cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.8224130
title: Supplementary Material for: A Case-Control Study of the Association of the Polymorphisms of <b><i>MTHFR</i></b> and <b><i>APOE</i></b> with Risk Factors and the Severity of Coronary Artery Disease

description: <b><i>Objectives:</i></b> To explore the association between single-nucleotide polymorphisms (SNPs) in <i>MTHFR</i> and <i>APOE</i> and the risk of CAD and, more importantly, the severity of CAD and the profile of serum lipids, we performed a case-control study in a Chinese Han population. <b><i>Methods:</i></b> A total of 1,207 cases of consecutive CAD-suspected inpatients were recruited, and 406 CAD cases and 231 non-CAD controls were enrolled for the final analysis after screening for exclusion criteria. All subjects had undergone coronary angiography, and the severity of CAD was evaluated by 2 cardiologists according to the Gensini scores. The genotypes of <i>MTHFR</i> and <i>APOE</i>were detected using real-time PCR, and then verified by Sanger sequencing. Environmental risk factors, such as age, sex, smoking, alcohol consumption, hypertension, diabetes, dyslipidemia, and BMI were collected. Statistical analyses (the χ<sup>2</sup> test, binary logistic regression analysis, and ordinal polytomous logistic regression analysis) were performed with SPSS v16.0. <b><i>Results:</i></b> The genotypes of<b><i></i></b>all the subjects included in the CAD and non-CAD groups in this study were successfully detected, with an agreement of 100% with Sanger sequencing. The distributions of genotypes<i> CT</i> and <i>TT</i> at <i>MTHFR C667T</i> were higher in CAD cases than in non-CAD controls (OR 1.99, 95% CI 1.34–2.95; OR 1.77, 95% CI 1.18–2.67; <i>p</i> &lt; 0.05), whereas genotype <i>AC</i> at <i>MTHFR A1298C</i>was lower in CAD cases (OR 0.71, 95% CI 0.50–1.02; <i>p</i> &lt; 0.05). A significant association was observed in genotypes <i>CT</i> and <i>TT</i> at <i>MTHFR C667T</i> and the risk of CAD (OR 1.44, 95% CI 1.27–3.67; OR 1.56, 95% CI 0.88–2.78;<i> p</i> &lt; 0.05). Both genotypes and alleles of <i>APOE</i> were comparable in the CAD cases and non-CAD controls (<i>p</i> &gt; 0.05). The genotype <i>TT</i> at <i>MTHFR C667T</i> and ε4<i>+</i> at <i>APOE</i> were more likely to be found in the CAD subgroup with a Gensini score ≥72 (<i>p</i> = 0.040 and <i>p</i> = 0.028, respectively). Meanwhile, in the patients with genotype <i>TT</i>,<i></i>a higher level of serum Hcy was detected, while genotype ε4+ patients possessed higher levels of serum apolipoprotein E (ApoE) and low-density lipoprotein cholesterol (LDL-C) than other genotypes. <b><i>Conclusion:</i></b> This study revealed that the SNP site of <i>MTHFR C667T</i>is associated<i></i>with the risk of CAD in this Chinese Han population. In addition, the genotypes of <i>TT</i> in <i>MTHFR C667T</i> and ε4<i>+</i>in <i>APOE</i> may increase the severity of CAD, and higher Hcy, LDL-C, and ApoE levels may be involved in this pathogenic process.
DOI: 10.6084/m9.figshare.8224175
title: Habitat loss does not always entail negative genetic consequences

description: Genotype and sequence data for two plant species: Brasilianthus carajensis (Melastomataceae) and Monogereion carajensis (Asteraceae). For each species we provide geographic coordinates in decimal degrees, genotypes in Variant Call Format and sequences in FASTA format.<br>The data belongs to the following published preprint:<br>Carvalho C da S., Lanes ECM., Silva AR., Caldeira CF., Carvalho-Filho N., Gastauer M., Imperatriz-Fonseca VL., Nascimento W., Oliveira G., Siqueira JO., Viana PL., Jaffe R. 2019. Habitat loss does not always entail negative genetic consequences. bioRxiv:528430. DOI: 10.1101/528430.<br>
DOI: 10.6084/m9.figshare.8224118
title: Genetic screening of Russian Usher syndrome patients toward selection for gene therapy

