PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
items: Field evaluation of Mosq-ovitrap, Ovitrap and a CO2-light trap for Aedes albopictus sampling in Shanghai, China
items: Effects of elevated pCO2 and nutrient enrichment on the growth, photosynthesis, and biochemical compositions of the brown alga Saccharina japonica (Laminariaceae, Phaeophyta)
items: Seasonal variation in apparent conductivity and soil salinity at two Narragansett Bay, RI salt marshes
items: Diatoms as indicators of the effects of river impoundment at multiple spatial scales
items: Evaluation of performance of leading algorithms for variant pathogenicity predictions and designing a combinatory predictor method: application to Rett syndrome variants
items: Arboreal twig-nesting ants form dominance hierarchies over nesting resources
items: Sarc-F and muscle function in community dwelling adults with aged care service needs: baseline and post-training relationship
items: Effect of vibration vs non-vibration foam rolling techniques on flexibility, dynamic balance and perceived joint stability after fatigue
items: A rapid spread of the stony coral tissue loss disease outbreak in the Mexican Caribbean
items: Complete mitogenome of Olidiana ritcheriina (Hemiptera: Cicadellidae) and phylogeny of Cicadellidae

Field evaluation of Mosq-ovitrap, Ovitrap and a CO2-light trap for Aedes albopictus sampling in Shanghai, China
type: item
type: AcademicArticle
description: Background The Mosq-ovitrap (MOT) is currently used for routine surveillance of container-breeding Aedes in China. However, the effectiveness of monitoring Aedes albopictus using the MOT and other mosquito monitoring methods, such as the Ovitrap (OT) and the CO2-light trap (CLT), have not been extensively compared. Moreover, little is known about the spatial-temporal correlations of eggs with adult Ae. albopictus abundance among these three types of traps. Methods Comparative field evaluation of MOT, OT and CLT for Ae. albopictus monitoring was conducted simultaneously at two city parks and three residential neighborhoods in downtown Shanghai for 8 months from April 21 to December 21, 2017. Results Significantly more Ae. albopictus eggs were collected from both MOTs and OTs when traps remained in the field for 10 d or 7 d compared with 3 d (MOT: 50.16, 34.15 vs. 12.38 per trap, P < 0.001; OT: 3.98, 2.92 vs. 0.63 per trap, P < 0.001). Egg collections of MOTs were significantly greater than OTs for all three exposure durations (Percent positive: X2 = 72.251, 52.420 and 51.429, P value all < 0.001; egg collections: t = 8.068, 8.517 and 10.021, P value all <0.001). Significant temporal correlations were observed between yields of MOT and CLT in all sampling locations and 3 different MOT exposure durations (correlation coefficient r ranged from 0.439 to 0.850, P values all < 0.05). However, great variation was found in the spatial distributions of Ae. albopictus density between MOT and CLT. MOT considerably underestimated Ae. albopictus abundances in areas with high Ae. albopictus density (>25.56 per day ⋅ trap by CLT). Conclusion The MOT was more efficient than the OT in percent positive scores and egg collections of Ae. albopictus. The minimum length of time that MOTs are deployed in the field should not be less than 7 d, as Ae. albopictus collections during this period were much greater than for 3 d of monitoring. MOT considerably underestimated Ae. albopictus abundan…
format: application/pdf
format: text/html
creator: Qiang Gao
creator: Hui Cao
creator: Jian Fan
creator: Zhendong Zhang
creator: Shuqing Jin
creator: Fei Su
creator: Peien Leng
creator: Chenglong Xiong
subject: Entomology
subject: Parasitology
description: doi:10.7717/peerj.8031
publisher: PeerJ Inc.
rights: © 2019 Gao et al.
abstract: Background The Mosq-ovitrap (MOT) is currently used for routine surveillance of container-breeding Aedes in China. However, the effectiveness of monitoring Aedes albopictus using the MOT and other mosquito monitoring methods, such as the Ovitrap (OT) and the CO2-light trap (CLT), have not been extensively compared. Moreover, little is known about the spatial-temporal correlations of eggs with adult Ae. albopictus abundance among these three types of traps. Methods Comparative field evaluation of MOT, OT and CLT for Ae. albopictus monitoring was conducted simultaneously at two city parks and three residential neighborhoods in downtown Shanghai for 8 months from April 21 to December 21, 2017. Results Significantly more Ae. albopictus eggs were collected from both MOTs and OTs when traps remained in the field for 10 d or 7 d compared with 3 d (MOT: 50.16, 34.15 vs. 12.38 per trap, P < 0.001; OT: 3.98, 2.92 vs. 0.63 per trap, P < 0.001). Egg collections of MOTs were significantly greater than OTs for all three exposure durations (Percent positive: X2 = 72.251, 52.420 and 51.429, P value all < 0.001; egg collections: t = 8.068, 8.517 and 10.021, P value all <0.001). Significant temporal correlations were observed between yields of MOT and CLT in all sampling locations and 3 different MOT exposure durations (correlation coefficient r ranged from 0.439 to 0.850, P values all < 0.05). However, great variation was found in the spatial distributions of Ae. albopictus density between MOT and CLT. MOT considerably underestimated Ae. albopictus abundances in areas with high Ae. albopictus density (>25.56 per day ⋅ trap by CLT). Conclusion The MOT was more efficient than the OT in percent positive scores and egg collections of Ae. albopictus. The minimum length of time that MOTs are deployed in the field should not be less than 7 d, as Ae. albopictus collections during this period were much greater than for 3 d of monitoring. MOT considerably underestimated Ae. albopictus abundan…
bibliographic citation: Gao et al. (2019) Field evaluation of Mosq-ovitrap, Ovitrap and a CO2-light trap for Aedes albopictus sampling in Shanghai, China. PeerJ 7:e8031 https://doi.org/10.7717/peerj.8031
date submitted: 2019-06-13
date accepted: 2019-10-14
issued: 2019-11-27
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Gao
  given name: Qiang
author list: Agent
  family name: Cao
  given name: Hui
author list: Agent
  family name: Fan
  given name: Jian
author list: Agent
  family name: Zhang
  given name: Zhendong
author list: Agent
  family name: Jin
  given name: Shuqing
author list: Agent
  family name: Su
  given name: Fei
author list: Agent
  family name: Leng
  given name: Peien
author list: Agent
  family name: Xiong
  given name: Chenglong
doi: 10.7717/peerj.8031
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-11-27
copyright: ©2019 Gao et al.
