PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
items: Conspicuous carotenoid-based pelvic spine ornament in three-spined stickleback populations—occurrence and inheritance
items: Psychosocial interventions for adults with visible differences: a systematic review
items: Self-regulatory mode (locomotion and assessment), well-being (subjective and psychological), and exercise behavior (frequency and intensity) in relation to high school pupils’ academic achievement
items: The effects of set volume during isolated lumbar extension resistance training in recreationally trained males
items: Proteomic responses to hypoxia at different temperatures in the great scallop (Pecten maximus)
items: A questions-based investigation of consumer mental-health information
items: The right whale mandatory ship reporting system: a retrospective
items: Effect of different heterotrophic plate count methods on the estimation of the composition of the culturable microbial community
items: A reproducible approach to high-throughput biological data acquisition and integration
items: Effects of preservation methods of muscle tissue from upper-trophic level reef fishes on stable isotope values (δ13C and δ15N)

Conspicuous carotenoid-based pelvic spine ornament in three-spined stickleback populations—occurrence and inheritance
type: item
type: AcademicArticle
description: Reports on reddish carotenoid-based ornaments in female three-spined sticklebacks (Gasterosteus aculeatus) are few, despite the large interest in the species’ behaviour, ornamentation, morphology and evolution. We sampled sticklebacks from 17 sites in north-western Europe in this first extensive study on the occurrence of carotenoid-based female pelvic spines and throat ornaments. The field results showed that females, and males, with reddish spines were found in all 17 populations. Specimens of both sexes with conspicuous red spines were found in several of the sites. The pelvic spines of males were more intensely red compared to the females’ spines, and large specimens were more red than small ones. Fish infected with the tapeworm (Schistocephalus solidus) had drabber spines than uninfected fish. Both sexes had red spines both during and after the spawning period, but the intensity of the red colour was more exaggerated during the spawning period. As opposed to pelvic spines, no sign of red colour at the throat was observed in any female from any of the 17 populations. A rearing experiment was carried out to estimate a potential genetic component of the pelvic spine ornament by artificial crossing and rearing of 15 family groups during a 12 months period. The results indicated that the genetic component of the red colour at the spines was low or close to zero. Although reddish pelvic spines seem common in populations of stickleback, the potential adaptive function of the reddish pelvic spines remains largely unexplained.
format: application/pdf
format: text/html
creator: CR Amundsen
creator: JT Nordeide
creator: HM Gjøen
creator: B Larsen
creator: ES Egeland
subject: Animal Behavior
subject: Aquaculture, Fisheries and Fish Science
subject: Evolutionary Studies
subject: Zoology
description: doi:10.7717/peerj.872
publisher: PeerJ Inc.
rights: © 2015 Amundsen et al.
abstract: Reports on reddish carotenoid-based ornaments in female three-spined sticklebacks (Gasterosteus aculeatus) are few, despite the large interest in the species’ behaviour, ornamentation, morphology and evolution. We sampled sticklebacks from 17 sites in north-western Europe in this first extensive study on the occurrence of carotenoid-based female pelvic spines and throat ornaments. The field results showed that females, and males, with reddish spines were found in all 17 populations. Specimens of both sexes with conspicuous red spines were found in several of the sites. The pelvic spines of males were more intensely red compared to the females’ spines, and large specimens were more red than small ones. Fish infected with the tapeworm (Schistocephalus solidus) had drabber spines than uninfected fish. Both sexes had red spines both during and after the spawning period, but the intensity of the red colour was more exaggerated during the spawning period. As opposed to pelvic spines, no sign of red colour at the throat was observed in any female from any of the 17 populations. A rearing experiment was carried out to estimate a potential genetic component of the pelvic spine ornament by artificial crossing and rearing of 15 family groups during a 12 months period. The results indicated that the genetic component of the red colour at the spines was low or close to zero. Although reddish pelvic spines seem common in populations of stickleback, the potential adaptive function of the reddish pelvic spines remains largely unexplained.
bibliographic citation: Amundsen et al. (2015) Conspicuous carotenoid-based pelvic spine ornament in three-spined stickleback populations—occurrence and inheritance. PeerJ 3:e872 https://doi.org/10.7717/peerj.872
date submitted: 2015-01-13
date accepted: 2015-03-11
issued: 2015-04-02
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Amundsen
  given name: CR
author list: Agent
  family name: Nordeide
  given name: JT
author list: Agent
  family name: Gjøen
  given name: HM
author list: Agent
  family name: Larsen
  given name: B
author list: Agent
  family name: Egeland
  given name: ES
doi: 10.7717/peerj.872
volume: 3
issn: 2167-8359
publication name: PeerJ
publication date: 2015-04-02
copyright: © 2015 Amundsen et al.
attribution name: Amundsen et al.

