cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.5393203.v1
title: Appendix_S2.biom

description: Operational Taxonomic Unit (OTU) table in the Biological Observation Matrix (BIOM) format associated with the following publication in the American Journal of Botany: "Fungal endophyte communities in the temperate fern <i>Polystichum munitum</i> show early colonization and extensive temporal turnover"
DOI: 10.6084/m9.figshare.5388361
title: Whole cell cancer vaccines

description: This is a lay cartoon to explain whole cell cancer vaccines
DOI: 10.6084/m9.figshare.5393164.v2
title: Fonseca_etal_Ecological_Applications

description: Results of Fonseca et al. (In Press) Ecological Applications<br>
DOI: 10.6084/m9.figshare.5388310
title: Mapping functional and anatomical connections within the human auditory pathway with ultra-high field MRI

description: Presentation and poster prepared for International Conference on Auditory Cortex (ICAC) 2017, Banf, Canada.
DOI: 10.6084/m9.figshare.5388361.v4
title: Whole cell cancer vaccines

description: This is a lay cartoon to explain whole cell cancer vaccines
DOI: 10.6084/m9.figshare.5388361.v3
title: GVAX cartoon

description: This is a lay cartoon to explain whole cell cancer vaccines
DOI: 10.6084/m9.figshare.5388106
title: Bibliography: Terenz-Rezeption Im Buchdruck Bis 1550. Deutsche Terenzdrucke Als Träger Der Humanistischen Terenzrezeption. (1994)

description: Bibliography of research literature and some early prints extracted from:<br>Dortmund, Annette. 1994. “Terenz-Rezeption Im Buchdruck Bis 1550. Deutsche Terenzdrucke Als Träger Der Humanistischen Terenzrezeption.” Univ. Mainz. <br>(http://www.worldcat.org/oclc/180638075).The bibliography was re-created in Mendeley. Capturing early printings metadata there was not easy. However, this might be useful to someone working in the field or on the topic. <br>
DOI: 10.6084/m9.figshare.5388106.v1
title: Bibliography: Terenz-Rezeption Im Buchdruck Bis 1550. Deutsche Terenzdrucke Als Träger Der Humanistischen Terenzrezeption. (1994)

description: Bibliography of research literature and some early prints extracted from:<br>Dortmund, Annette. 1994. “Terenz-Rezeption Im Buchdruck Bis 1550. Deutsche Terenzdrucke Als Träger Der Humanistischen Terenzrezeption.” Univ. Mainz. <br>(http://www.worldcat.org/oclc/180638075).The bibliography was re-created in Mendeley. Capturing early printings metadata there was not easy. However, this might be useful to someone working in the field or on the topic. <br>
DOI: 10.6084/m9.figshare.5388088
title: Supplementary Material for: The Association of Combined Total Kidney and Liver Volume with Pain and Gastrointestinal Symptoms in Patients with Later Stage Autosomal Dominant Polycystic Kidney Disease

description: <strong><em>Background:</em></strong> There is an ongoing debate if and how kidney and liver volume are associated with pain and gastrointestinal (GI) symptoms in autosomal dominant polycystic kidney disease (ADPKD) patients. Since both kidney and liver volume could interact, we investigated whether combined total kidney and liver volume had stronger associations with ADPKD-related pain and GI symptoms than the volumes of the organs separately. <b><i>Methods:</i></b> We used baseline data from the DIPAK-1 study, which included ADPKD patients with an estimated glomerular filtration rate (eGFR) between 30 and 60 mL/min/1.73 m<sup>2</sup>. MR imaging was performed to measure height-adjusted total kidney volume (hTKV), height-adjusted total liver volume (hTLV) and the combination of both (height-adjusted total kidney liver volume [hTKLV]). <b><i>Results:</i></b> Three hundred nine ADPKD patients were included with a mean age of 48 ± 7 years, 53% female, eGFR 50 ± 11 mL/min/1.73 m<sup>2</sup> and median hTKV, hTLV and hTKLV of 1,095 (758-1,669), 1,173 (994-1,523) and 2,496 (1,972-3,352) mL/m, respectively. ADPKD-related pain and GI symptoms were present in, respectively, 27.5 and 61.2% of patients. Gender was no effect modifier in the association between kidney and/or liver volume, and symptom burden, indicating that all models could be tested in the overall study population. hTKLV and hTLV were significantly associated with pain and GI symptoms, whereas hTKV was not. Model testing revealed that the associations of pain and GI symptoms with hTKLV were significantly stronger than with hTKV (<i>p</i> = 0.04 and <i>p</i> = 0.04, respectively) but not when compared to hTLV (<i>p</i> = 0.2 and <i>p</i> = 0.5, respectively). <b><i>Conclusions:</i></b> This study indicates that combined kidney and liver volume was associated with the presence and severity of pain and GI symptoms in ADPKD, with a more prominent role for hTLV than for hTKV.
DOI: 10.6084/m9.figshare.5388085
title: Fake News Game Data

