PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
items: Medial knee joint contact force in the intact limb during walking in recently ambulatory service members with unilateral limb loss: a cross-sectional study
items: Demographic, ecological, and physiological responses of ringed seals to an abrupt decline in sea ice availability
items: Are sawfishes still present in Mozambique? A baseline ecological study
items: Comparison of admission random glucose, fasting glucose, and glycated hemoglobin in predicting the neurological outcome of acute ischemic stroke: a retrospective study
items: Do syntopic host species harbour similar symbiotic communities? The case of Chaetopterus spp. (Annelida: Chaetopteridae)
items: The embryonic life history of the tropical sea hare Stylocheilus striatus (Gastropoda: Opisthobranchia) under ambient and elevated ocean temperatures
items: What has been missed for predicting human attention in viewing driving clips?
items: Epidermal cell death in frogs with chytridiomycosis
items: Untargeted metabolomics approach for unraveling robust biomarkers of nutritional status in fasted gilthead sea bream (Sparus aurata)
items: Successive DNA extractions improve characterization of soil microbial communities

Medial knee joint contact force in the intact limb during walking in recently ambulatory service members with unilateral limb loss: a cross-sectional study
type: item
type: AcademicArticle
description: Background Individuals with unilateral lower limb amputation have a high risk of developing knee osteoarthritis (OA) in their intact limb as they age. This risk may be related to joint loading experienced earlier in life. We hypothesized that loading during walking would be greater in the intact limb of young US military service members with limb loss than in controls with no limb loss. Methods Cross-sectional instrumented gait analysis at self-selected walking speeds with a limb loss group (N = 10, age 27 ± 5 years, 170 ± 36 days since last surgery) including five service members with transtibial limb loss and five with transfemoral limb loss, all walking independently with their first prosthesis for approximately two months. Controls (N = 10, age 30 ± 4 years) were service members with no overt demographical risk factors for knee OA. 3D inverse dynamics modeling was performed to calculate joint moments and medial knee joint contact forces (JCF) were calculated using a reduction-based musculoskeletal modeling method and expressed relative to body weight (BW). Results Peak JCF and maximum JCF loading rate were significantly greater in limb loss (184% BW, 2,469% BW/s) vs. controls (157% BW, 1,985% BW/s), with large effect sizes. Results were robust to probabilistic perturbations to the knee model parameters. Discussion Assuming these data are reflective of joint loading experienced in daily life, they support a “mechanical overloading” hypothesis for the risk of developing knee OA in the intact limb of limb loss subjects. Examination of the evolution of gait mechanics, joint loading, and joint health over time, as well as interventions to reduce load or strengthen the ability of the joint to withstand loads, is warranted.
format: application/pdf
format: text/html
creator: Ross H. Miller
creator: Rebecca L. Krupenevich
creator: Alison L. Pruziner
creator: Erik J. Wolf
creator: Barri L. Schnall
subject: Bioengineering
subject: Anatomy and Physiology
subject: Kinesiology
description: doi:10.7717/peerj.2960
publisher: PeerJ Inc.
rights: © 2017 Miller et al.
abstract: Background Individuals with unilateral lower limb amputation have a high risk of developing knee osteoarthritis (OA) in their intact limb as they age. This risk may be related to joint loading experienced earlier in life. We hypothesized that loading during walking would be greater in the intact limb of young US military service members with limb loss than in controls with no limb loss. Methods Cross-sectional instrumented gait analysis at self-selected walking speeds with a limb loss group (N = 10, age 27 ± 5 years, 170 ± 36 days since last surgery) including five service members with transtibial limb loss and five with transfemoral limb loss, all walking independently with their first prosthesis for approximately two months. Controls (N = 10, age 30 ± 4 years) were service members with no overt demographical risk factors for knee OA. 3D inverse dynamics modeling was performed to calculate joint moments and medial knee joint contact forces (JCF) were calculated using a reduction-based musculoskeletal modeling method and expressed relative to body weight (BW). Results Peak JCF and maximum JCF loading rate were significantly greater in limb loss (184% BW, 2,469% BW/s) vs. controls (157% BW, 1,985% BW/s), with large effect sizes. Results were robust to probabilistic perturbations to the knee model parameters. Discussion Assuming these data are reflective of joint loading experienced in daily life, they support a “mechanical overloading” hypothesis for the risk of developing knee OA in the intact limb of limb loss subjects. Examination of the evolution of gait mechanics, joint loading, and joint health over time, as well as interventions to reduce load or strengthen the ability of the joint to withstand loads, is warranted.
bibliographic citation: Miller et al. (2017) Medial knee joint contact force in the intact limb during walking in recently ambulatory service members with unilateral limb loss: a cross-sectional study. PeerJ 5:e2960 https://doi.org/10.7717/peerj.2960
date submitted: 2016-10-24
date accepted: 2017-01-05
issued: 2017-02-02
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Miller
  given name: Ross H.
author list: Agent
  family name: Krupenevich
  given name: Rebecca L.
author list: Agent
  family name: Pruziner
  given name: Alison L.
author list: Agent
  family name: Wolf
  given name: Erik J.
author list: Agent
  family name: Schnall
  given name: Barri L.
doi: 10.7717/peerj.2960
volume: 5
issn: 2167-8359
publication name: PeerJ
publication date: 2017-02-02
copyright: ©2017 Miller et al.
attribution name: Miller et al.

