PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
items: Data challenges of biomedical researchers in the age of omics
items: Tibia functionality and Division II female and male collegiate athletes from multiple sports
items: A short, robust brain activation control task optimised for pharmacological fMRI studies
items: DNA mismatch repair and CD133-marked cancer stem cells in colorectal carcinoma
items: Growth under cold conditions in a wide perennial ryegrass panel is under tight physiological control
items: A comparison of perceptions of nuts between the general public, dietitians, general practitioners, and nurses
items: A novel experimental design for the measurement of metacarpal bone loading and deformation and fingertip force
items: Effects of resveratrol, exercises and their combination on Farnesoid X receptor, Liver X receptor and Sirtuin 1 gene expression and apoptosis in the liver of elderly rats with nonalcoholic fatty liver
items: Association of burnout with doctor–patient relationship and common stressors among postgraduate trainees and house officers in Lahore—a cross-sectional study
items: Effects of environmental and anthropogenic landscape features on mule deer harvest in Nebraska

Data challenges of biomedical researchers in the age of omics
type: item
type: AcademicArticle
description: Background High-throughput technologies are rapidly generating large amounts of diverse omics data. Although this offers a great opportunity, it also poses great challenges as data analysis becomes more complex. The purpose of this study was to identify the main challenges researchers face in analyzing data, and how academic libraries can support them in this endeavor. Methods A multimodal needs assessment analysis combined an online survey sent to 860 Yale-affiliated researchers (176 responded) and 15 in-depth one-on-one semi-structured interviews. Interviews were recorded, transcribed, and analyzed using NVivo 10 software according to the thematic analysis approach. Results The survey response rate was 20%. Most respondents (78%) identified lack of adequate data analysis training (e.g., R, Python) as a main challenge, in addition to not having the proper database or software (54%) to expedite analysis. Two main themes emerged from the interviews: personnel and training needs. Researchers feel they could improve data analyses practices by having better access to the appropriate bioinformatics expertise, and/or training in data analyses tools. They also reported lack of time to acquire expertise in using bioinformatics tools and poor understanding of the resources available to facilitate analysis. Conclusions The main challenges identified by our study are: lack of adequate training for data analysis (including need to learn scripting language), need for more personnel at the University to provide data analysis and training, and inadequate communication between bioinformaticians and researchers. The authors identified the positive impact of medical and/or science libraries by establishing bioinformatics support to researchers.
format: application/pdf
format: text/html
creator: Rolando Garcia-Milian
creator: Denise Hersey
creator: Milica Vukmirovic
creator: Fanny Duprilot
subject: Bioinformatics
subject: Genomics
subject: Human–Computer Interaction
subject: Data Science
description: doi:10.7717/peerj.5553
publisher: PeerJ Inc.
rights: © 2018 Garcia-Milian et al.
abstract: Background High-throughput technologies are rapidly generating large amounts of diverse omics data. Although this offers a great opportunity, it also poses great challenges as data analysis becomes more complex. The purpose of this study was to identify the main challenges researchers face in analyzing data, and how academic libraries can support them in this endeavor. Methods A multimodal needs assessment analysis combined an online survey sent to 860 Yale-affiliated researchers (176 responded) and 15 in-depth one-on-one semi-structured interviews. Interviews were recorded, transcribed, and analyzed using NVivo 10 software according to the thematic analysis approach. Results The survey response rate was 20%. Most respondents (78%) identified lack of adequate data analysis training (e.g., R, Python) as a main challenge, in addition to not having the proper database or software (54%) to expedite analysis. Two main themes emerged from the interviews: personnel and training needs. Researchers feel they could improve data analyses practices by having better access to the appropriate bioinformatics expertise, and/or training in data analyses tools. They also reported lack of time to acquire expertise in using bioinformatics tools and poor understanding of the resources available to facilitate analysis. Conclusions The main challenges identified by our study are: lack of adequate training for data analysis (including need to learn scripting language), need for more personnel at the University to provide data analysis and training, and inadequate communication between bioinformaticians and researchers. The authors identified the positive impact of medical and/or science libraries by establishing bioinformatics support to researchers.
bibliographic citation: Garcia-Milian et al. (2018) Data challenges of biomedical researchers in the age of omics. PeerJ 6:e5553 https://doi.org/10.7717/peerj.5553
date submitted: 2018-03-07
date accepted: 2018-08-10
issued: 2018-09-11
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Garcia-Milian
  given name: Rolando
author list: Agent
  family name: Hersey
  given name: Denise
author list: Agent
  family name: Vukmirovic
  given name: Milica
author list: Agent
  family name: Duprilot
  given name: Fanny
doi: 10.7717/peerj.5553
volume: 6
issn: 2167-8359
publication name: PeerJ
publication date: 2018-09-11
copyright: ©2018 Garcia-Milian et al.
attribution name: Garcia-Milian et al.

