PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
items: Antibodies to Bordetella pertussis antigens in maternal and cord blood pairs: a Thai cohort study
items: https://peerj.com/articles/4012
items: Modus operandi and affect in Sweden: the Swedish version of the Regulatory Mode Questionnaire
items: I-ATAC: interactive pipeline for the management and pre-processing of ATAC-seq samples
items: Assessment of brain functional connectome alternations and correlation with depression and anxiety in major depressive disorders
items: Morphological convergence in ‘river dolphin’ skulls
items: Diversity of bacterial communities on the facial skin of different age-group Thai males
items: Development of medical informatics in China over the past 30 years from a conference perspective and a Sino-American comparison
items: Genome-wide survey of single-nucleotide polymorphisms reveals fine-scale population structure and signs of selection in the threatened Caribbean elkhorn coral, Acropora palmata
items: The ability of laying pullets to negotiate two ramp designs as measured by bird preference and behaviour

Antibodies to Bordetella pertussis antigens in maternal and cord blood pairs: a Thai cohort study
type: item
type: AcademicArticle
description: Background Pertussis is a vaccine-preventable disease, yet an increasing incidence of pertussis occurs in many countries. Thailand has a long-standing pertussis vaccination policy, therefore most expectant mothers today had received vaccines as children. The resurgence of pertussis among Thai infants in recent years led us to examine the pre-existing antibodies to Bordetella pertussis antigens in a cohort of 90 pregnant women. Methods We evaluated the IgG to the Pertussis toxin (PT), filamentous hemagglutinin (FHA) and pertactin (PRN) in maternal and cord blood sera using commercial enzyme-linked immunosorbent assays (ELISA). Results When values of >10 IU/ml were accepted as potential protective concentrations, we found that the percentages of unprotected infants were 73.3%, 43.3% and 75.5% for anti-PT, anti-FHA and anti-PRN IgG, respectively. Discussion These results may explain the susceptibility for pertussis among newborn infants in Thailand and support the requirement for a pertussis booster vaccine during pregnancy, which may contribute to the passive seroprotection among newborns during the first months of life.
format: application/pdf
format: text/html
creator: Nasamon Wanlapakorn
creator: Thanunrat Thongmee
creator: Preeyaporn Vichaiwattana
creator: Elke Leuridan
creator: Sompong Vongpunsawad
creator: Yong Poovorawan
subject: Immunology
subject: Infectious Diseases
subject: Women's Health
description: doi:10.7717/peerj.4043
publisher: PeerJ Inc.
rights: © 2017 Wanlapakorn et al.
abstract: Background Pertussis is a vaccine-preventable disease, yet an increasing incidence of pertussis occurs in many countries. Thailand has a long-standing pertussis vaccination policy, therefore most expectant mothers today had received vaccines as children. The resurgence of pertussis among Thai infants in recent years led us to examine the pre-existing antibodies to Bordetella pertussis antigens in a cohort of 90 pregnant women. Methods We evaluated the IgG to the Pertussis toxin (PT), filamentous hemagglutinin (FHA) and pertactin (PRN) in maternal and cord blood sera using commercial enzyme-linked immunosorbent assays (ELISA). Results When values of >10 IU/ml were accepted as potential protective concentrations, we found that the percentages of unprotected infants were 73.3%, 43.3% and 75.5% for anti-PT, anti-FHA and anti-PRN IgG, respectively. Discussion These results may explain the susceptibility for pertussis among newborn infants in Thailand and support the requirement for a pertussis booster vaccine during pregnancy, which may contribute to the passive seroprotection among newborns during the first months of life.
bibliographic citation: Wanlapakorn et al. (2017) Antibodies to Bordetella pertussis antigens in maternal and cord blood pairs: a Thai cohort study. PeerJ 5:e4043 https://doi.org/10.7717/peerj.4043
date submitted: 2017-09-26
date accepted: 2017-10-25
issued: 2017-11-23
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Wanlapakorn
  given name: Nasamon
author list: Agent
  family name: Thongmee
  given name: Thanunrat
author list: Agent
  family name: Vichaiwattana
  given name: Preeyaporn
author list: Agent
  family name: Leuridan
  given name: Elke
author list: Agent
  family name: Vongpunsawad
  given name: Sompong
author list: Agent
  family name: Poovorawan
  given name: Yong
doi: 10.7717/peerj.4043
volume: 5
issn: 2167-8359
publication name: PeerJ
publication date: 2017-11-23
copyright: ©2017 Wanlapakorn et al.
attribution name: Wanlapakorn et al.