description: Raw data accompanying Roozenbeek & van der Linden (2017).<br>
DOI: 10.6084/m9.figshare.5388079
title: Bibliography: Römisches Buchwesen um die Zeitenwende : War T. Pomponius Atticus (110-32 v. Chr.) Verleger? (2001)

description: Bibliography of research literature / extracted from: <br>Dortmund, Annette. 2001. “Römisches Buchwesen um die Zeitenwende : War T. Pomponius Atticus (110-32 v. Chr.) Verleger?” Wiesbaden: Harrassowitz.(http://www.worldcat.org/oclc/47632356)<br>The bibliography might be useful to someone working in the field or on related topics. <br>
DOI: 10.6084/m9.figshare.5388079.v1
title: Bibliography: Römisches Buchwesen um die Zeitenwende : War T. Pomponius Atticus (110-32 v. Chr.) Verleger? (2001)

description: Bibliography of research literature / extracted from: <br>Dortmund, Annette. 2001. “Römisches Buchwesen um die Zeitenwende : War T. Pomponius Atticus (110-32 v. Chr.) Verleger?” Wiesbaden: Harrassowitz.(http://www.worldcat.org/oclc/47632356)<br>The bibliography might be useful to someone working in the field or on related topics. <br>
DOI: 10.6084/m9.figshare.5388058
title: Supplementary Material for: The Edinburgh Feeding Evaluation in Dementia Scale: A Longitudinal Study in Nursing Home Residents

description: <strong><em>Aims/Background:</em></strong> The Edinburgh Feeding Evaluation in Dementia (EdFED) scale has been shown to have good psychometric properties using a range of methods including Mokken scaling. We aimed to study the Italian version of the EdFED using Mokken scaling. <b><i>Methods:</i></b> Data were gathered at 7 time points from 401 nursing home residents affected by dementia in the course of a 6-month intervention study using analysis of variance, Mokken scaling, and person-item fit statistics. <b><i>Results:</i></b> The properties of the EdFED-I scale were stable over the course of the study with 4 items showing invariant item ordering at all time points. Some items behaved differently at different levels of difficulty in the scale and also depending on the mean level of feeding difficulty. The test information function showed a dip in the mid-range of difficulty scores.
DOI: 10.6084/m9.figshare.5388058.v1
title: Supplementary Material for: The Edinburgh Feeding Evaluation in Dementia Scale: A Longitudinal Study in Nursing Home Residents

description: <strong><em>Aims/Background:</em></strong> The Edinburgh Feeding Evaluation in Dementia (EdFED) scale has been shown to have good psychometric properties using a range of methods including Mokken scaling. We aimed to study the Italian version of the EdFED using Mokken scaling. <b><i>Methods:</i></b> Data were gathered at 7 time points from 401 nursing home residents affected by dementia in the course of a 6-month intervention study using analysis of variance, Mokken scaling, and person-item fit statistics. <b><i>Results:</i></b> The properties of the EdFED-I scale were stable over the course of the study with 4 items showing invariant item ordering at all time points. Some items behaved differently at different levels of difficulty in the scale and also depending on the mean level of feeding difficulty. The test information function showed a dip in the mid-range of difficulty scores.
DOI: 10.6084/m9.figshare.5388085.v1
title: Untitled Item