Tibia functionality and Division II female and male collegiate athletes from multiple sports
type: item
type: AcademicArticle
description: Background Bone strength is developed through a combination of the size and shape (architecture) of a bone as well as the bone’s material properties; and therefore, no one outcome variable can measure a positive or negative adaptation in bone. Skeletal robusticity (total area/ bone length) a measure of bones external size varies within the population and is independent of body size, but robusticity has been associated with bone strength. Athletes may have similar variability in robusticity values as the general population and thus have a wide range of bone strengths based on the robustness of their bones. Therefore, the purpose of this study was to determine if an athlete’s bone strength and cortical area relative to body size was dependent on robusticity. The second aim was to determine if anthropometry or muscle function measurements were associated with bone robusticity. Methods Bone variables contributing to bone strength were measured in collegiate athletes and a reference group using peripheral quantitative computed tomography (pQCT) at the 50% tibial site. Bone functionality was assessed by plotting bone strength and cortical area vs body size (body weight x tibial length) and robustness (total area/length) vs body size. Bone strength was measured using the polar strength-strain index (SSIp). Based on the residuals from the regression, an athlete’s individual functionality was determined, and two groups were formed “weaker for size” (WS) and “stronger for size” (SS). Grip strength, leg extensor strength and lower body power were also measured. Results Division II athletes exhibited a natural variation in (SSIp) relative to robusticity consistent with previous studies. Bone strength (SSIp) was dependent on the robusticity of the tibia. The bone traits that comprise bone strength (SSIp) were significantly different between the SS and WS groups, yet there were minimal differences in the anthropometric data and muscle function measures between groups. A lower per…
format: application/pdf
format: text/html
creator: Vanessa R. Yingling
creator: Benjamin Ferrari-Church
creator: Ariana Strickland
subject: Anthropology
subject: Kinesiology
description: doi:10.7717/peerj.5550
publisher: PeerJ Inc.
rights: © 2018 Yingling et al.
abstract: Background Bone strength is developed through a combination of the size and shape (architecture) of a bone as well as the bone’s material properties; and therefore, no one outcome variable can measure a positive or negative adaptation in bone. Skeletal robusticity (total area/ bone length) a measure of bones external size varies within the population and is independent of body size, but robusticity has been associated with bone strength. Athletes may have similar variability in robusticity values as the general population and thus have a wide range of bone strengths based on the robustness of their bones. Therefore, the purpose of this study was to determine if an athlete’s bone strength and cortical area relative to body size was dependent on robusticity. The second aim was to determine if anthropometry or muscle function measurements were associated with bone robusticity. Methods Bone variables contributing to bone strength were measured in collegiate athletes and a reference group using peripheral quantitative computed tomography (pQCT) at the 50% tibial site. Bone functionality was assessed by plotting bone strength and cortical area vs body size (body weight x tibial length) and robustness (total area/length) vs body size. Bone strength was measured using the polar strength-strain index (SSIp). Based on the residuals from the regression, an athlete’s individual functionality was determined, and two groups were formed “weaker for size” (WS) and “stronger for size” (SS). Grip strength, leg extensor strength and lower body power were also measured. Results Division II athletes exhibited a natural variation in (SSIp) relative to robusticity consistent with previous studies. Bone strength (SSIp) was dependent on the robusticity of the tibia. The bone traits that comprise bone strength (SSIp) were significantly different between the SS and WS groups, yet there were minimal differences in the anthropometric data and muscle function measures between groups. A lower per…
bibliographic citation: Yingling et al. (2018) Tibia functionality and Division II female and male collegiate athletes from multiple sports. PeerJ 6:e5550 https://doi.org/10.7717/peerj.5550
date submitted: 2018-03-19
date accepted: 2018-08-10
issued: 2018-09-11
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Yingling
  given name: Vanessa R.
author list: Agent
  family name: Ferrari-Church
  given name: Benjamin
author list: Agent
  family name: Strickland
  given name: Ariana
doi: 10.7717/peerj.5550
volume: 6
issn: 2167-8359
publication name: PeerJ
publication date: 2018-09-11
copyright: ©2018 Yingling et al.
attribution name: Yingling et al.

A short, robust brain activation control task optimised for pharmacological fMRI studies
type: item
type: AcademicArticle
description: Background Functional magnetic resonance imaging (fMRI) is a popular method for examining pharmacological effects on the brain; however, the BOLD response is dependent on intact neurovascular coupling, and potentially modulated by a number of physiological factors. Pharmacological fMRI is therefore vulnerable to confounding effects of pharmacological probes on general physiology or neurovascular coupling. Controlling for such non-specific effects in pharmacological fMRI studies is therefore an important consideration, and there is an additional need for well-validated fMRI task paradigms that could be used to control for such effects, or for general testing purposes. Methods We have developed two variants of a standardized control task that are short (5 minutes duration) simple (for both the subject and experimenter), widely applicable, and yield a number of readouts in a spatially diverse set of brain networks. The tasks consist of four functionally discrete three-second trial types (plus additional null trials) and contain visual, auditory, motor and cognitive (eye-movements, and working memory tasks in the two task variants) stimuli. Performance of the tasks was assessed in a group of 15 subjects scanned on two separate occasions, with test-retest reliability explicitly assessed using intra-class correlation coefficients. Results Both tasks produced robust patterns of brain activation in the expected brain regions, and region of interest-derived reliability coefficients for the tasks were generally high, with four out of eight task conditions rated as ‘excellent’ or ‘good’, and only one out of eight rated as ‘poor’. Median values in the voxel-wise reliability measures were also >0.7 for all task conditions, and therefore classed as ‘excellent’ or ‘good’. The spatial concordance between the most highly activated voxels and those with the highest reliability coefficients was greater for the sensory (auditory, visual) conditions than the other (motor, cognitive) con…
format: application/pdf
format: text/html
creator: Jessica-Lily Harvey
creator: Lysia Demetriou
creator: John McGonigle
creator: Matthew B. Wall
subject: Neuroscience
subject: Radiology and Medical Imaging
description: doi:10.7717/peerj.5540
publisher: PeerJ Inc.
