PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
items: Alexithymia and facial emotion recognition in patients with craniofacial pain and association of alexithymia with anxiety and depression: a systematic review with meta-analysis
items: Innate and learnt color preferences in the common green-eyed white butterfly (Leptophobia aripa): experimental evidence
items: Whole-limb scaling of muscle mass and force-generating capacity in amniotes
items: Helicobacter pylori virulence factors: relationship between genetic variability and phylogeographic origin
items: Systematic review and meta-analysis on the effect of continuous subjective tinnitus on attention and habituation
items: Monitoring newt communities in urban area using eDNA metabarcoding
items: Quadriceps femoris cross-sectional area and specific leg strength: relationship between different muscles and squat variations
items: treedata.table: a wrapper for data.table that enables fast manipulation of large phylogenetic trees matched to data
items: The influence of storage time on ponazuril concentrations in feline plasma
items: Nutritional properties of selected superfood extracts and their potential health benefits

Alexithymia and facial emotion recognition in patients with craniofacial pain and association of alexithymia with anxiety and depression: a systematic review with meta-analysis
type: item
type: AcademicArticle
description: Background We aimed to determine the presence of alexithymia in patients with craniofacial pain (CFP) compared with asymptomatic individuals. Our secondary aims were to assess the relationship of alexithymia with anxiety and depression levels, as well as to assess the presence of facial emotion recognition deficit. Methods Medline, Scielo and Google Scholar were searched, with the last search performed in 8 September 2021. Standardized mean differences (SMDs) and 95% CIs were calculated for relevant outcomes and were pooled in a meta-analysis using the random effects model. In addition, meta-analyses of correlations and a meta-regression of alexithymia with depression and anxiety were performed. Results Regarding alexithymia, assessed through the Toronto Alexithymia Scale (TAS), the results showed significant differences, with higher values in patients compared with asymptomatic individuals, with a large clinical effect (SMD 0.46; 95% CI [0.22–0.71]; heterogeneity-Q 66.86; p < 0.001; inconsistency (I2) = 81%). We found statistically significant correlations with a small clinical effect of alexithymia with anxiety and depression. The meta-regression showed no significant association between the TAS and anxiety or depression. With respect to facial emotion recognition, the results showed statistically significant differences, with greater recognition difficulty in patients compared with asymptomatic individuals, with a large clinical effect (SMD −1.17; 95% CI [−2.01 to −0.33]; heterogeneity-Q 2.97; p = 0.080; I2 = 66%). Conclusions Patients with CFP showed alexithymia with moderate evidence. There was also moderate evidence indicating that these patients had significant deficits in facial emotion recognition compared with asymptomatic individuals. Furthermore, alexithymia showed statistically significant correlations with anxiety and depression levels.
format: application/pdf
format: text/html
creator: Roy La Touche
creator: Alberto García-Salgado
creator: Ferran Cuenca-Martínez
creator: Santiago Angulo-Díaz-Parreño
creator: Alba Paris-Alemany
creator: Luis Suso-Martí
creator: Aida Herranz-Gómez
subject: Neuroscience
subject: Anesthesiology and Pain Management
subject: Global Health
subject: Psychiatry and Psychology
description: doi:10.7717/peerj.12545
publisher: PeerJ Inc.
rights: © 2021 La Touche et al.
abstract: Background We aimed to determine the presence of alexithymia in patients with craniofacial pain (CFP) compared with asymptomatic individuals. Our secondary aims were to assess the relationship of alexithymia with anxiety and depression levels, as well as to assess the presence of facial emotion recognition deficit. Methods Medline, Scielo and Google Scholar were searched, with the last search performed in 8 September 2021. Standardized mean differences (SMDs) and 95% CIs were calculated for relevant outcomes and were pooled in a meta-analysis using the random effects model. In addition, meta-analyses of correlations and a meta-regression of alexithymia with depression and anxiety were performed. Results Regarding alexithymia, assessed through the Toronto Alexithymia Scale (TAS), the results showed significant differences, with higher values in patients compared with asymptomatic individuals, with a large clinical effect (SMD 0.46; 95% CI [0.22–0.71]; heterogeneity-Q 66.86; p < 0.001; inconsistency (I2) = 81%). We found statistically significant correlations with a small clinical effect of alexithymia with anxiety and depression. The meta-regression showed no significant association between the TAS and anxiety or depression. With respect to facial emotion recognition, the results showed statistically significant differences, with greater recognition difficulty in patients compared with asymptomatic individuals, with a large clinical effect (SMD −1.17; 95% CI [−2.01 to −0.33]; heterogeneity-Q 2.97; p = 0.080; I2 = 66%). Conclusions Patients with CFP showed alexithymia with moderate evidence. There was also moderate evidence indicating that these patients had significant deficits in facial emotion recognition compared with asymptomatic individuals. Furthermore, alexithymia showed statistically significant correlations with anxiety and depression levels.
