PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
items: Genome-wide identification and characterization of TCP family genes in Brassica juncea var. tumida
items: Drivers of beta diversity in modern and ancient reef-associated soft-bottom environments
items: A low caffeine dose improves maximal strength, but not relative muscular endurance in either heavier-or lighter-loads, or perceptions of effort or discomfort at task failure in females
items: Effects of rumen bypass melatonin feeding (RBMF) on milk quality and mastitis of Holstein cows
items: Inventory statistics meet big data: complications for estimating numbers of species
items: The mitochondrial genome of Acrobeloides varius (Cephalobomorpha) confirms non-monophyly of Tylenchina (Nematoda)
items: Nonalcoholic fatty liver disease, a potential risk factor of non-specific ST-T segment changes: data from a cross-sectional study
items: Application of 16S rRNA gene sequencing in Helicobacter pylori detection
items: The biomarkers of key miRNAs and target genes associated with acute myocardial infarction
items: Dental fear association between mothers and adolescents—a longitudinal study

Genome-wide identification and characterization of TCP family genes in Brassica juncea var. tumida
type: item
type: AcademicArticle
description: Background Teosinte branched1/Cycloidea/proliferating cell factors (TCPs) are plant-specific transcription factors widely involved in leaf development, flowering, shoot branching, the circadian rhythm, hormone signaling, and stress responses. However, the TCP function in Brassica juncea var. tumida, the tumorous stem mustard, has not yet been reported. This study identified and characterized the entire TCP family members in B. juncea var. tumida. Methods We identified 62 BjTCP genes from the B. juncea var. tumida genome and analyzed their phylogenetic relationship, gene structure, protein motifs, chromosome location, and expression profile in different tissues. Results Of the 62 BjTCP genes we identified in B. juncea var. tumida, containing 34 class I and 28 class II subfamily members, 61 were distributed on 18 chromosomes. Gene structure and conserved motif analysis showed that the same clade genes displayed a similar exon/intron gene structure and conserved motifs. Cis-acting element results showed that the same clade genes also had a similar cis-acting element; however, subtle differences implied a different regulatory pathway. The BjTCP18s members were low-expressed in Dayejie strains and the unswelling stage of Yonganxiaoye strains. Treatment with gibberellin (GA) and salicylic acid (SA) showed that GA and SA affect the expression levels of multiple TCP genes. Conclusion We performed the first genome-wide analysis of the TCP gene family of B. juncea var. tumida. Our results have provided valuable information for understanding the classification and functions of TCP genes in B. juncea var. tumida.
format: application/pdf
format: text/html
creator: Jing He
creator: Xiaohong He
creator: Pingan Chang
creator: Huaizhong Jiang
creator: Daping Gong
creator: Quan Sun
subject: Agricultural Science
subject: Genomics
subject: Plant Science
description: doi:10.7717/peerj.9130
publisher: PeerJ Inc.
rights: © 2020 He et al.
abstract: Background Teosinte branched1/Cycloidea/proliferating cell factors (TCPs) are plant-specific transcription factors widely involved in leaf development, flowering, shoot branching, the circadian rhythm, hormone signaling, and stress responses. However, the TCP function in Brassica juncea var. tumida, the tumorous stem mustard, has not yet been reported. This study identified and characterized the entire TCP family members in B. juncea var. tumida. Methods We identified 62 BjTCP genes from the B. juncea var. tumida genome and analyzed their phylogenetic relationship, gene structure, protein motifs, chromosome location, and expression profile in different tissues. Results Of the 62 BjTCP genes we identified in B. juncea var. tumida, containing 34 class I and 28 class II subfamily members, 61 were distributed on 18 chromosomes. Gene structure and conserved motif analysis showed that the same clade genes displayed a similar exon/intron gene structure and conserved motifs. Cis-acting element results showed that the same clade genes also had a similar cis-acting element; however, subtle differences implied a different regulatory pathway. The BjTCP18s members were low-expressed in Dayejie strains and the unswelling stage of Yonganxiaoye strains. Treatment with gibberellin (GA) and salicylic acid (SA) showed that GA and SA affect the expression levels of multiple TCP genes. Conclusion We performed the first genome-wide analysis of the TCP gene family of B. juncea var. tumida. Our results have provided valuable information for understanding the classification and functions of TCP genes in B. juncea var. tumida.
bibliographic citation: He et al. (2020) Genome-wide identification and characterization of TCP family genes in Brassica juncea var. tumida. PeerJ 8:e9130 https://doi.org/10.7717/peerj.9130
date submitted: 2019-11-26
date accepted: 2020-04-14
issued: 2020-05-14
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: He
  given name: Jing
author list: Agent
  family name: He
  given name: Xiaohong
author list: Agent
  family name: Chang
  given name: Pingan
author list: Agent
  family name: Jiang
  given name: Huaizhong
author list: Agent
  family name: Gong
  given name: Daping
author list: Agent
  family name: Sun
  given name: Quan
doi: 10.7717/peerj.9130
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-05-14
copyright: ©2020 He et al.
attribution name: He et al.

