PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
items: Association of military-specific reaction time performance with physical fitness and visual skills
items: Non-synonymous to synonymous substitutions suggest that orthologs tend to keep their functions, while paralogs are a source of functional novelty
items: An insight into the invasion of breast ductal carcinoma in situ based on clinical, pathological and hematological data
items: Fine scale population structure of Acropora palmata and Acropora cervicornis in the Colombian Caribbean
items: Be aware of the allele-specific bias and compositional effects in multi-template PCR
items: Cardiorespiratory function, resting metabolic rate and heart rate variability in coal miners exposed to hypobaric hypoxia in highland workplace
items: Prior experience of captivity affects behavioural responses to ‘novel’ environments
items: The relationship between the Functional Movement Screen and the Y Balance Test in youth footballers
items: Proteomic profile of serum from patients with schizophrenia spectrum disorders
items: Analysis of endophyte diversity of Gentiana officinalis among different tissue types and ages and their association with four medicinal secondary metabolites

Association of military-specific reaction time performance with physical fitness and visual skills
type: item
type: AcademicArticle
description: Background The aim of the present study was to explore whether military-specific reaction time (RT) test performance is affected by individuals’ physical and visual skills. Method In a single testing session, the military-specific Simple and Go, No-Go RT, aerobic power (20-m Multistage Shuttle Run test), maximal upper- and lower-body mechanical capacities (bench press and squat against different loads), and visual skills (multiple object tracking and dynamic visual acuity) of 30 young men (15 active-duty military personnel and 15 sport science students) were evaluated. Results The main findings revealed that the Simple RT and Go, No-Go RT presented (1) with aerobic power non-significant small correlations in military personnel (r = −0.39 and −0.35, respectively) and non-significant negligible correlations in sport science students (r = −0.10 and 0.06, respectively), (2) inconsistent and generally non-significant correlations with the maximal mechanical capacities of the upper- and lower-body muscles (r range = −0.10, 0.67 and −0.27, 0.48, respectively), (3) non-significant correlations with visual skills (r magnitude ≥ 0.58) with the only exception of the Go, No-Go RT that was significantly correlated to all visual variables in the group of students (i.e., students who achieved better results during visual tests had shorter RT; r magnitude ≥ 0.58), and (4) none of the physical and visual variables significantly predicted the Simple RT or Go, No-Go RT. Conclusion Altogether, these results indicate that military-specific RT performance is generally independent of physical and visual skills in both military personnel and active university students.
format: application/pdf
format: text/html
creator: Danica Janicijevic
creator: Sergio Miras-Moreno
creator: Alejandro Pérez Castilla
creator: Jesus Vera
creator: Beatriz Redondo
creator: Raimundo Jiménez
creator: Amador García-Ramos
subject: Neuroscience
subject: Ophthalmology
subject: Public Health
subject: Sports Medicine
description: doi:10.7717/peerj.14007
publisher: PeerJ Inc.
rights: © 2022 Janicijevic et al.
abstract: Background The aim of the present study was to explore whether military-specific reaction time (RT) test performance is affected by individuals’ physical and visual skills. Method In a single testing session, the military-specific Simple and Go, No-Go RT, aerobic power (20-m Multistage Shuttle Run test), maximal upper- and lower-body mechanical capacities (bench press and squat against different loads), and visual skills (multiple object tracking and dynamic visual acuity) of 30 young men (15 active-duty military personnel and 15 sport science students) were evaluated. Results The main findings revealed that the Simple RT and Go, No-Go RT presented (1) with aerobic power non-significant small correlations in military personnel (r = −0.39 and −0.35, respectively) and non-significant negligible correlations in sport science students (r = −0.10 and 0.06, respectively), (2) inconsistent and generally non-significant correlations with the maximal mechanical capacities of the upper- and lower-body muscles (r range = −0.10, 0.67 and −0.27, 0.48, respectively), (3) non-significant correlations with visual skills (r magnitude ≥ 0.58) with the only exception of the Go, No-Go RT that was significantly correlated to all visual variables in the group of students (i.e., students who achieved better results during visual tests had shorter RT; r magnitude ≥ 0.58), and (4) none of the physical and visual variables significantly predicted the Simple RT or Go, No-Go RT. Conclusion Altogether, these results indicate that military-specific RT performance is generally independent of physical and visual skills in both military personnel and active university students.
bibliographic citation: Janicijevic et al. (2022) Association of military-specific reaction time performance with physical fitness and visual skills. PeerJ 10:e14007 https://doi.org/10.7717/peerj.14007
date submitted: 2022-04-26
date accepted: 2022-08-14
issued: 2022-09-01
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Janicijevic
  given name: Danica
author list: Agent
  family name: Miras-Moreno
  given name: Sergio
author list: Agent
  family name: Pérez Castilla
  given name: Alejandro
author list: Agent
  family name: Vera
  given name: Jesus
author list: Agent
  family name: Redondo
  given name: Beatriz
author list: Agent
  family name: Jiménez
  given name: Raimundo
author list: Agent
  family name: García-Ramos
  given name: Amador
doi: 10.7717/peerj.14007
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-09-01
copyright: © 2022 Janicijevic et al.
attribution name: Janicijevic et al.

