PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
items: The contribution of Nintendo Wii Fit series in the field of health: a systematic review and meta-analysis
items: Urbanization alters communities of flying arthropods in parks and gardens of a medium-sized city
items: How long should the fully hillside-closed forest protection be implemented on the Loess Plateau, Shaanxi, China?
items: Preferences for achromatic horizontal, vertical, and square patterns in zebrafish (Danio rerio)
items: Stress responses to conspecific visual cues of predation risk in zebrafish
items: Minimum infusion rate and adrenocortical function after continuous infusion of the novel etomidate analog ET-26-HCl in rats
items: Trophic analysis of the fish community in the Ciénega Churince, Cuatro Ciénegas, Coahuila
items: Prediction of endoplasmic reticulum resident proteins using fragmented amino acid composition and support vector machine
items: Onset of human preterm and term birth is related to unique inflammatory transcriptome profiles at the maternal fetal interface
items: Measuring coral calcification under ocean acidification: methodological considerations for the 45Ca-uptake and total alkalinity anomaly technique

The contribution of Nintendo Wii Fit series in the field of health: a systematic review and meta-analysis
type: item
type: AcademicArticle
description: Background Wii Fit was originally designed as a health and fitness interactive training experience for the general public. There are, however, many examples of Wii Fit being utilized in clinical settings. This article aims to identify the contribution of Wii Fit in the field of health promotion and rehabilitation by: (1) identifying the health-related domains for which the Wii Fit series has been tested, (2) clarifying the effect of Wii Fit in those identified health-related domains and (3) quantifying this effect. Method A systematic literature review was undertaken. The MEDLINE database and Games for Health Journal published content were explored using the search term “Wii-Fit.” Occurrences resulting from manual searches on Google and material suggested by experts in the field were also considered. Included articles were required to have measurements from Wii Fit activities for at least one relevant health indicator. The effect of Wii Fit interventions was assessed using meta-analyses for the following outcomes: activity-specific balance confidence score, Berg balance score (BBC) and time-up-and-go test (TUG). Findings A total of 115 articles highlighted that the Wii Fit has been tested in numerous healthy and pathological populations. Out of these, only a few intervention studies have focused on the prevention of chronic diseases. A large proportion of the studies focus on balance training (N = 55). This systematic review highlights several potential benefits of Wii Fit interventions and these positive observations are supported by meta-analyses data (N = 25). For example, the BBC and the TUG respond to a similar extend to Wii Fit interventions compared with traditional training. Conclusion Wii Fit has the potential to be used as a rehabilitation tool in different clinical situations. However, the current literature includes relatively few randomized controlled trials in each population. Further research is therefore required.
format: application/pdf
format: text/html
creator: Julien Tripette
creator: Haruka Murakami
creator: Katie Rose Ryan
creator: Yuji Ohta
creator: Motohiko Miyachi
subject: Drugs and Devices
subject: Geriatrics
subject: Kinesiology
description: doi:10.7717/peerj.3600
publisher: PeerJ Inc.
rights: © 2017 Tripette et al.
abstract: Background Wii Fit was originally designed as a health and fitness interactive training experience for the general public. There are, however, many examples of Wii Fit being utilized in clinical settings. This article aims to identify the contribution of Wii Fit in the field of health promotion and rehabilitation by: (1) identifying the health-related domains for which the Wii Fit series has been tested, (2) clarifying the effect of Wii Fit in those identified health-related domains and (3) quantifying this effect. Method A systematic literature review was undertaken. The MEDLINE database and Games for Health Journal published content were explored using the search term “Wii-Fit.” Occurrences resulting from manual searches on Google and material suggested by experts in the field were also considered. Included articles were required to have measurements from Wii Fit activities for at least one relevant health indicator. The effect of Wii Fit interventions was assessed using meta-analyses for the following outcomes: activity-specific balance confidence score, Berg balance score (BBC) and time-up-and-go test (TUG). Findings A total of 115 articles highlighted that the Wii Fit has been tested in numerous healthy and pathological populations. Out of these, only a few intervention studies have focused on the prevention of chronic diseases. A large proportion of the studies focus on balance training (N = 55). This systematic review highlights several potential benefits of Wii Fit interventions and these positive observations are supported by meta-analyses data (N = 25). For example, the BBC and the TUG respond to a similar extend to Wii Fit interventions compared with traditional training. Conclusion Wii Fit has the potential to be used as a rehabilitation tool in different clinical situations. However, the current literature includes relatively few randomized controlled trials in each population. Further research is therefore required.
bibliographic citation: Tripette et al. (2017) The contribution of Nintendo Wii Fit series in the field of health: a systematic review and meta-analysis. PeerJ 5:e3600 https://doi.org/10.7717/peerj.3600
date submitted: 2017-04-04
date accepted: 2017-06-29
issued: 2017-09-05
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Tripette
  given name: Julien
author list: Agent
  family name: Murakami
  given name: Haruka
author list: Agent
  family name: Ryan
  given name: Katie Rose
author list: Agent
  family name: Ohta
  given name: Yuji
author list: Agent
  family name: Miyachi
  given name: Motohiko
doi: 10.7717/peerj.3600
volume: 5
issn: 2167-8359
publication name: PeerJ
publication date: 2017-09-05
copyright: © 2017 Tripette et al.
attribution name: Tripette et al.

