PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
items: Environmental stressors may cause equine herpesvirus reactivation in captive Grévy’s zebras (Equus grevyi)
items: Expectancy effects in the Autonomous Sensory Meridian Response
items: What affects power to estimate speciation rate shifts?
items: Seed bank and growth comparisons of native (Virgilia divaricata) and invasive alien (Acacia mearnsii and A. melanoxylon) plants: implications for conservation
items: Smokeless tobacco use: pattern of use, knowledge and perceptions among rural Bangladeshi adolescents
items: Disentangling the mechanisms of mate choice in a captive koala population
items: Children’s physical activity and sedentary time compared using assessments of accelerometry counts and muscle activity level
items: Comprehensive analysis of metastasis-related genes reveals a gene signature predicting the survival of colon cancer patients
items: RNA-Seq analysis of differential gene expression in Betula luminifera xylem during the early stages of tension wood formation
items: Influence of hydrolysis rate of urea on ruminal bacterial diversity level and cellulolytic bacteria abundance in vitro

Environmental stressors may cause equine herpesvirus reactivation in captive Grévy’s zebras (Equus grevyi)
type: item
type: AcademicArticle
description: Equine Herpesviruses (EHV) are common and often latent pathogens of equids which can cause fatalities when transmitted to non-equids. Stress and elevated glucocorticoids have been associated with EHV reactivation in domestic horses, but little is known about the correlation between stress and viral reactivation in wild equids. We investigated the effect of an environmental stressor (social group restructuring following a translocation event) on EHV reactivation in captive Grévy’s zebras (Equus grevyi). A mare was translocated by road transport from Zoo Mulhouse, France, to join a resident group of three mares in Tierpark Berlin, Germany. We used an indirect sampling method to assess the frequency of EHV shedding for 14 days immediately after the translocation event (termed the ‘experimental period’). The results were compared with those from two control periods, one preceding and one subsequent to the experimental period. In addition, we measured fecal glucocorticoid metabolite (fGCM) concentrations daily in all individuals from 6 days before, to 14 days after translocation. We found significantly higher EHV shedding frequencies during the experimental period, compared to each of the two control periods. All animals showed significantly elevated fGCM concentrations, compared to fGCM levels before translocation. Finally, we found that an increase in fGCM concentration was significantly associated with an increased likelihood of EHV shedding. Although the small number of animals in the study limits the conclusions that can be drawn from the study, taken together, our results support the hypothesis that environmental stressors induce viral reactivation in wild equids. Our results suggest that potentials stressors such as group restructuring and translocation should be considered in the management of zoological collections to reduce the risk of fatal EHV infections in novel hosts. Moreover, environmental stressors may play an important role in EHV reactivation and sprea…
format: application/pdf
format: text/html
creator: Peter A. Seeber
creator: Benoît Quintard
creator: Florian Sicks
creator: Martin Dehnhard
creator: Alex D. Greenwood
creator: Mathias Franz
subject: Ecology
subject: Virology
subject: Zoology
description: doi:10.7717/peerj.5422
publisher: PeerJ Inc.
rights: © 2018 Seeber et al.
abstract: Equine Herpesviruses (EHV) are common and often latent pathogens of equids which can cause fatalities when transmitted to non-equids. Stress and elevated glucocorticoids have been associated with EHV reactivation in domestic horses, but little is known about the correlation between stress and viral reactivation in wild equids. We investigated the effect of an environmental stressor (social group restructuring following a translocation event) on EHV reactivation in captive Grévy’s zebras (Equus grevyi). A mare was translocated by road transport from Zoo Mulhouse, France, to join a resident group of three mares in Tierpark Berlin, Germany. We used an indirect sampling method to assess the frequency of EHV shedding for 14 days immediately after the translocation event (termed the ‘experimental period’). The results were compared with those from two control periods, one preceding and one subsequent to the experimental period. In addition, we measured fecal glucocorticoid metabolite (fGCM) concentrations daily in all individuals from 6 days before, to 14 days after translocation. We found significantly higher EHV shedding frequencies during the experimental period, compared to each of the two control periods. All animals showed significantly elevated fGCM concentrations, compared to fGCM levels before translocation. Finally, we found that an increase in fGCM concentration was significantly associated with an increased likelihood of EHV shedding. Although the small number of animals in the study limits the conclusions that can be drawn from the study, taken together, our results support the hypothesis that environmental stressors induce viral reactivation in wild equids. Our results suggest that potentials stressors such as group restructuring and translocation should be considered in the management of zoological collections to reduce the risk of fatal EHV infections in novel hosts. Moreover, environmental stressors may play an important role in EHV reactivation and sprea…
bibliographic citation: Seeber et al. (2018) Environmental stressors may cause equine herpesvirus reactivation in captive Grévy’s zebras (Equus grevyi). PeerJ 6:e5422 https://doi.org/10.7717/peerj.5422
date submitted: 2018-05-09
date accepted: 2018-07-20
issued: 2018-08-22
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Seeber
  given name: Peter A.
author list: Agent
  family name: Quintard
  given name: Benoît
author list: Agent
  family name: Sicks
  given name: Florian
author list: Agent
  family name: Dehnhard
  given name: Martin
author list: Agent
  family name: Greenwood
  given name: Alex D.
author list: Agent
  family name: Franz
  given name: Mathias
doi: 10.7717/peerj.5422
volume: 6
issn: 2167-8359
publication name: PeerJ
publication date: 2018-08-22
copyright: ©2018 Seeber et al.
attribution name: Seeber et al.

