cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.19723596.v2
title: Whole genome sequencing and phylogenomic analysis show support for the splitting of genus <i>Pythium</i>

description: The genus <i>Pythium</i> (nom. cons.) sensu lato (s.l.) is composed of many important species of plant pathogens. Early molecular phylogenetic studies suggested paraphyly of <i>Pythium</i>, which led to a formal proposal by Uzuhashi and colleagues in 2010 to split the genus into <i>Pythium</i> sensu stricto (s.s.), <i>Elongisporangium, Globisporangium, Ovatisporangium</i> (= <i>Phytopythium</i>), and <i>Pilasporangium</i> using morphological characters and phylogenies of the mt cytochrome <i>c</i> oxidase subunit 2 (<i>cox2</i>) and D1–D2 domains of nuc 28S rDNA. Although the split was fairly justified by the delineating morphological characters, there were weaknesses in the molecular analyses, which created reluctance in the scientific community to adopt these new genera for the description of new species. In this study, this issue was addressed using phylogenomics. Whole genomes of 109 strains of <i>Pythium</i> and close relatives were sequenced, assembled, and annotated. These data were combined with 10 genomes sequenced in previous studies. Phylogenomic analyses were performed with 148 single-copy genes represented in at least 90% of the taxa in the data set. The results showed support for the division of <i>Pythium</i> s.l. The status of alternative generic names that have been used for species of <i>Pythium</i> in the past (e.g., <i>Artotrogus, Cystosiphon, Eupythium, Nematosporangium, Rheosporangium, Sphaerosporangium</i>) was investigated. Based on our molecular analyses and review of the <i>Pythium</i> generic concepts, we urge the scientific community to adopt the generic names <i>Pythium, Elongisporangium, Globisporangium</i>, and their concepts as proposed by Uzuhashi and colleagues in 2010 in their work going forward. In order to consolidate the taxonomy of these genera, some of the recently described <i>Pythium</i> spp. are transferred to <i>Elongisporangium</i> and <i>Globisporangium</i>.
DOI: 10.6084/m9.figshare.19723596
title: Whole genome sequencing and phylogenomic analysis show support for the splitting of genus <i>Pythium</i>

description: The genus <i>Pythium</i> (nom. cons.) sensu lato (s.l.) is composed of many important species of plant pathogens. Early molecular phylogenetic studies suggested paraphyly of <i>Pythium</i>, which led to a formal proposal by Uzuhashi and colleagues in 2010 to split the genus into <i>Pythium</i> sensu stricto (s.s.), <i>Elongisporangium, Globisporangium, Ovatisporangium</i> (= <i>Phytopythium</i>), and <i>Pilasporangium</i> using morphological characters and phylogenies of the mt cytochrome <i>c</i> oxidase subunit 2 (<i>cox2</i>) and D1–D2 domains of nuc 28S rDNA. Although the split was fairly justified by the delineating morphological characters, there were weaknesses in the molecular analyses, which created reluctance in the scientific community to adopt these new genera for the description of new species. In this study, this issue was addressed using phylogenomics. Whole genomes of 109 strains of <i>Pythium</i> and close relatives were sequenced, assembled, and annotated. These data were combined with 10 genomes sequenced in previous studies. Phylogenomic analyses were performed with 148 single-copy genes represented in at least 90% of the taxa in the data set. The results showed support for the division of <i>Pythium</i> s.l. The status of alternative generic names that have been used for species of <i>Pythium</i> in the past (e.g., <i>Artotrogus, Cystosiphon, Eupythium, Nematosporangium, Rheosporangium, Sphaerosporangium</i>) was investigated. Based on our molecular analyses and review of the <i>Pythium</i> generic concepts, we urge the scientific community to adopt the generic names <i>Pythium, Elongisporangium, Globisporangium</i>, and their concepts as proposed by Uzuhashi and colleagues in 2010 in their work going forward. In order to consolidate the taxonomy of these genera, some of the recently described <i>Pythium</i> spp. are transferred to <i>Elongisporangium</i> and <i>Globisporangium</i>.
DOI: 10.6084/m9.figshare.19787707
title: <i>Diaporthe</i> species infecting sunflower (<i>Helianthus annuus</i>) in Russia, with the description of two new species