description: Raw data accompanying Roozenbeek & van der Linden (2015).<br>
DOI: 10.6084/m9.figshare.5388037
title: Supplementary Material for: Mild Cognitive Impairment and Progression to Dementia in Progressive Supranuclear Palsy

description: <strong><em>Background:</em></strong> Cognitive deficits are common in progressive supranuclear palsy (PSP), but their relevance and the progression to dementia are still poorly described. The recently revised criteria for PSP consider cognitive dysfunction in the diagnostic work-up. <b><i>Methods:</i></b> The study retrospectively evaluated a series of 99 PSP patients with Richardson syndrome (PSP-RS), subgrouped according to cognitive and behavioural performances into PSP with normal cognition (PSP-NC), PSP with mild cognitive impairment (PSP-MCI), and PSP with dementia (PSP-D). The progression to dementia at the 3-year follow-up was assessed. <b><i>Results:</i></b> At baseline, 15.2% of patients were classified as PSP-NC, 43.4% as PSP-MCI, and 41.4% as PSP-D. During the 3-year follow-up, 21 out of 29 patients, previously classified as PSP-NC or PSP-MCI, converted to dementia, with an incidence rate of 241 per 1,000 patients/year. Nineteen out of 21 PSP patients (90%) developed the behavioural variant frontotemporal dementia phenotype. The only factor associated with conversion to dementia was MCI diagnosis at baseline (<i>p</i> = 0.023). <b><i>Conclusion:</i></b> Cognitive decline occurs in a great proportion of PSP-RS patients early during the disease course. In the absence of a specific phenotype, the diagnosis of MCI might identify PSP patients at greatest risk of developing dementia and should be considered further in the diagnostic assessment.
DOI: 10.6084/m9.figshare.5388034
title: Supplementary Material for: Epstein-Barr Virus miR-BART6-3p Inhibits the RIG-I Pathway

description: Recognition of viral pathogen-associated molecular patterns by pattern recognition receptors (PRRs) is the first step in the initiation of a host innate immune response. As a PRR, RIG-I detects either viral RNA or replication transcripts. Avoiding RIG-I recognition is a strategy employed by viruses for immune evasion. Epstein-Barr virus (EBV) infects the majority of the human population worldwide. During the latent infection period there are only a few EBV proteins expressed, whereas EBV-encoded microRNAs, such as BART microRNAs, are highly expressed. BART microRNAs regulate both EBV and the host's gene expression, modulating virus proliferation and the immune response. Here, through gene expression profiling, we found that EBV miR-BART6-3ps inhibited genes of RIG-I-like receptor signaling and the type I interferon (IFN) response. We demonstrated that miR-BART6-3p rather than other BARTs specifically suppressed RIG-I-like receptor signaling-mediated IFN-β production. RNA-seq was used to analyze the global transcriptome change upon EBV infection and miR-BART6-3p mimics transfection, which revealed that EBV infection-triggered immune response signaling can be repressed by miR-BART6-3p overexpression. Furthermore, miR-BART6-3p inhibited the EBV-triggered IFN-β response and facilitated EBV infection through targeting the 3′UTR of RIG-I mRNA. These findings provide new insights into the mechanism underlying the strategies employed by EBV to evade immune surveillance.
DOI: 10.6084/m9.figshare.5388085.v2
title: Fake News Game Data

description: Raw data accompanying Roozenbeek & van der Linden (2015).<br>
DOI: 10.6084/m9.figshare.5388037.v1
title: Supplementary Material for: Mild Cognitive Impairment and Progression to Dementia in Progressive Supranuclear Palsy