description: <b>Background</b>: Usher syndrome (USH) is heterogeneous in nature and requires genetic test for diagnosis and management. Mutations in USH associated genes are reported in some populations except Russians. Here, we first time represented the mutation spectrum of a Russian USH cohort. <b>Methods</b>: Twenty-eight patients with USH were selected from 3214 patients from Deaf-Blind Support Foundation “Con-nection” during 2014–2016 following the observational study NCT03319524. Complete ophthalmologic, ENT, and vestibular medical tests were done for clinical characterization. NGS, MLPA, and Sanger sequencing were considered for genetic analysis. <b>Results</b>: Around 53.57% and 39.28% patients had USH1 and USH2, respectively; 17.85% cases (n = 5/28) had no known mutation. Eleven (73.33%) subjects showed variations in USH1 associated genes <i>MYO7A</i> (72.72%), <i>CDH23</i> (9.09%), <i>PCDH15</i> (9.09%), and USH1C (9.09%). Eleven mutations are detected in MYO7A where 54.54% are novel. <i>MYO7A</i>: p.Q18* was most frequent (27.27%) mutation and is associated with early manifestation and most severe clinical picture. Two novel mutations (p.E1301* and c.158-?_318+?del) are detected in <i>PCDH15</i> gene. Around 90.90% patients suspected to be USH2 are confirmed by genetic testing. Eleven mutations detected in the <i>USH2A</i> gene, where 27.27% were novel. Most common <i>USH2A</i> mutation is p.W3955* (50%) followed by p.E767fs, p.R1653*, and c.8682-9A&gt; G (20% each). <b>Conclusion</b>: The Russian USH cohort shows both novel and known USH mutations. Clinically the prevalence of USH2 is low (39.28%) and the frequency of <i>MYO7A</i> mutations responsible for USH1B is very high (63.63%, N = 7/11) compared to other cohorts. These seven patients carrying <i>MYO7A</i> mutations are preliminarily eligible for the UshStat® gene therapy.
DOI: 10.6084/m9.figshare.8224118.v1
title: Genetic screening of Russian Usher syndrome patients toward selection for gene therapy

description: <b>Background</b>: Usher syndrome (USH) is heterogeneous in nature and requires genetic test for diagnosis and management. Mutations in USH associated genes are reported in some populations except Russians. Here, we first time represented the mutation spectrum of a Russian USH cohort. <b>Methods</b>: Twenty-eight patients with USH were selected from 3214 patients from Deaf-Blind Support Foundation “Con-nection” during 2014–2016 following the observational study NCT03319524. Complete ophthalmologic, ENT, and vestibular medical tests were done for clinical characterization. NGS, MLPA, and Sanger sequencing were considered for genetic analysis. <b>Results</b>: Around 53.57% and 39.28% patients had USH1 and USH2, respectively; 17.85% cases (n = 5/28) had no known mutation. Eleven (73.33%) subjects showed variations in USH1 associated genes <i>MYO7A</i> (72.72%), <i>CDH23</i> (9.09%), <i>PCDH15</i> (9.09%), and USH1C (9.09%). Eleven mutations are detected in MYO7A where 54.54% are novel. <i>MYO7A</i>: p.Q18* was most frequent (27.27%) mutation and is associated with early manifestation and most severe clinical picture. Two novel mutations (p.E1301* and c.158-?_318+?del) are detected in <i>PCDH15</i> gene. Around 90.90% patients suspected to be USH2 are confirmed by genetic testing. Eleven mutations detected in the <i>USH2A</i> gene, where 27.27% were novel. Most common <i>USH2A</i> mutation is p.W3955* (50%) followed by p.E767fs, p.R1653*, and c.8682-9A&gt; G (20% each). <b>Conclusion</b>: The Russian USH cohort shows both novel and known USH mutations. Clinically the prevalence of USH2 is low (39.28%) and the frequency of <i>MYO7A</i> mutations responsible for USH1B is very high (63.63%, N = 7/11) compared to other cohorts. These seven patients carrying <i>MYO7A</i> mutations are preliminarily eligible for the UshStat® gene therapy.
DOI: 10.21954/ou.rd.8224100
title: Technology In Later Life (TILL) Project (2015-2017) - Technology Survey