Expectancy effects in the Autonomous Sensory Meridian Response
type: item
type: AcademicArticle
description: The Autonomous Sensory Meridian Response (ASMR) is a tingling, almost euphoric, sensation often elicited following certain visual or auditory stimulations (Barratt & Davis, 2015). Despite considerable media attention, little empirical work has investigated the underlying mechanisms. In the present study, ASMR enthusiasts and naïve observers listened to audio clips with and without ASMR-eliciting characteristics. We also manipulated participants’ expectations of ASMR, providing a measure of “placebo effects.” Although naïve participants were susceptible to suggestive instructions, experienced users were not, suggesting that initial exposure to ASMR media may evoke somatosensory responses consistent with one’s expectations. Implications for at-home stress management techniques are discussed.
format: application/pdf
format: text/html
creator: Daniella K. Cash
creator: Laura L. Heisick
creator: Megan H. Papesh
subject: Neuroscience
subject: Anesthesiology and Pain Management
subject: Psychiatry and Psychology
description: doi:10.7717/peerj.5229
publisher: PeerJ Inc.
rights: © 2018 Cash et al.
abstract: The Autonomous Sensory Meridian Response (ASMR) is a tingling, almost euphoric, sensation often elicited following certain visual or auditory stimulations (Barratt & Davis, 2015). Despite considerable media attention, little empirical work has investigated the underlying mechanisms. In the present study, ASMR enthusiasts and naïve observers listened to audio clips with and without ASMR-eliciting characteristics. We also manipulated participants’ expectations of ASMR, providing a measure of “placebo effects.” Although naïve participants were susceptible to suggestive instructions, experienced users were not, suggesting that initial exposure to ASMR media may evoke somatosensory responses consistent with one’s expectations. Implications for at-home stress management techniques are discussed.
bibliographic citation: Cash et al. (2018) Expectancy effects in the Autonomous Sensory Meridian Response. PeerJ 6:e5229 https://doi.org/10.7717/peerj.5229
date submitted: 2017-12-18
date accepted: 2018-06-22
issued: 2018-08-22
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Cash
  given name: Daniella K.
author list: Agent
  family name: Heisick
  given name: Laura L.
author list: Agent
  family name: Papesh
  given name: Megan H.
doi: 10.7717/peerj.5229
volume: 6
issn: 2167-8359
publication name: PeerJ
publication date: 2018-08-22
copyright: © 2018 Cash et al.
attribution name: Cash et al.

What affects power to estimate speciation rate shifts?
type: item
type: AcademicArticle
description: The development of methods to estimate rates of speciation and extinction from time-calibrated phylogenies has revolutionized evolutionary biology by allowing researchers to correlate diversification rate shifts with causal factors. A growing number of researchers are interested in testing whether the evolution of a trait or a trait variant has influenced speciation rate, and three modelling methods—BiSSE, MEDUSA and BAMM—have been widely used in such studies. We simulated phylogenies with a single speciation rate shift each, and evaluated the power of the three methods to detect these shifts. We varied the degree of increase in speciation rate (speciation rate asymmetry), the number of tips, the tip-ratio bias (ratio of number of tips with each character state) and the relative age in relation to overall tree age when the rate shift occurred. All methods had good power to detect rate shifts when the rate asymmetry was strong and the sizes of the two lineages with the distinct speciation rates were large. Even when lineage size was small, power was good when rate asymmetry was high. In our simulated scenarios, small lineage sizes appear to affect BAMM most strongly. Tip-ratio influenced the accuracy of speciation rate estimation but did not have a strong effect on power to detect rate shifts. Based on our results, we provide suggestions to users of these methods.
format: application/pdf
format: text/html
creator: Ullasa Kodandaramaiah
creator: Gopal Murali
subject: Bioinformatics
subject: Computational Biology
subject: Evolutionary Studies
description: doi:10.7717/peerj.5495
publisher: PeerJ Inc.
rights: © 2018 Kodandaramaiah and Murali
abstract: The development of methods to estimate rates of speciation and extinction from time-calibrated phylogenies has revolutionized evolutionary biology by allowing researchers to correlate diversification rate shifts with causal factors. A growing number of researchers are interested in testing whether the evolution of a trait or a trait variant has influenced speciation rate, and three modelling methods—BiSSE, MEDUSA and BAMM—have been widely used in such studies. We simulated phylogenies with a single speciation rate shift each, and evaluated the power of the three methods to detect these shifts. We varied the degree of increase in speciation rate (speciation rate asymmetry), the number of tips, the tip-ratio bias (ratio of number of tips with each character state) and the relative age in relation to overall tree age when the rate shift occurred. All methods had good power to detect rate shifts when the rate asymmetry was strong and the sizes of the two lineages with the distinct speciation rates were large. Even when lineage size was small, power was good when rate asymmetry was high. In our simulated scenarios, small lineage sizes appear to affect BAMM most strongly. Tip-ratio influenced the accuracy of speciation rate estimation but did not have a strong effect on power to detect rate shifts. Based on our results, we provide suggestions to users of these methods.