description: <strong><em>Background:</em></strong> Cognitive deficits are common in progressive supranuclear palsy (PSP), but their relevance and the progression to dementia are still poorly described. The recently revised criteria for PSP consider cognitive dysfunction in the diagnostic work-up. <b><i>Methods:</i></b> The study retrospectively evaluated a series of 99 PSP patients with Richardson syndrome (PSP-RS), subgrouped according to cognitive and behavioural performances into PSP with normal cognition (PSP-NC), PSP with mild cognitive impairment (PSP-MCI), and PSP with dementia (PSP-D). The progression to dementia at the 3-year follow-up was assessed. <b><i>Results:</i></b> At baseline, 15.2% of patients were classified as PSP-NC, 43.4% as PSP-MCI, and 41.4% as PSP-D. During the 3-year follow-up, 21 out of 29 patients, previously classified as PSP-NC or PSP-MCI, converted to dementia, with an incidence rate of 241 per 1,000 patients/year. Nineteen out of 21 PSP patients (90%) developed the behavioural variant frontotemporal dementia phenotype. The only factor associated with conversion to dementia was MCI diagnosis at baseline (<i>p</i> = 0.023). <b><i>Conclusion:</i></b> Cognitive decline occurs in a great proportion of PSP-RS patients early during the disease course. In the absence of a specific phenotype, the diagnosis of MCI might identify PSP patients at greatest risk of developing dementia and should be considered further in the diagnostic assessment.
DOI: 10.6084/m9.figshare.5387986
title: Supplementary Material for: Retinal Nerve Fiber Layer Thickness Changes in the Pseudoexfoliation Syndrome: A Meta-Analysis of Case-Control Studies

description: <strong><em>Purpose:</em></strong> To evaluate and compare changes in retinal nerve fiber layer (RNFL) thickness in patients with the pseudoexfoliation syndrome (PXS) and healthy controls. <b><i>Methods:</i></b> Case-control studies were selected through an electronic search of the Cochrane Controlled Trials Register, PubMed, and Embase. Results were reviewed to ensure that the included studies met prespecified inclusion/exclusion criteria, and the quality of each study was assessed using the Newcastle-Ottawa Scale. All included studies measured average and 4-quadrant (temporal, superior, nasal, and inferior) RNFL thickness using optical coherence tomography (OCT). For the continuous outcomes, we calculated the weighted mean difference (WMD) and 95% confidence intervals (CIs). <b><i>Results:</i></b> Eight case-control studies were included in this meta-analysis involving 225 eyes of PXS patients and 208 eyes of healthy controls in total. Statistical analysis revealed that the average RNFL thickness in PXS patients was significantly reduced compared to healthy controls (WMD = −6.91, 95% CI: −9.99 to −3.82, <i>p</i> &lt; 0.0001). Additionally, differences in RNFL thickness in the superior quadrant (WMD = −10.68, 95% CI: −16.40 to −4.95, <i>p</i> = 0.0003), inferior quadrant (WMD = −8.20, 95% CI: −10.85 to −5.55, <i>p</i> &lt; 0.00001), nasal quadrant (WMD = −3.05, 95% CI: −5.21 to −0.90, <i>p</i> = 0.005), and temporal quadrant (WMD = −6.39, 95% CI: −9.98 to −2.80, <i>p</i> = 0.0005) were all significant between the two groups. <b><i>Conclusions:</i></b> These results suggest that it is important to evaluate RNFL thickness and the optic nerve head through OCT in patients with PXS in order to determine early glaucomatous damage and start timely intervention prior to visual field loss.
DOI: 10.6084/m9.figshare.5388034.v1
title: Supplementary Material for: Epstein-Barr Virus miR-BART6-3p Inhibits the RIG-I Pathway

