PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
items: Trust and distrust in information systems at the workplace
items: Multielement analysis of plant extracts with potential use in the treatment of peptic ulcers by synchrotron radiation total reflection X-ray fluorescence
items: Complete paternally inherited mitogenomes of two freshwater mussels Unio pictorum and Sinanodonta woodiana (Bivalvia: Unionidae)
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

Trust and distrust in information systems at the workplace
type: item
type: AcademicArticle
description: Digitalization of work processes is advancing, and this is increasingly supported by complex information systems (IS). However, whether such systems are used by employees largely depends on users’ trust in these IS. Because there are few systematic studies on this topic, this research provides an initial exploration and validation of preconditions for trust in work-related IS. In Study 1, N = 30 professionals were asked to describe occupational incidents in which they had highly trusted or distrusted an IS. Content analysis of 111 critical incidents described in the in-depth interviews led to 12 predictors of trust and distrust in IS, which partly correspond to the structure of the established IS success model (Delone & McLean, 2003) but also exceed this structure. The resulting integrative model of trust in IS at work was validated in Study 2 using an online questionnaire with N = 179 professionals. Based on regression analyses, reliability (system quality) and credibility (information quality) of IS were identified as the most important predictors for both trust and distrust in IS at work. Contrasting analyses revealed diverging qualities of trust and distrust in IS : whereas well-being and performance were rated higher in trust events, experienced strain was rated higher in distrust events. Together, this study offers a first comprehensive model of trust in IS at work based on systematic empirical research. In addition to implications for theory advancement, we suggest practical implications for how to support trust and to avoid distrust in IS at work.
format: application/pdf
format: text/html
creator: Meinald T. Thielsch
creator: Sarah M. Meeßen
creator: Guido Hertel
subject: Psychiatry and Psychology
subject: Human-Computer Interaction
description: doi:10.7717/peerj.5483
publisher: PeerJ Inc.
rights: © 2018 Thielsch et al.
abstract: Digitalization of work processes is advancing, and this is increasingly supported by complex information systems (IS). However, whether such systems are used by employees largely depends on users’ trust in these IS. Because there are few systematic studies on this topic, this research provides an initial exploration and validation of preconditions for trust in work-related IS. In Study 1, N = 30 professionals were asked to describe occupational incidents in which they had highly trusted or distrusted an IS. Content analysis of 111 critical incidents described in the in-depth interviews led to 12 predictors of trust and distrust in IS, which partly correspond to the structure of the established IS success model (Delone & McLean, 2003) but also exceed this structure. The resulting integrative model of trust in IS at work was validated in Study 2 using an online questionnaire with N = 179 professionals. Based on regression analyses, reliability (system quality) and credibility (information quality) of IS were identified as the most important predictors for both trust and distrust in IS at work. Contrasting analyses revealed diverging qualities of trust and distrust in IS : whereas well-being and performance were rated higher in trust events, experienced strain was rated higher in distrust events. Together, this study offers a first comprehensive model of trust in IS at work based on systematic empirical research. In addition to implications for theory advancement, we suggest practical implications for how to support trust and to avoid distrust in IS at work.
bibliographic citation: Thielsch et al. (2018) Trust and distrust in information systems at the workplace. PeerJ 6:e5483 https://doi.org/10.7717/peerj.5483
date submitted: 2018-03-12
date accepted: 2018-07-29
issued: 2018-09-12
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Thielsch
  given name: Meinald T.
author list: Agent
  family name: Meeßen
  given name: Sarah M.
author list: Agent
  family name: Hertel
  given name: Guido
doi: 10.7717/peerj.5483
volume: 6
issn: 2167-8359
publication name: PeerJ
publication date: 2018-09-12
copyright: ©2018 Thielsch et al.
attribution name: Thielsch et al.

