cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.9901763
title: Metadata record for: Compendiums of cancer transcriptomes for machine learning applications

description: This dataset contains key characteristics about the data described in the Data Descriptor Compendiums of cancer transcriptomes for machine learning applications. <br> Contents: <br> 1. human readable metadata summary table in CSV format 2. machine readable metadata file in JSON format 3. machine readable metadata file in ISA-Tab format (zipped folder)<br><br>Versioning Note:A revised version was generated when the metadata format was updated from JSON to JSON-LD. This was an automatic process that changed only the format, not the contents, of the metadata.<br>
DOI: 10.6084/m9.figshare.9901838.v1
title: Metadata record for: Linkage Disequilibrium Maps for European and African Populations Constructed from Whole Genome Sequence Data

description: This dataset contains key characteristics about the data described in the Data Descriptor Linkage Disequilibrium Maps for European and African Populations Constructed from Whole Genome Sequence Data. <br> Contents: <br> 1. human readable metadata summary table in CSV format 2. machine readable metadata file in JSON format <br> <br> <br>
DOI: 10.6084/m9.figshare.9901763.v1
title: Metadata record for: Compendiums of cancer transcriptomes for machine learning applications

description: This dataset contains key characteristics about the data described in the Data Descriptor Compendiums of cancer transcriptomes for machine learning applications. <br> Contents: <br> 1. human readable metadata summary table in CSV format 2. machine readable metadata file in JSON format 3. machine readable metadata file in ISA-Tab format (zipped folder)<br><br>Versioning Note:A revised version was generated when the metadata format was updated from JSON to JSON-LD. This was an automatic process that changed only the format, not the contents, of the metadata.<br>
DOI: 10.6084/m9.figshare.9901709
title: Supplementary Material for: Associations of Urine Biomarkers with Kidney Function Decline in HIV-Infected and Uninfected Men

description: <b><i>Background:</i></b> HIV-infected (HIV+) persons are at increased risk of chronic kidney disease, but serum creatinine does not detect early losses in kidney function. We hypothesized that urine biomarkers of kidney damage would be associated with subsequent changes in kidney function in a contemporary cohort of HIV+ and HIV-uninfected (HIV–) men. <b><i>Methods:</i></b> In the Multicenter AIDS Cohort Study, we measured baseline urine concentrations of 5 biomarkers from 2009 to 2011 in 860 HIV+ and 337 HIV– men: albumin, alpha-1-microglobulin (α1m), interleukin-18 (IL-18), kidney injury molecule-1 (KIM-1), and procollagen type III N-terminal propeptide (PIIINP). We evaluated associations of urine biomarker concentrations with annual changes in estimated glomerular filtration rate (eGFR) using multivariable linear mixed models adjusted for demographics, traditional kidney disease risk factors, HIV-related risk factors, and baseline eGFR. <b><i>Results:</i></b> Over a median follow-up of 4.8 years, the average annual eGFR decline was 1.42 mL/min/1.73 m<sup>2</sup>/year in HIV+ men and 1.22 mL/min/1.73 m<sup>2</sup>/year in HIV– men. Among HIV+ men, the highest vs. lowest tertiles of albumin (–1.78 mL/min/1.73 m<sup>2</sup>/year, 95% CI –3.47 to –0.09) and α1m (–2.43 mL/min/1.73 m<sup>2</sup>/year, 95% CI –4.14 to –0.73) were each associated with faster annual eGFR declines after multivariable adjustment. Among HIV– men, the highest vs. lowest tertile of α1m (–2.49 mL/min/1.73 m<sup>2</sup>/year, 95% CI –4.48 to –0.50) was independently associated with faster annual eGFR decline. Urine IL-18, KIM-1, and PIIINP showed no independent associations with eGFR decline, regardless of HIV serostatus. <b><i>Conclusions:</i></b> Among HIV+ men, higher urine albumin and α1m are associated with subsequent declines in kidney function, independent of eGFR.
DOI: 10.6084/m9.figshare.9901709.v1
title: Supplementary Material for: Associations of Urine Biomarkers with Kidney Function Decline in HIV-Infected and Uninfected Men