description: Technology Survey administered as part of the Technology In Later Life (TILL) Project (2015-2017)
DOI: 10.6084/m9.figshare.8224175.v1
title: Habitat loss does not always entail negative genetic consequences

description: Genotype and sequence data for two plant species: Brasilianthus carajensis (Melastomataceae) and Monogereion carajensis (Asteraceae). For each species we provide genotypes in Variant Call Format and sequences in FASTA format.<br>The data belongs to the following published preprint:<br>Carvalho C da S., Lanes ECM., Silva AR., Caldeira CF., Carvalho-Filho N., Gastauer M., Imperatriz-Fonseca VL., Nascimento W., Oliveira G., Siqueira JO., Viana PL., Jaffe R. 2019. Habitat loss does not always entail negative genetic consequences. bioRxiv:528430. DOI: 10.1101/528430.<br>
DOI: 10.21954/ou.rd.8224100.v1
title: Technology In Later Life (TILL) Project (2015-2017) - Technology Survey

description: Technology Survey administered as part of the Technology In Later Life (TILL) Project (2015-2017)
DOI: 10.6084/m9.figshare.8224175.v2
title: Habitat loss does not always entail negative genetic consequences

description: Genotype and sequence data for two plant species: Brasilianthus carajensis (Melastomataceae) and Monogereion carajensis (Asteraceae). For each species we provide geographic coordinates in decimal degrees, genotypes in Variant Call Format and sequences in FASTA format.<br>The data belongs to the following published preprint:<br>Carvalho C da S., Lanes ECM., Silva AR., Caldeira CF., Carvalho-Filho N., Gastauer M., Imperatriz-Fonseca VL., Nascimento W., Oliveira G., Siqueira JO., Viana PL., Jaffe R. 2019. Habitat loss does not always entail negative genetic consequences. bioRxiv:528430. DOI: 10.1101/528430.<br>
DOI: 10.6084/m9.figshare.8224025
title: Cave_dwelling_spiders_Europe

description: Cave_description.csv= A dataset with all the information about the subterranean localities included in the CAWEB project. The R notation 'NA' is used for missing values.<br>Community_composition.csv= A dataset with the spider community composition (species presence/absence data) of each subterranean locality included in the CAWEB project. <br>A detailed description of these datasets is given in the Data Paper associated with this resource. When using these datasets, please cite it as follow:<br>Mammola S, Cardoso P, Angyal D, Balázs G, Blick T, Brustel H, Carter J, Ćurčić S, Danflous S, Dányi L, Déjean S, Deltshev C, Elverici M, Fernández J, Gasparo F, Komnenov M, Komposch C, Kováč L, Kunt KB, Mock A, Moldovan O, Naumova M, Pavlek M, Prieto CE, Ribera C, Rozwałka R, Růžička V, Vargovitsh RS, Zaenker S, Isaia M (2019): Continental data on cave-dwelling spider communities across Europe (Arachnida: Araneae). Biodiversity Data Journal, 7: e38492. https://doi.org/10.3897/BDJ.7.e38492<br>An example of macroecological analysis based on this dataset is given in:<br>Mammola S, Cardoso P, Angyal D, Balázs G, Blick T, Brustel H, Carter J, Ćurčić S, Danflous S, Dányi L, Déjean S, Deltshev C, Elverici M, Fernández J, Gasparo F, Komnenov M, Komposch C, Kováč L, Kunt KB, Mock A, Moldovan O, Naumova M, Pavlek M, Prieto CE, Ribera C, Rozwałka R, Růžička V, Vargovitsh RS, Zaenker S, Isaia M (2019): Local versus broad scale environmental drivers of continental beta diversity patterns in subterranean spider communities across Europe. Proceeding of the Royal Society B: Biological Sciences, https://doi.org/10.1098/rspb.2019.1579
DOI: 10.6084/m9.figshare.8223977
title: 3h1_vs_WT_nuclei