Psychosocial interventions for adults with visible differences: a systematic review
type: item
type: AcademicArticle
description: Background. Some individuals with visible differences have been found to experience psychosocial adjustment problems that can lead to social anxiety and isolation. Various models of psychosocial intervention have been used to reduce social anxiety and appearance related distress in this population. The objective of this review was to update a previous systematic review assessing the efficacy of psychosocial intervention programs for adults with visible differences. The original review (Bessell & Moss, 2007) identified 12 papers for inclusion. Methods. A search protocol identified studies from 13 electronic journal databases. Methods: Studies were selected in accordance with pre-set inclusion criteria and relevant data were extracted. Results. This update identified an additional four papers that met the inclusion criteria. Two papers provided very limited evidence for the efficacy of a combined cognitive-behavioural and social skills training approach. None of the papers provided sufficient evidence for the optimal duration, intensity or setting of psychosocial interventions for this population. Discussion. The review concluded that a greater number of Randomised Controlled Trials and experimental studies were required to increase the methodological validity of intervention studies.
format: application/pdf
format: text/html
creator: Alyson Norman
creator: Timothy P. Moss
subject: Evidence Based Medicine
subject: Nursing
subject: Psychiatry and Psychology
description: doi:10.7717/peerj.870
publisher: PeerJ Inc.
rights: © 2015 Norman and Moss
abstract: Background. Some individuals with visible differences have been found to experience psychosocial adjustment problems that can lead to social anxiety and isolation. Various models of psychosocial intervention have been used to reduce social anxiety and appearance related distress in this population. The objective of this review was to update a previous systematic review assessing the efficacy of psychosocial intervention programs for adults with visible differences. The original review (Bessell & Moss, 2007) identified 12 papers for inclusion. Methods. A search protocol identified studies from 13 electronic journal databases. Methods: Studies were selected in accordance with pre-set inclusion criteria and relevant data were extracted. Results. This update identified an additional four papers that met the inclusion criteria. Two papers provided very limited evidence for the efficacy of a combined cognitive-behavioural and social skills training approach. None of the papers provided sufficient evidence for the optimal duration, intensity or setting of psychosocial interventions for this population. Discussion. The review concluded that a greater number of Randomised Controlled Trials and experimental studies were required to increase the methodological validity of intervention studies.
bibliographic citation: Norman et al. (2015) Psychosocial interventions for adults with visible differences: a systematic review. PeerJ 3:e870 https://doi.org/10.7717/peerj.870
date submitted: 2014-11-24
date accepted: 2015-03-10
issued: 2015-04-02
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Norman
  given name: Alyson
author list: Agent
  family name: Moss
  given name: Timothy P.
doi: 10.7717/peerj.870
volume: 3
issn: 2167-8359
publication name: PeerJ
publication date: 2015-04-02
copyright: © 2015 Norman and Moss
attribution name: Norman and Moss

Self-regulatory mode (locomotion and assessment), well-being (subjective and psychological), and exercise behavior (frequency and intensity) in relation to high school pupils’ academic achievement
type: item
type: AcademicArticle
description: Background. Self-regulation is the procedure implemented by an individual striving to reach a goal and consists of two inter-related strategies: assessment and locomotion. Moreover, both subjective and psychological well-being along exercise behaviour might also play a role on adolescents academic achievement. Method. Participants were 160 Swedish high school pupils (111 boys and 49 girls) with an age mean of 17.74 (sd = 1.29). We used the Regulatory Mode Questionnaire to measure self-regulation strategies (i.e., locomotion and assessment). Well-being was measured using Ryff’s Psychological Well-Being Scales short version, the Temporal Satisfaction with Life Scale, and the Positive Affect and Negative Affect Schedule. Exercise behaviour was self-reported using questions pertaining to frequency and intensity of exercise compliance. Academic achievement was operationalized through the pupils’ mean value of final grades in Swedish, Mathematics, English, and Physical Education. Both correlation and regressions analyses were conducted. Results. Academic achievement was positively related to assessment, well-being, and frequent/intensive exercise behaviour. Assessment was, however, negatively related to well-being. Locomotion on the other hand was positively associated to well-being and also to exercise behaviour. Conclusions. The results suggest a dual (in)direct model to increase pupils’ academic achievement and well-being—assessment being directly related to higher academic achievement, while locomotion is related to frequently exercising and well-being, which in turn, increase academic achievement.
format: application/pdf
format: text/html
creator: Danilo Garcia
creator: Alexander Jimmefors
creator: Fariba Mousavi
creator: Lillemor Adrianson
creator: Patricia Rosenberg
creator: Trevor Archer
subject: Psychiatry and Psychology
subject: Public Health
description: doi:10.7717/peerj.847
publisher: PeerJ Inc.
rights: © 2015 Garcia et al.