attribution name: Gao et al.

Effects of elevated pCO2 and nutrient enrichment on the growth, photosynthesis, and biochemical compositions of the brown alga Saccharina japonica (Laminariaceae, Phaeophyta)
type: item
type: AcademicArticle
description: Ocean acidification and eutrophication are two major environmental issues affecting kelp mariculture. In this study, the growth, photosynthesis, and biochemical compositions of adult sporophytes of Saccharina japonica were evaluated at different levels of pCO2 (400 and 800 µatm) and nutrients (nutrient-enriched and non-enriched seawater). The relative growth rate (RGR), net photosynthetic rate, and all tested biochemical contents (including chlorophyll (Chl) a, Chl c, soluble carbohydrates, and soluble proteins) were significantly lower at 800 µatm than at 400 µatm pCO2. The RGR and the contents of Chl a and soluble proteins were significantly higher under nutrient-enriched conditions than under non-enriched conditions. Moreover, the negative effects of the elevated pCO2 level on the RGR, net photosynthetic rate, Chl c and the soluble carbohydrates and proteins contents were synergized by the elevated nutrient availability. These results implied that increased pCO2could suppress the growth and biochemical composition of adult sporophytes of S. japonica. The interactive effects of ocean acidification and eutrophication constitute a great threat to the cultivation of S. japonica due to growth inhibition and a reduction in quality.
format: application/pdf
format: text/html
creator: Yaoyao Chu
creator: Yan Liu
creator: Jingyu Li
creator: Qingli Gong
subject: Ecology
subject: Marine Biology
subject: Plant Science
subject: Synthetic Biology
subject: Environmental Contamination and Remediation
description: doi:10.7717/peerj.8040
publisher: PeerJ Inc.
rights: © 2019 Chu et al.
abstract: Ocean acidification and eutrophication are two major environmental issues affecting kelp mariculture. In this study, the growth, photosynthesis, and biochemical compositions of adult sporophytes of Saccharina japonica were evaluated at different levels of pCO2 (400 and 800 µatm) and nutrients (nutrient-enriched and non-enriched seawater). The relative growth rate (RGR), net photosynthetic rate, and all tested biochemical contents (including chlorophyll (Chl) a, Chl c, soluble carbohydrates, and soluble proteins) were significantly lower at 800 µatm than at 400 µatm pCO2. The RGR and the contents of Chl a and soluble proteins were significantly higher under nutrient-enriched conditions than under non-enriched conditions. Moreover, the negative effects of the elevated pCO2 level on the RGR, net photosynthetic rate, Chl c and the soluble carbohydrates and proteins contents were synergized by the elevated nutrient availability. These results implied that increased pCO2could suppress the growth and biochemical composition of adult sporophytes of S. japonica. The interactive effects of ocean acidification and eutrophication constitute a great threat to the cultivation of S. japonica due to growth inhibition and a reduction in quality.
bibliographic citation: Chu et al. (2019) Effects of elevated pCO2 and nutrient enrichment on the growth, photosynthesis, and biochemical compositions of the brown alga Saccharina japonica (Laminariaceae, Phaeophyta). PeerJ 7:e8040 https://doi.org/10.7717/peerj.8040
date submitted: 2019-07-24
date accepted: 2019-10-15
issued: 2019-11-27
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Chu
  given name: Yaoyao
author list: Agent
  family name: Liu
  given name: Yan
author list: Agent
  family name: Li
  given name: Jingyu
author list: Agent
  family name: Gong
  given name: Qingli
doi: 10.7717/peerj.8040
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-11-27
copyright: ©2019 Chu et al.
attribution name: Chu et al.

Seasonal variation in apparent conductivity and soil salinity at two Narragansett Bay, RI salt marshes
type: item
type: AcademicArticle
description: Measurement of the apparent conductivity of salt marsh sediments using electromagnetic induction (EMI) is a rapid alternative to traditional methods of salinity determination that can be used to map soil salinity across a marsh surface. Soil salinity measures can provide information about marsh processes, since salinity is important in determining the structure and function of tidally influenced marsh communities. While EMI has been shown to accurately reflect salinity to a specified depth, more information is needed on the potential for spatial and temporal variability in apparent conductivity measures that may impact the interpretation of salinity data. In this study we mapped soil salinity at two salt marshes in the Narragansett Bay, RI estuary monthly over the course of several years to examine spatial and temporal trends in marsh salinity. Mean monthly calculated salinity was 25.8 ± 5.5 ppt at Narrow River marsh (NAR), located near the mouth of the Bay, and 17.7 ± 5.3 ppt at Passeonkquis marsh (PAS) located in the upper Bay. Salinity varied seasonally with both marshes, showing the lowest values (16.3 and 8.3 ppt, respectively) in April and highest values (35.4 and 26.2 ppt, respectively) in August. Contour plots of calculated salinities showed that while the mean whole-marsh calculated salinity at both sites changed over time, within-marsh patterns of higher versus lower salinity were maintained at NAR but changed over time at PAS. Calculated salinity was significantly negatively correlated with elevation at NAR during a sub-set of 12 sample events, but not at PAS. Best-supported linear regression models for both sites included one-month and 6-month cumulative rainfall, and tide state as potential factors driving observed changes in calculated salinity. Mapping apparent conductivity of salt marsh sediments may be useful both identifying within-marsh micro-habitats, and documenting marsh-wide changes in salinity over time.