Urbanization alters communities of flying arthropods in parks and gardens of a medium-sized city
type: item
type: AcademicArticle
description: Urbanization transforms undeveloped landscapes into built environments, causing changes in communities and ecological processes. Flying arthropods play important roles in these processes as pollinators, decomposers, and predators, and can be important in structuring food webs. The goal of this study was to identify associations between urbanization and the composition of communities of flying (and floating) arthropods within gardens and parks in a medium-sized mesic city. We predicted that flying arthropod abundance and diversity would respond strongly to percent impervious surface and distance to city center, measurements of urbanization. Flying arthropods were sampled from 30 gardens and parks along an urbanization gradient in Toledo, Ohio, during July and August 2016, using elevated pan traps. A variety of potential predictor variables were also recorded at each site. We collected a total of 2,369 individuals representing nine orders. We found that flying arthropod community composition was associated with percent impervious surface and canopy cover. Overall flying arthropod abundance was negatively associated with percent impervious surface and positively associated with distance to city center. Hymenoptera (bees, wasps, ants), Lepidoptera (moths, butterflies), and Araneae (spiders) were positively associated with distance to city center. Hemiptera (true bugs), Diptera (flies), and Araneae were negatively associated with percent impervious surface. Both distance to city center and percent impervious surface are metrics of urbanization, and this study shows how these factors influence flying arthropod communities in urban gardens and city parks, including significant reductions in taxa that contain pollinators and predators important to urban agriculture and forestry. A variety of environmental factors also showed significant associations with responses (e.g. canopy cover and soil moisture), suggesting these factors may underlie or modulate the urbanization effec…
format: application/pdf
format: text/html
creator: Edward Lagucki
creator: Justin D. Burdine
creator: Kevin E. McCluney
subject: Biodiversity
subject: Ecology
subject: Entomology
subject: Biosphere Interactions
subject: Natural Resource Management
description: doi:10.7717/peerj.3620
publisher: PeerJ Inc.
rights: © 2017 Lagucki et al.
abstract: Urbanization transforms undeveloped landscapes into built environments, causing changes in communities and ecological processes. Flying arthropods play important roles in these processes as pollinators, decomposers, and predators, and can be important in structuring food webs. The goal of this study was to identify associations between urbanization and the composition of communities of flying (and floating) arthropods within gardens and parks in a medium-sized mesic city. We predicted that flying arthropod abundance and diversity would respond strongly to percent impervious surface and distance to city center, measurements of urbanization. Flying arthropods were sampled from 30 gardens and parks along an urbanization gradient in Toledo, Ohio, during July and August 2016, using elevated pan traps. A variety of potential predictor variables were also recorded at each site. We collected a total of 2,369 individuals representing nine orders. We found that flying arthropod community composition was associated with percent impervious surface and canopy cover. Overall flying arthropod abundance was negatively associated with percent impervious surface and positively associated with distance to city center. Hymenoptera (bees, wasps, ants), Lepidoptera (moths, butterflies), and Araneae (spiders) were positively associated with distance to city center. Hemiptera (true bugs), Diptera (flies), and Araneae were negatively associated with percent impervious surface. Both distance to city center and percent impervious surface are metrics of urbanization, and this study shows how these factors influence flying arthropod communities in urban gardens and city parks, including significant reductions in taxa that contain pollinators and predators important to urban agriculture and forestry. A variety of environmental factors also showed significant associations with responses (e.g. canopy cover and soil moisture), suggesting these factors may underlie or modulate the urbanization effec…
bibliographic citation: Lagucki et al. (2017) Urbanization alters communities of flying arthropods in parks and gardens of a medium-sized city. PeerJ 5:e3620 https://doi.org/10.7717/peerj.3620
date submitted: 2017-03-28
date accepted: 2017-07-07
issued: 2017-09-04
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Lagucki
  given name: Edward
author list: Agent
  family name: Burdine
  given name: Justin D.
author list: Agent
  family name: McCluney
  given name: Kevin E.
doi: 10.7717/peerj.3620
volume: 5
issn: 2167-8359
publication name: PeerJ
publication date: 2017-09-04
copyright: © 2017 Lagucki et al.
attribution name: Lagucki et al.

How long should the fully hillside-closed forest protection be implemented on the Loess Plateau, Shaanxi, China?