Non-synonymous to synonymous substitutions suggest that orthologs tend to keep their functions, while paralogs are a source of functional novelty
type: item
type: AcademicArticle
description: Orthologs separate after lineages split from each other and paralogs after gene duplications. Thus, orthologs are expected to remain more functionally coherent across lineages, while paralogs have been proposed as a source of new functions. Because protein functional divergence follows from non-synonymous substitutions, we performed an analysis based on the ratio of non-synonymous to synonymous substitutions (dN/dS), as proxy for functional divergence. We used five working definitions of orthology, including reciprocal best hits (RBH), among other definitions based on network analyses and clustering. The results showed that orthologs, by all definitions tested, had values of dN/dS noticeably lower than those of paralogs, suggesting that orthologs generally tend to be more functionally stable than paralogs. The differences in dN/dS ratios remained suggesting the functional stability of orthologs after eliminating gene comparisons with potential problems, such as genes with high codon usage biases, low coverage of either of the aligned sequences, or sequences with very high similarities. Separation by percent identity of the encoded proteins showed that the differences between the dN/dS ratios of orthologs and paralogs were more evident at high sequence identity, less so as identity dropped. The last results suggest that the differences between dN/dS ratios were partially related to differences in protein identity. However, they also suggested that paralogs undergo functional divergence relatively early after duplication. Our analyses indicate that choosing orthologs as probably functionally coherent remains the right approach in comparative genomics.
format: application/pdf
format: text/html
creator: Juan M. Escorcia-Rodríguez
creator: Mario Esposito
creator: Julio A. Freyre-González
creator: Gabriel Moreno-Hagelsieb
subject: Bioinformatics
subject: Computational Biology
subject: Evolutionary Studies
subject: Genomics
subject: Microbiology
description: doi:10.7717/peerj.13843
publisher: PeerJ Inc.
rights: © 2022 Escorcia-Rodriguez et al.
abstract: Orthologs separate after lineages split from each other and paralogs after gene duplications. Thus, orthologs are expected to remain more functionally coherent across lineages, while paralogs have been proposed as a source of new functions. Because protein functional divergence follows from non-synonymous substitutions, we performed an analysis based on the ratio of non-synonymous to synonymous substitutions (dN/dS), as proxy for functional divergence. We used five working definitions of orthology, including reciprocal best hits (RBH), among other definitions based on network analyses and clustering. The results showed that orthologs, by all definitions tested, had values of dN/dS noticeably lower than those of paralogs, suggesting that orthologs generally tend to be more functionally stable than paralogs. The differences in dN/dS ratios remained suggesting the functional stability of orthologs after eliminating gene comparisons with potential problems, such as genes with high codon usage biases, low coverage of either of the aligned sequences, or sequences with very high similarities. Separation by percent identity of the encoded proteins showed that the differences between the dN/dS ratios of orthologs and paralogs were more evident at high sequence identity, less so as identity dropped. The last results suggest that the differences between dN/dS ratios were partially related to differences in protein identity. However, they also suggested that paralogs undergo functional divergence relatively early after duplication. Our analyses indicate that choosing orthologs as probably functionally coherent remains the right approach in comparative genomics.
bibliographic citation: Escorcia-Rodríguez et al. (2022) Non-synonymous to synonymous substitutions suggest that orthologs tend to keep their functions, while paralogs are a source of functional novelty. PeerJ 10:e13843 https://doi.org/10.7717/peerj.13843
date submitted: 2020-08-25
date accepted: 2022-07-14
issued: 2022-08-31
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Escorcia-Rodríguez
  given name: Juan M.
author list: Agent
  family name: Esposito
  given name: Mario
author list: Agent
  family name: Freyre-González
  given name: Julio A.
author list: Agent
  family name: Moreno-Hagelsieb
  given name: Gabriel
doi: 10.7717/peerj.13843
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-08-31
copyright: © 2022 Escorcia-Rodríguez et al.
attribution name: Escorcia-Rodriguez et al.

