PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
items: Region-of-interest analyses of one-dimensional biomechanical trajectories: bridging 0D and 1D theory, augmenting statistical power
items: The Ecology of Stress: linking life-history traits with physiological control mechanisms in free-living guanacos
items: Elevational pattern of bird species richness and its causes along a central Himalaya gradient, China
items: Three-dimensional paleohistology of the scale and median fin spine of Lophosteus superbus (Pander 1856)
items: Comparison of the effectiveness of ISJ and SSR markers and detection of outlier loci in conservation genetics of Pulsatilla patens populations
items: Performance, usability and comparison of two versions of a new macular vision test: the handheld Radial Shape Discrimination test
items: The abundance of large, piscivorous Ferox Trout (Salmo trutta) in Loch Rannoch, Scotland
items: Non-target effects of a glyphosate-based herbicide on Common toad larvae (Bufo bufo, Amphibia) and associated algae are altered by temperature
items: Whole-brain ex-vivo quantitative MRI of the cuprizone mouse model
items: Therapeutic role of human hepatocyte growth factor (HGF) in treating hair loss

Region-of-interest analyses of one-dimensional biomechanical trajectories: bridging 0D and 1D theory, augmenting statistical power
type: item
type: AcademicArticle
description: One-dimensional (1D) kinematic, force, and EMG trajectories are often analyzed using zero-dimensional (0D) metrics like local extrema. Recently whole-trajectory 1D methods have emerged in the literature as alternatives. Since 0D and 1D methods can yield qualitatively different results, the two approaches may appear to be theoretically distinct. The purposes of this paper were (a) to clarify that 0D and 1D approaches are actually just special cases of a more general region-of-interest (ROI) analysis framework, and (b) to demonstrate how ROIs can augment statistical power. We first simulated millions of smooth, random 1D datasets to validate theoretical predictions of the 0D, 1D and ROI approaches and to emphasize how ROIs provide a continuous bridge between 0D and 1D results. We then analyzed a variety of public datasets to demonstrate potential effects of ROIs on biomechanical conclusions. Results showed, first, that a priori ROI particulars can qualitatively affect the biomechanical conclusions that emerge from analyses and, second, that ROIs derived from exploratory/pilot analyses can detect smaller biomechanical effects than are detectable using full 1D methods. We recommend regarding ROIs, like data filtering particulars and Type I error rate, as parameters which can affect hypothesis testing results, and thus as sensitivity analysis tools to ensure arbitrary decisions do not influence scientific interpretations. Last, we describe open-source Python and MATLAB implementations of 1D ROI analysis for arbitrary experimental designs ranging from one-sample t tests to MANOVA.
format: application/pdf
format: text/html
creator: Todd C. Pataky
creator: Mark A. Robinson
creator: Jos Vanrenterghem
subject: Animal Behavior
subject: Bioengineering
subject: Kinesiology
subject: Statistics
description: doi:10.7717/peerj.2652
publisher: PeerJ Inc.
rights: © 2016 Pataky et al.
abstract: One-dimensional (1D) kinematic, force, and EMG trajectories are often analyzed using zero-dimensional (0D) metrics like local extrema. Recently whole-trajectory 1D methods have emerged in the literature as alternatives. Since 0D and 1D methods can yield qualitatively different results, the two approaches may appear to be theoretically distinct. The purposes of this paper were (a) to clarify that 0D and 1D approaches are actually just special cases of a more general region-of-interest (ROI) analysis framework, and (b) to demonstrate how ROIs can augment statistical power. We first simulated millions of smooth, random 1D datasets to validate theoretical predictions of the 0D, 1D and ROI approaches and to emphasize how ROIs provide a continuous bridge between 0D and 1D results. We then analyzed a variety of public datasets to demonstrate potential effects of ROIs on biomechanical conclusions. Results showed, first, that a priori ROI particulars can qualitatively affect the biomechanical conclusions that emerge from analyses and, second, that ROIs derived from exploratory/pilot analyses can detect smaller biomechanical effects than are detectable using full 1D methods. We recommend regarding ROIs, like data filtering particulars and Type I error rate, as parameters which can affect hypothesis testing results, and thus as sensitivity analysis tools to ensure arbitrary decisions do not influence scientific interpretations. Last, we describe open-source Python and MATLAB implementations of 1D ROI analysis for arbitrary experimental designs ranging from one-sample t tests to MANOVA.
bibliographic citation: Pataky et al. (2016) Region-of-interest analyses of one-dimensional biomechanical trajectories: bridging 0D and 1D theory, augmenting statistical power. PeerJ 4:e2652 https://doi.org/10.7717/peerj.2652
date submitted: 2016-07-13
date accepted: 2016-10-04
issued: 2016-11-02
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Pataky
  given name: Todd C.
author list: Agent
  family name: Robinson
  given name: Mark A.
author list: Agent
  family name: Vanrenterghem
  given name: Jos
doi: 10.7717/peerj.2652
volume: 4
issn: 2167-8359
publication name: PeerJ
publication date: 2016-11-02
copyright: ©2016 Pataky et al.
attribution name: Pataky et al.

