PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
items: Percentile curves for skinfold thickness for Canadian children and youth
items: Emotional intelligence and depressive symptoms in Spanish institutionalized elders: does emotional self-efficacy act as a mediator?
items: Fast men slow more than fast women in a 10 kilometer road race
items: Computer-assisted initial diagnosis of rare diseases
items: A century of ecosystem change: human and seabird impacts on plant species extirpation and invasion on islands
items: Proteomic indicators of oxidation and hydration state in colorectal cancer
items: The relationship between different exercise modes and visuospatial working memory in older adults: a cross-sectional study
items: Evolutionary relationships within the lamioid tribe Synandreae (Lamiaceae) based on multiple low-copy nuclear loci
items: Morphological analysis of dendrites and spines by hybridization of ridge detection with twin support vector machine
items: DNA barcode data accurately assign higher spider taxa

Percentile curves for skinfold thickness for Canadian children and youth
type: item
type: AcademicArticle
description: Background. Skinfold thickness (SFT) measurements are a reliable and feasible method for assessing body fat in children but their use and interpretation is hindered by the scarcity of reference values in representative populations of children. The objective of the present study was to develop age- and sex-specific percentile curves for five SFT measures (biceps, triceps, subscapular, suprailiac, medial calf) in a representative population of Canadian children and youth. Methods. We analyzed data from 3,938 children and adolescents between 6 and 19 years of age who participated in the Canadian Health Measures Survey cycles 1 (2007/2009) and 2 (2009/2011). Standardized procedures were used to measure SFT. Age- and sex-specific centiles for SFT were calculated using the GAMLSS method. Results. Percentile curves were materially different in absolute value and shape for boys and girls. Percentile girls in girls steadily increased with age whereas percentile curves in boys were characterized by a pubertal centered peak. Conclusions. The current study has presented for the first time percentile curves for five SFT measures in a representative sample of Canadian children and youth.
format: application/pdf
format: text/html
creator: Stefan Kuhle
creator: Jillian Ashley-Martin
creator: Bryan Maguire
creator: David C. Hamilton
subject: Epidemiology
subject: Nutrition
subject: Pediatrics
subject: Public Health
subject: Statistics
description: doi:10.7717/peerj.2247
publisher: PeerJ Inc.
rights: © 2016 Kuhle et al.
abstract: Background. Skinfold thickness (SFT) measurements are a reliable and feasible method for assessing body fat in children but their use and interpretation is hindered by the scarcity of reference values in representative populations of children. The objective of the present study was to develop age- and sex-specific percentile curves for five SFT measures (biceps, triceps, subscapular, suprailiac, medial calf) in a representative population of Canadian children and youth. Methods. We analyzed data from 3,938 children and adolescents between 6 and 19 years of age who participated in the Canadian Health Measures Survey cycles 1 (2007/2009) and 2 (2009/2011). Standardized procedures were used to measure SFT. Age- and sex-specific centiles for SFT were calculated using the GAMLSS method. Results. Percentile curves were materially different in absolute value and shape for boys and girls. Percentile girls in girls steadily increased with age whereas percentile curves in boys were characterized by a pubertal centered peak. Conclusions. The current study has presented for the first time percentile curves for five SFT measures in a representative sample of Canadian children and youth.
bibliographic citation: Kuhle et al. (2016) Percentile curves for skinfold thickness for Canadian children and youth. PeerJ 4:e2247 https://doi.org/10.7717/peerj.2247
date submitted: 2016-05-17
date accepted: 2016-06-22
issued: 2016-07-21
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Kuhle
  given name: Stefan
author list: Agent
  family name: Ashley-Martin
  given name: Jillian
author list: Agent
  family name: Maguire
  given name: Bryan
author list: Agent
  family name: Hamilton
  given name: David C.
doi: 10.7717/peerj.2247
volume: 4
issn: 2167-8359
publication name: PeerJ
publication date: 2016-07-21
copyright: ©2016 Kuhle et al.
attribution name: Kuhle et al.

Emotional intelligence and depressive symptoms in Spanish institutionalized elders: does emotional self-efficacy act as a mediator?
type: item
type: AcademicArticle
description: Background. This work examines the relationship between emotional intelligence (EI) and depressive symptomatology in institutionalized older adults, delving into the mechanisms underlying this relationship. Considering that previous evidence of the variation of the EI-depression relationship depending on whether the emotional ability or the perception of that ability is evaluated, a model of multiple mediation was tested in which the dimensions of emotional self-efficacy (ESE) act as mediators in the relationship between ability EI and depressive symptomatology. Methods. The sample consisted of 115 institutionalized older adults (47.82% women; 80.3 ± 7.9 years of age) from the province of Jaén (Spain) who completed a test of ESE, a measure of ability EI, and a self-administered questionnaire of depressive symptoms. Results. The results showed a positive association between older adults’ emotional performance and depressive symptomatology, finding stronger associations with ESE than with EI abilities. In addition, multiple mediation analyses showed that two of the four dimensions of ESE fully mediated the relationship between ability EI and depressive symptoms. Discussion. These findings suggest that older adults’ high levels of emotional competence generate a feeling of ESE which can protect them against depressive symptoms. This work supports the predictive validity of emotional abilities and ESE for the mental health of a group that is particularly vulnerable to depression, institutionalized older adults. The limitations of the work are discussed, and future lines of research were considered.