https://peerj.com/articles/4012
type: item
type: AcademicArticle
title: Morphological and molecular data confirm the transfer of homostylous species in the typically distylous genus Galianthe (Rubiaceae), and the description of the new species Galianthe vasquezii from Peru and Colombia
description: Galianthe (Rubiaceae) is a neotropical genus comprising 50 species divided into two subgenera, Galianthe subgen. Galianthe, with 39 species and Galianthe subgen. Ebelia, with 11 species. The diagnostic features of the genus are: usually erect habit with xylopodium, distylous flowers arranged in lax thyrsoid inflorescences, bifid stigmas, 2-carpellate and longitudinally dehiscent fruits, with dehiscent valves or indehiscent mericarps, plump seeds or complanate with a wing-like strophiole, and pollen with double reticulum, rarely with a simple reticulum. This study focused on two species that were originally described under Diodia due to the occurrence of fruits indehiscent mericarps: Diodia palustris and D. spicata. In the present study, classical taxonomy is combined with molecular analyses. As a result, we propose that both Diodia species belong to Galianthe subgen. Ebelia. The molecular position within Galianthe, based on ITS and ETS sequences, has been supported by the following morphological characters: thyrsoid, spiciform or cymoidal inflorescences, bifid stigmas, pollen grains with a double reticulum, and indehiscent mericarps. However, both species, unlike the remainder of the genus Galianthe, have homostylous flowers, so the presence of this type of flower significantly modifies the generic concept. In this framework, a third homostylous species, Galianthe vasquezii, from the Andean region is also described. Until now, this species remained cryptic under specimens of Galianthe palustris It differs however from the latter by having longer calyx lobes, the presence of dispersed trichomes inside the corolla lobes (vs. glabrous), fruits that are acropetally dehiscent (vs. basipetally dehiscent), and its Andean geographical distribution (vs. Paranaense). Additionally, a lectotype has been chosen for Diodia palustris, Borreria pterophora has been placed under synonymy of Galianthe palustris, and Galianthe boliviana is reported for the first time from Peru. A key o…
format: application/pdf
format: text/html
creator: Javier Elias Florentín
creator: Andrea Alejandra Cabaña Fader
creator: Roberto Manuel Salas
creator: Steven Janssens
creator: Steven Dessein
creator: Elsa Leonor Cabral
subject: Conservation Biology
subject: Plant Science
subject: Taxonomy
description: doi:10.7717/peerj.4012
publisher: PeerJ Inc.
rights: © 2017 Florentín et al.
abstract: Galianthe (Rubiaceae) is a neotropical genus comprising 50 species divided into two subgenera, Galianthe subgen. Galianthe, with 39 species and Galianthe subgen. Ebelia, with 11 species. The diagnostic features of the genus are: usually erect habit with xylopodium, distylous flowers arranged in lax thyrsoid inflorescences, bifid stigmas, 2-carpellate and longitudinally dehiscent fruits, with dehiscent valves or indehiscent mericarps, plump seeds or complanate with a wing-like strophiole, and pollen with double reticulum, rarely with a simple reticulum. This study focused on two species that were originally described under Diodia due to the occurrence of fruits indehiscent mericarps: Diodia palustris and D. spicata. In the present study, classical taxonomy is combined with molecular analyses. As a result, we propose that both Diodia species belong to Galianthe subgen. Ebelia. The molecular position within Galianthe, based on ITS and ETS sequences, has been supported by the following morphological characters: thyrsoid, spiciform or cymoidal inflorescences, bifid stigmas, pollen grains with a double reticulum, and indehiscent mericarps. However, both species, unlike the remainder of the genus Galianthe, have homostylous flowers, so the presence of this type of flower significantly modifies the generic concept. In this framework, a third homostylous species, Galianthe vasquezii, from the Andean region is also described. Until now, this species remained cryptic under specimens of Galianthe palustris It differs however from the latter by having longer calyx lobes, the presence of dispersed trichomes inside the corolla lobes (vs. glabrous), fruits that are acropetally dehiscent (vs. basipetally dehiscent), and its Andean geographical distribution (vs. Paranaense). Additionally, a lectotype has been chosen for Diodia palustris, Borreria pterophora has been placed under synonymy of Galianthe palustris, and Galianthe boliviana is reported for the first time from Peru. A key o…
bibliographic citation: Florentín et al. (2017) Morphological and molecular data confirm the transfer of homostylous species in the typically distylous genus Galianthe (Rubiaceae), and the description of the new species Galianthe vasquezii from Peru and Colombia. PeerJ 5:e4012 https://doi.org/10.7717/peerj.4012
date submitted: 2017-06-10
date accepted: 2017-10-19
issued: 2017-11-23
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Florentín
  given name: Javier Elias
author list: Agent
  family name: Cabaña Fader
  given name: Andrea Alejandra
author list: Agent
  family name: Salas
  given name: Roberto Manuel
author list: Agent
  family name: Janssens
  given name: Steven
author list: Agent
  family name: Dessein
  given name: Steven
author list: Agent
  family name: Cabral
  given name: Elsa Leonor
doi: 10.7717/peerj.4012
volume: 5
issn: 2167-8359
publication name: PeerJ
publication date: 2017-11-23
copyright: ©2017 Florentín et al.
