PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
items: An integrated model of seasonal changes in stock composition and abundance with an application to Chinook salmon
items: Rainwater chemistry observation in a karst city: variations, influence factors, sources and potential environmental effects
items: Long non-coding RNA taurine upregulated gene 1 is downregulated in osteoporosis and influences the osteogenic differentiation of bone marrow mesenchymal stem cells
items: Development and validation of an oxidative stress—associated prognostic risk model for melanoma
items: Prediction and analysis of novel key genes ITGAX, LAPTM5, SERPINE1 in clear cell renal cell carcinoma through bioinformatics analysis
items: The impact of functional excess of footwear on the foot shape of 7-year-old girls and boys
items: Anti-atherosclerotic vaccination against Porphyromonas gingivalis as a potential comparator of statin in mice
items: Characteristics of craniofacial morphology and factors affecting them in patients with isolated cleft palate
items: Identification and comparison of circular RNAs in preeclampsia
items: Sexual dimorphism and skull size and shape in the highly specialized snake species, Aipysurus eydouxii (Elapidae: Hydrophiinae)

An integrated model of seasonal changes in stock composition and abundance with an application to Chinook salmon
type: item
type: AcademicArticle
description: Population-specific spatial and temporal distribution data are necessary to identify mechanisms regulating abundance and to manage anthropogenic impacts. However the distributions of highly migratory species are often difficult to resolve, particularly when multiple populations’ movements overlap. Here we present an integrated model to estimate spatially-stratified, seasonal trends in abundance and population composition, using data from extensive genetic sampling of commercial and recreational Chinook salmon (Oncorhynchus tshawytscha) fisheries in southern British Columbia. We use the model to estimate seasonal changes in population-specific standardized catch per unit effort (a proxy for abundance) across six marine regions, while accounting for annual variability in sampling effort and uncertain genetic stock assignment. We also share this model as an R package stockseasonr for application to other regions and species. Even at the relatively small spatial scales considered here, we found that patterns in seasonal abundance differed among regions and stocks. While certain locations were clearly migratory corridors, regions within the Salish Sea exhibited diverse, and often weak, seasonal patterns in abundance, emphasizing that they are important, year-round foraging habitats. Furthermore, we found evidence that stocks with similar freshwater life histories and adult run timing, as well as relatively proximate spawning locations, exhibited divergent distributions. Our findings highlight subtle, but important differences in how adult Chinook salmon use marine habitats. Down-scaled model outputs could be used to inform ecosystem-based management efforts by resolving the degree to which salmon overlap with other species of concern, as well as specific fisheries. More broadly, variation in stock-specific abundance among regions indicates efforts to identify mechanisms driving changes in size-at-maturity and natural mortality should account for distinct marine distribut…
format: application/pdf
format: text/html
creator: Cameron Freshwater
creator: Sean C. Anderson
creator: Terry D. Beacham
creator: Wilf Luedke
creator: Catarina Wor
creator: Jackie King
subject: Fisheries and Fish Science
subject: Conservation Biology
subject: Ecology
subject: Zoology
description: doi:10.7717/peerj.11163
publisher: PeerJ Inc.
rights: © 2021
abstract: Population-specific spatial and temporal distribution data are necessary to identify mechanisms regulating abundance and to manage anthropogenic impacts. However the distributions of highly migratory species are often difficult to resolve, particularly when multiple populations’ movements overlap. Here we present an integrated model to estimate spatially-stratified, seasonal trends in abundance and population composition, using data from extensive genetic sampling of commercial and recreational Chinook salmon (Oncorhynchus tshawytscha) fisheries in southern British Columbia. We use the model to estimate seasonal changes in population-specific standardized catch per unit effort (a proxy for abundance) across six marine regions, while accounting for annual variability in sampling effort and uncertain genetic stock assignment. We also share this model as an R package stockseasonr for application to other regions and species. Even at the relatively small spatial scales considered here, we found that patterns in seasonal abundance differed among regions and stocks. While certain locations were clearly migratory corridors, regions within the Salish Sea exhibited diverse, and often weak, seasonal patterns in abundance, emphasizing that they are important, year-round foraging habitats. Furthermore, we found evidence that stocks with similar freshwater life histories and adult run timing, as well as relatively proximate spawning locations, exhibited divergent distributions. Our findings highlight subtle, but important differences in how adult Chinook salmon use marine habitats. Down-scaled model outputs could be used to inform ecosystem-based management efforts by resolving the degree to which salmon overlap with other species of concern, as well as specific fisheries. More broadly, variation in stock-specific abundance among regions indicates efforts to identify mechanisms driving changes in size-at-maturity and natural mortality should account for distinct marine distribut…
bibliographic citation: Freshwater et al. (2021) An integrated model of seasonal changes in stock composition and abundance with an application to Chinook salmon. PeerJ 9:e11163 https://doi.org/10.7717/peerj.11163
date submitted: 2021-01-11
date accepted: 2021-03-04
issued: 2021-04-20
is part of: PeerJ
license: open-government-licence
author list: Agent
  family name: Freshwater
  given name: Cameron
author list: Agent
  family name: Anderson
  given name: Sean C.
author list: Agent
  family name: Beacham
  given name: Terry D.