description: Datasets for comparison of chromatin organisation in nuclei from wild-type Arabidopsis plants (Col, WT) or linker histone triple mutants (3h1) plants (~2 weeks old seedlings). 1) Images of isolated leaf nuclei stained for DNA (PI) or histone modifications as indicated in their label (lif files, readable by Fiji)2)TEM images (regions of interest) as used for chromatin density analyses (303=3h1, 277=wt, 276=3h1complemented) (Zip file, TIF images)3) FRAP series on H2B-RFP labelled nuclei used for mobility analyses (.lif file readable by Fiji/Bioformat), raw data (no crop, no registration). Datasheet, xls file with raw, normalised, relative recovery data and final graphs<br><br>Dataset related to: Rutowicz et al , (2019)Linker histones regulate fine-scale chromatin organization and modulate developmental decisions in Arabidopsis<br>
DOI: 10.6084/m9.figshare.8223974
title: Fellow Eye Deficits in Amblyopia

description: Amblyopia is a neurodevelopmental disorder of the visual system, as a result of discordant visual experience during infancy or early childhood. Because amblyopia is typically defined as monocularly reduced visual acuity accompanied by one or more known amblyogenic factors, it is often assumed that the fellow eye is normal and sufficient for tasks like reading and eye-hand coordination. Recent scientific evidence of ocular motor, visual, and visuomotor deficits that are present with fellow eye monocular viewing and with binocular viewing calls this assumption into question. This clinical update reviews the research that has revealed fellow ocular motor and visual deficits and the effect that these deficits have on an amblyopic child’s visuomotor and visuocognitive skills. We need to understand how to prevent and rehabilitate the effects of amblyopia not only on the nonpreferred eye but also on the fellow eye.
DOI: 10.6084/m9.figshare.8223977.v1
title: 3h1_vs_WT_nuclei

description: This dataset correspond to images of isolated leaf nuclei stained for DNA (PI) or histone modifications (as indicated in their label), from wild-type Arabidopsis plants (Col) or linker histone triple mutants (WT). Dataset related to: Rutowicz et al , (2019)Linker histones regulate fine-scale chromatin organization and modulate developmental decisions in Arabidopsis<br>
DOI: 10.6084/m9.figshare.8223974.v1
title: Fellow Eye Deficits in Amblyopia

description: Amblyopia is a neurodevelopmental disorder of the visual system, as a result of discordant visual experience during infancy or early childhood. Because amblyopia is typically defined as monocularly reduced visual acuity accompanied by one or more known amblyogenic factors, it is often assumed that the fellow eye is normal and sufficient for tasks like reading and eye-hand coordination. Recent scientific evidence of ocular motor, visual, and visuomotor deficits that are present with fellow eye monocular viewing and with binocular viewing calls this assumption into question. This clinical update reviews the research that has revealed fellow ocular motor and visual deficits and the effect that these deficits have on an amblyopic child’s visuomotor and visuocognitive skills. We need to understand how to prevent and rehabilitate the effects of amblyopia not only on the nonpreferred eye but also on the fellow eye.
DOI: 10.6084/m9.figshare.8223977.v3
title: 3h1_vs_WT_nuclei