rights: © 2018 Harvey et al.
abstract: Background Functional magnetic resonance imaging (fMRI) is a popular method for examining pharmacological effects on the brain; however, the BOLD response is dependent on intact neurovascular coupling, and potentially modulated by a number of physiological factors. Pharmacological fMRI is therefore vulnerable to confounding effects of pharmacological probes on general physiology or neurovascular coupling. Controlling for such non-specific effects in pharmacological fMRI studies is therefore an important consideration, and there is an additional need for well-validated fMRI task paradigms that could be used to control for such effects, or for general testing purposes. Methods We have developed two variants of a standardized control task that are short (5 minutes duration) simple (for both the subject and experimenter), widely applicable, and yield a number of readouts in a spatially diverse set of brain networks. The tasks consist of four functionally discrete three-second trial types (plus additional null trials) and contain visual, auditory, motor and cognitive (eye-movements, and working memory tasks in the two task variants) stimuli. Performance of the tasks was assessed in a group of 15 subjects scanned on two separate occasions, with test-retest reliability explicitly assessed using intra-class correlation coefficients. Results Both tasks produced robust patterns of brain activation in the expected brain regions, and region of interest-derived reliability coefficients for the tasks were generally high, with four out of eight task conditions rated as ‘excellent’ or ‘good’, and only one out of eight rated as ‘poor’. Median values in the voxel-wise reliability measures were also >0.7 for all task conditions, and therefore classed as ‘excellent’ or ‘good’. The spatial concordance between the most highly activated voxels and those with the highest reliability coefficients was greater for the sensory (auditory, visual) conditions than the other (motor, cognitive) con…
bibliographic citation: Harvey et al. (2018) A short, robust brain activation control task optimised for pharmacological fMRI studies. PeerJ 6:e5540 https://doi.org/10.7717/peerj.5540
date submitted: 2018-03-12
date accepted: 2018-08-07
issued: 2018-09-11
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Harvey
  given name: Jessica-Lily
author list: Agent
  family name: Demetriou
  given name: Lysia
author list: Agent
  family name: McGonigle
  given name: John
author list: Agent
  family name: Wall
  given name: Matthew B.
doi: 10.7717/peerj.5540
volume: 6
issn: 2167-8359
publication name: PeerJ
publication date: 2018-09-11
copyright: ©2018 Harvey et al.
attribution name: Harvey et al.

DNA mismatch repair and CD133-marked cancer stem cells in colorectal carcinoma
type: item
type: AcademicArticle
description: Background Except for a few studies with contradictory observations, information is lacking on the possibility of association between DNA mismatch repair (MMR) status and the presence of cancer stem cells in colorectal carcinoma (CRC), two important aspects in colorectal carcinogenesis. Methods Eighty (40 right-sided and 40 left-sided) formalin-fixed, paraffin-embedded primary CRC were immunohistochemically studied for CD133, a putative CRC stem cell marker, and MMR proteins MLH1, MSH2, MSH6 and PMS2. CD133 expression was semi-quantitated for proportion of tumor immunopositivity on a scale of 0–5 and staining intensity on a scale of 0–3 with a final score (units) being the product of proportion and intensity of tumor staining. The tumor was considered immunopositive only when the tumor demonstrated moderate to strong intensity of CD133 staining (a decision made after analysis of CD133 expression in normal colon). Deficient MMR (dMMR) was interpreted as unequivocal loss of tumor nuclear staining for any MMR protein despite immunoreactivity in the internal positive controls. Results CD133 was expressed in 36 (90.0%) left-sided and 28 (70.0%) right-sided tumors (p < 0.05) and CD133 score was significantly higher in left- (mean ± SD = 9.6 ± 5.3 units) compared with right-sided tumors (mean ± SD = 6.8 ± 5.6 units) p < 0.05). dMMR was noted in 14 (35%) right-sided and no (0%) left-sided CRC. When stratified according to MMR status, dMMR cases showed a lower frequency of CD133 expression (42.9%) and CD133 score (mean ± SD = 2.5 ± 3.6 units) compared with pMMR tumors on the right (frequency = 84.6%; mean score ± SD = 9.2 ± 5.0 units) as well as pMMR tumors on the left (frequency = 90.0%; mean score ± SD = 9.6 ± 5.3 units) (p < 0.05). Interestingly, frequencies of CD133 immunoreactivity and CD133 scores did not differ between pMMR CRC on the right versus the left (p > 0.05). Conclusion Proficient MMR correlated with high levels of CD133-marked putative cancer stem cells in b…
format: application/pdf
format: text/html
creator: Phaik-Leng Cheah
creator: Jing Li
creator: Lai-Meng Looi
creator: Kean-Hooi Teoh
creator: Diana Bee-Lan Ong
creator: Mark J. Arends
subject: Gastroenterology and Hepatology
subject: Pathology
description: doi:10.7717/peerj.5530
publisher: PeerJ Inc.
rights: © 2018 Cheah et al.