description: <b><i>Background:</i></b> HIV-infected (HIV+) persons are at increased risk of chronic kidney disease, but serum creatinine does not detect early losses in kidney function. We hypothesized that urine biomarkers of kidney damage would be associated with subsequent changes in kidney function in a contemporary cohort of HIV+ and HIV-uninfected (HIV–) men. <b><i>Methods:</i></b> In the Multicenter AIDS Cohort Study, we measured baseline urine concentrations of 5 biomarkers from 2009 to 2011 in 860 HIV+ and 337 HIV– men: albumin, alpha-1-microglobulin (α1m), interleukin-18 (IL-18), kidney injury molecule-1 (KIM-1), and procollagen type III N-terminal propeptide (PIIINP). We evaluated associations of urine biomarker concentrations with annual changes in estimated glomerular filtration rate (eGFR) using multivariable linear mixed models adjusted for demographics, traditional kidney disease risk factors, HIV-related risk factors, and baseline eGFR. <b><i>Results:</i></b> Over a median follow-up of 4.8 years, the average annual eGFR decline was 1.42 mL/min/1.73 m<sup>2</sup>/year in HIV+ men and 1.22 mL/min/1.73 m<sup>2</sup>/year in HIV– men. Among HIV+ men, the highest vs. lowest tertiles of albumin (–1.78 mL/min/1.73 m<sup>2</sup>/year, 95% CI –3.47 to –0.09) and α1m (–2.43 mL/min/1.73 m<sup>2</sup>/year, 95% CI –4.14 to –0.73) were each associated with faster annual eGFR declines after multivariable adjustment. Among HIV– men, the highest vs. lowest tertile of α1m (–2.49 mL/min/1.73 m<sup>2</sup>/year, 95% CI –4.48 to –0.50) was independently associated with faster annual eGFR decline. Urine IL-18, KIM-1, and PIIINP showed no independent associations with eGFR decline, regardless of HIV serostatus. <b><i>Conclusions:</i></b> Among HIV+ men, higher urine albumin and α1m are associated with subsequent declines in kidney function, independent of eGFR.
DOI: 10.6084/m9.figshare.9901472
title: Phenotypic and genotypic data

description: Raw Data of the following article (currently in preprint in bioRxiv): Common gardens in teosintes reveal the establishment of a syndrome of adaptation to altitude.
DOI: 10.6084/m9.figshare.9901472.v1
title: Phenotypic and genotypic data

description: Raw Data of the following article (currently in preprint in bioRxiv): Common gardens in teosintes reveal the establishment of a syndrome of adaptation to altitude.
DOI: 10.6084/m9.figshare.9901421
title: Enteric Fever Challenge Participant Survey Data

description: Participant questionnaire raw data from typhoid/paratyphoid challenge studies. Completed at day 28 or 60. Ethics approval for data collection tool received from South Central Oxfordshire Research Ethics Committee A.
DOI: 10.6084/m9.figshare.9901421.v1
title: Enteric Fever Challenge Participant Survey Data

description: Participant questionnaires from typhoid/paratyphoid challenge studies. Completed at day 28 or 60. Ethics approval for data collection tool received from South Central Oxfordshire Research Ethics Committee A.
DOI: 10.25392/leicester.data.9901388
title: uta_20180821_vv.pgd.gz

description: Repaired version of the UTA datadump uta_20180821.pgd.gz. Specifically, corrects the lacking REFRESH MATERIALIZED VIEWS. Will be required for VariantValidator and VerisntValidator in docker.<br>VariantValidator available at:https://github.com/openvar/variantValidator
DOI: 10.25392/leicester.data.9901388.v1
title: uta_20180821_vv.pgd.gz

description: Repaired version of the UTA datadump uta_20180821.pgd.gz. Specifically, corrects the lacking REFRESH MATERIALIZED VIEWS. Will be required for VariantValidator and VerisntValidator in docker.<br>VariantValidator available at:https://github.com/openvar/variantValidator
DOI: 10.6084/m9.figshare.9901376
title: Positive association between cerebral grey matter metabolism and dopamine D<sub>2</sub>/D<sub>3</sub> receptor availability in healthy and schizophrenia subjects: An <sup>18</sup>F-fluorodeoxyglucose and <sup>18</sup>F-fallypride positron emission tomography study

