cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.8094758.v1
title: Changes in asthma severity in the first year of school and difficulty learning to read

description: <b>Objective:</b> Asthma is a risk factor for poor early reading in children, for reasons that are unclear. This analysis examines the relationship between changes in asthma severity during the first year of school and being in the lowest quartile of reading achievement after 1 year of school. <b>Methods:</b> We used previously unreported data from our cohort study. Parent interviews and teacher questionnaires enquired about asthma and covariates of achievement at school entry (T1) and 12 months later (T2). Asthma severity scores at T1 and T2 showed that in 27 of 51 children with asthma, symptoms improved over the year, whereas in 24, symptoms persisted or worsened. Word and story reading were assessed at T1 and T2. We compared reading achievement at both timepoints between children with asthma and children who had no reported respiratory symptoms between birth and T2 (controls, <i>N</i> = 74), and between those with persistent versus improved symptoms. <b>Results:</b> More children with asthma than controls were in the lowest quartiles for reading. Further, significantly more children in the persistent group compared to the improved group were in the lowest quartiles for word reading (58 versus 30%, respectively) and story reading (54 versus 26%, respectively). School absences, increased behavior problems, stressful life events or parental mental health were not associated with the differences in either comparison. Logistic regression modeling identified persistent asthma as the most important variable associated with being in the lowest quartile of reading after 1 year in school. <b>Conclusions:</b> Active asthma symptoms during early school may influence early reading achievement.
DOI: 10.6084/m9.figshare.8094737.v1
title: Radiation-induced brachial plexus toxicity after SBRT of apically located lung lesions

description: <b>Purpose</b>: To evaluate the rate and dose response of brachial plexus toxicity post stereotactic body radiation therapy (SBRT) of apically situated lung lesions. <b>Material/methods:</b> We retrospectively identified all patients with apically located tumors, defined by the epicenter of the tumor being located superiorly to the aortic arch, and treated with SBRT between 2008 and 2013. Patients with a shorter follow-up than 6 months were excluded. Primary aim was to evaluate radiation-induced brachial plexopathy (RIBP). Dose to the plexus was assessed by a retrospective delineation of the brachial plexus on the CT used for treatment planning. Then, <i>D</i><sub>max</sub>, <i>D</i><sub>0.1cc</sub>, <i>D</i><sub>1cc</sub> and <i>D</i><sub>3.0cc</sub> of the brachial plexus were collected from the dose-volume histograms (DVH) and recalculated to the biologically effective dose (BED) using α/β = 3 Gy. A normal tissue complication probability (NTCP) model, based on four different dose-volume parameters (BED<sub>3,max</sub>, BED<sub>3,0.1cc,</sub> BED<sub>3,1.0cc,</sub> BED<sub>3,3.0cc</sub>) was fitted to the data. <b>Results:</b> Fifty-two patients with 56 apically located tumors were identified. Median prescription dose per fraction was 15 Gy (range 6–17) and median number of fractions was 3 (3–10). With a median follow-up of 30 months (6.1–72) seven patients experienced maximum grade 2 (scored 3 times) or 3 (scored 4 times) RIBP after a median of 8.7 months (range 4.0–31). Three patients had combined symptoms with pain, sensory and motor affection and four patients had isolated pain. Median BED<sub>3,max</sub> for the patients experiencing RIBP was 381 Gy (range 30–524) versus BED<sub>3,max</sub> of 34 Gy (range 0.10–483) for the patients without RIBP. The NTCP models showed a very high predictive ability (area under the receiver operating characteristic curve (AUC) 0.80–0.88). <b>Conclusion:</b> SBRT of apically located lung lesions may cause severe neurological symptoms; for a three-fraction treatment, we suggest that the maximum dose to the plexus should be kept ≤30 Gy (130 Gy BED<sub>3</sub>).
DOI: 10.6084/m9.figshare.8094728.v1
title: Anatomy and systematics of <i>Notohippus toxodontoides</i> Ameghino, 1891 (Mammalia, Notoungulata), from the Miocene of Santa Cruz Province, Argentina