An insight into the invasion of breast ductal carcinoma in situ based on clinical, pathological and hematological data
type: item
type: AcademicArticle
description: Background Ductal carcinoma in situ (DCIS) has become a non-negligible part of breast cancers owing to the greatly increased incidence. While its natural history was not fully elucidated, which is the reason for current controversies in clinical treatment. Exploration of this issue from a clinical perspective is meaningful. Methods Medical records of 389 patients diagnosed with DCIS or DCIS with invasive ductal carcinoma (IDC) were reviewed. All of them received appropriate medical care in our center. All 324 patients in training cohort were divided into invasion and non-invasion groups based on pathology. Differences in DCIS immunohistochemical markers and hematological indicators between them were analyzed. In the invasion group, differences between DCIS and matched IDC were compared to explore changes in the tumor heterogeneity during invasion. Conclusions are validated in the validation cohort of 65 patients. Results Patients in invasion and non-invasion groups were balanced in baseline characteristics and no statistically significant differences were noticed for DCIS immunohistochemical markers. For hematological indicators, high expression of platelet >291.50) (odds ratio, 2.46; CI [1.35–4.46]; p = 0.003) and SII (>347.20) (odds ratio, 2.54; CI [1.56–4.12]; p < 0.001) were established as independent predictors for invasion by logistic analysis and were validated in the validation cohort. Ki-67 of IDC was significantly higher than that of matched DCIS (p < 0.001). HER2 expression and histological grade of DCIS were separately linearly related to those of IDC. Conclusion The change in hematological indicators is an independent predictor for invasion and can be incorporated into the treatment decision-making process for DCIS. Invasion tumor cells exhibit a stronger proliferative capacity compared with the in-situ ones. There are linear relationships in HER2 expression and histological grades between DCIS and matched IDC. DCIS subclones with different histological…
format: application/pdf
format: text/html
creator: Yanbiao Liu
creator: Zining Jin
creator: Xinmiao Yu
creator: Ang Zheng
creator: Feng Jin
creator: Xu Wang
subject: Hematology
subject: Oncology
subject: Pathology
subject: Women’s Health
description: doi:10.7717/peerj.13966
publisher: PeerJ Inc.
rights: © 2022 Liu et al.
abstract: Background Ductal carcinoma in situ (DCIS) has become a non-negligible part of breast cancers owing to the greatly increased incidence. While its natural history was not fully elucidated, which is the reason for current controversies in clinical treatment. Exploration of this issue from a clinical perspective is meaningful. Methods Medical records of 389 patients diagnosed with DCIS or DCIS with invasive ductal carcinoma (IDC) were reviewed. All of them received appropriate medical care in our center. All 324 patients in training cohort were divided into invasion and non-invasion groups based on pathology. Differences in DCIS immunohistochemical markers and hematological indicators between them were analyzed. In the invasion group, differences between DCIS and matched IDC were compared to explore changes in the tumor heterogeneity during invasion. Conclusions are validated in the validation cohort of 65 patients. Results Patients in invasion and non-invasion groups were balanced in baseline characteristics and no statistically significant differences were noticed for DCIS immunohistochemical markers. For hematological indicators, high expression of platelet >291.50) (odds ratio, 2.46; CI [1.35–4.46]; p = 0.003) and SII (>347.20) (odds ratio, 2.54; CI [1.56–4.12]; p < 0.001) were established as independent predictors for invasion by logistic analysis and were validated in the validation cohort. Ki-67 of IDC was significantly higher than that of matched DCIS (p < 0.001). HER2 expression and histological grade of DCIS were separately linearly related to those of IDC. Conclusion The change in hematological indicators is an independent predictor for invasion and can be incorporated into the treatment decision-making process for DCIS. Invasion tumor cells exhibit a stronger proliferative capacity compared with the in-situ ones. There are linear relationships in HER2 expression and histological grades between DCIS and matched IDC. DCIS subclones with different histological…
bibliographic citation: Liu et al. (2022) An insight into the invasion of breast ductal carcinoma in situ based on clinical, pathological and hematological data. PeerJ 10:e13966 https://doi.org/10.7717/peerj.13966
date submitted: 2022-06-03
date accepted: 2022-08-08
issued: 2022-08-31
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Liu
  given name: Yanbiao
author list: Agent
  family name: Jin
  given name: Zining
author list: Agent
  family name: Yu
  given name: Xinmiao
author list: Agent
  family name: Zheng
  given name: Ang
author list: Agent
  family name: Jin
  given name: Feng
author list: Agent
  family name: Wang
  given name: Xu
doi: 10.7717/peerj.13966
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-08-31
copyright: ©2022 Liu et al.
attribution name: Liu et al.

Fine scale population structure of Acropora palmata and Acropora cervicornis in the Colombian Caribbean
type: item
type: AcademicArticle
description: Using a standardized SNP array, we identified two populations of Acropora cervicornis and one population of A. palmata in the Caribbean coast of Colombia. San Andrés was the most genetically differentiated location for both species. An average pairwise FST value of 0.131 and 0.050 between San Andrés and neighboring collection sites was estimated, for A. cervicornis and A. palmata, respectively. Based on population patterns of both acroporid species, we inferred that Magdalena River is not a barrier of genetic connectivity among Colombian populations. Genetic comparisons between the Colombian coast of Caribbean with other Caribbean locations agree with previous studies for both species, where four populations were identified in A. cervicornis and three in A. palmata. Our results support published bio-physical model predictions and highlight the Panama-Colombia gyre as a possible isolating mechanism within the western Caribbean. However, the genetic diversity in both species was about half (mean HE per site = 0.321 in A. palmata and 0.369 in A. cervicornis) than previous estimates in acroporid populations in the Caribbean. The lower genetic diversity as well their relative isolation and high levels of reef degradation may be of particular conservation concern that may require species-specific management coupled with science-based restoration efforts.
format: application/pdf
format: text/html
creator: Rocio García-Urueña
creator: Sheila A. Kitchen
creator: Nikolaos V. Schizas
subject: Conservation Biology
subject: Marine Biology
subject: Molecular Biology
subject: Biological Oceanography
subject: Population Biology
description: doi:10.7717/peerj.13854
publisher: PeerJ Inc.