The Ecology of Stress: linking life-history traits with physiological control mechanisms in free-living guanacos
type: item
type: AcademicArticle
description: Background Providing the context for the evolution of life-history traits, habitat features constrain successful ecological and physiological strategies. In vertebrates, a key response to life’s challenges is the activation of the Stress (HPA) and Gonadal (HPG) axes. Much of the interest in stress ecology is motivated by the desire to understand the physiological mechanisms in which the environment affects fitness. As reported in the literature, several intrinsic and extrinsic factors affect variability in hormone levels. In both social and non-social animals, the frequency and type of interaction with conspecifics, as well as the status in social species, can affect HPA axis activity, resulting in changes in the reproductive success of animals. We predicted that a social environment can affect both guanaco axes by increasing the secretion of testosterone (T) and Glucocorticoid (GCs) in response to individual social interactions and the energetic demands of breeding. Assuming that prolonged elevated levels of GCs over time can be harmful to individuals, it is predicted that the HPA axis suppresses the HPG axis and causes T levels to decrease, as GCs increase. Methods All of the data for individuals were collected by non-invasive methods (fecal samples) to address hormonal activities. This is a novel approach in physiological ecology because feces are easily obtained through non-invasive sampling in animal populations. Results As expected, there was a marked adrenal (p-value = .3.4e−12) and gonadal (p-value = 0.002656) response due to seasonal variation in Lama guanicoe. No significant differences were found in fecal GCs metabolites between males/females*season for the entire study period (p-value = 0.2839). Despite the seasonal activity variation in the hormonal profiles, our results show a positive correlation (p-value = 1.952e−11, COR = 0.50) between the adrenal and gonadal system. The marked endocrine (r2 = 0.806) and gonad (r2 = 0.7231) response due to seasonal …
format: application/pdf
format: text/html
creator: Ramiro J.A. Ovejero Aguilar
creator: Graciela A. Jahn
creator: Mauricio Soto-Gamboa
creator: Andrés J. Novaro
creator: Pablo Carmanchahi
subject: Ecology
subject: Zoology
description: doi:10.7717/peerj.2640
publisher: PeerJ Inc.
rights: © 2016 Ovejero Aguilar et al.
abstract: Background Providing the context for the evolution of life-history traits, habitat features constrain successful ecological and physiological strategies. In vertebrates, a key response to life’s challenges is the activation of the Stress (HPA) and Gonadal (HPG) axes. Much of the interest in stress ecology is motivated by the desire to understand the physiological mechanisms in which the environment affects fitness. As reported in the literature, several intrinsic and extrinsic factors affect variability in hormone levels. In both social and non-social animals, the frequency and type of interaction with conspecifics, as well as the status in social species, can affect HPA axis activity, resulting in changes in the reproductive success of animals. We predicted that a social environment can affect both guanaco axes by increasing the secretion of testosterone (T) and Glucocorticoid (GCs) in response to individual social interactions and the energetic demands of breeding. Assuming that prolonged elevated levels of GCs over time can be harmful to individuals, it is predicted that the HPA axis suppresses the HPG axis and causes T levels to decrease, as GCs increase. Methods All of the data for individuals were collected by non-invasive methods (fecal samples) to address hormonal activities. This is a novel approach in physiological ecology because feces are easily obtained through non-invasive sampling in animal populations. Results As expected, there was a marked adrenal (p-value = .3.4e−12) and gonadal (p-value = 0.002656) response due to seasonal variation in Lama guanicoe. No significant differences were found in fecal GCs metabolites between males/females*season for the entire study period (p-value = 0.2839). Despite the seasonal activity variation in the hormonal profiles, our results show a positive correlation (p-value = 1.952e−11, COR = 0.50) between the adrenal and gonadal system. The marked endocrine (r2 = 0.806) and gonad (r2 = 0.7231) response due to seasonal …
bibliographic citation: Ovejero Aguilar et al. (2016) The Ecology of Stress: linking life-history traits with physiological control mechanisms in free-living guanacos. PeerJ 4:e2640 https://doi.org/10.7717/peerj.2640
date submitted: 2016-06-05
date accepted: 2016-09-30
issued: 2016-11-02
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Ovejero Aguilar
  given name: Ramiro J.A.
author list: Agent
  family name: Jahn
  given name: Graciela A.
author list: Agent
  family name: Soto-Gamboa
  given name: Mauricio
author list: Agent
  family name: Novaro
  given name: Andrés J.
author list: Agent
  family name: Carmanchahi
  given name: Pablo
doi: 10.7717/peerj.2640
volume: 4
issn: 2167-8359
publication name: PeerJ
publication date: 2016-11-02
copyright: ©2016 Ovejero Aguilar et al.
attribution name: Ovejero Aguilar et al.

Elevational pattern of bird species richness and its causes along a central Himalaya gradient, China
type: item
type: AcademicArticle
description: This study examines the relative importance of six variables: area, the mid-domain effect, temperature, precipitation, productivity, and habitat heterogeneity on elevational patterns of species richness for breeding birds along a central Himalaya gradient in the Gyirong Valley, the longest of five canyons in the Mount Qomolangma National Nature Reserve. We conducted field surveys in each of twelve elevational bands of 300 m between 1,800 and 5,400 m asl four times throughout the entire wet season. A total of 169 breeding bird species were recorded and most of the species (74%) were small-ranged. The species richness patterns of overall, large-ranged and small-ranged birds were all hump-shaped, but with peaks at different elevations. Large-ranged species and small-ranged species contributed equally to the overall richness pattern. Based on the bivariate and multiple regression analyses, area and precipitation were not crucial factors in determining the species richness along this gradient. The mid-domain effect played an important role in shaping the richness pattern of large-ranged species. Temperature was negatively correlated with overall and large-ranged species but positively correlated with small-ranged species. Productivity was a strong explanatory factor among all the bird groups, and habitat heterogeneity played an important role in shaping the elevational richness patterns of overall and small-ranged species. Our results highlight the need to conserve primary forest and intact habitat in this area. Furthermore, we need to increase conservation efforts in this montane biodiversity hotspot in light of increasing anthropogenic activities and land use pressure.
