged from 1.00 to 8.90, and translocation rates were &gt;1 for Sr and Cu. Total metals extracted by the BS and percolation were 31%, 34%, 50%, 45%, and 57% for Zn, Cu, Mn, Cr, and Sr, respectively. Only the BS was capable of extracting 94% of Cu and 38% of Zn. VDM allowed us to calibrate the extractive performance of the studied elements in BS. This biotechnological development holds great potential for phytoremediation of polluted areas.
DOI: 10.6084/m9.figshare.7886921.v1
title: Pilot testing of a bioremediation system for water and soils contaminated with heavy metals: vegetable depuration module

description: We present a novel constructed wetland called a vegetable depuration module (VDM) as a pilot test of a bioremediation system (BS) for decontaminating water and soil polluted with heavy metals. The VDM consisted of a pool filled with stones of different granulometry and a substrate top layer composed of a mixture of soil and volcanic ash (50:50, v/v) supplemented with 350 ppm Zn. The BS of sunflower plants colonized by the arbuscular mycorrhizal fungus <i>Rhizophagus intraradices</i> was planted in the VDM. Initially, the substrate registered high concentrations of Zn, Cr, Mn, Cu, and Sr, and had Eh &gt; +500 mV and pH 8.4. Irrigation with a Cu solution by vertical flow was carried out. After 3 months, bioaccumulation factors ranged from 1.00 to 8.90, and translocation rates were &gt;1 for Sr and Cu. Total metals extracted by the BS and percolation were 31%, 34%, 50%, 45%, and 57% for Zn, Cu, Mn, Cr, and Sr, respectively. Only the BS was capable of extracting 94% of Cu and 38% of Zn. VDM allowed us to calibrate the extractive performance of the studied elements in BS. This biotechnological development holds great potential for phytoremediation of polluted areas.
DOI: 10.6084/m9.figshare.7886838
title: Understanding citizens views around routine genome sequencing for NHS patients

description: WT Public Engagement Fund application appendixes.
DOI: 10.6084/m9.figshare.7886838.v1
title: Understanding citizens views around routine genome sequencing for NHS patients

description: WT Public Engagement Fund application appendixes.
DOI: 10.6084/m9.figshare.7886800
title: Increased use of cross-sectional imaging for follow-up does not improve post-recurrence survival of surgically treated initially localized R.C.C.: results from a European multicenter database (R.E.C.U.R.)

description: <b>Objective:</b> Modality and frequency of image-based renal cell carcinoma (R.C.C.) follow-up strategies are based on risk of recurrence. Using the R.E.C.U.R.-database, frequency of imaging was studied in regard to prognostic risk groups. Furthermore, it was investigated whether imaging modality utilized in contemporary follow-up were associated with outcome after detection of recurrence. Moreover, outcome was compared based on whether the assessment of potential curability was a pre-defined set of criteria’s (per-protocol) or stated by the investigator. <b>Materials and methods:</b> Consecutive non-metastatic R.C.C. patients (<i>n</i> = 1,612) treated with curative intent at 12 institutes across eight European countries between 2006 and 2011 were included. Leibovich or U.I.S.S. risk group, recurrence characteristics, imaging modality, frequency and survival were recorded. Primary endpoints were overall survival (O.S.) after detection of recurrence and frequency of features associated with favourable outcome (non-symptomatic recurrences and detection within the follow-up-programme). <b>Results:</b> Recurrence occurred in 336 patients. Within low, intermediate and high risk for recurrence groups, the frequency of follow-up imaging was highest in the early phase of follow-up and decreased significantly over time (<i>p</i> <b>Conclusions:</b> As expected, the frequency of imaging was highest during early follow-up. Cross-sectional imaging use for detection of recurrences following surgery for localized R.C.C. did not improve O.S. post-recurrence. Prospective studies are needed to determine the value of imaging in follow-up.
DOI: 10.6084/m9.figshare.7886800.v2
title: Increased use of cross-sectional imaging for follow-up does not improve post-recurrence survival of surgically treated initially localized R.C.C.: results from a European multicenter database (R.E.C.U.R.)