rights: © 2022 García-Urueña et al.
abstract: Using a standardized SNP array, we identified two populations of Acropora cervicornis and one population of A. palmata in the Caribbean coast of Colombia. San Andrés was the most genetically differentiated location for both species. An average pairwise FST value of 0.131 and 0.050 between San Andrés and neighboring collection sites was estimated, for A. cervicornis and A. palmata, respectively. Based on population patterns of both acroporid species, we inferred that Magdalena River is not a barrier of genetic connectivity among Colombian populations. Genetic comparisons between the Colombian coast of Caribbean with other Caribbean locations agree with previous studies for both species, where four populations were identified in A. cervicornis and three in A. palmata. Our results support published bio-physical model predictions and highlight the Panama-Colombia gyre as a possible isolating mechanism within the western Caribbean. However, the genetic diversity in both species was about half (mean HE per site = 0.321 in A. palmata and 0.369 in A. cervicornis) than previous estimates in acroporid populations in the Caribbean. The lower genetic diversity as well their relative isolation and high levels of reef degradation may be of particular conservation concern that may require species-specific management coupled with science-based restoration efforts.
bibliographic citation: García-Urueña et al. (2022) Fine scale population structure of Acropora palmata and Acropora cervicornis in the Colombian Caribbean. PeerJ 10:e13854 https://doi.org/10.7717/peerj.13854
date submitted: 2022-03-11
date accepted: 2022-07-16
issued: 2022-08-30
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: García-Urueña
  given name: Rocio
author list: Agent
  family name: Kitchen
  given name: Sheila A.
author list: Agent
  family name: Schizas
  given name: Nikolaos V.
doi: 10.7717/peerj.13854
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-08-30
copyright: ©2022 García-Urueña et al.
attribution name: García-Urueña et al.

Be aware of the allele-specific bias and compositional effects in multi-template PCR
type: item
type: AcademicArticle
description: High-throughput sequencing of amplicon libraries is the most widespread and one of the most effective ways to study the taxonomic structure of microbial communities, even despite growing accessibility of whole metagenome sequencing. Due to the targeted amplification, the method provides unparalleled resolution of communities, but at the same time perturbs initial community structure thereby reducing data robustness and compromising downstream analyses. Experimental research of the perturbations is largely limited to comparative studies on different PCR protocols without considering other sources of experimental variation related to characteristics of the initial microbial composition itself. Here we analyse these sources and demonstrate how dramatically they effect the relative abundances of taxa during the PCR cycles. We developed the mathematical model of the PCR amplification assuming the heterogeneity of amplification efficiencies and considering the compositional nature of data. We designed the experiment—five consecutive amplicon cycles (22–26) with 12 replicates for one real human stool microbial sample—and estimated the dynamics of the microbial community in line with the model. We found the high heterogeneity in amplicon efficiencies of taxa that leads to the non-linear and substantial (up to fivefold) changes in relative abundances during PCR. The analysis of possible sources of heterogeneity revealed the significant association between amplicon efficiencies and the energy of secondary structures of the DNA templates. The result of our work highlights non-trivial changes in the dynamics of real-life microbial communities due to their compositional nature. Obtained effects are specific not only for amplicon libraries, but also for any studies of metagenome dynamics.
format: application/pdf
format: text/html
creator: Ilia Korvigo
creator: Anna A. Igolkina
creator: Arina A. Kichko
creator: Tatiana Aksenova
creator: Evgeny E. Andronov
subject: Bioinformatics
subject: Computational Biology
subject: Microbiology
subject: Molecular Biology
description: doi:10.7717/peerj.13888
publisher: PeerJ Inc.
rights: © 2022 Korvigo et al.
abstract: High-throughput sequencing of amplicon libraries is the most widespread and one of the most effective ways to study the taxonomic structure of microbial communities, even despite growing accessibility of whole metagenome sequencing. Due to the targeted amplification, the method provides unparalleled resolution of communities, but at the same time perturbs initial community structure thereby reducing data robustness and compromising downstream analyses. Experimental research of the perturbations is largely limited to comparative studies on different PCR protocols without considering other sources of experimental variation related to characteristics of the initial microbial composition itself. Here we analyse these sources and demonstrate how dramatically they effect the relative abundances of taxa during the PCR cycles. We developed the mathematical model of the PCR amplification assuming the heterogeneity of amplification efficiencies and considering the compositional nature of data. We designed the experiment—five consecutive amplicon cycles (22–26) with 12 replicates for one real human stool microbial sample—and estimated the dynamics of the microbial community in line with the model. We found the high heterogeneity in amplicon efficiencies of taxa that leads to the non-linear and substantial (up to fivefold) changes in relative abundances during PCR. The analysis of possible sources of heterogeneity revealed the significant association between amplicon efficiencies and the energy of secondary structures of the DNA templates. The result of our work highlights non-trivial changes in the dynamics of real-life microbial communities due to their compositional nature. Obtained effects are specific not only for amplicon libraries, but also for any studies of metagenome dynamics.