author list: Agent
  family name: Luedke
  given name: Wilf
author list: Agent
  family name: Wor
  given name: Catarina
author list: Agent
  family name: King
  given name: Jackie
doi: 10.7717/peerj.11163
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-04-20

Rainwater chemistry observation in a karst city: variations, influence factors, sources and potential environmental effects
type: item
type: AcademicArticle
description: The rainwater chemistry and related air contaminants are used to investigate the rainwater ions sources, variations, and influence factors from 2012 to 2014 in Guiyang city (the typical karst urban area of Southwest China). According to temporal rainwater ion concentrations, the obvious variations were presented in the study period, such as Ca2+ (125∼6,652 μeq L−1) and SO42− (11∼4,127 μeq L−1). Consequently, Ca2+, Mg2+, SO42− and Cl− are considered as the leading ions. Three critical influencing factors of rainwater ions concentrations, including sources variations, rainfall amount and long-distance migration (rainfall amount > 100 mm) are identified. Based on the typical ionic ratios, source identification suggested that anthropogenic inputs mainly contributed to F−, NO3− and SO42−, while the dusts (crustal sources) are the primary sources of Mg2+, Ca2+ and K+. Cl− Enrichment in long-distance transport is the main contributor of Cl−. According to the observation of high level of total wet acid deposition, the more detailed spatio-temporal monitoring of rainfall-related acid deposition (particularly sulfur deposition) is required to understand its potential environmental effects in the aquatic ecosystem of the earth surface.
format: application/pdf
format: text/html
creator: Jie Zeng
creator: Guilin Han
subject: Atmospheric Chemistry
subject: Ecohydrology
subject: Environmental Contamination and Remediation
subject: Environmental Impacts
description: doi:10.7717/peerj.11167
publisher: PeerJ Inc.
rights: © 2021 Zeng and Han
abstract: The rainwater chemistry and related air contaminants are used to investigate the rainwater ions sources, variations, and influence factors from 2012 to 2014 in Guiyang city (the typical karst urban area of Southwest China). According to temporal rainwater ion concentrations, the obvious variations were presented in the study period, such as Ca2+ (125∼6,652 μeq L−1) and SO42− (11∼4,127 μeq L−1). Consequently, Ca2+, Mg2+, SO42− and Cl− are considered as the leading ions. Three critical influencing factors of rainwater ions concentrations, including sources variations, rainfall amount and long-distance migration (rainfall amount > 100 mm) are identified. Based on the typical ionic ratios, source identification suggested that anthropogenic inputs mainly contributed to F−, NO3− and SO42−, while the dusts (crustal sources) are the primary sources of Mg2+, Ca2+ and K+. Cl− Enrichment in long-distance transport is the main contributor of Cl−. According to the observation of high level of total wet acid deposition, the more detailed spatio-temporal monitoring of rainfall-related acid deposition (particularly sulfur deposition) is required to understand its potential environmental effects in the aquatic ecosystem of the earth surface.
bibliographic citation: Zeng et al. (2021) Rainwater chemistry observation in a karst city: variations, influence factors, sources and potential environmental effects. PeerJ 9:e11167 https://doi.org/10.7717/peerj.11167
date submitted: 2020-12-15
date accepted: 2021-03-05
issued: 2021-04-20
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Zeng
  given name: Jie
author list: Agent
  family name: Han
  given name: Guilin
doi: 10.7717/peerj.11167
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-04-20
copyright: © 2021 Zeng and Han
attribution name: Zeng and Han

Long non-coding RNA taurine upregulated gene 1 is downregulated in osteoporosis and influences the osteogenic differentiation of bone marrow mesenchymal stem cells
type: item
type: AcademicArticle
description: Background With aging, an imbalance in bone remodeling leading to increased bone resorption and decreased bone formation is thought to contribute to osteoporosis. Osteoblastic differentiation of bone marrow mesenchymal stem cells (BMMSCs) plays a vital role in the pathogenesis of osteoporosis. However, the detailed molecular mechanisms of osteoporosis remain incompletely understood. Given that long non-coding RNA taurine upregulated gene 1 (lnc TUG1) plays a critical role in the osteogenic differentiation, and microRNA-23b (miR-23b) as a putative sponge for lnc TUG1 has upregulated expression in osteoporosis. Therefore, this study investigated the roles of TUG1/miR-23b in osteoporotic pathology. Material and Methods TUG1 and miR-23b expression in the plasma of osteoporotic patients were evaluated by quantitative real-time PCR (qRT-PCR). The osteogenic differentiation in human BMMSCs was evaluated by qRT-PCR, western blot, Alizarin red staining after knockdown of TUG1 by small interfering RNA (siRNA) treatment. Results Decreased expression of TUG1 and increased expression of miR-23b evident in the plasma of patients with osteoporosis than in that of age- and sex-matched healthy controls. Additionally, increased miR-23b expression inhibited runt-related transcription factor 2 (RUNX2), osteocalcin, and osteopontin expression and reduced calcified nodule formation based on the results of qRT-PCR, western blot, and Alizarin Red S staining. Conclusion The study for the first time reported that silence of lncRNA TUG1 significantly suppressed the osteogenic differentiation of BMMSCs possibly by targeting the miR-23b/RUNX2 signaling pathway. This mechanism of TUG1/miR-23b/RUNX2 signaling within the osteogenic differentiation of BMMSCs might provide new insight for the development of lncRNA-directed diagnostic and therapeutic strategies for osteoporosis.
format: application/pdf
format: text/html
creator: Zhaowei Teng
creator: Yun Zhu
creator: Qinggang Hao
creator: Xiaochao Yu
creator: Yirong Teng
creator: Qiaoning Yue
creator: Xiguang Zhang
creator: Sheng Lu
subject: Cell Biology
subject: Molecular Biology
subject: Geriatrics
subject: Orthopedics
subject: Medical Genetics
description: doi:10.7717/peerj.11251
publisher: PeerJ Inc.