description: <b>Objectives:</b> Overlapping decreases in extrastriatal dopamine D<sub>2</sub>/D<sub>3</sub>-receptor availability and glucose metabolism have been reported in subjects with schizophrenia. It remains unknown whether these findings are physiologically related or coincidental. <b>Methods:</b> To ascertain this, we used two consecutive <sup>18</sup>F-fluorodeoxyglucose and <sup>18</sup>F-fallypride positron emission tomography scans in 19 healthy and 25 unmedicated schizophrenia subjects. Matrices of correlations between <sup>18</sup>F-fluorodeoxyglucose uptake and <sup>18</sup>F-fallypride binding in voxels at the same xyz location and AFNI-generated regions of interest were evaluated in both diagnostic groups. <b>Results:</b><sup>18</sup>F-fluorodeoxyglucose uptake and <sup>18</sup>F-fallypride binding potential were predominantly positively correlated across the striatal and extrastriatal grey matter in both healthy and schizophrenia subjects. In comparison to healthy subjects, significantly weaker correlations in subjects with schizophrenia were confirmed in the right cingulate gyrus and thalamus, including the mediodorsal, lateral dorsal, anterior, and midline nuclei. Schizophrenia subjects showed decreased D<sub>2</sub>/D<sub>3</sub>-receptor availability in the hypothalamus, mamillary bodies, thalamus and several thalamic nuclei, and increased glucose uptake in three lobules of the cerebellar vermis. <b>Conclusions:</b> Dopaminergic system may be involved in modulation of grey matter metabolism and neurometabolic coupling in both healthy human brain and psychopathology. Hyperdopaminergic state in untreated schizophrenia may at least partly account for the corresponding decreases in grey matter metabolism.
DOI: 10.6084/m9.figshare.9901367
title: Evaluation of pyrazolopyrimidine derivatives as microtubule affinity regulating kinase 4 inhibitors: Towards therapeutic management of Alzheimer’s disease

description: Microtubule affinity regulating kinase 4 (MARK4) plays essential role in the tau-assisted regulation of microtubule dynamics. Over expression of MARK4 causes early phosphorylation of Ser262 of tau protein which is essential for microtubule binding. Hyperphosphorylation of tau protein causes the formation of paired helical fragments and neurofibrillary tangles, the hallmarks of Alzheimer’s disease. Targeting the modulation of MARK4 activity is an effective strategy for therapeutic intervention of Alzheimer’s and other MARK4 associated neurodegenerative diseases. Having role of pyrazolopyrimidine derivatives in the therapeutic management of neurodegenerative diseases, we have tried to estimate their binding affinity with the MARK4. We performed <i>in silico</i> screening of 59 pyrazolopyrimidine derivatives against MARK4 and obtained a few best possible inhibitors. Molecular docking-based interaction analysis suggested five potential leads that were further analyzed using molecular dynamics simulations, MM/PBSA, principal component analysis and graph theory based dynamic network analysis to observe structural changes caused due to ligand binding. All these computational analyses suggested that compounds with PubChem IDs: 91895678, 91895679, 91895692, 91145515 and 90794095 may be further exploited to address Alzheimer’s and other neurodegenerative diseases. Communicated by Ramaswamy H. Sarma
DOI: 10.6084/m9.figshare.9901376.v2
title: Positive association between cerebral grey matter metabolism and dopamine D<sub>2</sub>/D<sub>3</sub> receptor availability in healthy and schizophrenia subjects: An <sup>18</sup>F-fluorodeoxyglucose and <sup>18</sup>F-fallypride positron emission tomography study

description: <b>Objectives:</b> Overlapping decreases in extrastriatal dopamine D<sub>2</sub>/D<sub>3</sub>-receptor availability and glucose metabolism have been reported in subjects with schizophrenia. It remains unknown whether these findings are physiologically related or coincidental. <b>Methods:</b> To ascertain this, we used two consecutive <sup>18</sup>F-fluorodeoxyglucose and <sup>18</sup>F-fallypride positron emission tomography scans in 19 healthy and 25 unmedicated schizophrenia subjects. Matrices of correlations between <sup>18</sup>F-fluorodeoxyglucose uptake and <sup>18</sup>F-fallypride binding in voxels at the same xyz location and AFNI-generated regions of interest were evaluated in both diagnostic groups. <b>Results:</b><sup>18</sup>F-fluorodeoxyglucose uptake and <sup>18</sup>F-fallypride binding potential were predominantly positively correlated across the striatal and extrastriatal grey matter in both healthy and schizophrenia subjects. In comparison to healthy subjects, significantly weaker correlations in subjects with schizophrenia were confirmed in the right cingulate gyrus and thalamus, including the mediodorsal, lateral dorsal, anterior, and midline nuclei. Schizophrenia subjects showed decreased D<sub>2</sub>/D<sub>3</sub>-receptor availability in the hypothalamus, mamillary bodies, thalamus and several thalamic nuclei, and increased glucose uptake in three lobules of the cerebellar vermis. <b>Conclusions:</b> Dopaminergic system may be involved in modulation of grey matter metabolism and neurometabolic coupling in both healthy human brain and psychopathology. Hyperdopaminergic state in untreated schizophrenia may at least partly account for the corresponding decreases in grey matter metabolism.
DOI: 10.6084/m9.figshare.9901367.v1
title: Evaluation of pyrazolopyrimidine derivatives as microtubule affinity regulating kinase 4 inhibitors: Towards therapeutic management of Alzheimer’s disease

