PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
items: Escape and avoidance learning in the earthworm Eisenia hortensis
items: Sexual coevolution of spermatophore envelopes and female genital traits in butterflies: Evidence of male coercion?
items: A new model for simulating growth in fish
items: Ligand determinants of fatty acid activation of the pronociceptive ion channel TRPA1
items: Plant compensation to grazing and soil carbon dynamics in a tropical grassland
items: Snake venomics of Bothrops punctatus, a semiarboreal pitviper species from Antioquia, Colombia
items: Perioperative morbidity and mortality of cardiothoracic surgery in patients with a do-not-resuscitate order
items: Being there: a brief visit to a neighbourhood induces the social attitudes of that neighbourhood
items: PhyloSift: phylogenetic analysis of genomes and metagenomes
items: The Xanthomonas Ax21 protein is processed by the general secretory system and is secreted in association with outer membrane vesicles
items: Composable languages for bioinformatics: the NYoSh experiment
items: Development of a novel clinical scoring system for on-farm diagnosis of bovine respiratory disease in pre-weaned dairy calves
items: Effects of reduced dissolved oxygen concentrations on physiology and fluorescence of hermatypic corals and benthic algae
items: A new specimen of the Early Cretaceous bird Hongshanornis longicresta: insights into the aerodynamics and diet of a basal ornithuromorph
items: Inter-annual variability influences the eco-evolutionary dynamics of range-shifting

Escape and avoidance learning in the earthworm Eisenia hortensis
type: item
type: AcademicArticle
description: Interest in instrumental learning in earthworms dates back to 1912 when Yerkes concluded that they can learn a spatial discrimination in a T-maze. Rosenkoetter and Boice determined in the 1970s that the “learning” that Yerkes observed was probably chemotaxis and not learning at all. We examined a different form of instrumental learning: the ability to learn both to escape and to avoid an aversive stimulus. Freely moving “master” worms could turn off an aversive white light by increasing their movement; the behavior of yoked controls had no effect on the light. We demonstrate that in as few as 12 trials the behavior of the master worms comes under the control of this contingency.
format: application/pdf
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creator: W. Jeffrey Wilson
creator: Nicole C. Ferrara
creator: Amanda L. Blaker
creator: Charisa E. Giddings
subject: Animal Behavior
subject: Neuroscience
description: doi:10.7717/peerj.250
publisher: PeerJ Inc.
rights: © 2014 Wilson et al.
abstract: Interest in instrumental learning in earthworms dates back to 1912 when Yerkes concluded that they can learn a spatial discrimination in a T-maze. Rosenkoetter and Boice determined in the 1970s that the “learning” that Yerkes observed was probably chemotaxis and not learning at all. We examined a different form of instrumental learning: the ability to learn both to escape and to avoid an aversive stimulus. Freely moving “master” worms could turn off an aversive white light by increasing their movement; the behavior of yoked controls had no effect on the light. We demonstrate that in as few as 12 trials the behavior of the master worms comes under the control of this contingency.
bibliographic citation: Wilson et al. (2014) Escape and avoidance learning in the earthworm Eisenia hortensis. PeerJ 2:e250 https://doi.org/10.7717/peerj.250
date submitted: 2013-11-26
date accepted: 2014-01-02
issued: 2014-01-30
is part of: PeerJ
license: http://creativecommons.org/licenses/by/3.0/
author list: Agent
  family name: Wilson
  given name: W. Jeffrey
author list: Agent
  family name: Ferrara
  given name: Nicole C.
author list: Agent
  family name: Blaker
  given name: Amanda L.
author list: Agent
  family name: Giddings
  given name: Charisa E.
doi: 10.7717/peerj.250
volume: 2
issn: 2167-8359
publication name: PeerJ
publication date: 2014-01-30
copyright: © 2014 Wilson et al.
attribution name: Wilson et al.

Sexual coevolution of spermatophore envelopes and female genital traits in butterflies: Evidence of male coercion?
type: item
type: AcademicArticle
description: Signa are sclerotized structures located on the inner wall of the corpus bursa of female Lepidoptera whose main function is tearing open spermatophores. The sexually antagonistic coevolution (SAC) hypothesis proposes that the thickness of spermatophore envelopes has driven the evolution of the females signa; this idea is based in the fact that in many lepidopterans female sexual receptivity is at least partially controlled by the volume of ejaculate remaining in the corpus bursa. According to the SAC hypothesis, males evolved thick spermatophore envelopes to delay the post-mating recovery of female sexual receptivity thus reducing sperm competition; in response, females evolved signa for breaking spermatophore envelopes faster, gaining access to the resources contained in them and reducing their intermating intervals; the evolution of signa, in turn, favored the evolution of even thicker spermatophore envelopes, and so on. We tested two predictions of the SAC hypothesis with comparative data on the thickness of spermatophore envelopes of eleven species of Heliconiinae butterflies. The first prediction is that the spermatophore envelopes of polyandrous species with signa will be thicker than those of monandrous species without signa. In agreement with this prediction, we found that the spermatophore envelopes of a polyandrous Heliconius species with signa are thicker than those of two monandrous Heliconius species without signa. The second prediction is that in some species with signa males could enforce monandry in females by evolving “very thick” spermatophore envelopes, in these species we predict that their spermatophore envelopes will be thicker than those of their closer polyandrous relatives with signa. In agreement with this prediction, we found that in two out of three comparisons, spermatophore envelopes of monandrous species with signa have thicker spermatophore envelopes than their closer polyandrous relatives with signa. Thus, our results support the ide…
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creator: Víctor Sánchez
creator: Carlos Cordero
subject: Animal Behavior
subject: Entomology
subject: Evolutionary Studies
subject: Zoology
description: doi:10.7717/peerj.247
publisher: PeerJ Inc.
rights: © 2014 Sánchez et al.
abstract: Signa are sclerotized structures located on the inner wall of the corpus bursa of female Lepidoptera whose main function is tearing open spermatophores. The sexually antagonistic coevolution (SAC) hypothesis proposes that the thickness of spermatophore envelopes has driven the evolution of the females signa; this idea is based in the fact that in many lepidopterans female sexual receptivity is at least partially controlled by the volume of ejaculate remaining in the corpus bursa. According to the SAC hypothesis, males evolved thick spermatophore envelopes to delay the post-mating recovery of female sexual receptivity thus reducing sperm competition; in response, females evolved signa for breaking spermatophore envelopes faster, gaining access to the resources contained in them and reducing their intermating intervals; the evolution of signa, in turn, favored the evolution of even thicker spermatophore envelopes, and so on. We tested two predictions of the SAC hypothesis with comparative data on the thickness of spermatophore envelopes of eleven species of Heliconiinae butterflies. The first prediction is that the spermatophore envelopes of polyandrous species with signa will be thicker than those of monandrous species without signa. In agreement with this prediction, we found that the spermatophore envelopes of a polyandrous Heliconius species with signa are thicker than those of two monandrous Heliconius species without signa. The second prediction is that in some species with signa males could enforce monandry in females by evolving “very thick” spermatophore envelopes, in these species we predict that their spermatophore envelopes will be thicker than those of their closer polyandrous relatives with signa. In agreement with this prediction, we found that in two out of three comparisons, spermatophore envelopes of monandrous species with signa have thicker spermatophore envelopes than their closer polyandrous relatives with signa. Thus, our results support the ide…
bibliographic citation: Sánchez et al. (2014) Sexual coevolution of spermatophore envelopes and female genital traits in butterflies: Evidence of male coercion?. PeerJ 2:e247 https://doi.org/10.7717/peerj.247
date submitted: 2013-10-27
date accepted: 2013-12-29
issued: 2014-01-30
is part of: PeerJ
license: http://creativecommons.org/licenses/by/3.0/
author list: Agent
  family name: Sánchez
  given name: Víctor
author list: Agent
  family name: Cordero
  given name: Carlos
doi: 10.7717/peerj.247
volume: 2
issn: 2167-8359
publication name: PeerJ
publication date: 2014-01-30
copyright: © 2014 Sánchez et al.
attribution name: Sánchez et al.