format: application/pdf
format: text/html
creator: Octavio Luque-Reca
creator: José María Augusto-Landa
creator: Manuel Pulido-Martos
subject: Geriatrics
subject: Psychiatry and Psychology
description: doi:10.7717/peerj.2246
publisher: PeerJ Inc.
rights: © 2016 Luque-Reca et al.
abstract: Background. This work examines the relationship between emotional intelligence (EI) and depressive symptomatology in institutionalized older adults, delving into the mechanisms underlying this relationship. Considering that previous evidence of the variation of the EI-depression relationship depending on whether the emotional ability or the perception of that ability is evaluated, a model of multiple mediation was tested in which the dimensions of emotional self-efficacy (ESE) act as mediators in the relationship between ability EI and depressive symptomatology. Methods. The sample consisted of 115 institutionalized older adults (47.82% women; 80.3 ± 7.9 years of age) from the province of Jaén (Spain) who completed a test of ESE, a measure of ability EI, and a self-administered questionnaire of depressive symptoms. Results. The results showed a positive association between older adults’ emotional performance and depressive symptomatology, finding stronger associations with ESE than with EI abilities. In addition, multiple mediation analyses showed that two of the four dimensions of ESE fully mediated the relationship between ability EI and depressive symptoms. Discussion. These findings suggest that older adults’ high levels of emotional competence generate a feeling of ESE which can protect them against depressive symptoms. This work supports the predictive validity of emotional abilities and ESE for the mental health of a group that is particularly vulnerable to depression, institutionalized older adults. The limitations of the work are discussed, and future lines of research were considered.
bibliographic citation: Luque-Reca et al. (2016) Emotional intelligence and depressive symptoms in Spanish institutionalized elders: does emotional self-efficacy act as a mediator?. PeerJ 4:e2246 https://doi.org/10.7717/peerj.2246
date submitted: 2016-03-04
date accepted: 2016-06-22
issued: 2016-07-21
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Luque-Reca
  given name: Octavio
author list: Agent
  family name: Augusto-Landa
  given name: José María
author list: Agent
  family name: Pulido-Martos
  given name: Manuel
doi: 10.7717/peerj.2246
volume: 4
issn: 2167-8359
publication name: PeerJ
publication date: 2016-07-21
copyright: ©2016 Luque-Reca et al.
attribution name: Luque-Reca et al.

Fast men slow more than fast women in a 10 kilometer road race
type: item
type: AcademicArticle
description: Background. Previous studies have demonstrated that men are more likely than women to slow in the marathon (footrace). This study investigated whether the sex difference in pacing occurs for a shorter race distance. Materials & Methods. Data were acquired from the Bolder Boulder 10 km road race for the years 2008–2013, which encompassed 191,693 performances. There were two pacing measures, percentage change in pace of the first 3 miles relative to the final 3.2 miles and percentage change in pace of the first mile relative to the final 5.2 miles. Pacing was analyzed as a continuous variable and as two categorical variables, as follows: “maintain the pace,” defined as slowing <5% and “marked slowing,” defined as slowing ≥10%. Results. Among the fastest (men < 48:40; women < 55:27) and second fastest (men < 53:54; women < 60:28) sex-specific finishing time sextiles, men slowed significantly more than women with both pacing measures, but there were no consistently significant sex differences in pacing among the slower four sextiles. For the fastest sextile, the odds for women were 1.96 (first pacing measure) and 1.36 (second measure) times greater than men to maintain the pace. For the fastest sextile, the odds for women were 0.46 (first measure) and 0.65 (second measure) times that of men to exhibit marked slowing. Multiple regression indicated that being older was associated with lesser slowing, but the sex difference among faster runners persisted when age was controlled. Conclusions. There was a sex difference in pacing during a 10 km race where glycogen depletion is not typically relevant. These results support the hypothesis that the sex difference in pacing partly reflects a sex difference in decision making.
format: application/pdf
format: text/html
creator: Robert O. Deaner
creator: Vittorio Addona
creator: Rickey E. Carter
creator: Michael J. Joyner
creator: Sandra K. Hunter
subject: Kinesiology
subject: Psychiatry and Psychology
description: doi:10.7717/peerj.2235
publisher: PeerJ Inc.
rights: © 2016 Deaner et al.