Demographic, ecological, and physiological responses of ringed seals to an abrupt decline in sea ice availability
type: item
type: AcademicArticle
description: To assess whether demographic declines of Arctic species at the southern limit of their range will be gradual or punctuated, we compared large-scale environmental patterns including sea ice dynamics to ringed seal (Pusa hispida) reproduction, body condition, recruitment, and stress in Hudson Bay from 2003 to 2013. Aerial surveys suggested a gradual decline in seal density from 1995 to 2013, with the lowest density occurring in 2013. Body condition decreased and stress (cortisol) increased over time in relation to longer open water periods. The 2010 open water period in Hudson Bay coincided with extremes in large-scale atmospheric patterns (North Atlantic Oscillation, Arctic Oscillation, El Nino-Southern Oscillation) resulting in the earliest spring breakup and the latest ice formation on record. The warming event was coincident with high stress level, low ovulation rate, low pregnancy rate, few pups in the Inuit harvest, and observations of sick seals. Results provide evidence of changes in the condition of Arctic marine mammals in relation to climate mediated sea ice dynamics. We conclude that although negative demographic responses of Hudson Bay seals are occurring gradually with diminishing sea ice, a recent episodic environmental event played a significant role in a punctuated population decline.
format: application/pdf
format: text/html
creator: Steven H. Ferguson
creator: Brent G. Young
creator: David J. Yurkowski
creator: Randi Anderson
creator: Cornelia Willing
creator: Ole Nielsen
subject: Biogeography
subject: Climate Change Biology
subject: Conservation Biology
subject: Ecology
subject: Marine Biology
description: doi:10.7717/peerj.2957
publisher: PeerJ Inc.
rights: © 2017 Ferguson et al.
abstract: To assess whether demographic declines of Arctic species at the southern limit of their range will be gradual or punctuated, we compared large-scale environmental patterns including sea ice dynamics to ringed seal (Pusa hispida) reproduction, body condition, recruitment, and stress in Hudson Bay from 2003 to 2013. Aerial surveys suggested a gradual decline in seal density from 1995 to 2013, with the lowest density occurring in 2013. Body condition decreased and stress (cortisol) increased over time in relation to longer open water periods. The 2010 open water period in Hudson Bay coincided with extremes in large-scale atmospheric patterns (North Atlantic Oscillation, Arctic Oscillation, El Nino-Southern Oscillation) resulting in the earliest spring breakup and the latest ice formation on record. The warming event was coincident with high stress level, low ovulation rate, low pregnancy rate, few pups in the Inuit harvest, and observations of sick seals. Results provide evidence of changes in the condition of Arctic marine mammals in relation to climate mediated sea ice dynamics. We conclude that although negative demographic responses of Hudson Bay seals are occurring gradually with diminishing sea ice, a recent episodic environmental event played a significant role in a punctuated population decline.
bibliographic citation: Ferguson et al. (2017) Demographic, ecological, and physiological responses of ringed seals to an abrupt decline in sea ice availability. PeerJ 5:e2957 https://doi.org/10.7717/peerj.2957
date submitted: 2016-07-22
date accepted: 2017-01-04
issued: 2017-02-02
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Ferguson
  given name: Steven H.
author list: Agent
  family name: Young
  given name: Brent G.
author list: Agent
  family name: Yurkowski
  given name: David J.
author list: Agent
  family name: Anderson
  given name: Randi
author list: Agent
  family name: Willing
  given name: Cornelia
author list: Agent
  family name: Nielsen
  given name: Ole
doi: 10.7717/peerj.2957
volume: 5
issn: 2167-8359
publication name: PeerJ
publication date: 2017-02-02
copyright: © 2017 Ferguson et al.
attribution name: Ferguson et al.

Are sawfishes still present in Mozambique? A baseline ecological study
type: item
type: AcademicArticle
description: Sawfishes (Pristidae) were formerly abundant in the western Indian Ocean, but current data on sawfish presence and distribution are lacking for most of the region. This paper summarises historical records of sawfishes in Mozambican waters and presents the findings of the first assessment of the presence and status of sawfishes in Mozambique. A countrywide baseline assessment was undertaken between May and July 2014, using interviews with artisanal, semi-industrial and industrial fishers, fish traders and fisheries monitoring staff as the primary source of information on sawfish distribution, recent catches, socio-economic value and cultural importance. Additional interviews were conducted via email or telephone with individuals running sport fishing operations or who otherwise had considerable experience interacting with the fishing sectors or the marine environment in Mozambique. Where encountered, sawfish rostra were photographed and a series of measurements and associated data were collected. In total, 200 questionnaire surveys and seven interviews with recreational fishing and dive operators were conducted, and 19 rostra were documented from museum archives and private collections, belonging to two sawfish species, the Largetooth Sawfish (Pristis pristis) and Green Sawfish (P. zijsron). The most recent captures of sawfishes were reported to have occurred in 2014. Two key sites were identified where both recent encounters were reported and numerous Largetooth Sawfish rostra were documented. Gill nets were the fishing gear most commonly attributed to sawfish catches. Sawfishes did not hold any cultural importance in Mozambique, but they have at least some socio-economic importance to artisanal fishers, primarily through the sale of their fins. The meat did not appear to be held in high regard and was usually consumed locally. Sampling and further research is now required to confirm the presence of sawfishes and to assess the primary threats to sawfishes in those a…
format: application/pdf
format: text/html
creator: Ruth H. Leeney
subject: Aquaculture, Fisheries and Fish Science
subject: Conservation Biology
subject: Marine Biology
subject: Natural Resource Management
description: doi:10.7717/peerj.2950
publisher: PeerJ Inc.