type: item
type: AcademicArticle
description: Background Restoration of degraded forest ecosystem is crucial for regional sustainable development. To protect the country’s fragile and fragmented environment, the Chinese government initiated an ecological engineering project, the Natural Forest Protection Program, in seventeen provinces in China beginning in 1998. Fully hillside-closed forest protection (vegetation restoration naturally without any artificial disturbance) was one of vital measures of the Natural Forest Protection Program applied nation wide. Whether plant diversity, biomass and age structure of dominant tree species and soil nutrients in protected stands may become better with increase of protected period are still open problems. Methods We investigated community diversity, biomass of dominant tree species, age structures, and analyzed soil chemical properties of a Pinus tabulaeformis population at protected sites representing different protected ages at Huanglongshan Forest Bureau on the Loess Plateau, Shaanxi, China. Results Plant species richness of Pinus tabulaeformis community was significantly affected (p < 0.05) by forest protection and the effect attenuated with protection age. Shannon evenness index of plant species generally increased with protection age. Stands protected for 45 years had the highest tree biomass and considerable natural regeneration capacity. Contents of organic carbon, available phosphorus and available potassium in top soil increased in protected stands less than 45 years, however decreased significantly thereafter. Long-term forest protection also decreased the content of mineral nitrogen in top soil. Discussion We found that the richness of shrubs and herbs was significantly affected by forest protection, and evenness indices of tree, shrub and herb increased inconsistently with protected ages. Forest protection created more complex age structures and tree densities with increasing age of protection. Content of soil mineral nitrogen at 0–20 cm soil depth showed a …
format: application/pdf
format: text/html
creator: Lin Hou
creator: Sijia Hou
subject: Biodiversity
subject: Conservation Biology
subject: Ecology
subject: Plant Science
subject: Soil Science
description: doi:10.7717/peerj.3764
publisher: PeerJ Inc.
rights: © 2017 Hou and Hou
abstract: Background Restoration of degraded forest ecosystem is crucial for regional sustainable development. To protect the country’s fragile and fragmented environment, the Chinese government initiated an ecological engineering project, the Natural Forest Protection Program, in seventeen provinces in China beginning in 1998. Fully hillside-closed forest protection (vegetation restoration naturally without any artificial disturbance) was one of vital measures of the Natural Forest Protection Program applied nation wide. Whether plant diversity, biomass and age structure of dominant tree species and soil nutrients in protected stands may become better with increase of protected period are still open problems. Methods We investigated community diversity, biomass of dominant tree species, age structures, and analyzed soil chemical properties of a Pinus tabulaeformis population at protected sites representing different protected ages at Huanglongshan Forest Bureau on the Loess Plateau, Shaanxi, China. Results Plant species richness of Pinus tabulaeformis community was significantly affected (p < 0.05) by forest protection and the effect attenuated with protection age. Shannon evenness index of plant species generally increased with protection age. Stands protected for 45 years had the highest tree biomass and considerable natural regeneration capacity. Contents of organic carbon, available phosphorus and available potassium in top soil increased in protected stands less than 45 years, however decreased significantly thereafter. Long-term forest protection also decreased the content of mineral nitrogen in top soil. Discussion We found that the richness of shrubs and herbs was significantly affected by forest protection, and evenness indices of tree, shrub and herb increased inconsistently with protected ages. Forest protection created more complex age structures and tree densities with increasing age of protection. Content of soil mineral nitrogen at 0–20 cm soil depth showed a …
bibliographic citation: Hou et al. (2017) How long should the fully hillside-closed forest protection be implemented on the Loess Plateau, Shaanxi, China?. PeerJ 5:e3764 https://doi.org/10.7717/peerj.3764
date submitted: 2017-03-04
date accepted: 2017-08-15
issued: 2017-09-04
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Hou
  given name: Lin
author list: Agent
  family name: Hou
  given name: Sijia
doi: 10.7717/peerj.3764
volume: 5
issn: 2167-8359
publication name: PeerJ
publication date: 2017-09-04
copyright: ©2017 Hou and Hou
attribution name: Hou and Hou

Preferences for achromatic horizontal, vertical, and square patterns in zebrafish (Danio rerio)
type: item
type: AcademicArticle
description: The zebrafish (Danio rerio) is gaining popularity as a laboratory organism and is used to model many human diseases. Many behavioural measures of locomotion and cognition have been developed that involve the processing of visual stimuli. However, the innate preference for vertical and horizontal stripes in zebrafish is unknown. We tested the preference of adult zebrafish for three achromatic patterns (vertical stripes, horizontal stripes, and squares) at three different size conditions (1, 5, and 10 mm). Each animal was tested once in a rectangular arena, which had a different pattern of the same size condition on the walls of either half of the arena. We show that zebrafish have differential preferences for patterned stimuli at each of the three size conditions. These results suggest that zebrafish have naïve preferences that should be carefully considered when testing zebrafish in paradigms using visual stimuli.
format: application/pdf
format: text/html
creator: Lisa A. Rimstad
creator: Adam Holcombe
creator: Alicia Pope
creator: Trevor J. Hamilton
creator: Melike P. Schalomon
subject: Animal Behavior
subject: Aquaculture, Fisheries and Fish Science
subject: Neuroscience
description: doi:10.7717/peerj.3748
publisher: PeerJ Inc.
rights: © 2017 Rimstad et al.
abstract: The zebrafish (Danio rerio) is gaining popularity as a laboratory organism and is used to model many human diseases. Many behavioural measures of locomotion and cognition have been developed that involve the processing of visual stimuli. However, the innate preference for vertical and horizontal stripes in zebrafish is unknown. We tested the preference of adult zebrafish for three achromatic patterns (vertical stripes, horizontal stripes, and squares) at three different size conditions (1, 5, and 10 mm). Each animal was tested once in a rectangular arena, which had a different pattern of the same size condition on the walls of either half of the arena. We show that zebrafish have differential preferences for patterned stimuli at each of the three size conditions. These results suggest that zebrafish have naïve preferences that should be carefully considered when testing zebrafish in paradigms using visual stimuli.