bibliographic citation: Korvigo et al. (2022) Be aware of the allele-specific bias and compositional effects in multi-template PCR. PeerJ 10:e13888 https://doi.org/10.7717/peerj.13888
date submitted: 2020-06-12
date accepted: 2022-07-21
issued: 2022-08-30
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Korvigo
  given name: Ilia
author list: Agent
  family name: Igolkina
  given name: Anna A.
author list: Agent
  family name: Kichko
  given name: Arina A.
author list: Agent
  family name: Aksenova
  given name: Tatiana
author list: Agent
  family name: Andronov
  given name: Evgeny E.
doi: 10.7717/peerj.13888
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-08-30
copyright: ©2022 Korvigo et al.
attribution name: Korvigo et al.

Cardiorespiratory function, resting metabolic rate and heart rate variability in coal miners exposed to hypobaric hypoxia in highland workplace
type: item
type: AcademicArticle
description: Background Owing to intermittent/acute exposure to hypobaric hypoxia, highland miners may often suffer, the physiological characteristics between highland and lowland miners, however, are rarely reported. The objective of this study was to compare the physiological characteristics of coal miners working at disparate altitudes. Methods Twenty-three male coal mining workers acclimating to high altitude for 30 ± 6 days in Tibet (highland group; approx. 4500 m above sea level; 628.39 millibar), and 22 male coal mining workers in Hebei (lowland group; less than 100 m above sea level; 1021.82 millibar) were recruited. Tests were conducted to compare ventilatory parameters, circulation parameters, resting metabolic rate (RMR), and heart rate variability (HRV) indices between the two groups in resting state. Results Ventilation volume per minute (VE) of the highland group was markedly raised compared to that of the lowland group (11.70 ± 1.57 vs. 8.94 ± 1.97 L/min, p = 0.000). In the meanwhile, O2 intake per heart beat (VO2/HR) was strikingly decreased (3.54 ± 0.54 vs. 4.36 ± 0.69 ml/beat, p = 0.000). Resting metabolic rate relevant to body surface area (RMR/BSA) was found no significant difference between the two groups. Evident reduction in standard deviation of NN intervals (SDNN) and remarkable increase in ratio of low- and high- frequency bands (LF/HF) were manifest in highland miners compared to that of lowland ones (110.82 ± 33.34 vs. 141.44 ± 40.38, p = 0.008 and 858.86 ± 699.24 vs. 371.33 ± 171.46, p = 0.003; respectively). Conclusions These results implicate that long-term intermittent exposure to high altitude can lead miners to an intensified respiration, a compromised circulation and a profound sympathetic-parasympathetic imbalance, whereas the RMR in highland miners does not distinctly decline.
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creator: Sanjun Yang
creator: Chunhu Tian
creator: Fan Yang
creator: Qi Chen
creator: Ruiyuan Geng
creator: Chunyan Liu
creator: Xinrong Wu
creator: Wing-Kai Lam
subject: Cardiology
subject: Public Health
subject: Respiratory Medicine
subject: Metabolic Sciences
subject: Environmental Health
description: doi:10.7717/peerj.13899
publisher: PeerJ Inc.
rights: © 2022 Yang et al.
abstract: Background Owing to intermittent/acute exposure to hypobaric hypoxia, highland miners may often suffer, the physiological characteristics between highland and lowland miners, however, are rarely reported. The objective of this study was to compare the physiological characteristics of coal miners working at disparate altitudes. Methods Twenty-three male coal mining workers acclimating to high altitude for 30 ± 6 days in Tibet (highland group; approx. 4500 m above sea level; 628.39 millibar), and 22 male coal mining workers in Hebei (lowland group; less than 100 m above sea level; 1021.82 millibar) were recruited. Tests were conducted to compare ventilatory parameters, circulation parameters, resting metabolic rate (RMR), and heart rate variability (HRV) indices between the two groups in resting state. Results Ventilation volume per minute (VE) of the highland group was markedly raised compared to that of the lowland group (11.70 ± 1.57 vs. 8.94 ± 1.97 L/min, p = 0.000). In the meanwhile, O2 intake per heart beat (VO2/HR) was strikingly decreased (3.54 ± 0.54 vs. 4.36 ± 0.69 ml/beat, p = 0.000). Resting metabolic rate relevant to body surface area (RMR/BSA) was found no significant difference between the two groups. Evident reduction in standard deviation of NN intervals (SDNN) and remarkable increase in ratio of low- and high- frequency bands (LF/HF) were manifest in highland miners compared to that of lowland ones (110.82 ± 33.34 vs. 141.44 ± 40.38, p = 0.008 and 858.86 ± 699.24 vs. 371.33 ± 171.46, p = 0.003; respectively). Conclusions These results implicate that long-term intermittent exposure to high altitude can lead miners to an intensified respiration, a compromised circulation and a profound sympathetic-parasympathetic imbalance, whereas the RMR in highland miners does not distinctly decline.