Drivers of beta diversity in modern and ancient reef-associated soft-bottom environments
type: item
type: AcademicArticle
description: Beta diversity, the compositional variation among communities, is often associated with environmental gradients. Other drivers of beta diversity include stochastic processes, priority effects, predation, or competitive exclusion. Temporal turnover may also explain differences in faunal composition between fossil assemblages. To assess the drivers of beta diversity in reef-associated soft-bottom environments, we investigate community patterns in a Middle to Late Triassic reef basin assemblage from the Cassian Formation in the Dolomites, Northern Italy, and compare results with a Recent reef basin assemblage from the Northern Bay of Safaga, Red Sea, Egypt. We evaluate beta diversity with regard to age, water depth, and spatial distance, and compare the results with a null model to evaluate the stochasticity of these differences. Using pairwise proportional dissimilarity, we find very high beta diversity for the Cassian Formation (0.91 ± 0.02) and slightly lower beta diversity for the Bay of Safaga (0.89 ± 0.04). Null models show that stochasticity only plays a minor role in determining faunal differences. Spatial distance is also irrelevant. Contrary to expectations, there is no tendency of beta diversity to decrease with water depth. Although water depth has frequently been found to be a key factor in determining beta diversity, we find that it is not the major driver in these reef-associated soft-bottom environments. We postulate that priority effects and the biotic structuring of the sediment may be key determinants of beta diversity.
format: application/pdf
format: text/html
creator: Vanessa Julie Roden
creator: Martin Zuschin
creator: Alexander Nützel
creator: Imelda M. Hausmann
creator: Wolfgang Kiessling
subject: Biodiversity
subject: Ecology
subject: Marine Biology
subject: Paleontology
description: doi:10.7717/peerj.9139
publisher: PeerJ Inc.
rights: © 2020 Roden et al.
abstract: Beta diversity, the compositional variation among communities, is often associated with environmental gradients. Other drivers of beta diversity include stochastic processes, priority effects, predation, or competitive exclusion. Temporal turnover may also explain differences in faunal composition between fossil assemblages. To assess the drivers of beta diversity in reef-associated soft-bottom environments, we investigate community patterns in a Middle to Late Triassic reef basin assemblage from the Cassian Formation in the Dolomites, Northern Italy, and compare results with a Recent reef basin assemblage from the Northern Bay of Safaga, Red Sea, Egypt. We evaluate beta diversity with regard to age, water depth, and spatial distance, and compare the results with a null model to evaluate the stochasticity of these differences. Using pairwise proportional dissimilarity, we find very high beta diversity for the Cassian Formation (0.91 ± 0.02) and slightly lower beta diversity for the Bay of Safaga (0.89 ± 0.04). Null models show that stochasticity only plays a minor role in determining faunal differences. Spatial distance is also irrelevant. Contrary to expectations, there is no tendency of beta diversity to decrease with water depth. Although water depth has frequently been found to be a key factor in determining beta diversity, we find that it is not the major driver in these reef-associated soft-bottom environments. We postulate that priority effects and the biotic structuring of the sediment may be key determinants of beta diversity.
bibliographic citation: Roden et al. (2020) Drivers of beta diversity in modern and ancient reef-associated soft-bottom environments. PeerJ 8:e9139 https://doi.org/10.7717/peerj.9139
date submitted: 2019-09-26
date accepted: 2020-04-16
issued: 2020-05-14
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Roden
  given name: Vanessa Julie
author list: Agent
  family name: Zuschin
  given name: Martin
author list: Agent
  family name: Nützel
  given name: Alexander
author list: Agent
  family name: Hausmann
  given name: Imelda M.
author list: Agent
  family name: Kiessling
  given name: Wolfgang
doi: 10.7717/peerj.9139
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-05-14
copyright: ©2020 Roden et al.
attribution name: Roden et al.

A low caffeine dose improves maximal strength, but not relative muscular endurance in either heavier-or lighter-loads, or perceptions of effort or discomfort at task failure in females
type: item
type: AcademicArticle
description: Background The body of literature considering caffeine as an ergogenic aid has primarily considered typically aerobic based exercise, male participants and moderate-to large-caffeine doses. With this in mind the aim of this project was to explore the effects of a low-caffeine dose upon maximal voluntary contraction (MVC) and muscular endurance (time to task failure, TTF) at heavier-and lighter-loads. Methods Nineteen physically active, habitual caffeine consuming females randomly performed four testing conditions; two with a low-dose of caffeine (100 mg equating to mean = 1.5 ± 0.18 mg·kg−1) and two placebo conditions, where they performed a maximal strength test (MVC) knee extension at 45° followed by a task of relative muscular endurance (sustained isometric contraction for TTF) using either heavier-(70% MVC) and lighter-(30% MVC) loads. Each participant performed each load condition following both caffeine and placebo consumption. Immediately following cessation of the muscular endurance test participants were asked to report their rating of perceived effort (RPE) and rating of perceived discomfort (RPD). Results Analyses revealed a significant effect for caffeine upon MVC compared to placebo (p = 0.007). We also found a significantly greater TTF for the lighter-compared to the heavier-load condition (p < 0.0001); however, there was no significant effect comparing caffeine to placebo (p = 0.2368), but insufficient precision of estimates to infer equivalence in either lighter-(p = 0.750) or heavier-load (p = 0.262) conditions. There were no statistically significant effects for caffeine compared with placebo, or lighter-compared with heavier-loads, for RPE and RPD (all p > 0.05). RPE was statistically equivalent between caffeine and placebo for both lighter-(p = 0.007) and heavier-load (p = 0.002) conditions and RPD for heavier-(p = 0.006) but not lighter-load (p = 0.136). Discussion This is the first study to demonstrate a positive effect on strength from a low c…
format: application/pdf
format: text/html
creator: Georgina Waller
creator: Melissa Dolby
creator: James Steele
creator: James P. Fisher
subject: Anatomy and Physiology
subject: Evidence Based Medicine
subject: Kinesiology
subject: Pharmacology
subject: Public Health
description: doi:10.7717/peerj.9144
publisher: PeerJ Inc.
