PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
items: The chemistry and histology of sexually dimorphic mental glands in the freshwater turtle, Mauremys leprosa
items: Spirometric traits show quantile-dependent heritability, which may contribute to their gene-environment interactions with smoking and pollution
items: Depigmenting potential of lichen extracts evaluated by in vitro and in vivo tests
items: Comparing race, gender, age, and career categories in recognizing and grouping tasks
items: Personalized analysis of breast cancer using sample-specific networks
items: Application of High Resolution Melt analysis (HRM) for screening haplotype variation in a non-model plant genus: Cyclopia (Honeybush)
items: The prevalence of low back pain among female hospital staff at childbearing age
items: fRNAkenseq: a fully powered-by-CyVerse cloud integrated RNA-sequencing analysis tool
items: Transcriptomic changes across the life cycle of Trypanosoma cruzi II
items: An interaction mechanism for the maintenance of fission–fusion dynamics under different individual densities

The chemistry and histology of sexually dimorphic mental glands in the freshwater turtle, Mauremys leprosa
type: item
type: AcademicArticle
description: Despite evidence from anatomy, behavior and genomics indicating that the sense of smell in turtles is important, our understanding of chemical communication in this group is still rudimentary. Our aim was to describe the microanatomy of mental glands (MGs) in a freshwater turtle, Mauremys leprosa (Geoemydidae), and to assess the chemical composition of their secretions with respect to variation among individuals and between sexes. MGs are paired sac-like organs on the gular region of the neck and are dimorphic in this species with males having fully functional holocrine glands while those of females appear non-secretory and vestigial. In adult males, the glandular epithelium of the inner portion of the gland provides exocytotic products as well as cellular debris into the lumen of the gland. The contents of the lumen can be secreted through the narrow duct portion of the gland ending in an orifice on the surface of the skin. Females have invaginated structures similar in general outline to male glands, but lack a glandular epithelium. Using gas chromatography coupled to mass spectrometry, we identified a total of 61 compounds in mental gland secretions, the most numerous being carboxylic acids, carbohydrates, alkanes, steroids and alcohols. The number of compounds per individual varied widely (mean (median) ± SD = 14.54 (13) ± 8.44; min = 3; max = 40), but only cholesterol was found in all samples. We found that the relative abundances of only six chemicals were different between the sexes, although males tended to have larger amounts of particular compounds. Although the lipid fraction of mental gland secretions is rich in chemical compounds, most occur in both sexes suggesting that they are metabolic byproducts with no role in chemical signaling. However, the relative amounts of some compounds tended to be higher in males, with significantly larger amounts of two carboxylic acids and one steroid, suggesting their putative involvement in chemical communication.
format: application/pdf
format: text/html
creator: Alejandro Ibáñez
creator: Albert Martínez-Silvestre
creator: Dagmara Podkowa
creator: Aneta Woźniakiewicz
creator: Michał Woźniakiewicz
creator: Maciej Pabijan
subject: Animal Behavior
subject: Zoology
subject: Histology
description: doi:10.7717/peerj.9047
publisher: PeerJ Inc.
rights: © 2020 Ibáñez et al.
abstract: Despite evidence from anatomy, behavior and genomics indicating that the sense of smell in turtles is important, our understanding of chemical communication in this group is still rudimentary. Our aim was to describe the microanatomy of mental glands (MGs) in a freshwater turtle, Mauremys leprosa (Geoemydidae), and to assess the chemical composition of their secretions with respect to variation among individuals and between sexes. MGs are paired sac-like organs on the gular region of the neck and are dimorphic in this species with males having fully functional holocrine glands while those of females appear non-secretory and vestigial. In adult males, the glandular epithelium of the inner portion of the gland provides exocytotic products as well as cellular debris into the lumen of the gland. The contents of the lumen can be secreted through the narrow duct portion of the gland ending in an orifice on the surface of the skin. Females have invaginated structures similar in general outline to male glands, but lack a glandular epithelium. Using gas chromatography coupled to mass spectrometry, we identified a total of 61 compounds in mental gland secretions, the most numerous being carboxylic acids, carbohydrates, alkanes, steroids and alcohols. The number of compounds per individual varied widely (mean (median) ± SD = 14.54 (13) ± 8.44; min = 3; max = 40), but only cholesterol was found in all samples. We found that the relative abundances of only six chemicals were different between the sexes, although males tended to have larger amounts of particular compounds. Although the lipid fraction of mental gland secretions is rich in chemical compounds, most occur in both sexes suggesting that they are metabolic byproducts with no role in chemical signaling. However, the relative amounts of some compounds tended to be higher in males, with significantly larger amounts of two carboxylic acids and one steroid, suggesting their putative involvement in chemical communication.
bibliographic citation: Ibáñez et al. (2020) The chemistry and histology of sexually dimorphic mental glands in the freshwater turtle, Mauremys leprosa. PeerJ 8:e9047 https://doi.org/10.7717/peerj.9047
date submitted: 2020-01-14
date accepted: 2020-04-02
issued: 2020-05-15
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Ibáñez
  given name: Alejandro
author list: Agent
  family name: Martínez-Silvestre
  given name: Albert
author list: Agent
  family name: Podkowa
  given name: Dagmara
author list: Agent
  family name: Woźniakiewicz
  given name: Aneta
author list: Agent
  family name: Woźniakiewicz
  given name: Michał
author list: Agent
  family name: Pabijan
  given name: Maciej
doi: 10.7717/peerj.9047
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-05-15
copyright: © 2020 Ibáñez et al.
attribution name: Ibáñez et al.