abstract: Background Except for a few studies with contradictory observations, information is lacking on the possibility of association between DNA mismatch repair (MMR) status and the presence of cancer stem cells in colorectal carcinoma (CRC), two important aspects in colorectal carcinogenesis. Methods Eighty (40 right-sided and 40 left-sided) formalin-fixed, paraffin-embedded primary CRC were immunohistochemically studied for CD133, a putative CRC stem cell marker, and MMR proteins MLH1, MSH2, MSH6 and PMS2. CD133 expression was semi-quantitated for proportion of tumor immunopositivity on a scale of 0–5 and staining intensity on a scale of 0–3 with a final score (units) being the product of proportion and intensity of tumor staining. The tumor was considered immunopositive only when the tumor demonstrated moderate to strong intensity of CD133 staining (a decision made after analysis of CD133 expression in normal colon). Deficient MMR (dMMR) was interpreted as unequivocal loss of tumor nuclear staining for any MMR protein despite immunoreactivity in the internal positive controls. Results CD133 was expressed in 36 (90.0%) left-sided and 28 (70.0%) right-sided tumors (p < 0.05) and CD133 score was significantly higher in left- (mean ± SD = 9.6 ± 5.3 units) compared with right-sided tumors (mean ± SD = 6.8 ± 5.6 units) p < 0.05). dMMR was noted in 14 (35%) right-sided and no (0%) left-sided CRC. When stratified according to MMR status, dMMR cases showed a lower frequency of CD133 expression (42.9%) and CD133 score (mean ± SD = 2.5 ± 3.6 units) compared with pMMR tumors on the right (frequency = 84.6%; mean score ± SD = 9.2 ± 5.0 units) as well as pMMR tumors on the left (frequency = 90.0%; mean score ± SD = 9.6 ± 5.3 units) (p < 0.05). Interestingly, frequencies of CD133 immunoreactivity and CD133 scores did not differ between pMMR CRC on the right versus the left (p > 0.05). Conclusion Proficient MMR correlated with high levels of CD133-marked putative cancer stem cells in b…
bibliographic citation: Cheah et al. (2018) DNA mismatch repair and CD133-marked cancer stem cells in colorectal carcinoma. PeerJ 6:e5530 https://doi.org/10.7717/peerj.5530
date submitted: 2018-03-15
date accepted: 2018-08-07
issued: 2018-09-11
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Cheah
  given name: Phaik-Leng
author list: Agent
  family name: Li
  given name: Jing
author list: Agent
  family name: Looi
  given name: Lai-Meng
author list: Agent
  family name: Teoh
  given name: Kean-Hooi
author list: Agent
  family name: Ong
  given name: Diana Bee-Lan
author list: Agent
  family name: Arends
  given name: Mark J.
doi: 10.7717/peerj.5530
volume: 6
issn: 2167-8359
publication name: PeerJ
publication date: 2018-09-11
copyright: ©2018 Cheah et al.
attribution name: Cheah et al.

Growth under cold conditions in a wide perennial ryegrass panel is under tight physiological control
type: item
type: AcademicArticle
description: Background Perennial ryegrass is a cool-season grass species from the family Poaceae and is widely cultivated in temperate regions because it exhibits rapid growth and establishment, and possesses high forage quality. The extension of the growing season in Ireland in spring and autumn is a breeding target to make farming more profitable since a grass-fed diet based on grazing is the cheapest way of nutrition for ruminants. Methods Fifty-seven perennial ryegrass accessions were screened for their ability to grow under typical Irish spring conditions as taken from long term temperature records in controlled climate chambers. They were grown in low temperature (8 °C/2 °C day/night) and control conditions (15 °C/8 °C day/night) in three consecutive independent experiments. Fresh weight, height, chlorophyll content and electrolyte leakage were measured, and these parameters were used to rank plant performance under low temperature growth conditions. Results The results showed that height, yield and electrolyte leakage are excellent measures for the impact of cold stress tolerance. Little variation in growth was seen under cold stress, but a wide variety of responses were observed under control conditions. Discussion Our results suggest that cold stress is under tight physiological control. Interestingly, the various genotypes responded differentially to more amenable control conditions, indicating that a quick response to more amenable growth conditions is a better target for breeding programmes.
format: application/pdf
format: text/html
creator: Lena Förster
creator: Jim Grant
creator: Thibauld Michel
creator: Carl Ng
creator: Susanne Barth
subject: Agricultural Science
subject: Plant Science
description: doi:10.7717/peerj.5520
publisher: PeerJ Inc.
rights: © 2018 Förster et al.
abstract: Background Perennial ryegrass is a cool-season grass species from the family Poaceae and is widely cultivated in temperate regions because it exhibits rapid growth and establishment, and possesses high forage quality. The extension of the growing season in Ireland in spring and autumn is a breeding target to make farming more profitable since a grass-fed diet based on grazing is the cheapest way of nutrition for ruminants. Methods Fifty-seven perennial ryegrass accessions were screened for their ability to grow under typical Irish spring conditions as taken from long term temperature records in controlled climate chambers. They were grown in low temperature (8 °C/2 °C day/night) and control conditions (15 °C/8 °C day/night) in three consecutive independent experiments. Fresh weight, height, chlorophyll content and electrolyte leakage were measured, and these parameters were used to rank plant performance under low temperature growth conditions. Results The results showed that height, yield and electrolyte leakage are excellent measures for the impact of cold stress tolerance. Little variation in growth was seen under cold stress, but a wide variety of responses were observed under control conditions. Discussion Our results suggest that cold stress is under tight physiological control. Interestingly, the various genotypes responded differentially to more amenable control conditions, indicating that a quick response to more amenable growth conditions is a better target for breeding programmes.
bibliographic citation: Förster et al. (2018) Growth under cold conditions in a wide perennial ryegrass panel is under tight physiological control. PeerJ 6:e5520 https://doi.org/10.7717/peerj.5520
date submitted: 2018-02-23
date accepted: 2018-08-06
issued: 2018-09-11
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Förster
  given name: Lena
author list: Agent
  family name: Grant
  given name: Jim
author list: Agent
  family name: Michel
  given name: Thibauld
author list: Agent
  family name: Ng
  given name: Carl
author list: Agent
  family name: Barth
  given name: Susanne
doi: 10.7717/peerj.5520
volume: 6
issn: 2167-8359
publication name: PeerJ
publication date: 2018-09-11
copyright: ©2018 Förster et al.
attribution name: Förster et al.