bibliographic citation: La Touche et al. (2021) Alexithymia and facial emotion recognition in patients with craniofacial pain and association of alexithymia with anxiety and depression: a systematic review with meta-analysis. PeerJ 9:e12545 https://doi.org/10.7717/peerj.12545
date submitted: 2021-07-05
date accepted: 2021-11-04
issued: 2021-11-29
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: La Touche
  given name: Roy
author list: Agent
  family name: García-Salgado
  given name: Alberto
author list: Agent
  family name: Cuenca-Martínez
  given name: Ferran
author list: Agent
  family name: Angulo-Díaz-Parreño
  given name: Santiago
author list: Agent
  family name: Paris-Alemany
  given name: Alba
author list: Agent
  family name: Suso-Martí
  given name: Luis
author list: Agent
  family name: Herranz-Gómez
  given name: Aida
doi: 10.7717/peerj.12545
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-11-29
copyright: © 2021 La Touche et al.
attribution name: La Touche et al.

Innate and learnt color preferences in the common green-eyed white butterfly (Leptophobia aripa): experimental evidence
type: item
type: AcademicArticle
description: Background Learning abilities help animals modify their behaviors based on experience and innate sensory biases to confront environmental unpredictability. In a food acquisition context, the ability to detect, learn, and switch is fundamental in a wide range of insect species facing the ever-changing availability of their floral rewards. Here, we used an experimental approach to address the innate color preferences and learning abilities of the common green-eyed white butterfly (Leptophobia aripa). Methods In Experiment 1, we conducted innate preference choice-tests to determine whether butterflies had a strong innate color preference and to evaluate whether color preferences differed depending on the array of colors offered. We faced naïve butterflies to artificial flowers of four colors (quadruple choice-test): yellow, pink, white, and red; their choices were assessed. In Experiment 2, we examined the ability of this butterfly species to associate colors with rewards while exploring if the spectral reflectance value of a flower color can slow or accelerate this behavioral response. Butterflies were first trained to be fed from artificial yellow flowers inserted in a feeder. These were later replaced by artificial flowers with a similar (blue) or very different (white) spectral reflectance range. Each preference test comprised a dual-choice test (yellow vs blue, yellow vs white). Results Butterflies showed an innate strong preference for red flowers. Both the number of visits and the time spent probing these flowers were much greater than the pink, white, and yellow color flowers. Butterflies learn to associate colors with sugar rewards. They then learned the newly rewarded colors as quickly and proficiently as if the previously rewarded color was similar in spectral reflectance value; the opposite occurs if the newly rewarded color is very different than the previously rewarded color. Conclusions Our findings suggest that common green-eyed white butterflies have g…
format: application/pdf
format: text/html
creator: Deysi Muñoz-Galicia
creator: Citlalli Castillo-Guevara
creator: Carlos Lara
subject: Animal Behavior
description: doi:10.7717/peerj.12567
publisher: PeerJ Inc.
rights: © 2021 Muñoz-Galicia et al.
abstract: Background Learning abilities help animals modify their behaviors based on experience and innate sensory biases to confront environmental unpredictability. In a food acquisition context, the ability to detect, learn, and switch is fundamental in a wide range of insect species facing the ever-changing availability of their floral rewards. Here, we used an experimental approach to address the innate color preferences and learning abilities of the common green-eyed white butterfly (Leptophobia aripa). Methods In Experiment 1, we conducted innate preference choice-tests to determine whether butterflies had a strong innate color preference and to evaluate whether color preferences differed depending on the array of colors offered. We faced naïve butterflies to artificial flowers of four colors (quadruple choice-test): yellow, pink, white, and red; their choices were assessed. In Experiment 2, we examined the ability of this butterfly species to associate colors with rewards while exploring if the spectral reflectance value of a flower color can slow or accelerate this behavioral response. Butterflies were first trained to be fed from artificial yellow flowers inserted in a feeder. These were later replaced by artificial flowers with a similar (blue) or very different (white) spectral reflectance range. Each preference test comprised a dual-choice test (yellow vs blue, yellow vs white). Results Butterflies showed an innate strong preference for red flowers. Both the number of visits and the time spent probing these flowers were much greater than the pink, white, and yellow color flowers. Butterflies learn to associate colors with sugar rewards. They then learned the newly rewarded colors as quickly and proficiently as if the previously rewarded color was similar in spectral reflectance value; the opposite occurs if the newly rewarded color is very different than the previously rewarded color. Conclusions Our findings suggest that common green-eyed white butterflies have g…
bibliographic citation: Muñoz-Galicia et al. (2021) Innate and learnt color preferences in the common green-eyed white butterfly (Leptophobia aripa): experimental evidence. PeerJ 9:e12567 https://doi.org/10.7717/peerj.12567
date submitted: 2021-09-21
date accepted: 2021-11-08
issued: 2021-11-29
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Muñoz-Galicia
  given name: Deysi
author list: Agent
  family name: Castillo-Guevara
  given name: Citlalli
author list: Agent
  family name: Lara
  given name: Carlos
doi: 10.7717/peerj.12567
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-11-29
copyright: © 2021 Muñoz-Galicia et al.
attribution name: Muñoz-Galicia et al.