abstract: Background. Self-regulation is the procedure implemented by an individual striving to reach a goal and consists of two inter-related strategies: assessment and locomotion. Moreover, both subjective and psychological well-being along exercise behaviour might also play a role on adolescents academic achievement. Method. Participants were 160 Swedish high school pupils (111 boys and 49 girls) with an age mean of 17.74 (sd = 1.29). We used the Regulatory Mode Questionnaire to measure self-regulation strategies (i.e., locomotion and assessment). Well-being was measured using Ryff’s Psychological Well-Being Scales short version, the Temporal Satisfaction with Life Scale, and the Positive Affect and Negative Affect Schedule. Exercise behaviour was self-reported using questions pertaining to frequency and intensity of exercise compliance. Academic achievement was operationalized through the pupils’ mean value of final grades in Swedish, Mathematics, English, and Physical Education. Both correlation and regressions analyses were conducted. Results. Academic achievement was positively related to assessment, well-being, and frequent/intensive exercise behaviour. Assessment was, however, negatively related to well-being. Locomotion on the other hand was positively associated to well-being and also to exercise behaviour. Conclusions. The results suggest a dual (in)direct model to increase pupils’ academic achievement and well-being—assessment being directly related to higher academic achievement, while locomotion is related to frequently exercising and well-being, which in turn, increase academic achievement.
bibliographic citation: Garcia et al. (2015) Self-regulatory mode (locomotion and assessment), well-being (subjective and psychological), and exercise behavior (frequency and intensity) in relation to high school pupils’ academic achievement. PeerJ 3:e847 https://doi.org/10.7717/peerj.847
date submitted: 2014-09-03
date accepted: 2015-03-02
issued: 2015-04-02
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Garcia
  given name: Danilo
author list: Agent
  family name: Jimmefors
  given name: Alexander
author list: Agent
  family name: Mousavi
  given name: Fariba
author list: Agent
  family name: Adrianson
  given name: Lillemor
author list: Agent
  family name: Rosenberg
  given name: Patricia
author list: Agent
  family name: Archer
  given name: Trevor
doi: 10.7717/peerj.847
volume: 3
issn: 2167-8359
publication name: PeerJ
publication date: 2015-04-02
copyright: © 2015 Garcia et al.
attribution name: Garcia et al.

The effects of set volume during isolated lumbar extension resistance training in recreationally trained males
type: item
type: AcademicArticle
description: Background/Aim. Exercise designed to condition the lumbar extensor musculature is often included in resistance training (RT) programs. It is suggested that deconditioning of this musculature may be linked to low back pain. Thus effective means of conditioning these muscles are of interest to pursue. Evidence suggests that isolated lumbar extension (ILEX) RT might be most efficacious, however, the best means of manipulating resistance training variables in this regard is unknown. Set volume is an easily manipulated RT variable and one thought to also interact with training status. As such this study sought to examine the effect of set volume during ILEX RT in trained males. Methods. Trained males previously engaged in exercises designed to condition the lumbar extensors underwent a 6 week intervention and were randomised to either a single set (1ST, n = 9), multiple set (3ST, n = 8) or control group (CON, n = 9). Pre- and post-testing of ILEX strength was conducted. Results. Both 1ST and 3ST significantly increased ILEX strength (p < 0.05) with large effect sizes (d = 0.89 and 0.95 respectively) whereas the CON group produced significant losses (−8.9%) with a moderate effect size (d = − 0.53). There was no statistically significant difference in ILEX strength gains when 1ST and 3ST were directly compared (p = 0.336). Conclusions. The results of this study suggest that significant ILEX strength changes occur in trained males as a result of 6 weeks of ILEX RT and that these changes are unaffected by set volume.
format: application/pdf
format: text/html
creator: James Steele
creator: Adam Fitzpatrick
creator: Stewart Bruce-Low
creator: James Fisher
subject: Anatomy and Physiology
subject: Kinesiology
subject: Orthopedics
description: doi:10.7717/peerj.878
publisher: PeerJ Inc.
rights: © 2015 Steele et al.
abstract: Background/Aim. Exercise designed to condition the lumbar extensor musculature is often included in resistance training (RT) programs. It is suggested that deconditioning of this musculature may be linked to low back pain. Thus effective means of conditioning these muscles are of interest to pursue. Evidence suggests that isolated lumbar extension (ILEX) RT might be most efficacious, however, the best means of manipulating resistance training variables in this regard is unknown. Set volume is an easily manipulated RT variable and one thought to also interact with training status. As such this study sought to examine the effect of set volume during ILEX RT in trained males. Methods. Trained males previously engaged in exercises designed to condition the lumbar extensors underwent a 6 week intervention and were randomised to either a single set (1ST, n = 9), multiple set (3ST, n = 8) or control group (CON, n = 9). Pre- and post-testing of ILEX strength was conducted. Results. Both 1ST and 3ST significantly increased ILEX strength (p < 0.05) with large effect sizes (d = 0.89 and 0.95 respectively) whereas the CON group produced significant losses (−8.9%) with a moderate effect size (d = − 0.53). There was no statistically significant difference in ILEX strength gains when 1ST and 3ST were directly compared (p = 0.336). Conclusions. The results of this study suggest that significant ILEX strength changes occur in trained males as a result of 6 weeks of ILEX RT and that these changes are unaffected by set volume.
bibliographic citation: Steele et al. (2015) The effects of set volume during isolated lumbar extension resistance training in recreationally trained males. PeerJ 3:e878 https://doi.org/10.7717/peerj.878
date submitted: 2015-01-31
date accepted: 2015-03-13
issued: 2015-03-31
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Steele
  given name: James
author list: Agent
  family name: Fitzpatrick
  given name: Adam
author list: Agent
  family name: Bruce-Low
  given name: Stewart
author list: Agent
  family name: Fisher
  given name: James
doi: 10.7717/peerj.878
volume: 3
issn: 2167-8359
publication name: PeerJ
publication date: 2015-03-31
copyright: © 2015 Steele et al.
attribution name: Steele et al.

