cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.5852151.v1
title: Additional file 2: Table S2. of The genetic structure of the Belgian population

description: Population details of the samples analyzed in the BelPHG-21 study, Belgium 2016. Indication of the number of samples taken from NHIS-2013 participants in each region and province, total number of inhabitants in 2013, number of samples taken per million inhabitants, number of invited participants, and sampling percentages. (XLSX 10Â kb)
DOI: 10.6084/m9.figshare.5852139
title: Additional file 4: Table S2. of Nc886 is epigenetically repressed in prostate cancer and acts as a tumor suppressor through the inhibition of cell growth

description: Correlation of the differentially expressed genes identified in a knock down of nc886 in esophageal, gastric and thyroid cell lines and nc886 TSS200 methylation level in TCGA-PRAD tumor samples. (XLSX 11 kb)
DOI: 10.6084/m9.figshare.5852139.v1
title: Additional file 4: Table S2. of Nc886 is epigenetically repressed in prostate cancer and acts as a tumor suppressor through the inhibition of cell growth

description: Correlation of the differentially expressed genes identified in a knock down of nc886 in esophageal, gastric and thyroid cell lines and nc886 TSS200 methylation level in TCGA-PRAD tumor samples. (XLSX 11 kb)
DOI: 10.6084/m9.figshare.5852127
title: Additional file 1: Table S1. of The genetic structure of the Belgian population

description: SNP variant allele frequencies of the Belgian population, BelPHG-21 study, Belgium 2016. Variant allele frequencies (VAF) for all SNPs were calculated with reference to the human genome build hg19 on all samples or after exclusion of samples with a foreign origin (indicated by tab names). Columns indicate SNP ids, chromosome, position, reference allele, variant allele, VAF, and frequencies of homozygous reference (AA), heterozygous (AB), and homozygous variant (BB) alleles respectively. (XLSX 28534Â kb)
DOI: 10.6084/m9.figshare.5852127.v1
title: Additional file 1: Table S1. of The genetic structure of the Belgian population

description: SNP variant allele frequencies of the Belgian population, BelPHG-21 study, Belgium 2016. Variant allele frequencies (VAF) for all SNPs were calculated with reference to the human genome build hg19 on all samples or after exclusion of samples with a foreign origin (indicated by tab names). Columns indicate SNP ids, chromosome, position, reference allele, variant allele, VAF, and frequencies of homozygous reference (AA), heterozygous (AB), and homozygous variant (BB) alleles respectively. (XLSX 28534Â kb)
DOI: 10.6084/m9.figshare.5852115
title: Additional file 3: Table S1. of Nc886 is epigenetically repressed in prostate cancer and acts as a tumor suppressor through the inhibition of cell growth

description: Correlation of the expression of the DNMTs with nc886 TSS200 methylation level in TCGA-PRAD tumor samples. (XLSX 9 kb)
DOI: 10.6084/m9.figshare.5852115.v1
title: Additional file 3: Table S1. of Nc886 is epigenetically repressed in prostate cancer and acts as a tumor suppressor through the inhibition of cell growth

description: Correlation of the expression of the DNMTs with nc886 TSS200 methylation level in TCGA-PRAD tumor samples. (XLSX 9 kb)
DOI: 10.6084/m9.figshare.5852094
title: Additional file 1: Table S1. of Crawling-induced floor dust resuspension affects the microbiota of the infant breathing zone

description: QIIME mapping file. Table S2. Details on qPCR assays included in this study. Table S3. Microbial concentrations as determined with qPCR in 17 carpets used in the chamber experiments, expressed as loads (cell equivalents (CE) per square meter of carpet) and as concentrations (CE per milligram of carpet dust). Table S4. Means, minimum, and maximum of particulate matter (PM100 [μg/m3]) and microbial levels (cell equivalents/m3) in infant breathing zone (IBZ) during five individual crawling and walking experiments on different rugs and corresponding ratios of crawling versus walking resuspension experiments. Table S5. Spearman rank-order correlations between the top 10 most abundant bacterial genera in infant breathing zone air and carpet dust. Table S6. Differential features (OTUs) in carpet dust versus infant breathing zone air samples as determined via LEfSe analysis of 16 carpet dust and 16 corresponding IBZ samples. Table S7. Dust load, quantitative PCR measurements, and particle mass concentrations from crawling experiments on 17 carpets. Table S8. Dust load, quantitative PCR measurements, and particle mass concentrations from crawling and walking experiments on 5 carpets. (XLSX 72 kb)
DOI: 10.6084/m9.figshare.5852094.v1
title: Additional file 1: Table S1. of Crawling-induced floor dust resuspension affects the microbiota of the infant breathing zone