format: application/pdf
format: text/html
creator: Richard McKinney
creator: Alana Hanson
creator: Roxanne Johnson
creator: Michael Charpentier
subject: Ecosystem Science
subject: Soil Science
subject: Aquatic and Marine Chemistry
description: doi:10.7717/peerj.8074
publisher: PeerJ Inc.
rights: ©
abstract: Measurement of the apparent conductivity of salt marsh sediments using electromagnetic induction (EMI) is a rapid alternative to traditional methods of salinity determination that can be used to map soil salinity across a marsh surface. Soil salinity measures can provide information about marsh processes, since salinity is important in determining the structure and function of tidally influenced marsh communities. While EMI has been shown to accurately reflect salinity to a specified depth, more information is needed on the potential for spatial and temporal variability in apparent conductivity measures that may impact the interpretation of salinity data. In this study we mapped soil salinity at two salt marshes in the Narragansett Bay, RI estuary monthly over the course of several years to examine spatial and temporal trends in marsh salinity. Mean monthly calculated salinity was 25.8 ± 5.5 ppt at Narrow River marsh (NAR), located near the mouth of the Bay, and 17.7 ± 5.3 ppt at Passeonkquis marsh (PAS) located in the upper Bay. Salinity varied seasonally with both marshes, showing the lowest values (16.3 and 8.3 ppt, respectively) in April and highest values (35.4 and 26.2 ppt, respectively) in August. Contour plots of calculated salinities showed that while the mean whole-marsh calculated salinity at both sites changed over time, within-marsh patterns of higher versus lower salinity were maintained at NAR but changed over time at PAS. Calculated salinity was significantly negatively correlated with elevation at NAR during a sub-set of 12 sample events, but not at PAS. Best-supported linear regression models for both sites included one-month and 6-month cumulative rainfall, and tide state as potential factors driving observed changes in calculated salinity. Mapping apparent conductivity of salt marsh sediments may be useful both identifying within-marsh micro-habitats, and documenting marsh-wide changes in salinity over time.
bibliographic citation: McKinney et al. (2019) Seasonal variation in apparent conductivity and soil salinity at two Narragansett Bay, RI salt marshes. PeerJ 7:e8074 https://doi.org/10.7717/peerj.8074
date submitted: 2019-05-16
date accepted: 2019-10-21
issued: 2019-11-27
is part of: PeerJ
license: https://creativecommons.org/publicdomain/zero/1.0/
author list: Agent
  family name: McKinney
  given name: Richard
author list: Agent
  family name: Hanson
  given name: Alana
author list: Agent
  family name: Johnson
  given name: Roxanne
author list: Agent
  family name: Charpentier
  given name: Michael
doi: 10.7717/peerj.8074
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-11-27

Diatoms as indicators of the effects of river impoundment at multiple spatial scales
type: item
type: AcademicArticle
description: River impoundment constitutes one of the most important anthropogenic impacts on the World’s rivers. An increasing number of studies have tried to quantify the effects of river impoundment on riverine ecosystems over the past two decades, often focusing on the effects of individual large reservoirs. This study is one of the first to use a large-scale, multi-year diatom dataset from a routine biomonitoring network to analyse sample sites downstream of a large number of water supply reservoirs (n = 77) and to compare them with paired unregulated control sites. We analysed benthic diatom assemblage structure and a set of derived indices, including ecological guilds, in tandem with multiple spatio-temporal variables to disclose patterns of ecological responses to reservoirs beyond the site-specific scale. Diatom assemblage structure at sites downstream of water supply reservoirs was significantly different to control sites, with the effect being most evident at the regional scale. We found that regional influences were important drivers of differences in assemblage structure at the national scale, although this effect was weaker at downstream sites, indicating the homogenising effect of river impoundment on diatom assemblages. Sites downstream of reservoirs typically exhibited a higher taxonomic richness, with the strongest increases found within the motile guild. In addition, Trophic Diatom Index (TDI) values were typically higher at downstream sites. Water quality gradients appeared to be an important driver of diatom assemblages, but the influence of other abiotic factors could not be ruled out and should be investigated further. Our results demonstrate the value of diatom assemblage data from national-scale biomonitoring networks to detect the effects of water supply reservoirs on instream communities at large spatial scales. This information may assist water resource managers with the future implementation of mitigation measures such as setting environmental flow t…
format: application/pdf
format: text/html
creator: Hendrik J. Krajenbrink
creator: Mike Acreman
creator: Michael J. Dunbar
creator: Libby Greenway
creator: David M. Hannah
creator: Cédric L.R. Laizé
creator: David B. Ryves
creator: Paul J. Wood
subject: Freshwater Biology
subject: Ecohydrology
description: doi:10.7717/peerj.8092
publisher: PeerJ Inc.