description: Datasets for comparison of chromatin organisation in nuclei from wild-type Arabidopsis plants (Col, WT) or linker histone triple mutants (3h1) plants (~2 weeks old seedlings). 1) Images of isolated leaf nuclei stained for DNA (PI) or histone modifications as indicated in their label (lif files, readable by Fiji)2)TEM images (regions of interest) as used for chromatin density analyses (303=3h1, 277=wt, 276=3h1complemented) (Zip file, TIF images)3) FRAP series on H2B-RFP labelled nuclei used for mobility analyses (.lif file readable by Fiji/Bioformat), raw data (no crop, no registration). Datasheet, xls file with raw, normalised, relative recovery data and final graphs<br><br>Dataset related to: Rutowicz et al , (2019)Linker histones regulate fine-scale chromatin organization and modulate developmental decisions in Arabidopsis<br>
DOI: 10.6084/m9.figshare.8223965
title: #CC118.txt

description: sequence of CC118 gblock
DOI: 10.6084/m9.figshare.8223965.v1
title: #CC118.txt

description: sequence of CC118 gblock
DOI: 10.6084/m9.figshare.8223977.v2
title: 3h1_vs_WT_nuclei

description: This dataset correspond to images of isolated leaf nuclei stained for DNA (PI) or histone modifications (as indicated in their label), from wild-type Arabidopsis plants (Col) or linker histone triple mutants (WT). The Zip file TEM_ROI corresponds to TEM images (regions of interest) as used for chromatin density analyses (303=3h1, 277=wt, 276=3h1complemented)<br>Dataset related to: Rutowicz et al , (2019)Linker histones regulate fine-scale chromatin organization and modulate developmental decisions in Arabidopsis<br>
DOI: 10.6084/m9.figshare.8223941
title: Genetic structure and phylogeographic relationships of <i>Fagus sylvatica</i> L. woods in Lazio (Central Italy)

description: The genetic characterisation of beech woods in Lazio was performed by microsatellite approach. The phylogeographic relationship existing among stands was investigated, allowing us to identify a putative glacial refugium for this species. This work provides information for management policies and conservation strategies of <i>F. sylvatica</i> germplasm resources in central Italy.
DOI: 10.6084/m9.figshare.8223938
title: Efficiency and allometry of seed production in grassland forbs: site and year comparative study in the Italian Eastern Pre-Alps

description: Forbs are important biodiversity components of grasslands and are often threatened by management intensification. As most forbs propagate predominantly by seed, knowledge of their seed regenerative traits would improve the conservation and restoration of forb-rich ecosystems. The main seed production traits of six forbs that are common in European species-rich grasslands were studied by collecting fertile shoots from different sites and over several years. Among sites and years, variability was high, particularly in the number of inflorescences per shoot, which affected ovule production more than any other trait. Relationships between inflorescence size and the number of ovules were mainly negatively allometric or almost so, with lower flower densities in larger inflorescences. The average ovule-to-seed transformation efficiency was 58%. There was significant variation among collections of the same species, and even more between species. Species with a low ovule-to-seed transformation efficiency generally exhibited compensatory, high seed viability. Large inflorescences had high ovule to seed utilization values, probably because of better nutrient conditions. Seed germinability (average, 30%) was much lower than seed viability (average, 54%); therefore, seed dormancy was an important feature of the species studied.
DOI: 10.6084/m9.figshare.8223941.v1
title: Genetic structure and phylogeographic relationships of <i>Fagus sylvatica</i> L. woods in Lazio (Central Italy)

description: The genetic characterisation of beech woods in Lazio was performed by microsatellite approach. The phylogeographic relationship existing among stands was investigated, allowing us to identify a putative glacial refugium for this species. This work provides information for management policies and conservation strategies of <i>F. sylvatica</i> germplasm resources in central Italy.
DOI: 10.6084/m9.figshare.8223938.v1
title: Efficiency and allometry of seed production in grassland forbs: site and year comparative study in the Italian Eastern Pre-Alps