description: QIIME mapping file. Table S2. Details on qPCR assays included in this study. Table S3. Microbial concentrations as determined with qPCR in 17 carpets used in the chamber experiments, expressed as loads (cell equivalents (CE) per square meter of carpet) and as concentrations (CE per milligram of carpet dust). Table S4. Means, minimum, and maximum of particulate matter (PM100 [μg/m3]) and microbial levels (cell equivalents/m3) in infant breathing zone (IBZ) during five individual crawling and walking experiments on different rugs and corresponding ratios of crawling versus walking resuspension experiments. Table S5. Spearman rank-order correlations between the top 10 most abundant bacterial genera in infant breathing zone air and carpet dust. Table S6. Differential features (OTUs) in carpet dust versus infant breathing zone air samples as determined via LEfSe analysis of 16 carpet dust and 16 corresponding IBZ samples. Table S7. Dust load, quantitative PCR measurements, and particle mass concentrations from crawling experiments on 17 carpets. Table S8. Dust load, quantitative PCR measurements, and particle mass concentrations from crawling and walking experiments on 5 carpets. (XLSX 72 kb)
DOI: 10.6084/m9.figshare.5852064
title: Additional file 1: of The serostatus of Brucella spp., Chlamydia abortus, Coxiella burnetii and Neospora caninum in cattle in three cantons in Bosnia and Herzegovina

description: Softic_BMC_raw_dataset; The raw dataset used in this study. (XLSX 147 kb)
DOI: 10.6084/m9.figshare.5852064.v1
title: Additional file 1: of The serostatus of Brucella spp., Chlamydia abortus, Coxiella burnetii and Neospora caninum in cattle in three cantons in Bosnia and Herzegovina

description: Softic_BMC_raw_dataset; The raw dataset used in this study. (XLSX 147 kb)
DOI: 10.6084/m9.figshare.5852055
title: Additional file 1: of The Japanese Clinical Practice Guidelines for Management of Sepsis and Septic Shock 2016 (J-SSCG 2016)

description: Financial and academic COIs and roles of committee members. (XLSX 30 kb)
DOI: 10.6084/m9.figshare.5852055.v1
title: Additional file 1: of The Japanese Clinical Practice Guidelines for Management of Sepsis and Septic Shock 2016 (J-SSCG 2016)

description: Financial and academic COIs and roles of committee members. (XLSX 30 kb)
DOI: 10.17608/k6.auckland.5852034
title: List of species endemic to each realm

description: This is a list of species that only occurred in each ot the marine realms in the following paper:<br>Costello MJ, Tsai P, Wong PS, Cheung A, Basher Z., Chaudhary C. 2017. Marine biogeographic realms and species endemicity. Nature Communications 8 (1057).<br>DOI; 10.1038/s41467-017-01121-2 <br>
DOI: 10.17608/k6.auckland.5852034.v1
title: List of species endemic to each realm

description: This is a list of species that only occurred in each ot the marine realms in the following paper:<br>Costello MJ, Tsai P, Wong PS, Cheung A, Basher Z., Chaudhary C. 2017. Marine biogeographic realms and species endemicity. Nature Communications 8 (1057).<br>DOI; 10.1038/s41467-017-01121-2 <br>
DOI: 10.6084/m9.figshare.5851884
title: follow17

description: See https://gitlab.com/mulsimco/follow17
DOI: 10.6084/m9.figshare.5851884.v1
title: follow17

description: See https://gitlab.com/mulsimco/follow17
DOI: 10.6084/m9.figshare.5851821
title: MSP Challenge 2050 food web review