Spirometric traits show quantile-dependent heritability, which may contribute to their gene-environment interactions with smoking and pollution
type: item
type: AcademicArticle
description: Background “Quantile-dependent expressivity” refers to a genetic effect that is dependent upon whether the phenotype (e.g., spirometric data) is high or low relative to its population distribution. Forced vital capacity (FVC), forced expiratory volume in 1 second (FEV1), and the FEV1/FVC ratio are moderately heritable spirometric traits. The aim of the analyses is to test whether their heritability (h2) is constant over all quantiles of their distribution. Methods Quantile regression was applied to the mean age, sex, height and smoking-adjusted spirometric data over multiple visits in 9,993 offspring-parent pairs and 1,930 sibships from the Framingham Heart Study to obtain robust estimates of offspring-parent (βOP), offspring-midparent (βOM), and full-sib regression slopes (βFS). Nonparametric significance levels were obtained from 1,000 bootstrap samples. βOPs were used as simple indicators of quantile-specific heritability (i.e., h2 = 2βOP/(1+rspouse), where rspouse was the correlation between spouses). Results βOP ± standard error (SE) decreased by 0.0009 ± 0.0003 (P = 0.003) with every one-percent increment in the population distribution of FEV1/FVC, i.e., βOP ± SE were: 0.182 ± 0.031, 0.152 ± 0.015; 0.136 ± 0.011; 0.121 ± 0.013; and 0.099 ± 0.013 at the 10th, 25th, 50th, 75th, and 90th percentiles of the FEV1/FVC distribution, respectively. These correspond to h2 ± SEs of 0.350 ± 0.060 at the 10th, 0.292 ± 0.029 at the 25th, 0.262 ± 0.020 at the 50th, 0.234 ± 0.025 at the 75th, and 0.191 ± 0.025 at the 90th percentiles of the FEV1/FVC ratio. Maximum mid-expiratory flow (MMEF) h2 ± SEs increased 0.0025 ± 0.0007 (P = 0.0004) with every one-percent increment in its distribution, i.e.: 0.467 ± 0.046, 0.467 ± 0.033, 0.554 ± 0.038, 0.615 ± 0.042, and 0.675 ± 0.060 at the 10th, 25th, 50th, 75th, and 90th percentiles of its distribution. This was due to forced expiratory flow at 75% of FVC (FEF75%), whose quantile-specific h2 increased an average of 0.0042 ± 0.0008 for…
format: application/pdf
format: text/html
creator: Paul T. Williams
subject: Genetics
subject: Public Health
subject: Respiratory Medicine
subject: Medical Genetics
description: doi:10.7717/peerj.9145
publisher: PeerJ Inc.
rights: © 2020 Williams
abstract: Background “Quantile-dependent expressivity” refers to a genetic effect that is dependent upon whether the phenotype (e.g., spirometric data) is high or low relative to its population distribution. Forced vital capacity (FVC), forced expiratory volume in 1 second (FEV1), and the FEV1/FVC ratio are moderately heritable spirometric traits. The aim of the analyses is to test whether their heritability (h2) is constant over all quantiles of their distribution. Methods Quantile regression was applied to the mean age, sex, height and smoking-adjusted spirometric data over multiple visits in 9,993 offspring-parent pairs and 1,930 sibships from the Framingham Heart Study to obtain robust estimates of offspring-parent (βOP), offspring-midparent (βOM), and full-sib regression slopes (βFS). Nonparametric significance levels were obtained from 1,000 bootstrap samples. βOPs were used as simple indicators of quantile-specific heritability (i.e., h2 = 2βOP/(1+rspouse), where rspouse was the correlation between spouses). Results βOP ± standard error (SE) decreased by 0.0009 ± 0.0003 (P = 0.003) with every one-percent increment in the population distribution of FEV1/FVC, i.e., βOP ± SE were: 0.182 ± 0.031, 0.152 ± 0.015; 0.136 ± 0.011; 0.121 ± 0.013; and 0.099 ± 0.013 at the 10th, 25th, 50th, 75th, and 90th percentiles of the FEV1/FVC distribution, respectively. These correspond to h2 ± SEs of 0.350 ± 0.060 at the 10th, 0.292 ± 0.029 at the 25th, 0.262 ± 0.020 at the 50th, 0.234 ± 0.025 at the 75th, and 0.191 ± 0.025 at the 90th percentiles of the FEV1/FVC ratio. Maximum mid-expiratory flow (MMEF) h2 ± SEs increased 0.0025 ± 0.0007 (P = 0.0004) with every one-percent increment in its distribution, i.e.: 0.467 ± 0.046, 0.467 ± 0.033, 0.554 ± 0.038, 0.615 ± 0.042, and 0.675 ± 0.060 at the 10th, 25th, 50th, 75th, and 90th percentiles of its distribution. This was due to forced expiratory flow at 75% of FVC (FEF75%), whose quantile-specific h2 increased an average of 0.0042 ± 0.0008 for…
bibliographic citation: Williams (2020) Spirometric traits show quantile-dependent heritability, which may contribute to their gene-environment interactions with smoking and pollution. PeerJ 8:e9145 https://doi.org/10.7717/peerj.9145
date submitted: 2019-10-23
date accepted: 2020-04-17
issued: 2020-05-15
is part of: PeerJ
license: https://creativecommons.org/publicdomain/zero/1.0/
author list: Agent
  family name: Williams
  given name: Paul T.