rights: © 2020 Waller et al.
abstract: Background The body of literature considering caffeine as an ergogenic aid has primarily considered typically aerobic based exercise, male participants and moderate-to large-caffeine doses. With this in mind the aim of this project was to explore the effects of a low-caffeine dose upon maximal voluntary contraction (MVC) and muscular endurance (time to task failure, TTF) at heavier-and lighter-loads. Methods Nineteen physically active, habitual caffeine consuming females randomly performed four testing conditions; two with a low-dose of caffeine (100 mg equating to mean = 1.5 ± 0.18 mg·kg−1) and two placebo conditions, where they performed a maximal strength test (MVC) knee extension at 45° followed by a task of relative muscular endurance (sustained isometric contraction for TTF) using either heavier-(70% MVC) and lighter-(30% MVC) loads. Each participant performed each load condition following both caffeine and placebo consumption. Immediately following cessation of the muscular endurance test participants were asked to report their rating of perceived effort (RPE) and rating of perceived discomfort (RPD). Results Analyses revealed a significant effect for caffeine upon MVC compared to placebo (p = 0.007). We also found a significantly greater TTF for the lighter-compared to the heavier-load condition (p < 0.0001); however, there was no significant effect comparing caffeine to placebo (p = 0.2368), but insufficient precision of estimates to infer equivalence in either lighter-(p = 0.750) or heavier-load (p = 0.262) conditions. There were no statistically significant effects for caffeine compared with placebo, or lighter-compared with heavier-loads, for RPE and RPD (all p > 0.05). RPE was statistically equivalent between caffeine and placebo for both lighter-(p = 0.007) and heavier-load (p = 0.002) conditions and RPD for heavier-(p = 0.006) but not lighter-load (p = 0.136). Discussion This is the first study to demonstrate a positive effect on strength from a low c…
bibliographic citation: Waller et al. (2020) A low caffeine dose improves maximal strength, but not relative muscular endurance in either heavier-or lighter-loads, or perceptions of effort or discomfort at task failure in females. PeerJ 8:e9144 https://doi.org/10.7717/peerj.9144
date submitted: 2020-02-12
date accepted: 2020-04-16
issued: 2020-05-14
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Waller
  given name: Georgina
author list: Agent
  family name: Dolby
  given name: Melissa
author list: Agent
  family name: Steele
  given name: James
author list: Agent
  family name: Fisher
  given name: James P.
doi: 10.7717/peerj.9144
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-05-14
copyright: © 2020 Waller et al.
attribution name: Waller et al.

Effects of rumen bypass melatonin feeding (RBMF) on milk quality and mastitis of Holstein cows
type: item
type: AcademicArticle
description: Cow mastitis is a major problem frequently encountered by dairy farmers and it is manifested by the high number of somatic cells and the low quality of the milk. The conventional treatment for mastitis is use of antibiotics. In the current study, a new approach is applied to target this disorder: rumen bypass melatonin feeding (RBMF). The RBMF significantly reduced milk somatic cell count and improved milk nutritional values with the elevated protein, fat and dry matter levels. This approach also suppresses the stress and proinflammatory responses of the cows indicated by the reduced serum cortisol, TNF-α and IL-6 and increased IL-10 levels. Importantly, the beneficial effects of RBMF have lasted for several days after termination of the treatment. The effects of melatonin on the mastitis are probably attributed to the antioxidant and anti-inflammatory activities of melatonin. Considering the none or low toxicity of melatonin to organisms and the no invasive nature of this approach, we recommend that RBMF could be used in large scale in the dairy farming to target the cow mastitis.
format: application/pdf
format: text/html
creator: Songyang Yao
creator: Hao Wu
creator: Hui Ma
creator: Yao Fu
creator: Wenjuan Wei
creator: Tiankun Wang
creator: Shengyu Guan
creator: Hai Yang
creator: Xiubo Li
creator: Jiangpeng Guo
creator: Yongqiang Lu
creator: Lu Zhang
creator: Changwang He
creator: Yi Chang
creator: Guoshi Liu
subject: Agricultural Science
subject: Biochemistry
subject: Veterinary Medicine
description: doi:10.7717/peerj.9147
publisher: PeerJ Inc.