description: Forbs are important biodiversity components of grasslands and are often threatened by management intensification. As most forbs propagate predominantly by seed, knowledge of their seed regenerative traits would improve the conservation and restoration of forb-rich ecosystems. The main seed production traits of six forbs that are common in European species-rich grasslands were studied by collecting fertile shoots from different sites and over several years. Among sites and years, variability was high, particularly in the number of inflorescences per shoot, which affected ovule production more than any other trait. Relationships between inflorescence size and the number of ovules were mainly negatively allometric or almost so, with lower flower densities in larger inflorescences. The average ovule-to-seed transformation efficiency was 58%. There was significant variation among collections of the same species, and even more between species. Species with a low ovule-to-seed transformation efficiency generally exhibited compensatory, high seed viability. Large inflorescences had high ovule to seed utilization values, probably because of better nutrient conditions. Seed germinability (average, 30%) was much lower than seed viability (average, 54%); therefore, seed dormancy was an important feature of the species studied.
DOI: 10.6084/m9.figshare.8223839
title: Supplementary Material for: Systematic Review and Meta-Analysis of Postoperative Antibiotics for Patients with a Complex Appendicitis

description: Postoperative antibiotics are recommended after appendectomy for complex appendicitis to reduce infectious complications. The duration of this treatment varies considerably between and even within institutions. The aim of this review was to critically appraise studies on duration of antibiotic treatment following appendectomy for complex appendicitis. A systematic literature search according to the PRISMA guidelines was performed. Comparative studies evaluating different durations of postoperative antibiotic therapy. Primary endpoint was intra-abdominal abscess (IAA) after appendectomy. Secondary endpoints were surgical site infection, readmission and length of hospital stay. The quality of evidence was assessed with the Grading of Recommendations Assessment, Development and Evaluation (GRADE) tool. Pooled event rates were calculated using a random-effects model. Nine studies reporting 2006 patients with complex appendicitis were included. The methodological quality of the included articles was poor. IAA was seen in 138 patients (8,6%). Meta-analysis revealed a statistically significant difference in IAA incidence between antibiotic treatment of ≤5 vs. &gt;5 days (risk ratio (OR) 0.36 [95% CI 0.23–0.57] (<i>p</i> &lt; 0.0001)) but not between ≤3 vs. &gt;3 days (OR 0.81 [95% CI 0.38–1.74] (<i>p</i> = 0.59)). Descriptive statistics were used for secondary endpoints. The duration of postoperative antibiotic treatment is not associated with IAA following appendectomy for complex appendicitis.
DOI: 10.6084/m9.figshare.8223833
title: Supplementary Material for: Relevance of Collaterals for the Success of Neuroprotective Therapies in Acute Ischemic Stroke: Insights from the Randomized URICO-ICTUS Trial

description: <b><i>Background:</i></b> Collateral circulation may modify the effect of neuroprotective therapies. We report a post hoc analysis of the URICO-ICTUS trial (NCT00860366) assessing the modifying treatment effect of pretreatment collaterals on clinical and radiological outcomes in patients with large-vessel acute ischemic stroke receiving uric acid therapy or placebo. <b><i>Methods:</i></b> URICO-ICTUS was a randomized clinical trial where 411 alteplase-treated patients also received uric acid 1,000 mg (<i>n</i> = 211) or placebo (<i>n</i> = 200) before the end of alteplase infusion. Herein, we included a nested study of 84 patients (placebo = 40, uric acid = 44) who had a pretreatment CT-angiography (CTA) showing a proximal arterial occlusion in the carotid territory. Excellent collaterals were defined as 100% collateral supply on pretreatment CTA. Regression models assessed the interaction between therapy (uric acid/placebo) and collaterals on the main outcome (ordinal modified Rankin Scale [mRS] shift at 90 days). <b><i>Results:</i></b> Overall, excellent collaterals were associated with improved outcome. There was a significant interaction between therapy and pretreatment collaterals (<i>p</i> interaction = 0.02) for the prediction of improved mRS shift. The largest treatment contrast in favor of uric acid was found in patients with excellent collaterals (adjusted OR 9.2; 95% CI 1.23–68.6; <i>p</i> = 0.03). <b><i>Conclusions:</i></b> Collectively, the study found that collaterals were associated with the neuroprotective effect of uric acid therapy highlighting the importance of assessing collateral status in neuroprotection trials.