Whole-limb scaling of muscle mass and force-generating capacity in amniotes
type: item
type: AcademicArticle
description: Skeletal muscle mass, architecture and force-generating capacity are well known to scale with body size in animals, both throughout ontogeny and across species. Investigations of limb muscle scaling in terrestrial amniotes typically focus on individual muscles within select clades, but here this question was examined at the level of the whole limb across amniotes generally. In particular, the present study explored how muscle mass, force-generating capacity (measured by physiological cross-sectional area) and internal architecture (fascicle length) scales in the fore- and hindlimbs of extant mammals, non-avian saurians (‘reptiles’) and bipeds (birds and humans). Sixty species spanning almost five orders of magnitude in body mass were investigated, comprising previously published architectural data and new data obtained via dissections of the opossum Didelphis virginiana and the tegu lizard Salvator merianae. Phylogenetic generalized least squares was used to determine allometric scaling slopes (exponents) and intercepts, to assess whether patterns previously reported for individual muscles or functional groups were retained at the level of the whole limb, and to test whether mammals, reptiles and bipeds followed different allometric trajectories. In general, patterns of scaling observed in individual muscles were also observed in the whole limb. Reptiles generally have proportionately lower muscle mass and force-generating capacity compared to mammals, especially at larger body size, and bipeds exhibit strong to extreme positive allometry in the distal hindlimb. Remarkably, when muscle mass was accounted for in analyses of muscle force-generating capacity, reptiles, mammals and bipeds almost ubiquitously followed a single common scaling pattern, implying that differences in whole-limb force-generating capacity are principally driven by differences in muscle mass, not internal architecture. In addition to providing a novel perspective on skeletal muscle allometry in …
format: application/pdf
format: text/html
creator: Peter J. Bishop
creator: Mark A. Wright
creator: Stephanie E. Pierce
subject: Evolutionary Studies
subject: Zoology
subject: Biomechanics
description: doi:10.7717/peerj.12574
publisher: PeerJ Inc.
rights: © 2021 Bishop et al.
abstract: Skeletal muscle mass, architecture and force-generating capacity are well known to scale with body size in animals, both throughout ontogeny and across species. Investigations of limb muscle scaling in terrestrial amniotes typically focus on individual muscles within select clades, but here this question was examined at the level of the whole limb across amniotes generally. In particular, the present study explored how muscle mass, force-generating capacity (measured by physiological cross-sectional area) and internal architecture (fascicle length) scales in the fore- and hindlimbs of extant mammals, non-avian saurians (‘reptiles’) and bipeds (birds and humans). Sixty species spanning almost five orders of magnitude in body mass were investigated, comprising previously published architectural data and new data obtained via dissections of the opossum Didelphis virginiana and the tegu lizard Salvator merianae. Phylogenetic generalized least squares was used to determine allometric scaling slopes (exponents) and intercepts, to assess whether patterns previously reported for individual muscles or functional groups were retained at the level of the whole limb, and to test whether mammals, reptiles and bipeds followed different allometric trajectories. In general, patterns of scaling observed in individual muscles were also observed in the whole limb. Reptiles generally have proportionately lower muscle mass and force-generating capacity compared to mammals, especially at larger body size, and bipeds exhibit strong to extreme positive allometry in the distal hindlimb. Remarkably, when muscle mass was accounted for in analyses of muscle force-generating capacity, reptiles, mammals and bipeds almost ubiquitously followed a single common scaling pattern, implying that differences in whole-limb force-generating capacity are principally driven by differences in muscle mass, not internal architecture. In addition to providing a novel perspective on skeletal muscle allometry in …
bibliographic citation: Bishop et al. (2021) Whole-limb scaling of muscle mass and force-generating capacity in amniotes. PeerJ 9:e12574 https://doi.org/10.7717/peerj.12574
date submitted: 2021-09-02
date accepted: 2021-11-09
issued: 2021-11-29
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Bishop
  given name: Peter J.
author list: Agent
  family name: Wright
  given name: Mark A.
author list: Agent
  family name: Pierce
  given name: Stephanie E.
doi: 10.7717/peerj.12574
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-11-29
copyright: © 2021 Bishop et al.
attribution name: Bishop et al.