A new model for simulating growth in fish
type: item
type: AcademicArticle
description: A real dynamic population model calculates change in population sizes independent of time. The Beverton & Holt (B&H) model commonly used in fish assessment includes the von Bertalanffy growth function which has age or accumulated time as an independent variable. As a result the B&H model has to assume constant fish growth. However, growth in fish is highly variable depending on food availability and environmental conditions. We propose a new growth model where the length increment of fish living under constant conditions and unlimited food supply, decreases linearly with increasing fish length until it reaches zero at a maximal fish length. The model is independent of time and includes a term which accounts for the environmental variation. In the present study, the model was validated in zebrafish held at constant conditions. There was a good fit of the model to data on observed growth in Norwegian spring spawning herring, capelin from the Barents Sea, North Sea herring and in farmed coastal cod. Growth data from Walleye Pollock from the Eastern Bering Sea and blue whiting from the Norwegian Sea also fitted reasonably well to the model, whereas data from cod from the North Sea showed a good fit to the model only above a length of 70 cm. Cod from the Barents Sea did not grow according to the model. The last results can be explained by environmental factors and variable food availability in the time under study. The model implicates that the efficiency of energy conversion from food decreases as the individual animal approaches its maximal length and is postulated to represent a natural law of fish growth.
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creator: Johannes Hamre
creator: Espen Johnsen
creator: Kristin Hamre
subject: Aquaculture
subject: Fisheries and Fish Science
description: doi:10.7717/peerj.244
publisher: PeerJ Inc.
rights: © 2014 Hamre et al.
abstract: A real dynamic population model calculates change in population sizes independent of time. The Beverton & Holt (B&H) model commonly used in fish assessment includes the von Bertalanffy growth function which has age or accumulated time as an independent variable. As a result the B&H model has to assume constant fish growth. However, growth in fish is highly variable depending on food availability and environmental conditions. We propose a new growth model where the length increment of fish living under constant conditions and unlimited food supply, decreases linearly with increasing fish length until it reaches zero at a maximal fish length. The model is independent of time and includes a term which accounts for the environmental variation. In the present study, the model was validated in zebrafish held at constant conditions. There was a good fit of the model to data on observed growth in Norwegian spring spawning herring, capelin from the Barents Sea, North Sea herring and in farmed coastal cod. Growth data from Walleye Pollock from the Eastern Bering Sea and blue whiting from the Norwegian Sea also fitted reasonably well to the model, whereas data from cod from the North Sea showed a good fit to the model only above a length of 70 cm. Cod from the Barents Sea did not grow according to the model. The last results can be explained by environmental factors and variable food availability in the time under study. The model implicates that the efficiency of energy conversion from food decreases as the individual animal approaches its maximal length and is postulated to represent a natural law of fish growth.
bibliographic citation: Hamre et al. (2014) A new model for simulating growth in fish. PeerJ 2:e244 https://doi.org/10.7717/peerj.244
date submitted: 2013-09-23
date accepted: 2013-12-21
issued: 2014-01-30
is part of: PeerJ
license: http://creativecommons.org/licenses/by/3.0/
author list: Agent
  family name: Hamre
  given name: Johannes
author list: Agent
  family name: Johnsen
  given name: Espen
author list: Agent
  family name: Hamre
  given name: Kristin
doi: 10.7717/peerj.244
volume: 2
issn: 2167-8359
publication name: PeerJ
publication date: 2014-01-30
copyright: © 2014 Hamre et al.
attribution name: Hamre et al.

Ligand determinants of fatty acid activation of the pronociceptive ion channel TRPA1
type: item
type: AcademicArticle
description: Background and purpose. Arachidonic acid (AA) and its derivatives are important modulators of cellular signalling. The transient receptor potential cation channel subfamily A, member 1 (TRPA1) is a cation channel with important functions in mediating cellular responses to noxious stimuli and inflammation. There is limited information about the interactions between AA itself and TRPA1, so we investigated the effects of AA and key ethanolamide and amino acid/neurotransmitter derivatives of AA on hTRPA1. Experimental approach. HEK 293 cells expressing hTRPA1 were studied by measuring changes in intracellular calcium ([Ca]i) with a fluorescent dye and by standard whole cell patch clamp recordings. Key results. AA (30 μM) increased fluorescence in hTRPA1 expressing cells by 370% (notional EC50 13 μM). The covalent TRPA1 agonist cinnamaldehyde (300 μM) increased fluorescence by 430% (EC50, 11 μM). Anandamide (230%) and N-arachidonoyl tyrosine (170%) substantially activated hTRPA1 at 30 μM, however, N-arachidonoyl conjugates of glycine and taurine were less effective while N-acyl conjugates of 5-HT did not affect hTRPA1. Changing the acyl chain length or the number and position of double bonds reduced fatty acid efficacy at hTRPA1. Mutant hTRPA1 (Cys621, Cys641 and Cys665 changed to Ser) could be activated by AA (100 μM, 40% of wild type) but not by cinnamaldehyde (300 μM). Conclusions and implications. AA is a more potent activator of TRPA1 than its ethanolamide or amino acid/neurotransmitter derivatives and acts via a mechanism distinct from that of cinnamaldehyde, further underscoring the likelyhood of multiple pharmacologically exploitable sites on hTRPA1.
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creator: William John Redmond
creator: Liuqiong Gu
creator: Maxime Camo
creator: Peter McIntyre
creator: Mark Connor
subject: Biochemistry
subject: Pharmacology
description: doi:10.7717/peerj.248
publisher: PeerJ Inc.
rights: © 2014 Redmond et al.
abstract: Background and purpose. Arachidonic acid (AA) and its derivatives are important modulators of cellular signalling. The transient receptor potential cation channel subfamily A, member 1 (TRPA1) is a cation channel with important functions in mediating cellular responses to noxious stimuli and inflammation. There is limited information about the interactions between AA itself and TRPA1, so we investigated the effects of AA and key ethanolamide and amino acid/neurotransmitter derivatives of AA on hTRPA1. Experimental approach. HEK 293 cells expressing hTRPA1 were studied by measuring changes in intracellular calcium ([Ca]i) with a fluorescent dye and by standard whole cell patch clamp recordings. Key results. AA (30 μM) increased fluorescence in hTRPA1 expressing cells by 370% (notional EC50 13 μM). The covalent TRPA1 agonist cinnamaldehyde (300 μM) increased fluorescence by 430% (EC50, 11 μM). Anandamide (230%) and N-arachidonoyl tyrosine (170%) substantially activated hTRPA1 at 30 μM, however, N-arachidonoyl conjugates of glycine and taurine were less effective while N-acyl conjugates of 5-HT did not affect hTRPA1. Changing the acyl chain length or the number and position of double bonds reduced fatty acid efficacy at hTRPA1. Mutant hTRPA1 (Cys621, Cys641 and Cys665 changed to Ser) could be activated by AA (100 μM, 40% of wild type) but not by cinnamaldehyde (300 μM). Conclusions and implications. AA is a more potent activator of TRPA1 than its ethanolamide or amino acid/neurotransmitter derivatives and acts via a mechanism distinct from that of cinnamaldehyde, further underscoring the likelyhood of multiple pharmacologically exploitable sites on hTRPA1.
bibliographic citation: Redmond et al. (2014) Ligand determinants of fatty acid activation of the pronociceptive ion channel TRPA1. PeerJ 2:e248 https://doi.org/10.7717/peerj.248
date submitted: 2013-10-10
date accepted: 2013-12-31
issued: 2014-01-28
is part of: PeerJ
license: http://creativecommons.org/licenses/by/3.0/
author list: Agent
  family name: Redmond
  given name: William John
author list: Agent
  family name: Gu
  given name: Liuqiong
author list: Agent
  family name: Camo
  given name: Maxime
author list: Agent
  family name: McIntyre
  given name: Peter
author list: Agent
  family name: Connor
  given name: Mark
doi: 10.7717/peerj.248
volume: 2
issn: 2167-8359
publication name: PeerJ
publication date: 2014-01-28
copyright: © 2014 Redmond et al.
attribution name: Redmond et al.