rights: © 2017 Leeney
abstract: Sawfishes (Pristidae) were formerly abundant in the western Indian Ocean, but current data on sawfish presence and distribution are lacking for most of the region. This paper summarises historical records of sawfishes in Mozambican waters and presents the findings of the first assessment of the presence and status of sawfishes in Mozambique. A countrywide baseline assessment was undertaken between May and July 2014, using interviews with artisanal, semi-industrial and industrial fishers, fish traders and fisheries monitoring staff as the primary source of information on sawfish distribution, recent catches, socio-economic value and cultural importance. Additional interviews were conducted via email or telephone with individuals running sport fishing operations or who otherwise had considerable experience interacting with the fishing sectors or the marine environment in Mozambique. Where encountered, sawfish rostra were photographed and a series of measurements and associated data were collected. In total, 200 questionnaire surveys and seven interviews with recreational fishing and dive operators were conducted, and 19 rostra were documented from museum archives and private collections, belonging to two sawfish species, the Largetooth Sawfish (Pristis pristis) and Green Sawfish (P. zijsron). The most recent captures of sawfishes were reported to have occurred in 2014. Two key sites were identified where both recent encounters were reported and numerous Largetooth Sawfish rostra were documented. Gill nets were the fishing gear most commonly attributed to sawfish catches. Sawfishes did not hold any cultural importance in Mozambique, but they have at least some socio-economic importance to artisanal fishers, primarily through the sale of their fins. The meat did not appear to be held in high regard and was usually consumed locally. Sampling and further research is now required to confirm the presence of sawfishes and to assess the primary threats to sawfishes in those a…
bibliographic citation: Leeney (2017) Are sawfishes still present in Mozambique? A baseline ecological study. PeerJ 5:e2950 https://doi.org/10.7717/peerj.2950
date submitted: 2016-06-21
date accepted: 2016-12-30
issued: 2017-02-02
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Leeney
  given name: Ruth H.
doi: 10.7717/peerj.2950
volume: 5
issn: 2167-8359
publication name: PeerJ
publication date: 2017-02-02
copyright: ©2017 Leeney
attribution name: Leeney

Comparison of admission random glucose, fasting glucose, and glycated hemoglobin in predicting the neurological outcome of acute ischemic stroke: a retrospective study
type: item
type: AcademicArticle
description: Background Hyperglycemia is a known predictor of negative outcomes in stroke. Several glycemic measures, including admission random glucose, fasting glucose, and glycated hemoglobin (HbA1c), have been associated with bad neurological outcomes in acute ischemic stroke, particularly in nondiabetic patients. However, the predictive power of these glycemic measures is yet to be investigated. Methods This retrospective study enrolled 484 patients with acute ischemic stroke from January 2009 to March 2013, and complete records of initial stroke severity, neurological outcomes at three months, and glycemic measures were evaluated. We examined the predictive power of admission random glucose, fasting glucose, and HbA1c for neurological outcomes in acute ischemic stroke. Furthermore, subgroup analyses of nondiabetic patients and patients with diabetes were performed separately. Results Receiver operating characteristic (ROC) analysis revealed that admission random glucose and fasting glucose were significant predictors of poor neurological outcomes, whereas HbA1c was not (areas under the ROC curve (AUCs): admission random glucose = 0.564, p = 0.026; fasting glucose = 0.598, p = 0.001; HbA1c = 0.510, p = 0.742). Subgroup analyses of nondiabetic patients and those with diabetes revealed that only fasting glucose predicts neurological outcomes in patients with diabetes, and the AUCs of these three glycemic measures did not differ between the two groups. A multivariate logistic regression analysis of the study patients indicated that only age, initial stroke severity, and fasting glucose were independent predictors of poor neurological outcomes, whereas admission random glucose and HbA1c were not (adjusted odds ratio: admission random glucose = 1.002, p = 0.228; fasting glucose = 1.005, p = 0.039; HbA1c = 1.160, p = 0.076). Furthermore, subgroup multivariate logistic regression analyses of nondiabetic patients and those with diabetes indicated that none of the three glycemic mea…
format: application/pdf
format: text/html
creator: Jia-Ying Sung
creator: Chin-I Chen
creator: Yi-Chen Hsieh
creator: Yih-Ru Chen
creator: Hsin-Chiao Wu
creator: Lung Chan
creator: Chaur-Jong Hu
creator: Han-Hwa Hu
creator: Hung-Yi Chiou
creator: Nai-Fang Chi
subject: Diabetes and Endocrinology
subject: Neurology
description: doi:10.7717/peerj.2948
publisher: PeerJ Inc.
rights: © 2017 Sung et al.
