PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
items: Correlations between muscle strength and psychological health in Chinese adolescents: a cross-sectional analysis
items: Time-dependent effect of intense capsule-coffee and bleaching on the color of resin-infiltrated enamel white spot lesions: an in vitro study
items: Genomic differences between sequence types 1 and 104 of Streptococcus suis Serotype 2
items: Shallow epifaunal sea cucumber densities and their relationship with the benthic community in the Okinawa Islands
items: Histone H3K9 demethylase JMJD2B/KDM4B promotes osteogenic differentiation of bone marrow-derived mesenchymal stem cells by regulating H3K9me2 on RUNX2
items: Maximum aerobic speed, maximum oxygen consumption, and running spatiotemporal parameters during an incremental test among middle- and long-distance runners and endurance non-running athletes
items: Host generalists dominate fungal communities associated with alpine knotweed roots: a study of Sebacinales
items: The soccer season: performance variations and evolutionary trends
items: MicroRNA let-7f-5p regulates PI3K/AKT/COX2 signaling pathway in bacteria-induced pulmonary fibrosis via targeting of PIK3CA in forest musk deer
items: miR2Trait: an integrated resource for investigating miRNA-disease associations

Correlations between muscle strength and psychological health in Chinese adolescents: a cross-sectional analysis
type: item
type: AcademicArticle
description: Background Studies indicate that muscle strength is associated with good mental health. However, it remains unclear whether muscle strength is directly correlated with psychological symptoms in Chinese adolescents. Given the declining muscle strength and worrying mental health status of Chinese adolescents, the present study aimed to estimate the correlation between muscle strength and psychological symptoms as well as explore the gender differences in those correlations in Chinese adolescents. Method From April to July 2018, a total of 14,344 Chinese adolescents from eight provinces were selected using a stratified clustered sampling method. Psychological symptoms were evaluated using the Multidimensional Sub-health Questionnaire of Adolescents (MSQA), a verified and validated questionnaire that assesses three psychological areas: emotional symptoms, behavioral symptoms, and social adaptation difficulties. Muscle strength was assessed using grip strength, sit-ups, and standing long jump. The Chi-square test was used to compare the detection rates of the different categories of psychological symptoms. A logistic regression analysis was used to analyze the correlations between muscle strength and psychological symptoms and explore the gender differences in those correlations in Chinese adolescents. Results In general, the detection rate of psychological symptoms for Chinese adolescents was 21.39%. Males had a higher detection rate of psychological symptoms (22.12%) than females (20.66%, p < 0.05). Psychological symptoms were present in significantly fewer Chinese adolescents with a muscle strength index >P75 (19.26%) than among Chinese adolescents with a muscle strength index ≤P25 (23.00%) (χ2 = 23.417, p < 0.01). Compared with females, the OR values for males in most groups were over one (OR = 1.04–1.43), indicating that males have a higher risk of psychological symptoms than females. Conclusions The psychological symptom detection rate of Chinese adolescents is cor…
format: application/pdf
format: text/html
creator: Jinkui Lu
creator: Hao Sun
creator: Ningling Liu
creator: Jianhua Qiu
creator: Xiaofei Xia
subject: Kinesiology
subject: Pediatrics
subject: Public Health
subject: Mental Health
description: doi:10.7717/peerj.14133
publisher: PeerJ Inc.
rights: © 2022 Lu et al.
abstract: Background Studies indicate that muscle strength is associated with good mental health. However, it remains unclear whether muscle strength is directly correlated with psychological symptoms in Chinese adolescents. Given the declining muscle strength and worrying mental health status of Chinese adolescents, the present study aimed to estimate the correlation between muscle strength and psychological symptoms as well as explore the gender differences in those correlations in Chinese adolescents. Method From April to July 2018, a total of 14,344 Chinese adolescents from eight provinces were selected using a stratified clustered sampling method. Psychological symptoms were evaluated using the Multidimensional Sub-health Questionnaire of Adolescents (MSQA), a verified and validated questionnaire that assesses three psychological areas: emotional symptoms, behavioral symptoms, and social adaptation difficulties. Muscle strength was assessed using grip strength, sit-ups, and standing long jump. The Chi-square test was used to compare the detection rates of the different categories of psychological symptoms. A logistic regression analysis was used to analyze the correlations between muscle strength and psychological symptoms and explore the gender differences in those correlations in Chinese adolescents. Results In general, the detection rate of psychological symptoms for Chinese adolescents was 21.39%. Males had a higher detection rate of psychological symptoms (22.12%) than females (20.66%, p < 0.05). Psychological symptoms were present in significantly fewer Chinese adolescents with a muscle strength index >P75 (19.26%) than among Chinese adolescents with a muscle strength index ≤P25 (23.00%) (χ2 = 23.417, p < 0.01). Compared with females, the OR values for males in most groups were over one (OR = 1.04–1.43), indicating that males have a higher risk of psychological symptoms than females. Conclusions The psychological symptom detection rate of Chinese adolescents is cor…
bibliographic citation: Lu et al. (2022) Correlations between muscle strength and psychological health in Chinese adolescents: a cross-sectional analysis. PeerJ 10:e14133 https://doi.org/10.7717/peerj.14133
date submitted: 2022-03-10
date accepted: 2022-09-06
issued: 2022-10-06
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Lu
  given name: Jinkui
author list: Agent
  family name: Sun
  given name: Hao
author list: Agent
  family name: Liu
  given name: Ningling
author list: Agent
  family name: Qiu
  given name: Jianhua
author list: Agent
  family name: Xia
  given name: Xiaofei
doi: 10.7717/peerj.14133
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-10-06
copyright: © 2022 Lu et al.
attribution name: Lu et al.