Plant compensation to grazing and soil carbon dynamics in a tropical grassland
type: item
type: AcademicArticle
description: The effects of grazing on soil organic carbon (SOC) dynamics, particularly in the tropics, are still poorly understood. Plant compensation to grazing, whereby plants maintain leaf area (C input capacity) despite consumption (C removal) by grazers, has been demonstrated in tropical grasslands but its influence on SOC is largely unexplored. Here, the effect of grazing on plant leaf area index (LAI) was measured in a field experiment in Serengeti National Park, Tanzania. LAI changed little for grazing intensities up to 70%. The response curve of LAI versus grazing intensity was used in a mass balance model, called SNAP, of SOC dynamics based on previous data from the Serengeti. The model predicted SOC to increase at intermediate grazing intensity, but then to decline rapidly at the highest grazing intensities. The SNAP model predictions were compared with observed SOC stocks in the 24 grazed plots of a 10-year grazing exclosure experiment at eight sites across the park that varied in mean annual rainfall, soil texture, grazing intensity and plant lignin and cellulose. The model predicted current SOC stocks very well (R2 > 0.75), and suggests that compensatory plant responses to grazing are an important means of how herbivores might maintain or increase SOC in tropical grasslands.
format: application/pdf
format: text/html
creator: Mark E. Ritchie
subject: Ecology
subject: Ecosystem Science
subject: Environmental Sciences
subject: Soil Science
description: doi:10.7717/peerj.233
publisher: PeerJ Inc.
rights: © 2014 Ritchie
abstract: The effects of grazing on soil organic carbon (SOC) dynamics, particularly in the tropics, are still poorly understood. Plant compensation to grazing, whereby plants maintain leaf area (C input capacity) despite consumption (C removal) by grazers, has been demonstrated in tropical grasslands but its influence on SOC is largely unexplored. Here, the effect of grazing on plant leaf area index (LAI) was measured in a field experiment in Serengeti National Park, Tanzania. LAI changed little for grazing intensities up to 70%. The response curve of LAI versus grazing intensity was used in a mass balance model, called SNAP, of SOC dynamics based on previous data from the Serengeti. The model predicted SOC to increase at intermediate grazing intensity, but then to decline rapidly at the highest grazing intensities. The SNAP model predictions were compared with observed SOC stocks in the 24 grazed plots of a 10-year grazing exclosure experiment at eight sites across the park that varied in mean annual rainfall, soil texture, grazing intensity and plant lignin and cellulose. The model predicted current SOC stocks very well (R2 > 0.75), and suggests that compensatory plant responses to grazing are an important means of how herbivores might maintain or increase SOC in tropical grasslands.
bibliographic citation: Ritchie (2014) Plant compensation to grazing and soil carbon dynamics in a tropical grassland. PeerJ 2:e233 https://doi.org/10.7717/peerj.233
date submitted: 2013-08-20
date accepted: 2013-12-05
issued: 2014-01-28
is part of: PeerJ
license: http://creativecommons.org/licenses/by/3.0/
author list: Agent
  family name: Ritchie
  given name: Mark E.
doi: 10.7717/peerj.233
volume: 2
issn: 2167-8359
publication name: PeerJ
publication date: 2014-01-28
copyright: © 2014 Ritchie
attribution name: Ritchie

Snake venomics of Bothrops punctatus, a semiarboreal pitviper species from Antioquia, Colombia
type: item
type: AcademicArticle
description: Bothrops punctatus is an endangered, semi-arboreal pitviper species distributed in Panamá, Colombia, and Ecuador, whose venom is poorly characterized. In the present work, the protein composition of this venom was profiled using the ‘snake venomics’ analytical strategy. Decomplexation of the crude venom by RP-HPLC and SDS-PAGE, followed by tandem mass spectrometry of tryptic digests, showed that it consists of proteins assigned to at least nine snake toxin families. Metalloproteinases are predominant in this secretion (41.5% of the total proteins), followed by C-type lectin/lectin-like proteins (16.7%), bradykinin-potentiating peptides (10.7%), phospholipases A2 (93%), serine proteinases (5.4%), disintegrins (38%), L-amino acid oxidases (3.1%), vascular endothelial growth factors (17%), and cysteine-rich secretory proteins (1.2%). Altogether, 6.6% of the proteins were not identified. In vitro, the venom exhibited proteolytic, phospholipase A2, and L-amino acid oxidase activities, as well as angiotensin-converting enzyme (ACE)-inhibitory activity, in agreement with the obtained proteomic profile. Cytotoxic activity on murine C2C12 myoblasts was negative, suggesting that the majority of venom phospholipases A2 likely belong to the acidic type, which often lack major toxic effects. The protein composition of B. punctatus venom shows a good correlation with toxic activities here and previously reported, and adds further data in support of the wide diversity of strategies that have evolved in snake venoms to subdue prey, as increasingly being revealed by proteomic analyses.
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creator: Maritza Fernández Culma
creator: Jaime Andrés Pereañez
creator: Vitelbina Núñez Rangel
creator: Bruno Lomonte
subject: Biochemistry
subject: Biodiversity
subject: Toxicology
description: doi:10.7717/peerj.246
publisher: PeerJ Inc.
rights: © 2014 Fernández Culma et al.
abstract: Bothrops punctatus is an endangered, semi-arboreal pitviper species distributed in Panamá, Colombia, and Ecuador, whose venom is poorly characterized. In the present work, the protein composition of this venom was profiled using the ‘snake venomics’ analytical strategy. Decomplexation of the crude venom by RP-HPLC and SDS-PAGE, followed by tandem mass spectrometry of tryptic digests, showed that it consists of proteins assigned to at least nine snake toxin families. Metalloproteinases are predominant in this secretion (41.5% of the total proteins), followed by C-type lectin/lectin-like proteins (16.7%), bradykinin-potentiating peptides (10.7%), phospholipases A2 (93%), serine proteinases (5.4%), disintegrins (38%), L-amino acid oxidases (3.1%), vascular endothelial growth factors (17%), and cysteine-rich secretory proteins (1.2%). Altogether, 6.6% of the proteins were not identified. In vitro, the venom exhibited proteolytic, phospholipase A2, and L-amino acid oxidase activities, as well as angiotensin-converting enzyme (ACE)-inhibitory activity, in agreement with the obtained proteomic profile. Cytotoxic activity on murine C2C12 myoblasts was negative, suggesting that the majority of venom phospholipases A2 likely belong to the acidic type, which often lack major toxic effects. The protein composition of B. punctatus venom shows a good correlation with toxic activities here and previously reported, and adds further data in support of the wide diversity of strategies that have evolved in snake venoms to subdue prey, as increasingly being revealed by proteomic analyses.
bibliographic citation: Fernández Culma et al. (2014) Snake venomics of Bothrops punctatus, a semiarboreal pitviper species from Antioquia, Colombia. PeerJ 2:e246 https://doi.org/10.7717/peerj.246
date submitted: 2013-12-11
date accepted: 2013-12-27
issued: 2014-01-22
is part of: PeerJ
license: http://creativecommons.org/licenses/by/3.0/
author list: Agent
  family name: Fernández Culma
  given name: Maritza
author list: Agent
  family name: Andrés Pereañez
  given name: Jaime
author list: Agent
  family name: Núñez Rangel
  given name: Vitelbina
author list: Agent
  family name: Lomonte
  given name: Bruno
doi: 10.7717/peerj.246
volume: 2
issn: 2167-8359
publication name: PeerJ
publication date: 2014-01-22
copyright: © 2014 Fernández Culma et al.
attribution name: Fernández Culma et al.