description: The MSP Challenge 2050 serious game is being developed with the aim to provide maritime spatial planners the means to assess the environmental consequences of planning decisions in the marine and coastal ecosystem in space and time. The structure of the food web embedded in the MSP Challenge 2050 is a simplification of an EwE model of the North Sea (Mackinson and Daskalov, 2007), and model logic is loosely based on the Ecosim temporal model.<br><br>This review has been commissioned to answer four questions:<br>1. What are the advantages and disadvantages of the current food web model in the MSP Challenge 2050?<br>2. Is it correct that once the ecosystem in the food web model starts displaying a dropping trend, it is difficult to counter this trend? What could be done to fix this?<br>3. What type of (spatial) measures could enable players to benefit the ecosystem? <br>4. Other suggestions.<br>This review contains suggestions for modifications of the MSP Challenge 2050 software to mitigate problems. Please note that these suggestions, unless explicitly stated, aim to address structural computational issues without making the game more complex to play. <br>
DOI: 10.6084/m9.figshare.5851821.v2
title: MSP Challenge 2050 food web review

description: The MSP Challenge 2050 serious game is being developed with the aim to provide maritime spatial planners the means to assess the environmental consequences of planning decisions in the marine and coastal ecosystem in space and time. The structure of the food web embedded in the MSP Challenge 2050 is a simplification of an EwE model of the North Sea (Mackinson and Daskalov, 2007), and model logic is loosely based on the Ecosim temporal model.<br><br>This review has been commissioned to answer four questions:<br>1. What are the advantages and disadvantages of the current food web model in the MSP Challenge 2050?<br>2. Is it correct that once the ecosystem in the food web model starts displaying a dropping trend, it is difficult to counter this trend? What could be done to fix this?<br>3. What type of (spatial) measures could enable players to benefit the ecosystem? <br>4. Other suggestions.<br>This review contains suggestions for modifications of the MSP Challenge 2050 software to mitigate problems. Please note that these suggestions, unless explicitly stated, aim to address structural computational issues without making the game more complex to play. <br>
DOI: 10.25345/c5bx7k
title: MassIVE MSV000086039 - GNPS_Iridoids extract from Stereospermum accumuninatissimum.
title: A medium polar fraction from Stereospermum accuminatissimum containing Verminoside and specioside.
DOI: 10.6084/m9.figshare.5851734
title: The effect of temporal variation in sound exposure on swimming and foraging behaviour of captive zebrafish

description: Anthropogenic noise of variable temporal patterns is increasing in both marine and freshwater systems. Aquatic animals often rely on sounds for communication and orientation, which may therefore become more difficult. Predatoreprey interactions may be affected by masking of auditory cues, sound-related disturbance or attentional interference.
DOI: 10.6084/m9.figshare.5851707
title: ENCODE TF ChIP-seq data analysis

description: We downloaded 2,216 ChIP-seq experiment data from the ENCODE Project. The list of the data is in Supplementary Table S8. The data were lifted over from hg19 to hg38. We found overlapping peaks on four different categories: (1) 500bp upstream the promoter region of pcRNA-associated coding genes, (2) 500bp upstream promoter region of pcRNAs, (3) pcRNA genomic loci, and (4) pcRNA genomic loci but not overlapping with promoter region. To understand the correlation of TF binding patterns in the four categories, we made a binary matrix per category that consists of rows of TFs and columns of pcRNA/coding genes. Hence, the matrix contains connections between TF and pcRNA/associate coding genes. The matrix of category 2 is clustered by Euclidian Distance. To check the extent to which promoter sharing or proximity determines TFBS correlation, we also separated the clustered heat-map in the pcRNA bidirectional transcript (BIDIR) subgroup to the other subgroups (Non-BIDIR). To directly compare the TF binding patterns between each category, the other three matrices were sorted by the same order of the clustered matrix. We used the MatLab function corr2 to calculate r-value between category (1) and (2). We performed Monte Carlo simulation to calculate the p-value and test the significance of the r-value. <br>
DOI: 10.6084/m9.figshare.5851707.v1
title: ENCODE TF ChIP-seq data analysis

description: We downloaded 2,216 ChIP-seq experiment data from the ENCODE Project. The list of the data is in Supplementary Table S8. The data were lifted over from hg19 to hg38. We found overlapping peaks on four different categories: (1) 500bp upstream the promoter region of pcRNA-associated coding genes, (2) 500bp upstream promoter region of pcRNAs, (3) pcRNA genomic loci, and (4) pcRNA genomic loci but not overlapping with promoter region. To understand the correlation of TF binding patterns in the four categories, we made a binary matrix per category that consists of rows of TFs and columns of pcRNA/coding genes. Hence, the matrix contains connections between TF and pcRNA/associate coding genes. The matrix of category 2 is clustered by Euclidian Distance. To check the extent to which promoter sharing or proximity determines TFBS correlation, we also separated the clustered heat-map in the pcRNA bidirectional transcript (BIDIR) subgroup to the other subgroups (Non-BIDIR). To directly compare the TF binding patterns between each category, the other three matrices were sorted by the same order of the clustered matrix. We used the MatLab function corr2 to calculate r-value between category (1) and (2). We performed Monte Carlo simulation to calculate the p-value and test the significance of the r-value. <br>
DOI: 10.6084/m9.figshare.5851656
title: Saucedo et al 2019