attribution name: Florentín et al.

Modus operandi and affect in Sweden: the Swedish version of the Regulatory Mode Questionnaire
type: item
type: AcademicArticle
description: Background The Regulatory Mode Questionnaire (RMQ) is the most used and internationally well-known instrument for the measurement of individual differences in the two self-regulatory modes: locomotion (i.e., the aspect of self-regulation that is concerned with movement from state to state) and assessment (i.e., the comparative aspect of self-regulation). The aim of the present study was to verify the independence of the two regulatory modes, as postulated by the Regulatory Mode Theory (Kruglanski et al., 2000), and the psychometric properties of the RMQ in the Swedish context. Furthermore, we investigated the relationship between regulatory modes (locomotion and assessment) and affective well-being (i.e., positive affect and negative affect). Method A total of 655 university and high school students in the West of Sweden (males = 408 females = 242, and five participants who didn’t report their gender; agemean = 21.93 ± 6.51) responded to the RMQ and the Positive Affect Negative Affect Schedule. We conducted two confirmatory factor analyses using structural equation modeling (SEM). A third SEM was conducted to test the relationship between locomotion and assessment to positive affect and negative affect. Results The first analyses confirmed the unidimensional factor structure of locomotion and assessment and both scales showed good reliability. The assessment scale, however, was modified by dropping item 10 (“I don’t spend much time thinking about ways others could improve themselves”.) because it showed low loading (.07, p = .115). Furthermore, the effect of locomotion on positive affect was stronger than the effect of assessment on positive affect (Z = −15.16, p < .001), while the effect of assessment on negative affect was stronger than the effect of locomotion on negative affect (Z = 10.73, p < .001). Conclusion The factor structure of the Swedish version of the RMQ is, as Regulatory Mode Theory suggests, unidimensional and it showed good reliability. The scales …
format: application/pdf
format: text/html
creator: Clara Amato
creator: Ali Al Nima
creator: Marko Mihailovic
creator: Danilo Garcia
subject: Psychiatry and Psychology
subject: Public Health
description: doi:10.7717/peerj.4092
publisher: PeerJ Inc.
rights: © 2017 Amato et al.