Perioperative morbidity and mortality of cardiothoracic surgery in patients with a do-not-resuscitate order
type: item
type: AcademicArticle
description: Background. Do-not-resuscitate (DNR) orders are often active in patients with multiple comorbidities and a short natural life expectancy, but limited information exists as to how often these patients undergo high-risk operations and of the perioperative outcomes in this population. Methods. Using comprehensive inpatient administrative data from the Public Discharge Data file (years 2005 through 2010) of the California Office of Statewide Health Planning and Development, which includes a dedicated variable recording DNR status, we identified cohorts of DNR patients who underwent major cardiac or thoracic operations and compared themto age- and procedure-matched comparison cohorts. The primary study outcome was in-hospital mortality. Results. DNR status was not uncommon in cardiac (n = 2,678, 1.1% of all admissions for cardiac surgery, age 71.6 ± 15.9 years) and thoracic (n = 3,129, 3.7% of all admissions for thoracic surgery, age 73.8 ± 13.6 years) surgical patient populations. Relative to controls, patients who were DNR experienced significantly greater inhospital mortality after cardiac (37.5% vs. 11.2%, p < 0.0001 and thoracic (25.4% vs. 6.4%) operations. DNR status remained an independent predictor of in-hospital mortality onmultivariate analysis after adjustment for baseline and comorbid conditions in both the cardiac (OR 4.78, 95% confidence interval 4.21–5.41, p < 0.0001) and thoracic (OR 6.11, 95% confidence interval 5.37–6.94, p < 0.0001) cohorts. Conclusions. DNR status is associated with worse outcomes of cardiothoracic surgery even when controlling for age, race, insurance status, and serious comorbid disease. DNR status appears to be a marker of substantial perioperative risk, and may warrant substantial consideration when framing discussions of surgical risk and benefit, resource utilization, and biomedical ethics surrounding end-of-life care.
format: application/pdf
format: text/html
creator: Bryan G. Maxwell
creator: Robert L. Lobato
creator: Molly B. Cason
creator: Jim K. Wong
subject: Anesthesiology and Pain Management
subject: Emergency and Critical Care
subject: Palliative Care
subject: Public Health
subject: Surgery and Surgical Specialties
description: doi:10.7717/peerj.245
publisher: PeerJ Inc.
rights: © 2014 Maxwell et al.
abstract: Background. Do-not-resuscitate (DNR) orders are often active in patients with multiple comorbidities and a short natural life expectancy, but limited information exists as to how often these patients undergo high-risk operations and of the perioperative outcomes in this population. Methods. Using comprehensive inpatient administrative data from the Public Discharge Data file (years 2005 through 2010) of the California Office of Statewide Health Planning and Development, which includes a dedicated variable recording DNR status, we identified cohorts of DNR patients who underwent major cardiac or thoracic operations and compared themto age- and procedure-matched comparison cohorts. The primary study outcome was in-hospital mortality. Results. DNR status was not uncommon in cardiac (n = 2,678, 1.1% of all admissions for cardiac surgery, age 71.6 ± 15.9 years) and thoracic (n = 3,129, 3.7% of all admissions for thoracic surgery, age 73.8 ± 13.6 years) surgical patient populations. Relative to controls, patients who were DNR experienced significantly greater inhospital mortality after cardiac (37.5% vs. 11.2%, p < 0.0001 and thoracic (25.4% vs. 6.4%) operations. DNR status remained an independent predictor of in-hospital mortality onmultivariate analysis after adjustment for baseline and comorbid conditions in both the cardiac (OR 4.78, 95% confidence interval 4.21–5.41, p < 0.0001) and thoracic (OR 6.11, 95% confidence interval 5.37–6.94, p < 0.0001) cohorts. Conclusions. DNR status is associated with worse outcomes of cardiothoracic surgery even when controlling for age, race, insurance status, and serious comorbid disease. DNR status appears to be a marker of substantial perioperative risk, and may warrant substantial consideration when framing discussions of surgical risk and benefit, resource utilization, and biomedical ethics surrounding end-of-life care.
bibliographic citation: Maxwell et al. (2014) Perioperative morbidity and mortality of cardiothoracic surgery in patients with a do-not-resuscitate order. PeerJ 2:e245 https://doi.org/10.7717/peerj.245
date submitted: 2013-11-27
date accepted: 2013-12-21
issued: 2014-01-22
is part of: PeerJ
license: http://creativecommons.org/licenses/by/3.0/
author list: Agent
  family name: Maxwell
  given name: Bryan G.
author list: Agent
  family name: Lobato
  given name: Robert L.
author list: Agent
  family name: Cason
  given name: Molly B.
author list: Agent
  family name: Wong
  given name: Jim K.
doi: 10.7717/peerj.245
volume: 2
issn: 2167-8359
publication name: PeerJ
publication date: 2014-01-22
copyright: © 2014 Maxwell et al.
attribution name: Maxwell et al.