Multielement analysis of plant extracts with potential use in the treatment of peptic ulcers by synchrotron radiation total reflection X-ray fluorescence
type: item
type: AcademicArticle
description: Some plants popularly employed for the treatment of peptic ulcers have proved to be attractive sources of new drugs. Despite extensive research, the pharmacological and toxicological potentials of these plants are not fully understood. In this context, the aim of this work was to analyze the multielemental composition of the methanolic extracts of three of those plants, Alchornea glandulosa (AG), Davilla elliptica (DE) and Davilla nitida (DN), with the intention of contributing to the understanding of the mechanisms of action of these extracts. For this purpose, we used the analytical technique of total reflection X-ray fluorescence (TXRF) by synchrotron radiation at the Brazilian Synchrotron Light Source (LNLS/CNPEM). It was possible to determine the concentrations of the elements: P, S, Cl, K, Ca, Ti, Cr, Mn, Fe, Ni, Cu, Zn, Rb and Br in all of the samples. Selenium (Se) was detected only in the DN extract. An inverse relationship between the concentrations of elements with proven effectiveness and the gastroprotective activity of extracts considering induction protocols with ethanol and non-steroidal anti-inflammatory drugs (NSAIDs) was obtained. This data suggests that the function of the extract is not only associated with providing the elements for restoring the gastric mucosa but that it also promotes the displacement of these elements from other parts of the mucosa to the damaged area. Correlations between the concentrations of the elements were also obtained. In the DE extract, which is the most effective extract for both induction protocols, the obtained correlations were above 70% among almost all of the elements, and no anticorrelations were found. For the other two extracts, in the less effective extract (AG) anticorrelations above 70% were predominantly found. Meanwhile, in the DN extract, a few high anticorrelations were found, which may explain its intermediate stage of effectiveness.
format: application/pdf
format: text/html
creator: Leticia Diniz Vieira
creator: Káthia Takeda da Silva
creator: Rodrigo Sanchez Giarola
creator: Guilherme Franco Inocente
creator: Hélio Kushima
creator: Clelia Akiko Hiruma Lima
creator: Joel Mesa Hormaza
subject: Plant Science
subject: Drugs and Devices
subject: Gastroenterology and Hepatology
description: doi:10.7717/peerj.5375
publisher: PeerJ Inc.
rights: © 2018 Vieira et al.
abstract: Some plants popularly employed for the treatment of peptic ulcers have proved to be attractive sources of new drugs. Despite extensive research, the pharmacological and toxicological potentials of these plants are not fully understood. In this context, the aim of this work was to analyze the multielemental composition of the methanolic extracts of three of those plants, Alchornea glandulosa (AG), Davilla elliptica (DE) and Davilla nitida (DN), with the intention of contributing to the understanding of the mechanisms of action of these extracts. For this purpose, we used the analytical technique of total reflection X-ray fluorescence (TXRF) by synchrotron radiation at the Brazilian Synchrotron Light Source (LNLS/CNPEM). It was possible to determine the concentrations of the elements: P, S, Cl, K, Ca, Ti, Cr, Mn, Fe, Ni, Cu, Zn, Rb and Br in all of the samples. Selenium (Se) was detected only in the DN extract. An inverse relationship between the concentrations of elements with proven effectiveness and the gastroprotective activity of extracts considering induction protocols with ethanol and non-steroidal anti-inflammatory drugs (NSAIDs) was obtained. This data suggests that the function of the extract is not only associated with providing the elements for restoring the gastric mucosa but that it also promotes the displacement of these elements from other parts of the mucosa to the damaged area. Correlations between the concentrations of the elements were also obtained. In the DE extract, which is the most effective extract for both induction protocols, the obtained correlations were above 70% among almost all of the elements, and no anticorrelations were found. For the other two extracts, in the less effective extract (AG) anticorrelations above 70% were predominantly found. Meanwhile, in the DN extract, a few high anticorrelations were found, which may explain its intermediate stage of effectiveness.
bibliographic citation: Vieira et al. (2018) Multielement analysis of plant extracts with potential use in the treatment of peptic ulcers by synchrotron radiation total reflection X-ray fluorescence. PeerJ 6:e5375 https://doi.org/10.7717/peerj.5375
date submitted: 2018-04-15
date accepted: 2018-07-16
issued: 2018-09-12
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Vieira
  given name: Leticia Diniz
author list: Agent
  family name: da Silva
  given name: Káthia Takeda
author list: Agent
  family name: Giarola
  given name: Rodrigo Sanchez
author list: Agent
  family name: Inocente
  given name: Guilherme Franco
author list: Agent
  family name: Kushima
  given name: Hélio
author list: Agent
  family name: Hiruma Lima
  given name: Clelia Akiko
author list: Agent
  family name: Hormaza
  given name: Joel Mesa
doi: 10.7717/peerj.5375
volume: 6
issn: 2167-8359
publication name: PeerJ
publication date: 2018-09-12
copyright: ©2018 Vieira et al.
attribution name: Vieira et al.