rights: © 2021 Teng et al.
abstract: Background With aging, an imbalance in bone remodeling leading to increased bone resorption and decreased bone formation is thought to contribute to osteoporosis. Osteoblastic differentiation of bone marrow mesenchymal stem cells (BMMSCs) plays a vital role in the pathogenesis of osteoporosis. However, the detailed molecular mechanisms of osteoporosis remain incompletely understood. Given that long non-coding RNA taurine upregulated gene 1 (lnc TUG1) plays a critical role in the osteogenic differentiation, and microRNA-23b (miR-23b) as a putative sponge for lnc TUG1 has upregulated expression in osteoporosis. Therefore, this study investigated the roles of TUG1/miR-23b in osteoporotic pathology. Material and Methods TUG1 and miR-23b expression in the plasma of osteoporotic patients were evaluated by quantitative real-time PCR (qRT-PCR). The osteogenic differentiation in human BMMSCs was evaluated by qRT-PCR, western blot, Alizarin red staining after knockdown of TUG1 by small interfering RNA (siRNA) treatment. Results Decreased expression of TUG1 and increased expression of miR-23b evident in the plasma of patients with osteoporosis than in that of age- and sex-matched healthy controls. Additionally, increased miR-23b expression inhibited runt-related transcription factor 2 (RUNX2), osteocalcin, and osteopontin expression and reduced calcified nodule formation based on the results of qRT-PCR, western blot, and Alizarin Red S staining. Conclusion The study for the first time reported that silence of lncRNA TUG1 significantly suppressed the osteogenic differentiation of BMMSCs possibly by targeting the miR-23b/RUNX2 signaling pathway. This mechanism of TUG1/miR-23b/RUNX2 signaling within the osteogenic differentiation of BMMSCs might provide new insight for the development of lncRNA-directed diagnostic and therapeutic strategies for osteoporosis.
bibliographic citation: Teng et al. (2021) Long non-coding RNA taurine upregulated gene 1 is downregulated in osteoporosis and influences the osteogenic differentiation of bone marrow mesenchymal stem cells. PeerJ 9:e11251 https://doi.org/10.7717/peerj.11251
date submitted: 2020-09-21
date accepted: 2021-03-19
issued: 2021-04-20
is part of: PeerJ
license: https://creativecommons.org/licenses/by-nc/4.0
author list: Agent
  family name: Teng
  given name: Zhaowei
author list: Agent
  family name: Zhu
  given name: Yun
author list: Agent
  family name: Hao
  given name: Qinggang
author list: Agent
  family name: Yu
  given name: Xiaochao
author list: Agent
  family name: Teng
  given name: Yirong
author list: Agent
  family name: Yue
  given name: Qiaoning
author list: Agent
  family name: Zhang
  given name: Xiguang
author list: Agent
  family name: Lu
  given name: Sheng
doi: 10.7717/peerj.11251
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-04-20
copyright: ©2021 Teng et al.
attribution name: Teng et al.

Development and validation of an oxidative stress—associated prognostic risk model for melanoma
type: item
type: AcademicArticle
description: Background Oxidative stress (OS) is key to various diseases and is implicated in cancer progression and oncogenesis. However, the potential diagnostic value of OS-related genes in skin cutaneous melanoma (SKCM) remains unclear. Methods We used data of RNA sequencing from 471 tumor tissues and one healthy tissue acquired from The Cancer Genome Atlas (TCGA)-SKCM cohort. The Genome Tissue Expression database was used to acquire transcriptome data from 812 healthy samples. OS-related genes that were differentially expressed between SKCM and healthy samples were investigated and 16 prognosis-associated OS genes were identified. The prognostic risk model was built using univariate and Cox multivariate regressions. The prognostic value of the hub genes was validated in the GSE65904 cohort, which included 214 SKCM patients. Results The overall survival rate of SKCM patients in the high-risk group was decreased compared to the low-risk group. In both TCGA and GSE65904 cohorts, the ROC curves suggested that our prognostic risk model was more accurate than other clinicopathological characteristics to diagnose SKCM. Moreover, risk score and nomograms associated with the expression of hub genes were developed. These presented reiterated our prognostic risk model. Altogether, this study provides novel insights with regards to the pathogenesis of SKCM. The 16 hub genes identified may help in SKCM prognosis and individualized clinical treatment.
format: application/pdf
format: text/html
creator: Yu Yang
creator: Xuan Long
creator: Kun Li
creator: Guiyun Li
creator: Xiaohong Yu
creator: Ping Wen
creator: Jun Luo
creator: Xiaobin Tian
creator: Jinmin Zhao
subject: Bioinformatics
subject: Genetics
subject: Dermatology
subject: Oncology
subject: Medical Genetics
description: doi:10.7717/peerj.11258
publisher: PeerJ Inc.
rights: © 2021 Yang et al.
abstract: Background Oxidative stress (OS) is key to various diseases and is implicated in cancer progression and oncogenesis. However, the potential diagnostic value of OS-related genes in skin cutaneous melanoma (SKCM) remains unclear. Methods We used data of RNA sequencing from 471 tumor tissues and one healthy tissue acquired from The Cancer Genome Atlas (TCGA)-SKCM cohort. The Genome Tissue Expression database was used to acquire transcriptome data from 812 healthy samples. OS-related genes that were differentially expressed between SKCM and healthy samples were investigated and 16 prognosis-associated OS genes were identified. The prognostic risk model was built using univariate and Cox multivariate regressions. The prognostic value of the hub genes was validated in the GSE65904 cohort, which included 214 SKCM patients. Results The overall survival rate of SKCM patients in the high-risk group was decreased compared to the low-risk group. In both TCGA and GSE65904 cohorts, the ROC curves suggested that our prognostic risk model was more accurate than other clinicopathological characteristics to diagnose SKCM. Moreover, risk score and nomograms associated with the expression of hub genes were developed. These presented reiterated our prognostic risk model. Altogether, this study provides novel insights with regards to the pathogenesis of SKCM. The 16 hub genes identified may help in SKCM prognosis and individualized clinical treatment.