Being there: a brief visit to a neighbourhood induces the social attitudes of that neighbourhood
type: item
type: AcademicArticle
description: There are differences between human groups in social behaviours and the attitudes that underlie them, such as trust. However, the psychological mechanisms that produce and reproduce this variation are not well understood. In particular, it is not clear whether assimilation to the social culture of a group requires lengthy socialization within that group, or can be more rapidly and reversibly evoked by exposure to the group’s environment and the behaviour of its members. Here, we report the results of a two-part study in two neighbourhoods of a British city, one economically deprived with relatively high crime, and the other affluent and lower in crime. In the first part of the study, we surveyed residents and found that the residents of the deprived neighbourhood had lower levels of social trust and higher levels of paranoia than the residents of the affluent neighbourhood. In the second part, we experimentally transported student volunteers who resided in neither neighbourhood to one or the other, and had them walk around delivering questionnaires to houses. We surveyed their trust and paranoia, and found significant differences according to which neighbourhood they had been sent to. The differences in the visitors mirrored the differences seen in the residents, with visitors to the deprived neighbourhood reporting lower social trust and higher paranoia than visitors to the affluent one. The magnitudes of the neighbourhood differences in the visitors, who only spent up to 45 min in the locations, were nearly as great as the magnitudes of those amongst the residents. We discuss the relevance of our findings to differential psychology, neighbourhood effects on social outcomes, and models of cultural evolution.
format: application/pdf
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creator: Daniel Nettle
creator: Gillian V. Pepper
creator: Ruth Jobling
creator: Kari Britt Schroeder
subject: Anthropology
subject: Epidemiology
subject: Psychiatry and Psychology
subject: Public Health
description: doi:10.7717/peerj.236
publisher: PeerJ Inc.
rights: © 2014 Nettle et al.
abstract: There are differences between human groups in social behaviours and the attitudes that underlie them, such as trust. However, the psychological mechanisms that produce and reproduce this variation are not well understood. In particular, it is not clear whether assimilation to the social culture of a group requires lengthy socialization within that group, or can be more rapidly and reversibly evoked by exposure to the group’s environment and the behaviour of its members. Here, we report the results of a two-part study in two neighbourhoods of a British city, one economically deprived with relatively high crime, and the other affluent and lower in crime. In the first part of the study, we surveyed residents and found that the residents of the deprived neighbourhood had lower levels of social trust and higher levels of paranoia than the residents of the affluent neighbourhood. In the second part, we experimentally transported student volunteers who resided in neither neighbourhood to one or the other, and had them walk around delivering questionnaires to houses. We surveyed their trust and paranoia, and found significant differences according to which neighbourhood they had been sent to. The differences in the visitors mirrored the differences seen in the residents, with visitors to the deprived neighbourhood reporting lower social trust and higher paranoia than visitors to the affluent one. The magnitudes of the neighbourhood differences in the visitors, who only spent up to 45 min in the locations, were nearly as great as the magnitudes of those amongst the residents. We discuss the relevance of our findings to differential psychology, neighbourhood effects on social outcomes, and models of cultural evolution.
bibliographic citation: Nettle et al. (2014) Being there: a brief visit to a neighbourhood induces the social attitudes of that neighbourhood. PeerJ 2:e236 https://doi.org/10.7717/peerj.236
date submitted: 2013-10-04
date accepted: 2013-12-11
issued: 2014-01-14
is part of: PeerJ
license: http://creativecommons.org/licenses/by/3.0/
author list: Agent
  family name: Nettle
  given name: Daniel
author list: Agent
  family name: Pepper
  given name: Gillian V.
author list: Agent
  family name: Jobling
  given name: Ruth
author list: Agent
  family name: Schroeder
  given name: Kari Britt
doi: 10.7717/peerj.236
volume: 2
issn: 2167-8359
publication name: PeerJ
publication date: 2014-01-14
copyright: © 2014 Nettle et al.
attribution name: Nettle et al.

PhyloSift: phylogenetic analysis of genomes and metagenomes
type: item
type: AcademicArticle
description: Like all organisms on the planet, environmental microbes are subject to the forces of molecular evolution. Metagenomic sequencing provides a means to access the DNA sequence of uncultured microbes. By combining DNA sequencing of microbial communities with evolutionary modeling and phylogenetic analysis we might obtain new insights into microbiology and also provide a basis for practical tools such as forensic pathogen detection. In this work we present an approach to leverage phylogenetic analysis of metagenomic sequence data to conduct several types of analysis. First, we present a method to conduct phylogeny-driven Bayesian hypothesis tests for the presence of an organism in a sample. Second, we present a means to compare community structure across a collection of many samples and develop direct associations between the abundance of certain organisms and sample metadata. Third, we apply new tools to analyze the phylogenetic diversity of microbial communities and again demonstrate how this can be associated to sample metadata. These analyses are implemented in an open source software pipeline called PhyloSift. As a pipeline, PhyloSift incorporates several other programs including LAST, HMMER, and pplacer to automate phylogenetic analysis of protein coding and RNA sequences in metagenomic datasets generated by modern sequencing platforms (e.g., Illumina, 454).
format: application/pdf
format: text/html
creator: Aaron E. Darling
creator: Guillaume Jospin
creator: Eric Lowe
creator: Frederick A. Matsen
creator: Holly M. Bik
creator: Jonathan A. Eisen
subject: Bioinformatics
subject: Computational Biology
subject: Evolutionary Studies
subject: Genomics
subject: Microbiology
description: doi:10.7717/peerj.243
publisher: PeerJ Inc.
rights: © 2014 Darling et al.
abstract: Like all organisms on the planet, environmental microbes are subject to the forces of molecular evolution. Metagenomic sequencing provides a means to access the DNA sequence of uncultured microbes. By combining DNA sequencing of microbial communities with evolutionary modeling and phylogenetic analysis we might obtain new insights into microbiology and also provide a basis for practical tools such as forensic pathogen detection. In this work we present an approach to leverage phylogenetic analysis of metagenomic sequence data to conduct several types of analysis. First, we present a method to conduct phylogeny-driven Bayesian hypothesis tests for the presence of an organism in a sample. Second, we present a means to compare community structure across a collection of many samples and develop direct associations between the abundance of certain organisms and sample metadata. Third, we apply new tools to analyze the phylogenetic diversity of microbial communities and again demonstrate how this can be associated to sample metadata. These analyses are implemented in an open source software pipeline called PhyloSift. As a pipeline, PhyloSift incorporates several other programs including LAST, HMMER, and pplacer to automate phylogenetic analysis of protein coding and RNA sequences in metagenomic datasets generated by modern sequencing platforms (e.g., Illumina, 454).
bibliographic citation: Darling et al. (2014) PhyloSift: phylogenetic analysis of genomes and metagenomes. PeerJ 2:e243 https://doi.org/10.7717/peerj.243
date submitted: 2013-03-21
date accepted: 2013-12-19
issued: 2014-01-09
is part of: PeerJ
license: http://creativecommons.org/licenses/by/3.0/
author list: Agent
  family name: Darling
  given name: Aaron E.
author list: Agent
  family name: Jospin
  given name: Guillaume
author list: Agent
  family name: Lowe
  given name: Eric
author list: Agent
  family name: Matsen
  given name: Frederick A.
author list: Agent
  family name: Bik
  given name: Holly M.
author list: Agent
  family name: Eisen
  given name: Jonathan A.
doi: 10.7717/peerj.243
volume: 2
issn: 2167-8359
publication name: PeerJ
publication date: 2014-01-09
copyright: © 2014 Darling et al.
attribution name: Darling et al.