rights: © 2020 Yao et al.
abstract: Cow mastitis is a major problem frequently encountered by dairy farmers and it is manifested by the high number of somatic cells and the low quality of the milk. The conventional treatment for mastitis is use of antibiotics. In the current study, a new approach is applied to target this disorder: rumen bypass melatonin feeding (RBMF). The RBMF significantly reduced milk somatic cell count and improved milk nutritional values with the elevated protein, fat and dry matter levels. This approach also suppresses the stress and proinflammatory responses of the cows indicated by the reduced serum cortisol, TNF-α and IL-6 and increased IL-10 levels. Importantly, the beneficial effects of RBMF have lasted for several days after termination of the treatment. The effects of melatonin on the mastitis are probably attributed to the antioxidant and anti-inflammatory activities of melatonin. Considering the none or low toxicity of melatonin to organisms and the no invasive nature of this approach, we recommend that RBMF could be used in large scale in the dairy farming to target the cow mastitis.
bibliographic citation: Yao et al. (2020) Effects of rumen bypass melatonin feeding (RBMF) on milk quality and mastitis of Holstein cows. PeerJ 8:e9147 https://doi.org/10.7717/peerj.9147
date submitted: 2020-02-25
date accepted: 2020-04-17
issued: 2020-05-14
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Yao
  given name: Songyang
author list: Agent
  family name: Wu
  given name: Hao
author list: Agent
  family name: Ma
  given name: Hui
author list: Agent
  family name: Fu
  given name: Yao
author list: Agent
  family name: Wei
  given name: Wenjuan
author list: Agent
  family name: Wang
  given name: Tiankun
author list: Agent
  family name: Guan
  given name: Shengyu
author list: Agent
  family name: Yang
  given name: Hai
author list: Agent
  family name: Li
  given name: Xiubo
author list: Agent
  family name: Guo
  given name: Jiangpeng
author list: Agent
  family name: Lu
  given name: Yongqiang
author list: Agent
  family name: Zhang
  given name: Lu
author list: Agent
  family name: He
  given name: Changwang
author list: Agent
  family name: Chang
  given name: Yi
author list: Agent
  family name: Liu
  given name: Guoshi
doi: 10.7717/peerj.9147
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-05-14
copyright: ©2020 Yao et al.
attribution name: Yao et al.

Inventory statistics meet big data: complications for estimating numbers of species
type: item
type: AcademicArticle
description: We point out complications inherent in biodiversity inventory metrics when applied to large-scale datasets. The number of units of inventory effort (e.g., days of inventory effort) in which a species is detected saturates, such that crucial numbers of detections of rare species approach zero. Any rare errors can then come to dominate species richness estimates, creating upward biases in estimates of species numbers. We document the problem via simulations of sampling from virtual biotas, illustrate its potential using a large empirical dataset (bird records from Cape May, NJ, USA), and outline the circumstances under which these problems may be expected to emerge.
format: application/pdf
format: text/html
creator: Ali Khalighifar
creator: Laura Jiménez
creator: Claudia Nuñez-Penichet
creator: Benedictus Freeman
creator: Kate Ingenloff
creator: Daniel Jiménez-García
creator: Town Peterson
subject: Biodiversity
subject: Conservation Biology
description: doi:10.7717/peerj.8872
publisher: PeerJ Inc.
rights: © 2020 Khalighifar et al.
abstract: We point out complications inherent in biodiversity inventory metrics when applied to large-scale datasets. The number of units of inventory effort (e.g., days of inventory effort) in which a species is detected saturates, such that crucial numbers of detections of rare species approach zero. Any rare errors can then come to dominate species richness estimates, creating upward biases in estimates of species numbers. We document the problem via simulations of sampling from virtual biotas, illustrate its potential using a large empirical dataset (bird records from Cape May, NJ, USA), and outline the circumstances under which these problems may be expected to emerge.
bibliographic citation: Khalighifar et al. (2020) Inventory statistics meet big data: complications for estimating numbers of species. PeerJ 8:e8872 https://doi.org/10.7717/peerj.8872
date submitted: 2019-09-16
date accepted: 2020-03-09
issued: 2020-05-13
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Khalighifar
  given name: Ali
author list: Agent
  family name: Jiménez
  given name: Laura
author list: Agent
  family name: Nuñez-Penichet
  given name: Claudia
author list: Agent
  family name: Freeman
  given name: Benedictus
author list: Agent
  family name: Ingenloff
  given name: Kate
author list: Agent
  family name: Jiménez-García
  given name: Daniel
author list: Agent
  family name: Peterson
  given name: Town
doi: 10.7717/peerj.8872
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-05-13
copyright: © 2020 Khalighifar et al.
attribution name: Khalighifar et al.