abstract: Background The Regulatory Mode Questionnaire (RMQ) is the most used and internationally well-known instrument for the measurement of individual differences in the two self-regulatory modes: locomotion (i.e., the aspect of self-regulation that is concerned with movement from state to state) and assessment (i.e., the comparative aspect of self-regulation). The aim of the present study was to verify the independence of the two regulatory modes, as postulated by the Regulatory Mode Theory (Kruglanski et al., 2000), and the psychometric properties of the RMQ in the Swedish context. Furthermore, we investigated the relationship between regulatory modes (locomotion and assessment) and affective well-being (i.e., positive affect and negative affect). Method A total of 655 university and high school students in the West of Sweden (males = 408 females = 242, and five participants who didn’t report their gender; agemean = 21.93 ± 6.51) responded to the RMQ and the Positive Affect Negative Affect Schedule. We conducted two confirmatory factor analyses using structural equation modeling (SEM). A third SEM was conducted to test the relationship between locomotion and assessment to positive affect and negative affect. Results The first analyses confirmed the unidimensional factor structure of locomotion and assessment and both scales showed good reliability. The assessment scale, however, was modified by dropping item 10 (“I don’t spend much time thinking about ways others could improve themselves”.) because it showed low loading (.07, p = .115). Furthermore, the effect of locomotion on positive affect was stronger than the effect of assessment on positive affect (Z = −15.16, p < .001), while the effect of assessment on negative affect was stronger than the effect of locomotion on negative affect (Z = 10.73, p < .001). Conclusion The factor structure of the Swedish version of the RMQ is, as Regulatory Mode Theory suggests, unidimensional and it showed good reliability. The scales …
bibliographic citation: Amato et al. (2017) Modus operandi and affect in Sweden: the Swedish version of the Regulatory Mode Questionnaire. PeerJ 5:e4092 https://doi.org/10.7717/peerj.4092
date submitted: 2017-08-07
date accepted: 2017-11-04
issued: 2017-11-22
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Amato
  given name: Clara
author list: Agent
  family name: Nima
  given name: Ali Al
author list: Agent
  family name: Mihailovic
  given name: Marko
author list: Agent
  family name: Garcia
  given name: Danilo
doi: 10.7717/peerj.4092
volume: 5
issn: 2167-8359
publication name: PeerJ
publication date: 2017-11-22
copyright: ©2017 Amato et al.
attribution name: Amato et al.

I-ATAC: interactive pipeline for the management and pre-processing of ATAC-seq samples
type: item
type: AcademicArticle
description: Assay for Transposase Accessible Chromatin (ATAC-seq) is an open chromatin profiling assay that is adapted to interrogate chromatin accessibility from small cell numbers. ATAC-seq surmounted a major technical barrier and enabled epigenome profiling of clinical samples. With this advancement in technology, we are now accumulating ATAC-seq samples from clinical samples at an unprecedented rate. These epigenomic profiles hold the key to uncovering how transcriptional programs are established in diverse human cells and are disrupted by genetic or environmental factors. Thus, the barrier to deriving important clinical insights from clinical epigenomic samples is no longer one of data generation but of data analysis. Specifically, we are still missing easy-to-use software tools that will enable non-computational scientists to analyze their own ATAC-seq samples. To facilitate systematic pre-processing and management of ATAC-seq samples, we developed an interactive, cross-platform, user-friendly and customized desktop application: interactive-ATAC (I-ATAC). I-ATAC integrates command-line data processing tools (FASTQC, Trimmomatic, BWA, Picard, ATAC_BAM_shiftrt_gappedAlign.pl, Bedtools and Macs2) into an easy-to-use platform with user interface to automatically pre-process ATAC-seq samples with parallelized and customizable pipelines. Its performance has been tested using public ATAC-seq datasets in GM12878 and CD4+T cells and a feature-based comparison is performed with some available interactive LIMS (Galaxy, SMITH, SeqBench, Wasp, NG6, openBIS). I-ATAC is designed to empower non-computational scientists to process their own datasets and to break to exclusivity of data analyses to computational scientists. Additionally, I-ATAC is capable of processing WGS and ChIP-seq samples, and can be customized by the user for one-independent or multiple-sequential operations.
format: application/pdf
format: text/html
creator: Zeeshan Ahmed
creator: Duygu Ucar
subject: Bioinformatics
subject: Computational Biology
subject: Genomics
subject: Human-Computer Interaction
subject: Computational Science
description: doi:10.7717/peerj.4040
publisher: PeerJ Inc.