The Xanthomonas Ax21 protein is processed by the general secretory system and is secreted in association with outer membrane vesicles
type: item
type: AcademicArticle
description: Pattern recognition receptors (PRRs) play an important role in detecting invading pathogens and mounting a robust defense response to restrict infection. In rice, one of the best characterized PRRs is XA21, a leucine rich repeat receptor-like kinase that confers broad-spectrum resistance to multiple strains of the bacterial pathogen Xanthomonas oryzae pv. oryzae (Xoo). In 2009 we reported that an Xoo protein, called Ax21, is secreted by a type I-secretion system and that it serves to activate XA21-mediated immunity. This report has recently been retracted. Here we present data that corrects our previous model. We first show that Ax21 secretion does not depend on the predicted type I secretion system and that it is processed by the general secretion (Sec) system. We further show that Ax21 is an outer membrane protein, secreted in association with outer membrane vesicles. Finally, we provide data showing that ax21 knockout strains do not overcome XA21-mediated immunity.
format: application/pdf
format: text/html
creator: Ofir Bahar
creator: Rory Pruitt
creator: Dee Dee Luu
creator: Benjamin Schwessinger
creator: Arsalan Daudi
creator: Furong Liu
creator: Randy Ruan
creator: Lisa Fontaine-Bodin
creator: Ralf Koebnik
creator: Pamela Ronald
subject: Agricultural Science
subject: Genetics
subject: Microbiology
subject: Molecular Biology
subject: Plant Science
description: doi:10.7717/peerj.242
publisher: PeerJ Inc.
rights: © 2014 Bahar et al.
abstract: Pattern recognition receptors (PRRs) play an important role in detecting invading pathogens and mounting a robust defense response to restrict infection. In rice, one of the best characterized PRRs is XA21, a leucine rich repeat receptor-like kinase that confers broad-spectrum resistance to multiple strains of the bacterial pathogen Xanthomonas oryzae pv. oryzae (Xoo). In 2009 we reported that an Xoo protein, called Ax21, is secreted by a type I-secretion system and that it serves to activate XA21-mediated immunity. This report has recently been retracted. Here we present data that corrects our previous model. We first show that Ax21 secretion does not depend on the predicted type I secretion system and that it is processed by the general secretion (Sec) system. We further show that Ax21 is an outer membrane protein, secreted in association with outer membrane vesicles. Finally, we provide data showing that ax21 knockout strains do not overcome XA21-mediated immunity.
bibliographic citation: Bahar et al. (2014) The Xanthomonas Ax21 protein is processed by the general secretory system and is secreted in association with outer membrane vesicles. PeerJ 2:e242 https://doi.org/10.7717/peerj.242
date submitted: 2013-11-21
date accepted: 2013-12-19
issued: 2014-01-07
is part of: PeerJ
license: http://creativecommons.org/licenses/by/3.0/
author list: Agent
  family name: Bahar
  given name: Ofir
author list: Agent
  family name: Pruitt
  given name: Rory
author list: Agent
  family name: Luu
  given name: Dee Dee
author list: Agent
  family name: Schwessinger
  given name: Benjamin
author list: Agent
  family name: Daudi
  given name: Arsalan
author list: Agent
  family name: Liu
  given name: Furong
author list: Agent
  family name: Ruan
  given name: Randy
author list: Agent
  family name: Fontaine-Bodin
  given name: Lisa
author list: Agent
  family name: Koebnik
  given name: Ralf
author list: Agent
  family name: Ronald
  given name: Pamela
doi: 10.7717/peerj.242
volume: 2
issn: 2167-8359
publication name: PeerJ
publication date: 2014-01-07
copyright: © 2014 Bahar et al.
attribution name: Bahar et al.

Composable languages for bioinformatics: the NYoSh experiment
type: item
type: AcademicArticle
description: Language WorkBenches (LWBs) are software engineering tools that help domain experts develop solutions to various classes of problems. Some of these tools focus on non-technical users and provide languages to help organize knowledge while other workbenches provide means to create new programming languages. A key advantage of language workbenches is that they support the seamless composition of independently developed languages. This capability is useful when developing programs that can benefit from different levels of abstraction. We reasoned that language workbenches could be useful to develop bioinformatics software solutions. In order to evaluate the potential of language workbenches in bioinformatics, we tested a prominent workbench by developing an alternative to shell scripting. To illustrate what LWBs and Language Composition can bring to bioinformatics, we report on our design and development of NYoSh (Not Your ordinary Shell). NYoSh was implemented as a collection of languages that can be composed to write programs as expressive and concise as shell scripts. This manuscript offers a concrete illustration of the advantages and current minor drawbacks of using the MPS LWB. For instance, we found that we could implement an environment-aware editor for NYoSh that can assist the programmers when developing scripts for specific execution environments. This editor further provides semantic error detection and can be compiled interactively with an automatic build and deployment system. In contrast to shell scripts, NYoSh scripts can be written in a modern development environment, supporting context dependent intentions and can be extended seamlessly by end-users with new abstractions and language constructs. We further illustrate language extension and composition with LWBs by presenting a tight integration of NYoSh scripts with the GobyWeb system. The NYoSh Workbench prototype, which implements a fully featured integrated development environment for NYoSh is distr…
format: application/pdf
format: text/html
creator: Manuele Simi
creator: Fabien Campagne
subject: Bioinformatics
subject: Computational Science
description: doi:10.7717/peerj.241
publisher: PeerJ Inc.
rights: © 2014 Simi et al.
abstract: Language WorkBenches (LWBs) are software engineering tools that help domain experts develop solutions to various classes of problems. Some of these tools focus on non-technical users and provide languages to help organize knowledge while other workbenches provide means to create new programming languages. A key advantage of language workbenches is that they support the seamless composition of independently developed languages. This capability is useful when developing programs that can benefit from different levels of abstraction. We reasoned that language workbenches could be useful to develop bioinformatics software solutions. In order to evaluate the potential of language workbenches in bioinformatics, we tested a prominent workbench by developing an alternative to shell scripting. To illustrate what LWBs and Language Composition can bring to bioinformatics, we report on our design and development of NYoSh (Not Your ordinary Shell). NYoSh was implemented as a collection of languages that can be composed to write programs as expressive and concise as shell scripts. This manuscript offers a concrete illustration of the advantages and current minor drawbacks of using the MPS LWB. For instance, we found that we could implement an environment-aware editor for NYoSh that can assist the programmers when developing scripts for specific execution environments. This editor further provides semantic error detection and can be compiled interactively with an automatic build and deployment system. In contrast to shell scripts, NYoSh scripts can be written in a modern development environment, supporting context dependent intentions and can be extended seamlessly by end-users with new abstractions and language constructs. We further illustrate language extension and composition with LWBs by presenting a tight integration of NYoSh scripts with the GobyWeb system. The NYoSh Workbench prototype, which implements a fully featured integrated development environment for NYoSh is distr…
bibliographic citation: Simi et al. (2014) Composable languages for bioinformatics: the NYoSh experiment. PeerJ 2:e241 https://doi.org/10.7717/peerj.241
date submitted: 2013-11-26
date accepted: 2013-12-17
issued: 2014-01-02
is part of: PeerJ
license: http://creativecommons.org/licenses/by/3.0/
author list: Agent
  family name: Simi
  given name: Manuele
author list: Agent
  family name: Campagne
  given name: Fabien
doi: 10.7717/peerj.241
volume: 2
issn: 2167-8359
publication name: PeerJ
publication date: 2014-01-02
copyright: © 2014 Simi et al.
attribution name: Simi et al.

