cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.7910/dvn/v1rjpf/q0zmda
title: ykc20160308_03.txt.gz

description: :unav
DOI: 10.7910/dvn/v1rjpf/esbojz
title: ykc20170112_03.txt.gz

description: :unav
DOI: 10.7910/dvn/v1rjpf/iqys61
title: ykc20170313_03.txt.gz

description: :unav
DOI: 10.6084/m9.figshare.4003359
title: News stories as evidence for research? BBC citations from articles, books and Wikipedia

description: Although news stories target the general public and are sometimes inaccurate, they can serve as sources of real-world information for researchers. This article investigates the extent to which academics exploit journalism using content and citation analyses of online BBC News stories cited by Scopus articles. A total of 27,234 Scopus-indexed publications have cited at least one BBC News story, with a steady annual increase. Citations from arts and humanities (2.8% of publications in 2015) and social sciences (1.5%) were more likely than citations from medicine (0.1%) and science (&lt;0.1%). Surprisingly, half of the sampled Scopus-cited science and technology (53%) and medicine and health (47%) stories were based on academic research, rather than otherwise unpublished information, suggesting that researchers have chosen a lower quality secondary source for their citations. Nevertheless, the BBC News stories that were most frequently cited by Scopus, Google Books and Wikipedia introduced new information from many different topics, including politics, business, economics, statistics, and reports about events. Thus, news stories are mediating real world knowledge into the academic domain, a potential cause for concern.
DOI: 10.7910/dvn/v1rjpf/mcnq8f
title: ykc20170320_03.txt.gz

description: :unav
DOI: 10.6084/m9.figshare.4003359.v1
title: News stories as evidence for research? BBC citations from articles, books and Wikipedia

description: Although news stories target the general public and are sometimes inaccurate, they can serve as sources of real-world information for researchers. This article investigates the extent to which academics exploit journalism using content and citation analyses of online BBC News stories cited by Scopus articles. A total of 27,234 Scopus-indexed publications have cited at least one BBC News story, with a steady annual increase. Citations from arts and humanities (2.8% of publications in 2015) and social sciences (1.5%) were more likely than citations from medicine (0.1%) and science (&lt;0.1%). Surprisingly, half of the sampled Scopus-cited science and technology (53%) and medicine and health (47%) stories were based on academic research, rather than otherwise unpublished information, suggesting that researchers have chosen a lower quality secondary source for their citations. Nevertheless, the BBC News stories that were most frequently cited by Scopus, Google Books and Wikipedia introduced new information from many different topics, including politics, business, economics, statistics, and reports about events. Thus, news stories are mediating real world knowledge into the academic domain, a potential cause for concern.
DOI: 10.7910/dvn/v1rjpf/yhbld7
title: ykc20160822_03.txt.gz

description: :unav
DOI: 10.7910/dvn/v1rjpf/rijmtr
title: ykc20171223_03.txt.gz

description: :unav
DOI: 10.7910/dvn/v1rjpf/dzp0u9
title: ykc20171120_03.txt.gz

description: :unav
DOI: 10.7910/dvn/v1rjpf/ayo6ul
title: ykc20160814_03.txt.gz

description: :unav
DOI: 10.6084/m9.figshare.4003347.v2
title: msigDB-To-Geneset

description: Script that converts msigDB '.gmt' files into a tab-delimited gene-set ready for use in 'Genomica'
DOI: 10.7910/dvn/v1rjpf/cut7c9
title: ykc20171227_03.txt.gz

description: :unav
DOI: 10.7910/dvn/v1rjpf/sejbpy
title: ykc20170421_03.txt.gz

description: :unav
DOI: 10.6084/m9.figshare.4003347.v3
title: msigDB-To-Geneset

description: Script that converts msigDB '.gmt' files into a tab-delimited gene-set ready for use in 'Genomica'
DOI: 10.7910/dvn/v1rjpf/lxheax
title: ykc20171128_03.txt.gz