bibliographic citation: Rimstad et al. (2017) Preferences for achromatic horizontal, vertical, and square patterns in zebrafish (Danio rerio). PeerJ 5:e3748 https://doi.org/10.7717/peerj.3748
date submitted: 2017-05-19
date accepted: 2017-08-08
issued: 2017-09-04
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Rimstad
  given name: Lisa A.
author list: Agent
  family name: Holcombe
  given name: Adam
author list: Agent
  family name: Pope
  given name: Alicia
author list: Agent
  family name: Hamilton
  given name: Trevor J.
author list: Agent
  family name: Schalomon
  given name: Melike P.
doi: 10.7717/peerj.3748
volume: 5
issn: 2167-8359
publication name: PeerJ
publication date: 2017-09-04
copyright: ©2017 Rimstad et al.
attribution name: Rimstad et al.

Stress responses to conspecific visual cues of predation risk in zebrafish
type: item
type: AcademicArticle
description: Chemical communication relating to predation risk is a trait common among fish species. Prey fish under threat of predation can signal risk to conspecific fish, which then exhibit defensive responses. Fish also assess predation risk by visual cues and change their behavior accordingly. Here, we explored whether these behavioral changes act as visual alarm signals to conspecific fish that are not initially under risk. We show that shoals of zebrafish (Danio rerio) visually exposed to a predator display antipredator behaviors. In addition, these defensive maneuvers trigger antipredator reactions in conspecifics and, concomitantly, stimulate the hypothalamus-pituitary-interrenal axis, leading to cortisol increase. Thus, we conclude that zebrafish defensive behaviors act as visual alarm cues that induce antipredator and stress response in conspecific fish.
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format: text/html
creator: Thiago Acosta Oliveira
creator: Renan Idalencio
creator: Fabiana Kalichak
creator: João Gabriel dos Santos Rosa
creator: Gessi Koakoski
creator: Murilo Sander de Abreu
creator: Ana Cristina Varrone Giacomini
creator: Darlan Gusso
creator: Denis Brook Rosemberg
creator: Rodrigo Egydio Barreto
creator: Leonardo José Gil Barcellos
subject: Animal Behavior
subject: Ecology
subject: Zoology
description: doi:10.7717/peerj.3739
publisher: PeerJ Inc.
rights: © 2017 Oliveira et al.
abstract: Chemical communication relating to predation risk is a trait common among fish species. Prey fish under threat of predation can signal risk to conspecific fish, which then exhibit defensive responses. Fish also assess predation risk by visual cues and change their behavior accordingly. Here, we explored whether these behavioral changes act as visual alarm signals to conspecific fish that are not initially under risk. We show that shoals of zebrafish (Danio rerio) visually exposed to a predator display antipredator behaviors. In addition, these defensive maneuvers trigger antipredator reactions in conspecifics and, concomitantly, stimulate the hypothalamus-pituitary-interrenal axis, leading to cortisol increase. Thus, we conclude that zebrafish defensive behaviors act as visual alarm cues that induce antipredator and stress response in conspecific fish.
bibliographic citation: Oliveira et al. (2017) Stress responses to conspecific visual cues of predation risk in zebrafish. PeerJ 5:e3739 https://doi.org/10.7717/peerj.3739
date submitted: 2017-03-29
date accepted: 2017-08-04
issued: 2017-09-04
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Oliveira
  given name: Thiago Acosta
author list: Agent
  family name: Idalencio
  given name: Renan
author list: Agent
  family name: Kalichak
  given name: Fabiana
author list: Agent
  family name: dos Santos Rosa
  given name: João Gabriel
author list: Agent
  family name: Koakoski
  given name: Gessi
author list: Agent
  family name: de Abreu
  given name: Murilo Sander
author list: Agent
  family name: Giacomini
  given name: Ana Cristina Varrone
author list: Agent
  family name: Gusso
  given name: Darlan
author list: Agent
  family name: Rosemberg
  given name: Denis Brook
author list: Agent
  family name: Barreto
  given name: Rodrigo Egydio
author list: Agent
  family name: Barcellos
  given name: Leonardo José Gil
doi: 10.7717/peerj.3739
volume: 5
issn: 2167-8359
publication name: PeerJ
publication date: 2017-09-04
copyright: ©2017 Oliveira et al.
attribution name: Oliveira et al.

