PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
items: Influence of isoflurane on the diastolic pressure-flow relationship and critical occlusion pressure during arterial CABG surgery: a randomized controlled trial
items: Sustained attention in skilled and novice martial arts athletes: a study of event-related potentials and current sources
items: A method for histopathological study of the multifocal nature of spinal cord lesions in murine experimental autoimmune encephalomyelitis
items: First insights into the diversity of gill monogeneans of ‘Gnathochromis’ and Limnochromis (Teleostei, Cichlidae) in Burundi: do the parasites mirror host ecology and phylogenetic history?
items: Age-related changes of dental pulp tissue after experimental tooth movement in rats
items: An explicit solution for calculating optimum spawning stock size from Ricker’s stock recruitment model
items: Molecular evidence for sediment nitrogen fixation in a temperate New England estuary
items: Immunohistochemistry for the detection of neural and inflammatory cells in equine brain tissue
items: The feasibility and radiological features of sacral alar iliac fixation in an adult population: a 3D imaging study
items: Experimental modulation of external microbiome affects nestmate recognition in harvester ants (Pogonomyrmex barbatus)

Influence of isoflurane on the diastolic pressure-flow relationship and critical occlusion pressure during arterial CABG surgery: a randomized controlled trial
type: item
type: AcademicArticle
description: The effects of isoflurane on the determinants of blood flow during Coronary Artery Bypass Graft (CABG) surgery are not completely understood. This study characterized the influence of isoflurane on the diastolic Pressure-Flow (P-F) relationship and Critical Occlusion Pressure (COP) during CABG surgery. Twenty patients undergoing CABG surgery were studied. Patients were assigned to an isoflurane or control group. Hemodynamic and flow measurements during CABG surgery were performed twice (15 minutes after the discontinuation of extracorporeal circulation (T15) and again 15 minutes later (T30)). The zero flow pressure intercept (a measure of COP) was extrapolated from a linear regression analysis of the instantaneous diastolic P-F relationship. In the isoflurane group, the application of isoflurane significantly increased the slope of the diastolic P-F relationship by 215% indicating a mean reduction of Coronary Vascular Resistance (CVR) by 46%. Simultaneously, the Mean Diastolic Aortic Pressure (MDAP) decreased by 19% mainly due to a decrease in the systemic vascular resistance index by 21%. The COP, cardiac index, heart rate, Left Ventricular End-Diastolic Pressure (LVEDP) and Coronary Sinus Pressure (CSP) did not change significantly. In the control group, the parameters remained unchanged. In both groups, COP significantly exceeded the CSP and LVEDP at both time points. We conclude that short-term application of isoflurane at a sedative concentration markedly increases the slope of the instantaneous diastolic P-F relationship during CABG surgery implying a distinct decrease with CVR in patients undergoing CABG surgery.
format: application/pdf
format: text/html
creator: José Hinz
creator: Ashham Mansur
creator: Gerd G. Hanekop
creator: Andreas Weyland
creator: Aron F. Popov
creator: Jan D. Schmitto
creator: Frank F. G. Grüne
creator: Martin Bauer
creator: Stephan Kazmaier
subject: Anesthesiology and Pain Management
subject: Cardiology
subject: Clinical Trials
subject: Emergency and Critical Care
subject: Surgery and Surgical Specialties
description: doi:10.7717/peerj.1619
publisher: PeerJ Inc.
rights: © 2016 Hinz et al.
abstract: The effects of isoflurane on the determinants of blood flow during Coronary Artery Bypass Graft (CABG) surgery are not completely understood. This study characterized the influence of isoflurane on the diastolic Pressure-Flow (P-F) relationship and Critical Occlusion Pressure (COP) during CABG surgery. Twenty patients undergoing CABG surgery were studied. Patients were assigned to an isoflurane or control group. Hemodynamic and flow measurements during CABG surgery were performed twice (15 minutes after the discontinuation of extracorporeal circulation (T15) and again 15 minutes later (T30)). The zero flow pressure intercept (a measure of COP) was extrapolated from a linear regression analysis of the instantaneous diastolic P-F relationship. In the isoflurane group, the application of isoflurane significantly increased the slope of the diastolic P-F relationship by 215% indicating a mean reduction of Coronary Vascular Resistance (CVR) by 46%. Simultaneously, the Mean Diastolic Aortic Pressure (MDAP) decreased by 19% mainly due to a decrease in the systemic vascular resistance index by 21%. The COP, cardiac index, heart rate, Left Ventricular End-Diastolic Pressure (LVEDP) and Coronary Sinus Pressure (CSP) did not change significantly. In the control group, the parameters remained unchanged. In both groups, COP significantly exceeded the CSP and LVEDP at both time points. We conclude that short-term application of isoflurane at a sedative concentration markedly increases the slope of the instantaneous diastolic P-F relationship during CABG surgery implying a distinct decrease with CVR in patients undergoing CABG surgery.