The mitochondrial genome of Acrobeloides varius (Cephalobomorpha) confirms non-monophyly of Tylenchina (Nematoda)
type: item
type: AcademicArticle
description: The infraorder Cephalobomorpha is a diverse and ecologically important nematode group found in almost all terrestrial environments. In a recent nematode classification system based on SSU rDNA, Cephalobomorpha was classified within the suborder Tylenchina with Panagrolaimomorpha, Tylenchomorpha and Drilonematomorpha. However, phylogenetic relationships among species within Tylenchina are not always consistent, and the phylogenetic position of Cephalobomorpha is still uncertain. In this study, in order to examine phylogenetic relationships of Cephalobomorpha with other nematode groups, we determined the complete mitochondrial genome sequence of Acrobeloides varius, the first sequenced representative of Cephalobomorpha, and used this sequence for phylogenetic analyses along with 101 other nematode species. Phylogenetic analyses using amino acid and nucleotide sequence data of 12 protein-coding genes strongly support a sister relationship between the two cephalobomorpha species A. varius and Acrobeles complexus (represented by a partial mt genome sequence). In this mitochondrial genome phylogeny, Cephalobomorpha was sister to all chromadorean species (excluding Plectus acuminatus of Plectida) and separated from Panagrolaimomorpha and Tylenchomorpha, rendering Tylenchina non-monophyletic. Mitochondrial gene order among Tylenchina species is not conserved, and gene clusters shared between A. varius and A. complexus are very limited. Results from phylogenetic analysis and gene order comparison confirms Tylenchina is not monophyletic. To better understand phylogenetic relationships among Tylenchina members, additional mitochondrial genome information is needed from underrepresented taxa representing Panagrolaimomorpha and Cephalobomorpha.
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creator: Taeho Kim
creator: Yucheol Lee
creator: Hyun-Jong Kil
creator: Joong-Ki Park
subject: Evolutionary Studies
subject: Molecular Biology
subject: Taxonomy
description: doi:10.7717/peerj.9108
publisher: PeerJ Inc.
rights: © 2020 Kim et al.
abstract: The infraorder Cephalobomorpha is a diverse and ecologically important nematode group found in almost all terrestrial environments. In a recent nematode classification system based on SSU rDNA, Cephalobomorpha was classified within the suborder Tylenchina with Panagrolaimomorpha, Tylenchomorpha and Drilonematomorpha. However, phylogenetic relationships among species within Tylenchina are not always consistent, and the phylogenetic position of Cephalobomorpha is still uncertain. In this study, in order to examine phylogenetic relationships of Cephalobomorpha with other nematode groups, we determined the complete mitochondrial genome sequence of Acrobeloides varius, the first sequenced representative of Cephalobomorpha, and used this sequence for phylogenetic analyses along with 101 other nematode species. Phylogenetic analyses using amino acid and nucleotide sequence data of 12 protein-coding genes strongly support a sister relationship between the two cephalobomorpha species A. varius and Acrobeles complexus (represented by a partial mt genome sequence). In this mitochondrial genome phylogeny, Cephalobomorpha was sister to all chromadorean species (excluding Plectus acuminatus of Plectida) and separated from Panagrolaimomorpha and Tylenchomorpha, rendering Tylenchina non-monophyletic. Mitochondrial gene order among Tylenchina species is not conserved, and gene clusters shared between A. varius and A. complexus are very limited. Results from phylogenetic analysis and gene order comparison confirms Tylenchina is not monophyletic. To better understand phylogenetic relationships among Tylenchina members, additional mitochondrial genome information is needed from underrepresented taxa representing Panagrolaimomorpha and Cephalobomorpha.
bibliographic citation: Kim et al. (2020) The mitochondrial genome of Acrobeloides varius (Cephalobomorpha) confirms non-monophyly of Tylenchina (Nematoda). PeerJ 8:e9108 https://doi.org/10.7717/peerj.9108
date submitted: 2020-01-30
date accepted: 2020-04-10
issued: 2020-05-13
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Kim
  given name: Taeho
author list: Agent
  family name: Lee
  given name: Yucheol
author list: Agent
  family name: Kil
  given name: Hyun-Jong
author list: Agent
  family name: Park
  given name: Joong-Ki
doi: 10.7717/peerj.9108
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-05-13
copyright: ©2020 Kim et al.
attribution name: Kim et al.