format: application/pdf
format: text/html
creator: Xinyuan Pan
creator: Zhifeng Ding
creator: Yiming Hu
creator: Jianchao Liang
creator: Yongjie Wu
creator: Xingfeng Si
creator: Mingfang Guo
creator: Huijian Hu
creator: Kun Jin
subject: Biodiversity
subject: Biogeography
subject: Conservation Biology
subject: Ecology
subject: Zoology
description: doi:10.7717/peerj.2636
publisher: PeerJ Inc.
rights: © 2016 Pan et al.
abstract: This study examines the relative importance of six variables: area, the mid-domain effect, temperature, precipitation, productivity, and habitat heterogeneity on elevational patterns of species richness for breeding birds along a central Himalaya gradient in the Gyirong Valley, the longest of five canyons in the Mount Qomolangma National Nature Reserve. We conducted field surveys in each of twelve elevational bands of 300 m between 1,800 and 5,400 m asl four times throughout the entire wet season. A total of 169 breeding bird species were recorded and most of the species (74%) were small-ranged. The species richness patterns of overall, large-ranged and small-ranged birds were all hump-shaped, but with peaks at different elevations. Large-ranged species and small-ranged species contributed equally to the overall richness pattern. Based on the bivariate and multiple regression analyses, area and precipitation were not crucial factors in determining the species richness along this gradient. The mid-domain effect played an important role in shaping the richness pattern of large-ranged species. Temperature was negatively correlated with overall and large-ranged species but positively correlated with small-ranged species. Productivity was a strong explanatory factor among all the bird groups, and habitat heterogeneity played an important role in shaping the elevational richness patterns of overall and small-ranged species. Our results highlight the need to conserve primary forest and intact habitat in this area. Furthermore, we need to increase conservation efforts in this montane biodiversity hotspot in light of increasing anthropogenic activities and land use pressure.
bibliographic citation: Pan et al. (2016) Elevational pattern of bird species richness and its causes along a central Himalaya gradient, China. PeerJ 4:e2636 https://doi.org/10.7717/peerj.2636
date submitted: 2016-06-14
date accepted: 2016-09-30
issued: 2016-11-02
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Pan
  given name: Xinyuan
author list: Agent
  family name: Ding
  given name: Zhifeng
author list: Agent
  family name: Hu
  given name: Yiming
author list: Agent
  family name: Liang
  given name: Jianchao
author list: Agent
  family name: Wu
  given name: Yongjie
author list: Agent
  family name: Si
  given name: Xingfeng
author list: Agent
  family name: Guo
  given name: Mingfang
author list: Agent
  family name: Hu
  given name: Huijian
author list: Agent
  family name: Jin
  given name: Kun
doi: 10.7717/peerj.2636
volume: 4
issn: 2167-8359
publication name: PeerJ
publication date: 2016-11-02
copyright: ©2016 Pan et al.
attribution name: Pan et al.

Three-dimensional paleohistology of the scale and median fin spine of Lophosteus superbus (Pander 1856)
type: item
type: AcademicArticle
description: Lophosteus superbus is one of only a handful of probable stem-group osteichthyans known from the fossil record. First collected and described in the late 19th century from the upper Silurian Saaremaa Cliff locality in Estonia, it is known from a wealth of disarticulated scales, fin spines, and bone fragments. In this study we provide the first description of the morphology and paleohistology of a fin spine and scale from Lophosteus using virtual thin sections and 3D reconstructions that were segmented using phase-contrast synchrotron X-ray microtomography. These data reveal that both structures have fully or partially buried odontodes, which retain fine morphological details in older generations, including sharp nodes and serrated ridgelets. The vascular architecture of the fin spine tip, which is composed of several layers of longitudinally directed bone vascular canals, is much more complex compared to the bulbous horizontal canals within the scale, but they both have distinctive networks of ascending canals within each individual odontode. Other histological characteristics that can be observed from the data are cell spaces and Sharpey’s fibers that, when combined with the vascularization, could help to provide insights into the growth of the structure. The 3D data of the scales from Lophosteus superbus is similar to comparable data from other fossil osteichthyans, and the morphology of the reconstructed buried odontodes from this species is identical to scale material of Lophosteus ohesaarensis, casting doubt on the validity of that species. The 3D data presented in this paper is the first for fossil fin spines and so comparable data is not yet available. However, the overall morphology and histology seems to be similar to the structure of placoderm dermal plates. The 3D datasets presented here provide show that microtomography is a powerful tool for investigating the three-dimensional microstructure of fossils, which is difficult to study using traditional hist…
format: application/pdf
format: text/html
creator: Anna Jerve
creator: Qingming Qu
creator: Sophie Sanchez
creator: Henning Blom
creator: Per Erik Ahlberg
subject: Paleontology
subject: Histology
description: doi:10.7717/peerj.2521
publisher: PeerJ Inc.
rights: © 2016 Jerve et al.