bibliographic citation: Hinz et al. (2016) Influence of isoflurane on the diastolic pressure-flow relationship and critical occlusion pressure during arterial CABG surgery: a randomized controlled trial. PeerJ 4:e1619 https://doi.org/10.7717/peerj.1619
date submitted: 2015-09-08
date accepted: 2016-01-02
issued: 2016-01-26
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Hinz
  given name: José
author list: Agent
  family name: Mansur
  given name: Ashham
author list: Agent
  family name: Hanekop
  given name: Gerd G.
author list: Agent
  family name: Weyland
  given name: Andreas
author list: Agent
  family name: Popov
  given name: Aron F.
author list: Agent
  family name: Schmitto
  given name: Jan D.
author list: Agent
  family name: Grüne
  given name: Frank F. G.
author list: Agent
  family name: Bauer
  given name: Martin
author list: Agent
  family name: Kazmaier
  given name: Stephan
doi: 10.7717/peerj.1619
volume: 4
issn: 2167-8359
publication name: PeerJ
publication date: 2016-01-26
copyright: © 2016 Hinz et al.
attribution name: Hinz et al.

Sustained attention in skilled and novice martial arts athletes: a study of event-related potentials and current sources
type: item
type: AcademicArticle
description: Background. Research on sports has revealed that behavioral responses and event-related brain potentials (ERP) are better in expert than in novice athletes for sport-related tasks. Focused attention is essential for optimal athletic performance across different sports but mainly in combat disciplines. During combat, long periods of focused attention (i.e., sustained attention) are required for a good performance. Few investigations have reported effects of expertise on brain electrical activity and its neural generators during sport-unrelated attention tasks. The aim of the present study was to assess the effect of expertise (i.e., skilled and novice martial arts athletes) analyzing the ERP during a sustained attention task (Continuous Performance Task; CPT) and the cortical three-dimensional distribution of current density, using the sLORETA technique. Methods. CPT consisted in an oddball-type paradigm presentation of five stimuli (different pointing arrows) where only one of them (an arrow pointing up right) required a motor response (i.e., target). CPT was administered to skilled and novice martial arts athletes while EEG were recorded. Amplitude ERP data from target and non-target stimuli were compared between groups. Subsequently, current source analysis for each ERP component was performed on each subject. sLORETA images were compared by condition and group using Statistical Non-Parametric Mapping analysis. Results. Skilled athletes showed significant amplitude differences between target and non-target conditions in early ERP components (P100 and P200) as opposed to the novice group; however, skilled athletes showed no significant effect of condition in N200 but novices did show a significant effect. Current source analysis showed greater differences in activations in skilled compared with novice athletes between conditions in the frontal (mainly in the Superior Frontal Gyrus and Medial Frontal Gyrus) and limbic (mainly in the Anterior Cingulate Gyrus) lobes. …
format: application/pdf
format: text/html
creator: Javier Sanchez-Lopez
creator: Juan Silva-Pereyra
creator: Thalia Fernandez
subject: Neuroscience
subject: Psychiatry and Psychology
description: doi:10.7717/peerj.1614
publisher: PeerJ Inc.
rights: © 2016 Sanchez-Lopez et al.
abstract: Background. Research on sports has revealed that behavioral responses and event-related brain potentials (ERP) are better in expert than in novice athletes for sport-related tasks. Focused attention is essential for optimal athletic performance across different sports but mainly in combat disciplines. During combat, long periods of focused attention (i.e., sustained attention) are required for a good performance. Few investigations have reported effects of expertise on brain electrical activity and its neural generators during sport-unrelated attention tasks. The aim of the present study was to assess the effect of expertise (i.e., skilled and novice martial arts athletes) analyzing the ERP during a sustained attention task (Continuous Performance Task; CPT) and the cortical three-dimensional distribution of current density, using the sLORETA technique. Methods. CPT consisted in an oddball-type paradigm presentation of five stimuli (different pointing arrows) where only one of them (an arrow pointing up right) required a motor response (i.e., target). CPT was administered to skilled and novice martial arts athletes while EEG were recorded. Amplitude ERP data from target and non-target stimuli were compared between groups. Subsequently, current source analysis for each ERP component was performed on each subject. sLORETA images were compared by condition and group using Statistical Non-Parametric Mapping analysis. Results. Skilled athletes showed significant amplitude differences between target and non-target conditions in early ERP components (P100 and P200) as opposed to the novice group; however, skilled athletes showed no significant effect of condition in N200 but novices did show a significant effect. Current source analysis showed greater differences in activations in skilled compared with novice athletes between conditions in the frontal (mainly in the Superior Frontal Gyrus and Medial Frontal Gyrus) and limbic (mainly in the Anterior Cingulate Gyrus) lobes. …
bibliographic citation: Sanchez-Lopez et al. (2016) Sustained attention in skilled and novice martial arts athletes: a study of event-related potentials and current sources. PeerJ 4:e1614 https://doi.org/10.7717/peerj.1614
date submitted: 2015-10-19
date accepted: 2015-12-31
issued: 2016-01-26
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Sanchez-Lopez
  given name: Javier
author list: Agent
  family name: Silva-Pereyra
  given name: Juan
author list: Agent
  family name: Fernandez
  given name: Thalia
doi: 10.7717/peerj.1614
volume: 4
issn: 2167-8359
publication name: PeerJ
publication date: 2016-01-26
copyright: © 2016 Sanchez-Lopez et al.
attribution name: Sanchez-Lopez et al.