bibliographic citation: Yang et al. (2022) Cardiorespiratory function, resting metabolic rate and heart rate variability in coal miners exposed to hypobaric hypoxia in highland workplace. PeerJ 10:e13899 https://doi.org/10.7717/peerj.13899
date submitted: 2022-04-26
date accepted: 2022-07-23
issued: 2022-08-30
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Yang
  given name: Sanjun
author list: Agent
  family name: Tian
  given name: Chunhu
author list: Agent
  family name: Yang
  given name: Fan
author list: Agent
  family name: Chen
  given name: Qi
author list: Agent
  family name: Geng
  given name: Ruiyuan
author list: Agent
  family name: Liu
  given name: Chunyan
author list: Agent
  family name: Wu
  given name: Xinrong
author list: Agent
  family name: Lam
  given name: Wing-Kai
doi: 10.7717/peerj.13899
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-08-30
copyright: ©2022 Yang et al.
attribution name: Yang et al.

Prior experience of captivity affects behavioural responses to ‘novel’ environments
type: item
type: AcademicArticle
description: Information ecology theory predicts that prior experience influences current behaviour, even if the information is acquired under a different context. However, when individuals are tested to quantify personality, cognition, or stress, we usually assume that the novelty of the test is consistent among individuals. Surprisingly, this ‘gambit of prior experience’ has rarely been explored. Therefore, here we make use of a wild population of great tits (Parus major) to test if prior experience of handling and captivity influences common measures of exploration (open field tests in two novel contexts: room and cage arenas), social response (simulated using a mirror), and behavioural stress (breathing rate). We found that birds with prior experience of captivity (caught previously for unrelated learning and foraging experiments) were more exploratory, but this depended on age: exploration and captivity experience (in terms of both absolute binary experience and the length of time spent in captivity) were associated more strongly in young (first-winter) birds than in adults. However, there was no association of prior experience of captivity with social response and breathing rate, and nor did the measures of exploration correlate. Together our results suggest that re-testing of individuals requires careful consideration, particularly for younger birds, and previous experiences can carry over and affect behaviours differently.
format: application/pdf
format: text/html
creator: Edward Kluen
creator: Katja Rönkä
creator: Rose Thorogood
subject: Animal Behavior
subject: Ecology
subject: Zoology
description: doi:10.7717/peerj.13905
publisher: PeerJ Inc.
rights: © 2022 Kluen et al.
abstract: Information ecology theory predicts that prior experience influences current behaviour, even if the information is acquired under a different context. However, when individuals are tested to quantify personality, cognition, or stress, we usually assume that the novelty of the test is consistent among individuals. Surprisingly, this ‘gambit of prior experience’ has rarely been explored. Therefore, here we make use of a wild population of great tits (Parus major) to test if prior experience of handling and captivity influences common measures of exploration (open field tests in two novel contexts: room and cage arenas), social response (simulated using a mirror), and behavioural stress (breathing rate). We found that birds with prior experience of captivity (caught previously for unrelated learning and foraging experiments) were more exploratory, but this depended on age: exploration and captivity experience (in terms of both absolute binary experience and the length of time spent in captivity) were associated more strongly in young (first-winter) birds than in adults. However, there was no association of prior experience of captivity with social response and breathing rate, and nor did the measures of exploration correlate. Together our results suggest that re-testing of individuals requires careful consideration, particularly for younger birds, and previous experiences can carry over and affect behaviours differently.
bibliographic citation: Kluen et al. (2022) Prior experience of captivity affects behavioural responses to ‘novel’ environments. PeerJ 10:e13905 https://doi.org/10.7717/peerj.13905
date submitted: 2022-02-15
date accepted: 2022-07-27
issued: 2022-08-30
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Kluen
  given name: Edward
author list: Agent
  family name: Rönkä
  given name: Katja
author list: Agent
  family name: Thorogood
  given name: Rose
doi: 10.7717/peerj.13905
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-08-30
copyright: ©2022 Kluen et al.
attribution name: Kluen et al.

The relationship between the Functional Movement Screen and the Y Balance Test in youth footballers
type: item
type: AcademicArticle
description: Background The Functional Movement Screen (FMS) and the Y Balance Test (Y-BT) are screening tools to detect movement deficits and to identify footballers at high risk of injury. If these tools are able to identify athletes with high risk of injury, they should measure the same construct and also be highly correlated. Objectives The aim of the study was to determine the relationship between the FMS and Y-BT in youth footballers. The present study also aimed to assess the degree of association between the FMS and Y-BT considering high-injury-risk (FMS <= 14 points and Y-BT <= 89.6%) and low-injury-risk groups (FMS > 14 points and Y-BT > 89.6%). Method A sample of 226 healthy athletes (mean age: 14.0 ± 2.3 years) was selected from a football club. The FMS and Y-BT data were collected from all participants. The Y-BT raw data were normalised to the relative length of the lower limbs. Spearman’s correlation was used in the analysis. Results For the whole group, there was a moderate correlation (R = 0.41; p < 0.001) between the composite FMS score and composite Y-BT score. The strength of relationships varied from weak to moderate between the FMS subtests and most Y-BT results for each direction. In the high-injury-risk group, there was no correlation (R = 0.11; p = 0.61) between the composite FMS score and composite Y-BT score. For the low-injury-risk group, there was a weak significant correlation (R = 0.27; p < 0.007) between the composite FMS score and composite Y-BT score. Additionally, 56 and 53 athletes were classified to the high-injury-risk group based on the FMS and Y-BT, respectively. Only 23 athletes were classified to the high-risk group by both tests. Conclusions Youth footballers showed only weak to moderate correlations between the FMS and the Y-BT. Footballers classified in the high-injury-risk group based on the FMS and Y-BT presented a different relationship between the FMS and Y-BT tasks compared to the low-injury-risk group. The results confirmed that …
format: application/pdf
format: text/html
creator: Damian Sikora
creator: Pawel Linek
subject: Kinesiology
subject: Pediatrics
subject: Rehabilitation
description: doi:10.7717/peerj.13906
publisher: PeerJ Inc.