doi: 10.7717/peerj.9145
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-05-15
attribution name: Williams

Depigmenting potential of lichen extracts evaluated by in vitro and in vivo tests
type: item
type: AcademicArticle
description: Melanin is the main pigment of human skin, playing the primary role of protection from ultraviolet radiation. Alteration of the melanin production may lead to hyperpigmentation diseases, with both aesthetic and health consequences. Thus, suppressors of melanogenesis are considered useful tools for medical and cosmetic treatments. A great interest is focused on natural sources, aimed at finding safe and quantitatively available depigmenting substances. Lichens are thought to be possible sources of this kind of compounds, as the occurrence of many phenolic molecules suggests possible effects on phenolase enzymes involved in melanin synthesis, like tyrosinase. In this work, we used four lichen species, Cetraria islandica Ach., Flavoparmelia caperata Hale, Letharia vulpina (L.) Hue, and Parmotrema perlatum (Hudson) M. Choisy, to obtain extracts in solvents of increasing polarity, viz. chloroform, chloroform-methanol, methanol, and water. Cell-free, tyrosinase inhibition experiments showed highest inhibition for L. vulpina methanol extract, followed by C. islandica chloroform-methanol one. Comparable results for depigmenting activities were observed by means of in vitro and in vivo systems, such as MeWo melanoma cells and zebrafish larvae. Our study provides first evidence of depigmenting effects of lichen extracts, from tyrosinase inhibition to cell and in vivo models, suggesting that L. vulpina and C. islandica extracts deserve to be further studied for developing skin-whitening products.
format: application/pdf
format: text/html
creator: Paola Malaspina
creator: Erica Catellani
creator: Bruno Burlando
creator: Daniele Brignole
creator: Laura Cornara
creator: Miriam Bazzicalupo
creator: Simona Candiani
creator: Valentina Obino
creator: Vincenzo De Feo
creator: Lucia Caputo
creator: Paolo Giordani
subject: Plant Science
subject: Dermatology
description: doi:10.7717/peerj.9150
publisher: PeerJ Inc.
rights: © 2020 Malaspina et al.
abstract: Melanin is the main pigment of human skin, playing the primary role of protection from ultraviolet radiation. Alteration of the melanin production may lead to hyperpigmentation diseases, with both aesthetic and health consequences. Thus, suppressors of melanogenesis are considered useful tools for medical and cosmetic treatments. A great interest is focused on natural sources, aimed at finding safe and quantitatively available depigmenting substances. Lichens are thought to be possible sources of this kind of compounds, as the occurrence of many phenolic molecules suggests possible effects on phenolase enzymes involved in melanin synthesis, like tyrosinase. In this work, we used four lichen species, Cetraria islandica Ach., Flavoparmelia caperata Hale, Letharia vulpina (L.) Hue, and Parmotrema perlatum (Hudson) M. Choisy, to obtain extracts in solvents of increasing polarity, viz. chloroform, chloroform-methanol, methanol, and water. Cell-free, tyrosinase inhibition experiments showed highest inhibition for L. vulpina methanol extract, followed by C. islandica chloroform-methanol one. Comparable results for depigmenting activities were observed by means of in vitro and in vivo systems, such as MeWo melanoma cells and zebrafish larvae. Our study provides first evidence of depigmenting effects of lichen extracts, from tyrosinase inhibition to cell and in vivo models, suggesting that L. vulpina and C. islandica extracts deserve to be further studied for developing skin-whitening products.
bibliographic citation: Malaspina et al. (2020) Depigmenting potential of lichen extracts evaluated by in vitro and in vivo tests. PeerJ 8:e9150 https://doi.org/10.7717/peerj.9150
date submitted: 2019-07-17
date accepted: 2020-04-17
issued: 2020-05-15
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Malaspina
  given name: Paola
author list: Agent
  family name: Catellani
  given name: Erica
author list: Agent
  family name: Burlando
  given name: Bruno
author list: Agent
  family name: Brignole
  given name: Daniele
author list: Agent
  family name: Cornara
  given name: Laura
author list: Agent
  family name: Bazzicalupo
  given name: Miriam
author list: Agent
  family name: Candiani
  given name: Simona
author list: Agent
  family name: Obino
  given name: Valentina
author list: Agent
  family name: De Feo
  given name: Vincenzo
author list: Agent
  family name: Caputo
  given name: Lucia
author list: Agent
  family name: Giordani
  given name: Paolo
doi: 10.7717/peerj.9150
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-05-15
copyright: ©2020 Malaspina et al.
attribution name: Malaspina et al.