abstract: Background Hyperglycemia is a known predictor of negative outcomes in stroke. Several glycemic measures, including admission random glucose, fasting glucose, and glycated hemoglobin (HbA1c), have been associated with bad neurological outcomes in acute ischemic stroke, particularly in nondiabetic patients. However, the predictive power of these glycemic measures is yet to be investigated. Methods This retrospective study enrolled 484 patients with acute ischemic stroke from January 2009 to March 2013, and complete records of initial stroke severity, neurological outcomes at three months, and glycemic measures were evaluated. We examined the predictive power of admission random glucose, fasting glucose, and HbA1c for neurological outcomes in acute ischemic stroke. Furthermore, subgroup analyses of nondiabetic patients and patients with diabetes were performed separately. Results Receiver operating characteristic (ROC) analysis revealed that admission random glucose and fasting glucose were significant predictors of poor neurological outcomes, whereas HbA1c was not (areas under the ROC curve (AUCs): admission random glucose = 0.564, p = 0.026; fasting glucose = 0.598, p = 0.001; HbA1c = 0.510, p = 0.742). Subgroup analyses of nondiabetic patients and those with diabetes revealed that only fasting glucose predicts neurological outcomes in patients with diabetes, and the AUCs of these three glycemic measures did not differ between the two groups. A multivariate logistic regression analysis of the study patients indicated that only age, initial stroke severity, and fasting glucose were independent predictors of poor neurological outcomes, whereas admission random glucose and HbA1c were not (adjusted odds ratio: admission random glucose = 1.002, p = 0.228; fasting glucose = 1.005, p = 0.039; HbA1c = 1.160, p = 0.076). Furthermore, subgroup multivariate logistic regression analyses of nondiabetic patients and those with diabetes indicated that none of the three glycemic mea…
bibliographic citation: Sung et al. (2017) Comparison of admission random glucose, fasting glucose, and glycated hemoglobin in predicting the neurological outcome of acute ischemic stroke: a retrospective study. PeerJ 5:e2948 https://doi.org/10.7717/peerj.2948
date submitted: 2016-10-24
date accepted: 2016-12-30
issued: 2017-02-02
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Sung
  given name: Jia-Ying
author list: Agent
  family name: Chen
  given name: Chin-I
author list: Agent
  family name: Hsieh
  given name: Yi-Chen
author list: Agent
  family name: Chen
  given name: Yih-Ru
author list: Agent
  family name: Wu
  given name: Hsin-Chiao
author list: Agent
  family name: Chan
  given name: Lung
author list: Agent
  family name: Hu
  given name: Chaur-Jong
author list: Agent
  family name: Hu
  given name: Han-Hwa
author list: Agent
  family name: Chiou
  given name: Hung-Yi
author list: Agent
  family name: Chi
  given name: Nai-Fang
doi: 10.7717/peerj.2948
volume: 5
issn: 2167-8359
publication name: PeerJ
publication date: 2017-02-02
copyright: ©2017 Sung et al.
attribution name: Sung et al.

Do syntopic host species harbour similar symbiotic communities? The case of Chaetopterus spp. (Annelida: Chaetopteridae)
type: item
type: AcademicArticle
description: To assess whether closely related host species harbour similar symbiotic communities, we studied two polychaetes, Chaetopterus sp. (n = 11) and Chaetopterus cf. appendiculatus (n = 83) living in soft sediments of Nhatrang Bay (South China Sea, Vietnam). The former harboured the porcellanid crabs Polyonyx cf. heok and Polyonyx sp., the pinnotherid crab Tetrias sp. and the tergipedid nudibranch Phestilla sp. The latter harboured the polynoid polychaete Ophthalmonoe pettiboneae, the carapid fish Onuxodon fowleri and the porcellanid crab Eulenaios cometes, all of which, except O. fowleri, seemed to be specialized symbionts. The species richness and mean intensity of the symbionts were higher in Chaetopterus sp. than in C. cf. appendiculatus (1.8 and 1.02 species and 3.0 and 1.05 individuals per host respectively). We suggest that the lower density of Chaetopterus sp. may explain the higher number of associated symbionts observed, as well as the 100% prevalence (69.5% in C. cf. appenciculatus). Most Chaetopterus sp. harboured two symbiotic species, which was extremely rare in C. cf. appendiculatus, suggesting lower interspecific interactions in the former. The crab and nudibranch symbionts of Chaetopterus sp. often shared a host and lived in pairs, thus partitioning resources. This led to the species coexisting in the tubes of Chaetopterus sp., establishing a tightly packed community, indicating high species richness and mean intensity, together with a low species dominance. In contrast, the aggressive, strictly territorial species associated with C. cf. appendiculatus established a symbiotic community strongly dominated by single species and, thus, low species richness and mean intensity. Therefore, we suggest that interspecific interactions are determining species richness, intensity and dominance, while intraspecific interactions are influencing only intensity and abundance. It is possible that species composition may have influenced the differences in community struc…
format: application/pdf
format: text/html
creator: Temir A. Britayev
creator: Elena Mekhova
creator: Yury Deart
creator: Daniel Martin
subject: Biodiversity
subject: Ecology
subject: Marine Biology
subject: Zoology
description: doi:10.7717/peerj.2930
publisher: PeerJ Inc.
rights: © 2017 Britayev et al.