description: Microtubule affinity regulating kinase 4 (MARK4) plays essential role in the tau-assisted regulation of microtubule dynamics. Over expression of MARK4 causes early phosphorylation of Ser262 of tau protein which is essential for microtubule binding. Hyperphosphorylation of tau protein causes the formation of paired helical fragments and neurofibrillary tangles, the hallmarks of Alzheimer’s disease. Targeting the modulation of MARK4 activity is an effective strategy for therapeutic intervention of Alzheimer’s and other MARK4 associated neurodegenerative diseases. Having role of pyrazolopyrimidine derivatives in the therapeutic management of neurodegenerative diseases, we have tried to estimate their binding affinity with the MARK4. We performed <i>in silico</i> screening of 59 pyrazolopyrimidine derivatives against MARK4 and obtained a few best possible inhibitors. Molecular docking-based interaction analysis suggested five potential leads that were further analyzed using molecular dynamics simulations, MM/PBSA, principal component analysis and graph theory based dynamic network analysis to observe structural changes caused due to ligand binding. All these computational analyses suggested that compounds with PubChem IDs: 91895678, 91895679, 91895692, 91145515 and 90794095 may be further exploited to address Alzheimer’s and other neurodegenerative diseases. Communicated by Ramaswamy H. Sarma
DOI: 10.6084/m9.figshare.9901376.v1
title: Positive association between cerebral grey matter metabolism and dopamine D<sub>2</sub>/D<sub>3</sub> receptor availability in healthy and schizophrenia subjects: an <sup>18</sup>F-fluorodeoxyglucose and <sup>18</sup>F-fallypride positron emission tomography study

description: <b>Objectives</b>: Overlapping decreases in extrastriatal dopamine D<sub>2</sub>/D<sub>3</sub>-receptor availability and glucose metabolism have been reported in subjects with schizophrenia. It remains unknown whether these findings are physiologically related or coincidental. <b>Methods</b>: To ascertain this, we used two consecutive <sup>18</sup>F-fluorodeoxyglucose and <sup>18</sup>F-fallypride positron emission tomography scans in 19 healthy and 25 unmedicated schizophrenia subjects. Matrices of correlations between <sup>18</sup>F-fluorodeoxyglucose uptake and <sup>18</sup>F-fallypride binding in voxels at the same xyz location and AFNI-generated regions of interest were evaluated in both diagnostic groups. <b>Results</b>: <sup>18</sup>F-fluorodeoxyglucose uptake and <sup>18</sup>F-fallypride binding potential were predominantly positively correlated across the striatal and extrastriatal grey matter in both healthy and schizophrenia subjects. In comparison to healthy subjects, significantly weaker correlations in subjects with schizophrenia were confirmed in the right cingulate gyrus and thalamus, including the mediodorsal, lateral dorsal, anterior, and midline nuclei. Schizophrenia subjects showed decreased D<sub>2</sub>/D<sub>3</sub>-receptor availability in the hypothalamus, mammillary bodies, thalamus and several thalamic nuclei, and increased glucose uptake in three lobules of the cerebellar vermis. <b>Conclusions</b>: Dopaminergic system may be involved in modulation of grey matter metabolism and neurometabolic coupling in both healthy human brain and psychopathology. Hyperdopaminergic state in untreated schizophrenia may at least partly account for the corresponding decreases in grey matter metabolism.
DOI: 10.6084/m9.figshare.9901322
title: Smoking and blood DNA methylation: an epigenome-wide association study and assessment of reversibility

description: We conducted a genome-wide association study of blood DNA methylation and smoking, attempted replication of previously discovered associations, and assessed the reversibility of smoking-associated methylation changes. DNA methylation was measured in baseline peripheral blood samples for 5,044 participants in the Melbourne Collaborative Cohort Study. For 1,032 participants, these measures were repeated using blood samples collected at follow-up, a median of 11 years later. A cross-sectional analysis of the association between smoking and DNA methylation and a longitudinal analysis of changes in smoking status and changes in DNA methylation were conducted. We used our cross-sectional analysis to replicate previously reported associations for current (N = 3,327) and former (N = 172) smoking. A comprehensive smoking index accounting for the biological half-life of smoking compounds and several aspects of smoking history was constructed to assess the reversibility of smoking-induced methylation changes. This measure of lifetime exposure to smoking allowed us to detect more associations than comparing current with never smokers. We identified 4,496 cross-sectional associations at P −7, including 3,296 annotated to 1,326 genes that were not previously implicated in smoking-associated DNA methylation changes at this significance threshold. We replicated the majority of previously reported associations (P −7) for current and former smokers. In our data, we observed for former smokers a substantial degree of return to the methylation levels of never smokers, compared with current smokers (median: 74%, IQR = 63-86%), corresponding to small values (median: 2.75, IQR = 1.5–5.25) for the half-life parameter of the comprehensive smoking index. Longitudinal analyses identified 368 sites at which methylation changed upon smoking cessation. Our study demonstrates the usefulness of the comprehensive smoking index to detect associations between smoking and DNA methylation at CpGs across the genome, replicates the vast majority of previously reported associations, and quantifies the reversibility of smoking-induced methylation changes.
DOI: 10.6084/m9.figshare.9901334
title: Voltage vs. Ligand II: Structural insights of the intrinsic flexibility in cyclic nucleotide-gated channels