Comparing race, gender, age, and career categories in recognizing and grouping tasks
type: item
type: AcademicArticle
description: The purpose of our research was to compare how participants weighed age, gender, race, and career categories in recognizing and grouping tasks. In Study 1, we used a category recognition task to compare participants’ speeds in recognizing information from different categories. The results showed that participants recognized the gender information most quickly, followed by career, race, and age information. In Study 2, a categorization task was used to compare participants’ category preferences. The results showed that the career category had the greatest weight, and the gender category had the lowest weight. Two targets who had different career identities were more possible considered as belonging to different groups than two targets with different gender, race or age identities. Our results have implications in understanding the weight of different categories, with gender and career category are the most important category that affects perception and evaluation.
format: application/pdf
format: text/html
creator: Jingjing Song
creator: Lin Li
subject: Psychiatry and Psychology
subject: Public Health
description: doi:10.7717/peerj.9156
publisher: PeerJ Inc.
rights: © 2020 Song and Li
abstract: The purpose of our research was to compare how participants weighed age, gender, race, and career categories in recognizing and grouping tasks. In Study 1, we used a category recognition task to compare participants’ speeds in recognizing information from different categories. The results showed that participants recognized the gender information most quickly, followed by career, race, and age information. In Study 2, a categorization task was used to compare participants’ category preferences. The results showed that the career category had the greatest weight, and the gender category had the lowest weight. Two targets who had different career identities were more possible considered as belonging to different groups than two targets with different gender, race or age identities. Our results have implications in understanding the weight of different categories, with gender and career category are the most important category that affects perception and evaluation.
bibliographic citation: Song et al. (2020) Comparing race, gender, age, and career categories in recognizing and grouping tasks. PeerJ 8:e9156 https://doi.org/10.7717/peerj.9156
date submitted: 2020-01-21
date accepted: 2020-04-18
issued: 2020-05-15
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Song
  given name: Jingjing
author list: Agent
  family name: Li
  given name: Lin
doi: 10.7717/peerj.9156
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-05-15
copyright: ©2020 Song and Li
attribution name: Song and Li

Personalized analysis of breast cancer using sample-specific networks
type: item
type: AcademicArticle
description: Breast cancer is a disease with high heterogeneity. Cancer is not usually caused by a single gene, but by multiple genes and their interactions with others and surroundings. Estimating breast cancer-specific gene–gene interaction networks is critical to elucidate the mechanisms of breast cancer from a biological network perspective. In this study, sample-specific gene–gene interaction networks of breast cancer samples were established by using a sample-specific network analysis method based on gene expression profiles. Then, gene–gene interaction networks and pathways related to breast cancer and its subtypes and stages were further identified. The similarity and difference among these subtype-related (and stage-related) networks and pathways were studied, which showed highly specific for subtype Basal-like and Stages IV and V. Finally, gene pairwise interactions associated with breast cancer prognosis were identified by a Cox proportional hazards regression model, and a risk prediction model based on the gene pairs was established, which also performed very well on an independent validation data set. This work will help us to better understand the mechanism underlying the occurrence of breast cancer from the sample-specific network perspective.
format: application/pdf
format: text/html
creator: Ke Zhu
creator: Cong Pian
creator: Qiong Xiang
creator: Xin Liu
creator: Yuanyuan Chen
subject: Bioinformatics
subject: Genomics
subject: Epidemiology
subject: Oncology
description: doi:10.7717/peerj.9161
publisher: PeerJ Inc.
rights: © 2020 Zhu et al.
abstract: Breast cancer is a disease with high heterogeneity. Cancer is not usually caused by a single gene, but by multiple genes and their interactions with others and surroundings. Estimating breast cancer-specific gene–gene interaction networks is critical to elucidate the mechanisms of breast cancer from a biological network perspective. In this study, sample-specific gene–gene interaction networks of breast cancer samples were established by using a sample-specific network analysis method based on gene expression profiles. Then, gene–gene interaction networks and pathways related to breast cancer and its subtypes and stages were further identified. The similarity and difference among these subtype-related (and stage-related) networks and pathways were studied, which showed highly specific for subtype Basal-like and Stages IV and V. Finally, gene pairwise interactions associated with breast cancer prognosis were identified by a Cox proportional hazards regression model, and a risk prediction model based on the gene pairs was established, which also performed very well on an independent validation data set. This work will help us to better understand the mechanism underlying the occurrence of breast cancer from the sample-specific network perspective.
bibliographic citation: Zhu et al. (2020) Personalized analysis of breast cancer using sample-specific networks. PeerJ 8:e9161 https://doi.org/10.7717/peerj.9161
date submitted: 2020-03-06
date accepted: 2020-04-18
issued: 2020-05-15
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Zhu
  given name: Ke
author list: Agent
  family name: Pian
  given name: Cong
author list: Agent
  family name: Xiang
  given name: Qiong
author list: Agent
  family name: Liu
  given name: Xin
author list: Agent
  family name: Chen
  given name: Yuanyuan
doi: 10.7717/peerj.9161
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-05-15
copyright: © 2020 Zhu et al.
attribution name: Zhu et al.