abstract: To assess whether closely related host species harbour similar symbiotic communities, we studied two polychaetes, Chaetopterus sp. (n = 11) and Chaetopterus cf. appendiculatus (n = 83) living in soft sediments of Nhatrang Bay (South China Sea, Vietnam). The former harboured the porcellanid crabs Polyonyx cf. heok and Polyonyx sp., the pinnotherid crab Tetrias sp. and the tergipedid nudibranch Phestilla sp. The latter harboured the polynoid polychaete Ophthalmonoe pettiboneae, the carapid fish Onuxodon fowleri and the porcellanid crab Eulenaios cometes, all of which, except O. fowleri, seemed to be specialized symbionts. The species richness and mean intensity of the symbionts were higher in Chaetopterus sp. than in C. cf. appendiculatus (1.8 and 1.02 species and 3.0 and 1.05 individuals per host respectively). We suggest that the lower density of Chaetopterus sp. may explain the higher number of associated symbionts observed, as well as the 100% prevalence (69.5% in C. cf. appenciculatus). Most Chaetopterus sp. harboured two symbiotic species, which was extremely rare in C. cf. appendiculatus, suggesting lower interspecific interactions in the former. The crab and nudibranch symbionts of Chaetopterus sp. often shared a host and lived in pairs, thus partitioning resources. This led to the species coexisting in the tubes of Chaetopterus sp., establishing a tightly packed community, indicating high species richness and mean intensity, together with a low species dominance. In contrast, the aggressive, strictly territorial species associated with C. cf. appendiculatus established a symbiotic community strongly dominated by single species and, thus, low species richness and mean intensity. Therefore, we suggest that interspecific interactions are determining species richness, intensity and dominance, while intraspecific interactions are influencing only intensity and abundance. It is possible that species composition may have influenced the differences in community struc…
bibliographic citation: Britayev et al. (2017) Do syntopic host species harbour similar symbiotic communities? The case of Chaetopterus spp. (Annelida: Chaetopteridae). PeerJ 5:e2930 https://doi.org/10.7717/peerj.2930
date submitted: 2016-10-10
date accepted: 2016-12-21
issued: 2017-02-02
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Britayev
  given name: Temir A.
author list: Agent
  family name: Mekhova
  given name: Elena
author list: Agent
  family name: Deart
  given name: Yury
author list: Agent
  family name: Martin
  given name: Daniel
doi: 10.7717/peerj.2930
volume: 5
issn: 2167-8359
publication name: PeerJ
publication date: 2017-02-02
copyright: ©2017 Britayev et al.
attribution name: Britayev et al.

The embryonic life history of the tropical sea hare Stylocheilus striatus (Gastropoda: Opisthobranchia) under ambient and elevated ocean temperatures
type: item
type: AcademicArticle
description: Ocean warming represents a major threat to marine biota worldwide, and forecasting ecological ramifications is a high priority as atmospheric carbon dioxide (CO2) emissions continue to rise. Fitness of marine species relies critically on early developmental and reproductive stages, but their sensitivity to environmental stressors may be a bottleneck in future warming oceans. The present study focuses on the tropical sea hare, Stylocheilus striatus (Gastropoda: Opisthobranchia), a common species found throughout the Indo-West Pacific and Atlantic Oceans. Its ecological importance is well-established, particularly as a specialist grazer of the toxic cyanobacterium, Lyngbya majuscula. Although many aspects of its biology and ecology are well-known, description of its early developmental stages is lacking. First, a detailed account of this species’ life history is described, including reproductive behavior, egg mass characteristics and embryonic development phases. Key developmental features are then compared between embryos developed in present-day (ambient) and predicted end-of-century elevated ocean temperatures (+3 °C). Results showed developmental stages of embryos reared at ambient temperature were typical of other opisthobranch species, with hatching of planktotrophic veligers occurring 4.5 days post-oviposition. However, development times significantly decreased under elevated temperature, with key embryonic features such as the velum, statocysts, operculum, eyespots and protoconch developing approximately 24 h earlier when compared to ambient temperature. Although veligers hatched one day earlier under elevated temperature, their shell size decreased by approximately 20%. Our findings highlight how an elevated thermal environment accelerates planktotrophic development of this important benthic invertebrate, possibly at the cost of reducing fitness and increasing mortality.
format: application/pdf
format: text/html
creator: Rael Horwitz
creator: Matthew D. Jackson
creator: Suzanne C. Mills
subject: Climate Change Biology
subject: Developmental Biology
subject: Ecology
subject: Environmental Sciences
subject: Marine Biology
description: doi:10.7717/peerj.2956
publisher: PeerJ Inc.
rights: © 2017 Horwitz et al.
abstract: Ocean warming represents a major threat to marine biota worldwide, and forecasting ecological ramifications is a high priority as atmospheric carbon dioxide (CO2) emissions continue to rise. Fitness of marine species relies critically on early developmental and reproductive stages, but their sensitivity to environmental stressors may be a bottleneck in future warming oceans. The present study focuses on the tropical sea hare, Stylocheilus striatus (Gastropoda: Opisthobranchia), a common species found throughout the Indo-West Pacific and Atlantic Oceans. Its ecological importance is well-established, particularly as a specialist grazer of the toxic cyanobacterium, Lyngbya majuscula. Although many aspects of its biology and ecology are well-known, description of its early developmental stages is lacking. First, a detailed account of this species’ life history is described, including reproductive behavior, egg mass characteristics and embryonic development phases. Key developmental features are then compared between embryos developed in present-day (ambient) and predicted end-of-century elevated ocean temperatures (+3 °C). Results showed developmental stages of embryos reared at ambient temperature were typical of other opisthobranch species, with hatching of planktotrophic veligers occurring 4.5 days post-oviposition. However, development times significantly decreased under elevated temperature, with key embryonic features such as the velum, statocysts, operculum, eyespots and protoconch developing approximately 24 h earlier when compared to ambient temperature. Although veligers hatched one day earlier under elevated temperature, their shell size decreased by approximately 20%. Our findings highlight how an elevated thermal environment accelerates planktotrophic development of this important benthic invertebrate, possibly at the cost of reducing fitness and increasing mortality.