bibliographic citation: Yang et al. (2021) Development and validation of an oxidative stress—associated prognostic risk model for melanoma. PeerJ 9:e11258 https://doi.org/10.7717/peerj.11258
date submitted: 2021-01-22
date accepted: 2021-03-22
issued: 2021-04-20
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Yang
  given name: Yu
author list: Agent
  family name: Long
  given name: Xuan
author list: Agent
  family name: Li
  given name: Kun
author list: Agent
  family name: Li
  given name: Guiyun
author list: Agent
  family name: Yu
  given name: Xiaohong
author list: Agent
  family name: Wen
  given name: Ping
author list: Agent
  family name: Luo
  given name: Jun
author list: Agent
  family name: Tian
  given name: Xiaobin
author list: Agent
  family name: Zhao
  given name: Jinmin
doi: 10.7717/peerj.11258
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-04-20
copyright: ©2021 Yang et al.
attribution name: Yang et al.

Prediction and analysis of novel key genes ITGAX, LAPTM5, SERPINE1 in clear cell renal cell carcinoma through bioinformatics analysis
type: item
type: AcademicArticle
description: Background Clear Cell Renal Cell Carcinoma (CCRCC) is the most aggressive subtype of Renal Cell Carcinoma (RCC) with high metastasis and recurrence rates. This study aims to find new potential key genes of CCRCC. Methods Four gene expression profiles (GSE12606, GSE53000, GSE68417, and GSE66272) were downloaded from the Gene Expression Omnibus (GEO) database. The TCGA KIRC data was downloaded from The Cancer Genome Atlas (TCGA). Using GEO2R, the differentially expressed genes (DEG) in CCRCC tissues and normal samples were analyzed. Gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses were performed in DAVID database. A protein-protein interaction (PPI) network was constructed and the hub gene was predicted by STRING and Cytoscape. GEPIA and Kaplan-Meier plotter databases were used for further screening of Key genes. Expression verification and survival analysis of key genes were performed using TCGA database, GEPIA database, and Kaplan-Meier plotter. Receiver operating characteristic (ROC) curve was used to analyze the diagnostic value of key genes in CCRCC, which is plotted by R software based on TCGA database. UALCAN database was used to analyze the relationship between key genes and clinical pathology in CCRCC and the methylation level of the promoter of key genes in CCRCC. Results A total of 289 up-regulated and 449 down-regulated genes were identified based on GSE12606, GSE53000, GSE68417, and GSE66272 profiles in CCRCC. The upregulated DEGs were mainly enriched with protein binding and PI3K-Akt signaling pathway, whereas down-regulated genes were enriched with the integral component of the membrane and metabolic pathways. Next, the top 35 genes were screened out from the PPI network according to Degree, and three new key genes ITGAX, LAPTM5 and SERPINE1 were further screened out through survival and prognosis analysis. Further results showed that the ITGAX, LAPTM5, and SERPINE1 levels in CCRCC tumor tissues were significantl…
format: application/pdf
format: text/html
creator: Yingli Sui
creator: Kun Lu
creator: Lin Fu
subject: Bioinformatics
subject: Nephrology
subject: Oncology
description: doi:10.7717/peerj.11272
publisher: PeerJ Inc.
rights: © 2021 Sui et al.
abstract: Background Clear Cell Renal Cell Carcinoma (CCRCC) is the most aggressive subtype of Renal Cell Carcinoma (RCC) with high metastasis and recurrence rates. This study aims to find new potential key genes of CCRCC. Methods Four gene expression profiles (GSE12606, GSE53000, GSE68417, and GSE66272) were downloaded from the Gene Expression Omnibus (GEO) database. The TCGA KIRC data was downloaded from The Cancer Genome Atlas (TCGA). Using GEO2R, the differentially expressed genes (DEG) in CCRCC tissues and normal samples were analyzed. Gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses were performed in DAVID database. A protein-protein interaction (PPI) network was constructed and the hub gene was predicted by STRING and Cytoscape. GEPIA and Kaplan-Meier plotter databases were used for further screening of Key genes. Expression verification and survival analysis of key genes were performed using TCGA database, GEPIA database, and Kaplan-Meier plotter. Receiver operating characteristic (ROC) curve was used to analyze the diagnostic value of key genes in CCRCC, which is plotted by R software based on TCGA database. UALCAN database was used to analyze the relationship between key genes and clinical pathology in CCRCC and the methylation level of the promoter of key genes in CCRCC. Results A total of 289 up-regulated and 449 down-regulated genes were identified based on GSE12606, GSE53000, GSE68417, and GSE66272 profiles in CCRCC. The upregulated DEGs were mainly enriched with protein binding and PI3K-Akt signaling pathway, whereas down-regulated genes were enriched with the integral component of the membrane and metabolic pathways. Next, the top 35 genes were screened out from the PPI network according to Degree, and three new key genes ITGAX, LAPTM5 and SERPINE1 were further screened out through survival and prognosis analysis. Further results showed that the ITGAX, LAPTM5, and SERPINE1 levels in CCRCC tumor tissues were significantl…
bibliographic citation: Sui et al. (2021) Prediction and analysis of novel key genes ITGAX, LAPTM5, SERPINE1 in clear cell renal cell carcinoma through bioinformatics analysis. PeerJ 9:e11272 https://doi.org/10.7717/peerj.11272
date submitted: 2020-11-09
date accepted: 2021-03-23
issued: 2021-04-20
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Sui
  given name: Yingli
author list: Agent
  family name: Lu
  given name: Kun
author list: Agent
  family name: Fu
  given name: Lin
doi: 10.7717/peerj.11272
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-04-20
copyright: ©2021 Sui et al.
attribution name: Sui et al.