Time-dependent effect of intense capsule-coffee and bleaching on the color of resin-infiltrated enamel white spot lesions: an in vitro study
type: item
type: AcademicArticle
description: Background and Objectives White spot lesions (WSLs) are a common problem that can be conservatively managed by resin infiltration. Consumption of dark beverages such as coffee causes staining of dental hard tissues, which can deteriorate the esthetic qualities of treated WSLs. The aims of this study were to investigate the effect of dark coffee heavy consumption on ICON® resin infiltrated WSLs and the influence of bleaching on them after staining. Methods Twenty surfaces from sound human extracted third molars were used in the study. Two square-shaped buccal and lingual window areas had artificially created WSLs (received buccal resin infiltration afterward). Using VITA Easyshade, the baseline ΔE was recorded. Espresso coffee was used to immerse all surfaces for 8 days. The color coordinates according to CIE LAB were recorded for all surfaces at 2, 4, 6, and 8 days of immersion, and ΔE was calculated at each timepoint. After 8 days, in-office bleaching was applied to all surfaces according to the manufacturer’s instructions and the color. Coordinates and ΔE were recorded. For statistical analysis, an independent sample t-test was used to compare each group. A general linear mixed model (GLMM) repeated measure ANOVA was applied for statistical analysis of L*and changes due to staining over time. Results Analysis of time as a main effect on the L values of surfaces was statistically highly significant (p < 0.01). The interaction of time with surfaces under investigation and type of surface (test vs. control) as a main effect were non-significant (p = 0.47 and p = 0.35, respectively). Bleaching showed a significant difference in color lightness in both test and control surfaces compared to the mean L value at 8 days of staining (p < 0.01). Conclusion Capsule-coffee consumption gradually influences the esthetic of resin infiltration on treated teeth. However, bleaching materials might restore an esthetic shade.
format: application/pdf
format: text/html
creator: Hanin E. Yeslam
creator: Saeed J. AlZahrani
subject: Biochemistry
subject: Food Science and Technology
subject: Dentistry
description: doi:10.7717/peerj.14135
publisher: PeerJ Inc.
rights: © 2022 Yeslam and AlZahrani
abstract: Background and Objectives White spot lesions (WSLs) are a common problem that can be conservatively managed by resin infiltration. Consumption of dark beverages such as coffee causes staining of dental hard tissues, which can deteriorate the esthetic qualities of treated WSLs. The aims of this study were to investigate the effect of dark coffee heavy consumption on ICON® resin infiltrated WSLs and the influence of bleaching on them after staining. Methods Twenty surfaces from sound human extracted third molars were used in the study. Two square-shaped buccal and lingual window areas had artificially created WSLs (received buccal resin infiltration afterward). Using VITA Easyshade, the baseline ΔE was recorded. Espresso coffee was used to immerse all surfaces for 8 days. The color coordinates according to CIE LAB were recorded for all surfaces at 2, 4, 6, and 8 days of immersion, and ΔE was calculated at each timepoint. After 8 days, in-office bleaching was applied to all surfaces according to the manufacturer’s instructions and the color. Coordinates and ΔE were recorded. For statistical analysis, an independent sample t-test was used to compare each group. A general linear mixed model (GLMM) repeated measure ANOVA was applied for statistical analysis of L*and changes due to staining over time. Results Analysis of time as a main effect on the L values of surfaces was statistically highly significant (p < 0.01). The interaction of time with surfaces under investigation and type of surface (test vs. control) as a main effect were non-significant (p = 0.47 and p = 0.35, respectively). Bleaching showed a significant difference in color lightness in both test and control surfaces compared to the mean L value at 8 days of staining (p < 0.01). Conclusion Capsule-coffee consumption gradually influences the esthetic of resin infiltration on treated teeth. However, bleaching materials might restore an esthetic shade.
bibliographic citation: Yeslam et al. (2022) Time-dependent effect of intense capsule-coffee and bleaching on the color of resin-infiltrated enamel white spot lesions: an in vitro study. PeerJ 10:e14135 https://doi.org/10.7717/peerj.14135
date submitted: 2022-05-05
date accepted: 2022-09-06
issued: 2022-10-06
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Yeslam
  given name: Hanin E.
author list: Agent
  family name: AlZahrani
  given name: Saeed J.
doi: 10.7717/peerj.14135
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-10-06
copyright: ©2022 Yeslam and AlZahrani
attribution name: Yeslam and AlZahrani

Genomic differences between sequence types 1 and 104 of Streptococcus suis Serotype 2
type: item
type: AcademicArticle
description: Background Streptococcus suis is a zoonotic pathogen that can cause invasive infections in humans who are in close contact with infected pigs or contaminated pork-derived products. S. suis serotype 2 sequence type (ST) 1 strains are mostly associated with meningitis, whereas ST104 strains are mostly recovered from sepsis cases in humans. No data are available for comparison of the ST1 and ST104 strains at the genomic level, particularly concerning virulence-associated genes. Thus, genomic comparison of both STs was performed in this study. Methods An ST1 isolate (ID26154) from the cerebrospinal fluid of a patient with meningitis and an ST104 isolate (ID24525) from the blood of a patient with sepsis were subjected to shotgun pyrosequencing using the 454 GS Junior System. Genomic comparison was conducted between the ST1 isolate and the ST104 isolate using the Artemis Comparison Tool (ACT) to identify the region of differences (RDs) between ST1 and ST104. Results Fifty-eight RDs were unique to the ST104 genome and were mainly involved in metabolism and cell functional activities, cell wall anchored proteins, bacteriophages and mobile genetic elements, ABC-type transporters, two-component signal transductions, and lantibiotic proteins. Some virulence genes mostly found in ST1 strains were also present in the ST104 genome. Whole-genome comparison is a powerful tool for identifying genomic region differences between different STs of S. suis serotype 2, leading to the identification of the molecular basis of virulence involved in the pathogenesis of the infection.
format: application/pdf
format: text/html
creator: Anusak Kerdsin
creator: Dan Takeuchi
creator: Yukihiro Akeda
creator: Shota Nakamura
creator: Marcelo Gottschalk
creator: Kazunori Oishi
subject: Genomics
subject: Microbiology
subject: Molecular Biology
subject: Infectious Diseases
description: doi:10.7717/peerj.14144
publisher: PeerJ Inc.