abstract: Background. Previous studies have demonstrated that men are more likely than women to slow in the marathon (footrace). This study investigated whether the sex difference in pacing occurs for a shorter race distance. Materials & Methods. Data were acquired from the Bolder Boulder 10 km road race for the years 2008–2013, which encompassed 191,693 performances. There were two pacing measures, percentage change in pace of the first 3 miles relative to the final 3.2 miles and percentage change in pace of the first mile relative to the final 5.2 miles. Pacing was analyzed as a continuous variable and as two categorical variables, as follows: “maintain the pace,” defined as slowing <5% and “marked slowing,” defined as slowing ≥10%. Results. Among the fastest (men < 48:40; women < 55:27) and second fastest (men < 53:54; women < 60:28) sex-specific finishing time sextiles, men slowed significantly more than women with both pacing measures, but there were no consistently significant sex differences in pacing among the slower four sextiles. For the fastest sextile, the odds for women were 1.96 (first pacing measure) and 1.36 (second measure) times greater than men to maintain the pace. For the fastest sextile, the odds for women were 0.46 (first measure) and 0.65 (second measure) times that of men to exhibit marked slowing. Multiple regression indicated that being older was associated with lesser slowing, but the sex difference among faster runners persisted when age was controlled. Conclusions. There was a sex difference in pacing during a 10 km race where glycogen depletion is not typically relevant. These results support the hypothesis that the sex difference in pacing partly reflects a sex difference in decision making.
bibliographic citation: Deaner et al. (2016) Fast men slow more than fast women in a 10 kilometer road race. PeerJ 4:e2235 https://doi.org/10.7717/peerj.2235
date submitted: 2016-05-13
date accepted: 2016-06-20
issued: 2016-07-21
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Deaner
  given name: Robert O.
author list: Agent
  family name: Addona
  given name: Vittorio
author list: Agent
  family name: Carter
  given name: Rickey E.
author list: Agent
  family name: Joyner
  given name: Michael J.
author list: Agent
  family name: Hunter
  given name: Sandra K.
doi: 10.7717/peerj.2235
volume: 4
issn: 2167-8359
publication name: PeerJ
publication date: 2016-07-21
copyright: ©2016 Deaner et al.
attribution name: Deaner et al.

Computer-assisted initial diagnosis of rare diseases
type: item
type: AcademicArticle
description: Introduction. Most documented rare diseases have genetic origin. Because of their low individual frequency, an initial diagnosis based on phenotypic symptoms is not always easy, as practitioners might never have been exposed to patients suffering from the relevant disease. It is thus important to develop tools that facilitate symptom-based initial diagnosis of rare diseases by clinicians. In this work we aimed at developing a computational approach to aid in that initial diagnosis. We also aimed at implementing this approach in a user friendly web prototype. We call this tool Rare Disease Discovery. Finally, we also aimed at testing the performance of the prototype. Methods. Rare Disease Discovery uses the publicly available ORPHANET data set of association between rare diseases and their symptoms to automatically predict the most likely rare diseases based on a patient’s symptoms. We apply the method to retrospectively diagnose a cohort of 187 rare disease patients with confirmed diagnosis. Subsequently we test the precision, sensitivity, and global performance of the system under different scenarios by running large scale Monte Carlo simulations. All settings account for situations where absent and/or unrelated symptoms are considered in the diagnosis. Results. We find that this expert system has high diagnostic precision (≥80%) and sensitivity (≥99%), and is robust to both absent and unrelated symptoms. Discussion. The Rare Disease Discovery prediction engine appears to provide a fast and robust method for initial assisted differential diagnosis of rare diseases. We coupled this engine with a user-friendly web interface and it can be freely accessed at http://disease-discovery.udl.cat/. The code and most current database for the whole project can be downloaded from https://github.com/Wrrzag/DiseaseDiscovery/tree/no_classifiers.
format: application/pdf
format: text/html
creator: Rui Alves
creator: Marc Piñol
creator: Jordi Vilaplana
creator: Ivan Teixidó
creator: Joaquim Cruz
creator: Jorge Comas
creator: Ester Vilaprinyo
creator: Albert Sorribas
creator: Francesc Solsona
subject: Bioinformatics
subject: Evidence Based Medicine
subject: Translational Medicine
subject: Science and Medical Education
subject: Computational Science
description: doi:10.7717/peerj.2211
publisher: PeerJ Inc.
rights: © 2016 Alves et al.
abstract: Introduction. Most documented rare diseases have genetic origin. Because of their low individual frequency, an initial diagnosis based on phenotypic symptoms is not always easy, as practitioners might never have been exposed to patients suffering from the relevant disease. It is thus important to develop tools that facilitate symptom-based initial diagnosis of rare diseases by clinicians. In this work we aimed at developing a computational approach to aid in that initial diagnosis. We also aimed at implementing this approach in a user friendly web prototype. We call this tool Rare Disease Discovery. Finally, we also aimed at testing the performance of the prototype. Methods. Rare Disease Discovery uses the publicly available ORPHANET data set of association between rare diseases and their symptoms to automatically predict the most likely rare diseases based on a patient’s symptoms. We apply the method to retrospectively diagnose a cohort of 187 rare disease patients with confirmed diagnosis. Subsequently we test the precision, sensitivity, and global performance of the system under different scenarios by running large scale Monte Carlo simulations. All settings account for situations where absent and/or unrelated symptoms are considered in the diagnosis. Results. We find that this expert system has high diagnostic precision (≥80%) and sensitivity (≥99%), and is robust to both absent and unrelated symptoms. Discussion. The Rare Disease Discovery prediction engine appears to provide a fast and robust method for initial assisted differential diagnosis of rare diseases. We coupled this engine with a user-friendly web interface and it can be freely accessed at http://disease-discovery.udl.cat/. The code and most current database for the whole project can be downloaded from https://github.com/Wrrzag/DiseaseDiscovery/tree/no_classifiers.