description: <b>Objective:</b> Modality and frequency of image-based renal cell carcinoma (R.C.C.) follow-up strategies are based on risk of recurrence. Using the R.E.C.U.R.-database, frequency of imaging was studied in regard to prognostic risk groups. Furthermore, it was investigated whether imaging modality utilized in contemporary follow-up were associated with outcome after detection of recurrence. Moreover, outcome was compared based on whether the assessment of potential curability was a pre-defined set of criteria’s (per-protocol) or stated by the investigator. <b>Materials and methods:</b> Consecutive non-metastatic R.C.C. patients (<i>n</i> = 1,612) treated with curative intent at 12 institutes across eight European countries between 2006 and 2011 were included. Leibovich or U.I.S.S. risk group, recurrence characteristics, imaging modality, frequency and survival were recorded. Primary endpoints were overall survival (O.S.) after detection of recurrence and frequency of features associated with favourable outcome (non-symptomatic recurrences and detection within the follow-up-programme). <b>Results:</b> Recurrence occurred in 336 patients. Within low, intermediate and high risk for recurrence groups, the frequency of follow-up imaging was highest in the early phase of follow-up and decreased significantly over time (<i>p</i> <b>Conclusions:</b> As expected, the frequency of imaging was highest during early follow-up. Cross-sectional imaging use for detection of recurrences following surgery for localized R.C.C. did not improve O.S. post-recurrence. Prospective studies are needed to determine the value of imaging in follow-up.
DOI: 10.6084/m9.figshare.7886800.v1
title: Increased use of cross-sectional imaging for follow-up does not improve post-recurrence survival of surgically treated initially localized R.C.C.: results from a European multicenter database (R.E.C.U.R.)

description: <b>Objective:</b> Modality and frequency of image-based renal cell carcinoma (R.C.C.) follow-up strategies are based on risk of recurrence. Using the R.E.C.U.R.-database, frequency of imaging was studied in regard to prognostic risk groups. Furthermore, it was investigated whether imaging modality utilized in contemporary follow-up were associated with outcome after detection of recurrence. Moreover, outcome was compared based on whether the assessment of potential curability was a pre-defined set of criteria’s (per-protocol) or stated by the investigator. <b>Materials and methods:</b> Consecutive non-metastatic R.C.C. patients (<i>n</i> = 1,612) treated with curative intent at 12 institutes across eight European countries between 2006 and 2011 were included. Leibovich or U.I.S.S. risk group, recurrence characteristics, imaging modality, frequency and survival were recorded. Primary endpoints were overall survival (O.S.) after detection of recurrence and frequency of features associated with favourable outcome (non-symptomatic recurrences and detection within the follow-up-programme). <b>Results:</b> Recurrence occurred in 336 patients. Within low, intermediate and high risk for recurrence groups, the frequency of follow-up imaging was highest in the early phase of follow-up and decreased significantly over time (<i>p</i> <b>Conclusions:</b> As expected, the frequency of imaging was highest during early follow-up. Cross-sectional imaging use for detection of recurrences following surgery for localized R.C.C. did not improve O.S. post-recurrence. Prospective studies are needed to determine the value of imaging in follow-up.
DOI: 10.6084/m9.figshare.7886650
title: Supplementary Material for: Physical Activity and Mobility Differentially Predict Nondemented Executive Function Trajectories: Do Sex and <b><i>APOE</i></b> Moderate These Associations?