description: Phomopsis stem canker is economically important sunflower disease that caused by multiple <i>Diaporthe</i> species. Recent investigations resulted in the resolution that there are at least 13 <i>Diaporthe</i> species that can infect sunflower. A comprehensive analysis of the biodiversity and geographic distribution of <i>Diaporthe</i> species in Russia, particularly those that infect sunflower, has not been undertaken. For this study, 16 <i>Diaporthe</i> isolates were obtained from samples of stem canker and visually healthy seeds of <i>Helianthus annuus</i> from northwestern, central European, southern European Russia, North Caucasus, and the Urals in 2016–2019. The aim of this study was to identify these <i>Diaporthe</i> isolates based on morphology and sequence analyses of the nuclear ribosomal internal transcribed spacer (ITS) region, partial calmodulin (<i>cal</i>), DNA-lyase (<i>apn2</i>), histone H3 (<i>his3</i>), translation elongation factor-1α gene (<i>tef1</i>), and ß-tubulin (<i>tub2</i>) genes. The phylogenetic reconstruction revealed well-supported monophyletic clades corresponding to six <i>Diaporthe</i> species: <i>D. eres, D. gulyae, D. helianthi</i>, and <i>D. phaseolorum</i>. Two new species were described: <i>Diaporthe monetii</i> sp. nov. and <i>Diaporthe vangoghii</i> sp. nov. The isolates of <i>D. gulyae</i> and <i>D. phaseolorum</i> collected represent the first records of these species in Russia.
DOI: 10.6084/m9.figshare.19787707.v1
title: <i>Diaporthe</i> species infecting sunflower (<i>Helianthus annuus</i>) in Russia, with the description of two new species

description: Phomopsis stem canker is economically important sunflower disease that caused by multiple <i>Diaporthe</i> species. Recent investigations resulted in the resolution that there are at least 13 <i>Diaporthe</i> species that can infect sunflower. A comprehensive analysis of the biodiversity and geographic distribution of <i>Diaporthe</i> species in Russia, particularly those that infect sunflower, has not been undertaken. For this study, 16 <i>Diaporthe</i> isolates were obtained from samples of stem canker and visually healthy seeds of <i>Helianthus annuus</i> from northwestern, central European, southern European Russia, North Caucasus, and the Urals in 2016–2019. The aim of this study was to identify these <i>Diaporthe</i> isolates based on morphology and sequence analyses of the nuclear ribosomal internal transcribed spacer (ITS) region, partial calmodulin (<i>cal</i>), DNA-lyase (<i>apn2</i>), histone H3 (<i>his3</i>), translation elongation factor-1α gene (<i>tef1</i>), and ß-tubulin (<i>tub2</i>) genes. The phylogenetic reconstruction revealed well-supported monophyletic clades corresponding to six <i>Diaporthe</i> species: <i>D. eres, D. gulyae, D. helianthi</i>, and <i>D. phaseolorum</i>. Two new species were described: <i>Diaporthe monetii</i> sp. nov. and <i>Diaporthe vangoghii</i> sp. nov. The isolates of <i>D. gulyae</i> and <i>D. phaseolorum</i> collected represent the first records of these species in Russia.
DOI: 10.6084/m9.figshare.20006938.v1
title: The circumscription and phylogenetic position of <i>Bryonora</i> (Lecanoraceae, Ascomycota), with two additions to the genus

description: Lecanoraceae is one of the largest families of the Lecanoromycetes, with about 30 accepted genera, many of which, however, have uncertain status and/or circumscriptions. We assess the phylogenetic position of the genus <i>Bryonora</i> and its segregate <i>Bryodina</i> for the first time, using a six-locus phylogeny comprising the Lecanoraceae as well as closely related families. We find strong support for the placement of <i>Bryonora</i> in the Lecanoraceae, whereas there is no support for treating <i>Bryodina</i> as a genus separate from <i>Bryonora</i>. Hence, we reduce <i>Bryodina</i> to synonymy with <i>Bryonora</i>. Further, we describe <i>Bryonora microlepis</i> as new to science and transfer <i>Lecanora castaneoides</i> to <i>Bryonora</i> and <i>L. vicaria</i> to <i>Miriquidica</i>. A world key to <i>Bryonora</i> is included.
DOI: 10.6084/m9.figshare.19723596.v1
title: Whole genome sequencing and phylogenomic analysis show support for the splitting of genus <i>Pythium</i>

