cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.10298198
title: Efficacy of antiviral treatment in cytomegalovirus detected ulcerative colitis: meta-analysis of available data

description: <b>Aim:</b> This meta-analysis aimed to pool available data regarding the efficacy of ganciclovir treatment among cytomegalovirus-detected ulcerative colitis patients. <b>Methods:</b> We screened PubMed, Ovid, Web of Science and Cochrane databases for relevant studies, and four investigators independently evaluated the studies for eligibility. The primary outcome was surgical resection or death from ulcerative colitis. The data were then pooled via DerSimonian–Laird estimator and Mantel–Haenszel (MH) method, two points added for continuity correction and random-effects model fitted in the Bayesian framework. We first constructed a Bugs model with Student <i>t</i>-distribution as prior for between-study heterogeneity. The model was fitted by Gibbs sampler (JAGS) to produce a marginal posterior distribution. <b>Results:</b> Our screening identified 15 eligible studies for final data synthesis and combined data from 191 ganciclovir-treated and 166 non-treated patients. Effect estimates from the fixed-effects meta-analysis model did not encourage ganciclovir treatment (OR, 1.43; 95% CIs [0–95, 2.16]), with a negligible unaccounted heterogeneity (<i>I</i><sup>2</sup> = 0%). The Bayesian random-effects model generated high-density credible intervals, suggesting a high probability, that future studies will also not encourage ganciclovir treatment (mu, 1.028; 95% credible intervals [0.054, 2.238]; 80% credible intervals [0.401, 1.703]) which indicates that future studies will favor non-treatment of ulcerative colitis with ganciclovir. <b>Conclusions:</b> Data produced in this study do not encourage ganciclovir treatment for UC patients. However, studies included in this analysis were observational, and thus, inherited severe selection bias. We suggest randomized controlled studies be conducted to make firm recommendations in this context.
DOI: 10.6084/m9.figshare.10298198.v1
title: Efficacy of antiviral treatment in cytomegalovirus detected ulcerative colitis: meta-analysis of available data

description: <b>Aim:</b> This meta-analysis aimed to pool available data regarding the efficacy of ganciclovir treatment among cytomegalovirus-detected ulcerative colitis patients. <b>Methods:</b> We screened PubMed, Ovid, Web of Science and Cochrane databases for relevant studies, and four investigators independently evaluated the studies for eligibility. The primary outcome was surgical resection or death from ulcerative colitis. The data were then pooled via DerSimonian–Laird estimator and Mantel–Haenszel (MH) method, two points added for continuity correction and random-effects model fitted in the Bayesian framework. We first constructed a Bugs model with Student <i>t</i>-distribution as prior for between-study heterogeneity. The model was fitted by Gibbs sampler (JAGS) to produce a marginal posterior distribution. <b>Results:</b> Our screening identified 15 eligible studies for final data synthesis and combined data from 191 ganciclovir-treated and 166 non-treated patients. Effect estimates from the fixed-effects meta-analysis model did not encourage ganciclovir treatment (OR, 1.43; 95% CIs [0–95, 2.16]), with a negligible unaccounted heterogeneity (<i>I</i><sup>2</sup> = 0%). The Bayesian random-effects model generated high-density credible intervals, suggesting a high probability, that future studies will also not encourage ganciclovir treatment (mu, 1.028; 95% credible intervals [0.054, 2.238]; 80% credible intervals [0.401, 1.703]) which indicates that future studies will favor non-treatment of ulcerative colitis with ganciclovir. <b>Conclusions:</b> Data produced in this study do not encourage ganciclovir treatment for UC patients. However, studies included in this analysis were observational, and thus, inherited severe selection bias. We suggest randomized controlled studies be conducted to make firm recommendations in this context.
DOI: 10.25400/lincolnuninz.10298129
title: Research Data Compiled.xlsx

description: The data is comprised of search results of journal articles from Scopus and Web of Science databases using three Boolean search strings. The search strings are:<i>(“certification” AND “meat”) OR (“certification” AND “dairy”)</i>], (ii) [<i>(“credence” AND meat) OR (“experience” AND meat)</i>]<i>, and (iii) </i>[<i>(“meat” AND “intrinsic”) OR (“meat” AND “extrinsic”) OR (“meat” AND “quality cue”)</i>]
DOI: 10.6084/m9.figshare.10298132
title: The probability of MxxxxxK occurring by chance in three amino acid sequences

description: This project describes statistical analyses of the likelihood of the extended doubleton motif MxxxxxK arising by chance in three short amino acid sequences
DOI: 10.6084/m9.figshare.10298117
title: Query Sequences