bibliographic citation: Alves et al. (2016) Computer-assisted initial diagnosis of rare diseases. PeerJ 4:e2211 https://doi.org/10.7717/peerj.2211
date submitted: 2016-02-06
date accepted: 2016-06-13
issued: 2016-07-21
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Alves
  given name: Rui
author list: Agent
  family name: Piñol
  given name: Marc
author list: Agent
  family name: Vilaplana
  given name: Jordi
author list: Agent
  family name: Teixidó
  given name: Ivan
author list: Agent
  family name: Cruz
  given name: Joaquim
author list: Agent
  family name: Comas
  given name: Jorge
author list: Agent
  family name: Vilaprinyo
  given name: Ester
author list: Agent
  family name: Sorribas
  given name: Albert
author list: Agent
  family name: Solsona
  given name: Francesc
doi: 10.7717/peerj.2211
volume: 4
issn: 2167-8359
publication name: PeerJ
publication date: 2016-07-21
copyright: ©2016 Alves et al.
attribution name: Alves et al.

A century of ecosystem change: human and seabird impacts on plant species extirpation and invasion on islands
type: item
type: AcademicArticle
description: We used 116 years of floral and faunal records from Mandarte Island, British Columbia, Canada, to estimate the indirect effects of humans on plant communities via their effects on the population size of a surface-nesting, colonial seabird, the Glaucous-winged gull (Larus glaucescens). Comparing current to historical records revealed 18 extirpations of native plant species (32% of species historically present), 31 exotic species introductions, and one case of exotic introduction followed by extirpation. Contemporary surveys indicated that native species cover declined dramatically from 1986 to 2006, coincident with the extirpation of ‘old-growth’ conifers. Because vegetation change co-occurred with an increasing gull population locally and regionally, we tested several predictions from the hypothesis that the presence and activities of seabirds help to explain those changes. Specifically, we predicted that on Mandarte and nearby islands with gull colonies, we should observe higher nutrient loading and exotic plant species richness and cover than on nearby islands without gull colonies, as a consequence of competitive dominance in species adapted to high soil nitrogen and trampling. As predicted, we found that native plant species cover and richness were lower, and exotic species cover and richness higher, on islands with versus without gull colonies. In addition, we found that soil carbon and nitrogen on islands with nesting gulls were positively related to soil depth and exotic species richness and cover across plots and islands. Our results support earlier suggestions that nesting seabirds can drive rapid change in insular plant communities by increasing nutrients and disturbing vegetation, and that human activities that affect seabird abundance may therefore indirectly affect plant community composition on islands with seabird colonies.
format: application/pdf
format: text/html
creator: Thomas K. Lameris
creator: Joseph R. Bennett
creator: Louise K. Blight
creator: Marissa Giesen
creator: Michael H. Janssen
creator: Joop J.H.J. Schaminée
creator: Peter Arcese
subject: Biogeography
subject: Biosphere Interactions
subject: Conservation Biology
subject: Ecosystem Science
subject: Plant Science
description: doi:10.7717/peerj.2208
publisher: PeerJ Inc.
rights: © 2016 Lameris et al.
abstract: We used 116 years of floral and faunal records from Mandarte Island, British Columbia, Canada, to estimate the indirect effects of humans on plant communities via their effects on the population size of a surface-nesting, colonial seabird, the Glaucous-winged gull (Larus glaucescens). Comparing current to historical records revealed 18 extirpations of native plant species (32% of species historically present), 31 exotic species introductions, and one case of exotic introduction followed by extirpation. Contemporary surveys indicated that native species cover declined dramatically from 1986 to 2006, coincident with the extirpation of ‘old-growth’ conifers. Because vegetation change co-occurred with an increasing gull population locally and regionally, we tested several predictions from the hypothesis that the presence and activities of seabirds help to explain those changes. Specifically, we predicted that on Mandarte and nearby islands with gull colonies, we should observe higher nutrient loading and exotic plant species richness and cover than on nearby islands without gull colonies, as a consequence of competitive dominance in species adapted to high soil nitrogen and trampling. As predicted, we found that native plant species cover and richness were lower, and exotic species cover and richness higher, on islands with versus without gull colonies. In addition, we found that soil carbon and nitrogen on islands with nesting gulls were positively related to soil depth and exotic species richness and cover across plots and islands. Our results support earlier suggestions that nesting seabirds can drive rapid change in insular plant communities by increasing nutrients and disturbing vegetation, and that human activities that affect seabird abundance may therefore indirectly affect plant community composition on islands with seabird colonies.
bibliographic citation: Lameris et al. (2016) A century of ecosystem change: human and seabird impacts on plant species extirpation and invasion on islands. PeerJ 4:e2208 https://doi.org/10.7717/peerj.2208
date submitted: 2016-02-25
date accepted: 2016-06-11
issued: 2016-07-21
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Lameris
  given name: Thomas K.
author list: Agent
  family name: Bennett
  given name: Joseph R.
author list: Agent
  family name: Blight
  given name: Louise K.
author list: Agent
  family name: Giesen
  given name: Marissa
author list: Agent
  family name: Janssen
  given name: Michael H.
author list: Agent
  family name: Schaminée
  given name: Joop J.H.J.
author list: Agent
  family name: Arcese
  given name: Peter
doi: 10.7717/peerj.2208
volume: 4
issn: 2167-8359
publication name: PeerJ
publication date: 2016-07-21
copyright: © 2016 Lameris et al.
attribution name: Lameris et al.