rights: © 2022 Kerdsin et al.
abstract: Background Streptococcus suis is a zoonotic pathogen that can cause invasive infections in humans who are in close contact with infected pigs or contaminated pork-derived products. S. suis serotype 2 sequence type (ST) 1 strains are mostly associated with meningitis, whereas ST104 strains are mostly recovered from sepsis cases in humans. No data are available for comparison of the ST1 and ST104 strains at the genomic level, particularly concerning virulence-associated genes. Thus, genomic comparison of both STs was performed in this study. Methods An ST1 isolate (ID26154) from the cerebrospinal fluid of a patient with meningitis and an ST104 isolate (ID24525) from the blood of a patient with sepsis were subjected to shotgun pyrosequencing using the 454 GS Junior System. Genomic comparison was conducted between the ST1 isolate and the ST104 isolate using the Artemis Comparison Tool (ACT) to identify the region of differences (RDs) between ST1 and ST104. Results Fifty-eight RDs were unique to the ST104 genome and were mainly involved in metabolism and cell functional activities, cell wall anchored proteins, bacteriophages and mobile genetic elements, ABC-type transporters, two-component signal transductions, and lantibiotic proteins. Some virulence genes mostly found in ST1 strains were also present in the ST104 genome. Whole-genome comparison is a powerful tool for identifying genomic region differences between different STs of S. suis serotype 2, leading to the identification of the molecular basis of virulence involved in the pathogenesis of the infection.
bibliographic citation: Kerdsin et al. (2022) Genomic differences between sequence types 1 and 104 of Streptococcus suis Serotype 2. PeerJ 10:e14144 https://doi.org/10.7717/peerj.14144
date submitted: 2022-01-17
date accepted: 2022-09-07
issued: 2022-10-06
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Kerdsin
  given name: Anusak
author list: Agent
  family name: Takeuchi
  given name: Dan
author list: Agent
  family name: Akeda
  given name: Yukihiro
author list: Agent
  family name: Nakamura
  given name: Shota
author list: Agent
  family name: Gottschalk
  given name: Marcelo
author list: Agent
  family name: Oishi
  given name: Kazunori
doi: 10.7717/peerj.14144
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-10-06
copyright: © 2022 Kerdsin et al.
attribution name: Kerdsin et al.

Shallow epifaunal sea cucumber densities and their relationship with the benthic community in the Okinawa Islands
type: item
type: AcademicArticle
description: Sea cucumbers are important ecological engineers in marine ecosystems. However, the fishery demand of some species, especially large-epifaunal and commercially used (LEC) sea cucumbers, has risen drastically, resulting in serious depletion of local populations for many species. Despite this problem, basic ecological data on sea cucumbers, such as population densities and preferred habitats, are often still insufficient. Here, we report on the population densities of multiple LEC sea cucumber species, and their ambient benthic communities at eight sites around Okinawa Islands. Further, we discuss the correspondence between sea cucumber densities and the surrounding coral communities. Our results show two sites within national or quasi-national parks, Aka and Manza, where stricter rules have been placed on fisheries and land reclamation compared to other areas, had the highest and third highest sea cucumber population densities among sites, respectively. Holothuria atra was observed at all survey sites and made up the majority of sea cucumber populations at all sites except for Chatan and Sesoko, where Holothuria leucospilota and Stichopus chloronotus were most abundant, respectively. Regarding the relationships between benthic composition and LEC sea cucumber species, S. chloronotus was significantly correlated with dead corals, scleractinian corals, and coralline algae. As well, H. leucospilota had significant correlations with rubble. Although there were no significant correlations between any specific scleractinian coral genus and sea cucumber densities, S. chloronotus was marginally insignificant with Platygyra and Psammocora. Notably, medium- to highly valued species were sparse in our surveys, and most of them appeared at only one site. Additionally, at one site (Odo), only three LEC sea cucumber individuals were observed. Combining these facts with relatively low population densities around the Okinawa Islands compared to densities reported in previous researc…
format: application/pdf
format: text/html
creator: Kohei Hamamoto
creator: Angelo Poliseno
creator: Taha Soliman
creator: James Davis Reimer
subject: Biodiversity
subject: Conservation Biology
subject: Ecology
subject: Marine Biology
subject: Natural Resource Management
description: doi:10.7717/peerj.14181
publisher: PeerJ Inc.
rights: © 2022 Hamamoto et al.
abstract: Sea cucumbers are important ecological engineers in marine ecosystems. However, the fishery demand of some species, especially large-epifaunal and commercially used (LEC) sea cucumbers, has risen drastically, resulting in serious depletion of local populations for many species. Despite this problem, basic ecological data on sea cucumbers, such as population densities and preferred habitats, are often still insufficient. Here, we report on the population densities of multiple LEC sea cucumber species, and their ambient benthic communities at eight sites around Okinawa Islands. Further, we discuss the correspondence between sea cucumber densities and the surrounding coral communities. Our results show two sites within national or quasi-national parks, Aka and Manza, where stricter rules have been placed on fisheries and land reclamation compared to other areas, had the highest and third highest sea cucumber population densities among sites, respectively. Holothuria atra was observed at all survey sites and made up the majority of sea cucumber populations at all sites except for Chatan and Sesoko, where Holothuria leucospilota and Stichopus chloronotus were most abundant, respectively. Regarding the relationships between benthic composition and LEC sea cucumber species, S. chloronotus was significantly correlated with dead corals, scleractinian corals, and coralline algae. As well, H. leucospilota had significant correlations with rubble. Although there were no significant correlations between any specific scleractinian coral genus and sea cucumber densities, S. chloronotus was marginally insignificant with Platygyra and Psammocora. Notably, medium- to highly valued species were sparse in our surveys, and most of them appeared at only one site. Additionally, at one site (Odo), only three LEC sea cucumber individuals were observed. Combining these facts with relatively low population densities around the Okinawa Islands compared to densities reported in previous researc…
bibliographic citation: Hamamoto et al. (2022) Shallow epifaunal sea cucumber densities and their relationship with the benthic community in the Okinawa Islands. PeerJ 10:e14181 https://doi.org/10.7717/peerj.14181
date submitted: 2022-07-08
date accepted: 2022-09-14
issued: 2022-10-06
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Hamamoto
  given name: Kohei
author list: Agent
  family name: Poliseno
  given name: Angelo
author list: Agent
  family name: Soliman
  given name: Taha
author list: Agent
  family name: Reimer
  given name: James Davis
doi: 10.7717/peerj.14181
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-10-06
copyright: © 2022 Hamamoto et al.
attribution name: Hamamoto et al.