A comparison of perceptions of nuts between the general public, dietitians, general practitioners, and nurses
type: item
type: AcademicArticle
description: Background Nut consumption at the population level remains low despite the well-documented benefits of their consumption, including their cardioprotective effects. Studies have suggested that advice from health professionals may be a means to increase nut consumption levels. Understanding how nuts are perceived by the public and health professionals, along with understanding the public’s perceptions of motivators of and deterrents to consuming nuts, may inform the development of initiatives to improve on these low levels of consumption. The aim of this cross-sectional study was to compare perceptions of nuts among three groups of health professionals (dietitians, general practioners, and practice nurses) and the general public in New Zealand (NZ), along with motivators of and deterrents to consuming nuts amongst the general public and their experiences of receiving advice around nut consumption. Methods The NZ electoral roll was used to identify dietitians, general practitioners (GPs), and practice nurses, based on their free-text occupation descriptions, who were then invited to complete a questionnaire with 318, 292, and 149 respondents respectively. 1,600 members of the general public were randomly selected from the roll with 710 respondents. Analyses were performed using chi-squared tests to look at differences in categorical variables and linear regression for differences in other variables between the four survey groups. Results Although there were significant differences between the four groups regarding the perceptions of nuts, in general there was agreement that nuts are healthy, high in protein and fat, are filling, and some nuts are high in selenium. We noted frequent agreement that the general public participants would consume more if nuts: improved health (67%), were more affordable (60%), or improved the nutrient content (59%) and balance of fats (58%) within their diets. Over half the respondents reported they would eat more nuts if they were advised …
format: application/pdf
format: text/html
creator: Rachel Clare Brown
creator: Andrew Robert Gray
creator: Lee Ching Yong
creator: Alex Chisholm
creator: Sook Ling Leong
creator: Siew Ling Tey
subject: Allergy and Clinical Immunology
subject: Nutrition
subject: Public Health
description: doi:10.7717/peerj.5500
publisher: PeerJ Inc.
rights: © 2018 Brown et al.
abstract: Background Nut consumption at the population level remains low despite the well-documented benefits of their consumption, including their cardioprotective effects. Studies have suggested that advice from health professionals may be a means to increase nut consumption levels. Understanding how nuts are perceived by the public and health professionals, along with understanding the public’s perceptions of motivators of and deterrents to consuming nuts, may inform the development of initiatives to improve on these low levels of consumption. The aim of this cross-sectional study was to compare perceptions of nuts among three groups of health professionals (dietitians, general practioners, and practice nurses) and the general public in New Zealand (NZ), along with motivators of and deterrents to consuming nuts amongst the general public and their experiences of receiving advice around nut consumption. Methods The NZ electoral roll was used to identify dietitians, general practitioners (GPs), and practice nurses, based on their free-text occupation descriptions, who were then invited to complete a questionnaire with 318, 292, and 149 respondents respectively. 1,600 members of the general public were randomly selected from the roll with 710 respondents. Analyses were performed using chi-squared tests to look at differences in categorical variables and linear regression for differences in other variables between the four survey groups. Results Although there were significant differences between the four groups regarding the perceptions of nuts, in general there was agreement that nuts are healthy, high in protein and fat, are filling, and some nuts are high in selenium. We noted frequent agreement that the general public participants would consume more if nuts: improved health (67%), were more affordable (60%), or improved the nutrient content (59%) and balance of fats (58%) within their diets. Over half the respondents reported they would eat more nuts if they were advised …
bibliographic citation: Brown et al. (2018) A comparison of perceptions of nuts between the general public, dietitians, general practitioners, and nurses. PeerJ 6:e5500 https://doi.org/10.7717/peerj.5500
date submitted: 2018-03-01
date accepted: 2018-08-01
issued: 2018-09-11
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Brown
  given name: Rachel Clare
author list: Agent
  family name: Gray
  given name: Andrew Robert
author list: Agent
  family name: Yong
  given name: Lee Ching
author list: Agent
  family name: Chisholm
  given name: Alex
author list: Agent
  family name: Leong
  given name: Sook Ling
author list: Agent
  family name: Tey
  given name: Siew Ling
doi: 10.7717/peerj.5500
volume: 6
issn: 2167-8359
publication name: PeerJ
publication date: 2018-09-11
copyright: ©2018 Brown et al.
attribution name: Brown et al.