Proteomic indicators of oxidation and hydration state in colorectal cancer
type: item
type: AcademicArticle
description: New integrative approaches are needed to harness the potential of rapidly growing datasets of protein expression and microbial community composition in colorectal cancer. Chemical and thermodynamic models offer theoretical tools to describe populations of biomacromolecules and their relative potential for formation in different microenvironmental conditions. The average oxidation state of carbon (ZC) can be calculated as an elemental ratio from the chemical formulas of proteins, and water demand per residue ( ${\overline{n}}_{{\mathrm{H}}_{2}\mathrm{O}}$ n ¯ H 2 O ) is computed by writing the overall formation reactions of proteins from basis species. Using results reported in proteomic studies of clinical samples, many datasets exhibit higher mean ZC or ${\overline{n}}_{{\mathrm{H}}_{2}\mathrm{O}}$ n ¯ H 2 O of proteins in carcinoma or adenoma compared to normal tissue. In contrast, average protein compositions in bacterial genomes often have lower ZC for bacteria enriched in fecal samples from cancer patients compared to healthy donors. In thermodynamic calculations, the potential for formation of the cancer-related proteins is energetically favored by changes in the chemical activity of H2O and fugacity of O2 that reflect the compositional differences. The compositional analysis suggests that a systematic change in chemical composition is an essential feature of cancer proteomes, and the thermodynamic descriptions show that the observed proteomic transformations in host tissue could be promoted by relatively high microenvironmental oxidation and hydration states.
format: application/pdf
format: text/html
creator: Jeffrey M. Dick
subject: Biochemistry
subject: Mathematical Biology
subject: Oncology
description: doi:10.7717/peerj.2238
publisher: PeerJ Inc.
rights: © 2016 Dick
abstract: New integrative approaches are needed to harness the potential of rapidly growing datasets of protein expression and microbial community composition in colorectal cancer. Chemical and thermodynamic models offer theoretical tools to describe populations of biomacromolecules and their relative potential for formation in different microenvironmental conditions. The average oxidation state of carbon (ZC) can be calculated as an elemental ratio from the chemical formulas of proteins, and water demand per residue ( ${\overline{n}}_{{\mathrm{H}}_{2}\mathrm{O}}$ n ¯ H 2 O ) is computed by writing the overall formation reactions of proteins from basis species. Using results reported in proteomic studies of clinical samples, many datasets exhibit higher mean ZC or ${\overline{n}}_{{\mathrm{H}}_{2}\mathrm{O}}$ n ¯ H 2 O of proteins in carcinoma or adenoma compared to normal tissue. In contrast, average protein compositions in bacterial genomes often have lower ZC for bacteria enriched in fecal samples from cancer patients compared to healthy donors. In thermodynamic calculations, the potential for formation of the cancer-related proteins is energetically favored by changes in the chemical activity of H2O and fugacity of O2 that reflect the compositional differences. The compositional analysis suggests that a systematic change in chemical composition is an essential feature of cancer proteomes, and the thermodynamic descriptions show that the observed proteomic transformations in host tissue could be promoted by relatively high microenvironmental oxidation and hydration states.
bibliographic citation: Dick (2016) Proteomic indicators of oxidation and hydration state in colorectal cancer. PeerJ 4:e2238 https://doi.org/10.7717/peerj.2238
date submitted: 2016-04-14
date accepted: 2016-06-20
issued: 2016-07-20
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Dick
  given name: Jeffrey M.
doi: 10.7717/peerj.2238
volume: 4
issn: 2167-8359
publication name: PeerJ
publication date: 2016-07-20
copyright: ©2016 Dick
attribution name: Dick

The relationship between different exercise modes and visuospatial working memory in older adults: a cross-sectional study
type: item
type: AcademicArticle
description: The purpose of the study was to investigate the relationship between different exercise modes and visuospatial working memory in healthy older adults. A cross-sectional design was adopted. A total of 111 healthy older adults were enrolled in the study. They were classified by the exercise-related questionnaire to be in an open-skill group, closed-skill group or sedentary group. In experiment 1, the participants performed a visuospatial working memory task. The results indicated that both closed-skill (p < 0.05) and open-skill (p < 0.01) groups reached a higher accuracy than the sedentary group. Experiment 2 examined whether the exercise-induced benefit of working memory was manifested in passive maintenance or active manipulation of working memory which was assessed by visuospatial short-term memory task and visuospatial mental rotation task, respectively. The results showed that the open-skill (p < 0.01) group was more accurate than the sedentary group in the visuospatial short-term memory task, whereas the group difference in the visuospatial mental rotation task was not significant. These findings combined to suggest that physical exercise was associated with better visuospatial working memory in older adults. Furthermore, open-skill exercises that demand higher cognitive processing showed selective benefit for passive maintenance of working memory.