bibliographic citation: Kodandaramaiah et al. (2018) What affects power to estimate speciation rate shifts?. PeerJ 6:e5495 https://doi.org/10.7717/peerj.5495
date submitted: 2017-08-29
date accepted: 2018-07-30
issued: 2018-08-21
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Kodandaramaiah
  given name: Ullasa
author list: Agent
  family name: Murali
  given name: Gopal
doi: 10.7717/peerj.5495
volume: 6
issn: 2167-8359
publication name: PeerJ
publication date: 2018-08-21
copyright: ©2018 Kodandaramaiah and Murali
attribution name: Kodandaramaiah and Murali

Seed bank and growth comparisons of native (Virgilia divaricata) and invasive alien (Acacia mearnsii and A. melanoxylon) plants: implications for conservation
type: item
type: AcademicArticle
description: Background Invasive alien plants with long-lived dormant seed banks and fast growth rates are difficult to manage. Acacia mearnsii and Acacia melanoxylon are two such invaders in the southern Cape of South Africa which occasionally co-occur with a native, ecologically analogous species, Virgilia divaricata. We compared the performance of these three species to determine potential for the native species to be used in management of the invasives. Methods We compared the study species in terms of (i) soil seed bank densities, their vertical distribution, and the viability of seeds underneath the canopies of mature trees; (ii) seedling growth from planted seeds over a period of three months; and (iii) growth rates of saplings over a period of 10 months in stands that have naturally regenerated in the field (these stands were dominated by A. mearnsii) and where saplings have been exposed to varying levels of competition from surrounding saplings. Results Seed bank densities differed significantly among species but not among soil depth classes. Acacia mearnsii had the highest seed bank densities (mean of 7,596 seeds m−2), followed by V. divaricata (938 seeds m−2) and A. melanoxylon (274 seeds m−2). Seed viability was high (87–91%) in all three study species and did not differ significantly among species or soil depth classes. As seedlings, V. divaricata significantly outgrew A. mearnsii in terms of height, root and shoot dry mass, and root:shoot ratio. Relative growth (the relationship between growth in height and initial height) was negative in the seedlings of both species. Trends during the sapling stage were opposite to those during the seedling stage; A. mearnsii (but not A. melanoxylon) saplings significantly outgrew V. divaricata saplings in height, while relative growth rates were positive in all species. Sapling growth of all species was furthermore uninfluenced by the collective biomass of surrounding competitors. Discussion Our findings suggest that amongst the…
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creator: Stefan A. Goets
creator: Tineke Kraaij
creator: Keith M. Little
subject: Conservation Biology
subject: Plant Science
subject: Natural Resource Management
description: doi:10.7717/peerj.5466
publisher: PeerJ Inc.
rights: © 2018 Goets et al.
abstract: Background Invasive alien plants with long-lived dormant seed banks and fast growth rates are difficult to manage. Acacia mearnsii and Acacia melanoxylon are two such invaders in the southern Cape of South Africa which occasionally co-occur with a native, ecologically analogous species, Virgilia divaricata. We compared the performance of these three species to determine potential for the native species to be used in management of the invasives. Methods We compared the study species in terms of (i) soil seed bank densities, their vertical distribution, and the viability of seeds underneath the canopies of mature trees; (ii) seedling growth from planted seeds over a period of three months; and (iii) growth rates of saplings over a period of 10 months in stands that have naturally regenerated in the field (these stands were dominated by A. mearnsii) and where saplings have been exposed to varying levels of competition from surrounding saplings. Results Seed bank densities differed significantly among species but not among soil depth classes. Acacia mearnsii had the highest seed bank densities (mean of 7,596 seeds m−2), followed by V. divaricata (938 seeds m−2) and A. melanoxylon (274 seeds m−2). Seed viability was high (87–91%) in all three study species and did not differ significantly among species or soil depth classes. As seedlings, V. divaricata significantly outgrew A. mearnsii in terms of height, root and shoot dry mass, and root:shoot ratio. Relative growth (the relationship between growth in height and initial height) was negative in the seedlings of both species. Trends during the sapling stage were opposite to those during the seedling stage; A. mearnsii (but not A. melanoxylon) saplings significantly outgrew V. divaricata saplings in height, while relative growth rates were positive in all species. Sapling growth of all species was furthermore uninfluenced by the collective biomass of surrounding competitors. Discussion Our findings suggest that amongst the…
bibliographic citation: Goets et al. (2018) Seed bank and growth comparisons of native (Virgilia divaricata) and invasive alien (Acacia mearnsii and A. melanoxylon) plants: implications for conservation. PeerJ 6:e5466 https://doi.org/10.7717/peerj.5466
date submitted: 2018-03-03
date accepted: 2018-07-27
issued: 2018-08-21
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Goets
  given name: Stefan A.
author list: Agent
  family name: Kraaij
  given name: Tineke
author list: Agent
  family name: Little
  given name: Keith M.
doi: 10.7717/peerj.5466
volume: 6
issn: 2167-8359
publication name: PeerJ
publication date: 2018-08-21
copyright: ©2018 Goets et al.
attribution name: Goets et al.