rights: ©
abstract: River impoundment constitutes one of the most important anthropogenic impacts on the World’s rivers. An increasing number of studies have tried to quantify the effects of river impoundment on riverine ecosystems over the past two decades, often focusing on the effects of individual large reservoirs. This study is one of the first to use a large-scale, multi-year diatom dataset from a routine biomonitoring network to analyse sample sites downstream of a large number of water supply reservoirs (n = 77) and to compare them with paired unregulated control sites. We analysed benthic diatom assemblage structure and a set of derived indices, including ecological guilds, in tandem with multiple spatio-temporal variables to disclose patterns of ecological responses to reservoirs beyond the site-specific scale. Diatom assemblage structure at sites downstream of water supply reservoirs was significantly different to control sites, with the effect being most evident at the regional scale. We found that regional influences were important drivers of differences in assemblage structure at the national scale, although this effect was weaker at downstream sites, indicating the homogenising effect of river impoundment on diatom assemblages. Sites downstream of reservoirs typically exhibited a higher taxonomic richness, with the strongest increases found within the motile guild. In addition, Trophic Diatom Index (TDI) values were typically higher at downstream sites. Water quality gradients appeared to be an important driver of diatom assemblages, but the influence of other abiotic factors could not be ruled out and should be investigated further. Our results demonstrate the value of diatom assemblage data from national-scale biomonitoring networks to detect the effects of water supply reservoirs on instream communities at large spatial scales. This information may assist water resource managers with the future implementation of mitigation measures such as setting environmental flow t…
bibliographic citation: Krajenbrink et al. (2019) Diatoms as indicators of the effects of river impoundment at multiple spatial scales. PeerJ 7:e8092 https://doi.org/10.7717/peerj.8092
date submitted: 2019-07-08
date accepted: 2019-10-23
issued: 2019-11-27
is part of: PeerJ
license: open-government-licence
author list: Agent
  family name: Krajenbrink
  given name: Hendrik J.
author list: Agent
  family name: Acreman
  given name: Mike
author list: Agent
  family name: Dunbar
  given name: Michael J.
author list: Agent
  family name: Greenway
  given name: Libby
author list: Agent
  family name: Hannah
  given name: David M.
author list: Agent
  family name: Laizé
  given name: Cédric L.R.
author list: Agent
  family name: Ryves
  given name: David B.
author list: Agent
  family name: Wood
  given name: Paul J.
doi: 10.7717/peerj.8092
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-11-27

Evaluation of performance of leading algorithms for variant pathogenicity predictions and designing a combinatory predictor method: application to Rett syndrome variants
type: item
type: AcademicArticle
description: Background Genomics diagnostic tests are done for a wide spectrum of complex genetics conditions such as autism and cancer. The growth of technology has not only aided in successfully decoding the genetic variants that causes or trigger these disorders. However, interpretation of these variants is not a trivial task even at a level of distinguish pathogenic vs benign variants. Methods We used the clinically significant variants from ClinVar database to evaluate the performance of 14 most popular in-silico predictors using supervised learning methods. We implemented a feature selection and random forest classification algorithm to identify the best combination of predictors to evaluate the pathogenicity of a variant. Finally, we have also utilized this combination of predictors to reclassify the variants of unknown significance in MeCP2 gene that are associated with the Rett syndrome. Results The results from analysis shows an optimized selection of prediction algorithm and developed a combinatory predictor method. Our combinatory approach of using both best performing independent and ensemble predictors reduces any algorithm biases in variant characterization. The reclassification of variants (such as VUS) in MECP2 gene associated with RETT syndrome suggest that the combinatory in-silico predictor approach had a higher success rate in categorizing their pathogenicity.
format: application/pdf
format: text/html
creator: Satishkumar Ranganathan Ganakammal
creator: Emil Alexov
subject: Bioinformatics
subject: Computational Biology
subject: Pathology
subject: Medical Genetics
subject: Computational Science
description: doi:10.7717/peerj.8106
publisher: PeerJ Inc.
rights: © 2019 Ganakammal and Alexov
abstract: Background Genomics diagnostic tests are done for a wide spectrum of complex genetics conditions such as autism and cancer. The growth of technology has not only aided in successfully decoding the genetic variants that causes or trigger these disorders. However, interpretation of these variants is not a trivial task even at a level of distinguish pathogenic vs benign variants. Methods We used the clinically significant variants from ClinVar database to evaluate the performance of 14 most popular in-silico predictors using supervised learning methods. We implemented a feature selection and random forest classification algorithm to identify the best combination of predictors to evaluate the pathogenicity of a variant. Finally, we have also utilized this combination of predictors to reclassify the variants of unknown significance in MeCP2 gene that are associated with the Rett syndrome. Results The results from analysis shows an optimized selection of prediction algorithm and developed a combinatory predictor method. Our combinatory approach of using both best performing independent and ensemble predictors reduces any algorithm biases in variant characterization. The reclassification of variants (such as VUS) in MECP2 gene associated with RETT syndrome suggest that the combinatory in-silico predictor approach had a higher success rate in categorizing their pathogenicity.