description: Query sequences of all genes analysed and included in the paper "Phylogenetic evidence for the reductive evolution of stomata in bryophytes". Additional genes that were analysed, but not included in the paper are also included.
DOI: 10.25400/lincolnuninz.10298129.v1
title: Research Data Compiled.xlsx

description: The data is comprised of search results of journal articles from Scopus and Web of Science databases using three Boolean search strings. The search strings are:<i>(“certification” AND “meat”) OR (“certification” AND “dairy”)</i>], (ii) [<i>(“credence” AND meat) OR (“experience” AND meat)</i>]<i>, and (iii) </i>[<i>(“meat” AND “intrinsic”) OR (“meat” AND “extrinsic”) OR (“meat” AND “quality cue”)</i>]
DOI: 10.6084/m9.figshare.10298111
title: microscopy_MPIMM_039_QE_P_BP_CF.rar

description: Microscopy data (stereomicroscopy, widefield microscopy and CLSM) of the second control dataset for the MALDI-FISH study<br>
DOI: 10.6084/m9.figshare.10298111.v1
title: microscopy_MPIMM_039_QE_P_BP_CF.rar

description: Microscopy data (stereomicroscopy, widefield microscopy and CLSM) of the second control dataset for the MALDI-FISH study<br>
DOI: 10.6084/m9.figshare.10298117.v1
title: Query Sequences

description: Query sequences of all genes analysed and included in the paper "Phylogenetic evidence for the reductive evolution of stomata in bryophytes". Additional genes that were analysed, but not included in the paper are also included.
DOI: 10.6084/m9.figshare.10298096
title: Manuscript 476421 - LB 25 LB 26 search engine result files

description: 476421
DOI: 10.6084/m9.figshare.10298096.v1
title: Manuscript 476421 - LB 25 LB 26 search engine result files

description: 476421
DOI: 10.6084/m9.figshare.10298093
title: Alignment files

description: Mutliple sequence alignments for all genes analysed and included in the paper "Phylogenetic evidence for the reductive evolution of stomata in bryophytes". Additional genes that were analysed, but not included in the paper are also included.
DOI: 10.6084/m9.figshare.10298078
title: Newick tree files

description: Tree files (Newick) for all genes analysed and included in the paper "Phylogenetic evidence for the reductive evolution of stomata in bryophytes". Additional genes that were analysed, but not included in the paper are also included.
DOI: 10.6084/m9.figshare.10298054
title: Appendix to CRUS 3955

description: In this spreadsheet, the analysis as described in the papercan be examined.
DOI: 10.6084/m9.figshare.10298045
title: Programmed Cell Death in Neurospora crassa Is Controlled by the Allorecognition Determinant rcd-1

description: File 1: DNA sequences of rcd-1 homologs in Sordariaceae used for phylogeny and analyses of positive selection. File 2: Protein sequences of rcd-1 homologs in fungi and bacteria. File 3: DNA sequences of genes representing the genomic background in N. crassa used for analyses of balancing selection at rcd-1 in N. crassa. File 4: DNA sequences of genes representing the genomic background in N. discreta used for analyses of balancing selection at rcd-1 in N. discreta. File 5: DNA sequences of genes representing the genomic background in N. tetrasperma used for analyses of balancing selection at rcd-1 in N. tetrasperma.
DOI: 10.6084/m9.figshare.10298045.v1
title: Programmed Cell Death in Neurospora crassa Is Controlled by the Allorecognition Determinant rcd-1

description: File 1: DNA sequences of rcd-1 homologs in Sordariaceae used for phylogeny and analyses of positive selection. File 2: Protein sequences of rcd-1 homologs in fungi and bacteria. File 3: DNA sequences of genes representing the genomic background in N. crassa used for analyses of balancing selection at rcd-1 in N. crassa. File 4: DNA sequences of genes representing the genomic background in N. discreta used for analyses of balancing selection at rcd-1 in N. discreta. File 5: DNA sequences of genes representing the genomic background in N. tetrasperma used for analyses of balancing selection at rcd-1 in N. tetrasperma.
DOI: 10.6084/m9.figshare.10298054.v1
title: Appendix to CRUS 3955

description: In this spreadsheet, the analysis as described in the papercan be examined.
DOI: 10.6084/m9.figshare.10298039
title: Dataset for JGR-Planets paper: Quantitative Characterization of Impact Crater Materials on the Moon: Topographic Roughness and Thermophysical Properties