Helicobacter pylori virulence factors: relationship between genetic variability and phylogeographic origin
type: item
type: AcademicArticle
description: Background Helicobacter pylori is a pathogenic bacteria that colonize the gastrointestinal tract from human stomachs and causes diseases including gastritis, peptic ulcers, gastric lymphoma (MALT), and gastric cancer, with a higher prevalence in developing countries. Its high genetic diversity among strains is caused by a high mutation rate, observing virulence factors (VFs) variations in different geographic lineages. This study aimed to postulate the genetic variability associated with virulence factors present in the Helicobacter pylori strains, to identify the relationship of these genes with their phylogeographic origin. Methods The complete genomes of 135 strains available in NCBI, from different population origins, were analyzed using bioinformatics tools, identifying a high rate; as well as reorganization events in 87 virulence factor genes, divided into seven functional groups, to determine changes in position, number of copies, nucleotide identity and size, contrasting them with their geographical lineage and pathogenic phenotype. Results Bioinformatics analyses show a high rate of gene annotation errors in VF. Analysis of genetic variability of VFs shown that there is not a direct relationship between the reorganization and geographic lineage. However, regarding the pathogenic phenotype demonstrated in the analysis of many copies, size, and similarity when dividing the strains that possess and not the cag pathogenicity island (cagPAI), having a higher risk of developing gastritis and peptic ulcer was evidenced. Our data has shown that the analysis of the overall genetic variability of all VFs present in each strain of H. pylori is key information in understanding its pathogenic behavior.
format: application/pdf
format: text/html
creator: Aura M. Rodriguez
creator: Daniel A. Urrea
creator: Carlos F. Prada
subject: Bioinformatics
subject: Computational Biology
subject: Genomics
subject: Microbiology
subject: Gastroenterology and Hepatology
description: doi:10.7717/peerj.12272
publisher: PeerJ Inc.
rights: © 2021 Rodriguez et al.
abstract: Background Helicobacter pylori is a pathogenic bacteria that colonize the gastrointestinal tract from human stomachs and causes diseases including gastritis, peptic ulcers, gastric lymphoma (MALT), and gastric cancer, with a higher prevalence in developing countries. Its high genetic diversity among strains is caused by a high mutation rate, observing virulence factors (VFs) variations in different geographic lineages. This study aimed to postulate the genetic variability associated with virulence factors present in the Helicobacter pylori strains, to identify the relationship of these genes with their phylogeographic origin. Methods The complete genomes of 135 strains available in NCBI, from different population origins, were analyzed using bioinformatics tools, identifying a high rate; as well as reorganization events in 87 virulence factor genes, divided into seven functional groups, to determine changes in position, number of copies, nucleotide identity and size, contrasting them with their geographical lineage and pathogenic phenotype. Results Bioinformatics analyses show a high rate of gene annotation errors in VF. Analysis of genetic variability of VFs shown that there is not a direct relationship between the reorganization and geographic lineage. However, regarding the pathogenic phenotype demonstrated in the analysis of many copies, size, and similarity when dividing the strains that possess and not the cag pathogenicity island (cagPAI), having a higher risk of developing gastritis and peptic ulcer was evidenced. Our data has shown that the analysis of the overall genetic variability of all VFs present in each strain of H. pylori is key information in understanding its pathogenic behavior.
bibliographic citation: Rodriguez et al. (2021) Helicobacter pylori virulence factors: relationship between genetic variability and phylogeographic origin. PeerJ 9:e12272 https://doi.org/10.7717/peerj.12272
date submitted: 2021-07-01
date accepted: 2021-09-17
issued: 2021-11-26
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Rodriguez
  given name: Aura M.
author list: Agent
  family name: Urrea
  given name: Daniel A.
author list: Agent
  family name: Prada
  given name: Carlos F.
doi: 10.7717/peerj.12272
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-11-26
copyright: © 2021 Rodriguez et al.
attribution name: Rodriguez et al.

Systematic review and meta-analysis on the effect of continuous subjective tinnitus on attention and habituation
type: item
type: AcademicArticle
description: Background Attention and habituation are two domains known to play key roles in the perception and maintenance of tinnitus. The heterogeneous nature of tinnitus and the methodologies adopted by various studies make it difficult to generalize findings. The current review aims at assessing and synthesizing evidence on the possible roles of attention and habituation in continuous subjective tinnitus. Methodology The literature search included five databases (PubMed, Scopus, Web of Sciences, CINAHL and ProQuest) that resulted in 1,293 articles, published by July 2019. Studies on attention and/or habituation in individuals with tinnitus using either behavioural or electrophysiological tests were included in the review after a quality assessment. Results Seventeen studies on attention in tinnitus were included in the narrative synthesis. Two meta-analyses were performed to assess the role of attention in tinnitus using a behavioural methodology (z = 4.06; p < 0.0001) and P300 amplitude (z = 2.70; p = 0.007) with 531 participants. With respect to habituation, the review indicates the lack of quality articles for habituation inclusion in the narrative synthesis. Conclusions The review highlights that selective domains of attention were consistently impaired in individuals with tinnitus. Habituation, on the other hand, needs further exploration.