The impact of functional excess of footwear on the foot shape of 7-year-old girls and boys
type: item
type: AcademicArticle
description: Background Properly fitted shoes can support the development of growing feet and prevent problems and pathologies, not only in childhood, but also in adulthood. This points to the need to conduct research on the impact of shoe fitting on the structure of the foot in order to raise awareness and importance of this problem, to enable proper decisions regarding the purchase and use of shoes. The aim of this study was to analyze indoor footwear fit and its impact on foot structure in 7-year-old schoolchildren. Methods The CQ-ST podoscope and the Clevermess device were used for measurements. The analysis was carried out using the Mann Whitney U test, Wilcoxon signed-rank test, Chi-square test, regression analysis. Results About 40% of girls and boys had shoes that were incorrectly fitted in length, while as many as 74% of girls and 66% of boys wore shoes that were incorrectly fitted in width. Regression analysis demonstrated a statistically significant influence of the footwear length on longitudinal arch of the right and left foot and the transverse arch of the right foot. In boys, the length of the shoes shows associations with the right and left hallux valgus angle. Conclusion A significant percentage of the studied 7-year-olds, regardless of gender, wears inappropriately fitted shoes. In both sexes, the length of the footwear influenced the longitudinal arch of the right and left foot and the transverse arch of the right foot. Due to the deformity of the first metatarsophalangeal joint, the boys with hallux valgus require footwear which is wider and therefore their shoes need to be bigger in size.
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format: text/html
creator: Ewa Puszczalowska-Lizis
creator: Aleksandra Lukasiewicz
creator: Sabina Lizis
creator: Jaroslaw Omorczyk
subject: Health Policy
subject: Kinesiology
subject: Pediatrics
subject: Public Health
description: doi:10.7717/peerj.11277
publisher: PeerJ Inc.
rights: © 2021 Puszczalowska-Lizis et al.
abstract: Background Properly fitted shoes can support the development of growing feet and prevent problems and pathologies, not only in childhood, but also in adulthood. This points to the need to conduct research on the impact of shoe fitting on the structure of the foot in order to raise awareness and importance of this problem, to enable proper decisions regarding the purchase and use of shoes. The aim of this study was to analyze indoor footwear fit and its impact on foot structure in 7-year-old schoolchildren. Methods The CQ-ST podoscope and the Clevermess device were used for measurements. The analysis was carried out using the Mann Whitney U test, Wilcoxon signed-rank test, Chi-square test, regression analysis. Results About 40% of girls and boys had shoes that were incorrectly fitted in length, while as many as 74% of girls and 66% of boys wore shoes that were incorrectly fitted in width. Regression analysis demonstrated a statistically significant influence of the footwear length on longitudinal arch of the right and left foot and the transverse arch of the right foot. In boys, the length of the shoes shows associations with the right and left hallux valgus angle. Conclusion A significant percentage of the studied 7-year-olds, regardless of gender, wears inappropriately fitted shoes. In both sexes, the length of the footwear influenced the longitudinal arch of the right and left foot and the transverse arch of the right foot. Due to the deformity of the first metatarsophalangeal joint, the boys with hallux valgus require footwear which is wider and therefore their shoes need to be bigger in size.
bibliographic citation: Puszczalowska-Lizis et al. (2021) The impact of functional excess of footwear on the foot shape of 7-year-old girls and boys. PeerJ 9:e11277 https://doi.org/10.7717/peerj.11277
date submitted: 2021-01-07
date accepted: 2021-03-24
issued: 2021-04-20
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Puszczalowska-Lizis
  given name: Ewa
author list: Agent
  family name: Lukasiewicz
  given name: Aleksandra
author list: Agent
  family name: Lizis
  given name: Sabina
author list: Agent
  family name: Omorczyk
  given name: Jaroslaw
doi: 10.7717/peerj.11277
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-04-20
copyright: ©2021 Puszczalowska-Lizis et al.
attribution name: Puszczalowska-Lizis et al.

Anti-atherosclerotic vaccination against Porphyromonas gingivalis as a potential comparator of statin in mice
type: item
type: AcademicArticle
description: Background Porphyromonas gingivalis (Pg) is an oral anaerobe which damages teeth and periodontal tissues. Its body infection is known to cause chronic inflammation, thereby inducing an early stage of atherosclerosis through humoral immune actions. Hence, vaccination by immunizing the proteins of P. gingivalis (Pg) post sonication with heating may prevent atherosclerosis. This study aimed to compare the effect of its vaccination with statin, which effectively prevents atherosclerosis by lowering lipids. Methods The vaccine was produced by sonicating P. gingivalis through heating, and a total of 32 male APOE-/-mice (8-week old) were subjected Western diet for 8 weeks, in order to induce atherosclerosis in a physiological manner. Then, the mice were grouped to undergo four treatment conditions (i.e., no treatment, pitavastatin, vaccine, or pitavastatin with vaccine). Vaccination was conducted through nasal immunization and confirmed by a Pg-specific humoral immune reaction. Then, half of the mice in each group were orally injected with P. gingivalis for the next 5 weeks while the other half remained uninfected, generating a total of eight groups (n = 4/group). The mice were sacrificed at 3 weeks after the last injection. After harvesting the aorta, Oil Red O staining of en face was conducted with imaging and image analysis, and plaque formation was quantitatively determined. Results Compared to no treatment, the vaccination through nasal immunization significantly reduced the atherosclerotic plaque sizes in APOE -/- mice under Western diet to the comparable level of statin group. When both vaccine and statin were used, no clear synergistic effect was observed as opposed to expectation. Conclusions This study revealed that nasal immunization of heat shock P. gingivalis has a significant impact on the prevention of arteriosclerosis and acts as a potential comparator of statin.