rights: © 2017 Ahmed and Ucar
abstract: Assay for Transposase Accessible Chromatin (ATAC-seq) is an open chromatin profiling assay that is adapted to interrogate chromatin accessibility from small cell numbers. ATAC-seq surmounted a major technical barrier and enabled epigenome profiling of clinical samples. With this advancement in technology, we are now accumulating ATAC-seq samples from clinical samples at an unprecedented rate. These epigenomic profiles hold the key to uncovering how transcriptional programs are established in diverse human cells and are disrupted by genetic or environmental factors. Thus, the barrier to deriving important clinical insights from clinical epigenomic samples is no longer one of data generation but of data analysis. Specifically, we are still missing easy-to-use software tools that will enable non-computational scientists to analyze their own ATAC-seq samples. To facilitate systematic pre-processing and management of ATAC-seq samples, we developed an interactive, cross-platform, user-friendly and customized desktop application: interactive-ATAC (I-ATAC). I-ATAC integrates command-line data processing tools (FASTQC, Trimmomatic, BWA, Picard, ATAC_BAM_shiftrt_gappedAlign.pl, Bedtools and Macs2) into an easy-to-use platform with user interface to automatically pre-process ATAC-seq samples with parallelized and customizable pipelines. Its performance has been tested using public ATAC-seq datasets in GM12878 and CD4+T cells and a feature-based comparison is performed with some available interactive LIMS (Galaxy, SMITH, SeqBench, Wasp, NG6, openBIS). I-ATAC is designed to empower non-computational scientists to process their own datasets and to break to exclusivity of data analyses to computational scientists. Additionally, I-ATAC is capable of processing WGS and ChIP-seq samples, and can be customized by the user for one-independent or multiple-sequential operations.
bibliographic citation: Ahmed et al. (2017) I-ATAC: interactive pipeline for the management and pre-processing of ATAC-seq samples. PeerJ 5:e4040 https://doi.org/10.7717/peerj.4040
date submitted: 2017-04-21
date accepted: 2017-10-25
issued: 2017-11-22
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Ahmed
  given name: Zeeshan
author list: Agent
  family name: Ucar
  given name: Duygu
doi: 10.7717/peerj.4040
volume: 5
issn: 2167-8359
publication name: PeerJ
publication date: 2017-11-22
copyright: ©2017 Ahmed and Ucar
attribution name: Ahmed and Ucar

Assessment of brain functional connectome alternations and correlation with depression and anxiety in major depressive disorders
type: item
type: AcademicArticle
description: Major depressive disorder (MDD) is highly prevalent, recurrent, and associated with functional impairment, morbidity, and mortality. Herein, we aimed to identify disruptions in functional connectomics among subjects with MDD by using resting-state functional magnetic resonance imaging (rs-fMRI). Sixteen subjects with MDD and thirty health controls completed resting-state fMRI scans and clinical assessments (e.g., Hamilton Depression Rating Scale (HAMD) and Hospital Anxiety and Depression Scale (HADS)). We found higher amplitude of low frequency fluctuations (ALFF) bilaterally in the hippocampus and amygdala among MDD subjects when compared to healthy controls. Using graph theoretical analysis, we found decreased clustering coefficient, local efficiency, and transitivity in the MDD patients. Our findings suggest a potential biomarker for differentiating individuals with MDD from individuals without MDD.
format: application/pdf
format: text/html
creator: Vincent Chin-Hung Chen
creator: Chao-Yu Shen
creator: Sophie Hsin-Yi Liang
creator: Zhen-Hui Li
creator: Ming-Hong Hsieh
creator: Yeu-Sheng Tyan
creator: Mong-Liang Lu
creator: Yena Lee
creator: Roger S. McIntyre
creator: Jun-Cheng Weng
subject: Neuroscience
subject: Cognitive Disorders
subject: Neurology
description: doi:10.7717/peerj.3147
publisher: PeerJ Inc.
rights: © 2017 Chen et al.
abstract: Major depressive disorder (MDD) is highly prevalent, recurrent, and associated with functional impairment, morbidity, and mortality. Herein, we aimed to identify disruptions in functional connectomics among subjects with MDD by using resting-state functional magnetic resonance imaging (rs-fMRI). Sixteen subjects with MDD and thirty health controls completed resting-state fMRI scans and clinical assessments (e.g., Hamilton Depression Rating Scale (HAMD) and Hospital Anxiety and Depression Scale (HADS)). We found higher amplitude of low frequency fluctuations (ALFF) bilaterally in the hippocampus and amygdala among MDD subjects when compared to healthy controls. Using graph theoretical analysis, we found decreased clustering coefficient, local efficiency, and transitivity in the MDD patients. Our findings suggest a potential biomarker for differentiating individuals with MDD from individuals without MDD.