bibliographic citation: Horwitz et al. (2017) The embryonic life history of the tropical sea hare Stylocheilus striatus (Gastropoda: Opisthobranchia) under ambient and elevated ocean temperatures. PeerJ 5:e2956 https://doi.org/10.7717/peerj.2956
date submitted: 2016-10-17
date accepted: 2017-01-04
issued: 2017-02-01
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Horwitz
  given name: Rael
author list: Agent
  family name: Jackson
  given name: Matthew D.
author list: Agent
  family name: Mills
  given name: Suzanne C.
doi: 10.7717/peerj.2956
volume: 5
issn: 2167-8359
publication name: PeerJ
publication date: 2017-02-01
copyright: ©2017 Horwitz et al.
attribution name: Horwitz et al.

What has been missed for predicting human attention in viewing driving clips?
type: item
type: AcademicArticle
description: Recent research progress on the topic of human visual attention allocation in scene perception and its simulation is based mainly on studies with static images. However, natural vision requires us to extract visual information that constantly changes due to egocentric movements or dynamics of the world. It is unclear to what extent spatio-temporal regularity, an inherent regularity in dynamic vision, affects human gaze distribution and saliency computation in visual attention models. In this free-viewing eye-tracking study we manipulated the spatio-temporal regularity of traffic videos by presenting them in normal video sequence, reversed video sequence, normal frame sequence, and randomised frame sequence. The recorded human gaze allocation was then used as the ‘ground truth’ to examine the predictive ability of a number of state-of-the-art visual attention models. The analysis revealed high inter-observer agreement across individual human observers, but all the tested attention models performed significantly worse than humans. The inferior predictability of the models was evident from indistinguishable gaze prediction irrespective of stimuli presentation sequence, and weak central fixation bias. Our findings suggest that a realistic visual attention model for the processing of dynamic scenes should incorporate human visual sensitivity with spatio-temporal regularity and central fixation bias.
format: application/pdf
format: text/html
creator: Jiawei Xu
creator: Shigang Yue
creator: Federica Menchinelli
creator: Kun Guo
subject: Psychiatry and Psychology
description: doi:10.7717/peerj.2946
publisher: PeerJ Inc.
rights: © 2017 Xu et al.
abstract: Recent research progress on the topic of human visual attention allocation in scene perception and its simulation is based mainly on studies with static images. However, natural vision requires us to extract visual information that constantly changes due to egocentric movements or dynamics of the world. It is unclear to what extent spatio-temporal regularity, an inherent regularity in dynamic vision, affects human gaze distribution and saliency computation in visual attention models. In this free-viewing eye-tracking study we manipulated the spatio-temporal regularity of traffic videos by presenting them in normal video sequence, reversed video sequence, normal frame sequence, and randomised frame sequence. The recorded human gaze allocation was then used as the ‘ground truth’ to examine the predictive ability of a number of state-of-the-art visual attention models. The analysis revealed high inter-observer agreement across individual human observers, but all the tested attention models performed significantly worse than humans. The inferior predictability of the models was evident from indistinguishable gaze prediction irrespective of stimuli presentation sequence, and weak central fixation bias. Our findings suggest that a realistic visual attention model for the processing of dynamic scenes should incorporate human visual sensitivity with spatio-temporal regularity and central fixation bias.
bibliographic citation: Xu et al. (2017) What has been missed for predicting human attention in viewing driving clips?. PeerJ 5:e2946 https://doi.org/10.7717/peerj.2946
date submitted: 2016-06-24
date accepted: 2016-12-28
issued: 2017-02-01
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Xu
  given name: Jiawei
author list: Agent
  family name: Yue
  given name: Shigang
author list: Agent
  family name: Menchinelli
  given name: Federica
author list: Agent
  family name: Guo
  given name: Kun
doi: 10.7717/peerj.2946
volume: 5
issn: 2167-8359
publication name: PeerJ
publication date: 2017-02-01
copyright: ©2017 Xu et al.
attribution name: Xu et al.

Epidermal cell death in frogs with chytridiomycosis
type: item
type: AcademicArticle
description: Background Amphibians are declining at an alarming rate, and one of the major causes of decline is the infectious disease chytridiomycosis. Parasitic fungal sporangia occur within epidermal cells causing epidermal disruption, but these changes have not been well characterised. Apoptosis (planned cell death) can be a damaging response to the host but may alternatively be a mechanism of pathogen removal for some intracellular infections. Methods In this study we experimentally infected two endangered amphibian species Pseudophryne corroboree and Litoria verreauxii alpina with the causal agent of chytridiomycosis. We quantified cell death in the epidermis through two assays: terminal transferase-mediated dUTP nick end-labelling (TUNEL) and caspase 3/7. Results Cell death was positively associated with infection load and morbidity of clinically infected animals. In infected amphibians, TUNEL positive cells were concentrated in epidermal layers, correlating to the localisation of infection within the skin. Caspase activity was stable and low in early infection, where pathogen loads were light but increasing. In animals that recovered from infection, caspase activity gradually returned to normal as the infection cleared. Whereas, in amphibians that did not recover, caspase activity increased dramatically when infection loads peaked. Discussion Increased cell death may be a pathology of the fungal parasite, likely contributing to loss of skin homeostatic functions, but it is also possible that apoptosis suppression may be used initially by the pathogen to help establish infection. Further research should explore the specific mechanisms of cell death and more specifically apoptosis regulation during fungal infection.