format: application/pdf
format: text/html
creator: Wei Guo
creator: Biye Wang
creator: Yue Lu
creator: Qin Zhu
creator: Zhihao Shi
creator: Jie Ren
subject: Neuroscience
subject: Geriatrics
subject: Neurology
subject: Ophthalmology
description: doi:10.7717/peerj.2254
publisher: PeerJ Inc.
rights: © 2016 Guo et al.
abstract: The purpose of the study was to investigate the relationship between different exercise modes and visuospatial working memory in healthy older adults. A cross-sectional design was adopted. A total of 111 healthy older adults were enrolled in the study. They were classified by the exercise-related questionnaire to be in an open-skill group, closed-skill group or sedentary group. In experiment 1, the participants performed a visuospatial working memory task. The results indicated that both closed-skill (p < 0.05) and open-skill (p < 0.01) groups reached a higher accuracy than the sedentary group. Experiment 2 examined whether the exercise-induced benefit of working memory was manifested in passive maintenance or active manipulation of working memory which was assessed by visuospatial short-term memory task and visuospatial mental rotation task, respectively. The results showed that the open-skill (p < 0.01) group was more accurate than the sedentary group in the visuospatial short-term memory task, whereas the group difference in the visuospatial mental rotation task was not significant. These findings combined to suggest that physical exercise was associated with better visuospatial working memory in older adults. Furthermore, open-skill exercises that demand higher cognitive processing showed selective benefit for passive maintenance of working memory.
bibliographic citation: Guo et al. (2016) The relationship between different exercise modes and visuospatial working memory in older adults: a cross-sectional study. PeerJ 4:e2254 https://doi.org/10.7717/peerj.2254
date submitted: 2016-03-07
date accepted: 2016-06-23
issued: 2016-07-20
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Guo
  given name: Wei
author list: Agent
  family name: Wang
  given name: Biye
author list: Agent
  family name: Lu
  given name: Yue
author list: Agent
  family name: Zhu
  given name: Qin
author list: Agent
  family name: Shi
  given name: Zhihao
author list: Agent
  family name: Ren
  given name: Jie
doi: 10.7717/peerj.2254
volume: 4
issn: 2167-8359
publication name: PeerJ
publication date: 2016-07-20
copyright: ©2016 Guo et al.
attribution name: Guo et al.

Evolutionary relationships within the lamioid tribe Synandreae (Lamiaceae) based on multiple low-copy nuclear loci
type: item
type: AcademicArticle
description: The subfamily Lamioideae (Lamiaceae) comprises ten tribes, of which only Stachydeae and Synandreae include New World members. Previous studies have investigated the phylogenetic relationships among the members of Synandreae based on plastid and nuclear ribosomal DNA loci. In an effort to re-examine the phylogenetic relationships within Synandreae, the current study incorporates data from four low-copy nuclear loci, PHOT1, PHOT2, COR, and PPR. Our results confirm previous studies based on chloroplast and nuclear ribosomal markers in supporting the monophyly of tribe Synandreae, as well as sister relationships between Brazoria and Warnockia, and between that pair of genera and a monophyletic Physostegia. However, we observe incongruence in the relationships of Macbridea and Synandra. The placement of Synandreae within Lamioideae is poorly resolved and incongruent among different analyses, and the sister group of Synandreae remains enigmatic. Comparison of the colonization and migration patterns corroborates a single colonization of the New World by Synandreae during the Late Miocene/Tortonian age. This is in contrast to the only other lamioid tribe that includes New World members, Stachydeae, which colonized the New World at least twice—during the mid-Miocene and Pliocene. Edaphic conditions and intolerance of soil acidity may be factors that restricted the distribution of most genera of Synandreae to southeastern and south–central North America, whereas polyploidy could have increased the colonizing capability of the more wide-ranging genus, Physostegia.
format: application/pdf
format: text/html
creator: Tilottama Roy
creator: Nathan S. Catlin
creator: Drake M.G. Garner
creator: Philip D. Cantino
creator: Anne-Cathrine Scheen
creator: Charlotte Lindqvist
subject: Biogeography
subject: Evolutionary Studies
subject: Genetics
subject: Plant Science
subject: Taxonomy
description: doi:10.7717/peerj.2220
publisher: PeerJ Inc.
rights: © 2016 Roy et al.