description: :unav
DOI: 10.7910/dvn/v1rjpf/ayr4xd
title: ykc20160715_03.txt.gz

description: :unav
DOI: 10.7910/dvn/v1rjpf/tbzts6
title: ykc20170531_03.txt.gz

description: :unav
DOI: 10.7910/dvn/v1rjpf/0lluvu
title: ykc20161205_03.txt.gz

description: :unav
DOI: 10.6084/m9.figshare.4001454
title: Computed tomography for the diagnosis of varices in liver cirrhosis: a systematic review and meta-analysis of observational studies

description: <b>Objectives:</b> This systematic review and meta-analysis aimed to evaluate the diagnostic accuracy of contrast-enhanced computed tomography (CT) for varices in liver cirrhosis. <b>Methods</b>: PubMed and EMBASE databases were searched for the literature identification. The area under the summary receiver operating characteristic curve (AUSROC), sensitivity, specificity, positive and negative likelihood ratio (PLR and NLR), and diagnostic odds ratio (DOR) were calculated. We performed the subgroup analyses according to the location of varices, CT technique, and study design. The study quality was assessed according to the QUADAS-2 tool. <b>Results:</b> Seventeen papers were eligible. The study quality was modest. The AUSROC was 0.8975 and 0.9494 for predicting any size and high-risk varices, respectively. Summary sensitivity, specificity, PLR, NLR, and DOR of CT for predicting any size and high-risk varices were 0.87/0.80/3.67/0.18/22.70 and 0.87/0.88/7.52/0.12/65.55, respectively. According to the location of varices, the AUSROC was 0.9127 for predicting any size gastric varices alone; and the AUSROC was 0.8958 and 0.9461 for predicting any size and high-risk esophageal varices alone, respectively. According to the CT technique, the AUSROC of multi-detector CT (MDCT) was 0.9047 and 0.9490 for predicting any size and high-risk varices, respectively; and the AUSROC of MDCT esophagograms for predicting any size and high-risk varices was 0.8735 and 0.9664, respectively. In the subgroup analysis of prospective studies, the AUSROC was 0.9122 and 0.9507 for predicting any size and high-risk varices, respectively. <b>Conclusion:</b> CT had a high accuracy for the diagnosis of varices in liver cirrhosis.
DOI: 10.6084/m9.figshare.4001454.v1
title: Computed tomography for the diagnosis of varices in liver cirrhosis: a systematic review and meta-analysis of observational studies

description: <b>Objectives:</b> This systematic review and meta-analysis aimed to evaluate the diagnostic accuracy of contrast-enhanced computed tomography (CT) for varices in liver cirrhosis. <b>Methods</b>: PubMed and EMBASE databases were searched for the literature identification. The area under the summary receiver operating characteristic curve (AUSROC), sensitivity, specificity, positive and negative likelihood ratio (PLR and NLR), and diagnostic odds ratio (DOR) were calculated. We performed the subgroup analyses according to the location of varices, CT technique, and study design. The study quality was assessed according to the QUADAS-2 tool. <b>Results:</b> Seventeen papers were eligible. The study quality was modest. The AUSROC was 0.8975 and 0.9494 for predicting any size and high-risk varices, respectively. Summary sensitivity, specificity, PLR, NLR, and DOR of CT for predicting any size and high-risk varices were 0.87/0.80/3.67/0.18/22.70 and 0.87/0.88/7.52/0.12/65.55, respectively. According to the location of varices, the AUSROC was 0.9127 for predicting any size gastric varices alone; and the AUSROC was 0.8958 and 0.9461 for predicting any size and high-risk esophageal varices alone, respectively. According to the CT technique, the AUSROC of multi-detector CT (MDCT) was 0.9047 and 0.9490 for predicting any size and high-risk varices, respectively; and the AUSROC of MDCT esophagograms for predicting any size and high-risk varices was 0.8735 and 0.9664, respectively. In the subgroup analysis of prospective studies, the AUSROC was 0.9122 and 0.9507 for predicting any size and high-risk varices, respectively. <b>Conclusion:</b> CT had a high accuracy for the diagnosis of varices in liver cirrhosis.
DOI: 10.7910/dvn/v1rjpf/fscxsk
title: ykc20160510_03.txt.gz