abstract: Lophosteus superbus is one of only a handful of probable stem-group osteichthyans known from the fossil record. First collected and described in the late 19th century from the upper Silurian Saaremaa Cliff locality in Estonia, it is known from a wealth of disarticulated scales, fin spines, and bone fragments. In this study we provide the first description of the morphology and paleohistology of a fin spine and scale from Lophosteus using virtual thin sections and 3D reconstructions that were segmented using phase-contrast synchrotron X-ray microtomography. These data reveal that both structures have fully or partially buried odontodes, which retain fine morphological details in older generations, including sharp nodes and serrated ridgelets. The vascular architecture of the fin spine tip, which is composed of several layers of longitudinally directed bone vascular canals, is much more complex compared to the bulbous horizontal canals within the scale, but they both have distinctive networks of ascending canals within each individual odontode. Other histological characteristics that can be observed from the data are cell spaces and Sharpey’s fibers that, when combined with the vascularization, could help to provide insights into the growth of the structure. The 3D data of the scales from Lophosteus superbus is similar to comparable data from other fossil osteichthyans, and the morphology of the reconstructed buried odontodes from this species is identical to scale material of Lophosteus ohesaarensis, casting doubt on the validity of that species. The 3D data presented in this paper is the first for fossil fin spines and so comparable data is not yet available. However, the overall morphology and histology seems to be similar to the structure of placoderm dermal plates. The 3D datasets presented here provide show that microtomography is a powerful tool for investigating the three-dimensional microstructure of fossils, which is difficult to study using traditional hist…
bibliographic citation: Jerve et al. (2016) Three-dimensional paleohistology of the scale and median fin spine of Lophosteus superbus (Pander 1856). PeerJ 4:e2521 https://doi.org/10.7717/peerj.2521
date submitted: 2016-06-01
date accepted: 2016-09-02
issued: 2016-11-02
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Jerve
  given name: Anna
author list: Agent
  family name: Qu
  given name: Qingming
author list: Agent
  family name: Sanchez
  given name: Sophie
author list: Agent
  family name: Blom
  given name: Henning
author list: Agent
  family name: Ahlberg
  given name: Per Erik
doi: 10.7717/peerj.2521
volume: 4
issn: 2167-8359
publication name: PeerJ
publication date: 2016-11-02
copyright: ©2016 Jerve et al.
attribution name: Jerve et al.

Comparison of the effectiveness of ISJ and SSR markers and detection of outlier loci in conservation genetics of Pulsatilla patens populations
type: item
type: AcademicArticle
description: Background Research into the protection of rare and endangered plant species involves genetic analyses to determine their genetic variation and genetic structure. Various categories of genetic markers are used for this purpose. Microsatellites, also known as simple sequence repeats (SSR), are the most popular category of markers in population genetics research. In most cases, microsatellites account for a large part of the noncoding DNA and exert a neutral effect on the genome. Neutrality is a desirable feature in evaluations of genetic differences between populations, but it does not support analyses of a population’s ability to adapt to a given environment or its evolutionary potential. Despite the numerous advantages of microsatellites, non-neutral markers may supply important information in conservation genetics research. They are used to evaluate adaptation to specific environmental conditions and a population’s adaptive potential. The aim of this study was to compare the level of genetic variation in Pulsatilla patens populations revealed by neutral SSR markers and putatively adaptive ISJ markers (intron-exon splice junction). Methods The experiment was conducted on 14 Polish populations of P. patens and three P. patens populations from the nearby region of Vitebsk in Belarus. A total of 345 individuals were examined. Analyses were performed with the use of eight SSR primers specific to P. patens and three ISJ primers. Results SSR markers revealed a higher level of genetic variation than ISJ markers (He = 0.609, He = 0.145, respectively). An analysis of molecular variance (AMOVA) revealed that, the overall genetic diversity between the analyzed populations defined by parameters FST and ΦPT for SSR (20%) and ΦPT for ISJ (21%) markers was similar. Analysis conducted in the Structure program divided analyzed populations into two groups (SSR loci) and three groups (ISJ markers). Mantel test revealed correlations between the geographic distance and genetic diversit…
format: application/pdf
format: text/html
creator: Katarzyna Bilska
creator: Monika Szczecińska
subject: Conservation Biology
subject: Genetics
description: doi:10.7717/peerj.2504
publisher: PeerJ Inc.