description: The genus <i>Pythium</i> (nom. cons.) sensu lato (s.l.) is composed of many important species of plant pathogens. Early molecular phylogenetic studies suggested paraphyly of <i>Pythium</i>, which led to a formal proposal by Uzuhashi and colleagues in 2010 to split the genus into <i>Pythium</i> sensu stricto (s.s.), <i>Elongisporangium, Globisporangium, Ovatisporangium</i> (= <i>Phytopythium</i>), and <i>Pilasporangium</i> using morphological characters and phylogenies of the mt cytochrome <i>c</i> oxidase subunit 2 (<i>cox2</i>) and D1–D2 domains of nuc 28S rDNA. Although the split was fairly justified by the delineating morphological characters, there were weaknesses in the molecular analyses, which created reluctance in the scientific community to adopt these new genera for the description of new species. In this study, this issue was addressed using phylogenomics. Whole genomes of 109 strains of <i>Pythium</i> and close relatives were sequenced, assembled, and annotated. These data were combined with 10 genomes sequenced in previous studies. Phylogenomic analyses were performed with 148 single-copy genes represented in at least 90% of the taxa in the data set. The results showed support for the division of <i>Pythium</i> s.l. The status of alternative generic names that have been used for species of <i>Pythium</i> in the past (e.g., <i>Artotrogus, Cystosiphon, Eupythium, Nematosporangium, Rheosporangium, Sphaerosporangium</i>) was investigated. Based on our molecular analyses and review of the <i>Pythium</i> generic concepts, we urge the scientific community to adopt the generic names <i>Pythium, Elongisporangium, Globisporangium</i>, and their concepts as proposed by Uzuhashi and colleagues in 2010 in their work going forward. In order to consolidate the taxonomy of these genera, some of the recently described <i>Pythium</i> spp. are transferred to <i>Elongisporangium</i> and <i>Globisporangium</i>.
DOI: 10.6084/m9.figshare.20006938
title: The circumscription and phylogenetic position of <i>Bryonora</i> (Lecanoraceae, Ascomycota), with two additions to the genus

description: Lecanoraceae is one of the largest families of the Lecanoromycetes, with about 30 accepted genera, many of which, however, have uncertain status and/or circumscriptions. We assess the phylogenetic position of the genus <i>Bryonora</i> and its segregate <i>Bryodina</i> for the first time, using a six-locus phylogeny comprising the Lecanoraceae as well as closely related families. We find strong support for the placement of <i>Bryonora</i> in the Lecanoraceae, whereas there is no support for treating <i>Bryodina</i> as a genus separate from <i>Bryonora</i>. Hence, we reduce <i>Bryodina</i> to synonymy with <i>Bryonora</i>. Further, we describe <i>Bryonora microlepis</i> as new to science and transfer <i>Lecanora castaneoides</i> to <i>Bryonora</i> and <i>L. vicaria</i> to <i>Miriquidica</i>. A world key to <i>Bryonora</i> is included.
DOI: 10.6084/m9.figshare.20006935
title: Lateral wedge insole for knee osteoarthritis: randomized clinical trial

description: CONTEXT AND OBJECTIVE: Optimal management of knee osteoarthritis requires a combination of pharmacological and non-pharmacological methods. The use of lateral wedge insoles to treat medial knee osteoarthritis is recommended, but there is still controversy about its efficacy. The purpose of this study was to ascertain whether the use of lateral wedge insoles can diminish pain and improve function in patients with medial knee osteoarthritis. DESIGN AND SETTING: Prospective randomized trial conducted in a tertiary-level hospital. METHODS: We prospectively enrolled 58 patients with medial knee osteoarthritis and randomized them to use either a lateral wedge insole with subtalar strapping (Group W), or a neutral insole with subtalar strapping (Group N - control). All the patients were instructed to use the insole for five to ten hours per day. A visual analogue pain scale, the Western Ontario and McMaster Universities Arthritis Index (WOMAC) and the Lequesne questionnaire were applied at baseline and at weeks 2, 8 and 24. RESULTS: At weeks 8 and 24, both groups showed lower scores for WOMAC (P = 0,023 and P = 0,012 respectively). There were no statistically significant differences between the groups regarding the visual analogue pain scale, WOMAC or Lequesne results at any time evaluated. CONCLUSION: The use of a lateral wedge insole with subtalar strapping improved the patients' symptoms and function but was not superior to placebo insoles.
DOI: 10.6084/m9.figshare.20006935.v1
title: Lateral wedge insole for knee osteoarthritis: randomized clinical trial