Histone H3K9 demethylase JMJD2B/KDM4B promotes osteogenic differentiation of bone marrow-derived mesenchymal stem cells by regulating H3K9me2 on RUNX2
type: item
type: AcademicArticle
description: Background A variety of proteins including epigenetic factors are involved in the differentiation of human bone marrow mesenchymal stem cells. These cells also exhibited an epigenetic plasticity that enabled them to trans-differentiate from adipocytes to osteoblasts (and vice versa) after commitment. Further in-depth study of their epigenetic alterations may make sense. Methods Chromatin Immunoprecipitation-PCR (ChIP-PCR) was used to detect the methylation enrichment status of H3K9me2 in the Runx2 promoter, alizarin red and alkaline phosphatase (ALP) staining were used to detect osteogenic differentiation and mineralization ability, western blot and quantitative RT-PCR were used to measure the differential expression of osteogenesis-related proteins and genes. Recombinant Lentivirus mediated gain-of-function and loss-of-function study. The scale of epigenetic modification was detected by laser confocal. Results Our results showed that compared with human bone marrow mesenchymal stem cells (hBMSCs) without osteogenic differentiation treatment, hBMSCs after osteogenic differentiation significantly promoted osteogenic differentiation and mRNA expression such as JMJD2B/KDM4B, osteogenesis-related genes like Runx2 and FAM210A in hBMSCs cells, suggesting that upregulation of JMJD2B/KDM4B is involved in the promoting effect of osteogenesis. After overexpression and silencing expression of JMJD2B, we found a completely opposite and significant difference in mRNA expression of osteogenesis-related genes and staining in hBMSCs. Overexpression of JMJD2B/KDM4B significantly promoted osteogenic differentiation, suggesting that JMJD2B/KDM4B could promote osteogenesis. In addition, ChIP-PCR showed that overexpression of JMJD2B/KDM4B significantly reversed the methylation enrichment status of H3K9me2 in Runx2 promoter. Furthermore, overexpression of JMJD2B/KDM4B significantly reverses the inhibitory effect of BIX01294 on H3K9me2, suggesting that JMJD2B/KDM4B regulates the osteogeni…
format: application/pdf
format: text/html
creator: Pan Kang
creator: Zhiming Wu
creator: Yuxi Huang
creator: Zhen Luo
creator: Shaochuan Huo
creator: Qunqun Chen
subject: Biochemistry
subject: Cell Biology
subject: Molecular Biology
description: doi:10.7717/peerj.13862
publisher: PeerJ Inc.
rights: © 2022 Kang et al.
abstract: Background A variety of proteins including epigenetic factors are involved in the differentiation of human bone marrow mesenchymal stem cells. These cells also exhibited an epigenetic plasticity that enabled them to trans-differentiate from adipocytes to osteoblasts (and vice versa) after commitment. Further in-depth study of their epigenetic alterations may make sense. Methods Chromatin Immunoprecipitation-PCR (ChIP-PCR) was used to detect the methylation enrichment status of H3K9me2 in the Runx2 promoter, alizarin red and alkaline phosphatase (ALP) staining were used to detect osteogenic differentiation and mineralization ability, western blot and quantitative RT-PCR were used to measure the differential expression of osteogenesis-related proteins and genes. Recombinant Lentivirus mediated gain-of-function and loss-of-function study. The scale of epigenetic modification was detected by laser confocal. Results Our results showed that compared with human bone marrow mesenchymal stem cells (hBMSCs) without osteogenic differentiation treatment, hBMSCs after osteogenic differentiation significantly promoted osteogenic differentiation and mRNA expression such as JMJD2B/KDM4B, osteogenesis-related genes like Runx2 and FAM210A in hBMSCs cells, suggesting that upregulation of JMJD2B/KDM4B is involved in the promoting effect of osteogenesis. After overexpression and silencing expression of JMJD2B, we found a completely opposite and significant difference in mRNA expression of osteogenesis-related genes and staining in hBMSCs. Overexpression of JMJD2B/KDM4B significantly promoted osteogenic differentiation, suggesting that JMJD2B/KDM4B could promote osteogenesis. In addition, ChIP-PCR showed that overexpression of JMJD2B/KDM4B significantly reversed the methylation enrichment status of H3K9me2 in Runx2 promoter. Furthermore, overexpression of JMJD2B/KDM4B significantly reverses the inhibitory effect of BIX01294 on H3K9me2, suggesting that JMJD2B/KDM4B regulates the osteogeni…
bibliographic citation: Kang et al. (2022) Histone H3K9 demethylase JMJD2B/KDM4B promotes osteogenic differentiation of bone marrow-derived mesenchymal stem cells by regulating H3K9me2 on RUNX2. PeerJ 10:e13862 https://doi.org/10.7717/peerj.13862
date submitted: 2021-11-29
date accepted: 2022-07-18
issued: 2022-10-05
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Kang
  given name: Pan
author list: Agent
  family name: Wu
  given name: Zhiming
author list: Agent
  family name: Huang
  given name: Yuxi
author list: Agent
  family name: Luo
  given name: Zhen
author list: Agent
  family name: Huo
  given name: Shaochuan
author list: Agent
  family name: Chen
  given name: Qunqun
doi: 10.7717/peerj.13862
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-10-05
copyright: ©2022 Kang et al.
attribution name: Kang et al.