Proteomic responses to hypoxia at different temperatures in the great scallop (Pecten maximus)
type: item
type: AcademicArticle
description: Hypoxia and hyperthermia are two connected consequences of the ongoing global change and constitute major threats for coastal marine organisms. In the present study, we used a proteomic approach to characterize the changes induced by hypoxia in the great scallop, Pecten maximus, subjected to three different temperatures (10 °C, 18 °C and 25 °C). We did not observe any significant change induced by hypoxia in animals acclimated at 10 °C. At 18 °C and 25 °C, 16 and 11 protein spots were differentially accumulated between normoxia and hypoxia, respectively. Moreover, biochemical data (octopine dehydrogenase activity and arginine assays) suggest that animals grown at 25 °C switched their metabolism towards anaerobic metabolism when exposed to both normoxia and hypoxia, suggesting that this temperature is out of the scallops’ optimal thermal window. The 11 proteins identified with high confidence by mass spectrometry are involved in protein modifications and signaling (e.g., CK2, TBK1), energy metabolism (e.g., ENO3) or cytoskeleton (GSN), giving insights into the thermal-dependent response of scallops to hypoxia.
format: application/pdf
format: text/html
creator: Sébastien Artigaud
creator: Camille Lacroix
creator: Joëlle Richard
creator: Jonathan Flye-Sainte-Marie
creator: Luca Bargelloni
creator: Vianney Pichereau
subject: Aquaculture, Fisheries and Fish Science
subject: Ecology
subject: Environmental Sciences
subject: Marine Biology
subject: Molecular Biology
description: doi:10.7717/peerj.871
publisher: PeerJ Inc.
rights: © 2015 Artigaud et al.
abstract: Hypoxia and hyperthermia are two connected consequences of the ongoing global change and constitute major threats for coastal marine organisms. In the present study, we used a proteomic approach to characterize the changes induced by hypoxia in the great scallop, Pecten maximus, subjected to three different temperatures (10 °C, 18 °C and 25 °C). We did not observe any significant change induced by hypoxia in animals acclimated at 10 °C. At 18 °C and 25 °C, 16 and 11 protein spots were differentially accumulated between normoxia and hypoxia, respectively. Moreover, biochemical data (octopine dehydrogenase activity and arginine assays) suggest that animals grown at 25 °C switched their metabolism towards anaerobic metabolism when exposed to both normoxia and hypoxia, suggesting that this temperature is out of the scallops’ optimal thermal window. The 11 proteins identified with high confidence by mass spectrometry are involved in protein modifications and signaling (e.g., CK2, TBK1), energy metabolism (e.g., ENO3) or cytoskeleton (GSN), giving insights into the thermal-dependent response of scallops to hypoxia.
bibliographic citation: Artigaud et al. (2015) Proteomic responses to hypoxia at different temperatures in the great scallop (Pecten maximus). PeerJ 3:e871 https://doi.org/10.7717/peerj.871
date submitted: 2014-12-18
date accepted: 2015-03-11
issued: 2015-03-31
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Artigaud
  given name: Sébastien
author list: Agent
  family name: Lacroix
  given name: Camille
author list: Agent
  family name: Richard
  given name: Joëlle
author list: Agent
  family name: Flye-Sainte-Marie
  given name: Jonathan
author list: Agent
  family name: Bargelloni
  given name: Luca
author list: Agent
  family name: Pichereau
  given name: Vianney
doi: 10.7717/peerj.871
volume: 3
issn: 2167-8359
publication name: PeerJ
publication date: 2015-03-31
copyright: © 2015 Artigaud et al.
attribution name: Artigaud et al.

A questions-based investigation of consumer mental-health information
type: item
type: AcademicArticle
description: Despite the wealth of mental-health information available online to consumers, research has shown that the mental-health information needs of consumers are not being met. This study contributes to that research by soliciting consumer questions directly, categorizing them, analyzing their form, and assessing the extent to which they can be answered from a trusted and vetted source of online information, namely the website of the US National Institute of Mental Health (NIMH). As an alternative to surveys and analyses of online activity, this study shows how consumer questions provide new insight into what consumers do not know and how they express their information needs. The study crowdsourced 100 consumer questions through Amazon Inc.’s Mechanical Turk. Categorization of the questions shows broad agreement with earlier studies in terms of the content of consumer questions. It also suggests that consumers’ grasp of mental health issues may be low compared to other health topics. The majority of the questions (74%) were simple in form, with the remainder being multi-part, multifaceted or narrative. Even simple-form questions could, however, have complex interpretations. Fifty four questions were submitted to the search box at the NIMH website. For 32 questions, no answer could be found in the top one to three documents returned. Inadequacies in the search and retrieval technology deployed at websites account for some of the failure to find answers. The nature of consumer questions in mental health also plays a role. A question that has a false presupposition is less likely to have an answer in trusted and vetted sources of information. Consumer questions are also expressed with a degree of specificity that makes the retrieval of relevant information difficult. The significance of this study is that it shows what an analysis of consumer mental-health questions can tell us about consumer information needs and it provides new insight into the difficulties facing consumer…
format: application/pdf
format: text/html
creator: Colleen E. Crangle
creator: Joyce Brothers Kart
subject: Bioinformatics
subject: Cognitive Disorders
subject: Human-Computer Interaction
subject: Psychiatry and Psychology
subject: Public Health
description: doi:10.7717/peerj.867
publisher: PeerJ Inc.