Minimum infusion rate and adrenocortical function after continuous infusion of the novel etomidate analog ET-26-HCl in rats
type: item
type: AcademicArticle
description: Background Because etomidate induces prolonged adrenal suppression, even following a single bolus, its use as an infused anesthetic is limited. Our previous study indicated that a single administration of the novel etomidate analog methoxyethyletomidate hydrochloride (ET-26-HCl) shows little suppression of adrenocortical function. The aims of the present study were to (1) determine the minimum infusion rate of ET-26-HCl and compare it with those for etomidate and cyclopropyl-methoxycarbonylmetomidate (CPMM), a rapidly metabolized etomidate analog that is currently in clinical trials and (2) to evaluate adrenocortical function after a continuous infusion of ET-26-HCl as part of a broader study investigating whether this etomidate analog is suitable for long infusion in the maintenance of anesthesia. Method The up-and-down method was used to determine the minimum infusion rates for ET-26-HCl, etomidate and CPMM. Sprague-Dawley rats (n = 32) were then randomly divided into four groups: etomidate, ET-26-HCl, CPMM, and vehicle control. Rats in each group were infused for 60 min with one of the drugs at its predetermined minimum infusion rate. Blood samples were drawn initially and then every 30 min after drug infusion to determine the adrenocorticotropic hormone-stimulated concentration of serum corticosterone as a measure of adrenocortical function. Results The minimum infusion rates for etomidate, ET-26-HCl and CPMM were 0.29, 0.62, and 0.95 mg/kg/min, respectively. Compared with controls, etomidate decreased serum corticosterone, as expected, whereas serum corticosterone concentrations following infusion with the etomidate analogs ET-26-HCl or CPMM were not significantly different from those in the control group. Conclusion The corticosterone concentrations tended to be reduced for the first hour following ET-26-HCl infusion (as compared to vehicle infusion); however, this reduction did not reach statistical significance. Thus, further studies are warranted examining …
format: application/pdf
format: text/html
creator: Junli Jiang
creator: Bin Wang
creator: Zhaoqiong Zhu
creator: Jun Yang
creator: Jin Liu
creator: Wensheng Zhang
subject: Anesthesiology and Pain Management
subject: Animal Behavior
subject: Neuroscience
subject: Veterinary Medicine
description: doi:10.7717/peerj.3693
publisher: PeerJ Inc.
rights: © 2017 Jiang et al.
abstract: Background Because etomidate induces prolonged adrenal suppression, even following a single bolus, its use as an infused anesthetic is limited. Our previous study indicated that a single administration of the novel etomidate analog methoxyethyletomidate hydrochloride (ET-26-HCl) shows little suppression of adrenocortical function. The aims of the present study were to (1) determine the minimum infusion rate of ET-26-HCl and compare it with those for etomidate and cyclopropyl-methoxycarbonylmetomidate (CPMM), a rapidly metabolized etomidate analog that is currently in clinical trials and (2) to evaluate adrenocortical function after a continuous infusion of ET-26-HCl as part of a broader study investigating whether this etomidate analog is suitable for long infusion in the maintenance of anesthesia. Method The up-and-down method was used to determine the minimum infusion rates for ET-26-HCl, etomidate and CPMM. Sprague-Dawley rats (n = 32) were then randomly divided into four groups: etomidate, ET-26-HCl, CPMM, and vehicle control. Rats in each group were infused for 60 min with one of the drugs at its predetermined minimum infusion rate. Blood samples were drawn initially and then every 30 min after drug infusion to determine the adrenocorticotropic hormone-stimulated concentration of serum corticosterone as a measure of adrenocortical function. Results The minimum infusion rates for etomidate, ET-26-HCl and CPMM were 0.29, 0.62, and 0.95 mg/kg/min, respectively. Compared with controls, etomidate decreased serum corticosterone, as expected, whereas serum corticosterone concentrations following infusion with the etomidate analogs ET-26-HCl or CPMM were not significantly different from those in the control group. Conclusion The corticosterone concentrations tended to be reduced for the first hour following ET-26-HCl infusion (as compared to vehicle infusion); however, this reduction did not reach statistical significance. Thus, further studies are warranted examining …
bibliographic citation: Jiang et al. (2017) Minimum infusion rate and adrenocortical function after continuous infusion of the novel etomidate analog ET-26-HCl in rats. PeerJ 5:e3693 https://doi.org/10.7717/peerj.3693
date submitted: 2017-05-25
date accepted: 2017-07-25
issued: 2017-09-04
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Jiang
  given name: Junli
author list: Agent
  family name: Wang
  given name: Bin
author list: Agent
  family name: Zhu
  given name: Zhaoqiong
author list: Agent
  family name: Yang
  given name: Jun
author list: Agent
  family name: Liu
  given name: Jin
author list: Agent
  family name: Zhang
  given name: Wensheng
doi: 10.7717/peerj.3693
volume: 5
issn: 2167-8359
publication name: PeerJ
publication date: 2017-09-04
copyright: ©2017 Jiang et al.
attribution name: Jiang et al.

Trophic analysis of the fish community in the Ciénega Churince, Cuatro Ciénegas, Coahuila
type: item
type: AcademicArticle
description: Fish diets were analyzed to evaluate the dynamic trophs of the fish community in the Churince wetland system of the Cuatro Ciénegas, where the fauna consists of nine species: endemic, native and introduced. In nine sampling events (between February 2011 and May 2014) 556 specimens of all nine species were collected. Stomach contents were analyzed and the Relative Importance Index (IRI) was calculated. The feed coefficient (Q) of the diets and the accumulated trophic diversity (Hk), as well as the amplitude of the trophic niche were evaluated. Feeding strategies in the fish community were found to be eurifagic. The main foods in general were insects, crustaceans, gastropods, plants and teleosts. According to the average linkage method, four functional trophic groups were defined, with no higher consumption species; nevertheless all were regulators, mainly invertebrates. Therefore, the chain reaction in food control was higher from top to bottom, meaning a downwards dietary control.