description: :unav
DOI: 10.6084/m9.figshare.4001451
title: Defining the performance parameters of a rapid screening tool for myotonic dystrophy type 1 based on triplet-primed PCR and melt curve analysis

description: <b>Background:</b><i>DMPK</i> CTG-repeat expansions that cause myotonic dystrophy type 1 (DM1) can be detected more rapidly, cost-effectively, and simply by combining triplet-primed PCR (TP-PCR) with melting curve analysis (MCA). We undertook a detailed technical validation study to define the optimal operational parameters for performing bidirectional TP-PCR MCA assays. <b>Methods:</b> We determined the assays’ analytic specificity and sensitivity, assessed the effect of reaction volumes, DNA diluents, and common contaminants on melt peak temperature, determined the assays’ sensitivity in detecting low-level mosaicism for repeat expansion, and evaluated their performance on two real-time PCR platforms. <b>Results:</b> Both assays were highly specific and sensitive, and performed optimally under a broad range of parameters. Bidirectional TP-PCR MCA analysis also reduces the risk of generating false-negative results associated with the rare CCG-interruptions that may be present at either end of expanded alleles. <b>Conclusion:</b> The <i>DMPK</i> TP-PCR MCA is a highly specific, sensitive, and significantly cost-saving screening tool for DM1.
DOI: 10.7910/dvn/v1rjpf/waphva
title: ykc20160709_03.txt.gz

description: :unav
DOI: 10.6084/m9.figshare.4001451.v1
title: Defining the performance parameters of a rapid screening tool for myotonic dystrophy type 1 based on triplet-primed PCR and melt curve analysis

description: <b>Background:</b><i>DMPK</i> CTG-repeat expansions that cause myotonic dystrophy type 1 (DM1) can be detected more rapidly, cost-effectively, and simply by combining triplet-primed PCR (TP-PCR) with melting curve analysis (MCA). We undertook a detailed technical validation study to define the optimal operational parameters for performing bidirectional TP-PCR MCA assays. <b>Methods:</b> We determined the assays’ analytic specificity and sensitivity, assessed the effect of reaction volumes, DNA diluents, and common contaminants on melt peak temperature, determined the assays’ sensitivity in detecting low-level mosaicism for repeat expansion, and evaluated their performance on two real-time PCR platforms. <b>Results:</b> Both assays were highly specific and sensitive, and performed optimally under a broad range of parameters. Bidirectional TP-PCR MCA analysis also reduces the risk of generating false-negative results associated with the rare CCG-interruptions that may be present at either end of expanded alleles. <b>Conclusion:</b> The <i>DMPK</i> TP-PCR MCA is a highly specific, sensitive, and significantly cost-saving screening tool for DM1.
DOI: 10.7910/dvn/v1rjpf/al0mpb
title: ykc20170412_03.txt.gz

description: :unav
DOI: 10.6084/m9.figshare.4001445
title: Physical performance measures for predicting outcome in cancer patients: a systematic review

description: <b>Background:</b> Decision making regarding cancer treatment is challenging and there is a need for clinical parameters that can guide these decisions. As physical performance appears to be a reflection of health status, the aim of this systematic review is to assess whether physical performance tests (PPTs) are predictive of the clinical outcome and treatment tolerance in cancer patients. <b>Methods:</b> A literature search was conducted on 2 April 2015 in the electronic databases Medline and Embase to identify studies focusing on the association between objectively measured PPTs and outcome. No limitations in language or publication dates were applied. <b>Results:</b> The search retrieved 9680 articles, 16 publications were included involving 4187 patients with various cancer types and different treatments. Reported median or mean age varied from 58 to 78 years. Nine studies used the Timed Up & Go (TUG) test, five the Short Physical Performance Battery (SPPB) and five studies focused on gait speed. Poorer TUG, SPPB and gait speed outcome were associated with decreased survival. TUG, SPPB and gait speed were also associated with treatment-related complications. Furthermore, two studies reported an association between poorer TUG and SPPB outcome with higher rates of functional decline. <b>Conclusion:</b> PPTs appear to show a significant correlation with survival and these tests could be used as a prognostic tool, particular for older adult patients. A less explicit correlation for treatment-related complications and functional decline was also found. To optimize decision making, future research should focus on developing and validating individualized treatment algorithms that incorporate PPTs in addition to cancer- and treatment-related variables.
DOI: 10.7910/dvn/v1rjpf/y7xrx9
title: ykc20170330_03.txt.gz