description: We quantitatively characterized crater materials using 1) the topographic roughness calculated form LOLA, and 2) rock abundances and night-time soil temperatures derived from DIVINER measurements. We subdivided crater materials into central peak, floor, wall, and continuous ejecta, mapped 4770 crater-material subunits, and calculated the quantitative parameters for each of them. <br>
DOI: 10.6084/m9.figshare.10298042
title: Primers of all genes in Bacillus subtilis strain 168 without recognition sequence of NdeI and BamHI

description: Primer design is a critical part of the molecular cloning workflow for amplifying target genes from a template. Serving as a molecular marker for the region in which polymerase chain reaction should amplify a particular gene segment, primers should have perfect complementary base pairing with the target strand of the DNA duplex in which the gene resides. Beyond the binding sequence that anneals a primer to the target DNA strand at the correct location, recognition and flanking sequences are also typically appended to primer sequence to aid downstream restriction enzyme digestion for molecular cloning purposes. Specifically, recognition sequence appended to the primer facilitates recognition by specific restriction enzyme for digestion and excision of the gene fragment that is subsequently inserted into an expression vector. However, one critical requirement for the choice of restriction enzyme is that the gene of interest should not contain recognition sequence of the restriction enzyme. In this contribution, a primer database for all genes in <i>Bacillus subtilis</i> strain 168 (Genbank ID number: NC_000964.3) that do not contain recognition sequence of restriction enzymes, NdeI and BamHI was obtained using an in-house MATLAB software processing the annotated genome sequence of <i>B. subtilis</i> strain 168 from Genbank. The database comprises the gene identities together with the forward and reverse primers necessary for amplifying and inserting the gene of interest into an expression vector. NdeI recognition sequence was appended to the forward primer, while that of BamHI was appended to the reverse primer. Melting temperature of the primer was designed to be 55 <sup>o</sup>C. Two nucleotide flanking sequence of ‘AT’ was appended to the start of the forward and reverse primers to help anchor the RNA polymerase during transcription. Altogether, the database comprises 3202 genes that are without recognition sequence of NdeI and BamHI. Collectively, a primer database comprising genes in <i>B. subtilis</i> strain 168 that are without recognition sequence of NdeI and BamHI restriction enzymes was created using a MATLAB algorithm. Both forward and reverse primers sequence are available in the database and should find use in workflows attempting to clone specific genes from the <i>B. subtilis</i> strain 168 genome using NdeI and BamHI for the forward and reverse primers respectively.<br><br>
DOI: 10.6084/m9.figshare.10298024
title: Ground CO2 dataset

description: Dataset of CO2 concentrations and fluxes simulated by WRF-VPRM and observed at both CO2 monitoring sites and the Boseong flux tower
DOI: 10.6084/m9.figshare.10298000
title: Supplementary Material for: Interleukin-27 Ameliorates Renal Ischemia-Reperfusion Injury through Signal Transducers and Activators of Transcription 3 Signaling Pathway

description: <b><i>Background:</i></b> Acute kidney injury (AKI) is a clinical syndrome characterized by significant morbidity and a high death rate. Interleukin (IL)-27 is a newly described member of the IL-6/IL-12 heterodimeric cytokine family and displays anti-inflammatory and antiapoptotic properties. <b><i>Objectives:</i></b> To determine the effect and mechanism of IL-27 in AKI. <b><i>Method:</i></b> We used a mouse model of renal ischemia/reperfusion (I/R) injury to investigate whether IL-27 has a therapeutic potential for the treatment of AKI. For the IL-27 administration group, IL-27 protein was injected 1 h before ischemia. Human proximal tubular epithelial cells were exposed to ischemia for 2 h and followed by 2 h of reperfusion (I2h+R2h treatment) used as an in vitro model to investigate the effect of IL-27. <b><i>Results:</i></b> Two IL-27 subunits, Epstein-Barr virus gene 3 and p28, were upregulated in kidneys 24 h after I/R. Renal expression of IL-27 receptor subunits (gp130 and WSX-1) was also increased. Treatment with IL-27 reduced structural/functional damages, ameliorated renal inflammation, inhibited the cleaved caspase-3 expression, upregulated antiapoptotic protein Bcl-2 and downregulated proapoptotic protein Bax in the kidneys of mice subjected to I/R. Meanwhile, the level of IL-27 receptor on renal tubular epithelial cells was increased after I2h+R2h treatment, and IL-27 administration suppressed I2h+R2h-induced epithelial cell apoptosis. Furthermore, IL-27 treatment led to activation of signal transducer and activator of transcription 3 (STAT3) both in vivo and in vitro, and IL-27-mediated protection against I2h+R2h injury was abolished by STAT3 inhibition. <b><i>Conclusions:</i></b> IL-27 protects against renal I/R injury by activating STAT3, suggesting that IL-27 may represent a novel strategy for the treatment of AKI.
DOI: 10.6084/m9.figshare.10298009
title: DC-8 flight track data