format: application/pdf
format: text/html
creator: Ariana Hernández
creator: Hector S. Espinosa-Pérez
creator: Valeria Souza
subject: Aquaculture, Fisheries and Fish Science
subject: Biodiversity
subject: Ecology
subject: Zoology
description: doi:10.7717/peerj.3637
publisher: PeerJ Inc.
rights: © 2017 Hernández et al.
abstract: Fish diets were analyzed to evaluate the dynamic trophs of the fish community in the Churince wetland system of the Cuatro Ciénegas, where the fauna consists of nine species: endemic, native and introduced. In nine sampling events (between February 2011 and May 2014) 556 specimens of all nine species were collected. Stomach contents were analyzed and the Relative Importance Index (IRI) was calculated. The feed coefficient (Q) of the diets and the accumulated trophic diversity (Hk), as well as the amplitude of the trophic niche were evaluated. Feeding strategies in the fish community were found to be eurifagic. The main foods in general were insects, crustaceans, gastropods, plants and teleosts. According to the average linkage method, four functional trophic groups were defined, with no higher consumption species; nevertheless all were regulators, mainly invertebrates. Therefore, the chain reaction in food control was higher from top to bottom, meaning a downwards dietary control.
bibliographic citation: Hernández et al. (2017) Trophic analysis of the fish community in the Ciénega Churince, Cuatro Ciénegas, Coahuila. PeerJ 5:e3637 https://doi.org/10.7717/peerj.3637
date submitted: 2016-08-08
date accepted: 2017-07-12
issued: 2017-09-04
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Hernández
  given name: Ariana
author list: Agent
  family name: Espinosa-Pérez
  given name: Hector S.
author list: Agent
  family name: Souza
  given name: Valeria
doi: 10.7717/peerj.3637
volume: 5
issn: 2167-8359
publication name: PeerJ
publication date: 2017-09-04
copyright: ©2017 Hernández et al.
attribution name: Hernández et al.

Prediction of endoplasmic reticulum resident proteins using fragmented amino acid composition and support vector machine
type: item
type: AcademicArticle
description: Background The endoplasmic reticulum plays an important role in many cellular processes, which includes protein synthesis, folding and post-translational processing of newly synthesized proteins. It is also the site for quality control of misfolded proteins and entry point of extracellular proteins to the secretory pathway. Hence at any given point of time, endoplasmic reticulum contains two different cohorts of proteins, (i) proteins involved in endoplasmic reticulum-specific function, which reside in the lumen of the endoplasmic reticulum, called as endoplasmic reticulum resident proteins and (ii) proteins which are in process of moving to the extracellular space. Thus, endoplasmic reticulum resident proteins must somehow be distinguished from newly synthesized secretory proteins, which pass through the endoplasmic reticulum on their way out of the cell. Approximately only 50% of the proteins used in this study as training data had endoplasmic reticulum retention signal, which shows that these signals are not essentially present in all endoplasmic reticulum resident proteins. This also strongly indicates the role of additional factors in retention of endoplasmic reticulum-specific proteins inside the endoplasmic reticulum. Methods This is a support vector machine based method, where we had used different forms of protein features as inputs for support vector machine to develop the prediction models. During training leave-one-out approach of cross-validation was used. Maximum performance was obtained with a combination of amino acid compositions of different part of proteins. Results In this study, we have reported a novel support vector machine based method for predicting endoplasmic reticulum resident proteins, named as ERPred. During training we achieved a maximum accuracy of 81.42% with leave-one-out approach of cross-validation. When evaluated on independent dataset, ERPred did prediction with sensitivity of 72.31% and specificity of 83.69%. We have also annot…
format: application/pdf
format: text/html
creator: Ravindra Kumar
creator: Bandana Kumari
creator: Manish Kumar
subject: Bioinformatics
subject: Computational Biology
description: doi:10.7717/peerj.3561
publisher: PeerJ Inc.
rights: © 2017 Kumar et al.
abstract: Background The endoplasmic reticulum plays an important role in many cellular processes, which includes protein synthesis, folding and post-translational processing of newly synthesized proteins. It is also the site for quality control of misfolded proteins and entry point of extracellular proteins to the secretory pathway. Hence at any given point of time, endoplasmic reticulum contains two different cohorts of proteins, (i) proteins involved in endoplasmic reticulum-specific function, which reside in the lumen of the endoplasmic reticulum, called as endoplasmic reticulum resident proteins and (ii) proteins which are in process of moving to the extracellular space. Thus, endoplasmic reticulum resident proteins must somehow be distinguished from newly synthesized secretory proteins, which pass through the endoplasmic reticulum on their way out of the cell. Approximately only 50% of the proteins used in this study as training data had endoplasmic reticulum retention signal, which shows that these signals are not essentially present in all endoplasmic reticulum resident proteins. This also strongly indicates the role of additional factors in retention of endoplasmic reticulum-specific proteins inside the endoplasmic reticulum. Methods This is a support vector machine based method, where we had used different forms of protein features as inputs for support vector machine to develop the prediction models. During training leave-one-out approach of cross-validation was used. Maximum performance was obtained with a combination of amino acid compositions of different part of proteins. Results In this study, we have reported a novel support vector machine based method for predicting endoplasmic reticulum resident proteins, named as ERPred. During training we achieved a maximum accuracy of 81.42% with leave-one-out approach of cross-validation. When evaluated on independent dataset, ERPred did prediction with sensitivity of 72.31% and specificity of 83.69%. We have also annot…
bibliographic citation: Kumar et al. (2017) Prediction of endoplasmic reticulum resident proteins using fragmented amino acid composition and support vector machine. PeerJ 5:e3561 https://doi.org/10.7717/peerj.3561
date submitted: 2017-04-25
date accepted: 2017-06-20
issued: 2017-09-04
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Kumar
  given name: Ravindra
author list: Agent
  family name: Kumari
  given name: Bandana
author list: Agent
  family name: Kumar
  given name: Manish
doi: 10.7717/peerj.3561
volume: 5
issn: 2167-8359
publication name: PeerJ
publication date: 2017-09-04
copyright: ©2017 Kumar et al.