Application of High Resolution Melt analysis (HRM) for screening haplotype variation in a non-model plant genus: Cyclopia (Honeybush)
type: item
type: AcademicArticle
description: Aim This study has three broad aims: to (a) develop genus-specific primers for High Resolution Melt analysis (HRM) of members of Cyclopia Vent., (b) test the haplotype discrimination of HRM compared to Sanger sequencing, and (c) provide an example of using HRM to detect novel haplotype variation in wild C. subternata Vogel. populations. Location The Cape Floristic Region (CFR), located along the southern Cape of South Africa. Methods Polymorphic loci were detected through a screening process of sequencing 12 non-coding chloroplast DNA segments across 14 Cyclopia species. Twelve genus-specific primer combinations were designed around variable cpDNA loci, four of which failed to amplify under PCR; the eight remaining were applied to test the specificity, sensitivity and accuracy of HRM. The three top performing HRM Primer combinations were then applied to detect novel haplotypes in wild C. subternata populations, and phylogeographic patterns of C. subternata were explored. Results We present a framework for applying HRM to non-model systems. HRM accuracy varied across the PCR products screened using the genus-specific primers developed, ranging between 56 and 100%. The nucleotide variation failing to produce distinct melt curves is discussed. The top three performing regions, having 100% specificity (i.e. different haplotypes were never grouped into the same cluster, no false negatives), were able to detect novel haplotypes in wild C. subternata populations with high accuracy (96%). Sensitivity below 100% (i.e. a single haplotype being clustered into multiple unique groups during HRM curve analysis, false positives) was resolved through sequence confirmation of each cluster resulting in a final accuracy of 100%. Phylogeographic analyses revealed that wild C. subternata populations tend to exhibit phylogeographic structuring across mountain ranges (accounting for 73.8% of genetic variation base on an AMOVA), and genetic differentiation between populations increases wit…
format: application/pdf
format: text/html
creator: Nicholas C. Galuszynski
creator: Alastair J. Potts
subject: Molecular Biology
subject: Plant Science
description: doi:10.7717/peerj.9187
publisher: PeerJ Inc.
rights: © 2020 Galuszynski and Potts
abstract: Aim This study has three broad aims: to (a) develop genus-specific primers for High Resolution Melt analysis (HRM) of members of Cyclopia Vent., (b) test the haplotype discrimination of HRM compared to Sanger sequencing, and (c) provide an example of using HRM to detect novel haplotype variation in wild C. subternata Vogel. populations. Location The Cape Floristic Region (CFR), located along the southern Cape of South Africa. Methods Polymorphic loci were detected through a screening process of sequencing 12 non-coding chloroplast DNA segments across 14 Cyclopia species. Twelve genus-specific primer combinations were designed around variable cpDNA loci, four of which failed to amplify under PCR; the eight remaining were applied to test the specificity, sensitivity and accuracy of HRM. The three top performing HRM Primer combinations were then applied to detect novel haplotypes in wild C. subternata populations, and phylogeographic patterns of C. subternata were explored. Results We present a framework for applying HRM to non-model systems. HRM accuracy varied across the PCR products screened using the genus-specific primers developed, ranging between 56 and 100%. The nucleotide variation failing to produce distinct melt curves is discussed. The top three performing regions, having 100% specificity (i.e. different haplotypes were never grouped into the same cluster, no false negatives), were able to detect novel haplotypes in wild C. subternata populations with high accuracy (96%). Sensitivity below 100% (i.e. a single haplotype being clustered into multiple unique groups during HRM curve analysis, false positives) was resolved through sequence confirmation of each cluster resulting in a final accuracy of 100%. Phylogeographic analyses revealed that wild C. subternata populations tend to exhibit phylogeographic structuring across mountain ranges (accounting for 73.8% of genetic variation base on an AMOVA), and genetic differentiation between populations increases wit…
bibliographic citation: Galuszynski et al. (2020) Application of High Resolution Melt analysis (HRM) for screening haplotype variation in a non-model plant genus: Cyclopia (Honeybush). PeerJ 8:e9187 https://doi.org/10.7717/peerj.9187
date submitted: 2020-01-27
date accepted: 2020-04-23
issued: 2020-05-15
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Galuszynski
  given name: Nicholas C.
author list: Agent
  family name: Potts
  given name: Alastair J.
doi: 10.7717/peerj.9187
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-05-15
copyright: ©2020 Galuszynski and Potts
attribution name: Galuszynski and Potts

The prevalence of low back pain among female hospital staff at childbearing age
type: item
type: AcademicArticle
description: Background Low back pain (LBP) is considered the most common work-related musculoskeletal disorder among female healthcare workers. The aim of this study is to compare the prevalence of LBP and non-ergonomic risk factors between female nurses, office workers, and patient transporters, and the effect of pain on job performance. Methods Based on semi-structured interviews, we conducted a cross-sectional study on Jordanian female hospital workers between January and July, 2017. Results We included 209 participants with a mean age of 35.57 ± 8 years from four Jordanian medical centers. Nurses have significantly higher frequency of LBP (82.5%; p = 0.05) compared to both office workers (67.5%) and patient transporters (68.6%). The mean difference in pain score using Visual Analogue Scale (VAS) after treatment varied significantly (p = 0.003), since it was 28.2 (±35.4) for office workers, compared to 22.8 (±26.5) for nurses and 6.5 (±33.7) for patient transporters. A higher frequency of nurses reported that LBP affected their job performance (64.9%; p = 0.013), and 43.3% of them reported having previous sick leaves due to LBP (p = 0.008). Conclusions LBP is common among female hospital workers, with significantly higher prevalence among female nurses when compared to other female hospital staff.