description: The specimens described herein come from the Río Bote locality, Santa Cruz Formation (early Miocene), Santa Cruz Province, Argentina. They include the most complete cranial material of the ‘Notohippidae’ <i>Notohippus toxodontoides</i> and other remains that increase knowledge of the mandible and dentition<i>.</i> The new remains allow extension of the original description proposed by Ameghino in the 19th century and provide data on ontogenetic variation in the dental traits of this species. <i>Notohippus</i> differs from the Deseadan–Colhuehuapian genus <i>Argyrohippus</i> in the following features: discontinuous dentition; C and p1 absent; shorter P2–M3/p2–m3 series; crown of I1 highly curved; upper molars with less developed parastyle and paracone fold, less undulating ectoloph, deeper distolingual groove of M3 directed more lingually and presence of a very shallow distolabial groove; incisiform lower canine; and lower molars with posterolabial angle of talonid more rounded and narrower trigonid valley. As stated in previous works, our phylogenetic analysis indicates that the ‘Notohippidae’ do not constitute a monophyletic group, because <i>Argyrohippus</i>, <i>Notohippus</i>, and Toxodontidae are recovered as a clade. Internal relationships within this clade are not resolved in any of the phylogenetic analyses performed here. The presence of <i>N. toxodontoides</i> in the faunal assemblage found at the Río Bote locality adds to its previous records in Santa Cruz (Kar-Aiken and Cerro Centinela localities) Province, Argentina, and Sierra Baguales locality in Chile.
DOI: 10.6084/m9.figshare.8094581
title: Exploring the capacity of endophytic fungi isolated from medicinal plants for fermentation and phenolics biotransformation of rose oil distillation wastewater

description: A total of 139 endophytic fungal isolates derived from 20 medicinal and aromatic plants were tested for their capacity to ferment rose oil distillation wastewater (RODW). Internal transcribed spacer sequence-based phylogenetic analysis affiliated the collected isolates to seven genera and nine different species, of which <i>Alternaria alternata</i> was the most widely represented. The fungal fermentation of RODW was evaluated through analysis of the sugar and phenolics content and phenolics composition. After cultivation in a small volume of RODW, the performed cluster analysis grouped the isolates in four distinct clusters according to their capacity to ferment RODW sugars and phenolics. Further larger volume shake-flask cultivation of a selected subset of fungi with a pronounced RODW fermentation capacity, outlined three groups of isolates with a distinct pattern and dynamics of sugars and phenolics fermentation. High-performance liquid chromatography analysis of RODW phenolics extracts following the fermentation by the selected fungal isolates showed two main types of changes in phenolics composition: (1) changes in the relative abundance of part of the RODW phenolic compounds, mainly due to utilization of sugar residues from the RODW phenolic glycosides and (2) biosynthesis of new phenolic compounds, most of which are specific to the endophytic fungal isolates used for RODW fermentation. The overall results of the study clearly demonstrate that endophytic fungal isolates represent a rich and untapped source for efficient fermentation of RODW and other agro-industrial phenolics-rich wastewaters and highlight their capacity for directional changes and modification of RODW phenolics composition towards further wastewater phenolics valorization.
DOI: 10.6084/m9.figshare.8094587
title: Antifungal effects of the flavonoids kaempferol and quercetin: a possible alternative for the control of fungal biofilms

description: This study aimed to determine the minimum inhibitory concentration (MIC) of kaempferol and quercetin against planktonic and biofilm forms of the <i>Candida parapsilosis</i> complex. Initially, nine <i>C. parapsilosis sensu stricto</i>, nine <i>C. orthopsilosis</i> and nine <i>C. metapsilosis</i> strains were used. Planktonic susceptibility to kaempferol and quercetin was assessed. Growing and mature biofilms were then exposed to the flavonoids at MIC or 10xMIC, respectively, and theywere also analyzed by confocal laser scanning microscopy. The MIC ranges were 32-128 µg ml<sup>−1</sup> for kaempferol and 0.5-16 µg ml<sup>−1</sup> for quercetin. Kaempferol and quercetin decreased (P C. <i>parapsilosis</i> complex. As for mature biofilms, the metabolic effects of the flavonoids varied, according to the cryptic species, but kaempferol caused an overall reduction in biofilm biomass. Microscopic analyses showed restructuring of biofilms after flavonoid exposure. These results highlight the potential use of these compounds as sustainable resources for the control of fungal biofilms.
DOI: 10.6084/m9.figshare.8094581.v1
title: Exploring the capacity of endophytic fungi isolated from medicinal plants for fermentation and phenolics biotransformation of rose oil distillation wastewater