attribution name: Kumar et al.

Onset of human preterm and term birth is related to unique inflammatory transcriptome profiles at the maternal fetal interface
type: item
type: AcademicArticle
description: Background Preterm birth is a main determinant of neonatal mortality and morbidity and a major contributor to the overall mortality and burden of disease. However, research of the preterm birth is hindered by the imprecise definition of the clinical phenotype and complexity of the molecular phenotype due to multiple pregnancy tissue types and molecular processes that may contribute to the preterm birth. Here we comprehensively evaluate the mRNA transcriptome that characterizes preterm and term labor in tissues comprising the pregnancy using precisely phenotyped samples. The four complementary phenotypes together provide comprehensive insight into preterm and term parturition. Methods Samples of maternal blood, chorion, amnion, placenta, decidua, fetal blood, and myometrium from the uterine fundus and lower segment (n = 183) were obtained during cesarean delivery from women with four complementary phenotypes: delivering preterm with (PL) and without labor (PNL), term with (TL) and without labor (TNL). Enrolled were 35 pregnant women with four precisely and prospectively defined phenotypes: PL (n = 8), PNL (n = 10), TL (n = 7) and TNL (n = 10). Gene expression data were analyzed using shrunken centroid analysis to identify a minimal set of genes that uniquely characterizes each of the four phenotypes. Expression profiles of 73 genes and non-coding RNA sequences uniquely identified each of the four phenotypes. The shrunken centroid analysis and 10 times 10-fold cross-validation was also used to minimize false positive finings and overfitting. Identified were the pathways and molecular processes associated with and the cis-regulatory elements in gene’s 5′ promoter or 3′-UTR regions of the set of genes which expression uniquely characterized the four phenotypes. Results The largest differences in gene expression among the four groups occurred at maternal fetal interface in decidua, chorion and amnion. The gene expression profiles showed suppression of chemokines expressi…
format: application/pdf
format: text/html
creator: Radek Bukowski
creator: Yoel Sadovsky
creator: Hani Goodarzi
creator: Heping Zhang
creator: Joseph R. Biggio
creator: Michael Varner
creator: Samuel Parry
creator: Feifei Xiao
creator: Sean M. Esplin
creator: William Andrews
creator: George R. Saade
creator: John V. Ilekis
creator: Uma M. Reddy
creator: Donald A. Baldwin
subject: Gynecology and Obstetrics
subject: Women's Health
description: doi:10.7717/peerj.3685
publisher: PeerJ Inc.
rights: © 2017 Bukowski et al.
abstract: Background Preterm birth is a main determinant of neonatal mortality and morbidity and a major contributor to the overall mortality and burden of disease. However, research of the preterm birth is hindered by the imprecise definition of the clinical phenotype and complexity of the molecular phenotype due to multiple pregnancy tissue types and molecular processes that may contribute to the preterm birth. Here we comprehensively evaluate the mRNA transcriptome that characterizes preterm and term labor in tissues comprising the pregnancy using precisely phenotyped samples. The four complementary phenotypes together provide comprehensive insight into preterm and term parturition. Methods Samples of maternal blood, chorion, amnion, placenta, decidua, fetal blood, and myometrium from the uterine fundus and lower segment (n = 183) were obtained during cesarean delivery from women with four complementary phenotypes: delivering preterm with (PL) and without labor (PNL), term with (TL) and without labor (TNL). Enrolled were 35 pregnant women with four precisely and prospectively defined phenotypes: PL (n = 8), PNL (n = 10), TL (n = 7) and TNL (n = 10). Gene expression data were analyzed using shrunken centroid analysis to identify a minimal set of genes that uniquely characterizes each of the four phenotypes. Expression profiles of 73 genes and non-coding RNA sequences uniquely identified each of the four phenotypes. The shrunken centroid analysis and 10 times 10-fold cross-validation was also used to minimize false positive finings and overfitting. Identified were the pathways and molecular processes associated with and the cis-regulatory elements in gene’s 5′ promoter or 3′-UTR regions of the set of genes which expression uniquely characterized the four phenotypes. Results The largest differences in gene expression among the four groups occurred at maternal fetal interface in decidua, chorion and amnion. The gene expression profiles showed suppression of chemokines expressi…
bibliographic citation: Bukowski et al. (2017) Onset of human preterm and term birth is related to unique inflammatory transcriptome profiles at the maternal fetal interface. PeerJ 5:e3685 https://doi.org/10.7717/peerj.3685
date submitted: 2017-03-26
date accepted: 2017-07-22
issued: 2017-09-01
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Bukowski
  given name: Radek
author list: Agent
  family name: Sadovsky
  given name: Yoel
author list: Agent
  family name: Goodarzi
  given name: Hani
author list: Agent
  family name: Zhang
  given name: Heping
author list: Agent
  family name: Biggio
  given name: Joseph R.