format: application/pdf
format: text/html
creator: Fadi Al-Hadidi
creator: Isam Bsisu
creator: Bassem Haddad
creator: Saif Aldeen AlRyalat
creator: Mamoun Shaban
creator: Nada Matani
creator: Sondos Dehidi
creator: Yasmeen Khater
creator: Rana Shahrouri
creator: Tasnim Al Muzayen
creator: Hashem Al Hawamdeh
subject: Anesthesiology and Pain Management
subject: Nursing
subject: Orthopedics
subject: Women’s Health
description: doi:10.7717/peerj.9199
publisher: PeerJ Inc.
rights: © 2020 Al-Hadidi et al.
abstract: Background Low back pain (LBP) is considered the most common work-related musculoskeletal disorder among female healthcare workers. The aim of this study is to compare the prevalence of LBP and non-ergonomic risk factors between female nurses, office workers, and patient transporters, and the effect of pain on job performance. Methods Based on semi-structured interviews, we conducted a cross-sectional study on Jordanian female hospital workers between January and July, 2017. Results We included 209 participants with a mean age of 35.57 ± 8 years from four Jordanian medical centers. Nurses have significantly higher frequency of LBP (82.5%; p = 0.05) compared to both office workers (67.5%) and patient transporters (68.6%). The mean difference in pain score using Visual Analogue Scale (VAS) after treatment varied significantly (p = 0.003), since it was 28.2 (±35.4) for office workers, compared to 22.8 (±26.5) for nurses and 6.5 (±33.7) for patient transporters. A higher frequency of nurses reported that LBP affected their job performance (64.9%; p = 0.013), and 43.3% of them reported having previous sick leaves due to LBP (p = 0.008). Conclusions LBP is common among female hospital workers, with significantly higher prevalence among female nurses when compared to other female hospital staff.
bibliographic citation: Al-Hadidi et al. (2020) The prevalence of low back pain among female hospital staff at childbearing age. PeerJ 8:e9199 https://doi.org/10.7717/peerj.9199
date submitted: 2019-09-20
date accepted: 2020-04-24
issued: 2020-05-15
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Al-Hadidi
  given name: Fadi
author list: Agent
  family name: Bsisu
  given name: Isam
author list: Agent
  family name: Haddad
  given name: Bassem
author list: Agent
  family name: AlRyalat
  given name: Saif Aldeen
author list: Agent
  family name: Shaban
  given name: Mamoun
author list: Agent
  family name: Matani
  given name: Nada
author list: Agent
  family name: Dehidi
  given name: Sondos
author list: Agent
  family name: Khater
  given name: Yasmeen
author list: Agent
  family name: Shahrouri
  given name: Rana
author list: Agent
  family name: Al Muzayen
  given name: Tasnim
author list: Agent
  family name: Al Hawamdeh
  given name: Hashem
doi: 10.7717/peerj.9199
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-05-15
copyright: © 2020 Al-Hadidi et al.
attribution name: Al-Hadidi et al.

fRNAkenseq: a fully powered-by-CyVerse cloud integrated RNA-sequencing analysis tool
type: item
type: AcademicArticle
description: Background Decreasing costs make RNA sequencing technologies increasingly affordable for biologists. However, many researchers who can now afford sequencing lack access to resources necessary for downstream analysis. This means that even as algorithms to process RNA-Seq data improve, many biologists still struggle to manage the sheer volume of data produced by next generation sequencing (NGS) technologies. Scalable bioinformatics tools that exploit multiple platforms are needed to democratize bioinformatics resources in the sequencing era. This is essential for equipping many research groups in the life sciences with the tools to process the increasingly unwieldy datasets they produce. Methods One strategy to address this challenge is to develop a modern generation of sequence analysis tools capable of seamless data sharing and communication. Such tools will provide interoperability through offerings of interlinked resources. Systems of interlinked, scalable resources, which often incorporate cloud data storage, are broadly referred to as cyberinfrastructure. Cyberinfrastructure integrated tools will help researchers to robustly analyze large scale datasets by efficiently sharing data burdens across a distributed architecture. Additionally, interoperability will allow emerging tools to cross-adapt features of existing tools. It is important that these tools are designed to be easy to use for biologists. Results We introduce fRNAkenseq, a powered-by-CyVerse RNA sequencing analysis tool that exhibits interoperability with other resources and meets the needs of biologists for comprehensive, easy to use RNA sequencing analysis. fRNAkenseq leverages a complex set of Application Programming Interfaces (APIs) associated with the NSF-funded cyberinfrastructure project, CyVerse, to execute FASTQ-to-differential expression RNA-Seq analyses. Integrating across bioinformatics platforms, fRNAkenseq also exploits cloud integration and cross-talk with another CyVerse associated to…
format: application/pdf
format: text/html
creator: Allen Hubbard
creator: Matthew Bomhoff
creator: Carl J. Schmidt
subject: Bioinformatics
subject: Computational Biology
subject: Genomics
description: doi:10.7717/peerj.8592
publisher: PeerJ Inc.