Complete paternally inherited mitogenomes of two freshwater mussels Unio pictorum and Sinanodonta woodiana (Bivalvia: Unionidae)
type: item
type: AcademicArticle
description: Freshwater bivalves from the family Unionidae usually have two very divergent mitogenomes, inherited according to the doubly uniparental model. The early divergence of these two mitogenomic lineages gives a unique opportunity to use two mitogenomic data sets in a single phylogenetic context. However, the number of complete sequences of the maternally inherited mitogenomes of these animals available in GenBank greatly exceeds that of the paternally inherited mitogenomes. This is a problem for phylogenetic reconstruction because it limits the use of both mitogenomic data sets. Moreover, since long branch attraction phenomenon can bias reconstructions if only a few but highly divergent taxa are considered, the shortage of the faster evolving paternally inherited mitogenome sequences is a real problem. Here we provide, for the first time, complete sequences of the M mitogenomes sampled from Polish populations of two species: native Unio pictorum and invasive Sinanodonta woodiana. It increases the available set of mitogenomic pairs to 18 species per family, and allows unambiguous reconstruction of phylogenetic relationships among them. The reconstructions based on M and F mitogenomes which were separated for many millions of years, and subject to differing evolutionary dynamics, are fully congruent.
format: application/pdf
format: text/html
creator: Artur Burzyński
creator: Marianna Soroka
subject: Biogeography
subject: Conservation Biology
subject: Evolutionary Studies
subject: Genetics
subject: Freshwater Biology
description: doi:10.7717/peerj.5573
publisher: PeerJ Inc.
rights: © 2018 Burzyński and Soroka
abstract: Freshwater bivalves from the family Unionidae usually have two very divergent mitogenomes, inherited according to the doubly uniparental model. The early divergence of these two mitogenomic lineages gives a unique opportunity to use two mitogenomic data sets in a single phylogenetic context. However, the number of complete sequences of the maternally inherited mitogenomes of these animals available in GenBank greatly exceeds that of the paternally inherited mitogenomes. This is a problem for phylogenetic reconstruction because it limits the use of both mitogenomic data sets. Moreover, since long branch attraction phenomenon can bias reconstructions if only a few but highly divergent taxa are considered, the shortage of the faster evolving paternally inherited mitogenome sequences is a real problem. Here we provide, for the first time, complete sequences of the M mitogenomes sampled from Polish populations of two species: native Unio pictorum and invasive Sinanodonta woodiana. It increases the available set of mitogenomic pairs to 18 species per family, and allows unambiguous reconstruction of phylogenetic relationships among them. The reconstructions based on M and F mitogenomes which were separated for many millions of years, and subject to differing evolutionary dynamics, are fully congruent.
bibliographic citation: Burzyński et al. (2018) Complete paternally inherited mitogenomes of two freshwater mussels Unio pictorum and Sinanodonta woodiana (Bivalvia: Unionidae). PeerJ 6:e5573 https://doi.org/10.7717/peerj.5573
date submitted: 2018-03-16
date accepted: 2018-08-13
issued: 2018-09-11
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Burzyński
  given name: Artur
author list: Agent
  family name: Soroka
  given name: Marianna
doi: 10.7717/peerj.5573
volume: 6
issn: 2167-8359
publication name: PeerJ
publication date: 2018-09-11
copyright: ©2018 Burzyński and Soroka
attribution name: Burzyński and Soroka

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…
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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…
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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.
format: application/pdf
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.

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