rights: © 2022 Sikora and Linek
abstract: Background The Functional Movement Screen (FMS) and the Y Balance Test (Y-BT) are screening tools to detect movement deficits and to identify footballers at high risk of injury. If these tools are able to identify athletes with high risk of injury, they should measure the same construct and also be highly correlated. Objectives The aim of the study was to determine the relationship between the FMS and Y-BT in youth footballers. The present study also aimed to assess the degree of association between the FMS and Y-BT considering high-injury-risk (FMS <= 14 points and Y-BT <= 89.6%) and low-injury-risk groups (FMS > 14 points and Y-BT > 89.6%). Method A sample of 226 healthy athletes (mean age: 14.0 ± 2.3 years) was selected from a football club. The FMS and Y-BT data were collected from all participants. The Y-BT raw data were normalised to the relative length of the lower limbs. Spearman’s correlation was used in the analysis. Results For the whole group, there was a moderate correlation (R = 0.41; p < 0.001) between the composite FMS score and composite Y-BT score. The strength of relationships varied from weak to moderate between the FMS subtests and most Y-BT results for each direction. In the high-injury-risk group, there was no correlation (R = 0.11; p = 0.61) between the composite FMS score and composite Y-BT score. For the low-injury-risk group, there was a weak significant correlation (R = 0.27; p < 0.007) between the composite FMS score and composite Y-BT score. Additionally, 56 and 53 athletes were classified to the high-injury-risk group based on the FMS and Y-BT, respectively. Only 23 athletes were classified to the high-risk group by both tests. Conclusions Youth footballers showed only weak to moderate correlations between the FMS and the Y-BT. Footballers classified in the high-injury-risk group based on the FMS and Y-BT presented a different relationship between the FMS and Y-BT tasks compared to the low-injury-risk group. The results confirmed that …
bibliographic citation: Sikora et al. (2022) The relationship between the Functional Movement Screen and the Y Balance Test in youth footballers. PeerJ 10:e13906 https://doi.org/10.7717/peerj.13906
date submitted: 2022-02-24
date accepted: 2022-07-27
issued: 2022-08-30
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Sikora
  given name: Damian
author list: Agent
  family name: Linek
  given name: Pawel
doi: 10.7717/peerj.13906
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-08-30
copyright: © 2022 Sikora and Linek
attribution name: Sikora and Linek

Proteomic profile of serum from patients with schizophrenia spectrum disorders
type: item
type: AcademicArticle
description: This article describes the most likely classes of proteins and molecular processes that specifically characterize schizophrenic spectrum disorders such as simple and paranoid schizophrenia, schizotypal disorder, and acute polymorphic psychotic disorder (APPD). The identification of patients’ serum proteins was carried out using mass spectrometry. For patients with paranoid schizophrenia, the proteins responsible for translation and transcription are characteristic. A significant part of the proteins of patients with simple schizophrenia regulate the cell’s main metabolic and transport processes. These are proteins of the receptor system, vesicular transport, and extracellular matrix, which mainly carry out catabolic processes. The proteins of patients with schizotypal disorder mostly coincided with the classes of other patients, apart from chaperone proteins, which were not found in other studied groups. These proteins are mainly involved in anabolic processes. The main classes of proteins found in patients with APPD are responsible for the metabolism of nucleic acids. Active apoptosis processes were also revealed in these patients. These results from our basic knowledge about the molecular mechanisms of the pathogenesis of these disorders.
format: application/pdf
format: text/html
creator: Elena Dmitrieva
creator: Liudmila Smirnova
creator: Alexander Seregin
creator: Victor Zgoda
creator: Arkadij Semke
creator: Svetlana Ivanova
subject: Biochemistry
subject: Computational Biology
subject: Molecular Biology
subject: Cognitive Disorders
subject: Psychiatry and Psychology
description: doi:10.7717/peerj.13907
publisher: PeerJ Inc.
rights: © 2022 Dmitrieva et al.