Nonalcoholic fatty liver disease, a potential risk factor of non-specific ST-T segment changes: data from a cross-sectional study
type: item
type: AcademicArticle
description: Background Non-specific ST-T segment changes are prevalent and are proven risk factors for early onset of cardiovascular diseases. They can increase all-cause mortality by 100∼200% and are candidate for early signs of cardiovascular changes. Nonalcoholic fatty liver disease (NAFLD) is prevalent worldwide and is one facet of a multisystem disease that confers substantial increases morbidity and mortality of nonalcoholic fatty liver-related cardiovascular diseases. It is unclear whether NAFLD is associated with non-specific ST-T changes warning early signs of cardiovascular changes. Therefore, we investigated this association. Methods A cross-sectional study was designed that included a sample consisting of 32,922 participants who underwent health examinations. Participants with missing information, excessive alcohol intake, viral hepatitis, chronic liver disease or established cardiovascular diseases were excluded. Electrocardiograms were used for analysis of non-specific ST-T segment changes. NAFLD was diagnosed by ultrasonographic detection of hepatic steatosis without other liver diseases. A multivariable logistic regression model was served to calculate the OR and 95% CI for non-specific ST-T segment changes. Results The prevalence of non-specific ST-T segment changes was 6.5% in participants with NAFLD, however, the prevalence of NAFLD was 42.9% in participants with non-specific ST-T segment changes. NAFLD was independently associated with non-specific ST-T segment changes (OR: 1.925, 95% CI: 1.727-2.143, P < 0.001). After adjusting for age, sex, heart rate, hypertension, body mass index, fasting glucose, total cholesterol, triglycerides, HDL-C, NAFLD remained an independent risk factor of non-specific ST-T segment changes (OR: 1.289, 95% CI: 1.122-1.480). Conclusion Non-specific ST-T segment changes were independently associated with the presence of NAFLD after adjusting for potential confounders.
format: application/pdf
format: text/html
creator: Li Xiao
creator: Tao Bai
creator: Junchao Zeng
creator: Rui Yang
creator: Ling Yang
subject: Cardiology
subject: Gastroenterology and Hepatology
description: doi:10.7717/peerj.9090
publisher: PeerJ Inc.
rights: © 2020 Xiao et al.
abstract: Background Non-specific ST-T segment changes are prevalent and are proven risk factors for early onset of cardiovascular diseases. They can increase all-cause mortality by 100∼200% and are candidate for early signs of cardiovascular changes. Nonalcoholic fatty liver disease (NAFLD) is prevalent worldwide and is one facet of a multisystem disease that confers substantial increases morbidity and mortality of nonalcoholic fatty liver-related cardiovascular diseases. It is unclear whether NAFLD is associated with non-specific ST-T changes warning early signs of cardiovascular changes. Therefore, we investigated this association. Methods A cross-sectional study was designed that included a sample consisting of 32,922 participants who underwent health examinations. Participants with missing information, excessive alcohol intake, viral hepatitis, chronic liver disease or established cardiovascular diseases were excluded. Electrocardiograms were used for analysis of non-specific ST-T segment changes. NAFLD was diagnosed by ultrasonographic detection of hepatic steatosis without other liver diseases. A multivariable logistic regression model was served to calculate the OR and 95% CI for non-specific ST-T segment changes. Results The prevalence of non-specific ST-T segment changes was 6.5% in participants with NAFLD, however, the prevalence of NAFLD was 42.9% in participants with non-specific ST-T segment changes. NAFLD was independently associated with non-specific ST-T segment changes (OR: 1.925, 95% CI: 1.727-2.143, P < 0.001). After adjusting for age, sex, heart rate, hypertension, body mass index, fasting glucose, total cholesterol, triglycerides, HDL-C, NAFLD remained an independent risk factor of non-specific ST-T segment changes (OR: 1.289, 95% CI: 1.122-1.480). Conclusion Non-specific ST-T segment changes were independently associated with the presence of NAFLD after adjusting for potential confounders.
bibliographic citation: Xiao et al. (2020) Nonalcoholic fatty liver disease, a potential risk factor of non-specific ST-T segment changes: data from a cross-sectional study. PeerJ 8:e9090 https://doi.org/10.7717/peerj.9090
date submitted: 2019-12-16
date accepted: 2020-04-08
issued: 2020-05-13
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Xiao
  given name: Li
author list: Agent
  family name: Bai
  given name: Tao
author list: Agent
  family name: Zeng
  given name: Junchao
author list: Agent
  family name: Yang
  given name: Rui
author list: Agent
  family name: Yang
  given name: Ling
doi: 10.7717/peerj.9090
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-05-13
copyright: ©2020 Xiao et al.
attribution name: Xiao et al.

Application of 16S rRNA gene sequencing in Helicobacter pylori detection
type: item
type: AcademicArticle
description: Helicobacter pylori is one of the major stomach microbiome components, promoting development of inflammation and gastric cancer in humans. H. pylori has a unique ability to transform into a coccoidal form which is difficult to detect by many diagnostic methods, such as urease activity detection, and even histopathological examination. Here we present a comparison of three methods for H. pylori identification: histological assessment (with eosin, hematoxylin, and Giemsa staining), polymerase chain reaction (PCR) detection of urease (ureA specific primers), and detection by 16S rRNA gene sequencing. The study employed biopsies from the antral part of the stomach (N = 40). All samples were assessed histologically which revealed H. pylori in eight patients. Bacterial DNA isolated from the bioptates was used as a template for PCR reaction and 16S rRNA gene sequencing that revealed H. pylori in 13 and in 20 patients, respectively. Thus, 16S rRNA gene sequencing was the most sensitive method for detection of H. pylori in stomach biopsy samples.