description: A total of 139 endophytic fungal isolates derived from 20 medicinal and aromatic plants were tested for their capacity to ferment rose oil distillation wastewater (RODW). Internal transcribed spacer sequence-based phylogenetic analysis affiliated the collected isolates to seven genera and nine different species, of which <i>Alternaria alternata</i> was the most widely represented. The fungal fermentation of RODW was evaluated through analysis of the sugar and phenolics content and phenolics composition. After cultivation in a small volume of RODW, the performed cluster analysis grouped the isolates in four distinct clusters according to their capacity to ferment RODW sugars and phenolics. Further larger volume shake-flask cultivation of a selected subset of fungi with a pronounced RODW fermentation capacity, outlined three groups of isolates with a distinct pattern and dynamics of sugars and phenolics fermentation. High-performance liquid chromatography analysis of RODW phenolics extracts following the fermentation by the selected fungal isolates showed two main types of changes in phenolics composition: (1) changes in the relative abundance of part of the RODW phenolic compounds, mainly due to utilization of sugar residues from the RODW phenolic glycosides and (2) biosynthesis of new phenolic compounds, most of which are specific to the endophytic fungal isolates used for RODW fermentation. The overall results of the study clearly demonstrate that endophytic fungal isolates represent a rich and untapped source for efficient fermentation of RODW and other agro-industrial phenolics-rich wastewaters and highlight their capacity for directional changes and modification of RODW phenolics composition towards further wastewater phenolics valorization.
DOI: 10.6084/m9.figshare.8094587.v1
title: Antifungal effects of the flavonoids kaempferol and quercetin: a possible alternative for the control of fungal biofilms

description: This study aimed to determine the minimum inhibitory concentration (MIC) of kaempferol and quercetin against planktonic and biofilm forms of the <i>Candida parapsilosis</i> complex. Initially, nine <i>C. parapsilosis sensu stricto</i>, nine <i>C. orthopsilosis</i> and nine <i>C. metapsilosis</i> strains were used. Planktonic susceptibility to kaempferol and quercetin was assessed. Growing and mature biofilms were then exposed to the flavonoids at MIC or 10xMIC, respectively, and theywere also analyzed by confocal laser scanning microscopy. The MIC ranges were 32-128 µg ml<sup>−1</sup> for kaempferol and 0.5-16 µg ml<sup>−1</sup> for quercetin. Kaempferol and quercetin decreased (P C. <i>parapsilosis</i> complex. As for mature biofilms, the metabolic effects of the flavonoids varied, according to the cryptic species, but kaempferol caused an overall reduction in biofilm biomass. Microscopic analyses showed restructuring of biofilms after flavonoid exposure. These results highlight the potential use of these compounds as sustainable resources for the control of fungal biofilms.
DOI: 10.6084/m9.figshare.8094524
title: Dataset Glaucoma Symptom Scale

description: Results of the Serbian GSS
DOI: 10.6084/m9.figshare.8094515.v1
title: Model files for CTseg

description: These are the model files for the CTseg toolbox of SPM12, used to segment computed tomography (CT) scans. The toolbox is available at: https://github.com/WCHN/CTseg<br>
DOI: 10.25934/00003610.0
title: Available IPD datapackage for study 'A Phase III Randomised, Double-blind, Placebo-controlled, Parallel Group, Efficacy and Safety Study of BI 10773 (10 mg, 25 mg) Administered Orally, Once Daily Over 24 Weeks in Patients With Type 2 Diabetes Mellitus With Insufficient Glycaemic Control Despite Treatment With Metformin Alone or Metformin in Combination With a Sulfonylurea'

description: Vivli is an independent, non-profit organization that has developed a global data-sharing and analytics platform to serve all elements of the international research community. Our mission is to promote, coordinate, and facilitate scientific sharing and reuse of clinical research data through the creation and implementation of a sustainable global data-sharing enterprise. The Vivli platform includes an independent data repository, in-depth search engine and a cloud-based, secure analytics platform.
DOI: 10.25934/00003610.1
title: IPD datapackage for study 'A Phase III Randomised, Double-blind, Placebo-controlled, Parallel Group, Efficacy and Safety Study of BI 10773 (10 mg, 25 mg) Administered Orally, Once Daily Over 24 Weeks in Patients With Type 2 Diabetes Mellitus With Insufficient Glycaemic Control Despite Treatment With Metformin Alone or Metformin in Combination With a Sulfonylurea' and research request: 'Stratification of SGLT2 inhibitor glucose lowering therapy in Type 2 diabetes'