rights: © 2016 Bilska and Szczecińska
abstract: Background Research into the protection of rare and endangered plant species involves genetic analyses to determine their genetic variation and genetic structure. Various categories of genetic markers are used for this purpose. Microsatellites, also known as simple sequence repeats (SSR), are the most popular category of markers in population genetics research. In most cases, microsatellites account for a large part of the noncoding DNA and exert a neutral effect on the genome. Neutrality is a desirable feature in evaluations of genetic differences between populations, but it does not support analyses of a population’s ability to adapt to a given environment or its evolutionary potential. Despite the numerous advantages of microsatellites, non-neutral markers may supply important information in conservation genetics research. They are used to evaluate adaptation to specific environmental conditions and a population’s adaptive potential. The aim of this study was to compare the level of genetic variation in Pulsatilla patens populations revealed by neutral SSR markers and putatively adaptive ISJ markers (intron-exon splice junction). Methods The experiment was conducted on 14 Polish populations of P. patens and three P. patens populations from the nearby region of Vitebsk in Belarus. A total of 345 individuals were examined. Analyses were performed with the use of eight SSR primers specific to P. patens and three ISJ primers. Results SSR markers revealed a higher level of genetic variation than ISJ markers (He = 0.609, He = 0.145, respectively). An analysis of molecular variance (AMOVA) revealed that, the overall genetic diversity between the analyzed populations defined by parameters FST and ΦPT for SSR (20%) and ΦPT for ISJ (21%) markers was similar. Analysis conducted in the Structure program divided analyzed populations into two groups (SSR loci) and three groups (ISJ markers). Mantel test revealed correlations between the geographic distance and genetic diversit…
bibliographic citation: Bilska et al. (2016) Comparison of the effectiveness of ISJ and SSR markers and detection of outlier loci in conservation genetics of Pulsatilla patens populations. PeerJ 4:e2504 https://doi.org/10.7717/peerj.2504
date submitted: 2016-04-17
date accepted: 2016-08-30
issued: 2016-11-02
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Bilska
  given name: Katarzyna
author list: Agent
  family name: Szczecińska
  given name: Monika
doi: 10.7717/peerj.2504
volume: 4
issn: 2167-8359
publication name: PeerJ
publication date: 2016-11-02
copyright: © 2016 Bilska and Szczecińska
attribution name: Bilska and Szczecińska

Performance, usability and comparison of two versions of a new macular vision test: the handheld Radial Shape Discrimination test
type: item
type: AcademicArticle
description: Background Central vision, critical for everyday tasks such as reading and driving, is impacted by age-related changes in the eye and by diseases such as age-related macular degeneration. The detection of changes in macular function is therefore important. The Radial Shape Discrimination (RSD) test measures the threshold at which distortions in a radial frequency pattern can be detected and there is evidence that it is more sensitive to macular pathology than visual acuity (VA). It also provides a more quantitative measure of macular function than the commonly available Amsler grid. Recently, handheld versions of the test (hRSD) in which stimuli are presented on mobile devices (e.g., Apple iPod Touch, iPhone) have been developed. We investigated the characteristics of the hRSD test in healthy participants. Methods Data were collected using both three-alternative forced choice (3AFC) and 4AFC versions of the hRSD test, presented on an Apple iPod Touch. For the 3AFC version, data from a single test session were available for 186 (72 male; mean ± SD age 42 ± 17y; range 16–90y) healthy participants. Test-retest data were available for subgroups of participants (intra-session: N = 74; tests approximately 2 months apart: N = 30; tests 39 months apart: N = 15). The 3AFC and 4AFC versions were directly compared in 106 participants who also completed a usability questionnaire. Distance and near VA and Pelli Robson Contrast Sensitivity (CS) data were collected and undilated fundoscopy performed on the majority of participants. Results Mean (±SD) 3AFC hRSD threshold was −0.77 ± 0.14 logMAR, and was statistically significantly correlated with age (Pearson r = 0.35; p < 0.001). The linear regression of hRSD threshold on age had a slope of +0.0026 compared to +0.0051 for near VA (which also correlated with age: r = 0.51; p < 0.001). There were no statistically significant differences in hRSD thresholds for any of the test-retest subgroups. We also observed no statistically signif…
format: application/pdf
format: text/html
creator: Jae Y. Ku
creator: Ashli F. Milling
creator: Noelia Pitrelli Vazquez
creator: Paul C. Knox
subject: Drugs and Devices
subject: Global Health
subject: Ophthalmology
description: doi:10.7717/peerj.2650
publisher: PeerJ Inc.
rights: © 2016 Ku et al.
abstract: Background Central vision, critical for everyday tasks such as reading and driving, is impacted by age-related changes in the eye and by diseases such as age-related macular degeneration. The detection of changes in macular function is therefore important. The Radial Shape Discrimination (RSD) test measures the threshold at which distortions in a radial frequency pattern can be detected and there is evidence that it is more sensitive to macular pathology than visual acuity (VA). It also provides a more quantitative measure of macular function than the commonly available Amsler grid. Recently, handheld versions of the test (hRSD) in which stimuli are presented on mobile devices (e.g., Apple iPod Touch, iPhone) have been developed. We investigated the characteristics of the hRSD test in healthy participants. Methods Data were collected using both three-alternative forced choice (3AFC) and 4AFC versions of the hRSD test, presented on an Apple iPod Touch. For the 3AFC version, data from a single test session were available for 186 (72 male; mean ± SD age 42 ± 17y; range 16–90y) healthy participants. Test-retest data were available for subgroups of participants (intra-session: N = 74; tests approximately 2 months apart: N = 30; tests 39 months apart: N = 15). The 3AFC and 4AFC versions were directly compared in 106 participants who also completed a usability questionnaire. Distance and near VA and Pelli Robson Contrast Sensitivity (CS) data were collected and undilated fundoscopy performed on the majority of participants. Results Mean (±SD) 3AFC hRSD threshold was −0.77 ± 0.14 logMAR, and was statistically significantly correlated with age (Pearson r = 0.35; p < 0.001). The linear regression of hRSD threshold on age had a slope of +0.0026 compared to +0.0051 for near VA (which also correlated with age: r = 0.51; p < 0.001). There were no statistically significant differences in hRSD thresholds for any of the test-retest subgroups. We also observed no statistically signif…
bibliographic citation: Ku et al. (2016) Performance, usability and comparison of two versions of a new macular vision test: the handheld Radial Shape Discrimination test. PeerJ 4:e2650 https://doi.org/10.7717/peerj.2650
date submitted: 2016-08-15
date accepted: 2016-10-03
issued: 2016-11-01
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Ku
  given name: Jae Y.
author list: Agent
  family name: Milling
  given name: Ashli F.
author list: Agent
  family name: Pitrelli Vazquez
  given name: Noelia
author list: Agent
  family name: Knox
  given name: Paul C.
doi: 10.7717/peerj.2650
volume: 4
issn: 2167-8359
publication name: PeerJ
publication date: 2016-11-01
copyright: ©2016 Ku et al.
attribution name: Ku et al.