A method for histopathological study of the multifocal nature of spinal cord lesions in murine experimental autoimmune encephalomyelitis
type: item
type: AcademicArticle
description: Experimental autoimmune encephalomyelitis (EAE) is a well-established mouse model for multiple sclerosis and is characterized by infiltration of mononuclear cells and demyelination within the central nervous system along with the clinical symptoms of paralysis. EAE is a multifocal and random disease, which sometimes makes histopathologic analysis of lesions difficult as it may not be possible to predict where lesions will occur, especially when evaluating cross sections of spinal cord. Consequently, lesions may be easily missed due to limited sampling in traditional approaches. To evaluate the entire length of the spinal cord while maintaining anatomic integrity, we have developed a method to section the cord within the decalcified spinal column, which allows for the study of the multifocal nature of this disease and also minimizes handling artifact. HE and Luxol fast blue staining of these spinal cord sections revealed a paucity of lesions in some areas, while others showed marked inflammation and demyelination. The percentage of spinal cord affected by EAE was evaluated at four separate areas of longitudinally sectioned cord and it varied greatly within each animal. Immunohistochemical staining of in situ spinal cords which had undergone decalcification was successful for key immuno-markers used in EAE research including CD3 for T cells, B220 for B cells and F4/80 for murine macrophages. This method will allow investigators to look at the entire spinal cord on a single slide and evaluate the spinal cord with and without classic EAE lesions.
format: application/pdf
format: text/html
creator: Katherine N. Gibson-Corley
creator: Alexander W. Boyden
creator: Mariah R. Leidinger
creator: Allyn M. Lambertz
creator: Georgina Ofori-Amanfo
creator: Paul W. Naumann
creator: J. Adam Goeken
creator: Nitin J. Karandikar
subject: Neurology
subject: Pathology
subject: Histology
description: doi:10.7717/peerj.1600
publisher: PeerJ Inc.
rights: © 2016 Gibson-Corley et al.
abstract: Experimental autoimmune encephalomyelitis (EAE) is a well-established mouse model for multiple sclerosis and is characterized by infiltration of mononuclear cells and demyelination within the central nervous system along with the clinical symptoms of paralysis. EAE is a multifocal and random disease, which sometimes makes histopathologic analysis of lesions difficult as it may not be possible to predict where lesions will occur, especially when evaluating cross sections of spinal cord. Consequently, lesions may be easily missed due to limited sampling in traditional approaches. To evaluate the entire length of the spinal cord while maintaining anatomic integrity, we have developed a method to section the cord within the decalcified spinal column, which allows for the study of the multifocal nature of this disease and also minimizes handling artifact. HE and Luxol fast blue staining of these spinal cord sections revealed a paucity of lesions in some areas, while others showed marked inflammation and demyelination. The percentage of spinal cord affected by EAE was evaluated at four separate areas of longitudinally sectioned cord and it varied greatly within each animal. Immunohistochemical staining of in situ spinal cords which had undergone decalcification was successful for key immuno-markers used in EAE research including CD3 for T cells, B220 for B cells and F4/80 for murine macrophages. This method will allow investigators to look at the entire spinal cord on a single slide and evaluate the spinal cord with and without classic EAE lesions.
bibliographic citation: Gibson-Corley et al. (2016) A method for histopathological study of the multifocal nature of spinal cord lesions in murine experimental autoimmune encephalomyelitis. PeerJ 4:e1600 https://doi.org/10.7717/peerj.1600
date submitted: 2015-11-25
date accepted: 2015-12-23
issued: 2016-01-26
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Gibson-Corley
  given name: Katherine N.
author list: Agent
  family name: Boyden
  given name: Alexander W.
author list: Agent
  family name: Leidinger
  given name: Mariah R.
author list: Agent
  family name: Lambertz
  given name: Allyn M.
author list: Agent
  family name: Ofori-Amanfo
  given name: Georgina
author list: Agent
  family name: Naumann
  given name: Paul W.
author list: Agent
  family name: Goeken
  given name: J. Adam
author list: Agent
  family name: Karandikar
  given name: Nitin J.
doi: 10.7717/peerj.1600
volume: 4
issn: 2167-8359
publication name: PeerJ
publication date: 2016-01-26
copyright: © 2016 Gibson-Corley et al.
attribution name: Gibson-Corley et al.