description: Raw experimental data for publication.
DOI: 10.6084/m9.figshare.5851656.v1
title: Saucedo et al 2018

description: Raw experimental data for publication.
DOI: 10.6084/m9.figshare.5850342
title: HAL Workshop 1 Day 1

description: Audio Documentation of:Interdisciplinary perspectives: Machine Listening & Listening MachinesApril 27-28. Sussex Humanities Lab, University of Sussex, BrightonThe first workshop aims to lay the foundations for an interdisciplinary research agenda by bringing together researchers and practitioners from across music, humanities and computer science research to share archival, technical and critical perspectives on algorithmic listening.<em>What are the challenges and opportunities of working with large digital audio databases for humanities researchers, sound artists and archivists?</em><em>How is machine listening being applied in other areas of research and practice and what can we learn from this?</em><em>What are the cultural, epistemological or phenomenological implications of technologically mediated listening?</em><em>How can ideas from the history of philosophy of technology be applied to productively shape ethical and technical designs in the future?</em><em>How readily can digital audio software tools designed to classify, categorise and predict be used to afford discovery, reveal insights and new interpretations of sonic data?</em><em>What new approaches to the design of Listening Algorithms might historical or critical perspectives inspire? What new approaches to humanities research do Listening Algorithms inspire?</em>
DOI: 10.6084/m9.figshare.5850342.v1
title: HAL Workshop 1 Day 1

description: Audio Documentation of:Interdisciplinary perspectives: Machine Listening & Listening MachinesApril 27-28. Sussex Humanities Lab, University of Sussex, BrightonThe first workshop aims to lay the foundations for an interdisciplinary research agenda by bringing together researchers and practitioners from across music, humanities and computer science research to share archival, technical and critical perspectives on algorithmic listening.<em>What are the challenges and opportunities of working with large digital audio databases for humanities researchers, sound artists and archivists?</em><em>How is machine listening being applied in other areas of research and practice and what can we learn from this?</em><em>What are the cultural, epistemological or phenomenological implications of technologically mediated listening?</em><em>How can ideas from the history of philosophy of technology be applied to productively shape ethical and technical designs in the future?</em><em>How readily can digital audio software tools designed to classify, categorise and predict be used to afford discovery, reveal insights and new interpretations of sonic data?</em><em>What new approaches to the design of Listening Algorithms might historical or critical perspectives inspire? What new approaches to humanities research do Listening Algorithms inspire?</em>
DOI: 10.6084/m9.figshare.5850339
title: HAL Workshop 2 Day 1

description: Audio From:Understanding Distributed Agency Between Listening Algorithms and HumansMay 31-June 1 2017. Sonic Arts Research Centre, Queen’s University Belfast<em>What can improvisation and computer music performance practices teach us about human-machine agency?</em><em>How might this inform or challenge our understanding of how we can actively listen together with machines?</em><i><br></i>
DOI: 10.6084/m9.figshare.5850339.v1
title: HAL Workshop 2 Day 1

description: Audio From:Understanding Distributed Agency Between Listening Algorithms and HumansMay 31-June 1 2017. Sonic Arts Research Centre, Queen’s University Belfast<em>What can improvisation and computer music performance practices teach us about human-machine agency?</em><em>How might this inform or challenge our understanding of how we can actively listen together with machines?</em><i><br></i>
DOI: 10.6084/m9.figshare.5850267
title: Datafiles_PlosOne

description: PONE-D-17-18511R1 A smart all-in-one device to measure vital signs in admitted patientsDatafiles
DOI: 10.6084/m9.figshare.5850267.v1
title: Datafiles_PlosOne

description: PONE-D-17-18511R1 A smart all-in-one device to measure vital signs in admitted patientsDatafiles
DOI: 10.6084/m9.figshare.5850261
title: Review of the evidence of gender-focused interventions including men to reduce HIV risk and violence against women in sub-Saharan Africa