rights: © 2020 Hubbard et al.
abstract: Background Decreasing costs make RNA sequencing technologies increasingly affordable for biologists. However, many researchers who can now afford sequencing lack access to resources necessary for downstream analysis. This means that even as algorithms to process RNA-Seq data improve, many biologists still struggle to manage the sheer volume of data produced by next generation sequencing (NGS) technologies. Scalable bioinformatics tools that exploit multiple platforms are needed to democratize bioinformatics resources in the sequencing era. This is essential for equipping many research groups in the life sciences with the tools to process the increasingly unwieldy datasets they produce. Methods One strategy to address this challenge is to develop a modern generation of sequence analysis tools capable of seamless data sharing and communication. Such tools will provide interoperability through offerings of interlinked resources. Systems of interlinked, scalable resources, which often incorporate cloud data storage, are broadly referred to as cyberinfrastructure. Cyberinfrastructure integrated tools will help researchers to robustly analyze large scale datasets by efficiently sharing data burdens across a distributed architecture. Additionally, interoperability will allow emerging tools to cross-adapt features of existing tools. It is important that these tools are designed to be easy to use for biologists. Results We introduce fRNAkenseq, a powered-by-CyVerse RNA sequencing analysis tool that exhibits interoperability with other resources and meets the needs of biologists for comprehensive, easy to use RNA sequencing analysis. fRNAkenseq leverages a complex set of Application Programming Interfaces (APIs) associated with the NSF-funded cyberinfrastructure project, CyVerse, to execute FASTQ-to-differential expression RNA-Seq analyses. Integrating across bioinformatics platforms, fRNAkenseq also exploits cloud integration and cross-talk with another CyVerse associated to…
bibliographic citation: Hubbard et al. (2020) fRNAkenseq: a fully powered-by-CyVerse cloud integrated RNA-sequencing analysis tool. PeerJ 8:e8592 https://doi.org/10.7717/peerj.8592
date submitted: 2019-04-11
date accepted: 2020-01-18
issued: 2020-05-14
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Hubbard
  given name: Allen
author list: Agent
  family name: Bomhoff
  given name: Matthew
author list: Agent
  family name: Schmidt
  given name: Carl J.
doi: 10.7717/peerj.8592
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-05-14
copyright: © 2020 Hubbard et al.
attribution name: Hubbard et al.

Transcriptomic changes across the life cycle of Trypanosoma cruzi II
type: item
type: AcademicArticle
description: Trypanosoma cruzi is a flagellated protozoan that causes Chagas disease; it presents a complex life cycle comprising four morphological stages: epimastigote (EP), metacyclic trypomastigote (MT), cell-derived trypomastigote (CDT) and amastigote (AM). Previous transcriptomic studies on three stages (EPs, CDTs and AMs) have demonstrated differences in gene expressions among them; however, to the best of our knowledge, no studies have reported on gene expressions in MTs. Therefore, the present study compared differentially expressed genes (DEGs), and signaling pathway reconstruction in EPs, MTs, AMs and CDTs. The results revealed differences in gene expressions in the stages evaluated; these differences were greater between MTs and AMs-PTs. The signaling pathway that presented the highest number of DEGs in all the stages was associated with ribosomes protein profiles, whereas the other related pathways activated were processes related to energy metabolism from glucose, amino acid metabolism, or RNA regulation. However, the role of autophagy in the entire life cycle of T. cruzi and the presence of processes such as meiosis and homologous recombination in MTs (where the expressions of SPO11 and Rad51 plays a role) are crucial. These findings represent an important step towards the full understanding of the molecular basis during the life cycle of T. cruzi.
format: application/pdf
format: text/html
creator: Lissa Cruz-Saavedra
creator: Gustavo A. Vallejo
creator: Felipe Guhl
creator: Juan David Ramírez
subject: Genomics
subject: Microbiology
subject: Parasitology
description: doi:10.7717/peerj.8947
publisher: PeerJ Inc.
rights: © 2020 Cruz-Saavedra et al.
abstract: Trypanosoma cruzi is a flagellated protozoan that causes Chagas disease; it presents a complex life cycle comprising four morphological stages: epimastigote (EP), metacyclic trypomastigote (MT), cell-derived trypomastigote (CDT) and amastigote (AM). Previous transcriptomic studies on three stages (EPs, CDTs and AMs) have demonstrated differences in gene expressions among them; however, to the best of our knowledge, no studies have reported on gene expressions in MTs. Therefore, the present study compared differentially expressed genes (DEGs), and signaling pathway reconstruction in EPs, MTs, AMs and CDTs. The results revealed differences in gene expressions in the stages evaluated; these differences were greater between MTs and AMs-PTs. The signaling pathway that presented the highest number of DEGs in all the stages was associated with ribosomes protein profiles, whereas the other related pathways activated were processes related to energy metabolism from glucose, amino acid metabolism, or RNA regulation. However, the role of autophagy in the entire life cycle of T. cruzi and the presence of processes such as meiosis and homologous recombination in MTs (where the expressions of SPO11 and Rad51 plays a role) are crucial. These findings represent an important step towards the full understanding of the molecular basis during the life cycle of T. cruzi.