description: Recognition of viral pathogen-associated molecular patterns by pattern recognition receptors (PRRs) is the first step in the initiation of a host innate immune response. As a PRR, RIG-I detects either viral RNA or replication transcripts. Avoiding RIG-I recognition is a strategy employed by viruses for immune evasion. Epstein-Barr virus (EBV) infects the majority of the human population worldwide. During the latent infection period there are only a few EBV proteins expressed, whereas EBV-encoded microRNAs, such as BART microRNAs, are highly expressed. BART microRNAs regulate both EBV and the host's gene expression, modulating virus proliferation and the immune response. Here, through gene expression profiling, we found that EBV miR-BART6-3ps inhibited genes of RIG-I-like receptor signaling and the type I interferon (IFN) response. We demonstrated that miR-BART6-3p rather than other BARTs specifically suppressed RIG-I-like receptor signaling-mediated IFN-β production. RNA-seq was used to analyze the global transcriptome change upon EBV infection and miR-BART6-3p mimics transfection, which revealed that EBV infection-triggered immune response signaling can be repressed by miR-BART6-3p overexpression. Furthermore, miR-BART6-3p inhibited the EBV-triggered IFN-β response and facilitated EBV infection through targeting the 3′UTR of RIG-I mRNA. These findings provide new insights into the mechanism underlying the strategies employed by EBV to evade immune surveillance.
DOI: 10.6084/m9.figshare.5387959
title: <i>Araniella cucurbitina</i>: the first molecular evidence of a Palearctic species of genus <i>Araniella</i> inhabiting India

description: The present study represents first genetic record of single spider species <i>Araniella cucurbitina</i>, genus <i>Araniella</i> from Uttarakhand, India. There are 12 identified species under <i>Araniella</i> genus and they are distributed in Palearctic region. Here, we used known N = 47 (2 from present study and 45 from GenBank) cytochrome oxidase 1 (CO1) sequences of <i>A. cucurbitina</i> representing seven different geographical groups, additionally 23 sequences of eight <i>Araniella</i> species were used for phylogenetic relationship. The CO1 (561 bp) sequences of <i>A. cucurbitina</i> consisted of <i>n</i> = 14 haplotypes, where haplotype 14 (Hap 14) represents Indian species, while all 13 haplotypes (Hap1–13) shared between six <i>A. cucurbitina</i> groups. The overall ‘h’ and ‘π’ diversities among seven groups of <i>A. cucurbitina</i> were 0.85291 and 0.00888, respectively, while overall evolutionary divergence was 0.04. The Indian Hap 14, showed minimum sequence divergence (0.02) from Italy and Czech Republic haplotypes (Hap 6), it means it is the closest group compared to others. Evolutionary divergence among eight species of <i>Araniella</i> ranges from 0.003 to 0.114. The maximum likelihood (ML) topology based on 14 haplotypes of <i>A. cucurbitina</i> was divided into two major clades and further two subclades. Furthermore, ML topology between eight species of <i>Araniella</i> was divided into three major clades, where <i>A. cucurbitina</i> and <i>A. proxima</i> clustered together in clade ‘A’, while six others were present together in clade ‘B’ and ‘C’. This study helps to identify the Indian species from the rest of <i>Araniella</i> species and other <i>cucurbitina</i> population across the world. This study further needs to be on a large scale to know the exact status distribution and molecular phylogeography of this single species of genus <i>Araniella</i> from India.
DOI: 10.6084/m9.figshare.5387968
title: Supplementary Material for: Galectin-9 Produced by Intestinal Epithelial Cells Enhances Aldehyde Dehydrogenase Activity in Dendritic Cells in a PI3K- and p38-Dependent Manner

description: Intestinal epithelial cells (IEC) drive regulatory T cell (T<sub>reg</sub>) responses by promoting the differentiation of aldehyde dehydrogenase (ALDH)-expressing CD103<sup>+</sup> dendritic cells (DC). Apical stimulation of TLR9 by CpG DNA on IEC supports galectin-9 expression by IEC, which is promoted by short-chain galacto-oligosaccharides and long-chain fructo-oligosaccharides (GF). While galectin-9 can induce the maturation of monocyte-derived DC (moDC), the contribution of galectin-9 on the induction of ALDH activity in DC is not known. To this end, DC were stimulated with galectin-9, and ALDH activity and the expression of CD103 were assessed. ALDH activity was increased by moDC exposed to galectin-9, while the expression of CD103 remained unaltered. Galectin-9 secreted by IEC apically exposed to CpG DNA and GF enhanced ALDH activity, but not CD103 expression by moDC, which was abrogated upon galectin-9 neutralization. Similar observations were found in murine GM-CSF-cultured bone marrow-derived DC (BMDC). Using Flt3L-cultured BMDC and ex vivo murine splenic DC, it was observed that galectin-9 only enhanced ALDH activity in the presence of GM-CSF in CD103<sup>-</sup> cells. The induction of ALDH activity in BMDC was dependent on p38 and PI3K signaling. These data indicate a novel role for galectin-9 in modulating innate immunity by inducing ALDH activity in DC.
DOI: 10.6084/m9.figshare.5387986.v1
title: Supplementary Material for: Retinal Nerve Fiber Layer Thickness Changes in the Pseudoexfoliation Syndrome: A Meta-Analysis of Case-Control Studies