A novel experimental design for the measurement of metacarpal bone loading and deformation and fingertip force
type: item
type: AcademicArticle
description: Background Musculoskeletal and finite element modelling are often used to predict joint loading and bone strength within the human hand, but there is a lack of in vitro evidence of the force and strain experienced by hand bones. Methods This study presents a novel experimental setup that allows the positioning of a cadaveric digit in a variety of postures with the measurement of force and strain experienced by the third metacarpal. The setup allows for the measurement of fingertip force as well. We tested this experimental setup using three cadaveric human third digits in which the flexor tendons were loaded in two tendon pathways: (1) parallel to the metacarpal bone shaft, with bowstringing; (2) a semi-physiological condition in which the tendons were positioned closer to the bone shaft. Results There is substantial variation in metacarpal net force, metacarpal strain and fingertip force between the two tendon pathways. The net force acting on the metacarpal bone is oriented palmarly in the parallel tendon condition, causing tension along the dorsum of the metacarpal shaft, while the force increases and is oriented dorsally in the semi-physiological condition, causing compression of the dorsal metacarpal shaft. Fingertip force is also greater in the semi-physiological condition, implying a more efficient grip function. Inter-individual variation is observed in the radioulnar orientation of the force experienced by the metacarpal bone, the fingertip force, and the strain patterns on the metacarpal shaft. Conclusion This study demonstrates a new method for measuring force and strain experienced by the metacarpal, and fingertip force in cadaveric digits that can, in turn, inform computation models. Inter-individual variation in loads experienced by the third digit suggest that there are differences in joint contact and/or internal bone structure across individuals that are important to consider in clinical and evolutionary contexts.
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format: text/html
creator: Szu-Ching Lu
creator: Evie E. Vereecke
creator: Alexander Synek
creator: Dieter H. Pahr
creator: Tracy L. Kivell
subject: Anthropology
subject: Bioengineering
description: doi:10.7717/peerj.5480
publisher: PeerJ Inc.
rights: © 2018 Lu et al.
abstract: Background Musculoskeletal and finite element modelling are often used to predict joint loading and bone strength within the human hand, but there is a lack of in vitro evidence of the force and strain experienced by hand bones. Methods This study presents a novel experimental setup that allows the positioning of a cadaveric digit in a variety of postures with the measurement of force and strain experienced by the third metacarpal. The setup allows for the measurement of fingertip force as well. We tested this experimental setup using three cadaveric human third digits in which the flexor tendons were loaded in two tendon pathways: (1) parallel to the metacarpal bone shaft, with bowstringing; (2) a semi-physiological condition in which the tendons were positioned closer to the bone shaft. Results There is substantial variation in metacarpal net force, metacarpal strain and fingertip force between the two tendon pathways. The net force acting on the metacarpal bone is oriented palmarly in the parallel tendon condition, causing tension along the dorsum of the metacarpal shaft, while the force increases and is oriented dorsally in the semi-physiological condition, causing compression of the dorsal metacarpal shaft. Fingertip force is also greater in the semi-physiological condition, implying a more efficient grip function. Inter-individual variation is observed in the radioulnar orientation of the force experienced by the metacarpal bone, the fingertip force, and the strain patterns on the metacarpal shaft. Conclusion This study demonstrates a new method for measuring force and strain experienced by the metacarpal, and fingertip force in cadaveric digits that can, in turn, inform computation models. Inter-individual variation in loads experienced by the third digit suggest that there are differences in joint contact and/or internal bone structure across individuals that are important to consider in clinical and evolutionary contexts.
bibliographic citation: Lu et al. (2018) A novel experimental design for the measurement of metacarpal bone loading and deformation and fingertip force. PeerJ 6:e5480 https://doi.org/10.7717/peerj.5480
date submitted: 2018-04-15
date accepted: 2018-07-30
issued: 2018-09-11
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Lu
  given name: Szu-Ching
author list: Agent
  family name: Vereecke
  given name: Evie E.
author list: Agent
  family name: Synek
  given name: Alexander
author list: Agent
  family name: Pahr
  given name: Dieter H.
author list: Agent
  family name: Kivell
  given name: Tracy L.
doi: 10.7717/peerj.5480
volume: 6
issn: 2167-8359
publication name: PeerJ
publication date: 2018-09-11
copyright: © 2018 Lu et al.
attribution name: Lu et al.

Effects of resveratrol, exercises and their combination on Farnesoid X receptor, Liver X receptor and Sirtuin 1 gene expression and apoptosis in the liver of elderly rats with nonalcoholic fatty liver
type: item
type: AcademicArticle
description: Background Non-alcoholic fatty liver disease (NAFLD) is the most common chronic liver disorder. This study aims to consider effects of resveratrol, exercise and their combination on Farnesoid X receptor (Fxr), the liver X receptor (Lxr) and Sirtuin 1 (Sirt 1) genes expression in the liver of elderly rats with NAFLD. Methods Rats with NAFLD were randomly divided into seven groups including patient, saline, resveratrol (RSV), interval exercise, continuous exercise, interval exercise + RSV and continuous exercise + RSV. Levels of alanine aminotransferase (ALT), aspartate aminotransferase (AST) and alkaline phosphatase (ALP) in the liver tissue were measured using specific ELISA kits. A TUNEL assay kit was used for the assessment of hepatic cells apoptosis. Lipid profiles were considered by measuring the serum triglyceride, cholesterol, LDL, and HDL. Expression of Sirt1, Lxr and Fxr genes was considered using RT-PCR. Results Resveratrol administration alone or combined with exercise training significantly improved the expression of Sirt1, Lxr and Fxr genes (p < 0.05) in the hepatic tissue of rats with NAFLD, while levels of AST, ALT, ALP enzymes, as well as apoptotic cells were significantly decreased (p < 0.05). Discussion Although resveratrol alone improves the expression of Sirt1, Lxr and Fxr, as well as liver function, combined therapy with exercise training is more effective to improve NAFLD.
format: application/pdf
format: text/html
creator: Amir Hajighasem
creator: Parvin Farzanegi
creator: Zohreh Mazaheri
creator: Marjan Naghizadeh
creator: Ghoncheh Salehi
subject: Biochemistry
subject: Molecular Biology
subject: Anatomy and Physiology
subject: Metabolic Sciences
description: doi:10.7717/peerj.5522
publisher: PeerJ Inc.