bibliographic citation: Cruz-Saavedra et al. (2020) Transcriptomic changes across the life cycle of Trypanosoma cruzi II. PeerJ 8:e8947 https://doi.org/10.7717/peerj.8947
date submitted: 2019-11-22
date accepted: 2020-03-19
issued: 2020-05-14
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Cruz-Saavedra
  given name: Lissa
author list: Agent
  family name: Vallejo
  given name: Gustavo A.
author list: Agent
  family name: Guhl
  given name: Felipe
author list: Agent
  family name: Ramírez
  given name: Juan David
doi: 10.7717/peerj.8947
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-05-14
copyright: © 2020 Cruz-Saavedra et al.
attribution name: Cruz-Saavedra et al.

An interaction mechanism for the maintenance of fission–fusion dynamics under different individual densities
type: item
type: AcademicArticle
description: Animals often show high consistency in their social organisation despite facing changing environmental conditions. Especially in shoaling fish, fission–fusion dynamics that describe for which periods individuals are solitary or social have been found to remain unaltered even when density changed. This compensatory ability is assumed to be an adaptation towards constant predation pressure, but the mechanism through which individuals can actively compensate for density changes is yet unknown. The aim of the current study is to identify behavioural patterns that enable this active compensation. We compared the fission–fusion dynamics of two populations of the live-bearing Atlantic molly (Poecilia mexicana) that live in adjacent habitats with very different predator regimes: cave mollies that inhabit a low-predation environment inside a sulfidic cave with a low density of predatory water bugs (Belostoma sp.), and mollies that live directly outside the cave (henceforth called “surface” mollies) in a high-predation environment. We analysed their fission–fusion dynamics under two different fish densities of 12 and 6 fish per 0.36 m2. As expected, surface mollies spent more time being social than cave mollies, and this difference in social time was a result of surface mollies being less likely to discontinue social contact (once they had a social partner) and being more likely to resume social contact (once alone) than cave mollies. Interestingly, surface mollies were also less likely to switch among social partners than cave mollies. A random walk simulation predicted each population to show reduced social encounters in the low density treatment. While cave mollies largely followed this prediction, surface mollies maintained their interaction probabilities even at low density. Surface mollies achieved this by a reduction in the size of a convex polygon formed by the group as density decreased. This may allow them to largely maintain their fission–fusion dynamics while stil…
format: application/pdf
format: text/html
creator: David Bierbach
creator: Stefan Krause
creator: Pawel Romanczuk
creator: Juliane Lukas
creator: Lenin Arias-Rodriguez
creator: Jens Krause
subject: Animal Behavior
subject: Zoology
subject: Freshwater Biology
description: doi:10.7717/peerj.8974
publisher: PeerJ Inc.
rights: © 2020 Bierbach et al.
abstract: Animals often show high consistency in their social organisation despite facing changing environmental conditions. Especially in shoaling fish, fission–fusion dynamics that describe for which periods individuals are solitary or social have been found to remain unaltered even when density changed. This compensatory ability is assumed to be an adaptation towards constant predation pressure, but the mechanism through which individuals can actively compensate for density changes is yet unknown. The aim of the current study is to identify behavioural patterns that enable this active compensation. We compared the fission–fusion dynamics of two populations of the live-bearing Atlantic molly (Poecilia mexicana) that live in adjacent habitats with very different predator regimes: cave mollies that inhabit a low-predation environment inside a sulfidic cave with a low density of predatory water bugs (Belostoma sp.), and mollies that live directly outside the cave (henceforth called “surface” mollies) in a high-predation environment. We analysed their fission–fusion dynamics under two different fish densities of 12 and 6 fish per 0.36 m2. As expected, surface mollies spent more time being social than cave mollies, and this difference in social time was a result of surface mollies being less likely to discontinue social contact (once they had a social partner) and being more likely to resume social contact (once alone) than cave mollies. Interestingly, surface mollies were also less likely to switch among social partners than cave mollies. A random walk simulation predicted each population to show reduced social encounters in the low density treatment. While cave mollies largely followed this prediction, surface mollies maintained their interaction probabilities even at low density. Surface mollies achieved this by a reduction in the size of a convex polygon formed by the group as density decreased. This may allow them to largely maintain their fission–fusion dynamics while stil…
bibliographic citation: Bierbach et al. (2020) An interaction mechanism for the maintenance of fission–fusion dynamics under different individual densities. PeerJ 8:e8974 https://doi.org/10.7717/peerj.8974
date submitted: 2019-01-17
date accepted: 2020-03-24
issued: 2020-05-14
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Bierbach
  given name: David
author list: Agent
  family name: Krause
  given name: Stefan
author list: Agent
  family name: Romanczuk
  given name: Pawel
author list: Agent
  family name: Lukas
  given name: Juliane
author list: Agent
  family name: Arias-Rodriguez
  given name: Lenin
author list: Agent
  family name: Krause
  given name: Jens
doi: 10.7717/peerj.8974
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-05-14
copyright: ©2020 Bierbach et al.
attribution name: Bierbach et al.

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