description: :unav
DOI: 10.6084/m9.figshare.4001445.v1
title: Physical performance measures for predicting outcome in cancer patients: a systematic review

description: <b>Background:</b> Decision making regarding cancer treatment is challenging and there is a need for clinical parameters that can guide these decisions. As physical performance appears to be a reflection of health status, the aim of this systematic review is to assess whether physical performance tests (PPTs) are predictive of the clinical outcome and treatment tolerance in cancer patients. <b>Methods:</b> A literature search was conducted on 2 April 2015 in the electronic databases Medline and Embase to identify studies focusing on the association between objectively measured PPTs and outcome. No limitations in language or publication dates were applied. <b>Results:</b> The search retrieved 9680 articles, 16 publications were included involving 4187 patients with various cancer types and different treatments. Reported median or mean age varied from 58 to 78 years. Nine studies used the Timed Up & Go (TUG) test, five the Short Physical Performance Battery (SPPB) and five studies focused on gait speed. Poorer TUG, SPPB and gait speed outcome were associated with decreased survival. TUG, SPPB and gait speed were also associated with treatment-related complications. Furthermore, two studies reported an association between poorer TUG and SPPB outcome with higher rates of functional decline. <b>Conclusion:</b> PPTs appear to show a significant correlation with survival and these tests could be used as a prognostic tool, particular for older adult patients. A less explicit correlation for treatment-related complications and functional decline was also found. To optimize decision making, future research should focus on developing and validating individualized treatment algorithms that incorporate PPTs in addition to cancer- and treatment-related variables.
DOI: 10.6084/m9.figshare.4001349
title: Link prediction in multilayered network

description: Dataset consists of 5 files.<br> First 4 files describe protein-protein interactions(PPI) in homo sapiens. They are obtained from IntAct database(http://www.ebi.ac.uk/intact/).Selected interaction are filtered based on MI score &gt;= 0.45 from IntAct and considered to be highly confident.<br>Protein names are translated to unique Ensemble(http://www.ensembl.org/index.html) gene identifiers (ENSG). 1. Dataset containing expert curated interactions related to Parkinson's disease parkinson_intact_int_PPI.txt<br>2. All highly confident interactions in hs available in IntAct database intact_int.txt<br>3. Aumatically curated interactions related to synaptic activity synapse_intact_int.txt<br>4. Dataset containing expert curated interactions related to Alzheimer's diseasealz_intact_int_PPI.txtThe 5th file describes genes, that are coexpressed in the Alzheimer's patients and healthy individuals.<br>Correlation profiles are calculated using the set of microarray data obtained from ArrayExpress database (https://www.ebi.ac.uk/arrayexpress/). Final coexpression score is calculated by applying Robust Rank Aggregation method to aggregate correlation scores in individual microarray datasets.Coexpression scores are filtered based on pvalue &lt;=0.00001.<br>Gene names are translated to unique Ensemble(http://www.ensembl.org/index.html) gene identifiers (ENSG). alzcoexp_int_31052016.txt
DOI: 10.7910/dvn/v1rjpf/qdhbib
title: ykc20170617_03.txt.gz

description: :unav
DOI: 10.7910/dvn/v1rjpf/d2w47s
title: ykc20160808_03.txt.gz

description: :unav
DOI: 10.6084/m9.figshare.4001349.v1
title: Link prediction in multilayered network