Maximum aerobic speed, maximum oxygen consumption, and running spatiotemporal parameters during an incremental test among middle- and long-distance runners and endurance non-running athletes
type: item
type: AcademicArticle
description: Background Maximal aerobic speed (MAS) is a useful parameter to assess aerobic capacity and estimate training intensity in middle- and long-distance runners. However, whether middle- and long-distance runners reach different levels of MAS compared to other endurance athletes with similar V̇O2max has not been previously studied. Therefore, we aimed to compare V̇O2max, MAS and spatiotemporal parameters between sub-elite middle- and long-distance runners (n = 6) and endurance non-runners (n = 6). In addition, we aimed to compare the maximal blood lactate concentration [BLa] experienced by participants after conducting these tests. Methods Telemetric portable respiratory gas analysis, contact and flight time, and stride length and rate were measured using a 5-m contact platform during an incremental test at a synthetic athletics track. V̇O2, heart rate, respiratory quotient values in any 15 s average period during the test were measured. [BLa] was analyzed after the test . Running spatiotemporal parameters were recorded at the last two steps of each 400 m lap. A coefficient of variation (%CV) was calculated for each spatiotemporal variable in each participant from 8 km h−1 onwards. Results Whereas runners reported faster MAS (21.0 vs. 18.2 km h−1) than non-runners (p = 0.0001, ES = 3.0), no differences were found for V̇O2max and maximum blood lactate concentration during the running tests (p > 0.05). While significant increases in flight time and stride length and frequency (p < 0.001, 0.52 ≤ ${\eta }_{p}^{2}$ η p 2 ≤ 0.8) were observed throughout the tests, decreases in contact time (p < 0.001, ${\eta }_{p}^{2}=0.9$ η p 2 = 0 . 9 ) were reported. Runners displayed a greater %CV (p = 0.015) in stride length than non-runners. We conclude that middle- and long-distance runners can achieve a faster MAS compared to non-running endurance athletes despite exhibiting a similar V̇O2max. This superior performance may be associated to a greater mechanical efficiency. Overall, run…
format: application/pdf
format: text/html
creator: Arturo Casado
creator: José Luis Tuimil
creator: Xavier Iglesias
creator: Miguel Fernández-del-Olmo
creator: Pedro Jiménez-Reyes
creator: Rafael Martín-Acero
creator: Ferran A. Rodríguez
subject: Kinesiology
subject: Respiratory Medicine
subject: Biomechanics
subject: Sports Medicine
description: doi:10.7717/peerj.14035
publisher: PeerJ Inc.
rights: © 2022 Casado et al.
abstract: Background Maximal aerobic speed (MAS) is a useful parameter to assess aerobic capacity and estimate training intensity in middle- and long-distance runners. However, whether middle- and long-distance runners reach different levels of MAS compared to other endurance athletes with similar V̇O2max has not been previously studied. Therefore, we aimed to compare V̇O2max, MAS and spatiotemporal parameters between sub-elite middle- and long-distance runners (n = 6) and endurance non-runners (n = 6). In addition, we aimed to compare the maximal blood lactate concentration [BLa] experienced by participants after conducting these tests. Methods Telemetric portable respiratory gas analysis, contact and flight time, and stride length and rate were measured using a 5-m contact platform during an incremental test at a synthetic athletics track. V̇O2, heart rate, respiratory quotient values in any 15 s average period during the test were measured. [BLa] was analyzed after the test . Running spatiotemporal parameters were recorded at the last two steps of each 400 m lap. A coefficient of variation (%CV) was calculated for each spatiotemporal variable in each participant from 8 km h−1 onwards. Results Whereas runners reported faster MAS (21.0 vs. 18.2 km h−1) than non-runners (p = 0.0001, ES = 3.0), no differences were found for V̇O2max and maximum blood lactate concentration during the running tests (p > 0.05). While significant increases in flight time and stride length and frequency (p < 0.001, 0.52 ≤ ${\eta }_{p}^{2}$ η p 2 ≤ 0.8) were observed throughout the tests, decreases in contact time (p < 0.001, ${\eta }_{p}^{2}=0.9$ η p 2 = 0 . 9 ) were reported. Runners displayed a greater %CV (p = 0.015) in stride length than non-runners. We conclude that middle- and long-distance runners can achieve a faster MAS compared to non-running endurance athletes despite exhibiting a similar V̇O2max. This superior performance may be associated to a greater mechanical efficiency. Overall, run…
bibliographic citation: Casado et al. (2022) Maximum aerobic speed, maximum oxygen consumption, and running spatiotemporal parameters during an incremental test among middle- and long-distance runners and endurance non-running athletes. PeerJ 10:e14035 https://doi.org/10.7717/peerj.14035
date submitted: 2022-06-09
date accepted: 2022-08-18
issued: 2022-10-05
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Casado
  given name: Arturo
author list: Agent
  family name: Tuimil
  given name: José Luis
author list: Agent
  family name: Iglesias
  given name: Xavier
author list: Agent
  family name: Fernández-del-Olmo
  given name: Miguel
author list: Agent
  family name: Jiménez-Reyes
  given name: Pedro
author list: Agent
  family name: Martín-Acero
  given name: Rafael
author list: Agent
  family name: Rodríguez
  given name: Ferran A.
doi: 10.7717/peerj.14035
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-10-05
copyright: ©2022 Casado et al.
attribution name: Casado et al.