author list: Agent
  family name: Varner
  given name: Michael
author list: Agent
  family name: Parry
  given name: Samuel
author list: Agent
  family name: Xiao
  given name: Feifei
author list: Agent
  family name: Esplin
  given name: Sean M.
author list: Agent
  family name: Andrews
  given name: William
author list: Agent
  family name: Saade
  given name: George R.
author list: Agent
  family name: Ilekis
  given name: John V.
author list: Agent
  family name: Reddy
  given name: Uma M.
author list: Agent
  family name: Baldwin
  given name: Donald A.
doi: 10.7717/peerj.3685
volume: 5
issn: 2167-8359
publication name: PeerJ
publication date: 2017-09-01
copyright: ©2017 Bukowski et al.
attribution name: Bukowski et al.

Measuring coral calcification under ocean acidification: methodological considerations for the 45Ca-uptake and total alkalinity anomaly technique
type: item
type: AcademicArticle
description: As the oceans become less alkaline due to rising CO2 levels, deleterious consequences are expected for calcifying corals. Predicting how coral calcification will be affected by on-going ocean acidification (OA) requires an accurate assessment of CaCO3 deposition and an understanding of the relative importance that decreasing calcification and/or increasing dissolution play for the overall calcification budget of individual corals. Here, we assessed the compatibility of the 45Ca-uptake and total alkalinity (TA) anomaly techniques as measures of gross and net calcification (GC, NC), respectively, to determine coral calcification at pHT 8.1 and 7.5. Considering the differing buffering capacity of seawater at both pH values, we were also interested in how strongly coral calcification alters the seawater carbonate chemistry under prolonged incubation in sealed chambers, potentially interfering with physiological functioning. Our data indicate that NC estimates by TA are erroneously ∼5% and ∼21% higher than GC estimates from 45Ca for ambient and reduced pH, respectively. Considering also previous data, we show that the consistent discrepancy between both techniques across studies is not constant, but largely depends on the absolute value of CaCO3 deposition. Deriving rates of coral dissolution from the difference between NC and GC was not possible and we advocate a more direct approach for the future by simultaneously measuring skeletal calcium influx and efflux. Substantial changes in carbonate system parameters for incubation times beyond two hours in our experiment demonstrate the necessity to test and optimize experimental incubation setups when measuring coral calcification in closed systems, especially under OA conditions.
format: application/pdf
format: text/html
creator: Stephanie Cohen
creator: Thomas Krueger
creator: Maoz Fine
subject: Ecology
subject: Marine Biology
description: doi:10.7717/peerj.3749
publisher: PeerJ Inc.
rights: © 2017 Cohen et al.
abstract: As the oceans become less alkaline due to rising CO2 levels, deleterious consequences are expected for calcifying corals. Predicting how coral calcification will be affected by on-going ocean acidification (OA) requires an accurate assessment of CaCO3 deposition and an understanding of the relative importance that decreasing calcification and/or increasing dissolution play for the overall calcification budget of individual corals. Here, we assessed the compatibility of the 45Ca-uptake and total alkalinity (TA) anomaly techniques as measures of gross and net calcification (GC, NC), respectively, to determine coral calcification at pHT 8.1 and 7.5. Considering the differing buffering capacity of seawater at both pH values, we were also interested in how strongly coral calcification alters the seawater carbonate chemistry under prolonged incubation in sealed chambers, potentially interfering with physiological functioning. Our data indicate that NC estimates by TA are erroneously ∼5% and ∼21% higher than GC estimates from 45Ca for ambient and reduced pH, respectively. Considering also previous data, we show that the consistent discrepancy between both techniques across studies is not constant, but largely depends on the absolute value of CaCO3 deposition. Deriving rates of coral dissolution from the difference between NC and GC was not possible and we advocate a more direct approach for the future by simultaneously measuring skeletal calcium influx and efflux. Substantial changes in carbonate system parameters for incubation times beyond two hours in our experiment demonstrate the necessity to test and optimize experimental incubation setups when measuring coral calcification in closed systems, especially under OA conditions.
bibliographic citation: Cohen et al. (2017) Measuring coral calcification under ocean acidification: methodological considerations for the 45Ca-uptake and total alkalinity anomaly technique. PeerJ 5:e3749 https://doi.org/10.7717/peerj.3749
date submitted: 2017-05-24
date accepted: 2017-08-08
issued: 2017-09-01
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Cohen
  given name: Stephanie
author list: Agent
  family name: Krueger
  given name: Thomas
author list: Agent
  family name: Fine
  given name: Maoz
doi: 10.7717/peerj.3749
volume: 5
issn: 2167-8359
publication name: PeerJ
publication date: 2017-09-01
copyright: ©2017 Cohen et al.
attribution name: Cohen et al.

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