description: CONTEXT AND OBJECTIVE: Optimal management of knee osteoarthritis requires a combination of pharmacological and non-pharmacological methods. The use of lateral wedge insoles to treat medial knee osteoarthritis is recommended, but there is still controversy about its efficacy. The purpose of this study was to ascertain whether the use of lateral wedge insoles can diminish pain and improve function in patients with medial knee osteoarthritis. DESIGN AND SETTING: Prospective randomized trial conducted in a tertiary-level hospital. METHODS: We prospectively enrolled 58 patients with medial knee osteoarthritis and randomized them to use either a lateral wedge insole with subtalar strapping (Group W), or a neutral insole with subtalar strapping (Group N - control). All the patients were instructed to use the insole for five to ten hours per day. A visual analogue pain scale, the Western Ontario and McMaster Universities Arthritis Index (WOMAC) and the Lequesne questionnaire were applied at baseline and at weeks 2, 8 and 24. RESULTS: At weeks 8 and 24, both groups showed lower scores for WOMAC (P = 0,023 and P = 0,012 respectively). There were no statistically significant differences between the groups regarding the visual analogue pain scale, WOMAC or Lequesne results at any time evaluated. CONCLUSION: The use of a lateral wedge insole with subtalar strapping improved the patients' symptoms and function but was not superior to placebo insoles.
DOI: 10.6084/m9.figshare.20006941.v1
title: Diagnostic accuracy of a noninvasive hepatic ultrasound score for non-alcoholic fatty liver disease (NAFLD) in the Brazilian Longitudinal Study of Adult Health (ELSA-Brasil)

description: CONTEXT AND OBJECTIVE: Noninvasive strategies for evaluating non-alcoholic fatty liver disease (NAFLD) have been investigated over the last few decades. Our aim was to evaluate the diagnostic accuracy of a new hepatic ultrasound score for NAFLD in the ELSA-Brasil study.DESIGN AND SETTINGS: Diagnostic accuracy study conducted in the ELSA center, in the hospital of a public university.METHODS: Among the 15,105 participants of the ELSA study who were evaluated for NAFLD, 195 individuals were included in this sub-study. Hepatic ultrasound was performed (deep beam attenuation, hepatorenal index and anteroposterior diameter of the right hepatic lobe) and compared with the hepatic steatosis findings from 64-channel high-resolution computed tomography (CT). We also evaluated two clinical indices relating to NAFLD: the fatty liver index (FLI) and the hepatic steatosis index (HSI).RESULTS: Among the 195 participants, the NAFLD frequency was 34.4%. High body mass index, high waist circumference, diabetes and hypertriglyceridemia were associated with high hepatic attenuation and large anteroposterior diameter of the right hepatic lobe, but not with the hepatorenal index. The hepatic ultrasound score, based on hepatic attenuation and the anteroposterior diameter of the right hepatic lobe, presented the best performance for NAFLD screening at the cutoff point ≥ 1 point; sensitivity: 85.1%; specificity: 73.4%; accuracy: 79.3%; and area under the curve (AUC 0.85; 95% confidence interval, CI: 0.78-0.91)]. FLI and HSI presented lower performance (AUC 0.76; 95% CI: 0.69-0.83) than CT.CONCLUSION: The hepatic ultrasound score based on hepatic attenuation and the anteroposterior diameter of the right hepatic lobe has good reproducibility and accuracy for NAFLD screening.
DOI: 10.6084/m9.figshare.20006942
title: Frequency of obesity and related risk factors among school children and adolescents in a low-income community. A cross-sectional study

description: CONTEXT AND OBJECTIVE: The frequency of obesity at an early age may contribute to atherosclerosis and cardiovascular disease (CVD) in adults. This study measured the frequency of obesity and cardiovascular risk factors in children and adolescents aged 6 to 17 years.DESIGN AND SETTING: Cross-sectional study in a school located in a region of low income and socioeconomic status in Santa Rita do Sapucai, Minas Gerais, Brazil.METHODS: A total of 175 students were classified using body mass index (BMI) and their waist circumference, blood pressure, number of hours of sedentary behavior and school meals were evaluated. Serum concentrations of fasting blood glucose, total cholesterol (TC), triglycerides (TG), low-density lipoprotein (LDL-C) and high-density lipoprotein (HDL-C) were analyzed.RESULTS: 37.2% of the students had BMI above the 85th percentile and had significantly lower age, higher prevalence of hypertension, higher serum TC, LDL-C and TG, and greater waist circumference than those with BMI below the 85th percentile. Hypertension was observed in 2.9% of the students; 5.1% presented impaired glucose tolerance, 40% had two risk factors for atherosclerosis and 26.9% had three risk factors. A sedentary lifestyle was significantly less prevalent among subjects with BMI above the 85thpercentile and was significantly correlated with serum TC and LDL-C. The school meals were hypoglycemic, hyperproteic and hyperlipidemic.CONCLUSION: One third of the children and adolescents had weights greater than or equal to the age-adjusted weight, and this was associated with greater waist circumference, hypertension and prevalence of dyslipidemia.
DOI: 10.6084/m9.figshare.20006942.v1
title: Frequency of obesity and related risk factors among school children and adolescents in a low-income community. A cross-sectional study