description: This review investigates gender-informed intervention studies conducted in sub-Saharan Africa that measure an outcome related to HIV. The review included 20,340 abstracts published between January 1990 and July 2015, 84 of which met our inclusion criteria for full review, resulting in 17 articles that are the current analysis. The findings demonstrate a wide variation in the types of interventions, from low-intensity educational content to multicomponent interventions. The review groups study outcomes into biological, HIV risk interventions, behavioral, violence, and risk reduction. Most interventions showed positive effects, and although research methodologies varied considerably, longer interventions appeared to be more effective. Cultural and behavioral practices require a multidimensional interventional approach to prevent the spread of HIV in sub-Saharan Africa. Studies of sexual violence, oppressive cultural norms, and cultural acceptance of men having multiple partners may contribute to disproportionate HIV rates in the region.
DOI: 10.6084/m9.figshare.5850261.v1
title: Review of the evidence of gender-focused interventions including men to reduce HIV risk and violence against women in sub-Saharan Africa

description: This review investigates gender-informed intervention studies conducted in sub-Saharan Africa that measure an outcome related to HIV. The review included 20,340 abstracts published between January 1990 and July 2015, 84 of which met our inclusion criteria for full review, resulting in 17 articles that are the current analysis. The findings demonstrate a wide variation in the types of interventions, from low-intensity educational content to multicomponent interventions. The review groups study outcomes into biological, HIV risk interventions, behavioral, violence, and risk reduction. Most interventions showed positive effects, and although research methodologies varied considerably, longer interventions appeared to be more effective. Cultural and behavioral practices require a multidimensional interventional approach to prevent the spread of HIV in sub-Saharan Africa. Studies of sexual violence, oppressive cultural norms, and cultural acceptance of men having multiple partners may contribute to disproportionate HIV rates in the region.
DOI: 10.6084/m9.figshare.5850228
title: Geochronological data. Tectonic evolution of syn- to late-orogenic sedimentary–volcanic basins in the central Norwegian Caledonides

description: Geochronological data from LA–ICP–MS analysis of zircons.
DOI: 10.6084/m9.figshare.5850228.v1
title: Geochronological data. Tectonic evolution of syn- to late-orogenic sedimentary–volcanic basins in the central Norwegian Caledonides

description: Geochronological data from LA–ICP–MS analysis of zircons.
DOI: 10.6084/m9.figshare.5850177
title: stones.jpg

description: Close up of rounded pebbles from a stone beach in Denmark
DOI: 10.6084/m9.figshare.5850051
title: Relationship between disease activity and patient-reported outcomes in rheumatoid arthritis: <i>Post hoc</i> analyses of overall and Japanese results from two phase 3 clinical trials

description: <b>Objective:</b> To examine patient-reported outcomes (PROs) in patients with different rheumatoid arthritis (RA) disease activity levels and identify residual symptoms. <b>Methods:</b><i>Post hoc</i> analyses of overall and Japanese data from two randomized controlled trials including RA patients with previous inadequate responses to methotrexate (NCT01710358) or no/minimal previous disease-modifying antirheumatic drug treatment (NCT01711359) (sponsor: Eli Lilly and Company). Week 24 assessments were disease activity (Simplified Disease Activity Index, Disease Activity Score/Disease Activity Score 28 joints-erythrocyte sedimentation rate) and PROs (pain visual analog scale [VAS], morning joint stiffness [MJS], Health Assessment Questionnaire-Disability Index, Functional Assessment of Chronic Illness Therapy-Fatigue, and Medical Outcomes Study Short Form 36 Health Survey Physical and Mental Component Scores). <b>Results:</b> Patients achieving remission/low disease activity (LDA) at Week 24 had larger/significant improvements from baseline in pain, MJS, disability, fatigue, and physical and emotional quality of life versus patients with high/moderate disease activity. Some patients achieving remission and LDA, reported residual pain (pain VAS &gt;10 mm): 20.8–39.3% and 48.7–70.0% (overall study populations), 16.0–34.5% and 47.1–62.0% (Japanese patients). Residual MJS and fatigue were also reported. <b>Conclusion:</b> Remission/LDA were associated with improvements in PROs in overall and Japanese patient populations; however, some patients achieving remission had residual symptoms, including pain.