Host generalists dominate fungal communities associated with alpine knotweed roots: a study of Sebacinales
type: item
type: AcademicArticle
description: Bistorta vivipara is a widespread herbaceous perennial plant with a discontinuous pattern of distribution in arctic, alpine, subalpine and boreal habitats across the northern Hemisphere. Studies of the fungi associated with the roots of B. vivipara have mainly been conducted in arctic and alpine ecosystems. This study examined the fungal diversity and specificity from root tips of B. vivipara in two local mountain ecosystems as well as on a global scale. Sequences were generated by Sanger sequencing of the internal transcribed spacer (ITS) region followed by an analysis of accurately annotated nuclear segments including ITS1-5.8S-ITS2 sequences available from public databases. In total, 181 different UNITE species hypotheses (SHs) were detected to be fungi associated with B. vivipara, 73 of which occurred in the Bavarian Alps and nine in the Swabian Alps–with one SH shared among both mountains. In both sites as well as in additional public data, individuals of B. vivipara were found to contain phylogenetically diverse fungi, with the Basidiomycota, represented by the Thelephorales and Sebacinales, being the most dominant. A comparative analysis of the diversity of the Sebacinales associated with B. vivipara and other co-occurring plant genera showed that the highest number of sebacinoid SHs were associated with Quercus and Pinus, followed by Bistorta. A comparison of B. vivipara with plant families such as Ericaceae, Fagaceae, Orchidaceae, and Pinaceae showed a clear trend: Only a few species were specific to B. vivipara and a large number of SHs were shared with other co-occurring non-B. vivipara plant species. In Sebacinales, the majority of SHs associated with B. vivipara belonged to the ectomycorrhiza (ECM)-forming Sebacinaceae, with fewer SHs belonging to the Serendipitaceae encompassing diverse ericoid–orchid–ECM–endophytic associations. The large proportion of non-host-specific fungi able to form a symbiosis with other non-B. vivipara plants could suggest tha…
format: application/pdf
format: text/html
creator: Max Emil Schön
creator: Kessy Abarenkov
creator: Sigisfredo Garnica
subject: Biodiversity
subject: Ecology
subject: Mycology
description: doi:10.7717/peerj.14047
publisher: PeerJ Inc.
rights: © 2022 Schön et al.
abstract: Bistorta vivipara is a widespread herbaceous perennial plant with a discontinuous pattern of distribution in arctic, alpine, subalpine and boreal habitats across the northern Hemisphere. Studies of the fungi associated with the roots of B. vivipara have mainly been conducted in arctic and alpine ecosystems. This study examined the fungal diversity and specificity from root tips of B. vivipara in two local mountain ecosystems as well as on a global scale. Sequences were generated by Sanger sequencing of the internal transcribed spacer (ITS) region followed by an analysis of accurately annotated nuclear segments including ITS1-5.8S-ITS2 sequences available from public databases. In total, 181 different UNITE species hypotheses (SHs) were detected to be fungi associated with B. vivipara, 73 of which occurred in the Bavarian Alps and nine in the Swabian Alps–with one SH shared among both mountains. In both sites as well as in additional public data, individuals of B. vivipara were found to contain phylogenetically diverse fungi, with the Basidiomycota, represented by the Thelephorales and Sebacinales, being the most dominant. A comparative analysis of the diversity of the Sebacinales associated with B. vivipara and other co-occurring plant genera showed that the highest number of sebacinoid SHs were associated with Quercus and Pinus, followed by Bistorta. A comparison of B. vivipara with plant families such as Ericaceae, Fagaceae, Orchidaceae, and Pinaceae showed a clear trend: Only a few species were specific to B. vivipara and a large number of SHs were shared with other co-occurring non-B. vivipara plant species. In Sebacinales, the majority of SHs associated with B. vivipara belonged to the ectomycorrhiza (ECM)-forming Sebacinaceae, with fewer SHs belonging to the Serendipitaceae encompassing diverse ericoid–orchid–ECM–endophytic associations. The large proportion of non-host-specific fungi able to form a symbiosis with other non-B. vivipara plants could suggest tha…
bibliographic citation: Schön et al. (2022) Host generalists dominate fungal communities associated with alpine knotweed roots: a study of Sebacinales. PeerJ 10:e14047 https://doi.org/10.7717/peerj.14047
date submitted: 2021-09-02
date accepted: 2022-08-22
issued: 2022-10-05
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Schön
  given name: Max Emil
author list: Agent
  family name: Abarenkov
  given name: Kessy
author list: Agent
  family name: Garnica
  given name: Sigisfredo
doi: 10.7717/peerj.14047
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-10-05
copyright: © 2022 Schön et al.
attribution name: Schön et al.

The soccer season: performance variations and evolutionary trends
type: item
type: AcademicArticle
description: The physiological demands of soccer challenge the entire spectrum of the response capacity of the biological systems and fitness requirements of the players. In this review we examined variations and evolutionary trends in body composition, neuromuscular and endurance-related parameters, as well as in game-related physical parameters of professional players. Further, we explore aspects relevant for training monitoring and we reference how different training stimulus and situational variables (e.g., competition exposure) affect the physiological and performance parameters of players. Generally, improvements of small magnitude in non- (non-CMJ) and countermovement-based jumps (CMJBased) and in the sprint acceleration (ACCPhase) and maximal velocity phase (MVPhase) are observed from start of preparation phase (PPS) to beginning of competition phase (BCP). A greater magnitude of increases is observed in physiological and endurance performance measures within this period; moderate magnitude in sub-maximal intensity exercise (velocity at fixed blood lactate concentrations; V2–4mmol/l) and large magnitude in VO2max, maximal aerobic speed (MAS) and intense intermittent exercise performance (IE). In the middle of competition phase (MCP), small (CMJBased and ACCPhase), moderate (non-CMJ; MVPhase; VO2max; sub-maximal exercise) and large (MAS and IE) improvements were observed compared to PPS. In the end of competition period (ECP), CMJBased and MVPhase improve to a small extent with non-CMJ, and ACCPhase, VO2max, MAS, sub-maximal intensity exercise and IE revealing moderate increments compared to PPS. Although less investigated, there are generally observed alterations of trivial magnitude in neuromuscular and endurance-related parameters between in-season assessments; only substantial alterations are examined for IE and sub-maximal exercise performance (decrease and increase of small magnitude, respectively) from BCP to MCP and in VO2max and IE (decrements of small magnitude)…
format: application/pdf
format: text/html
creator: Joao Renato Silva
subject: Anatomy and Physiology
subject: Kinesiology
subject: Biomechanics
subject: Sports Medicine
description: doi:10.7717/peerj.14082
publisher: PeerJ Inc.