Smokeless tobacco use: pattern of use, knowledge and perceptions among rural Bangladeshi adolescents
type: item
type: AcademicArticle
description: Background The aim of the study was to investigate the practice and pattern of smokeless tobacco (SLT) use as well as the knowledge and perception about its ill effects among rural Bangladeshi adolescents. Methods A cross-sectional survey was conducted among students aged 13–18 years in two rural secondary schools in Bangladesh in August 2015. Data were collected through a self-administered questionnaire which consists of topics derived from the Social Cognitive Theory and Health Belief Model (personal characteristics, environmental factors, self-efficacy, outcome expectancies, perceived susceptibility, perceived severity, perceived benefits, perceived barriers, and cues to action). Data analysis was performed using SPSS version 24. A descriptive analysis was conducted to determine the current pattern of SLT use and knowledge about its ill effects. A chi-square test and Fisher exact test were conducted to explore associations between variables. Lastly, a logistic regression model was used to locate the predictors for current SLT use. Results A total of 790 students participated in the study. Among them, 9.5% (75) had used SLT at least once and 3.7% (29) were current SLT users. Males had a higher incidence of SLT use compared with females. The majority of students (77.3%) initiated SLT use between 10–13 years of age. ‘Zarda’ was the most common type of SLT used and most of the current users (86%) were able to buy SLT without age restrictions. Most of the current users (90%) wanted to quit SLT immediately; however, professional help was not available in schools. Overall, students had a good knowledge about the harmful effects of SLT with 54.8% (428) of respondents scoring in the good knowledge category. However, the majority of never SLT users (55.4%; 396) had a good knowledge compared to ever SLT users (42.7%; 32). Significant predictors of current SLT use included being a student aged 14 years and above (OR = 6.58, 95% CI [2.23–28.31]) as well as the variables of se…
format: application/pdf
format: text/html
creator: Md Zahid Ullah
creator: Jennifer NW Lim
creator: Marie-Ann Ha
creator: Md Mostafizur Rahman
subject: Epidemiology
subject: Public Health
description: doi:10.7717/peerj.5463
publisher: PeerJ Inc.
rights: © 2018 Ullah et al.
abstract: Background The aim of the study was to investigate the practice and pattern of smokeless tobacco (SLT) use as well as the knowledge and perception about its ill effects among rural Bangladeshi adolescents. Methods A cross-sectional survey was conducted among students aged 13–18 years in two rural secondary schools in Bangladesh in August 2015. Data were collected through a self-administered questionnaire which consists of topics derived from the Social Cognitive Theory and Health Belief Model (personal characteristics, environmental factors, self-efficacy, outcome expectancies, perceived susceptibility, perceived severity, perceived benefits, perceived barriers, and cues to action). Data analysis was performed using SPSS version 24. A descriptive analysis was conducted to determine the current pattern of SLT use and knowledge about its ill effects. A chi-square test and Fisher exact test were conducted to explore associations between variables. Lastly, a logistic regression model was used to locate the predictors for current SLT use. Results A total of 790 students participated in the study. Among them, 9.5% (75) had used SLT at least once and 3.7% (29) were current SLT users. Males had a higher incidence of SLT use compared with females. The majority of students (77.3%) initiated SLT use between 10–13 years of age. ‘Zarda’ was the most common type of SLT used and most of the current users (86%) were able to buy SLT without age restrictions. Most of the current users (90%) wanted to quit SLT immediately; however, professional help was not available in schools. Overall, students had a good knowledge about the harmful effects of SLT with 54.8% (428) of respondents scoring in the good knowledge category. However, the majority of never SLT users (55.4%; 396) had a good knowledge compared to ever SLT users (42.7%; 32). Significant predictors of current SLT use included being a student aged 14 years and above (OR = 6.58, 95% CI [2.23–28.31]) as well as the variables of se…
bibliographic citation: Ullah et al. (2018) Smokeless tobacco use: pattern of use, knowledge and perceptions among rural Bangladeshi adolescents. PeerJ 6:e5463 https://doi.org/10.7717/peerj.5463
date submitted: 2018-02-23
date accepted: 2018-07-26
issued: 2018-08-21
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Ullah
  given name: Md Zahid
author list: Agent
  family name: Lim
  given name: Jennifer NW
author list: Agent
  family name: Ha
  given name: Marie-Ann
author list: Agent
  family name: Rahman
  given name: Md Mostafizur
doi: 10.7717/peerj.5463
volume: 6
issn: 2167-8359
publication name: PeerJ
publication date: 2018-08-21
copyright: ©2018 Ullah et al.
attribution name: Ullah et al.

Disentangling the mechanisms of mate choice in a captive koala population
type: item
type: AcademicArticle
description: Successful captive breeding programs are crucial to the long-term survival of many threatened species. However, pair incompatibility (breeding failure) limits sustainability of many captive populations. Understanding whether the drivers of this incompatibility are behavioral, genetic, or a combination of both, is crucial to improving breeding programs. We used 28 years of pairing data from the San Diego Zoo koala colony, plus genetic analyses using both major histocompatibility complex (MHC)-linked and non-MHC-linked microsatellite markers, to show that both genetic and non-genetic factors can influence mating success. Male age was reconfirmed to be a contributing factor to the likelihood of a koala pair copulating. This trend could also be related to a pair’s age difference, which was highly correlated with male age in our dataset. Familiarity was reconfirmed to increase the probability of a successful copulation. Our data provided evidence that females select mates based on MHC and genome-wide similarity. Male heterozygosity at MHC class II loci was associated with both pre- and post-copulatory female choice. Genome-wide similarity, and similarity at the MHC class II DAB locus, were also associated with female choice at the post-copulatory level. Finally, certain MHC-linked alleles were associated with either increased or decreased mating success. We predict that utilizing a variety of behavioral and MHC-dependent mate choice mechanisms improves female fitness through increased reproductive success. This study highlights the complexity of mate choice mechanisms in a species, and the importance of ascertaining mate choice mechanisms to improve the success of captive breeding programs.