description: Dataset consists of 5 files.<br> First 4 files describe protein-protein interactions(PPI) in homo sapiens. They are obtained from IntAct database(http://www.ebi.ac.uk/intact/).Selected interaction are filtered based on MI score &gt;= 0.45 from IntAct and considered to be highly confident.<br>Protein names are translated to unique Ensemble(http://www.ensembl.org/index.html) gene identifiers (ENSG). 1. Dataset containing expert curated interactions related to Parkinson's disease parkinson_intact_int_PPI.txt<br>2. All highly confident interactions in hs available in IntAct database intact_int.txt<br>3. Aumatically curated interactions related to synaptic activity synapse_intact_int.txt<br>4. Dataset containing expert curated interactions related to Alzheimer's diseasealz_intact_int_PPI.txtThe 5th file describes genes, that are coexpressed in the Alzheimer's patients and healthy individuals.<br>Correlation profiles are calculated using the set of microarray data obtained from ArrayExpress database (https://www.ebi.ac.uk/arrayexpress/). Final coexpression score is calculated by applying Robust Rank Aggregation method to aggregate correlation scores in individual microarray datasets.Coexpression scores are filtered based on pvalue &lt;=0.00001.<br>Gene names are translated to unique Ensemble(http://www.ensembl.org/index.html) gene identifiers (ENSG). alzcoexp_int_31052016.txt
DOI: 10.7910/dvn/v1rjpf/dk4vai
title: ykc20161111_03.txt.gz

description: :unav
DOI: 10.6084/m9.figshare.4001349.v2
title: Link prediction in multilayered network

description: Dataset consists of 5 files.<br> First 4 files describe protein-protein interactions(PPI) in homo sapiens. They are obtained from IntAct database(http://www.ebi.ac.uk/intact/).Selected interaction are filtered based on MI score &gt;= 0.45 from IntAct and considered to be highly confident.<br>Protein names are translated to unique Ensemble(http://www.ensembl.org/index.html) gene identifiers (ENSG). 1. Dataset containing expert curated interactions related to Parkinson's disease parkinson_intact_int_PPI.txt<br>2. All highly confident interactions in hs available in IntAct database intact_int.txt<br>3. Aumatically curated interactions related to synaptic activity synapse_intact_int.txt<br>4. Dataset containing expert curated interactions related to Alzheimer's diseasealz_intact_int_PPI.txtThe 5th file describes genes, that are coexpressed in the Alzheimer's patients and healthy individuals.<br>Correlation profiles are calculated using the set of microarray data obtained from ArrayExpress database (https://www.ebi.ac.uk/arrayexpress/). Final coexpression score is calculated by applying Robust Rank Aggregation method to aggregate correlation scores in individual microarray datasets.Coexpression scores are filtered based on pvalue &lt;=0.00001.<br>Gene names are translated to unique Ensemble(http://www.ensembl.org/index.html) gene identifiers (ENSG). alzcoexp_int_31052016.txt
DOI: 10.7910/dvn/v1rjpf/0mkgww
title: ykc20160906_03.txt.gz

description: :unav
DOI: 10.6084/m9.figshare.4001349.v3
title: Link prediction in multilayered network

description: Dataset consists of 5 files.<br> First 4 files describe protein-protein interactions(PPI) in homo sapiens. They are obtained from IntAct database(http://www.ebi.ac.uk/intact/).Selected interaction are filtered based on MI score &gt;= 0.45 from IntAct and considered to be highly confident.<br>Protein names are translated to unique Ensemble(http://www.ensembl.org/index.html) gene identifiers (ENSG). 1. Dataset containing expert curated interactions related to Parkinson's disease parkinson_intact_int_PPI.txt<br>2. All highly confident interactions in hs available in IntAct database intact_int.txt<br>3. Aumatically curated interactions related to synaptic activity synapse_intact_int.txt<br>4. Dataset containing expert curated interactions related to Alzheimer's diseasealz_intact_int_PPI.txtThe 5th file describes genes, that are coexpressed in the Alzheimer's patients and healthy individuals.<br>Correlation profiles are calculated using the set of microarray data obtained from ArrayExpress database (https://www.ebi.ac.uk/arrayexpress/). Final coexpression score is calculated by applying Robust Rank Aggregation method to aggregate correlation scores in individual microarray datasets.Coexpression scores are filtered based on pvalue &lt;=0.00001.<br>Gene names are translated to unique Ensemble(http://www.ensembl.org/index.html) gene identifiers (ENSG). alzcoexp_int_31052016.txt
DOI: 10.7910/dvn/v1rjpf/5497wp
title: ykc20171207_03.txt.gz