The abundance of large, piscivorous Ferox Trout (Salmo trutta) in Loch Rannoch, Scotland
type: item
type: AcademicArticle
description: Background Ferox Trout are large, long-lived piscivorous Brown Trout (Salmo trutta). Due to their exceptionally large size, Ferox Trout are highly sought after by anglers while their life-history strategy, which includes delayed maturation, multiphasic growth and extended longevity, is of interest to ecological and evolutionary modelers. However, despite their recreational and theoretical importance, little is known about the typical abundance of Ferox Trout. Methods To rectify this situation a 16 year angling-based mark-recapture study was conducted on Loch Rannoch, which at 19 km2 is one of the largest lakes in the United Kingdom. Results A hierarchical Bayesian Jolly-Seber analysis of the data suggest that if individual differences in catchability are negligible the population of Ferox Trout in Loch Rannoch in 2009 was approximately 71 fish. The results also suggest that a single, often unaccompanied, highly-experienced angler was able to catch roughly 8% of the available fish on an annual basis. Discussion It is recommended that anglers adopt a precautionary approach and release all trout with a fork length ≥400 mm caught by trolling in Loch Rannoch. There is an urgent need to assess the status of Ferox Trout in other lakes.
format: application/pdf
format: text/html
creator: Alastair Thorne
creator: Alisdair I. MacDonald
creator: Joseph L. Thorley
subject: Aquaculture, Fisheries and Fish Science
subject: Conservation Biology
subject: Ecology
subject: Freshwater Biology
subject: Statistics
description: doi:10.7717/peerj.2646
publisher: PeerJ Inc.
rights: © 2016 Thorne et al.
abstract: Background Ferox Trout are large, long-lived piscivorous Brown Trout (Salmo trutta). Due to their exceptionally large size, Ferox Trout are highly sought after by anglers while their life-history strategy, which includes delayed maturation, multiphasic growth and extended longevity, is of interest to ecological and evolutionary modelers. However, despite their recreational and theoretical importance, little is known about the typical abundance of Ferox Trout. Methods To rectify this situation a 16 year angling-based mark-recapture study was conducted on Loch Rannoch, which at 19 km2 is one of the largest lakes in the United Kingdom. Results A hierarchical Bayesian Jolly-Seber analysis of the data suggest that if individual differences in catchability are negligible the population of Ferox Trout in Loch Rannoch in 2009 was approximately 71 fish. The results also suggest that a single, often unaccompanied, highly-experienced angler was able to catch roughly 8% of the available fish on an annual basis. Discussion It is recommended that anglers adopt a precautionary approach and release all trout with a fork length ≥400 mm caught by trolling in Loch Rannoch. There is an urgent need to assess the status of Ferox Trout in other lakes.
bibliographic citation: Thorne et al. (2016) The abundance of large, piscivorous Ferox Trout (Salmo trutta) in Loch Rannoch, Scotland. PeerJ 4:e2646 https://doi.org/10.7717/peerj.2646
date submitted: 2016-05-11
date accepted: 2016-10-03
issued: 2016-11-01
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Thorne
  given name: Alastair
author list: Agent
  family name: MacDonald
  given name: Alisdair I.
author list: Agent
  family name: Thorley
  given name: Joseph L.
doi: 10.7717/peerj.2646
volume: 4
issn: 2167-8359
publication name: PeerJ
publication date: 2016-11-01
copyright: ©2016 Thorne et al.
attribution name: Thorne et al.

Non-target effects of a glyphosate-based herbicide on Common toad larvae (Bufo bufo, Amphibia) and associated algae are altered by temperature
type: item
type: AcademicArticle
description: Background Glyphosate-based herbicides are the most widely used pesticides in agriculture, horticulture, municipalities and private gardens that can potentially contaminate nearby water bodies inhabited by amphibians and algae. Moreover, the development and diversity of these aquatic organisms could also be affected by human-induced climate change that might lead to more periods with extreme temperatures. However, to what extent non-target effects of these herbicides on amphibians or algae are altered by varying temperature is not well known. Methods We studied effects of five concentrations of the glyphosate-based herbicide formulation Roundup PowerFlex (0, 1.5, 3, 4 mg acid equivalent glyphosate L−1 as a one time addition and a pulse treatment of totally 4 mg a.e. glyphosate L−1) on larval development of Common toads (Bufo bufo, L.; Amphibia: Anura) and associated algae communities under two temperature regimes (15 vs. 20 °C). Results Herbicide contamination reduced tail growth (−8%), induced the occurrence of tail deformations (i.e. lacerated or crooked tails) and reduced algae diversity (−6%). Higher water temperature increased tadpole growth (tail and body length (tl/bl) +66%, length-to-width ratio +4%) and decreased algae diversity (−21%). No clear relation between herbicide concentrations and tadpole growth or algae density or diversity was observed. Interactive effects of herbicides and temperature affected growth parameters, tail deformation and tadpole mortality indicating that the herbicide effects are temperature-dependent. Remarkably, herbicide-temperature interactions resulted in deformed tails in 34% of all herbicide treated tadpoles at 15 °C whereas no tail deformations were observed for the herbicide-free control at 15 °C or any tadpole at 20 °C; herbicide-induced mortality was higher at 15 °C but lower at 20 °C. Discussion These herbicide- and temperature-induced changes may have decided effects on ecological interactions in freshwater ecosystems. …
format: application/pdf
format: text/html
creator: Fabian Baier
creator: Edith Gruber
creator: Thomas Hein
creator: Elisabeth Bondar-Kunze
creator: Marina Ivanković
creator: Axel Mentler
creator: Carsten A. Brühl
creator: Bernhard Spangl
creator: Johann G. Zaller
subject: Agricultural Science
subject: Biodiversity
subject: Conservation Biology
subject: Ecology
subject: Ecotoxicology
description: doi:10.7717/peerj.2641
publisher: PeerJ Inc.