bibliographic citation: Chen et al. (2017) Assessment of brain functional connectome alternations and correlation with depression and anxiety in major depressive disorders. PeerJ 5:e3147 https://doi.org/10.7717/peerj.3147
date submitted: 2016-12-18
date accepted: 2017-03-05
issued: 2017-11-22
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Chen
  given name: Vincent Chin-Hung
author list: Agent
  family name: Shen
  given name: Chao-Yu
author list: Agent
  family name: Liang
  given name: Sophie Hsin-Yi
author list: Agent
  family name: Li
  given name: Zhen-Hui
author list: Agent
  family name: Hsieh
  given name: Ming-Hong
author list: Agent
  family name: Tyan
  given name: Yeu-Sheng
author list: Agent
  family name: Lu
  given name: Mong-Liang
author list: Agent
  family name: Lee
  given name: Yena
author list: Agent
  family name: McIntyre
  given name: Roger S.
author list: Agent
  family name: Weng
  given name: Jun-Cheng
doi: 10.7717/peerj.3147
volume: 5
issn: 2167-8359
publication name: PeerJ
publication date: 2017-11-22
copyright: ©2017 Chen et al.
attribution name: Chen et al.

Morphological convergence in ‘river dolphin’ skulls
type: item
type: AcademicArticle
description: Convergent evolution can provide insights into the predictability of, and constraints on, the evolution of biodiversity. One striking example of convergence is seen in the ‘river dolphins’. The four dolphin genera that make up the ‘river dolphins’ (Inia geoffrensis, Pontoporia blainvillei, Platanista gangetica and Lipotes vexillifer) do not represent a single monophyletic group, despite being very similar in morphology. This has led many to using the ‘river dolphins’ as an example of convergent evolution. We investigate whether the skulls of the four ‘river dolphin’ genera are convergent when compared to other toothed dolphin taxa in addition to identifying convergent cranial and mandibular features. We use geometric morphometrics to uncover shape variation in the skulls of the ‘river dolphins’ and then apply a number of phylogenetic techniques to test for convergence. We find significant convergence in the skull morphology of the ‘river dolphins’. The four genera seem to have evolved similar skull shapes, leading to a convergent morphotype characterised by elongation of skull features. The cause of this morphological convergence remains unclear. However, the features we uncover as convergent, in particular elongation of the rostrum, support hypotheses of shared feeding mode or diet and thus provide the foundation for future work into convergence within the Odontoceti.
format: application/pdf
format: text/html
creator: Charlotte E. Page
creator: Natalie Cooper
subject: Evolutionary Studies
subject: Taxonomy
subject: Zoology
description: doi:10.7717/peerj.4090
publisher: PeerJ Inc.
rights: © 2017 Page and Cooper
abstract: Convergent evolution can provide insights into the predictability of, and constraints on, the evolution of biodiversity. One striking example of convergence is seen in the ‘river dolphins’. The four dolphin genera that make up the ‘river dolphins’ (Inia geoffrensis, Pontoporia blainvillei, Platanista gangetica and Lipotes vexillifer) do not represent a single monophyletic group, despite being very similar in morphology. This has led many to using the ‘river dolphins’ as an example of convergent evolution. We investigate whether the skulls of the four ‘river dolphin’ genera are convergent when compared to other toothed dolphin taxa in addition to identifying convergent cranial and mandibular features. We use geometric morphometrics to uncover shape variation in the skulls of the ‘river dolphins’ and then apply a number of phylogenetic techniques to test for convergence. We find significant convergence in the skull morphology of the ‘river dolphins’. The four genera seem to have evolved similar skull shapes, leading to a convergent morphotype characterised by elongation of skull features. The cause of this morphological convergence remains unclear. However, the features we uncover as convergent, in particular elongation of the rostrum, support hypotheses of shared feeding mode or diet and thus provide the foundation for future work into convergence within the Odontoceti.
bibliographic citation: Page et al. (2017) Morphological convergence in ‘river dolphin’ skulls. PeerJ 5:e4090 https://doi.org/10.7717/peerj.4090
date submitted: 2017-09-01
date accepted: 2017-11-02
issued: 2017-11-21
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Page
  given name: Charlotte E.