description: Vivli is an independent, non-profit organization that has developed a global data-sharing and analytics platform to serve all elements of the international research community. Our mission is to promote, coordinate, and facilitate scientific sharing and reuse of clinical research data through the creation and implementation of a sustainable global data-sharing enterprise. The Vivli platform includes an independent data repository, in-depth search engine and a cloud-based, secure analytics platform.
DOI: 10.6084/m9.figshare.8094515.v2
title: Model files for CTseg

description: These are the model files for the CTseg toolbox of SPM12, used to segment computed tomography (CT) scans. The toolbox is available at: https://github.com/WCHN/CTseg<br>
DOI: 10.6084/m9.figshare.8094362
title: links.bulk.csv

description: Using a web scraper, we checked the status of internet links detected in scientific papers.<br><br>The data schema is detailed below:<br>* type - In which part of the manuscript the link was found.<br>* journal - Title of the journal where the paper was published.<br>* id - Pubmed's primary identifier for the paper.<br>* year - When the paper was published.<br>* link - URL parsed from the manuscript text.<br>* code - HTTP/FTP status code returned when trying to access the URL. (-1 indicates a timeout.)<br>* flag.uniqueness - Whether the link appears only once in the data. '0' means it is unique.<br>* newtest - The protocol used to determine the status code in our revised pipeline. Only listed for links that were reevaluated.<br>* oldcode - The status recorded for this link prior to the pipeline revision. Only listed for links that were reevaluated.
DOI: 10.6084/m9.figshare.8094362.v1
title: links.bulk.csv

description: Using a web scraper, we checked the status of internet links detected in scientific papers.<br><br>The data schema is detailed below:<br>* type - In which part of the manuscript the link was found.<br>* journal - Title of the journal where the paper was published.<br>* id - Pubmed's primary identifier for the paper.<br>* year - When the paper was published.<br>* link - URL parsed from the manuscript text.<br>* code - HTTP/FTP status code returned when trying to access the URL. (-1 indicates a timeout.)<br>* flag.uniqueness - Whether the link appears only once in the data. '0' means it is unique.<br>* newtest - The protocol used to determine the status code in our revised pipeline. Only listed for links that were reevaluated.<br>* oldcode - The status recorded for this link prior to the pipeline revision. Only listed for links that were reevaluated.
DOI: 10.6084/m9.figshare.8094116
title: Supplementary Material for: Single-Field Non-Mydriatic Fundus Photography for Diabetic Retinopathy Screening: A Systematic Review and Meta-Analysis

description: <b><i>Purpose:</i></b> Single-field non-mydriatic fundus photography (NMFP) has been used to detect diabetic retinopathy (DR) in many studies; however, its value in a general clinical setting has not been established. Here we performed a meta-analysis to evaluate its diagnostic effectiveness. <b><i>Method:</i></b> We systematically searched PubMed, EMBASE, and Cochrane databases for candidate studies published through May 19, 2018. A random-effect model was used to calculate the diagnostic indicators including the sensitivity, specificity, positive likelihood ratio (PLR), negative likelihood ratio (NLR), diagnostic odds ratio (DOR), area under the curve (AUC), and 95% confidence intervals. <b><i>Results:</i></b> Ten prospective studies were ultimately included. The pooled sensitivity, specificity, PLR, NLR, and DOR were 0.68, 0.94, 11.2, 0.34 and 33, respectively. The AUC was 0.88. Subgroup analysis showed that single-field NMFP had a respective sensitivity and specificity of 0.73 and 0.91 when compared to standard 7-field mydriatic stereoscopic photography (7SF), and 0.54 and 0.98 when compared to slit-lamp biomicroscopy as reference standard. <b><i>Conclusions:</i></b> Single-field NMFP is inadequate to detect DR. Additionally, it showed higher sensitivity and lower specificity when 7SF was used as reference standard, as compared to slit-lamp biomicroscopy, suggesting that different reference standards used in DR screening might have affected the diagnostic results.
DOI: 10.6084/m9.figshare.8094119
title: Baselines for the WMT 2019 Biomedical Translation Shared Task