description: The dataset of CO2 concentrations simulated by WRF-VPRM and observed by the DC-8 aircraft.
DOI: 10.6084/m9.figshare.10298024.v2
title: Ground CO2 dataset

description: Dataset of CO2 concentrations and fluxes simulated by WRF-VPRM and observed at both CO2 monitoring sites and the Boseong flux tower
DOI: 10.6084/m9.figshare.10298000.v1
title: Supplementary Material for: Interleukin-27 Ameliorates Renal Ischemia-Reperfusion Injury through Signal Transducers and Activators of Transcription 3 Signaling Pathway

description: <b><i>Background:</i></b> Acute kidney injury (AKI) is a clinical syndrome characterized by significant morbidity and a high death rate. Interleukin (IL)-27 is a newly described member of the IL-6/IL-12 heterodimeric cytokine family and displays anti-inflammatory and antiapoptotic properties. <b><i>Objectives:</i></b> To determine the effect and mechanism of IL-27 in AKI. <b><i>Method:</i></b> We used a mouse model of renal ischemia/reperfusion (I/R) injury to investigate whether IL-27 has a therapeutic potential for the treatment of AKI. For the IL-27 administration group, IL-27 protein was injected 1 h before ischemia. Human proximal tubular epithelial cells were exposed to ischemia for 2 h and followed by 2 h of reperfusion (I2h+R2h treatment) used as an in vitro model to investigate the effect of IL-27. <b><i>Results:</i></b> Two IL-27 subunits, Epstein-Barr virus gene 3 and p28, were upregulated in kidneys 24 h after I/R. Renal expression of IL-27 receptor subunits (gp130 and WSX-1) was also increased. Treatment with IL-27 reduced structural/functional damages, ameliorated renal inflammation, inhibited the cleaved caspase-3 expression, upregulated antiapoptotic protein Bcl-2 and downregulated proapoptotic protein Bax in the kidneys of mice subjected to I/R. Meanwhile, the level of IL-27 receptor on renal tubular epithelial cells was increased after I2h+R2h treatment, and IL-27 administration suppressed I2h+R2h-induced epithelial cell apoptosis. Furthermore, IL-27 treatment led to activation of signal transducer and activator of transcription 3 (STAT3) both in vivo and in vitro, and IL-27-mediated protection against I2h+R2h injury was abolished by STAT3 inhibition. <b><i>Conclusions:</i></b> IL-27 protects against renal I/R injury by activating STAT3, suggesting that IL-27 may represent a novel strategy for the treatment of AKI.
DOI: 10.6084/m9.figshare.10298009.v1
title: DC-8 flight track data

description: The dataset of CO2 concentrations simulated by WRF-VPRM and observed by the DC-8 aircraft.
DOI: 10.6084/m9.figshare.10297991
title: Supplementary Material for: Changes in CD4<sup>+</sup>CD25<sup>+</sup>FoxP3<sup>+</sup> Regulatory T Cells and Serum Cytokines in Sublingual and Subcutaneous Immunotherapy in Allergic Rhinitis with or without Asthma