rights: © 2016 Baier et al.
abstract: Background Glyphosate-based herbicides are the most widely used pesticides in agriculture, horticulture, municipalities and private gardens that can potentially contaminate nearby water bodies inhabited by amphibians and algae. Moreover, the development and diversity of these aquatic organisms could also be affected by human-induced climate change that might lead to more periods with extreme temperatures. However, to what extent non-target effects of these herbicides on amphibians or algae are altered by varying temperature is not well known. Methods We studied effects of five concentrations of the glyphosate-based herbicide formulation Roundup PowerFlex (0, 1.5, 3, 4 mg acid equivalent glyphosate L−1 as a one time addition and a pulse treatment of totally 4 mg a.e. glyphosate L−1) on larval development of Common toads (Bufo bufo, L.; Amphibia: Anura) and associated algae communities under two temperature regimes (15 vs. 20 °C). Results Herbicide contamination reduced tail growth (−8%), induced the occurrence of tail deformations (i.e. lacerated or crooked tails) and reduced algae diversity (−6%). Higher water temperature increased tadpole growth (tail and body length (tl/bl) +66%, length-to-width ratio +4%) and decreased algae diversity (−21%). No clear relation between herbicide concentrations and tadpole growth or algae density or diversity was observed. Interactive effects of herbicides and temperature affected growth parameters, tail deformation and tadpole mortality indicating that the herbicide effects are temperature-dependent. Remarkably, herbicide-temperature interactions resulted in deformed tails in 34% of all herbicide treated tadpoles at 15 °C whereas no tail deformations were observed for the herbicide-free control at 15 °C or any tadpole at 20 °C; herbicide-induced mortality was higher at 15 °C but lower at 20 °C. Discussion These herbicide- and temperature-induced changes may have decided effects on ecological interactions in freshwater ecosystems. …
bibliographic citation: Baier et al. (2016) Non-target effects of a glyphosate-based herbicide on Common toad larvae (Bufo bufo, Amphibia) and associated algae are altered by temperature. PeerJ 4:e2641 https://doi.org/10.7717/peerj.2641
date submitted: 2016-08-22
date accepted: 2016-09-30
issued: 2016-11-01
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Baier
  given name: Fabian
author list: Agent
  family name: Gruber
  given name: Edith
author list: Agent
  family name: Hein
  given name: Thomas
author list: Agent
  family name: Bondar-Kunze
  given name: Elisabeth
author list: Agent
  family name: Ivanković
  given name: Marina
author list: Agent
  family name: Mentler
  given name: Axel
author list: Agent
  family name: Brühl
  given name: Carsten A.
author list: Agent
  family name: Spangl
  given name: Bernhard
author list: Agent
  family name: Zaller
  given name: Johann G.
doi: 10.7717/peerj.2641
volume: 4
issn: 2167-8359
publication name: PeerJ
publication date: 2016-11-01
copyright: © 2016 Baier et al.
attribution name: Baier et al.

Whole-brain ex-vivo quantitative MRI of the cuprizone mouse model
type: item
type: AcademicArticle
description: Myelin is a critical component of the nervous system and a major contributor to contrast in Magnetic Resonance (MR) images. However, the precise contribution of myelination to multiple MR modalities is still under debate. The cuprizone mouse is a well-established model of demyelination that has been used in several MR studies, but these have often imaged only a single slice and analysed a small region of interest in the corpus callosum. We imaged and analyzed the whole brain of the cuprizone mouse ex-vivo using high-resolution quantitative MR methods (multi-component relaxometry, Diffusion Tensor Imaging (DTI) and morphometry) and found changes in multiple regions, including the corpus callosum, cerebellum, thalamus and hippocampus. The presence of inflammation, confirmed with histology, presents difficulties in isolating the sensitivity and specificity of these MR methods to demyelination using this model.
format: application/pdf
format: text/html
creator: Tobias C. Wood
creator: Camilla Simmons
creator: Samuel A. Hurley
creator: Anthony C. Vernon
creator: Joel Torres
creator: Flavio Dell’Acqua
creator: Steve C.R. Williams
creator: Diana Cash
subject: Neuroscience
subject: Radiology and Medical Imaging
subject: Histology
description: doi:10.7717/peerj.2632
publisher: PeerJ Inc.