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creator: Parice A. Brandies
creator: Catherine E. Grueber
creator: Jamie A. Ivy
creator: Carolyn J. Hogg
creator: Katherine Belov
subject: Animal Behavior
subject: Conservation Biology
description: doi:10.7717/peerj.5438
publisher: PeerJ Inc.
rights: © 2018 Brandies et al.
abstract: Successful captive breeding programs are crucial to the long-term survival of many threatened species. However, pair incompatibility (breeding failure) limits sustainability of many captive populations. Understanding whether the drivers of this incompatibility are behavioral, genetic, or a combination of both, is crucial to improving breeding programs. We used 28 years of pairing data from the San Diego Zoo koala colony, plus genetic analyses using both major histocompatibility complex (MHC)-linked and non-MHC-linked microsatellite markers, to show that both genetic and non-genetic factors can influence mating success. Male age was reconfirmed to be a contributing factor to the likelihood of a koala pair copulating. This trend could also be related to a pair’s age difference, which was highly correlated with male age in our dataset. Familiarity was reconfirmed to increase the probability of a successful copulation. Our data provided evidence that females select mates based on MHC and genome-wide similarity. Male heterozygosity at MHC class II loci was associated with both pre- and post-copulatory female choice. Genome-wide similarity, and similarity at the MHC class II DAB locus, were also associated with female choice at the post-copulatory level. Finally, certain MHC-linked alleles were associated with either increased or decreased mating success. We predict that utilizing a variety of behavioral and MHC-dependent mate choice mechanisms improves female fitness through increased reproductive success. This study highlights the complexity of mate choice mechanisms in a species, and the importance of ascertaining mate choice mechanisms to improve the success of captive breeding programs.
bibliographic citation: Brandies et al. (2018) Disentangling the mechanisms of mate choice in a captive koala population. PeerJ 6:e5438 https://doi.org/10.7717/peerj.5438
date submitted: 2017-12-22
date accepted: 2018-07-23
issued: 2018-08-21
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Brandies
  given name: Parice A.
author list: Agent
  family name: Grueber
  given name: Catherine E.
author list: Agent
  family name: Ivy
  given name: Jamie A.
author list: Agent
  family name: Hogg
  given name: Carolyn J.
author list: Agent
  family name: Belov
  given name: Katherine
doi: 10.7717/peerj.5438
volume: 6
issn: 2167-8359
publication name: PeerJ
publication date: 2018-08-21
copyright: © 2018 Brandies et al.
attribution name: Brandies et al.

Children’s physical activity and sedentary time compared using assessments of accelerometry counts and muscle activity level
type: item
type: AcademicArticle
description: Background This research compared accelerometry (ACC)-derived and muscle electromyography (EMG)-based estimates of physical activity (PA) and sedentary time in typical PA tasks and during the daily lives of children. Methods Data was included from two exploratory studies. In Study I, 6–7-year-old children (n = 11, 64% girls) were assessed for eight PA tasks (walking, stair negotiation, climbing, crawling, swinging, balancing, trampoline jumping and a game of tag). In Study II, 7–9-year-old children (n = 14, 38% girls) were assessed for six PA tasks (walking, sitting, static squat, single leg hops, jump for height and standing long jump), and daily PA during one day with and one day without structured exercise. Quadriceps and hamstring muscle activity and inactivity using EMG shorts and acceleration by waist-mounted accelerometer were simultaneously measured and classified as sedentary, light, moderate and vigorous activity. Data from ACC was further analyzed using five different published cut-off points and varying time windows (1−60 s) for comparison with EMG. Results In the PA tasks ACC counts and EMG amplitude showed marked differences in swinging, trampoline jumping, crawling, static squat, single leg hops, standing long jump and jump for height, the difference being over 170% when signals were normalized to that during walking. Furthermore, in walking, swinging, trampoline jumping, stair negotiation and crawling ACC classified over 60% of the time as vigorous-intensity activity, while EMG indicated primarily light- and moderate-intensity activities. During both days with and without exercise, ACC resulted in greater proportion of light activity (p < 0.01) and smaller proportion of moderate activity compared to EMG (p < 0.05). The choice of cut-off points and epoch length in ACC analysis influenced the classification of PA level and sedentary time. In the analysis of daily activities the cut-off points by Evenson et al. (2008) with epochs of 7.5 s and 15 s yield…
format: application/pdf
format: text/html
creator: Ying Gao
creator: Martti Melin
creator: Karoliina Mäkäräinen
creator: Timo Rantalainen
creator: Arto J. Pesola
creator: Arto Laukkanen
creator: Arja Sääkslahti
creator: Taija Finni
subject: Kinesiology
subject: Public Health
description: doi:10.7717/peerj.5437
publisher: PeerJ Inc.
rights: © 2018 Gao et al.