format: application/pdf
format: text/html
creator: Aleksander Szymczak
creator: Stanisław Ferenc
creator: Joanna Majewska
creator: Paulina Miernikiewicz
creator: Jan Gnus
creator: Wojciech Witkiewicz
creator: Krystyna Dąbrowska
subject: Bioinformatics
subject: Genomics
subject: Microbiology
subject: Molecular Biology
subject: Gastroenterology and Hepatology
description: doi:10.7717/peerj.9099
publisher: PeerJ Inc.
rights: © 2020 Szymczak et al.
abstract: Helicobacter pylori is one of the major stomach microbiome components, promoting development of inflammation and gastric cancer in humans. H. pylori has a unique ability to transform into a coccoidal form which is difficult to detect by many diagnostic methods, such as urease activity detection, and even histopathological examination. Here we present a comparison of three methods for H. pylori identification: histological assessment (with eosin, hematoxylin, and Giemsa staining), polymerase chain reaction (PCR) detection of urease (ureA specific primers), and detection by 16S rRNA gene sequencing. The study employed biopsies from the antral part of the stomach (N = 40). All samples were assessed histologically which revealed H. pylori in eight patients. Bacterial DNA isolated from the bioptates was used as a template for PCR reaction and 16S rRNA gene sequencing that revealed H. pylori in 13 and in 20 patients, respectively. Thus, 16S rRNA gene sequencing was the most sensitive method for detection of H. pylori in stomach biopsy samples.
bibliographic citation: Szymczak et al. (2020) Application of 16S rRNA gene sequencing in Helicobacter pylori detection. PeerJ 8:e9099 https://doi.org/10.7717/peerj.9099
date submitted: 2019-10-29
date accepted: 2020-04-09
issued: 2020-05-13
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Szymczak
  given name: Aleksander
author list: Agent
  family name: Ferenc
  given name: Stanisław
author list: Agent
  family name: Majewska
  given name: Joanna
author list: Agent
  family name: Miernikiewicz
  given name: Paulina
author list: Agent
  family name: Gnus
  given name: Jan
author list: Agent
  family name: Witkiewicz
  given name: Wojciech
author list: Agent
  family name: Dąbrowska
  given name: Krystyna
doi: 10.7717/peerj.9099
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-05-13
copyright: ©2020 Szymczak et al.
attribution name: Szymczak et al.

The biomarkers of key miRNAs and target genes associated with acute myocardial infarction
type: item
type: AcademicArticle
description: Background Acute myocardial infarction (AMI) is considered one of the most prominent causes of death from cardiovascular disease worldwide. Knowledge of the molecular mechanisms underlying AMI remains limited. Accurate biomarkers are needed to predict the risk of AMI and would be beneficial for managing the incidence rate. The gold standard for the diagnosis of AMI, the cardiac troponin T (cTnT) assay, requires serial testing, and the timing of measurement with respect to symptoms affects the results. As attractive candidate diagnostic biomarkers in AMI, circulating microRNAs (miRNAs) are easily detectable, generally stable and tissue specific. Methods The Gene Expression Omnibus (GEO) database was used to compare miRNA expression between AMI and control samples, and the interactions between miRNAs and mRNAs were analysed for expression and function. Furthermore, a protein-protein interaction (PPI) network was constructed. The miRNAs identified in the bioinformatic analysis were verified by RT-qPCR in an H9C2 cell line. The miRNAs in plasma samples from patients with AMI (n = 11) and healthy controls (n = 11) were used to construct receiver operating characteristic (ROC) curves to evaluate the clinical prognostic value of the identified miRNAs. Results We identified eight novel miRNAs as potential candidate diagnostic biomarkers for patients with AMI. In addition, the predicted target genes provide insight into the molecular mechanisms underlying AMI.
format: application/pdf
format: text/html
creator: Qi Wang
creator: Bingyan Liu
creator: Yuanyong Wang
creator: Baochen Bai
creator: Tao Yu
creator: Xian–ming Chu
subject: Bioinformatics
subject: Cardiology
description: doi:10.7717/peerj.9129
publisher: PeerJ Inc.
rights: © 2020 Wang et al.
abstract: Background Acute myocardial infarction (AMI) is considered one of the most prominent causes of death from cardiovascular disease worldwide. Knowledge of the molecular mechanisms underlying AMI remains limited. Accurate biomarkers are needed to predict the risk of AMI and would be beneficial for managing the incidence rate. The gold standard for the diagnosis of AMI, the cardiac troponin T (cTnT) assay, requires serial testing, and the timing of measurement with respect to symptoms affects the results. As attractive candidate diagnostic biomarkers in AMI, circulating microRNAs (miRNAs) are easily detectable, generally stable and tissue specific. Methods The Gene Expression Omnibus (GEO) database was used to compare miRNA expression between AMI and control samples, and the interactions between miRNAs and mRNAs were analysed for expression and function. Furthermore, a protein-protein interaction (PPI) network was constructed. The miRNAs identified in the bioinformatic analysis were verified by RT-qPCR in an H9C2 cell line. The miRNAs in plasma samples from patients with AMI (n = 11) and healthy controls (n = 11) were used to construct receiver operating characteristic (ROC) curves to evaluate the clinical prognostic value of the identified miRNAs. Results We identified eight novel miRNAs as potential candidate diagnostic biomarkers for patients with AMI. In addition, the predicted target genes provide insight into the molecular mechanisms underlying AMI.