description: <b><i>Background:</i></b> Few studies have directly compared the immunologic responses to specific subcutaneous immunotherapy (SCIT) and sublingual immunotherapy (SLIT). <b><i>Objective:</i></b> We aimed to directly compare clinical efficacy and immunological responses between SLIT and SCIT in allergic rhinitis (AR) sensitized to house dust mites. <b><i>Methods:</i></b> Sixty-seven patients (age 5–55 years) with moderate-severe <i>Dermatophagoides pteronyssinus</i> (Der-p) and <i>Dermatophagoides farinae</i> AR with or without asthma were randomized (2:2:1) into SLIT (<i>n</i> = 27), SCIT (<i>n</i> = 26) and placebo (<i>n</i> = 14) groups. Symptom and medication scores, visual analogue score, serum Der-p specific immunoglobulin G4 (Der-p-sIgG4), CD4<sup>+</sup>CD25<sup>+</sup>FoxP3<sup>+</sup> regulatory T cells (Tregs) and serum cytokines were measured. <b><i>Results:</i></b> After 1-year treatment, a significant improvement of total rhinitis score (TRS), total rhinitis medication score (TRMS) and visual analogue score occurred in both SLIT and SCIT. There were no differences in clinical efficacy except for TRMS (<i>p</i> = 0.026) when SLIT and SCIT were directly compared. CD4<sup>+</sup>CD25<sup>+</sup>FoxP3<sup>+</sup> Tregs had a trend towards upregulation in the 2 modes and inversely correlated with TRS (<i>p</i> = 0.024) only in SLIT. Der-p-sIgG4 significantly increased in SLIT and SCIT (<i>p</i> &lt; 0.05), and it was 30 times higher in SCIT than SLIT after the treatment (<i>p</i> &lt; 0.05). Serum interferon-γ significantly increased only in SCIT after 1 (<i>p</i> = 0.008), 6 (<i>p</i> = 0.007) and 12 (<i>p</i> = 0.008) months of treatment and inversely correlated with TRS (<i>p</i> = 0.032). <b><i>Conclusion:</i></b> While SCIT and SLIT have similar rates of clinical improvement, the 2 modes reveal heterogeneous changes of CD4<sup>+</sup>CD25<sup>+</sup>Foxp3<sup>+</sup> Tregs, sIgG4 and cytokines.
DOI: 10.6084/m9.figshare.10298024.v1
title: BO_sim.obs_60m.300m_new_ysu.pblmix.topo_x-1y-1_.csv

description: Dataset of CO2 concentrations and fluxes simulated by WRF-VPRM and observed at Boseong flux tower during Korus-AQ 2016.
DOI: 10.6084/m9.figshare.10297946
title: Prevalence and determinants of C-section HtR areas Bangladesh

description: Prevalence and determinants of C-section at Hard to reach areas, Bangladesh
DOI: 10.6084/m9.figshare.10297946.v2
title: Prevalence and determinants of C-section HtR areas Bangladesh

description: Prevalence and determinants of C-section at Hard to reach areas, Bangladesh
DOI: 10.6084/m9.figshare.10297946.v1
title: Prevalence and determinants of C-section HtR areas Bangladesh

description: Prevalence and determinants of C-section at Hard to reach areas, Bangladesh
DOI: 10.6084/m9.figshare.10297694
title: Data of "Upper mantle seismic anisotropy beneath the Northern Transantarctic Mountains inferred from mantle xenoliths near Mt Melbourne, northern Victoria Land, Antarctica"

description: The samples included in the data set are J04-A5, B2, C, D, E and F. The files are formed as .ctf and exported from HKL channel 5 software after processes of basic noise reduction and rotation of olivine [100] and [010] aligned to horizontal and vertical directions, respectively. A table includes major elements of representative minerals.
DOI: 10.6084/m9.figshare.10297679
title: MOESM9 of An integrative methodology based on protein-protein interaction networks for identification and functional annotation of disease-relevant genes applied to channelopathies

description: Additional file 9 Quantitative validation by significance analysis of DAVID search against other phenotype-oriented resources. We searched the nine relevant genes resulted from the workflow in PheGenI [56], ToppGene [57] and g:Profiler [58]. We quantitatively evaluated this search selecting those terms with a significance less than 0.05 using Benjamini-Hochberg FDR statistic. We obtained a minor result in DAVID search (OMIM search did not offer the phenotypes p-values, unlike GAP DISEASE database). Even so, results are useful to develop a quantitative comparison between semiautomatic platforms and bibliographic search systems (sheet 1). From these results we represented the genotype-phenotype association networks to compare easily each p-value phenotype obtained (sheet 2). It should be noted that p-values of clinical phenotypes could be only obtained from one of the two databases explored through DAVID (GAP DISEASE database), and so the genotype-phenotype association network is sparser than the network of the manuscript (section A in Figs. 5, 6, 7). Yet, it is demonstrated that the workflow results are statistically significant and are as valid as or even better than systematic or exhaustive reviews. Then, we created three Boolean tables (in sheets 3, 4, 5) comparing each phenotype obtained from each search; these tables were then converted to binary matrices and clustering multivariate statistical analyses and bootstrap validations were carried out. This approach demonstrated that the results provided in the manuscript, obtained from DAVID (DAVID_m) and systematic and exhaustive reviews, clustered together in a robust and significant way (sheets 3, 4, 5). Hence, this workflow builds as productive results as a non-automatic research but in a quicker way allowing the extraction of information which a priori might not seem relevant when the starting point is a very large group of genes in disease. Moreover, the results obtained using just significant FDR corrected p-values also cluster in particular branches.