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format: text/html
creator: Hyun-Su Ha
creator: Tae Young Kim
creator: Soo Jung Han
creator: Hak-Joon Sung
creator: Kyoung Yul Seo
creator: Jong-Won Ha
subject: Biochemistry
subject: Microbiology
subject: Cardiology
subject: Infectious Diseases
description: doi:10.7717/peerj.11293
publisher: PeerJ Inc.
rights: © 2021 Ha et al.
abstract: Background Porphyromonas gingivalis (Pg) is an oral anaerobe which damages teeth and periodontal tissues. Its body infection is known to cause chronic inflammation, thereby inducing an early stage of atherosclerosis through humoral immune actions. Hence, vaccination by immunizing the proteins of P. gingivalis (Pg) post sonication with heating may prevent atherosclerosis. This study aimed to compare the effect of its vaccination with statin, which effectively prevents atherosclerosis by lowering lipids. Methods The vaccine was produced by sonicating P. gingivalis through heating, and a total of 32 male APOE-/-mice (8-week old) were subjected Western diet for 8 weeks, in order to induce atherosclerosis in a physiological manner. Then, the mice were grouped to undergo four treatment conditions (i.e., no treatment, pitavastatin, vaccine, or pitavastatin with vaccine). Vaccination was conducted through nasal immunization and confirmed by a Pg-specific humoral immune reaction. Then, half of the mice in each group were orally injected with P. gingivalis for the next 5 weeks while the other half remained uninfected, generating a total of eight groups (n = 4/group). The mice were sacrificed at 3 weeks after the last injection. After harvesting the aorta, Oil Red O staining of en face was conducted with imaging and image analysis, and plaque formation was quantitatively determined. Results Compared to no treatment, the vaccination through nasal immunization significantly reduced the atherosclerotic plaque sizes in APOE -/- mice under Western diet to the comparable level of statin group. When both vaccine and statin were used, no clear synergistic effect was observed as opposed to expectation. Conclusions This study revealed that nasal immunization of heat shock P. gingivalis has a significant impact on the prevention of arteriosclerosis and acts as a potential comparator of statin.
bibliographic citation: Ha et al. (2021) Anti-atherosclerotic vaccination against Porphyromonas gingivalis as a potential comparator of statin in mice. PeerJ 9:e11293 https://doi.org/10.7717/peerj.11293
date submitted: 2020-10-16
date accepted: 2021-03-26
issued: 2021-04-20
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Ha
  given name: Hyun-Su
author list: Agent
  family name: Kim
  given name: Tae Young
author list: Agent
  family name: Han
  given name: Soo Jung
author list: Agent
  family name: Sung
  given name: Hak-Joon
author list: Agent
  family name: Seo
  given name: Kyoung Yul
author list: Agent
  family name: Ha
  given name: Jong-Won
doi: 10.7717/peerj.11293
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-04-20
copyright: ©2021 Ha et al.
attribution name: Ha et al.

Characteristics of craniofacial morphology and factors affecting them in patients with isolated cleft palate
type: item
type: AcademicArticle
description: Background Myriad maxillo-mandibular occlusal relationships are observed in patients with isolated cleft palate (ICP), unlike in patients with other cleft types, such as cleft lip and palate. Objectives This study aimed to categorise the characteristics of craniofacial morphology in patients with ICP, and investigate the clinical factors affecting these categorised morphological characteristics. Methods Thirty-six girls with ICP (age (mean ± SD): 5.36 ± 0.36 years) underwent cephalometric measurement. Their craniofacial morphology was categorised using cluster analysis. Profilograms were created and superimposed onto the standard Japanese profilograms to visualise the morphological characteristics of each group (cluster). The mean values and variations in the linear and angular measurements of each group were compared with the Japanese standards and statistically analysed using Dunnett’s test after the analysis of variance. Fisher’s exact test was used to analyse the differences between the cleft types (cleft in the hard and/or soft palate) and skills of the operating surgeons in the groups. Results Cluster analysis of craniofacial morphologies in patients with ICP resulted in the formation of three categories: the first cluster exhibited a relatively harmonious anteroposterior relationship between the maxilla and the mandible (22.2%); the second cluster exhibited crossbite owing to a significantly smaller maxilla (33.3%); and the third cluster exhibited a smaller mandible with posterior rotation showing skeletal class II malocclusion (44.4%). Differences in cleft types and surgeons were not associated with the distribution of patients in each cluster. Conclusions Patients with ICP exhibited characteristic morphological patterns, such as bimaxillary retrusion or severe mandibular retrusion, besides the anterior crossbite frequently found in patients with cleft lip and palate . Understanding the typical morphological characteristics could enable better diagnostic cat…
format: application/pdf
format: text/html
creator: Kyoko Tsuji
creator: Naoto Haruyama
creator: Shunsuke Nomura
creator: Naohisa Murata
creator: Keigo Yoshizaki
creator: Takeshi Mitsuyasu
creator: Hiroyuki Nakano
creator: Seiji Nakamura
creator: Yoshihide Mori
creator: Ichiro Takahashi
subject: Dentistry
subject: Pediatrics
subject: Surgery and Surgical Specialties
description: doi:10.7717/peerj.11297
publisher: PeerJ Inc.