Development of a novel clinical scoring system for on-farm diagnosis of bovine respiratory disease in pre-weaned dairy calves
type: item
type: AcademicArticle
description: Several clinical scoring systems for diagnosis of bovine respiratory disease (BRD) in calves have been proposed. However, such systems were based on subjective judgment, rather than statistical methods, to weight scores. Data from a pair-matched case-control study on a California calf raising facility was used to develop three novel scoring systems to diagnose BRD in preweaned dairy calves. Disease status was assigned using both clinical signs and diagnostic test results for BRD-associated pathogens. Regression coefficients were used to weight score values. The systems presented use nasal and ocular discharge, rectal temperature, ear and head carriage, coughing, and respiratory quality as predictors. The systems developed in this research utilize fewer severity categories of clinical signs, require less calf handling, and had excellent agreement (Kappa > 0.8) when compared to an earlier scoring system. The first scoring system dichotomized all clinical predictors but required inducing a cough. The second scoring system removed induced cough as a clinical abnormality but required distinguishing between three levels of nasal discharge severity. The third system removed induced cough and forced a dichotomized variable for nasal discharge. The first system presented in this study used the following predictors and assigned values: coughing (induced or spontaneous coughing, 2 points), nasal discharge (any discharge, 3 points), ocular discharge (any discharge, 2 points), ear and head carriage (ear droop or head tilt, 5 points), fever (≥39.2°C or 102.5°F, 2 points), and respiratory quality (abnormal respiration, 2 points). Calves were categorized “BRD positive” if their total score was ≥4. This system correctly classified 95.4% cases and 88.6% controls. The second presented system categorized the predictors and assigned weights as follows: coughing (spontaneous only, 2 points), mild nasal discharge (unilateral, serous, or watery discharge, 3 points), moderate to severe nasa…
format: application/pdf
format: text/html
creator: William J. Love
creator: Terry W. Lehenbauer
creator: Philip H. Kass
creator: Alison L. Van Eenennaam
creator: Sharif S. Aly
subject: Veterinary Medicine
subject: Epidemiology
subject: Statistics
description: doi:10.7717/peerj.238
publisher: PeerJ Inc.
rights: © 2014 Love et al.
abstract: Several clinical scoring systems for diagnosis of bovine respiratory disease (BRD) in calves have been proposed. However, such systems were based on subjective judgment, rather than statistical methods, to weight scores. Data from a pair-matched case-control study on a California calf raising facility was used to develop three novel scoring systems to diagnose BRD in preweaned dairy calves. Disease status was assigned using both clinical signs and diagnostic test results for BRD-associated pathogens. Regression coefficients were used to weight score values. The systems presented use nasal and ocular discharge, rectal temperature, ear and head carriage, coughing, and respiratory quality as predictors. The systems developed in this research utilize fewer severity categories of clinical signs, require less calf handling, and had excellent agreement (Kappa > 0.8) when compared to an earlier scoring system. The first scoring system dichotomized all clinical predictors but required inducing a cough. The second scoring system removed induced cough as a clinical abnormality but required distinguishing between three levels of nasal discharge severity. The third system removed induced cough and forced a dichotomized variable for nasal discharge. The first system presented in this study used the following predictors and assigned values: coughing (induced or spontaneous coughing, 2 points), nasal discharge (any discharge, 3 points), ocular discharge (any discharge, 2 points), ear and head carriage (ear droop or head tilt, 5 points), fever (≥39.2°C or 102.5°F, 2 points), and respiratory quality (abnormal respiration, 2 points). Calves were categorized “BRD positive” if their total score was ≥4. This system correctly classified 95.4% cases and 88.6% controls. The second presented system categorized the predictors and assigned weights as follows: coughing (spontaneous only, 2 points), mild nasal discharge (unilateral, serous, or watery discharge, 3 points), moderate to severe nasa…
bibliographic citation: Love et al. (2014) Development of a novel clinical scoring system for on-farm diagnosis of bovine respiratory disease in pre-weaned dairy calves. PeerJ 2:e238 https://doi.org/10.7717/peerj.238
date submitted: 2013-09-26
date accepted: 2013-12-16
issued: 2014-01-02
is part of: PeerJ
license: http://creativecommons.org/licenses/by/3.0/
author list: Agent
  family name: Love
  given name: William J.
author list: Agent
  family name: Lehenbauer
  given name: Terry W.
author list: Agent
  family name: Kass
  given name: Philip H.
author list: Agent
  family name: Van Eenennaam
  given name: Alison L.
author list: Agent
  family name: Aly
  given name: Sharif S.
doi: 10.7717/peerj.238
volume: 2
issn: 2167-8359
publication name: PeerJ
publication date: 2014-01-02
copyright: © 2014 Love et al.
attribution name: Love et al.

Effects of reduced dissolved oxygen concentrations on physiology and fluorescence of hermatypic corals and benthic algae
type: item
type: AcademicArticle
description: While shifts from coral to seaweed dominance have become increasingly common on coral reefs and factors triggering these shifts successively identified, the primary mechanisms involved in coral-algae interactions remain unclear. Amongst various potential mechanisms, algal exudates can mediate increases in microbial activity, leading to localized hypoxic conditions which may cause coral mortality in the direct vicinity. Most of the processes likely causing such algal exudate induced coral mortality have been quantified (e.g., labile organic matter release, increased microbial metabolism, decreased dissolved oxygen availability), yet little is known about how reduced dissolved oxygen concentrations affect competitive dynamics between seaweeds and corals. The goals of this study were to investigate the effects of different levels of oxygen including hypoxic conditions on a common hermatypic coral Acropora yongei and the common green alga Bryopsis pennata. Specifically, we examined how photosynthetic oxygen production, dark and daylight adapted quantum yield, intensity and anatomical distribution of the coral innate fluorescence, and visual estimates of health varied with differing background oxygen conditions. Our results showed that the algae were significantly more tolerant to extremely low oxygen concentrations (2–4 mg L−1) than corals. Furthermore corals could tolerate reduced oxygen concentrations, but only until a given threshold determined by a combination of exposure time and concentration. Exceeding this threshold led to rapid loss of coral tissue and mortality. This study concludes that hypoxia may indeed play a significant role, or in some cases may even be the main cause, for coral tissue loss during coral-algae interaction processes.
format: application/pdf
format: text/html
creator: Andreas F. Haas
creator: Jennifer E. Smith
creator: Melissa Thompson
creator: Dimitri D. Deheyn
subject: Ecology
subject: Marine Biology
description: doi:10.7717/peerj.235
publisher: PeerJ Inc.
rights: © 2014 Haas et al.
abstract: While shifts from coral to seaweed dominance have become increasingly common on coral reefs and factors triggering these shifts successively identified, the primary mechanisms involved in coral-algae interactions remain unclear. Amongst various potential mechanisms, algal exudates can mediate increases in microbial activity, leading to localized hypoxic conditions which may cause coral mortality in the direct vicinity. Most of the processes likely causing such algal exudate induced coral mortality have been quantified (e.g., labile organic matter release, increased microbial metabolism, decreased dissolved oxygen availability), yet little is known about how reduced dissolved oxygen concentrations affect competitive dynamics between seaweeds and corals. The goals of this study were to investigate the effects of different levels of oxygen including hypoxic conditions on a common hermatypic coral Acropora yongei and the common green alga Bryopsis pennata. Specifically, we examined how photosynthetic oxygen production, dark and daylight adapted quantum yield, intensity and anatomical distribution of the coral innate fluorescence, and visual estimates of health varied with differing background oxygen conditions. Our results showed that the algae were significantly more tolerant to extremely low oxygen concentrations (2–4 mg L−1) than corals. Furthermore corals could tolerate reduced oxygen concentrations, but only until a given threshold determined by a combination of exposure time and concentration. Exceeding this threshold led to rapid loss of coral tissue and mortality. This study concludes that hypoxia may indeed play a significant role, or in some cases may even be the main cause, for coral tissue loss during coral-algae interaction processes.
bibliographic citation: Haas et al. (2014) Effects of reduced dissolved oxygen concentrations on physiology and fluorescence of hermatypic corals and benthic algae. PeerJ 2:e235 https://doi.org/10.7717/peerj.235
date submitted: 2013-10-01
date accepted: 2013-12-11
issued: 2014-01-02
is part of: PeerJ
license: http://creativecommons.org/licenses/by/3.0/
author list: Agent
  family name: Haas
  given name: Andreas F.
author list: Agent
  family name: Smith
  given name: Jennifer E.
author list: Agent
  family name: Thompson
  given name: Melissa
author list: Agent
  family name: Deheyn
  given name: Dimitri D.
doi: 10.7717/peerj.235
volume: 2
issn: 2167-8359
publication name: PeerJ
publication date: 2014-01-02
copyright: © 2014 Haas et al.
attribution name: Haas et al.