format: application/pdf
format: text/html
creator: Laura A. Brannelly
creator: Alexandra A. Roberts
creator: Lee F. Skerratt
creator: Lee Berger
subject: Ecology
subject: Mycology
subject: Veterinary Medicine
subject: Histology
description: doi:10.7717/peerj.2925
publisher: PeerJ Inc.
rights: © 2017 Brannelly et al.
abstract: Background Amphibians are declining at an alarming rate, and one of the major causes of decline is the infectious disease chytridiomycosis. Parasitic fungal sporangia occur within epidermal cells causing epidermal disruption, but these changes have not been well characterised. Apoptosis (planned cell death) can be a damaging response to the host but may alternatively be a mechanism of pathogen removal for some intracellular infections. Methods In this study we experimentally infected two endangered amphibian species Pseudophryne corroboree and Litoria verreauxii alpina with the causal agent of chytridiomycosis. We quantified cell death in the epidermis through two assays: terminal transferase-mediated dUTP nick end-labelling (TUNEL) and caspase 3/7. Results Cell death was positively associated with infection load and morbidity of clinically infected animals. In infected amphibians, TUNEL positive cells were concentrated in epidermal layers, correlating to the localisation of infection within the skin. Caspase activity was stable and low in early infection, where pathogen loads were light but increasing. In animals that recovered from infection, caspase activity gradually returned to normal as the infection cleared. Whereas, in amphibians that did not recover, caspase activity increased dramatically when infection loads peaked. Discussion Increased cell death may be a pathology of the fungal parasite, likely contributing to loss of skin homeostatic functions, but it is also possible that apoptosis suppression may be used initially by the pathogen to help establish infection. Further research should explore the specific mechanisms of cell death and more specifically apoptosis regulation during fungal infection.
bibliographic citation: Brannelly et al. (2017) Epidermal cell death in frogs with chytridiomycosis. PeerJ 5:e2925 https://doi.org/10.7717/peerj.2925
date submitted: 2016-08-10
date accepted: 2016-12-19
issued: 2017-02-01
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Brannelly
  given name: Laura A.
author list: Agent
  family name: Roberts
  given name: Alexandra A.
author list: Agent
  family name: Skerratt
  given name: Lee F.
author list: Agent
  family name: Berger
  given name: Lee
doi: 10.7717/peerj.2925
volume: 5
issn: 2167-8359
publication name: PeerJ
publication date: 2017-02-01
copyright: ©2017 Brannelly et al.
attribution name: Brannelly et al.

Untargeted metabolomics approach for unraveling robust biomarkers of nutritional status in fasted gilthead sea bream (Sparus aurata)
type: item
type: AcademicArticle
description: A metabolomic study has been performed to identify sensitive and robust biomarkers of malnutrition in farmed fish, using gilthead sea bream (Sparus aurata) as a model. The metabolomic fingerprinting of serum from fasted fish was assessed by means of ultra-high performance liquid chromatography coupled to quadrupole time-of-flight mass spectrometry. More than 15,000 different m/z ions were detected and Partial Least Squares–Discriminant analysis allowed a clear differentiation between the two experimental groups (fed and 10-day fasted fish) with more than 90% of total variance explained by the two first components. The most significant metabolites (up to 45) were elucidated on the basis of their tandem mass spectra with a broad representation of amino acids, oligopeptides, urea cycle metabolites, L-carnitine-related metabolites, glutathione-related metabolites, fatty acids, lysophosphatidic acids, phosphatidylcholines as well as biotin- and noradrenaline-related metabolites. This untargeted approach highlighted important adaptive responses in energy and oxidative metabolism, contributing to identify robust and nutritionally-regulated biomarkers of health and metabolic condition that will serve to assess the welfare status of farmed fish.
format: application/pdf
format: text/html
creator: Ruben Gil-Solsona
creator: Jaime Nácher-Mestre
creator: Leticia Lacalle-Bergeron
creator: Juan Vicente Sancho
creator: Josep Alvar Calduch-Giner
creator: Félix Hernández
creator: Jaume Pérez-Sánchez
subject: Aquaculture, Fisheries and Fish Science
subject: Biochemistry
subject: Bioinformatics
subject: Nutrition
subject: Metabolic Sciences
description: doi:10.7717/peerj.2920
publisher: PeerJ Inc.
rights: © 2017 Gil-Solsona et al.
abstract: A metabolomic study has been performed to identify sensitive and robust biomarkers of malnutrition in farmed fish, using gilthead sea bream (Sparus aurata) as a model. The metabolomic fingerprinting of serum from fasted fish was assessed by means of ultra-high performance liquid chromatography coupled to quadrupole time-of-flight mass spectrometry. More than 15,000 different m/z ions were detected and Partial Least Squares–Discriminant analysis allowed a clear differentiation between the two experimental groups (fed and 10-day fasted fish) with more than 90% of total variance explained by the two first components. The most significant metabolites (up to 45) were elucidated on the basis of their tandem mass spectra with a broad representation of amino acids, oligopeptides, urea cycle metabolites, L-carnitine-related metabolites, glutathione-related metabolites, fatty acids, lysophosphatidic acids, phosphatidylcholines as well as biotin- and noradrenaline-related metabolites. This untargeted approach highlighted important adaptive responses in energy and oxidative metabolism, contributing to identify robust and nutritionally-regulated biomarkers of health and metabolic condition that will serve to assess the welfare status of farmed fish.