bibliographic citation: Ganakammal et al. (2019) Evaluation of performance of leading algorithms for variant pathogenicity predictions and designing a combinatory predictor method: application to Rett syndrome variants. PeerJ 7:e8106 https://doi.org/10.7717/peerj.8106
date submitted: 2019-07-24
date accepted: 2019-10-27
issued: 2019-11-27
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Ganakammal
  given name: Satishkumar Ranganathan
author list: Agent
  family name: Alexov
  given name: Emil
doi: 10.7717/peerj.8106
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-11-27
copyright: © 2019 Ganakammal and Alexov
attribution name: Ganakammal and Alexov

Arboreal twig-nesting ants form dominance hierarchies over nesting resources
type: item
type: AcademicArticle
description: Interspecific dominance hierarchies have been widely reported across animal systems. High-ranking species are expected to monopolize more resources than low-ranking species via resource monopolization. In some ant species, dominance hierarchies have been used to explain species coexistence and community structure. However, it remains unclear whether or in what contexts dominance hierarchies occur in tropical ant communities. This study seeks to examine whether arboreal twig-nesting ants competing for nesting resources in a Mexican coffee agricultural ecosystem are arranged in a linear dominance hierarchy. We described the dominance relationships among 10 species of ants and measured the uncertainty and steepness of the inferred dominance hierarchy. We also assessed the orderliness of the hierarchy by considering species interactions at the network level. Based on the randomized Elo-rating method, we found that the twig-nesting ant species Myrmelachista mexicana ranked highest in the ranking, while Pseudomyrmex ejectus was ranked as the lowest in the hierarchy. Our results show that the hierarchy was intermediate in its steepness, suggesting that the probability of higher ranked species winning contests against lower ranked species was fairly high. Motif analysis and significant excess of triads further revealed that the species networks were largely transitive. This study highlights that some tropical arboreal ant communities organize into dominance hierarchies.
format: application/pdf
format: text/html
creator: Senay Yitbarek
creator: Stacy M. Philpott
subject: Agricultural Science
subject: Biodiversity
subject: Ecology
subject: Entomology
subject: Population Biology
description: doi:10.7717/peerj.8124
publisher: PeerJ Inc.
rights: © 2019 Yitbarek and Philpott
abstract: Interspecific dominance hierarchies have been widely reported across animal systems. High-ranking species are expected to monopolize more resources than low-ranking species via resource monopolization. In some ant species, dominance hierarchies have been used to explain species coexistence and community structure. However, it remains unclear whether or in what contexts dominance hierarchies occur in tropical ant communities. This study seeks to examine whether arboreal twig-nesting ants competing for nesting resources in a Mexican coffee agricultural ecosystem are arranged in a linear dominance hierarchy. We described the dominance relationships among 10 species of ants and measured the uncertainty and steepness of the inferred dominance hierarchy. We also assessed the orderliness of the hierarchy by considering species interactions at the network level. Based on the randomized Elo-rating method, we found that the twig-nesting ant species Myrmelachista mexicana ranked highest in the ranking, while Pseudomyrmex ejectus was ranked as the lowest in the hierarchy. Our results show that the hierarchy was intermediate in its steepness, suggesting that the probability of higher ranked species winning contests against lower ranked species was fairly high. Motif analysis and significant excess of triads further revealed that the species networks were largely transitive. This study highlights that some tropical arboreal ant communities organize into dominance hierarchies.
bibliographic citation: Yitbarek et al. (2019) Arboreal twig-nesting ants form dominance hierarchies over nesting resources. PeerJ 7:e8124 https://doi.org/10.7717/peerj.8124
date submitted: 2019-08-08
date accepted: 2019-10-30
issued: 2019-11-27
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Yitbarek
  given name: Senay
author list: Agent
  family name: Philpott
  given name: Stacy M.
doi: 10.7717/peerj.8124
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-11-27
copyright: ©2019 Yitbarek and Philpott
attribution name: Yitbarek and Philpott

Sarc-F and muscle function in community dwelling adults with aged care service needs: baseline and post-training relationship
type: item
type: AcademicArticle
description: Background This study sought to better understand the psychometric properties of the SARC-F, by examining the baseline and training-related relationships between the five SARC-F items and objective measures of muscle function. Each of the five items of the SARC-F are scored from 0 to 2, with total score of four or more indicative of likely sarcopenia. Methods This manuscript describes a sub-study of a larger step-wedge, randomised controlled 24-week progressive resistance and balance training (PRBT) program trial for Australian community dwelling older adults accessing government supported aged care. Muscle function was assessed using handgrip strength, isometric knee extension, 5-time repeated chair stand and walking speed over 4 m. Associations within and between SARC-F categories and muscle function were assessed using multiple correspondence analysis (MCA) and multinomial regression, respectively. Results Significant associations were identified at baseline between SARC-F total score and measures of lower-body muscle function (r = − 0.62 to 0.57; p ≤ 0.002) in 245 older adults. MCA analysis indicated the first three dimensions of the SARC-F data explained 48.5% of the cumulative variance. The initial dimension represented overall sarcopenia diagnosis, Dimension 2 the ability to displace the body vertically, and Dimension 3 walking ability and falls status. The majority of the 168 older adults who completed the PRBT program reported no change in their SARC-F diagnosis or individual item scores (56.5–79.2%). However, significant associations were obtained between training-related changes in SARC-F total and item scores and changes in walking speed and chair stand test performance (r = − 0.30 to 0.33; p < 0.001 and relative risk ratio = 0.40–2.24; p < 0.05, respectively). MCA analysis of the change score data indicated that the first two dimensions explained 32.2% of the cumulative variance, with these dimensions representing whether a change occurred and the direc…
format: application/pdf
format: text/html
creator: Justin W.L. Keogh
creator: Tim Henwood
creator: Paul A. Gardiner
creator: Anthony G. Tuckett
creator: Sharon Hetherington
creator: Kevin Rouse
creator: Paul Swinton
subject: Geriatrics
subject: Kinesiology
description: doi:10.7717/peerj.8140
publisher: PeerJ Inc.