rights: © 2022 Silva
abstract: The physiological demands of soccer challenge the entire spectrum of the response capacity of the biological systems and fitness requirements of the players. In this review we examined variations and evolutionary trends in body composition, neuromuscular and endurance-related parameters, as well as in game-related physical parameters of professional players. Further, we explore aspects relevant for training monitoring and we reference how different training stimulus and situational variables (e.g., competition exposure) affect the physiological and performance parameters of players. Generally, improvements of small magnitude in non- (non-CMJ) and countermovement-based jumps (CMJBased) and in the sprint acceleration (ACCPhase) and maximal velocity phase (MVPhase) are observed from start of preparation phase (PPS) to beginning of competition phase (BCP). A greater magnitude of increases is observed in physiological and endurance performance measures within this period; moderate magnitude in sub-maximal intensity exercise (velocity at fixed blood lactate concentrations; V2–4mmol/l) and large magnitude in VO2max, maximal aerobic speed (MAS) and intense intermittent exercise performance (IE). In the middle of competition phase (MCP), small (CMJBased and ACCPhase), moderate (non-CMJ; MVPhase; VO2max; sub-maximal exercise) and large (MAS and IE) improvements were observed compared to PPS. In the end of competition period (ECP), CMJBased and MVPhase improve to a small extent with non-CMJ, and ACCPhase, VO2max, MAS, sub-maximal intensity exercise and IE revealing moderate increments compared to PPS. Although less investigated, there are generally observed alterations of trivial magnitude in neuromuscular and endurance-related parameters between in-season assessments; only substantial alterations are examined for IE and sub-maximal exercise performance (decrease and increase of small magnitude, respectively) from BCP to MCP and in VO2max and IE (decrements of small magnitude)…
bibliographic citation: Silva (2022) The soccer season: performance variations and evolutionary trends. PeerJ 10:e14082 https://doi.org/10.7717/peerj.14082
date submitted: 2022-07-01
date accepted: 2022-08-29
issued: 2022-10-05
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Silva
  given name: Joao Renato
doi: 10.7717/peerj.14082
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-10-05
copyright: © 2022 Silva
attribution name: Silva

MicroRNA let-7f-5p regulates PI3K/AKT/COX2 signaling pathway in bacteria-induced pulmonary fibrosis via targeting of PIK3CA in forest musk deer
type: item
type: AcademicArticle
description: Background Recent studies have characterized that microRNA (miRNA) is a suitable candidate for the study of bleomycin/LPS-induced pulmonary fibrosis, but the knowledge on miRNA in bacteria-induced pulmonary fibrosis (BIPF) is limited. Forest musk deer (Moschus berezovskii, FMD) is an important endangered species that has been seriously affected by BIPF. We sought to determine whether miRNA exist that modulates the pathogenesis of BIPF in FMD. Methods High-throughput sequencing and RT-qPCR were used to determine the differentially expressed miRNAs (DEmiRNAs) in the blood of BIPF FMD. The DEmiRNAs were further detected in the blood and lung of BIPF model rat by RT-qPCR, and the targeting relationship between candidate miRNA and its potential target gene was verified by dual-luciferase reporter activity assay. Furthermore, the function of the candidate miRNA was verified in the FMD lung fibroblast cells (FMD-C1). Results Here we found that five dead FMD were suffered from BIPF, and six circulating miRNAs (miR-30g, let-7f-5p, miR-27-3p, miR-25-3p, miR-9-5p and miR-652) were differentially expressed in the blood of the BIPF FMD. Of these, let-7f-5p showed reproducibly lower level in the blood and lung of the BIPF model rat, and the expression levels of PI3K/AKT/COX2 signaling pathway genes (PIK3CA, PDK1, Akt1, IKBKA, NF-κB1 and COX2) were increased in the lung of BIPF model rats, suggesting that there is a potential correlation between BIPF and the PI3K/AKT/COX2 signaling pathway. Notably, using bioinformatic prediction and experimental verification, we demonstrated that let-7f-5p is conserved across mammals, and the seed sequence of let-7f-5p displays perfect complementarity with the 3’ UTR of PIK3CA gene and the expression of the PIK3CA gene was regulated by let-7f-5p. In order to determine the regulatory relationship between let-7f-5p and the PI3K/AKT/COX2 signaling pathway in FMD, we successfully cultured FMD-C1, and found that let-7f-5p could act as a negative regul…
format: application/pdf
format: text/html
creator: Wei Zhao
creator: Jianguo Cheng
creator: Yan Luo
creator: Wenlong Fu
creator: Lei Zhou
creator: Xiang Wang
creator: Yin Wang
creator: Zexiao Yang
creator: Xueping Yao
creator: Meishen Ren
creator: Zhijun Zhong
creator: Xi Wu
creator: Ziwei Ren
creator: Yimeng Li
subject: Biochemistry
subject: Cell Biology
subject: Microbiology
subject: Molecular Biology
subject: Veterinary Medicine
description: doi:10.7717/peerj.14097
publisher: PeerJ Inc.
rights: © 2022 Zhao et al.