author list: Agent
  family name: Cooper
  given name: Natalie
doi: 10.7717/peerj.4090
volume: 5
issn: 2167-8359
publication name: PeerJ
publication date: 2017-11-21
copyright: ©2017 Page and Cooper
attribution name: Page and Cooper

Diversity of bacterial communities on the facial skin of different age-group Thai males
type: item
type: AcademicArticle
description: Background Skin microbiome varies from person to person due to a combination of various factors, including age, biogeography, sex, cosmetics and genetics. Many skin disorders appear to be related to the resident microflora, yet databases of facial skin microbiome of many biogeographies, including Thai, are limited. Methods Metagenomics derived B-RISA and 16S rRNA gene sequencing was utilized to identify the culture-independent bacterial diversity on Thai male faces (cheek and forehead areas). Skin samples were categorized (grouped) into (i) normal (teenage.hea) and (ii) acne-prone (teenage.acn) young adults, and normal (iii) middle-aged (middle.hea) and (iv) elderly (elderly.hea) adults. Results The 16S rRNA gene sequencing was successful as the sequencing depth had an estimated >98% genus coverage of the true community. The major diversity was found between the young and elderly adults in both cheek and forehead areas, followed by that between normal and acne young adults. Detection of representative characteristics indicated that bacteria from the order Rhizobiales, genera Sphingomonas and Pseudoalteromonas, distinguished the elderly.hea microbiota, along the clinical features of wrinkles and pores. Prediction of the metabolic potential revealed reduced metabolic pathways involved in replication and repair, nucleotide metabolism and genetic translation in the elderly.hea compared with that in the teenage.hea. For young adults, some unique compositions such as abundance of Propionibacterium acnes and Staphylococcus epidermidis, with a minor diversity between normal and acne skins, were detected. The metabolic potentials of the acne vs. normal young adults showed that teenage.acn was low in many cellular processes (e.g., cell motility and environmental adaptation), but high in carbohydrate metabolism, which could support acne growth. Moreover, comparison with the age-matched males from the US (Boulder, Colorado) to gain insight into the diversity across national bio…
format: application/pdf
format: text/html
creator: Alisa Wilantho
creator: Pamornya Deekaew
creator: Chutika Srisuttiyakorn
creator: Sissades Tongsima
creator: Naraporn Somboonna
subject: Microbiology
subject: Dermatology
description: doi:10.7717/peerj.4084
publisher: PeerJ Inc.
rights: © 2017 Wilantho et al.
abstract: Background Skin microbiome varies from person to person due to a combination of various factors, including age, biogeography, sex, cosmetics and genetics. Many skin disorders appear to be related to the resident microflora, yet databases of facial skin microbiome of many biogeographies, including Thai, are limited. Methods Metagenomics derived B-RISA and 16S rRNA gene sequencing was utilized to identify the culture-independent bacterial diversity on Thai male faces (cheek and forehead areas). Skin samples were categorized (grouped) into (i) normal (teenage.hea) and (ii) acne-prone (teenage.acn) young adults, and normal (iii) middle-aged (middle.hea) and (iv) elderly (elderly.hea) adults. Results The 16S rRNA gene sequencing was successful as the sequencing depth had an estimated >98% genus coverage of the true community. The major diversity was found between the young and elderly adults in both cheek and forehead areas, followed by that between normal and acne young adults. Detection of representative characteristics indicated that bacteria from the order Rhizobiales, genera Sphingomonas and Pseudoalteromonas, distinguished the elderly.hea microbiota, along the clinical features of wrinkles and pores. Prediction of the metabolic potential revealed reduced metabolic pathways involved in replication and repair, nucleotide metabolism and genetic translation in the elderly.hea compared with that in the teenage.hea. For young adults, some unique compositions such as abundance of Propionibacterium acnes and Staphylococcus epidermidis, with a minor diversity between normal and acne skins, were detected. The metabolic potentials of the acne vs. normal young adults showed that teenage.acn was low in many cellular processes (e.g., cell motility and environmental adaptation), but high in carbohydrate metabolism, which could support acne growth. Moreover, comparison with the age-matched males from the US (Boulder, Colorado) to gain insight into the diversity across national bio…
bibliographic citation: Wilantho et al. (2017) Diversity of bacterial communities on the facial skin of different age-group Thai males. PeerJ 5:e4084 https://doi.org/10.7717/peerj.4084
date submitted: 2017-04-08
date accepted: 2017-11-02
issued: 2017-11-21
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Wilantho
  given name: Alisa
author list: Agent
  family name: Deekaew
  given name: Pamornya
author list: Agent
  family name: Srisuttiyakorn
  given name: Chutika
author list: Agent
  family name: Tongsima
  given name: Sissades
author list: Agent
  family name: Somboonna
  given name: Naraporn
doi: 10.7717/peerj.4084
volume: 5
issn: 2167-8359
publication name: PeerJ
publication date: 2017-11-21
copyright: ©2017 Wilantho et al.
attribution name: Wilantho et al.