description: This repository contains the OpenNMT-py files for the models developed as baselines for the WMT19 Biomedical Translation Shared Task.
DOI: 10.6084/m9.figshare.8094098.v1
title: Genetic determination of sex and shell color in the Pacific abalone Haliotis discus hannai revealed by an integrated linkage map

description: Genotype data for the mapping families; Phenotype data for shell color and sex.
DOI: 10.6084/m9.figshare.8094119.v1
title: Baselines for the WMT 2019 Biomedical Translation Shared Task

description: This repository contains the OpenNMT-py files for the models developed as baselines for the WMT19 Biomedical Translation Shared Task.
DOI: 10.6084/m9.figshare.8094080.v1
title: Genetic determination of sex and shell color in the Pacific abalone Haliotis discus hannai revealed by an integrated linkage map

description: Genotype data for the mapping families; Phenotype data for shell color and sex.
DOI: 10.6084/m9.figshare.8094014
title: Diverse yet endangered: pollen dispersal and mating system reveal inbreeding in a narrow endemic plant

description: <b>Background</b>: Mating system and allele dispersal through pollen and seeds influence population genetic constitution and are directly associated with structure and diversity. <i>Petunia secreta</i> is a rare and endemic species that is characterised by high levels of genetic variability and, despite being dependent on bee-pollination, its breeding system is unknown. <b>Aims</b>: In order to understand how a rare and narrowly distributed species presents levels of genetic diversity compatible with that of widely distributed congeneric species, the aims of this study were to investigate the mating system of <i>P. secreta</i>; to evaluate its pollen and seed dispersal; and to estimate the level of inbreeding. <b>Methods</b>: We geographically mapped and genotyped all adult individuals from the type origin of <i>P. secreta</i> during one reproductive season and 125 offspring originating from 11 mother plants at nine polymorphic microsatellite loci and using population genetics tools and paternity analysis. <b>Results</b>: No geographical structure was observed in adult individuals. The species has mixed mating system, with predominant self-fertilisation and few outcrossing events. All outcrossing events occurred within the respective maternal plant’s collection site. High, positive <i>F</i><sub>is</sub> values were observed among adult plants, and inbreeding depression was observed in progenies. <b>Conclusions</b>: In the long term, the main threat for this species consists of the high level of inbreeding depression resulting mainly from the biparental inbreeding, which affects the genetic diversity. These results should be considered in the development of strategies for <i>in situ</i> species conservation.
DOI: 10.6084/m9.figshare.8094014.v1
title: Diverse yet endangered: pollen dispersal and mating system reveal inbreeding in a narrow endemic plant

description: <b>Background</b>: Mating system and allele dispersal through pollen and seeds influence population genetic constitution and are directly associated with structure and diversity. <i>Petunia secreta</i> is a rare and endemic species that is characterised by high levels of genetic variability and, despite being dependent on bee-pollination, its breeding system is unknown. <b>Aims</b>: In order to understand how a rare and narrowly distributed species presents levels of genetic diversity compatible with that of widely distributed congeneric species, the aims of this study were to investigate the mating system of <i>P. secreta</i>; to evaluate its pollen and seed dispersal; and to estimate the level of inbreeding. <b>Methods</b>: We geographically mapped and genotyped all adult individuals from the type origin of <i>P. secreta</i> during one reproductive season and 125 offspring originating from 11 mother plants at nine polymorphic microsatellite loci and using population genetics tools and paternity analysis. <b>Results</b>: No geographical structure was observed in adult individuals. The species has mixed mating system, with predominant self-fertilisation and few outcrossing events. All outcrossing events occurred within the respective maternal plant’s collection site. High, positive <i>F</i><sub>is</sub> values were observed among adult plants, and inbreeding depression was observed in progenies. <b>Conclusions</b>: In the long term, the main threat for this species consists of the high level of inbreeding depression resulting mainly from the biparental inbreeding, which affects the genetic diversity. These results should be considered in the development of strategies for <i>in situ</i> species conservation.