rights: © 2018 Hajighasem et al.
abstract: Background Non-alcoholic fatty liver disease (NAFLD) is the most common chronic liver disorder. This study aims to consider effects of resveratrol, exercise and their combination on Farnesoid X receptor (Fxr), the liver X receptor (Lxr) and Sirtuin 1 (Sirt 1) genes expression in the liver of elderly rats with NAFLD. Methods Rats with NAFLD were randomly divided into seven groups including patient, saline, resveratrol (RSV), interval exercise, continuous exercise, interval exercise + RSV and continuous exercise + RSV. Levels of alanine aminotransferase (ALT), aspartate aminotransferase (AST) and alkaline phosphatase (ALP) in the liver tissue were measured using specific ELISA kits. A TUNEL assay kit was used for the assessment of hepatic cells apoptosis. Lipid profiles were considered by measuring the serum triglyceride, cholesterol, LDL, and HDL. Expression of Sirt1, Lxr and Fxr genes was considered using RT-PCR. Results Resveratrol administration alone or combined with exercise training significantly improved the expression of Sirt1, Lxr and Fxr genes (p < 0.05) in the hepatic tissue of rats with NAFLD, while levels of AST, ALT, ALP enzymes, as well as apoptotic cells were significantly decreased (p < 0.05). Discussion Although resveratrol alone improves the expression of Sirt1, Lxr and Fxr, as well as liver function, combined therapy with exercise training is more effective to improve NAFLD.
bibliographic citation: Hajighasem et al. (2018) Effects of resveratrol, exercises and their combination on Farnesoid X receptor, Liver X receptor and Sirtuin 1 gene expression and apoptosis in the liver of elderly rats with nonalcoholic fatty liver. PeerJ 6:e5522 https://doi.org/10.7717/peerj.5522
date submitted: 2018-02-16
date accepted: 2018-08-04
issued: 2018-09-10
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Hajighasem
  given name: Amir
author list: Agent
  family name: Farzanegi
  given name: Parvin
author list: Agent
  family name: Mazaheri
  given name: Zohreh
author list: Agent
  family name: Naghizadeh
  given name: Marjan
author list: Agent
  family name: Salehi
  given name: Ghoncheh
doi: 10.7717/peerj.5522
volume: 6
issn: 2167-8359
publication name: PeerJ
publication date: 2018-09-10
copyright: ©2018 Hajighasem et al.
attribution name: Hajighasem et al.

Association of burnout with doctor–patient relationship and common stressors among postgraduate trainees and house officers in Lahore—a cross-sectional study
type: item
type: AcademicArticle
description: Introduction Burnout is defined as a prolonged state of physical and psychological exhaustion. Doctors, due to the demanding nature of their job, are susceptible to facing burnout, which has far reaching implications on their productivity and motivation. It affects the quality of care they provide to patients, thus eroding the doctor–patient relationship which embodies patient centeredness and autonomy. The study aims at addressing the stressors leading to burnout and its effect on the doctor–patient relationship. Methods A descriptive, cross-sectional study design with convenience (non-probability) sampling technique was employed in six major hospitals of Lahore, Pakistan. A total of 600 doctors were approached for the study which included house officers or “HOs” (recent graduates doing their 1 year long internship) and post-graduate trainees or “PGRs” (residents for 4–5 years in their specialties). Burnout was measured using the Copenhagen Burnout Inventor (CBI) while attitudes towards the doctor–patient relationship was measured using the Patient Practitioner Orientation Scale (PPOS), which measures two components of the relationship: power sharing and patient caring. Pearson correlation and linear regression analysis were used to analyze the data via SPSS v.21. Results A total of 515 doctors consented to take part in the study (response rate 85.83%). The final sample consisted of 487 doctors. The burnout score was not associated with the total and caring domain scores of PPOS (P > 0.05). However, it was associated with the power sharing sub-scale of PPOS. Multiple linear regression analysis yielded a significant model, by virtue of which CBI scores were positively associated with factors such as female gender, feeling of burn out, scoring high on sharing domain of PPOS and a lack of personal control while CBI scores were negatively associated with private medical college education, having a significant other, accommodation away from home and a sense of never end…
format: application/pdf
format: text/html
creator: Waqas Ahmad
creator: Huma Ashraf
creator: Afnan Talat
creator: Aleena Ahmad Khan
creator: Ammad Anwar Baig
creator: Iqra Zia
creator: Zohak Sarfraz
creator: Hifsa Sajid
creator: Marium Tahir
creator: Usman Sadiq
creator: Hira Imtiaz
subject: Psychiatry and Psychology
subject: Public Health
description: doi:10.7717/peerj.5519
publisher: PeerJ Inc.
rights: © 2018 Ahmad et al.