rights: © 2015 Crangle and Kart
abstract: Despite the wealth of mental-health information available online to consumers, research has shown that the mental-health information needs of consumers are not being met. This study contributes to that research by soliciting consumer questions directly, categorizing them, analyzing their form, and assessing the extent to which they can be answered from a trusted and vetted source of online information, namely the website of the US National Institute of Mental Health (NIMH). As an alternative to surveys and analyses of online activity, this study shows how consumer questions provide new insight into what consumers do not know and how they express their information needs. The study crowdsourced 100 consumer questions through Amazon Inc.’s Mechanical Turk. Categorization of the questions shows broad agreement with earlier studies in terms of the content of consumer questions. It also suggests that consumers’ grasp of mental health issues may be low compared to other health topics. The majority of the questions (74%) were simple in form, with the remainder being multi-part, multifaceted or narrative. Even simple-form questions could, however, have complex interpretations. Fifty four questions were submitted to the search box at the NIMH website. For 32 questions, no answer could be found in the top one to three documents returned. Inadequacies in the search and retrieval technology deployed at websites account for some of the failure to find answers. The nature of consumer questions in mental health also plays a role. A question that has a false presupposition is less likely to have an answer in trusted and vetted sources of information. Consumer questions are also expressed with a degree of specificity that makes the retrieval of relevant information difficult. The significance of this study is that it shows what an analysis of consumer mental-health questions can tell us about consumer information needs and it provides new insight into the difficulties facing consumer…
bibliographic citation: Crangle et al. (2015) A questions-based investigation of consumer mental-health information. PeerJ 3:e867 https://doi.org/10.7717/peerj.867
date submitted: 2015-01-02
date accepted: 2015-03-10
issued: 2015-03-31
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Crangle
  given name: Colleen E.
author list: Agent
  family name: Kart
  given name: Joyce Brothers
doi: 10.7717/peerj.867
volume: 3
issn: 2167-8359
publication name: PeerJ
publication date: 2015-03-31
copyright: © 2015 Crangle and Kart
attribution name: Crangle and Kart

The right whale mandatory ship reporting system: a retrospective
type: item
type: AcademicArticle
description: In 1998, the United States sought and received International Maritime Organization-endorsement of two Mandatory Ship Reporting (MSR) systems designed to improve mariner awareness about averting ship collisions with the endangered North Atlantic right whale (Eubalaena glacialis). Vessel collisions are a serious threat to the right whale and the program was among the first formal attempts to reduce this threat. Under the provisions of the MSR, all ships >300 gross tons are required to report their location, speed, and destination to a shore-based station when entering two key right whale habitats: one in waters off New England and one off coastal Georgia and Florida. In return, reporting ships receive an automatically-generated message, delivered directly to the ship’s bridge, that provides information about right whale vulnerability to vessel collisions and actions mariners can take to avoid collisions. The MSR has been in operation continuously from July 1999 to the present. Archived incoming reports provided a 15-plus year history of ship operations in these two locations. We analyzed a total of 26,772 incoming MSR messages logged between July 1999 and December 2013. Most ships that were required to report did so, and compliance rates were generally constant throughout the study period. Self-reported vessel speeds when entering the systems indicated that most ships travelled between 10 and 16 (range = 5–20 +) knots. Ship speeds generally decreased in 2009 to 2013 following implementation of vessel speed restrictions. The number of reports into the southern system remained relatively constant following a steady increase through 2007, but numbers in the northern system decreased annually beginning in 2008. If reporting is indicative of long-term patterns in shipping operations, it reflects noteworthy changes in marine transportation. Observed declines in ship traffic are likely attributable to the 2008–2009 economic recession, the containerized shipping industry maki…
format: application/pdf
format: text/html
creator: Gregory K. Silber
creator: Jeffrey D. Adams
creator: Michael J. Asaro
creator: Timothy V.N. Cole
creator: Katie S. Moore
creator: Leslie I. Ward-Geiger
creator: Barbara J. Zoodsma
subject: Biosphere Interactions
subject: Conservation Biology
subject: Legal Issues
subject: Marine Biology
subject: Science Policy
description: doi:10.7717/peerj.866
publisher: PeerJ Inc.