description: CONTEXT AND OBJECTIVE: The frequency of obesity at an early age may contribute to atherosclerosis and cardiovascular disease (CVD) in adults. This study measured the frequency of obesity and cardiovascular risk factors in children and adolescents aged 6 to 17 years.DESIGN AND SETTING: Cross-sectional study in a school located in a region of low income and socioeconomic status in Santa Rita do Sapucai, Minas Gerais, Brazil.METHODS: A total of 175 students were classified using body mass index (BMI) and their waist circumference, blood pressure, number of hours of sedentary behavior and school meals were evaluated. Serum concentrations of fasting blood glucose, total cholesterol (TC), triglycerides (TG), low-density lipoprotein (LDL-C) and high-density lipoprotein (HDL-C) were analyzed.RESULTS: 37.2% of the students had BMI above the 85th percentile and had significantly lower age, higher prevalence of hypertension, higher serum TC, LDL-C and TG, and greater waist circumference than those with BMI below the 85th percentile. Hypertension was observed in 2.9% of the students; 5.1% presented impaired glucose tolerance, 40% had two risk factors for atherosclerosis and 26.9% had three risk factors. A sedentary lifestyle was significantly less prevalent among subjects with BMI above the 85thpercentile and was significantly correlated with serum TC and LDL-C. The school meals were hypoglycemic, hyperproteic and hyperlipidemic.CONCLUSION: One third of the children and adolescents had weights greater than or equal to the age-adjusted weight, and this was associated with greater waist circumference, hypertension and prevalence of dyslipidemia.
DOI: 10.6084/m9.figshare.20006941
title: Diagnostic accuracy of a noninvasive hepatic ultrasound score for non-alcoholic fatty liver disease (NAFLD) in the Brazilian Longitudinal Study of Adult Health (ELSA-Brasil)

description: CONTEXT AND OBJECTIVE: Noninvasive strategies for evaluating non-alcoholic fatty liver disease (NAFLD) have been investigated over the last few decades. Our aim was to evaluate the diagnostic accuracy of a new hepatic ultrasound score for NAFLD in the ELSA-Brasil study.DESIGN AND SETTINGS: Diagnostic accuracy study conducted in the ELSA center, in the hospital of a public university.METHODS: Among the 15,105 participants of the ELSA study who were evaluated for NAFLD, 195 individuals were included in this sub-study. Hepatic ultrasound was performed (deep beam attenuation, hepatorenal index and anteroposterior diameter of the right hepatic lobe) and compared with the hepatic steatosis findings from 64-channel high-resolution computed tomography (CT). We also evaluated two clinical indices relating to NAFLD: the fatty liver index (FLI) and the hepatic steatosis index (HSI).RESULTS: Among the 195 participants, the NAFLD frequency was 34.4%. High body mass index, high waist circumference, diabetes and hypertriglyceridemia were associated with high hepatic attenuation and large anteroposterior diameter of the right hepatic lobe, but not with the hepatorenal index. The hepatic ultrasound score, based on hepatic attenuation and the anteroposterior diameter of the right hepatic lobe, presented the best performance for NAFLD screening at the cutoff point ≥ 1 point; sensitivity: 85.1%; specificity: 73.4%; accuracy: 79.3%; and area under the curve (AUC 0.85; 95% confidence interval, CI: 0.78-0.91)]. FLI and HSI presented lower performance (AUC 0.76; 95% CI: 0.69-0.83) than CT.CONCLUSION: The hepatic ultrasound score based on hepatic attenuation and the anteroposterior diameter of the right hepatic lobe has good reproducibility and accuracy for NAFLD screening.
DOI: 10.7916/d8-45tz-em54
title:  GRID3 Namibia Settlement Extents Version 01, Alpha

description: NOTE: This initial version of the Namibia settlement extents has been superseded by the final version, "GRID3 Namibia Settlement Extents, Version 01", now available here: https://doi.org/10.7916/d8-s0ae-xf56 The database constitutes a comprehensive set of settlement polygons nationwide. It is in geodatabase format and consists of three feature classes for built up areas (BUA), small settlement areas (SSA), and hamlets (hamlets). This work has been undertaken as part of the Geo-referenced Infrastructure and Demographic Data for Development (GRID3) initiative in Namibia. GRID3 works with countries to generate, validate and use geospatial data on population, settlements, infrastructure, and subnational boundaries. For more information, see https://grid3.org/ Keywords: built up areas, BUA, small settlement areas, SSA, hamlets, settlement aggregation, settlement extent, CIESIN, GRID3, Novel-T