abstract: The subfamily Lamioideae (Lamiaceae) comprises ten tribes, of which only Stachydeae and Synandreae include New World members. Previous studies have investigated the phylogenetic relationships among the members of Synandreae based on plastid and nuclear ribosomal DNA loci. In an effort to re-examine the phylogenetic relationships within Synandreae, the current study incorporates data from four low-copy nuclear loci, PHOT1, PHOT2, COR, and PPR. Our results confirm previous studies based on chloroplast and nuclear ribosomal markers in supporting the monophyly of tribe Synandreae, as well as sister relationships between Brazoria and Warnockia, and between that pair of genera and a monophyletic Physostegia. However, we observe incongruence in the relationships of Macbridea and Synandra. The placement of Synandreae within Lamioideae is poorly resolved and incongruent among different analyses, and the sister group of Synandreae remains enigmatic. Comparison of the colonization and migration patterns corroborates a single colonization of the New World by Synandreae during the Late Miocene/Tortonian age. This is in contrast to the only other lamioid tribe that includes New World members, Stachydeae, which colonized the New World at least twice—during the mid-Miocene and Pliocene. Edaphic conditions and intolerance of soil acidity may be factors that restricted the distribution of most genera of Synandreae to southeastern and south–central North America, whereas polyploidy could have increased the colonizing capability of the more wide-ranging genus, Physostegia.
bibliographic citation: Roy et al. (2016) Evolutionary relationships within the lamioid tribe Synandreae (Lamiaceae) based on multiple low-copy nuclear loci. PeerJ 4:e2220 https://doi.org/10.7717/peerj.2220
date submitted: 2016-02-06
date accepted: 2016-06-15
issued: 2016-07-20
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Roy
  given name: Tilottama
author list: Agent
  family name: Catlin
  given name: Nathan S.
author list: Agent
  family name: Garner
  given name: Drake M.G.
author list: Agent
  family name: Cantino
  given name: Philip D.
author list: Agent
  family name: Scheen
  given name: Anne-Cathrine
author list: Agent
  family name: Lindqvist
  given name: Charlotte
doi: 10.7717/peerj.2220
volume: 4
issn: 2167-8359
publication name: PeerJ
publication date: 2016-07-20
copyright: ©2016 Roy et al.
attribution name: Roy et al.

Morphological analysis of dendrites and spines by hybridization of ridge detection with twin support vector machine
type: item
type: AcademicArticle
description: Dendritic spines are described as neuronal protrusions. The morphology of dendritic spines and dendrites has a strong relationship to its function, as well as playing an important role in understanding brain function. Quantitative analysis of dendrites and dendritic spines is essential to an understanding of the formation and function of the nervous system. However, highly efficient tools for the quantitative analysis of dendrites and dendritic spines are currently undeveloped. In this paper we propose a novel three-step cascaded algorithm–RTSVM— which is composed of ridge detection as the curvature structure identifier for backbone extraction, boundary location based on differences in density, the Hu moment as features and Twin Support Vector Machine (TSVM) classifiers for spine classification. Our data demonstrates that this newly developed algorithm has performed better than other available techniques used to detect accuracy and false alarm rates. This algorithm will be used effectively in neuroscience research.
format: application/pdf
format: text/html
creator: Shuihua Wang
creator: Mengmeng Chen
creator: Yang Li
creator: Ying Shao
creator: Yudong Zhang
creator: Sidan Du
creator: Jane Wu
subject: Neuroscience
subject: Computational Science
description: doi:10.7717/peerj.2207
publisher: PeerJ Inc.
rights: © 2016 Wang et al.
abstract: Dendritic spines are described as neuronal protrusions. The morphology of dendritic spines and dendrites has a strong relationship to its function, as well as playing an important role in understanding brain function. Quantitative analysis of dendrites and dendritic spines is essential to an understanding of the formation and function of the nervous system. However, highly efficient tools for the quantitative analysis of dendrites and dendritic spines are currently undeveloped. In this paper we propose a novel three-step cascaded algorithm–RTSVM— which is composed of ridge detection as the curvature structure identifier for backbone extraction, boundary location based on differences in density, the Hu moment as features and Twin Support Vector Machine (TSVM) classifiers for spine classification. Our data demonstrates that this newly developed algorithm has performed better than other available techniques used to detect accuracy and false alarm rates. This algorithm will be used effectively in neuroscience research.
bibliographic citation: Wang et al. (2016) Morphological analysis of dendrites and spines by hybridization of ridge detection with twin support vector machine. PeerJ 4:e2207 https://doi.org/10.7717/peerj.2207
date submitted: 2016-03-29
date accepted: 2016-06-12
issued: 2016-07-20
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Wang
  given name: Shuihua
author list: Agent
  family name: Chen
  given name: Mengmeng
author list: Agent
  family name: Li
  given name: Yang
author list: Agent
  family name: Shao
  given name: Ying
author list: Agent
  family name: Zhang
  given name: Yudong
author list: Agent
  family name: Du
  given name: Sidan
author list: Agent
  family name: Wu
  given name: Jane
doi: 10.7717/peerj.2207
volume: 4
issn: 2167-8359
publication name: PeerJ
publication date: 2016-07-20
copyright: ©2016 Wang et al.
attribution name: Wang et al.