First insights into the diversity of gill monogeneans of ‘Gnathochromis’ and Limnochromis (Teleostei, Cichlidae) in Burundi: do the parasites mirror host ecology and phylogenetic history?
type: item
type: AcademicArticle
description: Monogenea is one of the most species-rich groups of parasitic flatworms worldwide, with many species described only recently, which is particularly true for African monogeneans. For example, Cichlidogyrus, a genus mostly occurring on African cichlids, comprises more than 100 nominal species. Twenty-two of these have been described from Lake Tanganyika, a famous biodiversity hotspot in which many vertebrate and invertebrate taxa, including monogeneans, underwent unique and spectacular radiations. Given their often high degrees of host specificity, parasitic monogeneans were also used as a potential tool to uncover host species relationships. This study presents the first investigation of the monogenean fauna occurring on the gills of endemic ‘Gnathochromis’ species along the Burundese coastline of Lake Tanganyika. We test whether their monogenean fauna reflects the different phylogenetic position and ecological niche of ‘Gnathochromis’ pfefferi and Gnathochromis permaxillaris. Worms collected from specimens of Limnochromis auritus, a cichlid belonging to the same cichlid tribe as G. permaxillaris, were used for comparison. Morphological as well as genetic characterisation was used for parasite identification. In total, all 73 Cichlidogyrus individuals collected from ‘G.’ pfefferi were identified as C. irenae. This is the only representative of Cichlidogyrus previously described from ‘G.’ pfefferi, its type host. Gnathochromis permaxillaris is infected by a species of Cichlidogyrus morphologically very similar to C. gillardinae. The monogenean species collected from L. auritus is considered as new for science, but sample size was insufficient for a formal description. Our results confirm previous suggestions that ‘G.’ pfefferi as a good disperser is infected by a single monogenean species across the entire Lake Tanganyika. Although G. permaxillaris and L. auritus are placed in the same tribe, Cichlidogyrus sp. occurring on G. permaxillaris is morphologically more simi…
format: application/pdf
format: text/html
creator: Nikol Kmentová
creator: Milan Gelnar
creator: Stephan Koblmüller
creator: Maarten P.M. Vanhove
subject: Aquaculture, Fisheries and Fish Science
subject: Biodiversity
subject: Parasitology
description: doi:10.7717/peerj.1629
publisher: PeerJ Inc.
rights: © 2016 Kmentová et al.
abstract: Monogenea is one of the most species-rich groups of parasitic flatworms worldwide, with many species described only recently, which is particularly true for African monogeneans. For example, Cichlidogyrus, a genus mostly occurring on African cichlids, comprises more than 100 nominal species. Twenty-two of these have been described from Lake Tanganyika, a famous biodiversity hotspot in which many vertebrate and invertebrate taxa, including monogeneans, underwent unique and spectacular radiations. Given their often high degrees of host specificity, parasitic monogeneans were also used as a potential tool to uncover host species relationships. This study presents the first investigation of the monogenean fauna occurring on the gills of endemic ‘Gnathochromis’ species along the Burundese coastline of Lake Tanganyika. We test whether their monogenean fauna reflects the different phylogenetic position and ecological niche of ‘Gnathochromis’ pfefferi and Gnathochromis permaxillaris. Worms collected from specimens of Limnochromis auritus, a cichlid belonging to the same cichlid tribe as G. permaxillaris, were used for comparison. Morphological as well as genetic characterisation was used for parasite identification. In total, all 73 Cichlidogyrus individuals collected from ‘G.’ pfefferi were identified as C. irenae. This is the only representative of Cichlidogyrus previously described from ‘G.’ pfefferi, its type host. Gnathochromis permaxillaris is infected by a species of Cichlidogyrus morphologically very similar to C. gillardinae. The monogenean species collected from L. auritus is considered as new for science, but sample size was insufficient for a formal description. Our results confirm previous suggestions that ‘G.’ pfefferi as a good disperser is infected by a single monogenean species across the entire Lake Tanganyika. Although G. permaxillaris and L. auritus are placed in the same tribe, Cichlidogyrus sp. occurring on G. permaxillaris is morphologically more simi…
bibliographic citation: Kmentová et al. (2016) First insights into the diversity of gill monogeneans of ‘Gnathochromis’ and Limnochromis (Teleostei, Cichlidae) in Burundi: do the parasites mirror host ecology and phylogenetic history?. PeerJ 4:e1629 https://doi.org/10.7717/peerj.1629
date submitted: 2015-11-02
date accepted: 2016-01-05
issued: 2016-01-25
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Kmentová
  given name: Nikol
author list: Agent
  family name: Gelnar
  given name: Milan
author list: Agent
  family name: Koblmüller
  given name: Stephan
author list: Agent
  family name: Vanhove
  given name: Maarten P.M.
doi: 10.7717/peerj.1629
volume: 4
issn: 2167-8359
publication name: PeerJ
publication date: 2016-01-25
copyright: ©2016 Kmentová et al.
attribution name: Kmentová et al.

Age-related changes of dental pulp tissue after experimental tooth movement in rats
type: item
type: AcademicArticle
description: It is generally accepted that the effect of orthodontic tooth movement on the dental pulp in adolescents is reversible and that it has no long-lasting effect on pulpal physiology. However, it is not clear yet if the same conclusion is also valid for adult subjects. Thus, in two groups of rats, aged 6 and 40 weeks respectively, 3 molars at one side of the maxilla were moved together in a mesial direction with a standardized orthodontic appliance delivering a force of 10 cN. The contralateral side served as a control. Parasagittal histological sections were prepared after tooth movement for 1, 2, 4, 8, and 12 weeks. The pulp tissue was characterized for the different groups, with special emphasis on cell density, inflammatory cells, vascularity, and odontoblasts. Dimensions of dentin and the pulpal horns was determined and related with the duration of orthodontic force application and age ware evaluated. We found that neither in young nor in adult rats, force application led to long-lasting or irreversible changes in pulpal tissues. Dimensional variables showed significant age-related changes. In conclusion, orthodontic tooth movement per se has no long-lasting or irreversible effect on pulpal tissues, neither in the young nor in the adult animals.