bibliographic citation: Wang et al. (2020) The biomarkers of key miRNAs and target genes associated with acute myocardial infarction. PeerJ 8:e9129 https://doi.org/10.7717/peerj.9129
date submitted: 2019-12-23
date accepted: 2020-04-14
issued: 2020-05-13
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Wang
  given name: Qi
author list: Agent
  family name: Liu
  given name: Bingyan
author list: Agent
  family name: Wang
  given name: Yuanyong
author list: Agent
  family name: Bai
  given name: Baochen
author list: Agent
  family name: Yu
  given name: Tao
author list: Agent
  family name: Chu
  given name: Xian–ming
doi: 10.7717/peerj.9129
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-05-13
copyright: ©2020 Wang et al.
attribution name: Wang et al.

Dental fear association between mothers and adolescents—a longitudinal study
type: item
type: AcademicArticle
description: Aim To assess the longitudinal association between adolescents’ and their mothers’ dental fear. Study Design A longitudinal questionnaire survey study. Methods A randomized sample of 12-year-old adolescents were selected from local Hong Kong schools. Adolescents and their mothers self-completed the Modified Dental Anxiety Scale (MDAS). The sociodemographic background of the mothers and the oral health habits of the adolescents were also collected and these measurements were repeated at 15- and 18-years-old. Non-parametric tests (Mann–Whitney U test/Kruskall Wallis test) were used to test associations between MDAS dental fear items and independent variables. Logistic regression (adjusted for family’s sociodemographic background and adolescent’s oral health habits) was performed to evaluate the longitudinal association between adolescents’ and mothers’ dental fear. Results A total of 212 mother-child pairs were recruited at baseline (12-year-old adolescents). In the first and second follow-ups (15- and 18-years-old), 195 and 182 mother-child pairs completed the survey. Significant associations between mother’s and child’s scores in “feeling about having their teeth scraped and polished”, “having teeth drilled”, and ‘having an injection in the gum’ were found when adolescents were 12- years-old (P < 0.01) and 18-years-old (P < 0.05), but not at 15-years-old. Conclusion Adolescents’ and mothers’ dental fear is associated at 12-years-old and 18-years-old, but not at 15-years-old, which is likely specific to the Hong Kong context but may be extrapolated to other industrialized countries with caution.
format: application/pdf
format: text/html
creator: Hai Ming Wong
creator: Yu Yuan Zhang
creator: Antonio Perfecto
creator: Colman P.J. McGrath
subject: Dentistry
subject: Public Health
description: doi:10.7717/peerj.9154
publisher: PeerJ Inc.
rights: © 2020 Wong et al.
abstract: Aim To assess the longitudinal association between adolescents’ and their mothers’ dental fear. Study Design A longitudinal questionnaire survey study. Methods A randomized sample of 12-year-old adolescents were selected from local Hong Kong schools. Adolescents and their mothers self-completed the Modified Dental Anxiety Scale (MDAS). The sociodemographic background of the mothers and the oral health habits of the adolescents were also collected and these measurements were repeated at 15- and 18-years-old. Non-parametric tests (Mann–Whitney U test/Kruskall Wallis test) were used to test associations between MDAS dental fear items and independent variables. Logistic regression (adjusted for family’s sociodemographic background and adolescent’s oral health habits) was performed to evaluate the longitudinal association between adolescents’ and mothers’ dental fear. Results A total of 212 mother-child pairs were recruited at baseline (12-year-old adolescents). In the first and second follow-ups (15- and 18-years-old), 195 and 182 mother-child pairs completed the survey. Significant associations between mother’s and child’s scores in “feeling about having their teeth scraped and polished”, “having teeth drilled”, and ‘having an injection in the gum’ were found when adolescents were 12- years-old (P < 0.01) and 18-years-old (P < 0.05), but not at 15-years-old. Conclusion Adolescents’ and mothers’ dental fear is associated at 12-years-old and 18-years-old, but not at 15-years-old, which is likely specific to the Hong Kong context but may be extrapolated to other industrialized countries with caution.
bibliographic citation: Wong et al. (2020) Dental fear association between mothers and adolescents—a longitudinal study. PeerJ 8:e9154 https://doi.org/10.7717/peerj.9154
date submitted: 2019-10-28
date accepted: 2020-04-18
issued: 2020-05-13
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Wong
  given name: Hai Ming
author list: Agent
  family name: Zhang
  given name: Yu Yuan
author list: Agent
  family name: Perfecto
  given name: Antonio
author list: Agent
  family name: McGrath
  given name: Colman P.J.
doi: 10.7717/peerj.9154
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-05-13
copyright: © 2020 Wong et al.
attribution name: Wong et al.

PeerJ
type: Periodical
uri: PeerJ
issn: 2167-8359