DNA barcode data accurately assign higher spider taxa
type: item
type: AcademicArticle
description: The use of unique DNA sequences as a method for taxonomic identification is no longer fundamentally controversial, even though debate continues on the best markers, methods, and technology to use. Although both existing databanks such as GenBank and BOLD, as well as reference taxonomies, are imperfect, in best case scenarios “barcodes” (whether single or multiple, organelle or nuclear, loci) clearly are an increasingly fast and inexpensive method of identification, especially as compared to manual identification of unknowns by increasingly rare expert taxonomists. Because most species on Earth are undescribed, a complete reference database at the species level is impractical in the near term. The question therefore arises whether unidentified species can, using DNA barcodes, be accurately assigned to more inclusive groups such as genera and families—taxonomic ranks of putatively monophyletic groups for which the global inventory is more complete and stable. We used a carefully chosen test library of CO1 sequences from 49 families, 313 genera, and 816 species of spiders to assess the accuracy of genus and family-level assignment. We used BLAST queries of each sequence against the entire library and got the top ten hits. The percent sequence identity was reported from these hits (PIdent, range 75–100%). Accurate assignment of higher taxa (PIdent above which errors totaled less than 5%) occurred for genera at PIdent values >95 and families at PIdent values ≥ 91, suggesting these as heuristic thresholds for accurate generic and familial identifications in spiders. Accuracy of identification increases with numbers of species/genus and genera/family in the library; above five genera per family and fifteen species per genus all higher taxon assignments were correct. We propose that using percent sequence identity between conventional barcode sequences may be a feasible and reasonably accurate method to identify animals to family/genus. However, the quality of the underlyin…
format: application/pdf
format: text/html
creator: Jonathan A. Coddington
creator: Ingi Agnarsson
creator: Ren-Chung Cheng
creator: Klemen Čandek
creator: Amy Driskell
creator: Holger Frick
creator: Matjaž Gregorič
creator: Rok Kostanjšek
creator: Christian Kropf
creator: Matthew Kweskin
creator: Tjaša Lokovšek
creator: Miha Pipan
creator: Nina Vidergar
creator: Matjaž Kuntner
subject: Biodiversity
subject: Bioinformatics
subject: Ecology
subject: Genetics
subject: Taxonomy
description: doi:10.7717/peerj.2201
publisher: PeerJ Inc.
rights: © 2016 Coddington et al.
abstract: The use of unique DNA sequences as a method for taxonomic identification is no longer fundamentally controversial, even though debate continues on the best markers, methods, and technology to use. Although both existing databanks such as GenBank and BOLD, as well as reference taxonomies, are imperfect, in best case scenarios “barcodes” (whether single or multiple, organelle or nuclear, loci) clearly are an increasingly fast and inexpensive method of identification, especially as compared to manual identification of unknowns by increasingly rare expert taxonomists. Because most species on Earth are undescribed, a complete reference database at the species level is impractical in the near term. The question therefore arises whether unidentified species can, using DNA barcodes, be accurately assigned to more inclusive groups such as genera and families—taxonomic ranks of putatively monophyletic groups for which the global inventory is more complete and stable. We used a carefully chosen test library of CO1 sequences from 49 families, 313 genera, and 816 species of spiders to assess the accuracy of genus and family-level assignment. We used BLAST queries of each sequence against the entire library and got the top ten hits. The percent sequence identity was reported from these hits (PIdent, range 75–100%). Accurate assignment of higher taxa (PIdent above which errors totaled less than 5%) occurred for genera at PIdent values >95 and families at PIdent values ≥ 91, suggesting these as heuristic thresholds for accurate generic and familial identifications in spiders. Accuracy of identification increases with numbers of species/genus and genera/family in the library; above five genera per family and fifteen species per genus all higher taxon assignments were correct. We propose that using percent sequence identity between conventional barcode sequences may be a feasible and reasonably accurate method to identify animals to family/genus. However, the quality of the underlyin…
bibliographic citation: Coddington et al. (2016) DNA barcode data accurately assign higher spider taxa. PeerJ 4:e2201 https://doi.org/10.7717/peerj.2201
date submitted: 2016-01-11
date accepted: 2016-06-10
issued: 2016-07-20
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Coddington
  given name: Jonathan A.
author list: Agent
  family name: Agnarsson
  given name: Ingi
author list: Agent
  family name: Cheng
  given name: Ren-Chung
author list: Agent
  family name: Čandek
  given name: Klemen
author list: Agent
  family name: Driskell
  given name: Amy
author list: Agent
  family name: Frick
  given name: Holger
author list: Agent
  family name: Gregorič
  given name: Matjaž
author list: Agent
  family name: Kostanjšek
  given name: Rok
author list: Agent
  family name: Kropf
  given name: Christian
author list: Agent
  family name: Kweskin
  given name: Matthew
author list: Agent
  family name: Lokovšek
  given name: Tjaša
author list: Agent
  family name: Pipan
  given name: Miha
author list: Agent
  family name: Vidergar
  given name: Nina
author list: Agent
  family name: Kuntner
  given name: Matjaž
doi: 10.7717/peerj.2201
volume: 4
issn: 2167-8359
publication name: PeerJ
publication date: 2016-07-20
copyright: ©2016 Coddington et al.
attribution name: Coddington et al.

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