format: application/pdf
format: text/html
creator: Harini Vasudevan
creator: Kanaka Ganapathy
creator: Hari Prakash Palaniswamy
creator: Grant Searchfield
creator: Bellur Rajashekhar
subject: Neuroscience
subject: Otorhinolaryngology
subject: Psychiatry and Psychology
description: doi:10.7717/peerj.12340
publisher: PeerJ Inc.
rights: © 2021 Vasudevan et al.
abstract: Background Attention and habituation are two domains known to play key roles in the perception and maintenance of tinnitus. The heterogeneous nature of tinnitus and the methodologies adopted by various studies make it difficult to generalize findings. The current review aims at assessing and synthesizing evidence on the possible roles of attention and habituation in continuous subjective tinnitus. Methodology The literature search included five databases (PubMed, Scopus, Web of Sciences, CINAHL and ProQuest) that resulted in 1,293 articles, published by July 2019. Studies on attention and/or habituation in individuals with tinnitus using either behavioural or electrophysiological tests were included in the review after a quality assessment. Results Seventeen studies on attention in tinnitus were included in the narrative synthesis. Two meta-analyses were performed to assess the role of attention in tinnitus using a behavioural methodology (z = 4.06; p < 0.0001) and P300 amplitude (z = 2.70; p = 0.007) with 531 participants. With respect to habituation, the review indicates the lack of quality articles for habituation inclusion in the narrative synthesis. Conclusions The review highlights that selective domains of attention were consistently impaired in individuals with tinnitus. Habituation, on the other hand, needs further exploration.
bibliographic citation: Vasudevan et al. (2021) Systematic review and meta-analysis on the effect of continuous subjective tinnitus on attention and habituation. PeerJ 9:e12340 https://doi.org/10.7717/peerj.12340
date submitted: 2021-04-05
date accepted: 2021-09-28
issued: 2021-11-26
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Vasudevan
  given name: Harini
author list: Agent
  family name: Ganapathy
  given name: Kanaka
author list: Agent
  family name: Palaniswamy
  given name: Hari Prakash
author list: Agent
  family name: Searchfield
  given name: Grant
author list: Agent
  family name: Rajashekhar
  given name: Bellur
doi: 10.7717/peerj.12340
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-11-26
copyright: ©2021 Vasudevan et al.
attribution name: Vasudevan et al.

Monitoring newt communities in urban area using eDNA metabarcoding
type: item
type: AcademicArticle
description: Newts are amphibians commonly present in small ponds or garden pools in urban areas. They are protected in many countries and their presence is monitored through visual observation and/or trapping. However, newts are not easy to spot as they are small, elusive and often hidden at the bottom of water bodies. In recent years, environmental DNA (eDNA) has become a popular tool for detecting newts, with a focus on individual species using qPCR assays. Here, we assess the effectiveness of eDNA metabarcoding compared to conventional visual surveys of newt diversity in 45 ponds within urban areas of Geneva canton, Switzerland. We designed newt-specific mitochondrial 16S rRNA primers, which assign the majority of amplicons to newts, and were able to detect four species known to be present in the region, including the invasive subspecies Lissotriton vulgaris meridionalis, native to the Italian peninsula, that has been introduced in the Geneva area recently. The obtained eDNA results were congruent overall with conventional surveys, confirming the morphological observations in the majority of cases (67%). In 25% of cases, a species was only detected genetically, while in 8% of cases, the observations were not supported by eDNA metabarcoding. Our study confirms the usefulness of eDNA metabarcoding as a tool for the effective and non-invasive monitoring of newt community and suggests its broader use for the survey of newt diversity in urban area at larger scales.
format: application/pdf
format: text/html
creator: Léo Charvoz
creator: Laure Apothéloz-Perret-Gentil
creator: Emanuela Reo
creator: Jacques Thiébaud
creator: Jan Pawlowski
subject: Biodiversity
subject: Conservation Biology
subject: Molecular Biology
subject: Zoology
subject: Freshwater Biology
description: doi:10.7717/peerj.12357
publisher: PeerJ Inc.
rights: © 2021 Charvoz et al.
abstract: Newts are amphibians commonly present in small ponds or garden pools in urban areas. They are protected in many countries and their presence is monitored through visual observation and/or trapping. However, newts are not easy to spot as they are small, elusive and often hidden at the bottom of water bodies. In recent years, environmental DNA (eDNA) has become a popular tool for detecting newts, with a focus on individual species using qPCR assays. Here, we assess the effectiveness of eDNA metabarcoding compared to conventional visual surveys of newt diversity in 45 ponds within urban areas of Geneva canton, Switzerland. We designed newt-specific mitochondrial 16S rRNA primers, which assign the majority of amplicons to newts, and were able to detect four species known to be present in the region, including the invasive subspecies Lissotriton vulgaris meridionalis, native to the Italian peninsula, that has been introduced in the Geneva area recently. The obtained eDNA results were congruent overall with conventional surveys, confirming the morphological observations in the majority of cases (67%). In 25% of cases, a species was only detected genetically, while in 8% of cases, the observations were not supported by eDNA metabarcoding. Our study confirms the usefulness of eDNA metabarcoding as a tool for the effective and non-invasive monitoring of newt community and suggests its broader use for the survey of newt diversity in urban area at larger scales.