rights: © 2015 Silber et al.
abstract: In 1998, the United States sought and received International Maritime Organization-endorsement of two Mandatory Ship Reporting (MSR) systems designed to improve mariner awareness about averting ship collisions with the endangered North Atlantic right whale (Eubalaena glacialis). Vessel collisions are a serious threat to the right whale and the program was among the first formal attempts to reduce this threat. Under the provisions of the MSR, all ships >300 gross tons are required to report their location, speed, and destination to a shore-based station when entering two key right whale habitats: one in waters off New England and one off coastal Georgia and Florida. In return, reporting ships receive an automatically-generated message, delivered directly to the ship’s bridge, that provides information about right whale vulnerability to vessel collisions and actions mariners can take to avoid collisions. The MSR has been in operation continuously from July 1999 to the present. Archived incoming reports provided a 15-plus year history of ship operations in these two locations. We analyzed a total of 26,772 incoming MSR messages logged between July 1999 and December 2013. Most ships that were required to report did so, and compliance rates were generally constant throughout the study period. Self-reported vessel speeds when entering the systems indicated that most ships travelled between 10 and 16 (range = 5–20 +) knots. Ship speeds generally decreased in 2009 to 2013 following implementation of vessel speed restrictions. The number of reports into the southern system remained relatively constant following a steady increase through 2007, but numbers in the northern system decreased annually beginning in 2008. If reporting is indicative of long-term patterns in shipping operations, it reflects noteworthy changes in marine transportation. Observed declines in ship traffic are likely attributable to the 2008–2009 economic recession, the containerized shipping industry maki…
bibliographic citation: Silber et al. (2015) The right whale mandatory ship reporting system: a retrospective. PeerJ 3:e866 https://doi.org/10.7717/peerj.866
date submitted: 2014-12-08
date accepted: 2015-03-10
issued: 2015-03-31
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Silber
  given name: Gregory K.
author list: Agent
  family name: Adams
  given name: Jeffrey D.
author list: Agent
  family name: Asaro
  given name: Michael J.
author list: Agent
  family name: Cole
  given name: Timothy V.N.
author list: Agent
  family name: Moore
  given name: Katie S.
author list: Agent
  family name: Ward-Geiger
  given name: Leslie I.
author list: Agent
  family name: Zoodsma
  given name: Barbara J.
doi: 10.7717/peerj.866
volume: 3
issn: 2167-8359
publication name: PeerJ
publication date: 2015-03-31
copyright: © 2015 Silber et al.
attribution name: Silber et al.

Effect of different heterotrophic plate count methods on the estimation of the composition of the culturable microbial community
type: item
type: AcademicArticle
description: Heterotrophic plate counts (HPC) are routinely determined within the scope of water quality assessment. However, variable HPC methods with different cultivation parameters (i.e., temperature and media type) are applied, which could lead to significant effects in the outcome of the analysis. Therefore the effect of different HPC methods, according to DIN EN ISO 6222 and EPA, on the culturable microbial community composition was investigated by 16S rRNA gene sequence analysis and statistical evaluation was performed. The culturable community composition revealed significant effects assigned to temperature (p < 0.01), while for media type no statistical significance was observed. However, the abundance of certain detected bacteria was affected. Lower temperature (22 °C) showed the abundance of naturally occurring Pseudomonadaceae and Aeromonadaceae, whereas at high temperature (37 °C) numerous Enterobacteriaceae, Citrobacter spp. and Bacilli were identified. The highest biodiversity was detected at lower temperature, especially on R2A medium. These results indicate that different temperatures (low and high) should be included into HPC measurement and selection of media should, ideally, be adjusted to the monitored water source. Accordingly, it can be inferred that the HPC method is more suitable for continuous monitoring of the same water source than for single assessments of a water sample.
format: application/pdf
format: text/html
creator: Eva Theres Gensberger
creator: Eva-Maria Gössl
creator: Livio Antonielli
creator: Angela Sessitsch
creator: Tanja Kostić
subject: Microbiology
subject: Molecular Biology
description: doi:10.7717/peerj.862
publisher: PeerJ Inc.
rights: © 2015 Gensberger et al.
abstract: Heterotrophic plate counts (HPC) are routinely determined within the scope of water quality assessment. However, variable HPC methods with different cultivation parameters (i.e., temperature and media type) are applied, which could lead to significant effects in the outcome of the analysis. Therefore the effect of different HPC methods, according to DIN EN ISO 6222 and EPA, on the culturable microbial community composition was investigated by 16S rRNA gene sequence analysis and statistical evaluation was performed. The culturable community composition revealed significant effects assigned to temperature (p < 0.01), while for media type no statistical significance was observed. However, the abundance of certain detected bacteria was affected. Lower temperature (22 °C) showed the abundance of naturally occurring Pseudomonadaceae and Aeromonadaceae, whereas at high temperature (37 °C) numerous Enterobacteriaceae, Citrobacter spp. and Bacilli were identified. The highest biodiversity was detected at lower temperature, especially on R2A medium. These results indicate that different temperatures (low and high) should be included into HPC measurement and selection of media should, ideally, be adjusted to the monitored water source. Accordingly, it can be inferred that the HPC method is more suitable for continuous monitoring of the same water source than for single assessments of a water sample.