A new specimen of the Early Cretaceous bird Hongshanornis longicresta: insights into the aerodynamics and diet of a basal ornithuromorph
type: item
type: AcademicArticle
description: The discovery of Hongshanornis longicresta, a small ornithuromorph bird with unusually long hindlimb proportions, was followed by the discovery of two closely related species, Longicrusavis houi and Parahongshanornis chaoyangensis. Together forming the Hongshanornithidae, these species reveal important information about the early diversity and morphological specialization of ornithuromorphs, the clade that contains all living birds. Here we report on a new specimen (DNHM D2945/6) referable to Hongshanornis longicresta that contributes significant information to better understand the morphology, trophic ecology, and aerodynamics of this species, as well as the taxonomy of the Hongshanornithidae. Most notable are the well-preserved wings and feathered tail of DNHM D2945/6, which afford an accurate reconstruction of aerodynamic parameters indicating that as early as 125 million years ago, basal ornithuromorphs had evolved aerodynamic surfaces comparable in size and design to those of many modern birds, and flight modes alike to those of some small living birds.
format: application/pdf
format: text/html
creator: Luis M. Chiappe
creator: Bo Zhao
creator: Jingmai K. O’Connor
creator: Gao Chunling
creator: Xuri Wang
creator: Michael Habib
creator: Jesus Marugan-Lobon
creator: Qingjin Meng
creator: Xiaodong Cheng
subject: Paleontology
subject: Taxonomy
subject: Zoology
description: doi:10.7717/peerj.234
publisher: PeerJ Inc.
rights: © 2014 Chiappe et al.
abstract: The discovery of Hongshanornis longicresta, a small ornithuromorph bird with unusually long hindlimb proportions, was followed by the discovery of two closely related species, Longicrusavis houi and Parahongshanornis chaoyangensis. Together forming the Hongshanornithidae, these species reveal important information about the early diversity and morphological specialization of ornithuromorphs, the clade that contains all living birds. Here we report on a new specimen (DNHM D2945/6) referable to Hongshanornis longicresta that contributes significant information to better understand the morphology, trophic ecology, and aerodynamics of this species, as well as the taxonomy of the Hongshanornithidae. Most notable are the well-preserved wings and feathered tail of DNHM D2945/6, which afford an accurate reconstruction of aerodynamic parameters indicating that as early as 125 million years ago, basal ornithuromorphs had evolved aerodynamic surfaces comparable in size and design to those of many modern birds, and flight modes alike to those of some small living birds.
bibliographic citation: Chiappe et al. (2014) A new specimen of the Early Cretaceous bird Hongshanornis longicresta: insights into the aerodynamics and diet of a basal ornithuromorph. PeerJ 2:e234 https://doi.org/10.7717/peerj.234
date submitted: 2013-08-30
date accepted: 2013-12-11
issued: 2014-01-02
is part of: PeerJ
license: http://creativecommons.org/licenses/by/3.0/
author list: Agent
  family name: Chiappe
  given name: Luis M.
author list: Agent
  family name: Zhao
  given name: Bo
author list: Agent
  family name: O’Connor
  given name: Jingmai K.
author list: Agent
  family name: Chunling
  given name: Gao
author list: Agent
  family name: Wang
  given name: Xuri
author list: Agent
  family name: Habib
  given name: Michael
author list: Agent
  family name: Marugan-Lobon
  given name: Jesus
author list: Agent
  family name: Meng
  given name: Qingjin
author list: Agent
  family name: Cheng
  given name: Xiaodong
doi: 10.7717/peerj.234
volume: 2
issn: 2167-8359
publication name: PeerJ
publication date: 2014-01-02
copyright: © 2014 Chiappe et al.
attribution name: Chiappe et al.

Inter-annual variability influences the eco-evolutionary dynamics of range-shifting
type: item
type: AcademicArticle
description: Understanding the eco-evolutionary dynamics of species under rapid climate change is vital for both accurate forecasting of biodiversity responses and for developing effective management strategies. Using an individual-based model we demonstrate that the presence and form (colour) of inter-annual variability in environmental conditions can impact the evolution of dispersal during range shifts. Under stable climate, temporal variability typically results in higher dispersal. However, at expanding margins, inter-annual variability actually inhibits the evolution of higher emigration propensities by disrupting the spatial sorting and natural selection processes. These results emphasize the need for future theoretical studies, as well as predictive modelling, to account for the potential impacts of inter-annual variability.
format: application/pdf
format: text/html
creator: Roslyn C. Henry
creator: Greta Bocedi
creator: Calvin Dytham
creator: Justin M.J. Travis
subject: Computational Biology
subject: Ecology
subject: Environmental Sciences
subject: Evolutionary Studies
subject: Mathematical Biology
description: doi:10.7717/peerj.228
publisher: PeerJ Inc.
rights: © 2013 Henry et al.
abstract: Understanding the eco-evolutionary dynamics of species under rapid climate change is vital for both accurate forecasting of biodiversity responses and for developing effective management strategies. Using an individual-based model we demonstrate that the presence and form (colour) of inter-annual variability in environmental conditions can impact the evolution of dispersal during range shifts. Under stable climate, temporal variability typically results in higher dispersal. However, at expanding margins, inter-annual variability actually inhibits the evolution of higher emigration propensities by disrupting the spatial sorting and natural selection processes. These results emphasize the need for future theoretical studies, as well as predictive modelling, to account for the potential impacts of inter-annual variability.
bibliographic citation: Henry et al. (2014) Inter-annual variability influences the eco-evolutionary dynamics of range-shifting. PeerJ 1:e228 https://doi.org/10.7717/peerj.228
date submitted: 2013-10-21
date accepted: 2013-11-30
issued: 2014-01-02
is part of: PeerJ
license: http://creativecommons.org/licenses/by/3.0/
author list: Agent
  family name: Henry
  given name: Roslyn C.
author list: Agent
  family name: Bocedi
  given name: Greta
author list: Agent
  family name: Dytham
  given name: Calvin
author list: Agent
  family name: Travis
  given name: Justin M.J.
doi: 10.7717/peerj.228
volume: 1
issn: 2167-8359
publication name: PeerJ
publication date: 2014-01-02
copyright: © 2013 Henry et al.
attribution name: Henry et al.

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