bibliographic citation: Charvoz et al. (2021) Monitoring newt communities in urban area using eDNA metabarcoding. PeerJ 9:e12357 https://doi.org/10.7717/peerj.12357
date submitted: 2021-04-30
date accepted: 2021-09-30
issued: 2021-11-26
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Charvoz
  given name: Léo
author list: Agent
  family name: Apothéloz-Perret-Gentil
  given name: Laure
author list: Agent
  family name: Reo
  given name: Emanuela
author list: Agent
  family name: Thiébaud
  given name: Jacques
author list: Agent
  family name: Pawlowski
  given name: Jan
doi: 10.7717/peerj.12357
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-11-26
copyright: ©2021 Charvoz et al.
attribution name: Charvoz et al.

Quadriceps femoris cross-sectional area and specific leg strength: relationship between different muscles and squat variations
type: item
type: AcademicArticle
description: Background The aim was to determine the relationship between the cross-sectional area of the quadriceps femoris and strength performance in the deep and parallel barbell squat. Methods The sample included 16 university students (seven female, 24.1 ± 1.7 years). Muscle strength was expressed as external load, including the one-repetition maximum and the body mass segments involved (calculated according to Dempster’s method). The cross-sectional area of the quadriceps femoris muscles was determined using ultrasound, while leg muscle mass was measured using the Bioelectrical Impedance method. Results The cross-sectional areas of the three vastii muscles and leg muscle mass showed moderate to strong correlation with external load in both squat types (r = 0.509–0.873). However, partial correlation (cross-sectional area of quadriceps femoris muscles were controlled) showed significant association only between leg muscle mass and deep squat (r = 0.64, p < 0.05). The cross-sectional area of the vastus lateralis showed a slightly higher correlation with external load in the parallel than in the deep squat (r = 0.67, p < 0.01 vs. r = 0.59, p < 0.05). The regression analysis extracted the vastus medialis cross-sectional area as the most important factor in manifesting strength (parallel squat: R2 = 0.569; deep squat: R2 = 0.499, both p < 0.01). The obtained results suggest that parallel squat strength depends mainly on the cross-sectional area of the vastii muscles, while it seems that the performance in the deep squat requires an additional engagement of the hip and back extensor muscle groups.
format: application/pdf
format: text/html
creator: Filip Kojic
creator: Saša Ðurić
creator: Igor Ranisavljev
creator: Stanimir Stojiljkovic
creator: Vladimir Ilic
subject: Anatomy and Physiology
subject: Kinesiology
subject: Orthopedics
description: doi:10.7717/peerj.12435
publisher: PeerJ Inc.
rights: © 2021 Kojic et al.
abstract: Background The aim was to determine the relationship between the cross-sectional area of the quadriceps femoris and strength performance in the deep and parallel barbell squat. Methods The sample included 16 university students (seven female, 24.1 ± 1.7 years). Muscle strength was expressed as external load, including the one-repetition maximum and the body mass segments involved (calculated according to Dempster’s method). The cross-sectional area of the quadriceps femoris muscles was determined using ultrasound, while leg muscle mass was measured using the Bioelectrical Impedance method. Results The cross-sectional areas of the three vastii muscles and leg muscle mass showed moderate to strong correlation with external load in both squat types (r = 0.509–0.873). However, partial correlation (cross-sectional area of quadriceps femoris muscles were controlled) showed significant association only between leg muscle mass and deep squat (r = 0.64, p < 0.05). The cross-sectional area of the vastus lateralis showed a slightly higher correlation with external load in the parallel than in the deep squat (r = 0.67, p < 0.01 vs. r = 0.59, p < 0.05). The regression analysis extracted the vastus medialis cross-sectional area as the most important factor in manifesting strength (parallel squat: R2 = 0.569; deep squat: R2 = 0.499, both p < 0.01). The obtained results suggest that parallel squat strength depends mainly on the cross-sectional area of the vastii muscles, while it seems that the performance in the deep squat requires an additional engagement of the hip and back extensor muscle groups.
bibliographic citation: Kojic et al. (2021) Quadriceps femoris cross-sectional area and specific leg strength: relationship between different muscles and squat variations. PeerJ 9:e12435 https://doi.org/10.7717/peerj.12435
date submitted: 2021-07-22
date accepted: 2021-10-14
issued: 2021-11-26
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Kojic
  given name: Filip
author list: Agent
  family name: Ðurić
  given name: Saša
author list: Agent
  family name: Ranisavljev
  given name: Igor
author list: Agent
  family name: Stojiljkovic
  given name: Stanimir
author list: Agent
  family name: Ilic
  given name: Vladimir
doi: 10.7717/peerj.12435
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-11-26
copyright: ©2021 Kojic et al.
attribution name: Kojic et al.