bibliographic citation: Gil-Solsona et al. (2017) Untargeted metabolomics approach for unraveling robust biomarkers of nutritional status in fasted gilthead sea bream (Sparus aurata). PeerJ 5:e2920 https://doi.org/10.7717/peerj.2920
date submitted: 2016-11-10
date accepted: 2016-12-17
issued: 2017-02-01
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Gil-Solsona
  given name: Ruben
author list: Agent
  family name: Nácher-Mestre
  given name: Jaime
author list: Agent
  family name: Lacalle-Bergeron
  given name: Leticia
author list: Agent
  family name: Sancho
  given name: Juan Vicente
author list: Agent
  family name: Calduch-Giner
  given name: Josep Alvar
author list: Agent
  family name: Hernández
  given name: Félix
author list: Agent
  family name: Pérez-Sánchez
  given name: Jaume
doi: 10.7717/peerj.2920
volume: 5
issn: 2167-8359
publication name: PeerJ
publication date: 2017-02-01
copyright: ©2017 Gil-Solsona et al.
attribution name: Gil-Solsona et al.

Successive DNA extractions improve characterization of soil microbial communities
type: item
type: AcademicArticle
description: Currently, characterization of soil microbial communities relies heavily on the use of molecular approaches. Independently of the approach used, soil DNA extraction is a crucial step, and success of downstream procedures will depend on how well DNA extraction was performed. Often, studies describing and comparing soil microbial communities are based on a single DNA extraction, which may not lead to a representative recovery of DNA from all organisms present in the soil. The use of successive DNA extractions might improve soil microbial characterization, but the benefit of this approach has only been limitedly studied. To determine whether successive DNA extractions of the same soil sample would lead to different observations in terms of microbial abundance and community composition, we performed three successive extractions, with two widely used commercial kits, on a range of clay and sandy soils. Successive extractions increased DNA yield considerably (1–374%), as well as total bacterial and fungal abundances in most of the soil samples. Analysis of the 16S and 18S ribosomal RNA genes using 454-pyrosequencing, revealed that microbial community composition (taxonomic groups) observed in the successive DNA extractions were similar. However, successive DNA extractions did reveal several additional microbial groups. For some soil samples, shifts in microbial community composition were observed, mainly due to shifts in relative abundance of a number of microbial groups. Our results highlight that performing successive DNA extractions optimize DNA yield, and can lead to a better picture of overall community composition.
format: application/pdf
format: text/html
creator: Mauricio R. Dimitrov
creator: Annelies J. Veraart
creator: Mattias de Hollander
creator: Hauke Smidt
creator: Johannes A. van Veen
creator: Eiko E. Kuramae
subject: Microbiology
subject: Soil Science
description: doi:10.7717/peerj.2915
publisher: PeerJ Inc.
rights: © 2017 Dimitrov et al.
abstract: Currently, characterization of soil microbial communities relies heavily on the use of molecular approaches. Independently of the approach used, soil DNA extraction is a crucial step, and success of downstream procedures will depend on how well DNA extraction was performed. Often, studies describing and comparing soil microbial communities are based on a single DNA extraction, which may not lead to a representative recovery of DNA from all organisms present in the soil. The use of successive DNA extractions might improve soil microbial characterization, but the benefit of this approach has only been limitedly studied. To determine whether successive DNA extractions of the same soil sample would lead to different observations in terms of microbial abundance and community composition, we performed three successive extractions, with two widely used commercial kits, on a range of clay and sandy soils. Successive extractions increased DNA yield considerably (1–374%), as well as total bacterial and fungal abundances in most of the soil samples. Analysis of the 16S and 18S ribosomal RNA genes using 454-pyrosequencing, revealed that microbial community composition (taxonomic groups) observed in the successive DNA extractions were similar. However, successive DNA extractions did reveal several additional microbial groups. For some soil samples, shifts in microbial community composition were observed, mainly due to shifts in relative abundance of a number of microbial groups. Our results highlight that performing successive DNA extractions optimize DNA yield, and can lead to a better picture of overall community composition.
bibliographic citation: Dimitrov et al. (2017) Successive DNA extractions improve characterization of soil microbial communities. PeerJ 5:e2915 https://doi.org/10.7717/peerj.2915
date submitted: 2016-06-27
date accepted: 2016-12-15
issued: 2017-02-01
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Dimitrov
  given name: Mauricio R.
author list: Agent
  family name: Veraart
  given name: Annelies J.
author list: Agent
  family name: de Hollander
  given name: Mattias
author list: Agent
  family name: Smidt
  given name: Hauke
author list: Agent
  family name: van Veen
  given name: Johannes A.
author list: Agent
  family name: Kuramae
  given name: Eiko E.
doi: 10.7717/peerj.2915
volume: 5
issn: 2167-8359
publication name: PeerJ
publication date: 2017-02-01
copyright: © 2017 Dimitrov et al.
attribution name: Dimitrov et al.

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