rights: © 2021 Tsuji et al.
abstract: Background Myriad maxillo-mandibular occlusal relationships are observed in patients with isolated cleft palate (ICP), unlike in patients with other cleft types, such as cleft lip and palate. Objectives This study aimed to categorise the characteristics of craniofacial morphology in patients with ICP, and investigate the clinical factors affecting these categorised morphological characteristics. Methods Thirty-six girls with ICP (age (mean ± SD): 5.36 ± 0.36 years) underwent cephalometric measurement. Their craniofacial morphology was categorised using cluster analysis. Profilograms were created and superimposed onto the standard Japanese profilograms to visualise the morphological characteristics of each group (cluster). The mean values and variations in the linear and angular measurements of each group were compared with the Japanese standards and statistically analysed using Dunnett’s test after the analysis of variance. Fisher’s exact test was used to analyse the differences between the cleft types (cleft in the hard and/or soft palate) and skills of the operating surgeons in the groups. Results Cluster analysis of craniofacial morphologies in patients with ICP resulted in the formation of three categories: the first cluster exhibited a relatively harmonious anteroposterior relationship between the maxilla and the mandible (22.2%); the second cluster exhibited crossbite owing to a significantly smaller maxilla (33.3%); and the third cluster exhibited a smaller mandible with posterior rotation showing skeletal class II malocclusion (44.4%). Differences in cleft types and surgeons were not associated with the distribution of patients in each cluster. Conclusions Patients with ICP exhibited characteristic morphological patterns, such as bimaxillary retrusion or severe mandibular retrusion, besides the anterior crossbite frequently found in patients with cleft lip and palate . Understanding the typical morphological characteristics could enable better diagnostic cat…
bibliographic citation: Tsuji et al. (2021) Characteristics of craniofacial morphology and factors affecting them in patients with isolated cleft palate. PeerJ 9:e11297 https://doi.org/10.7717/peerj.11297
date submitted: 2020-10-15
date accepted: 2021-03-28
issued: 2021-04-20
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Tsuji
  given name: Kyoko
author list: Agent
  family name: Haruyama
  given name: Naoto
author list: Agent
  family name: Nomura
  given name: Shunsuke
author list: Agent
  family name: Murata
  given name: Naohisa
author list: Agent
  family name: Yoshizaki
  given name: Keigo
author list: Agent
  family name: Mitsuyasu
  given name: Takeshi
author list: Agent
  family name: Nakano
  given name: Hiroyuki
author list: Agent
  family name: Nakamura
  given name: Seiji
author list: Agent
  family name: Mori
  given name: Yoshihide
author list: Agent
  family name: Takahashi
  given name: Ichiro
doi: 10.7717/peerj.11297
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-04-20
copyright: © 2021 Tsuji et al.
attribution name: Tsuji et al.

Identification and comparison of circular RNAs in preeclampsia
type: item
type: AcademicArticle
description: Background Preeclampsia (PE) is a pregnancy-specific syndrome, belongs to the gestational hypertension diseases category and is considered among the causes of maternal and perinatal mortality and morbidity. However, the pathogenesis of PE is still vague. Methods In the present study, the circular RNA (circRNA) expression patterns of normal pregnant women and PE patients were investigated using whole RNA sequencing. Results A total of 151 differential expressed circRNAs were identified including 121 upregulated and 30 downregulated ones. Functional and pathway enrichment analysis was conducted on the differentially expressed circRNAs using Gene Ontology and KEGG databases. The results of this analysis indicated that several crucial biological processes and pathways were enriched in PE patients. circRNA–microRNA (miRNA) interaction analysis indicated that the reported differentially expresse circRNAs may be associated with some regulatory functions through miRNAs in PE patients. Two ceRNAs networks were constructed according to the targeting relationship between circRNAs/miRNAs and miRNAs/mRNAs. One sub-network contained one upregulated circRNA, four downregulated miRNAs and five upregulated mRNAs, and another sub-network contained 10 downregulated circRNAs, 21 upregulated miRNAs and 15 downregulated mRNAs. Conclusion CircRNA expression patterns have been investigated and this analysis revealed their potential regulatory mechanisms in PE patients. We constructed the ceRNAs (competing endogenous RNA) to reveal the potential molecular roles of dysregulated circRNAs in the PE patients using RNA sequencing data. circRNA_13301 was the only one upregulated circRNA in ceRNA being targeted by four miRNAs.
format: application/pdf
format: text/html
creator: Zepeng Ping
creator: Ling Ai
creator: Huaxiang Shen
creator: Xing Zhang
creator: Huling Jiang
creator: Ye Song
subject: Bioinformatics
subject: Molecular Biology
subject: Gynecology and Obstetrics
subject: Women’s Health
subject: Medical Genetics
description: doi:10.7717/peerj.11299
publisher: PeerJ Inc.
rights: © 2021 Ping et al.