description: <b><i>Background:</i></b> In nondemented aging, higher levels of everyday physical activity (EPA) and mobility performance are associated with better executive function (EF) trajectories. However, these associations may be moderated by both sex and Alzheimer’s disease (AD) genetic risk. <b><i>Objectives:</i></b> In a longitudinal study, we investigate sex differences in (a) EPA and mobility effects on EF performance (level) and change (slope) and (b) AD genetic risk moderation of these associations. <b><i>Methods:</i></b> The longitudinal design included nondemented adults (<i>n =</i> 532, mean age = 70.4 years, range 53–95) from the Victoria Longitudinal Study. Using structural equation analyses on an EF latent variable, we tested (a) sex moderation and (b) interactive effects of sex and <i>APOE</i> on<i></i> observed EPA-EF and mobility-EF performance and change relationships. <b><i>Results:</i></b> First, we observed independent sex effects for the EPA-EF and mobility-EF predictions. Whereas EPA had a significant effect on EF performance and change only for females, mobility had a significant effect for both sexes. Notably, males with lower mobility levels experienced steeper EF decline than females with lower mobility levels. Second, we observed significant sex × <i>APOE</i> interaction effects. The combination of lower genetic risk and higher EPA benefitted females but not males. In contrast, lower genetic risk and higher mobility benefited both sexes, although male <i>APOE</i> no-risk carriers with lower mobility levels had EF decline patterns that were similar to <i>APOE</i> risk carriers. <b><i>Conclusions:</i></b> Longitudinal analyses across a broad band of aging show that sex moderates the effects of both EPA and mobility on EF performance and change. Notably, this moderation occurs differentially across the AD genetic risk status. These results point to a precision health approach to observational and interventional research in which effects of physical activity and mobility on EF trajectories and dementia are examined in the personalized and interactive context of sex and AD risk.
DOI: 10.6084/m9.figshare.7886656
title: Online Appendix - The Development and Validation of the Intellectual Virtue Scale.docx

description: Online supplemental material for the article on intellectual virtue
DOI: 10.17045/sthlmuni.7886641
title: ATP-cone sequence clusters

description: The NCBI RefSeq database (2019-03-19; Haft et al. 2018 https://doi.org/10.1093/nar/gkx1068) was searched with Pfam's ATP-cone profile (accno: PF03477; Finn et al. 2010 https://doi.org/10.1093/nar/gkp985) returning 44367 NCBI accessions. Ribonucleotide reductase proteins were identified using HMMER (Eddy 2011 https://doi.org/10.1371/journal.pcbi.1002195) profiles from the RNRdb database (http://rnrdb.pfitmap.org). Subsequently, sequences were clustered with UCLUST (Edgar 2010 https://doi.org/10.1093/bioinformatics/btq461) at identity to remove sequence duplicates (24477 sequences remaning).<br>All sequences were pairwise aligned to each other using LAST (Kiełbasa et al. 2011 https://doi.org/10.1101/gr.113985.110) and a bitscore matrix was constructed. The bitscore matrix was clustered with MCL (Enright, Dongen & Ouzounis 2002 https://doi.org/10.1093/nar/30.7.1575) using the Cluster Maker 2 (Morris et al. 2011 https://doi.org/10.1186/1471-2105-12-436) Cytoscape (Shannon et al. 2003 https://doi.org/10.1101/gr.1239303) app. Bitscores &lt; 200 were not included in the initial network and an inflation parameter of 2.5 was used.<br>The file "atp-cone_mcl_clustering.tsv" contains all information necessary to recreate the clustering as well as the assigned cluster numbers to each sequence. <br><br>Column names: SUID: Cytoscape's id, accno: NCBI's accession number, mcl2.0ewc200-mcl3.0: cluster assignments with inflation parameters and bitscore cutoff (ewc; when used), name: sequence identifier composed of accno plus cone number, outer_inner: "inner", "middle" or "outer" when more than one cone present in full sequence, pclass and psubclass: RNR class and subclass, ptype: protein type, taxon, tdomain: taxonomic domain, title: NCBI's description of the sequence.<br>The "precluster_assignments.tsv" file contains the results of the preclustering with USEARCH, i.e. which usearch cluster (first column) each accession number (second column) belong to.<br>
DOI: 10.6084/m9.figshare.7886650.v1
title: Supplementary Material for: Physical Activity and Mobility Differentially Predict Nondemented Executive Function Trajectories: Do Sex and <b><i>APOE</i></b> Moderate These Associations?