format: application/pdf
format: text/html
creator: Martina Von Böhl
creator: Yijin Ren
creator: Anne M. Kuijpers-Jagtman
creator: Piotr S. Fudalej
creator: Jaap C. Maltha
subject: Zoology
subject: Dentistry
subject: Histology
description: doi:10.7717/peerj.1625
publisher: PeerJ Inc.
rights: © 2016 Von Böhl et al.
abstract: It is generally accepted that the effect of orthodontic tooth movement on the dental pulp in adolescents is reversible and that it has no long-lasting effect on pulpal physiology. However, it is not clear yet if the same conclusion is also valid for adult subjects. Thus, in two groups of rats, aged 6 and 40 weeks respectively, 3 molars at one side of the maxilla were moved together in a mesial direction with a standardized orthodontic appliance delivering a force of 10 cN. The contralateral side served as a control. Parasagittal histological sections were prepared after tooth movement for 1, 2, 4, 8, and 12 weeks. The pulp tissue was characterized for the different groups, with special emphasis on cell density, inflammatory cells, vascularity, and odontoblasts. Dimensions of dentin and the pulpal horns was determined and related with the duration of orthodontic force application and age ware evaluated. We found that neither in young nor in adult rats, force application led to long-lasting or irreversible changes in pulpal tissues. Dimensional variables showed significant age-related changes. In conclusion, orthodontic tooth movement per se has no long-lasting or irreversible effect on pulpal tissues, neither in the young nor in the adult animals.
bibliographic citation: Von Böhl et al. (2016) Age-related changes of dental pulp tissue after experimental tooth movement in rats. PeerJ 4:e1625 https://doi.org/10.7717/peerj.1625
date submitted: 2015-08-10
date accepted: 2016-01-05
issued: 2016-01-25
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Von Böhl
  given name: Martina
author list: Agent
  family name: Ren
  given name: Yijin
author list: Agent
  family name: Kuijpers-Jagtman
  given name: Anne M.
author list: Agent
  family name: Fudalej
  given name: Piotr S.
author list: Agent
  family name: Maltha
  given name: Jaap C.
doi: 10.7717/peerj.1625
volume: 4
issn: 2167-8359
publication name: PeerJ
publication date: 2016-01-25
copyright: ©2016 Von Böhl et al.
attribution name: Von Böhl et al.

An explicit solution for calculating optimum spawning stock size from Ricker’s stock recruitment model
type: item
type: AcademicArticle
description: Stock-recruitment models have been used for decades in fisheries management as a means of formalizing the expected number of offspring that recruit to a fishery based on the number of parents. In particular, Ricker’s stock recruitment model is widely used due to its flexibility and ease with which the parameters can be estimated. After model fitting, the spawning stock size that produces the maximum sustainable yield (SMSY) to a fishery, and the harvest corresponding to it (UMSY), are two of the most common biological reference points of interest to fisheries managers. However, to date there has been no explicit solution for either reference point because of the transcendental nature of the equation needed to solve for them. Therefore, numerical or statistical approximations have been used for more than 30 years. Here I provide explicit formulae for calculating both SMSY and UMSY in terms of the productivity and density-dependent parameters of Ricker’s model.
format: application/pdf
format: text/html
creator: Mark D. Scheuerell
subject: Ecology
subject: Mathematical Biology
description: doi:10.7717/peerj.1623
publisher: PeerJ Inc.
rights: © 2016 Scheuerell
abstract: Stock-recruitment models have been used for decades in fisheries management as a means of formalizing the expected number of offspring that recruit to a fishery based on the number of parents. In particular, Ricker’s stock recruitment model is widely used due to its flexibility and ease with which the parameters can be estimated. After model fitting, the spawning stock size that produces the maximum sustainable yield (SMSY) to a fishery, and the harvest corresponding to it (UMSY), are two of the most common biological reference points of interest to fisheries managers. However, to date there has been no explicit solution for either reference point because of the transcendental nature of the equation needed to solve for them. Therefore, numerical or statistical approximations have been used for more than 30 years. Here I provide explicit formulae for calculating both SMSY and UMSY in terms of the productivity and density-dependent parameters of Ricker’s model.
bibliographic citation: Scheuerell (2016) An explicit solution for calculating optimum spawning stock size from Ricker’s stock recruitment model. PeerJ 4:e1623 https://doi.org/10.7717/peerj.1623
date submitted: 2015-10-16
date accepted: 2016-01-04
issued: 2016-01-25
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Scheuerell
  given name: Mark D.