bibliographic citation: Gensberger et al. (2015) Effect of different heterotrophic plate count methods on the estimation of the composition of the culturable microbial community. PeerJ 3:e862 https://doi.org/10.7717/peerj.862
date submitted: 2014-02-21
date accepted: 2015-03-08
issued: 2015-03-31
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Gensberger
  given name: Eva Theres
author list: Agent
  family name: Gössl
  given name: Eva-Maria
author list: Agent
  family name: Antonielli
  given name: Livio
author list: Agent
  family name: Sessitsch
  given name: Angela
author list: Agent
  family name: Kostić
  given name: Tanja
doi: 10.7717/peerj.862
volume: 3
issn: 2167-8359
publication name: PeerJ
publication date: 2015-03-31
copyright: © 2015 Gensberger et al.
attribution name: Gensberger et al.

A reproducible approach to high-throughput biological data acquisition and integration
type: item
type: AcademicArticle
description: Modern biological research requires rapid, complex, and reproducible integration of multiple experimental results generated both internally and externally (e.g., from public repositories). Although large systematic meta-analyses are among the most effective approaches both for clinical biomarker discovery and for computational inference of biomolecular mechanisms, identifying, acquiring, and integrating relevant experimental results from multiple sources for a given study can be time-consuming and error-prone. To enable efficient and reproducible integration of diverse experimental results, we developed a novel approach for standardized acquisition and analysis of high-throughput and heterogeneous biological data. This allowed, first, novel biomolecular network reconstruction in human prostate cancer, which correctly recovered and extended the NFκB signaling pathway. Next, we investigated host-microbiome interactions. In less than an hour of analysis time, the system retrieved data and integrated six germ-free murine intestinal gene expression datasets to identify the genes most influenced by the gut microbiota, which comprised a set of immune-response and carbohydrate metabolism processes. Finally, we constructed integrated functional interaction networks to compare connectivity of peptide secretion pathways in the model organisms Escherichia coli, Bacillus subtilis, and Pseudomonas aeruginosa.
format: application/pdf
format: text/html
creator: Daniela Börnigen
creator: Yo Sup Moon
creator: Gholamali Rahnavard
creator: Levi Waldron
creator: Lauren McIver
creator: Afrah Shafquat
creator: Eric A. Franzosa
creator: Larissa Miropolsky
creator: Christopher Sweeney
creator: Xochitl C. Morgan
creator: Wendy S. Garrett
creator: Curtis Huttenhower
subject: Bioinformatics
subject: Computational Biology
description: doi:10.7717/peerj.791
publisher: PeerJ Inc.
rights: © 2015 Boernigen et al.
abstract: Modern biological research requires rapid, complex, and reproducible integration of multiple experimental results generated both internally and externally (e.g., from public repositories). Although large systematic meta-analyses are among the most effective approaches both for clinical biomarker discovery and for computational inference of biomolecular mechanisms, identifying, acquiring, and integrating relevant experimental results from multiple sources for a given study can be time-consuming and error-prone. To enable efficient and reproducible integration of diverse experimental results, we developed a novel approach for standardized acquisition and analysis of high-throughput and heterogeneous biological data. This allowed, first, novel biomolecular network reconstruction in human prostate cancer, which correctly recovered and extended the NFκB signaling pathway. Next, we investigated host-microbiome interactions. In less than an hour of analysis time, the system retrieved data and integrated six germ-free murine intestinal gene expression datasets to identify the genes most influenced by the gut microbiota, which comprised a set of immune-response and carbohydrate metabolism processes. Finally, we constructed integrated functional interaction networks to compare connectivity of peptide secretion pathways in the model organisms Escherichia coli, Bacillus subtilis, and Pseudomonas aeruginosa.
bibliographic citation: Börnigen et al. (2015) A reproducible approach to high-throughput biological data acquisition and integration. PeerJ 3:e791 https://doi.org/10.7717/peerj.791
date submitted: 2014-10-21
date accepted: 2015-02-04
issued: 2015-03-31
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Börnigen
  given name: Daniela
author list: Agent
  family name: Moon
  given name: Yo Sup
author list: Agent
  family name: Rahnavard
  given name: Gholamali
author list: Agent
  family name: Waldron
  given name: Levi
author list: Agent
  family name: McIver
  given name: Lauren
author list: Agent
  family name: Shafquat
  given name: Afrah
author list: Agent
  family name: Franzosa
  given name: Eric A.
author list: Agent
  family name: Miropolsky
  given name: Larissa
author list: Agent
  family name: Sweeney
  given name: Christopher
author list: Agent
  family name: Morgan
  given name: Xochitl C.
author list: Agent
  family name: Garrett
  given name: Wendy S.
author list: Agent
  family name: Huttenhower
  given name: Curtis
doi: 10.7717/peerj.791
volume: 3
issn: 2167-8359
publication name: PeerJ
publication date: 2015-03-31
copyright: © 2015 Boernigen et al.
attribution name: Boernigen et al.