treedata.table: a wrapper for data.table that enables fast manipulation of large phylogenetic trees matched to data
type: item
type: AcademicArticle
description: The number of terminals in phylogenetic trees has significantly increased over the last decade. This trend reflects recent advances in next-generation sequencing, accessibility of public data repositories, and the increased use of phylogenies in many fields. Despite R being central to the analysis of phylogenetic data, manipulation of phylogenetic comparative datasets remains slow, complex, and poorly reproducible. Here, we describe the first R package extending the functionality and syntax of data.table to explicitly deal with phylogenetic comparative datasets. treedata.table significantly increases speed and reproducibility during the data manipulation steps involved in the phylogenetic comparative workflow in R. The latest release of treedata.table is currently available through CRAN (https://cran.r-project.org/web/packages/treedata.table/). Additional documentation can be accessed through rOpenSci (https://ropensci.github.io/treedata.table/).
format: application/pdf
format: text/html
creator: Cristian Román Palacios
creator: April Wright
creator: Josef Uyeda
subject: Bioinformatics
subject: Computational Biology
subject: Evolutionary Studies
description: doi:10.7717/peerj.12450
publisher: PeerJ Inc.
rights: © 2021 Román Palacios et al.
abstract: The number of terminals in phylogenetic trees has significantly increased over the last decade. This trend reflects recent advances in next-generation sequencing, accessibility of public data repositories, and the increased use of phylogenies in many fields. Despite R being central to the analysis of phylogenetic data, manipulation of phylogenetic comparative datasets remains slow, complex, and poorly reproducible. Here, we describe the first R package extending the functionality and syntax of data.table to explicitly deal with phylogenetic comparative datasets. treedata.table significantly increases speed and reproducibility during the data manipulation steps involved in the phylogenetic comparative workflow in R. The latest release of treedata.table is currently available through CRAN (https://cran.r-project.org/web/packages/treedata.table/). Additional documentation can be accessed through rOpenSci (https://ropensci.github.io/treedata.table/).
bibliographic citation: Román Palacios et al. (2021) treedata.table: a wrapper for data.table that enables fast manipulation of large phylogenetic trees matched to data. PeerJ 9:e12450 https://doi.org/10.7717/peerj.12450
date submitted: 2021-07-27
date accepted: 2021-10-18
issued: 2021-11-26
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Román Palacios
  given name: Cristian
author list: Agent
  family name: Wright
  given name: April
author list: Agent
  family name: Uyeda
  given name: Josef
doi: 10.7717/peerj.12450
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-11-26
copyright: ©2021 Román Palacios et al.
attribution name: Román Palacios et al.

The influence of storage time on ponazuril concentrations in feline plasma
type: item
type: AcademicArticle
description: Background The pharmacokinetics of ponazuril have been determined in several species; however, there is very little information on the stability of the drug after storage for long periods of time. This study was undertaken to determine the stability of ponazuril in plasma samples stored at −80 °C, which is the temperature most commonly used in the author’s laboratory. Method Spiked plasma samples (0.3, 7.5, and 15 µg/mL) were stored at −80 °C for three months. Analysis occurred on the first day and then once a week for the following twelve weeks. The drug was extracted using a chloroform extraction and separated by high performance liquid chromatography using ultraviolet detection. Results There was no loss of drug for any concentration for the first four weeks of storage. There was an average loss of less than 5% from day 35 through day 70 and an average loss of 6% on day 77 and 84. The data suggest that ponazuril is stable for 4 weeks when stored at −80 °C and undergoes minimal loss in the remaining 8 weeks.
format: application/pdf
format: text/html
creator: Sherry Cox
creator: Lainey Harvill
creator: Sarah Singleton
creator: Joan B. Bergman
creator: Becky DeBolt
subject: Parasitology
subject: Veterinary Medicine
subject: Pharmacology
description: doi:10.7717/peerj.12516
publisher: PeerJ Inc.
rights: © 2021 Cox et al.
abstract: Background The pharmacokinetics of ponazuril have been determined in several species; however, there is very little information on the stability of the drug after storage for long periods of time. This study was undertaken to determine the stability of ponazuril in plasma samples stored at −80 °C, which is the temperature most commonly used in the author’s laboratory. Method Spiked plasma samples (0.3, 7.5, and 15 µg/mL) were stored at −80 °C for three months. Analysis occurred on the first day and then once a week for the following twelve weeks. The drug was extracted using a chloroform extraction and separated by high performance liquid chromatography using ultraviolet detection. Results There was no loss of drug for any concentration for the first four weeks of storage. There was an average loss of less than 5% from day 35 through day 70 and an average loss of 6% on day 77 and 84. The data suggest that ponazuril is stable for 4 weeks when stored at −80 °C and undergoes minimal loss in the remaining 8 weeks.
bibliographic citation: Cox et al. (2021) The influence of storage time on ponazuril concentrations in feline plasma. PeerJ 9:e12516 https://doi.org/10.7717/peerj.12516
date submitted: 2021-08-20
date accepted: 2021-10-27
issued: 2021-11-26
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Cox
  given name: Sherry
author list: Agent
  family name: Harvill
  given name: Lainey
author list: Agent
  family name: Singleton
  given name: Sarah
author list: Agent
  family name: Bergman
  given name: Joan B.
author list: Agent
  family name: DeBolt
  given name: Becky
doi: 10.7717/peerj.12516
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-11-26
copyright: ©2021 Cox et al.
attribution name: Cox et al.