description: <strong><em>Purpose:</em></strong> To evaluate and compare changes in retinal nerve fiber layer (RNFL) thickness in patients with the pseudoexfoliation syndrome (PXS) and healthy controls. <b><i>Methods:</i></b> Case-control studies were selected through an electronic search of the Cochrane Controlled Trials Register, PubMed, and Embase. Results were reviewed to ensure that the included studies met prespecified inclusion/exclusion criteria, and the quality of each study was assessed using the Newcastle-Ottawa Scale. All included studies measured average and 4-quadrant (temporal, superior, nasal, and inferior) RNFL thickness using optical coherence tomography (OCT). For the continuous outcomes, we calculated the weighted mean difference (WMD) and 95% confidence intervals (CIs). <b><i>Results:</i></b> Eight case-control studies were included in this meta-analysis involving 225 eyes of PXS patients and 208 eyes of healthy controls in total. Statistical analysis revealed that the average RNFL thickness in PXS patients was significantly reduced compared to healthy controls (WMD = −6.91, 95% CI: −9.99 to −3.82, <i>p</i> &lt; 0.0001). Additionally, differences in RNFL thickness in the superior quadrant (WMD = −10.68, 95% CI: −16.40 to −4.95, <i>p</i> = 0.0003), inferior quadrant (WMD = −8.20, 95% CI: −10.85 to −5.55, <i>p</i> &lt; 0.00001), nasal quadrant (WMD = −3.05, 95% CI: −5.21 to −0.90, <i>p</i> = 0.005), and temporal quadrant (WMD = −6.39, 95% CI: −9.98 to −2.80, <i>p</i> = 0.0005) were all significant between the two groups. <b><i>Conclusions:</i></b> These results suggest that it is important to evaluate RNFL thickness and the optic nerve head through OCT in patients with PXS in order to determine early glaucomatous damage and start timely intervention prior to visual field loss.
DOI: 10.6084/m9.figshare.5387956
title: Supplementary Material for: Chromosomal Microarray Analysis in Fetuses with Growth Restriction and Normal Karyotype: A Systematic Review and Meta-Analysis

description: <strong><em>Objective:</em></strong> To perform a systematic review of the literature and a meta-analysis to estimate the incremental yield of chromosomal microarray analysis (CMA) over karyotyping in fetal growth restriction (FGR). <b><i>Methods:</i></b> This was a systematic review conducted in accordance with the PRISMA criteria. All articles identified in PubMed, Ovid Medline, and ISI Web of Knowledge (Web of Science) from January 2009 to November 2016 describing pathogenic copy number variants (CNVs) in fetuses with growth restriction were included. Case reports were excluded. Risk differences were pooled to estimate the overall and stratified CMA incremental yield. <b><i>Results:</i></b> Ten studies with full data available met the inclusion criteria for analysis. Combined data from these studies revealed a 4% (95% confidence interval [CI] 1-6%) incremental yield of CMA over karyotyping in nonmalformed growth-restricted fetuses, and a 10% (95% CI 6-14%) incremental yield in FGR when associated with fetal malformations. The most frequently found pathogenic CNVs were 22q11.2 duplication, Xp22.3 deletion, and 7q11.23 deletion (Williams-Beuren syndrome), particularly in isolated FGR. <b><i>Conclusion:</i></b> The use of genomic CMA provides a 4% incremental yield of detecting pathogenic CNVs in fetuses with isolated growth restriction and normal karyotype.