Effects of preservation methods of muscle tissue from upper-trophic level reef fishes on stable isotope values (δ13C and δ15N)
type: item
type: AcademicArticle
description: Research that uses stable isotope analysis often involves a delay between sample collection in the field and laboratory processing, therefore requiring preservation to prevent or reduce tissue degradation and associated isotopic compositions. Although there is a growing literature describing the effects of various preservation techniques, the results are often contextual, unpredictable and vary among taxa, suggesting the need to treat each species individually. We conducted a controlled experiment to test the effects of four preservation methods of muscle tissue from four species of upper trophic-level reef fish collected from the eastern Gulf of Mexico (Red Grouper Epinephelus morio, Gag Mycteroperca microlepis, Scamp Mycteroperca phenax, and Red Snapper Lutjanus campechanus). We used a paired design to measure the effects on isotopic values for carbon and nitrogen after storage using ice, 95% ethanol, and sodium chloride (table salt), against that in a liquid nitrogen control. Mean offsets for both δ13C and δ15N values from controls were lowest for samples preserved on ice, intermediate for those preserved with salt, and highest with ethanol. Within species, both salt and ethanol significantly enriched the δ15N values in nearly all comparisons. Ethanol also had strong effects on the δ13C values in all three groupers. Conversely, for samples preserved on ice, we did not detect a significant offset in either isotopic ratio for any of the focal species. Previous studies have addressed preservation-induced offsets in isotope values using a mass balance correction that accounts for changes in the isotope value to that in the C/N ratio. We tested the application of standard mass balance corrections for isotope values that were significantly affected by the preservation methods and found generally poor agreement between corrected and control values. The poor performance by the correction may have been due to preferential loss of lighter isotopes and corresponding low lev…
format: application/pdf
format: text/html
creator: Christopher D. Stallings
creator: James A. Nelson
creator: Katherine L. Rozar
creator: Charles S. Adams
creator: Kara R. Wall
creator: Theodore S. Switzer
creator: Brent L. Winner
creator: David J. Hollander
subject: Aquaculture, Fisheries and Fish Science
subject: Biochemistry
subject: Ecology
subject: Ecosystem Science
subject: Marine Biology
description: doi:10.7717/peerj.874
publisher: PeerJ Inc.
rights: © 2015 Stallings et al.
abstract: Research that uses stable isotope analysis often involves a delay between sample collection in the field and laboratory processing, therefore requiring preservation to prevent or reduce tissue degradation and associated isotopic compositions. Although there is a growing literature describing the effects of various preservation techniques, the results are often contextual, unpredictable and vary among taxa, suggesting the need to treat each species individually. We conducted a controlled experiment to test the effects of four preservation methods of muscle tissue from four species of upper trophic-level reef fish collected from the eastern Gulf of Mexico (Red Grouper Epinephelus morio, Gag Mycteroperca microlepis, Scamp Mycteroperca phenax, and Red Snapper Lutjanus campechanus). We used a paired design to measure the effects on isotopic values for carbon and nitrogen after storage using ice, 95% ethanol, and sodium chloride (table salt), against that in a liquid nitrogen control. Mean offsets for both δ13C and δ15N values from controls were lowest for samples preserved on ice, intermediate for those preserved with salt, and highest with ethanol. Within species, both salt and ethanol significantly enriched the δ15N values in nearly all comparisons. Ethanol also had strong effects on the δ13C values in all three groupers. Conversely, for samples preserved on ice, we did not detect a significant offset in either isotopic ratio for any of the focal species. Previous studies have addressed preservation-induced offsets in isotope values using a mass balance correction that accounts for changes in the isotope value to that in the C/N ratio. We tested the application of standard mass balance corrections for isotope values that were significantly affected by the preservation methods and found generally poor agreement between corrected and control values. The poor performance by the correction may have been due to preferential loss of lighter isotopes and corresponding low lev…
bibliographic citation: Stallings et al. (2015) Effects of preservation methods of muscle tissue from upper-trophic level reef fishes on stable isotope values (δ13C and δ15N). PeerJ 3:e874 https://doi.org/10.7717/peerj.874
date submitted: 2014-12-22
date accepted: 2015-03-12
issued: 2015-03-26
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Stallings
  given name: Christopher D.
author list: Agent
  family name: Nelson
  given name: James A.
author list: Agent
  family name: Rozar
  given name: Katherine L.
author list: Agent
  family name: Adams
  given name: Charles S.
author list: Agent
  family name: Wall
  given name: Kara R.
author list: Agent
  family name: Switzer
  given name: Theodore S.
author list: Agent
  family name: Winner
  given name: Brent L.
author list: Agent
  family name: Hollander
  given name: David J.
doi: 10.7717/peerj.874
volume: 3
issn: 2167-8359
publication name: PeerJ
publication date: 2015-03-26
copyright: © 2015 Stallings et al.
attribution name: Stallings et al.

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