description: <b><i>Background:</i></b> In nondemented aging, higher levels of everyday physical activity (EPA) and mobility performance are associated with better executive function (EF) trajectories. However, these associations may be moderated by both sex and Alzheimer’s disease (AD) genetic risk. <b><i>Objectives:</i></b> In a longitudinal study, we investigate sex differences in (a) EPA and mobility effects on EF performance (level) and change (slope) and (b) AD genetic risk moderation of these associations. <b><i>Methods:</i></b> The longitudinal design included nondemented adults (<i>n =</i> 532, mean age = 70.4 years, range 53–95) from the Victoria Longitudinal Study. Using structural equation analyses on an EF latent variable, we tested (a) sex moderation and (b) interactive effects of sex and <i>APOE</i> on<i></i> observed EPA-EF and mobility-EF performance and change relationships. <b><i>Results:</i></b> First, we observed independent sex effects for the EPA-EF and mobility-EF predictions. Whereas EPA had a significant effect on EF performance and change only for females, mobility had a significant effect for both sexes. Notably, males with lower mobility levels experienced steeper EF decline than females with lower mobility levels. Second, we observed significant sex × <i>APOE</i> interaction effects. The combination of lower genetic risk and higher EPA benefitted females but not males. In contrast, lower genetic risk and higher mobility benefited both sexes, although male <i>APOE</i> no-risk carriers with lower mobility levels had EF decline patterns that were similar to <i>APOE</i> risk carriers. <b><i>Conclusions:</i></b> Longitudinal analyses across a broad band of aging show that sex moderates the effects of both EPA and mobility on EF performance and change. Notably, this moderation occurs differentially across the AD genetic risk status. These results point to a precision health approach to observational and interventional research in which effects of physical activity and mobility on EF trajectories and dementia are examined in the personalized and interactive context of sex and AD risk.
DOI: 10.17045/sthlmuni.7886641.v1
title: ATP-cone sequence clusters

description: The NCBI RefSeq database (2019-03-19; Haft et al. 2018 https://doi.org/10.1093/nar/gkx1068) was searched with Pfam's ATP-cone profile (accno: PF03477; Finn et al. 2010 https://doi.org/10.1093/nar/gkp985) returning 44367 NCBI accessions. Ribonucleotide reductase proteins were identified using HMMER (Eddy 2011 https://doi.org/10.1371/journal.pcbi.1002195) profiles from the RNRdb database (http://rnrdb.pfitmap.org). Subsequently, sequences were clustered with UCLUST (Edgar 2010 https://doi.org/10.1093/bioinformatics/btq461) at identity to remove sequence duplicates (24477 sequences remaning).<br>All sequences were pairwise aligned to each other using LAST (Kiełbasa et al. 2011 https://doi.org/10.1101/gr.113985.110) and a bitscore matrix was constructed. The bitscore matrix was clustered with MCL (Enright, Dongen & Ouzounis 2002 https://doi.org/10.1093/nar/30.7.1575) using the Cluster Maker 2 (Morris et al. 2011 https://doi.org/10.1186/1471-2105-12-436) Cytoscape (Shannon et al. 2003 https://doi.org/10.1101/gr.1239303) app. Bitscores &lt; 200 were not included in the initial network and an inflation parameter of 2.5 was used.<br>The file "atp-cone_mcl_clustering.tsv" contains all information necessary to recreate the clustering as well as the assigned cluster numbers to each sequence. <br><br>Column names: SUID: Cytoscape's id, accno: NCBI's accession number, mcl2.0ewc200-mcl3.0: cluster assignments with inflation parameters and bitscore cutoff (ewc; when used), name: sequence identifier composed of accno plus cone number, outer_inner: "inner", "middle" or "outer" when more than one cone present in full sequence, pclass and psubclass: RNR class and subclass, ptype: protein type, taxon, tdomain: taxonomic domain, title: NCBI's description of the sequence.<br>The "precluster_assignments.tsv" file contains the results of the preclustering with USEARCH, i.e. which usearch cluster (first column) each accession number (second column) belong to.<br>