abstract: Background This research compared accelerometry (ACC)-derived and muscle electromyography (EMG)-based estimates of physical activity (PA) and sedentary time in typical PA tasks and during the daily lives of children. Methods Data was included from two exploratory studies. In Study I, 6–7-year-old children (n = 11, 64% girls) were assessed for eight PA tasks (walking, stair negotiation, climbing, crawling, swinging, balancing, trampoline jumping and a game of tag). In Study II, 7–9-year-old children (n = 14, 38% girls) were assessed for six PA tasks (walking, sitting, static squat, single leg hops, jump for height and standing long jump), and daily PA during one day with and one day without structured exercise. Quadriceps and hamstring muscle activity and inactivity using EMG shorts and acceleration by waist-mounted accelerometer were simultaneously measured and classified as sedentary, light, moderate and vigorous activity. Data from ACC was further analyzed using five different published cut-off points and varying time windows (1−60 s) for comparison with EMG. Results In the PA tasks ACC counts and EMG amplitude showed marked differences in swinging, trampoline jumping, crawling, static squat, single leg hops, standing long jump and jump for height, the difference being over 170% when signals were normalized to that during walking. Furthermore, in walking, swinging, trampoline jumping, stair negotiation and crawling ACC classified over 60% of the time as vigorous-intensity activity, while EMG indicated primarily light- and moderate-intensity activities. During both days with and without exercise, ACC resulted in greater proportion of light activity (p < 0.01) and smaller proportion of moderate activity compared to EMG (p < 0.05). The choice of cut-off points and epoch length in ACC analysis influenced the classification of PA level and sedentary time. In the analysis of daily activities the cut-off points by Evenson et al. (2008) with epochs of 7.5 s and 15 s yield…
bibliographic citation: Gao et al. (2018) Children’s physical activity and sedentary time compared using assessments of accelerometry counts and muscle activity level. PeerJ 6:e5437 https://doi.org/10.7717/peerj.5437
date submitted: 2018-03-16
date accepted: 2018-07-24
issued: 2018-08-21
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Gao
  given name: Ying
author list: Agent
  family name: Melin
  given name: Martti
author list: Agent
  family name: Mäkäräinen
  given name: Karoliina
author list: Agent
  family name: Rantalainen
  given name: Timo
author list: Agent
  family name: Pesola
  given name: Arto J.
author list: Agent
  family name: Laukkanen
  given name: Arto
author list: Agent
  family name: Sääkslahti
  given name: Arja
author list: Agent
  family name: Finni
  given name: Taija
doi: 10.7717/peerj.5437
volume: 6
issn: 2167-8359
publication name: PeerJ
publication date: 2018-08-21
copyright: ©2018 Gao et al.
attribution name: Gao et al.

Comprehensive analysis of metastasis-related genes reveals a gene signature predicting the survival of colon cancer patients
type: item
type: AcademicArticle
description: Objective The mechanism underlying colon cancer metastasis remain unclear. This study aimed to elucidate the genes alteration during the metastasis of colon cancer and identify genes that crucial to the metastasis and survival of colon cancer patients. Methods The dataset of primary and metastasis tissue of colon cancer, and dataset of high and low metastasis capability of colon cancer cells were selected as training cohort, and the overlapped differentially expressed genes (DEGs) were screened from the training cohort. The functional enrichment analysis for the overlapped DEGs was performed. The prognostic value of overlapped DEGs were analyzed in The Cancer Genome Atlas dataset, and a gene signature was developed using genes that related to the overall survival (OS). The prognostic value of the gene signature was further confirmed in a validation cohort. Results A total of 184 overlapped DEGs were screened from the training cohort. Functional enrichment analysis revealed the significant gene functions and pathways of the overlapped DEGs. Four hub genes (3-oxoacid CoA-transferase 1, actinin alpha 4, interleukin 8, integrin subunit alpha 3) were identified using protein–protein network analysis. Six genes (aldehyde dehydrogenase 2, neural precursor cell expressed, developmentally down-regulated 9, filamin A, lamin B receptor, twinfilin actin binding protein 1, serine and arginine rich splicing factor 1) were closely related to the OS of colon cancer patients. A gene signature was developed using these six genes based on their risk score, and the validation cohort indicated that the prognostic value of this gene signature was high in the prediction of colon cancer patients. Conclusions Our study demonstrates a gene profiles related to the metastasis of colon cancer, and identify a six-gene signature that acts as an independent biomarker on the prognosis of colon cancer.
format: application/pdf
format: text/html
creator: Haotang Wei
creator: Jilin Li
creator: Minzhi Xie
creator: Ronger Lei
creator: Bangli Hu
subject: Gastroenterology and Hepatology
subject: Oncology
description: doi:10.7717/peerj.5433
publisher: PeerJ Inc.
rights: © 2018 Wei et al.