rights: © 2019 Keogh et al.
abstract: Background This study sought to better understand the psychometric properties of the SARC-F, by examining the baseline and training-related relationships between the five SARC-F items and objective measures of muscle function. Each of the five items of the SARC-F are scored from 0 to 2, with total score of four or more indicative of likely sarcopenia. Methods This manuscript describes a sub-study of a larger step-wedge, randomised controlled 24-week progressive resistance and balance training (PRBT) program trial for Australian community dwelling older adults accessing government supported aged care. Muscle function was assessed using handgrip strength, isometric knee extension, 5-time repeated chair stand and walking speed over 4 m. Associations within and between SARC-F categories and muscle function were assessed using multiple correspondence analysis (MCA) and multinomial regression, respectively. Results Significant associations were identified at baseline between SARC-F total score and measures of lower-body muscle function (r = − 0.62 to 0.57; p ≤ 0.002) in 245 older adults. MCA analysis indicated the first three dimensions of the SARC-F data explained 48.5% of the cumulative variance. The initial dimension represented overall sarcopenia diagnosis, Dimension 2 the ability to displace the body vertically, and Dimension 3 walking ability and falls status. The majority of the 168 older adults who completed the PRBT program reported no change in their SARC-F diagnosis or individual item scores (56.5–79.2%). However, significant associations were obtained between training-related changes in SARC-F total and item scores and changes in walking speed and chair stand test performance (r = − 0.30 to 0.33; p < 0.001 and relative risk ratio = 0.40–2.24; p < 0.05, respectively). MCA analysis of the change score data indicated that the first two dimensions explained 32.2% of the cumulative variance, with these dimensions representing whether a change occurred and the direc…
bibliographic citation: Keogh et al. (2019) Sarc-F and muscle function in community dwelling adults with aged care service needs: baseline and post-training relationship. PeerJ 7:e8140 https://doi.org/10.7717/peerj.8140
date submitted: 2019-06-17
date accepted: 2019-11-01
issued: 2019-11-27
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Keogh
  given name: Justin W.L.
author list: Agent
  family name: Henwood
  given name: Tim
author list: Agent
  family name: Gardiner
  given name: Paul A.
author list: Agent
  family name: Tuckett
  given name: Anthony G.
author list: Agent
  family name: Hetherington
  given name: Sharon
author list: Agent
  family name: Rouse
  given name: Kevin
author list: Agent
  family name: Swinton
  given name: Paul
doi: 10.7717/peerj.8140
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-11-27
copyright: ©2019 Keogh et al.
attribution name: Keogh et al.

Effect of vibration vs non-vibration foam rolling techniques on flexibility, dynamic balance and perceived joint stability after fatigue
type: item
type: AcademicArticle
description: Background Foam roller and vibration techniques are currently used to assist in recovery after fatigue. The main purpose of this study was to determine the effects of the use of a foam roller with and without vibration on dynamic balance, ankle dorsiflexion, hamstring and lumbar spine flexibility and perceived knee and ankle stability after an induced fatigue protocol. Methods A total of 24 healthy recreationally active participants (17 males and seven females) were recruited to a randomized cross over trial consisting of; no treatment (NT), foam roller treatment (FR) and vibration foam roller treatment (VFR). The assessments included; the Sit & Reach test, Y balance test and post-treatment perceived knee and ankle stability. Measurements were taken after a standardized warm up (baseline) and repeated following an exercise-induced muscle fatigue protocol consisting of repeated lunges until volitional fatigue. The three treatment conditions were assessed on three separate days in a randomized order. A 3 × 3 repeated measures ANOVA was used to investigate differences between the three treatments over the three time points and a one factor repeated measures ANOVA was used to determine any differences between treatments using the Global Rate of Change scale when considering perceived stability. Results FR and VFR conditions both showed a greater ankle dorsiflexion range of motion (ROM) (p < 0.001), greater posteromedial and posterolateral reach distances (p < 0.001) and a better knee and ankle perceived stability (p < 0.001) when compared to the NT condition. A trend toward significance was observed in the hamstring and lumbar spine flexibility (p = 0.074) in both treatment conditions when compared to the NT condition. However, no differences were seen between the FR and VFR conditions. Conclusions Both FR conditions seem to assist in exercise-induced muscle fatigue recovery with improvements in ROM, balance and perceived stability.
format: application/pdf
format: text/html
creator: Ana María de Benito
creator: Raúl Valldecabres
creator: Diego Ceca
creator: Jim Richards
creator: Joaquín Barrachina Igual
creator: Ana Pablos
subject: Kinesiology
description: doi:10.7717/peerj.8000
publisher: PeerJ Inc.
rights: © 2019 de Benito et al.