doi: 10.7717/peerj.1623
volume: 4
issn: 2167-8359
publication name: PeerJ
publication date: 2016-01-25
copyright: ©2016 Scheuerell
attribution name: Scheuerell

Molecular evidence for sediment nitrogen fixation in a temperate New England estuary
type: item
type: AcademicArticle
description: Primary production in coastal waters is generally nitrogen (N) limited with denitrification outpacing nitrogen fixation (N2-fixation). However, recent work suggests that we have potentially underestimated the importance of heterotrophic sediment N2-fixation in marine ecosystems. We used clone libraries to examine transcript diversity of nifH (a gene associated with N2-fixation) in sediments at three sites in a temperate New England estuary (Waquoit Bay, Massachusetts, USA) and compared our results to net sediment N2 fluxes previously measured at these sites. We observed nifH expression at all sites, including a site heavily impacted by anthropogenic N. At this N impacted site, we also observed mean net sediment N2-fixation, linking the geochemical rate measurement with nifH expression. This same site also had the lowest diversity (non-parametric Shannon = 2.75). At the two other sites, we also detected nifH transcripts, however, the mean N2 flux indicated net denitrification. These results suggest that N2-fixation and denitrification co-occur in these sediments. Of the unique sequences in this study, 67% were most closely related to uncultured bacteria from various marine environments, 17% to Cluster III, 15% to Cluster I, and only 1% to Cluster II. These data add to the growing body of literature that sediment heterotrophic N2-fixation, even under high inorganic nitrogen concentrations, may be an important yet overlooked source of N in coastal systems.
format: application/pdf
format: text/html
creator: Silvia E. Newell
creator: Kaitlyn R. Pritchard
creator: Sarah Q. Foster
creator: Robinson W. Fulweiler
subject: Biogeochemistry
subject: Biological Oceanography
subject: Ecosystem Science
subject: Environmental Sciences
description: doi:10.7717/peerj.1615
publisher: PeerJ Inc.
rights: © 2016 Newell et al.
abstract: Primary production in coastal waters is generally nitrogen (N) limited with denitrification outpacing nitrogen fixation (N2-fixation). However, recent work suggests that we have potentially underestimated the importance of heterotrophic sediment N2-fixation in marine ecosystems. We used clone libraries to examine transcript diversity of nifH (a gene associated with N2-fixation) in sediments at three sites in a temperate New England estuary (Waquoit Bay, Massachusetts, USA) and compared our results to net sediment N2 fluxes previously measured at these sites. We observed nifH expression at all sites, including a site heavily impacted by anthropogenic N. At this N impacted site, we also observed mean net sediment N2-fixation, linking the geochemical rate measurement with nifH expression. This same site also had the lowest diversity (non-parametric Shannon = 2.75). At the two other sites, we also detected nifH transcripts, however, the mean N2 flux indicated net denitrification. These results suggest that N2-fixation and denitrification co-occur in these sediments. Of the unique sequences in this study, 67% were most closely related to uncultured bacteria from various marine environments, 17% to Cluster III, 15% to Cluster I, and only 1% to Cluster II. These data add to the growing body of literature that sediment heterotrophic N2-fixation, even under high inorganic nitrogen concentrations, may be an important yet overlooked source of N in coastal systems.
bibliographic citation: Newell et al. (2016) Molecular evidence for sediment nitrogen fixation in a temperate New England estuary. PeerJ 4:e1615 https://doi.org/10.7717/peerj.1615
date submitted: 2015-10-19
date accepted: 2016-01-01
issued: 2016-01-25
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Newell
  given name: Silvia E.
author list: Agent
  family name: Pritchard
  given name: Kaitlyn R.
author list: Agent
  family name: Foster
  given name: Sarah Q.
author list: Agent
  family name: Fulweiler
  given name: Robinson W.
doi: 10.7717/peerj.1615
volume: 4
issn: 2167-8359
publication name: PeerJ
publication date: 2016-01-25
copyright: ©2016 Newell et al.
attribution name: Newell et al.

Immunohistochemistry for the detection of neural and inflammatory cells in equine brain tissue
type: item
type: AcademicArticle
description: Phenotypic characterization of cellular responses in equine infectious encephalitides has had limited description of both peripheral and resident cell populations in central nervous system (CNS) tissues due to limited species-specific reagents that react with formalin-fixed, paraffin embedded tissue (FFPE). This study identified a set of antibodies for investigating the immunopathology of infectious CNS diseases in horses. Multiple commercially available staining reagents and antibodies derived from antigens of various species for manual immunohistochemistry (IHC) were screened. Several techniques and reagents for heat-induced antigen retrieval, non-specific protein blocking, endogenous peroxidase blocking, and visualization-detection systems were tested during IHC protocol development. Boiling of slides in a low pH, citrate-based buffer solution in a double-boiler system was most consistent for epitope retrieval. Pressure-cooking, microwaving, high pH buffers, and proteinase K solutions often resulted in tissue disruption or no reactivity. Optimal blocking reagents and concentrations of each working antibody were determined. Ultimately, a set of monoclonal (mAb) and polyclonal antibodies (pAb) were identified for CD3+ (pAb A0452, Dako) T-lymphocytes, CD79αcy+ B-lymphocytes (mAb HM57, Dako), macrophages (mAb MAC387, Leica), NF-H+ neurons (mAb NAP4, EnCor Biotechnology), microglia/macrophage (pAb Iba-1, Wako), and GFAP+ astrocytes (mAb 5C10, EnCor Biotechnology). In paraffin embedded tissues, mAbs and pAbs derived from human and swine antigens were very successful at binding equine tissue targets. Individual, optimized protocols are provided for each positively reactive antibody for analyzing equine neuroinflammatory disease histopathology.