abstract: Objective The mechanism underlying colon cancer metastasis remain unclear. This study aimed to elucidate the genes alteration during the metastasis of colon cancer and identify genes that crucial to the metastasis and survival of colon cancer patients. Methods The dataset of primary and metastasis tissue of colon cancer, and dataset of high and low metastasis capability of colon cancer cells were selected as training cohort, and the overlapped differentially expressed genes (DEGs) were screened from the training cohort. The functional enrichment analysis for the overlapped DEGs was performed. The prognostic value of overlapped DEGs were analyzed in The Cancer Genome Atlas dataset, and a gene signature was developed using genes that related to the overall survival (OS). The prognostic value of the gene signature was further confirmed in a validation cohort. Results A total of 184 overlapped DEGs were screened from the training cohort. Functional enrichment analysis revealed the significant gene functions and pathways of the overlapped DEGs. Four hub genes (3-oxoacid CoA-transferase 1, actinin alpha 4, interleukin 8, integrin subunit alpha 3) were identified using protein–protein network analysis. Six genes (aldehyde dehydrogenase 2, neural precursor cell expressed, developmentally down-regulated 9, filamin A, lamin B receptor, twinfilin actin binding protein 1, serine and arginine rich splicing factor 1) were closely related to the OS of colon cancer patients. A gene signature was developed using these six genes based on their risk score, and the validation cohort indicated that the prognostic value of this gene signature was high in the prediction of colon cancer patients. Conclusions Our study demonstrates a gene profiles related to the metastasis of colon cancer, and identify a six-gene signature that acts as an independent biomarker on the prognosis of colon cancer.
bibliographic citation: Wei et al. (2018) Comprehensive analysis of metastasis-related genes reveals a gene signature predicting the survival of colon cancer patients. PeerJ 6:e5433 https://doi.org/10.7717/peerj.5433
date submitted: 2018-03-14
date accepted: 2018-07-10
issued: 2018-08-21
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Wei
  given name: Haotang
author list: Agent
  family name: Li
  given name: Jilin
author list: Agent
  family name: Xie
  given name: Minzhi
author list: Agent
  family name: Lei
  given name: Ronger
author list: Agent
  family name: Hu
  given name: Bangli
doi: 10.7717/peerj.5433
volume: 6
issn: 2167-8359
publication name: PeerJ
publication date: 2018-08-21
copyright: © 2018 Wei et al.
attribution name: Wei et al.

RNA-Seq analysis of differential gene expression in Betula luminifera xylem during the early stages of tension wood formation
type: item
type: AcademicArticle
description: Background Betula luminifera H. Winkler, which is widely distributed in southern China, is an economically important broadleaf tree species. However, little genomic information of B. luminifera is available, and little is known about the molecular mechanisms of wood formation in this species. Meanwhile, few efforts have focused on investigating the early transcriptional changes during tension wood formation in woody plants. Results A reference transcriptome dataset was first generated containing 45,700 Unigenes, and 35,135 (76.9%) Unigenes were annotated by a BLAST similarity search against four public databases. Then, based on an anatomical investigation, the global gene expression changes during the early stages of tension wood formation were analyzed. Gene expression profiling showed that a total of 13,273 Unigenes were differentially regulated during the early stages of tension wood formation. Most genes involved in cellulose and lignin biosynthesis were highlighted to reveal their biological importance in tension wood formation. In addition, the transcription levels of many genes involved in the auxin response pathway were significantly changed during the early stages of tension wood formation. Furthermore, 18 TFs co-expressed with key enzymes of cellulose synthesis were identified. Conclusions Our results revealed the transcriptional changes associated with TW formation and identified potential key genes in the regulation of this process. These results will help to dissect the molecular mechanism of wood formation and provide key candidate genes for marker-assisted selection in B. luminifera.
format: application/pdf
format: text/html
creator: Miaomiao Cai
creator: Huahong Huang
creator: Fei Ni
creator: Zaikang Tong
creator: Erpei Lin
creator: Muyuan Zhu
subject: Agricultural Science
subject: Bioinformatics
subject: Plant Science
description: doi:10.7717/peerj.5427
publisher: PeerJ Inc.
rights: © 2018 Cai et al.
abstract: Background Betula luminifera H. Winkler, which is widely distributed in southern China, is an economically important broadleaf tree species. However, little genomic information of B. luminifera is available, and little is known about the molecular mechanisms of wood formation in this species. Meanwhile, few efforts have focused on investigating the early transcriptional changes during tension wood formation in woody plants. Results A reference transcriptome dataset was first generated containing 45,700 Unigenes, and 35,135 (76.9%) Unigenes were annotated by a BLAST similarity search against four public databases. Then, based on an anatomical investigation, the global gene expression changes during the early stages of tension wood formation were analyzed. Gene expression profiling showed that a total of 13,273 Unigenes were differentially regulated during the early stages of tension wood formation. Most genes involved in cellulose and lignin biosynthesis were highlighted to reveal their biological importance in tension wood formation. In addition, the transcription levels of many genes involved in the auxin response pathway were significantly changed during the early stages of tension wood formation. Furthermore, 18 TFs co-expressed with key enzymes of cellulose synthesis were identified. Conclusions Our results revealed the transcriptional changes associated with TW formation and identified potential key genes in the regulation of this process. These results will help to dissect the molecular mechanism of wood formation and provide key candidate genes for marker-assisted selection in B. luminifera.
bibliographic citation: Cai et al. (2018) RNA-Seq analysis of differential gene expression in Betula luminifera xylem during the early stages of tension wood formation. PeerJ 6:e5427 https://doi.org/10.7717/peerj.5427
date submitted: 2018-02-08
date accepted: 2018-07-20
issued: 2018-08-21
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Cai
  given name: Miaomiao
author list: Agent
  family name: Huang
  given name: Huahong
author list: Agent
  family name: Ni
  given name: Fei
author list: Agent
  family name: Tong
  given name: Zaikang
author list: Agent
  family name: Lin
  given name: Erpei
author list: Agent
  family name: Zhu
  given name: Muyuan
doi: 10.7717/peerj.5427
volume: 6
issn: 2167-8359
publication name: PeerJ
publication date: 2018-08-21
copyright: ©2018 Cai et al.
attribution name: Cai et al.