abstract: Background Foam roller and vibration techniques are currently used to assist in recovery after fatigue. The main purpose of this study was to determine the effects of the use of a foam roller with and without vibration on dynamic balance, ankle dorsiflexion, hamstring and lumbar spine flexibility and perceived knee and ankle stability after an induced fatigue protocol. Methods A total of 24 healthy recreationally active participants (17 males and seven females) were recruited to a randomized cross over trial consisting of; no treatment (NT), foam roller treatment (FR) and vibration foam roller treatment (VFR). The assessments included; the Sit & Reach test, Y balance test and post-treatment perceived knee and ankle stability. Measurements were taken after a standardized warm up (baseline) and repeated following an exercise-induced muscle fatigue protocol consisting of repeated lunges until volitional fatigue. The three treatment conditions were assessed on three separate days in a randomized order. A 3 × 3 repeated measures ANOVA was used to investigate differences between the three treatments over the three time points and a one factor repeated measures ANOVA was used to determine any differences between treatments using the Global Rate of Change scale when considering perceived stability. Results FR and VFR conditions both showed a greater ankle dorsiflexion range of motion (ROM) (p < 0.001), greater posteromedial and posterolateral reach distances (p < 0.001) and a better knee and ankle perceived stability (p < 0.001) when compared to the NT condition. A trend toward significance was observed in the hamstring and lumbar spine flexibility (p = 0.074) in both treatment conditions when compared to the NT condition. However, no differences were seen between the FR and VFR conditions. Conclusions Both FR conditions seem to assist in exercise-induced muscle fatigue recovery with improvements in ROM, balance and perceived stability.
bibliographic citation: de Benito et al. (2019) Effect of vibration vs non-vibration foam rolling techniques on flexibility, dynamic balance and perceived joint stability after fatigue. PeerJ 7:e8000 https://doi.org/10.7717/peerj.8000
date submitted: 2019-07-18
date accepted: 2019-10-07
issued: 2019-11-26
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: de Benito
  given name: Ana María
author list: Agent
  family name: Valldecabres
  given name: Raúl
author list: Agent
  family name: Ceca
  given name: Diego
author list: Agent
  family name: Richards
  given name: Jim
author list: Agent
  family name: Barrachina Igual
  given name: Joaquín
author list: Agent
  family name: Pablos
  given name: Ana
doi: 10.7717/peerj.8000
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-11-26
copyright: © 2019 de Benito et al.
attribution name: de Benito et al.

A rapid spread of the stony coral tissue loss disease outbreak in the Mexican Caribbean
type: item
type: AcademicArticle
description: Caribbean reef corals have experienced unprecedented declines from climate change, anthropogenic stressors and infectious diseases in recent decades. Since 2014, a highly lethal, new disease, called stony coral tissue loss disease, has impacted many reef-coral species in Florida. During the summer of 2018, we noticed an anomalously high disease prevalence affecting different coral species in the northern portion of the Mexican Caribbean. We assessed the severity of this outbreak in 2018/2019 using the AGRRA coral protocol to survey 82 reef sites across the Mexican Caribbean. Then, using a subset of 14 sites, we detailed information from before the outbreak (2016/2017) to explore the consequences of the disease on the condition and composition of coral communities. Our findings show that the disease outbreak has already spread across the entire region by affecting similar species (with similar disease patterns) to those previously described for Florida. However, we observed a great variability in prevalence and tissue mortality that was not attributable to any geographical gradient. Using long-term data, we determined that there is no evidence of such high coral disease prevalence anywhere in the region before 2018, which suggests that the entire Mexican Caribbean was afflicted by the disease within a few months. The analysis of sites that contained pre-outbreak information showed that this event considerably increased coral mortality and severely changed the structure of coral communities in the region. Given the high prevalence and lethality of this disease, and the high number of susceptible species, we encourage reef researchers, managers and stakeholders across the Western Atlantic to accord it the highest priority for the near future.
format: application/pdf
format: text/html
creator: Lorenzo Alvarez-Filip
creator: Nuria Estrada-Saldívar
creator: Esmeralda Pérez-Cervantes
creator: Ana Molina-Hernández
creator: Francisco J. González-Barrios
subject: Conservation Biology
subject: Ecology
subject: Marine Biology
description: doi:10.7717/peerj.8069
publisher: PeerJ Inc.
rights: © 2019 Alvarez-Filip et al.
abstract: Caribbean reef corals have experienced unprecedented declines from climate change, anthropogenic stressors and infectious diseases in recent decades. Since 2014, a highly lethal, new disease, called stony coral tissue loss disease, has impacted many reef-coral species in Florida. During the summer of 2018, we noticed an anomalously high disease prevalence affecting different coral species in the northern portion of the Mexican Caribbean. We assessed the severity of this outbreak in 2018/2019 using the AGRRA coral protocol to survey 82 reef sites across the Mexican Caribbean. Then, using a subset of 14 sites, we detailed information from before the outbreak (2016/2017) to explore the consequences of the disease on the condition and composition of coral communities. Our findings show that the disease outbreak has already spread across the entire region by affecting similar species (with similar disease patterns) to those previously described for Florida. However, we observed a great variability in prevalence and tissue mortality that was not attributable to any geographical gradient. Using long-term data, we determined that there is no evidence of such high coral disease prevalence anywhere in the region before 2018, which suggests that the entire Mexican Caribbean was afflicted by the disease within a few months. The analysis of sites that contained pre-outbreak information showed that this event considerably increased coral mortality and severely changed the structure of coral communities in the region. Given the high prevalence and lethality of this disease, and the high number of susceptible species, we encourage reef researchers, managers and stakeholders across the Western Atlantic to accord it the highest priority for the near future.
bibliographic citation: Alvarez-Filip et al. (2019) A rapid spread of the stony coral tissue loss disease outbreak in the Mexican Caribbean. PeerJ 7:e8069 https://doi.org/10.7717/peerj.8069
date submitted: 2019-08-12
date accepted: 2019-10-20
issued: 2019-11-26
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Alvarez-Filip
  given name: Lorenzo
author list: Agent
  family name: Estrada-Saldívar
  given name: Nuria
author list: Agent
  family name: Pérez-Cervantes
  given name: Esmeralda
author list: Agent
  family name: Molina-Hernández
  given name: Ana
author list: Agent
  family name: González-Barrios
  given name: Francisco J.
doi: 10.7717/peerj.8069
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-11-26
copyright: © 2019 Alvarez-Filip et al.
attribution name: Alvarez-Filip et al.