Nutritional properties of selected superfood extracts and their potential health benefits
type: item
type: AcademicArticle
description: Background The term ‘superfoods’ is used to market foods considered to have significant health benefits. ‘Superfoods’ are claimed to prevent diseases as well as improving overall health, though the lack of explicit criteria means that any food can be labelled ‘super’ without support from scientific research. Typically, these ‘superfoods’ are rich in a particular nutrient for example antioxidants or omega-3 fatty acids. The objective of this study was to investigate the nutritional properties of a selection of superfood seeds: flax, chia, hulled sunflower and two types of processed hemp seeds and determine whether they may have potential health benefits. Methods We developed a simple aqueous extraction method for ground seeds and analysed their composition by mineral, protein and monosaccharide analyses. Cell viability assays were performed on Caco-2 and IEC-6 intestinal epithelial cells using increasing doses of the prepared extracts. Results Increased cell viability was observed in both cell lines with increasing concentrations of the flax seed, chia seed or hulled sunflower extracts (P < 0.05). Compositional analyses revealed the presence of polysaccharides, proteins and essential minerals in the aqueous extracts and in vitro assays showed sunflower had the highest antioxidant activity. However, differences in extract composition and antioxidant properties could not be directly related to the observed increase in cell viability suggesting that other components in the extracts may be responsible. Future studies will further characterize these extracts and investigate whether they are beneficial for gastrointestinal health.
format: application/pdf
format: text/html
creator: Jacqueline P. Barsby
creator: James M. Cowley
creator: Shalem Y. Leemaqz
creator: Jessica A. Grieger
creator: Daniel R. McKeating
creator: Anthony V. Perkins
creator: Susan E. P. Bastian
creator: Rachel A. Burton
creator: Tina Bianco-Miotto
subject: Biochemistry
subject: Cell Biology
subject: Food Science and Technology
description: doi:10.7717/peerj.12525
publisher: PeerJ Inc.
rights: © 2021 Barsby et al.
abstract: Background The term ‘superfoods’ is used to market foods considered to have significant health benefits. ‘Superfoods’ are claimed to prevent diseases as well as improving overall health, though the lack of explicit criteria means that any food can be labelled ‘super’ without support from scientific research. Typically, these ‘superfoods’ are rich in a particular nutrient for example antioxidants or omega-3 fatty acids. The objective of this study was to investigate the nutritional properties of a selection of superfood seeds: flax, chia, hulled sunflower and two types of processed hemp seeds and determine whether they may have potential health benefits. Methods We developed a simple aqueous extraction method for ground seeds and analysed their composition by mineral, protein and monosaccharide analyses. Cell viability assays were performed on Caco-2 and IEC-6 intestinal epithelial cells using increasing doses of the prepared extracts. Results Increased cell viability was observed in both cell lines with increasing concentrations of the flax seed, chia seed or hulled sunflower extracts (P < 0.05). Compositional analyses revealed the presence of polysaccharides, proteins and essential minerals in the aqueous extracts and in vitro assays showed sunflower had the highest antioxidant activity. However, differences in extract composition and antioxidant properties could not be directly related to the observed increase in cell viability suggesting that other components in the extracts may be responsible. Future studies will further characterize these extracts and investigate whether they are beneficial for gastrointestinal health.
bibliographic citation: Barsby et al. (2021) Nutritional properties of selected superfood extracts and their potential health benefits. PeerJ 9:e12525 https://doi.org/10.7717/peerj.12525
date submitted: 2021-06-10
date accepted: 2021-10-29
issued: 2021-11-26
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Barsby
  given name: Jacqueline P.
author list: Agent
  family name: Cowley
  given name: James M.
author list: Agent
  family name: Leemaqz
  given name: Shalem Y.
author list: Agent
  family name: Grieger
  given name: Jessica A.
author list: Agent
  family name: McKeating
  given name: Daniel R.
author list: Agent
  family name: Perkins
  given name: Anthony V.
author list: Agent
  family name: Bastian
  given name: Susan E. P.
author list: Agent
  family name: Burton
  given name: Rachel A.
author list: Agent
  family name: Bianco-Miotto
  given name: Tina
doi: 10.7717/peerj.12525
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-11-26
copyright: © 2021 Barsby et al.
attribution name: Barsby et al.

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