abstract: Introduction Burnout is defined as a prolonged state of physical and psychological exhaustion. Doctors, due to the demanding nature of their job, are susceptible to facing burnout, which has far reaching implications on their productivity and motivation. It affects the quality of care they provide to patients, thus eroding the doctor–patient relationship which embodies patient centeredness and autonomy. The study aims at addressing the stressors leading to burnout and its effect on the doctor–patient relationship. Methods A descriptive, cross-sectional study design with convenience (non-probability) sampling technique was employed in six major hospitals of Lahore, Pakistan. A total of 600 doctors were approached for the study which included house officers or “HOs” (recent graduates doing their 1 year long internship) and post-graduate trainees or “PGRs” (residents for 4–5 years in their specialties). Burnout was measured using the Copenhagen Burnout Inventor (CBI) while attitudes towards the doctor–patient relationship was measured using the Patient Practitioner Orientation Scale (PPOS), which measures two components of the relationship: power sharing and patient caring. Pearson correlation and linear regression analysis were used to analyze the data via SPSS v.21. Results A total of 515 doctors consented to take part in the study (response rate 85.83%). The final sample consisted of 487 doctors. The burnout score was not associated with the total and caring domain scores of PPOS (P > 0.05). However, it was associated with the power sharing sub-scale of PPOS. Multiple linear regression analysis yielded a significant model, by virtue of which CBI scores were positively associated with factors such as female gender, feeling of burn out, scoring high on sharing domain of PPOS and a lack of personal control while CBI scores were negatively associated with private medical college education, having a significant other, accommodation away from home and a sense of never end…
bibliographic citation: Ahmad et al. (2018) Association of burnout with doctor–patient relationship and common stressors among postgraduate trainees and house officers in Lahore—a cross-sectional study. PeerJ 6:e5519 https://doi.org/10.7717/peerj.5519
date submitted: 2018-02-24
date accepted: 2018-08-06
issued: 2018-09-10
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Ahmad
  given name: Waqas
author list: Agent
  family name: Ashraf
  given name: Huma
author list: Agent
  family name: Talat
  given name: Afnan
author list: Agent
  family name: Khan
  given name: Aleena Ahmad
author list: Agent
  family name: Baig
  given name: Ammad Anwar
author list: Agent
  family name: Zia
  given name: Iqra
author list: Agent
  family name: Sarfraz
  given name: Zohak
author list: Agent
  family name: Sajid
  given name: Hifsa
author list: Agent
  family name: Tahir
  given name: Marium
author list: Agent
  family name: Sadiq
  given name: Usman
author list: Agent
  family name: Imtiaz
  given name: Hira
doi: 10.7717/peerj.5519
volume: 6
issn: 2167-8359
publication name: PeerJ
publication date: 2018-09-10
copyright: ©2018 Ahmad et al.
attribution name: Ahmad et al.

Effects of environmental and anthropogenic landscape features on mule deer harvest in Nebraska
type: item
type: AcademicArticle
description: Understanding the habitat use of wildlife species is important for effective management. Nebraska has a variety of habitat types, with the majority being covered by rangeland and cropland. These habitat types likely influence the harvest of mule deer (MD; Odocoileus hemionus) in Nebraska, but their specific effects are unknown, and moreover, harvest may also be influenced by the accessibility of deer habitats for hunters. We modeled which environmental and anthropogenic landscape features influenced harvest densities. Spatial analysis in a Geographic Information System was used to determine the mean values of environmental and anthropogenic landscape features at the county level. We then used a generalized linear model to determine which of those factors influenced MD harvest from 2014–2016. We found that NDVI amplitude, hunter effort, road density, terrain roughness, and canopy cover influence MD harvest in Nebraska. According to our model, MD harvest densities are significantly greater areas with NDVI amplitude ∼38, increasing hunter effort, road densities near 1,750 m/km2, increasing terrain roughness, and decreasing canopy cover. Understanding increased harvest densities of MD can be beneficial for wildlife managers, allowing for more efficient allocation of efforts and expenses by managers for population management.
format: application/pdf
format: text/html
creator: Bryan J. O’Connor
creator: Nicolas J. Fryda
creator: Dustin H. Ranglack
subject: Coupled Natural and Human Systems
subject: Natural Resource Management
description: doi:10.7717/peerj.5510
publisher: PeerJ Inc.
rights: © 2018 O’Connor et al.
abstract: Understanding the habitat use of wildlife species is important for effective management. Nebraska has a variety of habitat types, with the majority being covered by rangeland and cropland. These habitat types likely influence the harvest of mule deer (MD; Odocoileus hemionus) in Nebraska, but their specific effects are unknown, and moreover, harvest may also be influenced by the accessibility of deer habitats for hunters. We modeled which environmental and anthropogenic landscape features influenced harvest densities. Spatial analysis in a Geographic Information System was used to determine the mean values of environmental and anthropogenic landscape features at the county level. We then used a generalized linear model to determine which of those factors influenced MD harvest from 2014–2016. We found that NDVI amplitude, hunter effort, road density, terrain roughness, and canopy cover influence MD harvest in Nebraska. According to our model, MD harvest densities are significantly greater areas with NDVI amplitude ∼38, increasing hunter effort, road densities near 1,750 m/km2, increasing terrain roughness, and decreasing canopy cover. Understanding increased harvest densities of MD can be beneficial for wildlife managers, allowing for more efficient allocation of efforts and expenses by managers for population management.
bibliographic citation: O’Connor et al. (2018) Effects of environmental and anthropogenic landscape features on mule deer harvest in Nebraska. PeerJ 6:e5510 https://doi.org/10.7717/peerj.5510
date submitted: 2018-03-01
date accepted: 2018-08-02
issued: 2018-09-10
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: O’Connor
  given name: Bryan J.
author list: Agent
  family name: Fryda
  given name: Nicolas J.
author list: Agent
  family name: Ranglack
  given name: Dustin H.
doi: 10.7717/peerj.5510
volume: 6
issn: 2167-8359
publication name: PeerJ
publication date: 2018-09-10
copyright: ©2018 O’Connor et al.
attribution name: O’Connor et al.

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