Complete mitogenome of Olidiana ritcheriina (Hemiptera: Cicadellidae) and phylogeny of Cicadellidae
type: item
type: AcademicArticle
description: Background Coelidiinae, a relatively large subfamily within the family Cicadellidae, includes 129 genera and ∼1,300 species distributed worldwide. However, the mitogenomes of only two species (Olidiana sp. and Taharana fasciana) in the subfamily Coelidiinae have been assembled. Here, we report the first complete mitogenome assembly of the genus Olidiana. Methods Specimens were collected from Wenxian County (Gansu Province, China) and identified on the basis of their morphology. Mitogenomes were sequenced by next-generation sequencing, following which an NGS template was generated, and this was confirmed using polymerase chain reaction and Sanger sequencing. Phylogenic trees were constructed using maximum likelihood and Bayesian analyses. Results The mitogenome of O. ritcheriina was 15,166 bp long, with an A + T content of 78.0%. Compared with the mitogenome of other Cicadellidae sp., the gene order, gene content, gene size, base composition, and codon usage of protein-coding genes (PCGs) in O. ritcheriina were highly conserved. The standard start codon of all PCGs was ATN and stop codon was TAA or TAG; COII, COIII, and ND4L ended with a single T. All tRNA genes showed the typical cloverleaf secondary structure, except for trnSer, which did not have the dihydrouridine arm. Furthermore, the secondary structures of rRNAs (rrnL and rrnS) in O. ritcheriina were predicted. Overall, five domains and 42 helices were predicted for rrnL (domain III is absent in arthropods), and three structural domains and 27 helices were predicted for rrnS. Maximum likelihood and Bayesian analyses indicated that O. ritcheriina and other Coelidiinae members were clustered into a clade, indicating the relationships among their subfamilies; the main topology was as follows: (Deltocephalinae + ((Coelidiinae + Iassinae) + ((Typhlocybinae + Cicadellinae) + (Idiocerinae + (Treehopper + Megophthalminae))))). The phylogenetic relationships indicated that the molecular taxonomy of O. ritcheriina is co…
format: application/pdf
format: text/html
creator: Xian-Yi Wang
creator: Jia-Jia Wang
creator: Zhi-Hua Fan
creator: Ren-Huai Dai
subject: Biodiversity
subject: Entomology
subject: Evolutionary Studies
subject: Genomics
subject: Taxonomy
description: doi:10.7717/peerj.8072
publisher: PeerJ Inc.
rights: © 2019 Wang et al.
abstract: Background Coelidiinae, a relatively large subfamily within the family Cicadellidae, includes 129 genera and ∼1,300 species distributed worldwide. However, the mitogenomes of only two species (Olidiana sp. and Taharana fasciana) in the subfamily Coelidiinae have been assembled. Here, we report the first complete mitogenome assembly of the genus Olidiana. Methods Specimens were collected from Wenxian County (Gansu Province, China) and identified on the basis of their morphology. Mitogenomes were sequenced by next-generation sequencing, following which an NGS template was generated, and this was confirmed using polymerase chain reaction and Sanger sequencing. Phylogenic trees were constructed using maximum likelihood and Bayesian analyses. Results The mitogenome of O. ritcheriina was 15,166 bp long, with an A + T content of 78.0%. Compared with the mitogenome of other Cicadellidae sp., the gene order, gene content, gene size, base composition, and codon usage of protein-coding genes (PCGs) in O. ritcheriina were highly conserved. The standard start codon of all PCGs was ATN and stop codon was TAA or TAG; COII, COIII, and ND4L ended with a single T. All tRNA genes showed the typical cloverleaf secondary structure, except for trnSer, which did not have the dihydrouridine arm. Furthermore, the secondary structures of rRNAs (rrnL and rrnS) in O. ritcheriina were predicted. Overall, five domains and 42 helices were predicted for rrnL (domain III is absent in arthropods), and three structural domains and 27 helices were predicted for rrnS. Maximum likelihood and Bayesian analyses indicated that O. ritcheriina and other Coelidiinae members were clustered into a clade, indicating the relationships among their subfamilies; the main topology was as follows: (Deltocephalinae + ((Coelidiinae + Iassinae) + ((Typhlocybinae + Cicadellinae) + (Idiocerinae + (Treehopper + Megophthalminae))))). The phylogenetic relationships indicated that the molecular taxonomy of O. ritcheriina is co…
bibliographic citation: Wang et al. (2019) Complete mitogenome of Olidiana ritcheriina (Hemiptera: Cicadellidae) and phylogeny of Cicadellidae. PeerJ 7:e8072 https://doi.org/10.7717/peerj.8072
date submitted: 2019-04-27
date accepted: 2019-10-21
issued: 2019-11-26
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Wang
  given name: Xian-Yi
author list: Agent
  family name: Wang
  given name: Jia-Jia
author list: Agent
  family name: Fan
  given name: Zhi-Hua
author list: Agent
  family name: Dai
  given name: Ren-Huai
doi: 10.7717/peerj.8072
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-11-26
copyright: ©2019 Wang et al.
attribution name: Wang et al.

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