abstract: Background Preeclampsia (PE) is a pregnancy-specific syndrome, belongs to the gestational hypertension diseases category and is considered among the causes of maternal and perinatal mortality and morbidity. However, the pathogenesis of PE is still vague. Methods In the present study, the circular RNA (circRNA) expression patterns of normal pregnant women and PE patients were investigated using whole RNA sequencing. Results A total of 151 differential expressed circRNAs were identified including 121 upregulated and 30 downregulated ones. Functional and pathway enrichment analysis was conducted on the differentially expressed circRNAs using Gene Ontology and KEGG databases. The results of this analysis indicated that several crucial biological processes and pathways were enriched in PE patients. circRNA–microRNA (miRNA) interaction analysis indicated that the reported differentially expresse circRNAs may be associated with some regulatory functions through miRNAs in PE patients. Two ceRNAs networks were constructed according to the targeting relationship between circRNAs/miRNAs and miRNAs/mRNAs. One sub-network contained one upregulated circRNA, four downregulated miRNAs and five upregulated mRNAs, and another sub-network contained 10 downregulated circRNAs, 21 upregulated miRNAs and 15 downregulated mRNAs. Conclusion CircRNA expression patterns have been investigated and this analysis revealed their potential regulatory mechanisms in PE patients. We constructed the ceRNAs (competing endogenous RNA) to reveal the potential molecular roles of dysregulated circRNAs in the PE patients using RNA sequencing data. circRNA_13301 was the only one upregulated circRNA in ceRNA being targeted by four miRNAs.
bibliographic citation: Ping et al. (2021) Identification and comparison of circular RNAs in preeclampsia. PeerJ 9:e11299 https://doi.org/10.7717/peerj.11299
date submitted: 2020-10-01
date accepted: 2021-03-29
issued: 2021-04-20
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Ping
  given name: Zepeng
author list: Agent
  family name: Ai
  given name: Ling
author list: Agent
  family name: Shen
  given name: Huaxiang
author list: Agent
  family name: Zhang
  given name: Xing
author list: Agent
  family name: Jiang
  given name: Huling
author list: Agent
  family name: Song
  given name: Ye
doi: 10.7717/peerj.11299
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-04-20
copyright: ©2021 Ping et al.
attribution name: Ping et al.

Sexual dimorphism and skull size and shape in the highly specialized snake species, Aipysurus eydouxii (Elapidae: Hydrophiinae)
type: item
type: AcademicArticle
description: Background Snakes exhibit sexual dimorphism in both head size and shape. Such differences are often attributed to different reproductive roles and feeding habits. We aim to investigate how sexual dimorphism is displayed in the highly specialised fish-egg-eating snake, Aipysurus eydouxii, by analysing two complementary features: body size and skull morphology. Methods We used data on body length, weight, and skull shape from 27 measurements of 116 males and females of A. eydouxii. We investigated both sexual dimorphism and allometric (multivariate and bi-variate) properties of skull growth in the analysed data set. Results We found that although there was female-biased sexual size dimorphism in body length, females were not heavier than males, contrary to what is commonly observed pattern among snakes. Moreover, females tend to possess relatively smaller heads than males. However, we only found very subtle differences in skull shape reflected in nasal width, mandibular fossa, quadrate crest and quadrate length. Discussion We suggest that the feeding specialisation in A. eydouxii does not allow for an increase in body thickness and the size of the head above a certain threshold. Our results may be interpreted as support for prey-size divergence as a factor driving skull dimorphism since such species in which the sexes do not differ in prey size also shows very subtle or no differences in skull morphology.
format: application/pdf
format: text/html
creator: Bartosz Borczyk
creator: Łukasz Paśko
creator: Jan Kusznierz
creator: Stanisław Bury
subject: Evolutionary Studies
subject: Zoology
description: doi:10.7717/peerj.11311
publisher: PeerJ Inc.
rights: © 2021 Borczyk et al.
abstract: Background Snakes exhibit sexual dimorphism in both head size and shape. Such differences are often attributed to different reproductive roles and feeding habits. We aim to investigate how sexual dimorphism is displayed in the highly specialised fish-egg-eating snake, Aipysurus eydouxii, by analysing two complementary features: body size and skull morphology. Methods We used data on body length, weight, and skull shape from 27 measurements of 116 males and females of A. eydouxii. We investigated both sexual dimorphism and allometric (multivariate and bi-variate) properties of skull growth in the analysed data set. Results We found that although there was female-biased sexual size dimorphism in body length, females were not heavier than males, contrary to what is commonly observed pattern among snakes. Moreover, females tend to possess relatively smaller heads than males. However, we only found very subtle differences in skull shape reflected in nasal width, mandibular fossa, quadrate crest and quadrate length. Discussion We suggest that the feeding specialisation in A. eydouxii does not allow for an increase in body thickness and the size of the head above a certain threshold. Our results may be interpreted as support for prey-size divergence as a factor driving skull dimorphism since such species in which the sexes do not differ in prey size also shows very subtle or no differences in skull morphology.
bibliographic citation: Borczyk et al. (2021) Sexual dimorphism and skull size and shape in the highly specialized snake species, Aipysurus eydouxii (Elapidae: Hydrophiinae). PeerJ 9:e11311 https://doi.org/10.7717/peerj.11311
date submitted: 2018-07-18
date accepted: 2021-03-29
issued: 2021-04-20
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Borczyk
  given name: Bartosz
author list: Agent
  family name: Paśko
  given name: Łukasz
author list: Agent
  family name: Kusznierz
  given name: Jan
author list: Agent
  family name: Bury
  given name: Stanisław
doi: 10.7717/peerj.11311
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-04-20
copyright: © 2021 Borczyk et al.
attribution name: Borczyk et al.

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