Influence of hydrolysis rate of urea on ruminal bacterial diversity level and cellulolytic bacteria abundance in vitro
type: item
type: AcademicArticle
description: The objective of this experiment was to evaluate the effects of urea hydrolysis rate on ruminal bacterial diversity level and cellulolytic bacteria abundance in vitro. To control urea hydrolysis rate, urea and urease inhibitor (acetohydroxamic acid, AHA) were supplemented to a 2 × 2 factorial design, with urea supplemented at 0 or 20 g/kg dry matter (DM) of substrate, and AHA equivalent to 0 or 450 mg/kg DM of substrate. Ruminal fluid was collected from three Chinese Holstein dairy cows, fed a TMR, and incubated at 39 °C for 12 h after the addition of urea and AHA. Rumen fermentation parameters, which indicated the rate of ammonia formation (including ammonia-nitrogen (NH3-N) and urea-nitrogen concentrations, urease activity, and microbial crude protein) were measured by chemical analysis. Bacterial diversity was analyzed by denaturing gradient gel electrophoresis (DGGE). Total bacteria and cellulolytic bacteria abundance was detected by quantitative PCR. Results showed that AHA addition significantly decreased the rate of ammonia formation when urea was supplemented. Urea and AHA supplementation significantly increased the bacterial community diversity level according to the Shannon–Weiner index of 16S DGGE images. Furthermore, ruminal bacterial profiles were separated by ammonia release rate when urea was supplemented, according to the DGGE and hierarchical cluster analysis. Urea supplementation reduced the abundance of cellulolytic bacteria, such as Ruminococcus albus, R. flavefaciens, Fibrobacter succinogenes, and Butyrivibrio fibrosolvens, but inhibition of urea hydrolysis by AHA addition alleviated the reductions during the early period of incubation. In conclusion, slow release of ammonia induced by urease inhibitor influenced the ruminal bacterial diversity level and lessened the inhibition of total bacteria growth at the incubation of 12 h and F. succinogenes during the early period of incubation.
format: application/pdf
format: text/html
creator: Pengpeng Wang
creator: Shengguo Zhao
creator: Xuemei Nan
creator: Di Jin
creator: Jiaqi Wang
subject: Agricultural Science
subject: Biotechnology
subject: Microbiology
subject: Molecular Biology
description: doi:10.7717/peerj.5475
publisher: PeerJ Inc.
rights: © 2018 Wang et al.
abstract: The objective of this experiment was to evaluate the effects of urea hydrolysis rate on ruminal bacterial diversity level and cellulolytic bacteria abundance in vitro. To control urea hydrolysis rate, urea and urease inhibitor (acetohydroxamic acid, AHA) were supplemented to a 2 × 2 factorial design, with urea supplemented at 0 or 20 g/kg dry matter (DM) of substrate, and AHA equivalent to 0 or 450 mg/kg DM of substrate. Ruminal fluid was collected from three Chinese Holstein dairy cows, fed a TMR, and incubated at 39 °C for 12 h after the addition of urea and AHA. Rumen fermentation parameters, which indicated the rate of ammonia formation (including ammonia-nitrogen (NH3-N) and urea-nitrogen concentrations, urease activity, and microbial crude protein) were measured by chemical analysis. Bacterial diversity was analyzed by denaturing gradient gel electrophoresis (DGGE). Total bacteria and cellulolytic bacteria abundance was detected by quantitative PCR. Results showed that AHA addition significantly decreased the rate of ammonia formation when urea was supplemented. Urea and AHA supplementation significantly increased the bacterial community diversity level according to the Shannon–Weiner index of 16S DGGE images. Furthermore, ruminal bacterial profiles were separated by ammonia release rate when urea was supplemented, according to the DGGE and hierarchical cluster analysis. Urea supplementation reduced the abundance of cellulolytic bacteria, such as Ruminococcus albus, R. flavefaciens, Fibrobacter succinogenes, and Butyrivibrio fibrosolvens, but inhibition of urea hydrolysis by AHA addition alleviated the reductions during the early period of incubation. In conclusion, slow release of ammonia induced by urease inhibitor influenced the ruminal bacterial diversity level and lessened the inhibition of total bacteria growth at the incubation of 12 h and F. succinogenes during the early period of incubation.
bibliographic citation: Wang et al. (2018) Influence of hydrolysis rate of urea on ruminal bacterial diversity level and cellulolytic bacteria abundance in vitro. PeerJ 6:e5475 https://doi.org/10.7717/peerj.5475
date submitted: 2017-12-19
date accepted: 2018-07-27
issued: 2018-08-17
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Wang
  given name: Pengpeng
author list: Agent
  family name: Zhao
  given name: Shengguo
author list: Agent
  family name: Nan
  given name: Xuemei
author list: Agent
  family name: Jin
  given name: Di
author list: Agent
  family name: Wang
  given name: Jiaqi
doi: 10.7717/peerj.5475
volume: 6
issn: 2167-8359
publication name: PeerJ
publication date: 2018-08-17
copyright: © 2018 Wang et al.
attribution name: Wang et al.

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