format: application/pdf
format: text/html
creator: Gretchen H. Delcambre
creator: Junjie Liu
creator: Jenna M. Herrington
creator: Kelsey Vallario
creator: Maureen T. Long
subject: Histology
subject: Infectious Diseases
subject: Pathology
subject: Veterinary Medicine
description: doi:10.7717/peerj.1601
publisher: PeerJ Inc.
rights: © 2016 Delcambre et al.
abstract: Phenotypic characterization of cellular responses in equine infectious encephalitides has had limited description of both peripheral and resident cell populations in central nervous system (CNS) tissues due to limited species-specific reagents that react with formalin-fixed, paraffin embedded tissue (FFPE). This study identified a set of antibodies for investigating the immunopathology of infectious CNS diseases in horses. Multiple commercially available staining reagents and antibodies derived from antigens of various species for manual immunohistochemistry (IHC) were screened. Several techniques and reagents for heat-induced antigen retrieval, non-specific protein blocking, endogenous peroxidase blocking, and visualization-detection systems were tested during IHC protocol development. Boiling of slides in a low pH, citrate-based buffer solution in a double-boiler system was most consistent for epitope retrieval. Pressure-cooking, microwaving, high pH buffers, and proteinase K solutions often resulted in tissue disruption or no reactivity. Optimal blocking reagents and concentrations of each working antibody were determined. Ultimately, a set of monoclonal (mAb) and polyclonal antibodies (pAb) were identified for CD3+ (pAb A0452, Dako) T-lymphocytes, CD79αcy+ B-lymphocytes (mAb HM57, Dako), macrophages (mAb MAC387, Leica), NF-H+ neurons (mAb NAP4, EnCor Biotechnology), microglia/macrophage (pAb Iba-1, Wako), and GFAP+ astrocytes (mAb 5C10, EnCor Biotechnology). In paraffin embedded tissues, mAbs and pAbs derived from human and swine antigens were very successful at binding equine tissue targets. Individual, optimized protocols are provided for each positively reactive antibody for analyzing equine neuroinflammatory disease histopathology.
bibliographic citation: Delcambre et al. (2016) Immunohistochemistry for the detection of neural and inflammatory cells in equine brain tissue. PeerJ 4:e1601 https://doi.org/10.7717/peerj.1601
date submitted: 2015-10-02
date accepted: 2015-12-23
issued: 2016-01-25
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Delcambre
  given name: Gretchen H.
author list: Agent
  family name: Liu
  given name: Junjie
author list: Agent
  family name: Herrington
  given name: Jenna M.
author list: Agent
  family name: Vallario
  given name: Kelsey
author list: Agent
  family name: Long
  given name: Maureen T.
doi: 10.7717/peerj.1601
volume: 4
issn: 2167-8359
publication name: PeerJ
publication date: 2016-01-25
copyright: © 2016 Delcambre et al.
attribution name: Delcambre et al.

The feasibility and radiological features of sacral alar iliac fixation in an adult population: a 3D imaging study
type: item
type: AcademicArticle
description: Background: Surgical treatments for adult spinal deformities often include pelvic fixation, and the feasibility of sacral-2 alar iliac (S2AI) screw fixation has been shown previously. However, sometimes S2AI screw fixation cannot be applied due to the presence of an osteolytic lesion or trauma or because the biomechanical properties of only an S2AI screw is insufficient. Therefore, we questioned the feasibility of using sacral AI screws in other segments and determined whether S3AI and S4AI screws have the potential to be used for sacral fractures. The aim of this study was to investigate the feasibility and radiological features of sacral AI fixation in S1–S4 in an adult population using 3D imaging techniques. Methods: Computed tomography (CT) scans were taken of 45 patients and were imported into Mimics (Version 10.01, Materialise, Belgium) software to reconstruct the 3D digital images. Next, a cylinder (radius of 3.5 mm) was drawn to imitate the screw trajectory of a S1–4 AI screw, and every imitated screw in each segment was adjusted to a maximum upward and downward angle to acquire the feasible region. The parameters of the S1–4AI screw trajectories were measured. Results: Sacral AI screws could be successfully imitated using 3D digital imaging. The S4AI screw trajectory could be obtained in 19 of 45 patient images (42.2%), while the feasibility rates of S1AI, S2AI, and S3AI screw fixation were 100%, 100%, and 91.1% (41/45), respectively. The feasible regions of S1AI, S2AI, and S3AI screw trajectories were wide enough, while the adjustable angle of S4AI screws was very small. Conclusion: It is feasible to place S1–2AI screws in the entire adult population and S3–4AI screws in some of the adult population. Furthermore, our study suggested that 3D digital images are suitable to study the feasibility of new screw fixation.
format: application/pdf
format: text/html
creator: Ai-Min Wu
creator: Yong-Long Chi
creator: Wen-Fei Ni
creator: Yi-Xing Huang
subject: Orthopedics
subject: Radiology and Medical Imaging
subject: Surgery and Surgical Specialties
description: doi:10.7717/peerj.1587
publisher: PeerJ Inc.