description: In the preceding article, we present a flexibility analysis of the voltage-gated ion channel (VGIC) superfamily. In this study, we describe in detail the flexibility profile of the voltage-sensor domain (VSD) and the pore domain (PD) concerning the evolution of 6TM ion channels. In particular, we highlight the role of flexibility in the emergence of CNG channels and describe a significant level of sequence similarity between the archetypical VSD and the TolQ proteins. A highly flexible S4-like segment exhibiting Lys instead Arg for these membrane proteins is reported. Sequence analysis indicates that, in addition to this S4-like segment, TolQ proteins also show similarity with specific motifs in S2 and S3 from typical V-sensors. Notably, S3 flexibility profiles from typical VSDs and S3-like in TolQ proteins are also similar. Interestingly, TolQ from early divergent prokaryotes are comparatively more flexible than those in modern counterparts or true V-sensors. Regarding the PD, we also found that 2TM K<sup>+</sup>-channels in early prokaryotes are considerably more flexible than the ones in modern microbes, and such flexibility is comparable to the one present in CNG channels. Voltage dependence is mainly exhibited in prokaryotic CNG channels whose VSD is rigid whereas the eukaryotic CNG channels are considerably more flexible and poorly V-dependent. The implication of the flexibility present in CNG channels, their sensitivity to cyclic nucleotides and the cation selectivity are discussed. Finally, we generated a structural model of the putative cyclic nucleotide-modulated ion channel, which we coined here as AqK, from the thermophilic bacteria <i>Aquifex aeolicus</i>, one of the earliest diverging prokaryotes known. Overall, our analysis suggests that V-sensors in CNG-like channels were essentially rigid in early prokaryotes but raises the possibility that this module was probably part of a very flexible stator protein of the bacterial flagellum motor complex.
DOI: 10.6084/m9.figshare.9901313
title: Effect of D-ring C-3’ methylation of strigolactone analogs on their transcription regulating activity in rice

description: Strigolactones (SLs) are a well-known class of plant hormones, which are involved in a number of developmental and adaptation processes and mediate different interspecific interactions. In spite of the growing knowledge on SL biosynthesis and signal transduction, effects of structural modifications on the activity and efficiency of SLs and their analogs remain largely elusive. SLs are characterized by the presence of a lactone ring (D-ring) that is connected by an enol ether bridge to a second moiety. In this study, we investigated the effect of additional D-ring methylation of SL analogs on their transcription regulating activity. For this purpose, we compared the SL analogs MP13 and AR8, which differ only by the presence of a methyl group at the C-3ʹ atom in the latter. Transcription regulating activity was determined by quantitative real-time PCR measurement of transcript levels of SL-dependent, feed-back regulated genes in treated wild type and <i>ccd7</i> mutant rice seedlings. Results obtained indicate that C-3ʹ methylation reduces the transcription regulating activity, as shown by the more pronounced suppression of the SL biosynthesis genes <i>DWARF27</i> (<i>D27</i>) and <i>CAROTENOID CLEAVAGE DIOXYGENASES</i> (<i>CCD7</i> and <i>CCD8</i>) and higher induction of the SL signaling repressor gene <i>DWARF53</i> (<i>D53</i>) in MP13 treated seedlings. These results are consistent with a recent study on the biological activities of MP13 and AR8.
DOI: 10.6084/m9.figshare.9901307
title: Immunohistochemical Expression of p53 in Type I and II Epithelial Ovarian Cancer among Sudanese women

description: Immunohistochemical Expression of p53 in Type I and II Epithelial Ovarian Cancer among Sudanese women. In this cross-sectional, hospital-based study a total of 114 paraffin-embedded tissue blocks previously diagnosed as epithelial ovarian cancer were collected from six governmental hospitals in Khartoum state, Sudan, in the period 2013-2016. Immunohistochemistry was performed on tissue microarray slides to measure the protein expression of p53 in the EOC.<br>