abstract: Background Recent studies have characterized that microRNA (miRNA) is a suitable candidate for the study of bleomycin/LPS-induced pulmonary fibrosis, but the knowledge on miRNA in bacteria-induced pulmonary fibrosis (BIPF) is limited. Forest musk deer (Moschus berezovskii, FMD) is an important endangered species that has been seriously affected by BIPF. We sought to determine whether miRNA exist that modulates the pathogenesis of BIPF in FMD. Methods High-throughput sequencing and RT-qPCR were used to determine the differentially expressed miRNAs (DEmiRNAs) in the blood of BIPF FMD. The DEmiRNAs were further detected in the blood and lung of BIPF model rat by RT-qPCR, and the targeting relationship between candidate miRNA and its potential target gene was verified by dual-luciferase reporter activity assay. Furthermore, the function of the candidate miRNA was verified in the FMD lung fibroblast cells (FMD-C1). Results Here we found that five dead FMD were suffered from BIPF, and six circulating miRNAs (miR-30g, let-7f-5p, miR-27-3p, miR-25-3p, miR-9-5p and miR-652) were differentially expressed in the blood of the BIPF FMD. Of these, let-7f-5p showed reproducibly lower level in the blood and lung of the BIPF model rat, and the expression levels of PI3K/AKT/COX2 signaling pathway genes (PIK3CA, PDK1, Akt1, IKBKA, NF-κB1 and COX2) were increased in the lung of BIPF model rats, suggesting that there is a potential correlation between BIPF and the PI3K/AKT/COX2 signaling pathway. Notably, using bioinformatic prediction and experimental verification, we demonstrated that let-7f-5p is conserved across mammals, and the seed sequence of let-7f-5p displays perfect complementarity with the 3’ UTR of PIK3CA gene and the expression of the PIK3CA gene was regulated by let-7f-5p. In order to determine the regulatory relationship between let-7f-5p and the PI3K/AKT/COX2 signaling pathway in FMD, we successfully cultured FMD-C1, and found that let-7f-5p could act as a negative regul…
bibliographic citation: Zhao et al. (2022) MicroRNA let-7f-5p regulates PI3K/AKT/COX2 signaling pathway in bacteria-induced pulmonary fibrosis via targeting of PIK3CA in forest musk deer. PeerJ 10:e14097 https://doi.org/10.7717/peerj.14097
date submitted: 2022-06-07
date accepted: 2022-08-31
issued: 2022-10-05
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Zhao
  given name: Wei
author list: Agent
  family name: Cheng
  given name: Jianguo
author list: Agent
  family name: Luo
  given name: Yan
author list: Agent
  family name: Fu
  given name: Wenlong
author list: Agent
  family name: Zhou
  given name: Lei
author list: Agent
  family name: Wang
  given name: Xiang
author list: Agent
  family name: Wang
  given name: Yin
author list: Agent
  family name: Yang
  given name: Zexiao
author list: Agent
  family name: Yao
  given name: Xueping
author list: Agent
  family name: Ren
  given name: Meishen
author list: Agent
  family name: Zhong
  given name: Zhijun
author list: Agent
  family name: Wu
  given name: Xi
author list: Agent
  family name: Ren
  given name: Ziwei
author list: Agent
  family name: Li
  given name: Yimeng
doi: 10.7717/peerj.14097
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-10-05
copyright: ©2022 Zhao et al.
attribution name: Zhao et al.

miR2Trait: an integrated resource for investigating miRNA-disease associations
type: item
type: AcademicArticle
description: MicroRNAs are key components of cellular regulatory networks, and breakdown in miRNA function causes cascading effects leading to pathophenotypes. A better understanding of the role of miRNAs in diseases is essential for human health. Here, we have devised a method for comprehensively mapping the associations between miRNAs and diseases by merging on a common key between two curated omics databases. The resulting bidirectional resource, miR2Trait, is more detailed than earlier catalogs, uncovers new relationships, and includes analytical utilities to interrogate and extract knowledge from these datasets. miR2Trait provides resources to compute the disease enrichment of a user-given set of miRNAs and analyze the miRNA profile of a specified diseasome. Reproducible examples demonstrating use-cases for each of these resource components are illustrated. Furthermore we used these tools to construct pairwise miRNA-miRNA and disease-disease enrichment networks, and identified 23 central miRNAs that could underlie major regulatory functions in the human genome. miR2Trait is available as an open-source command-line interface in Python3 (URL: https://github.com/miR2Trait) with a companion wiki documenting the scripts and data resources developed, under MIT license for commercial and non-commercial use. A minimal web-based implementation has been made available at https://sas.sastra.edu/pymir18. Supplementary information is available at: https://doi.org/10.6084/m9.figshare.8288825.v3.
format: application/pdf
format: text/html
creator: Poornima Babu
creator: Ashok Palaniappan
subject: Bioinformatics
subject: Biotechnology
subject: Computational Biology
subject: Genomics
subject: Molecular Biology
description: doi:10.7717/peerj.14146
publisher: PeerJ Inc.
rights: © 2022 Babu and Palaniappan
abstract: MicroRNAs are key components of cellular regulatory networks, and breakdown in miRNA function causes cascading effects leading to pathophenotypes. A better understanding of the role of miRNAs in diseases is essential for human health. Here, we have devised a method for comprehensively mapping the associations between miRNAs and diseases by merging on a common key between two curated omics databases. The resulting bidirectional resource, miR2Trait, is more detailed than earlier catalogs, uncovers new relationships, and includes analytical utilities to interrogate and extract knowledge from these datasets. miR2Trait provides resources to compute the disease enrichment of a user-given set of miRNAs and analyze the miRNA profile of a specified diseasome. Reproducible examples demonstrating use-cases for each of these resource components are illustrated. Furthermore we used these tools to construct pairwise miRNA-miRNA and disease-disease enrichment networks, and identified 23 central miRNAs that could underlie major regulatory functions in the human genome. miR2Trait is available as an open-source command-line interface in Python3 (URL: https://github.com/miR2Trait) with a companion wiki documenting the scripts and data resources developed, under MIT license for commercial and non-commercial use. A minimal web-based implementation has been made available at https://sas.sastra.edu/pymir18. Supplementary information is available at: https://doi.org/10.6084/m9.figshare.8288825.v3.
bibliographic citation: Babu et al. (2022) miR2Trait: an integrated resource for investigating miRNA-disease associations. PeerJ 10:e14146 https://doi.org/10.7717/peerj.14146
date submitted: 2022-06-07
date accepted: 2022-09-07
issued: 2022-10-05
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Babu
  given name: Poornima
author list: Agent
  family name: Palaniappan
  given name: Ashok
doi: 10.7717/peerj.14146
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-10-05
copyright: ©2022 Babu and Palaniappan
attribution name: Babu and Palaniappan

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