rights: © 2016 Wu et al.
abstract: Background: Surgical treatments for adult spinal deformities often include pelvic fixation, and the feasibility of sacral-2 alar iliac (S2AI) screw fixation has been shown previously. However, sometimes S2AI screw fixation cannot be applied due to the presence of an osteolytic lesion or trauma or because the biomechanical properties of only an S2AI screw is insufficient. Therefore, we questioned the feasibility of using sacral AI screws in other segments and determined whether S3AI and S4AI screws have the potential to be used for sacral fractures. The aim of this study was to investigate the feasibility and radiological features of sacral AI fixation in S1–S4 in an adult population using 3D imaging techniques. Methods: Computed tomography (CT) scans were taken of 45 patients and were imported into Mimics (Version 10.01, Materialise, Belgium) software to reconstruct the 3D digital images. Next, a cylinder (radius of 3.5 mm) was drawn to imitate the screw trajectory of a S1–4 AI screw, and every imitated screw in each segment was adjusted to a maximum upward and downward angle to acquire the feasible region. The parameters of the S1–4AI screw trajectories were measured. Results: Sacral AI screws could be successfully imitated using 3D digital imaging. The S4AI screw trajectory could be obtained in 19 of 45 patient images (42.2%), while the feasibility rates of S1AI, S2AI, and S3AI screw fixation were 100%, 100%, and 91.1% (41/45), respectively. The feasible regions of S1AI, S2AI, and S3AI screw trajectories were wide enough, while the adjustable angle of S4AI screws was very small. Conclusion: It is feasible to place S1–2AI screws in the entire adult population and S3–4AI screws in some of the adult population. Furthermore, our study suggested that 3D digital images are suitable to study the feasibility of new screw fixation.
bibliographic citation: Wu et al. (2016) The feasibility and radiological features of sacral alar iliac fixation in an adult population: a 3D imaging study. PeerJ 4:e1587 https://doi.org/10.7717/peerj.1587
date submitted: 2015-07-30
date accepted: 2015-12-20
issued: 2016-01-25
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Wu
  given name: Ai-Min
author list: Agent
  family name: Chi
  given name: Yong-Long
author list: Agent
  family name: Ni
  given name: Wen-Fei
author list: Agent
  family name: Huang
  given name: Yi-Xing
doi: 10.7717/peerj.1587
volume: 4
issn: 2167-8359
publication name: PeerJ
publication date: 2016-01-25
copyright: © 2016 Wu et al.
attribution name: Wu et al.

Experimental modulation of external microbiome affects nestmate recognition in harvester ants (Pogonomyrmex barbatus)
type: item
type: AcademicArticle
description: Social insects use odors as cues for a variety of behavioral responses, including nestmate recognition. Past research on nestmate recognition indicates cuticular hydrocarbons are important nestmate discriminators for social insects, but other factors are likely to contribute to colony-specific odors. Here we experimentally tested whether external microbes contribute to nestmate recognition in red harvester ants (Pogonomyrmex barbatus). We changed the external microbiome of ants through topical application of either antibiotics or microbial cultures. We then observed behavior of nestmates when treated ants were returned to the nest. Ants whose external microbiome was augmented with microbial cultures were much more likely to be rejected than controls, but ants treated with antibiotics were not. This result is consistent with the possibility that external microbes are used for nestmate recognition.
format: application/pdf
format: text/html
creator: Andy Dosmann
creator: Nassim Bahet
creator: Deborah M. Gordon
subject: Animal Behavior
subject: Entomology
description: doi:10.7717/peerj.1566
publisher: PeerJ Inc.
rights: © 2016 Dosmann et al.
abstract: Social insects use odors as cues for a variety of behavioral responses, including nestmate recognition. Past research on nestmate recognition indicates cuticular hydrocarbons are important nestmate discriminators for social insects, but other factors are likely to contribute to colony-specific odors. Here we experimentally tested whether external microbes contribute to nestmate recognition in red harvester ants (Pogonomyrmex barbatus). We changed the external microbiome of ants through topical application of either antibiotics or microbial cultures. We then observed behavior of nestmates when treated ants were returned to the nest. Ants whose external microbiome was augmented with microbial cultures were much more likely to be rejected than controls, but ants treated with antibiotics were not. This result is consistent with the possibility that external microbes are used for nestmate recognition.
bibliographic citation: Dosmann et al. (2016) Experimental modulation of external microbiome affects nestmate recognition in harvester ants (Pogonomyrmex barbatus). PeerJ 4:e1566 https://doi.org/10.7717/peerj.1566
date submitted: 2015-09-29
date accepted: 2015-12-15
issued: 2016-01-25
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Dosmann
  given name: Andy
author list: Agent
  family name: Bahet
  given name: Nassim
author list: Agent
  family name: Gordon
  given name: Deborah M.
doi: 10.7717/peerj.1566
volume: 4
issn: 2167-8359
publication name: PeerJ
publication date: 2016-01-25
copyright: ©2016 Dosmann et al.
attribution name: Dosmann et al.

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