description: :unav
DOI: 10.7910/dvn/v1rjpf/sxcxj8
title: ykc20160514_03.txt.gz

description: :unav
DOI: 10.7910/dvn/v1rjpf/3qmtub
title: ykc20170622_03.txt.gz

description: :unav
DOI: 10.7910/dvn/v1rjpf/hgu9kf
title: ykc20160526_03.txt.gz

description: :unav
DOI: 10.7910/dvn/v1rjpf/oxp8n4
title: ykc20160105_03.txt.gz

description: :unav
DOI: 10.7910/dvn/v1rjpf/urbrct
title: ykc20160731_03.txt.gz

description: :unav
DOI: 10.7910/dvn/v1rjpf/pzdr1x
title: ykc20170515_03.txt.gz

description: :unav
DOI: 10.7910/dvn/v1rjpf/8a5bjj
title: ykc20170928_03.txt.gz

description: :unav
DOI: 10.7910/dvn/v1rjpf/qpwexi
title: ykc20160519_03.txt.gz

description: :unav
DOI: 10.7910/dvn/v1rjpf/yz8rsw
title: ykc20160414_03.txt.gz

description: :unav
DOI: 10.7910/dvn/v1rjpf/zu0nqy
title: ykc20170212_03.txt.gz

description: :unav
DOI: 10.7910/dvn/v1rjpf/ytye2d
title: ykc20170815_03.txt.gz

description: :unav
DOI: 10.6084/m9.figshare.4001265
title: Theoretical and experimental vibrational property of 1,3,4,6-tetramethylpiperazine-2,5-dione

description: 1,3,4,6-tetramethylpiperazine-2,5-dione was synthesized, and the crystal structure was characterized by single-crystal X-ray diffraction method, vibrational spectral measurements were obtained by Fourier transform infrared spectroscopy and Fourier transform Raman spectroscopy. The measurements agree well with the calculated geometrical structure and harmonic vibrational wavenumbers (using<i>ab initio</i> and density functional theory Becke’s three parameters hybrid method with the Lee, Yang, and Parr non-local functions methods with 6-311G and 6-311G** basis sets).
DOI: 10.7910/dvn/v1rjpf/e0zxsd
title: ykc20170510_03.txt.gz

description: :unav
DOI: 10.6084/m9.figshare.4001265.v1
title: Theoretical and Experimental Vibrational Property of 1,3,4,6- Tetramethylpiperazine-2,5-dione

description: 1,3,4,6–tetramethylpiperazine-2,5-dione was synthesized, and the crystal structure was characterized by single crystal X-ray diffraction method, vibrational spectral measurements were obtained by Fourier transform infrared spectoscopy and Fourier transform raman spectroscopy. The measurements agree well with the calculated geometrical structure and harmonic vibrational wavenumbers (using <i>ab initio</i> and density functional theory Becke's three parameters hybrid method with the Lee, Yang and Parr non-local functions methods with 6-311 G and 6-311G** basis sets).
DOI: 10.7910/dvn/v1rjpf/tcofbp
title: ykc20160622_03.txt.gz

description: :unav
DOI: 10.7910/dvn/v1rjpf/b0uio8
title: ykc20160419_03.txt.gz

description: :unav
DOI: 10.7910/dvn/v1rjpf/9bcu8f
title: ykc20161115_03.txt.gz

description: :unav
DOI: 10.7910/dvn/v1rjpf/o3m8n6
title: ykc20170518_03.txt.gz

description: :unav
DOI: 10.7910/dvn/v1rjpf/zyqlkt
title: ykc20170115_03.txt.gz

description: :unav
DOI: 10.7910/dvn/v1rjpf/4aycux
title: ykc20171029_03.txt.gz

description: :unav
DOI: 10.7910/dvn/v1rjpf/ogyvv6
title: ykc20160702_03.txt.gz

description: :unav
DOI: 10.7910/dvn/v1rjpf/lm5vjq
title: ykc20161206_03.txt.gz

description: :unav
DOI: 10.7910/dvn/v1rjpf/jl3cmk
title: ykc20170822_03.txt.gz

description: :unav