rights: © 2016 Wood et al.
abstract: Myelin is a critical component of the nervous system and a major contributor to contrast in Magnetic Resonance (MR) images. However, the precise contribution of myelination to multiple MR modalities is still under debate. The cuprizone mouse is a well-established model of demyelination that has been used in several MR studies, but these have often imaged only a single slice and analysed a small region of interest in the corpus callosum. We imaged and analyzed the whole brain of the cuprizone mouse ex-vivo using high-resolution quantitative MR methods (multi-component relaxometry, Diffusion Tensor Imaging (DTI) and morphometry) and found changes in multiple regions, including the corpus callosum, cerebellum, thalamus and hippocampus. The presence of inflammation, confirmed with histology, presents difficulties in isolating the sensitivity and specificity of these MR methods to demyelination using this model.
bibliographic citation: Wood et al. (2016) Whole-brain ex-vivo quantitative MRI of the cuprizone mouse model. PeerJ 4:e2632 https://doi.org/10.7717/peerj.2632
date submitted: 2016-07-28
date accepted: 2016-09-29
issued: 2016-11-01
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Wood
  given name: Tobias C.
author list: Agent
  family name: Simmons
  given name: Camilla
author list: Agent
  family name: Hurley
  given name: Samuel A.
author list: Agent
  family name: Vernon
  given name: Anthony C.
author list: Agent
  family name: Torres
  given name: Joel
author list: Agent
  family name: Dell’Acqua
  given name: Flavio
author list: Agent
  family name: Williams
  given name: Steve C.R.
author list: Agent
  family name: Cash
  given name: Diana
doi: 10.7717/peerj.2632
volume: 4
issn: 2167-8359
publication name: PeerJ
publication date: 2016-11-01
copyright: © 2016 Wood et al.
attribution name: Wood et al.

Therapeutic role of human hepatocyte growth factor (HGF) in treating hair loss
type: item
type: AcademicArticle
description: Hepatocyte growth factor (HGF) is a paracrine hormone that plays an important role in epithelial-mesenchymal transition. HGF secreted by mesenchymal cells affects many properties of epithelial cells, such as proliferation, motility, and morphology. HGF has been reported to promote follicular growth. The purpose of the present study is to investigate the therapeutic role of HGF in hair loss treatment. A recombinant vector containing the human HGF (hHGF) gene (pTARGET-hHGF) was constructed, and the expression of hHGF in vitro was quantitatively and qualitatively evaluated. The effect of hHGF on hair growth was tested in mice, and results demonstrated that pTARGET-hHGF was successfully delivered into fibroblasts in vitro leading to a high expression of hHGF. Local injections of the pTARGET-hHGF recombinant vector into mice resulted in multiple beneficial effects compared to placebo, including faster hair regeneration, improved follicle development, and significantly increased HGF receptor (HGF-R). In conclusion, we have established a nonviral vector of hHGF which could be utilized to manipulate the sheath fibroblasts surrounding hair follicles (HF), thereby stimulating hair regeneration.
format: application/pdf
format: text/html
creator: Yonghao Qi
creator: Miao Li
creator: Lian Xu
creator: Zhijing Chang
creator: Xiong Shu
creator: Lijun Zhou
subject: Biochemistry
subject: Cell Biology
subject: Molecular Biology
subject: Toxicology
description: doi:10.7717/peerj.2624
publisher: PeerJ Inc.
rights: © 2016 Qi et al.
abstract: Hepatocyte growth factor (HGF) is a paracrine hormone that plays an important role in epithelial-mesenchymal transition. HGF secreted by mesenchymal cells affects many properties of epithelial cells, such as proliferation, motility, and morphology. HGF has been reported to promote follicular growth. The purpose of the present study is to investigate the therapeutic role of HGF in hair loss treatment. A recombinant vector containing the human HGF (hHGF) gene (pTARGET-hHGF) was constructed, and the expression of hHGF in vitro was quantitatively and qualitatively evaluated. The effect of hHGF on hair growth was tested in mice, and results demonstrated that pTARGET-hHGF was successfully delivered into fibroblasts in vitro leading to a high expression of hHGF. Local injections of the pTARGET-hHGF recombinant vector into mice resulted in multiple beneficial effects compared to placebo, including faster hair regeneration, improved follicle development, and significantly increased HGF receptor (HGF-R). In conclusion, we have established a nonviral vector of hHGF which could be utilized to manipulate the sheath fibroblasts surrounding hair follicles (HF), thereby stimulating hair regeneration.
bibliographic citation: Qi et al. (2016) Therapeutic role of human hepatocyte growth factor (HGF) in treating hair loss. PeerJ 4:e2624 https://doi.org/10.7717/peerj.2624
date submitted: 2016-06-04
date accepted: 2016-09-27
issued: 2016-11-01
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Qi
  given name: Yonghao
author list: Agent
  family name: Li
  given name: Miao
author list: Agent
  family name: Xu
  given name: Lian
author list: Agent
  family name: Chang
  given name: Zhijing
author list: Agent
  family name: Shu
  given name: Xiong
author list: Agent
  family name: Zhou
  given name: Lijun
doi: 10.7717/peerj.2624
volume: 4
issn: 2167-8359
publication name: PeerJ
publication date: 2016-11-01
copyright: © 2016 Qi et al.
attribution name: Qi et al.

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