abstract: This article describes the most likely classes of proteins and molecular processes that specifically characterize schizophrenic spectrum disorders such as simple and paranoid schizophrenia, schizotypal disorder, and acute polymorphic psychotic disorder (APPD). The identification of patients’ serum proteins was carried out using mass spectrometry. For patients with paranoid schizophrenia, the proteins responsible for translation and transcription are characteristic. A significant part of the proteins of patients with simple schizophrenia regulate the cell’s main metabolic and transport processes. These are proteins of the receptor system, vesicular transport, and extracellular matrix, which mainly carry out catabolic processes. The proteins of patients with schizotypal disorder mostly coincided with the classes of other patients, apart from chaperone proteins, which were not found in other studied groups. These proteins are mainly involved in anabolic processes. The main classes of proteins found in patients with APPD are responsible for the metabolism of nucleic acids. Active apoptosis processes were also revealed in these patients. These results from our basic knowledge about the molecular mechanisms of the pathogenesis of these disorders.
bibliographic citation: Dmitrieva et al. (2022) Proteomic profile of serum from patients with schizophrenia spectrum disorders. PeerJ 10:e13907 https://doi.org/10.7717/peerj.13907
date submitted: 2022-05-19
date accepted: 2022-07-27
issued: 2022-08-30
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Dmitrieva
  given name: Elena
author list: Agent
  family name: Smirnova
  given name: Liudmila
author list: Agent
  family name: Seregin
  given name: Alexander
author list: Agent
  family name: Zgoda
  given name: Victor
author list: Agent
  family name: Semke
  given name: Arkadij
author list: Agent
  family name: Ivanova
  given name: Svetlana
doi: 10.7717/peerj.13907
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-08-30
copyright: ©2022 Dmitrieva et al.
attribution name: Dmitrieva et al.

Analysis of endophyte diversity of Gentiana officinalis among different tissue types and ages and their association with four medicinal secondary metabolites
type: item
type: AcademicArticle
description: Background The difference of metabolites in medicinal plants has always been concerned to be influenced by external environmental factors. However, the relationship between endophytes and host metabolites remains unclear. Methods In this study, we used 16S and ITS amplicon sequencing to compare endophyte diversity among different tissue types and ages of Gentiana officinalis. Endophyte diversity and abundance was also analyzed in relation to the abundance of four secondary metabolites (Gentiopicroside, Loganic acid, Swertiamarine and Sweroside). Results The diversity and richness of G. officinalis endophyte differed as a function of tissue types and ages. Four metabolites of G. officinalis were significantly correlated with the abundance of dominant endophyte genera. The predictive function analysis showed that metabolism was main function of endophytic bacteria in different tissue and year root samples, while saprotroph was dominant trophic modes of endophytic fungi in the different year root samples. The dominant trophic modes of endophytic fungi was saprotroph and pathotroph, and relative abundances differed in the different tissue samples. The results of this study will help to elucidate the plant-microbial interactions and provide key information on the role of endophytes in the production of G.officinalis and its important metabolites.
format: application/pdf
format: text/html
creator: QinZheng Hou
creator: DaWei Chen
creator: Yu-pei Wang
creator: Nurbiye Ehmet
creator: Jing Ma
creator: Kun Sun
subject: Agricultural Science
subject: Food Science and Technology
subject: Microbiology
subject: Mycology
subject: Plant Science
description: doi:10.7717/peerj.13949
publisher: PeerJ Inc.
rights: © 2022 Hou et al.
abstract: Background The difference of metabolites in medicinal plants has always been concerned to be influenced by external environmental factors. However, the relationship between endophytes and host metabolites remains unclear. Methods In this study, we used 16S and ITS amplicon sequencing to compare endophyte diversity among different tissue types and ages of Gentiana officinalis. Endophyte diversity and abundance was also analyzed in relation to the abundance of four secondary metabolites (Gentiopicroside, Loganic acid, Swertiamarine and Sweroside). Results The diversity and richness of G. officinalis endophyte differed as a function of tissue types and ages. Four metabolites of G. officinalis were significantly correlated with the abundance of dominant endophyte genera. The predictive function analysis showed that metabolism was main function of endophytic bacteria in different tissue and year root samples, while saprotroph was dominant trophic modes of endophytic fungi in the different year root samples. The dominant trophic modes of endophytic fungi was saprotroph and pathotroph, and relative abundances differed in the different tissue samples. The results of this study will help to elucidate the plant-microbial interactions and provide key information on the role of endophytes in the production of G.officinalis and its important metabolites.
bibliographic citation: Hou et al. (2022) Analysis of endophyte diversity of Gentiana officinalis among different tissue types and ages and their association with four medicinal secondary metabolites. PeerJ 10:e13949 https://doi.org/10.7717/peerj.13949
date submitted: 2021-12-01
date accepted: 2022-08-04
issued: 2022-08-30
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Hou
  given name: QinZheng
author list: Agent
  family name: Chen
  given name: DaWei
author list: Agent
  family name: Wang
  given name: Yu-pei
author list: Agent
  family name: Ehmet
  given name: Nurbiye
author list: Agent
  family name: Ma
  given name: Jing
author list: Agent
  family name: Sun
  given name: Kun
doi: 10.7717/peerj.13949
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-08-30
copyright: © 2022 Hou et al.
attribution name: Hou et al.

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