Development of medical informatics in China over the past 30 years from a conference perspective and a Sino-American comparison
type: item
type: AcademicArticle
description: Background As the world’s second-largest economy, China has launched health reforms for the second time and invested significant funding in medical informatics (MI) since 2010; however, few studies have been conducted on the outcomes of this ambitious cause. Objective This study analyzed the features of major MI meetings held in China and compared them with similar MI conferences in the United States, aiming at informing researchers on the outcomes of MI in China and the US from the professional conference perspective and encouraging greater international cooperation for the advancement of the field of medical informatics in China and, ultimately, the promotion of China’s health reform. Methods Qualitative and quantitative analyses of four MI meetings in China (i.e., CMIAAS, CHINC, CHITEC, and CPMI) and two in the US (i.e., AMIA and HIMSS) were conducted. Furthermore, the size, constituent parts and regional allocation of participants, topics, and fields of research for each meeting were determined and compared. Results From 1985 to 2016, approximately 45,000 individuals attended the CMIAAS and CPMI (academic), CHINC and CHITEC (industry), resulting in 5,085 documented articles. In contrast, in 2015, 38,000 and 3,700 individuals, respectively, attended the American HIMSS (industry) and AMIA (academic) conferences and published 1,926 papers in the latter. Compared to those of HIMSS in 2015, the meeting duration of Chinese industry CHITEC was 3 vs. 5 days, the number of vendors was 100 vs. 1,500+, the number of sub-forums was 10 vs. 250; while compared to those of AMIA, the meeting duration of Chinese CMIAAS was 2 vs. 8 days, the number of vendors was 5 vs. 65+, the number of sub-forums was 4 vs. 26. HIMSS and AMIA were more open, international, and comprehensive in comparison to the aforementioned Chinese conferences. Conclusions The current MI in China can be characterized as “hot in industry application, and cold in academic research.” Taking into consideration the…
format: application/pdf
format: text/html
creator: Jun Liang
creator: Kunyan Wei
creator: Qun Meng
creator: Zhenying Chen
creator: Jiajie Zhang
creator: Jianbo Lei
subject: Bioinformatics
subject: Clinical Trials
subject: Science and Medical Education
description: doi:10.7717/peerj.4082
publisher: PeerJ Inc.
rights: © 2017 Liang et al.
abstract: Background As the world’s second-largest economy, China has launched health reforms for the second time and invested significant funding in medical informatics (MI) since 2010; however, few studies have been conducted on the outcomes of this ambitious cause. Objective This study analyzed the features of major MI meetings held in China and compared them with similar MI conferences in the United States, aiming at informing researchers on the outcomes of MI in China and the US from the professional conference perspective and encouraging greater international cooperation for the advancement of the field of medical informatics in China and, ultimately, the promotion of China’s health reform. Methods Qualitative and quantitative analyses of four MI meetings in China (i.e., CMIAAS, CHINC, CHITEC, and CPMI) and two in the US (i.e., AMIA and HIMSS) were conducted. Furthermore, the size, constituent parts and regional allocation of participants, topics, and fields of research for each meeting were determined and compared. Results From 1985 to 2016, approximately 45,000 individuals attended the CMIAAS and CPMI (academic), CHINC and CHITEC (industry), resulting in 5,085 documented articles. In contrast, in 2015, 38,000 and 3,700 individuals, respectively, attended the American HIMSS (industry) and AMIA (academic) conferences and published 1,926 papers in the latter. Compared to those of HIMSS in 2015, the meeting duration of Chinese industry CHITEC was 3 vs. 5 days, the number of vendors was 100 vs. 1,500+, the number of sub-forums was 10 vs. 250; while compared to those of AMIA, the meeting duration of Chinese CMIAAS was 2 vs. 8 days, the number of vendors was 5 vs. 65+, the number of sub-forums was 4 vs. 26. HIMSS and AMIA were more open, international, and comprehensive in comparison to the aforementioned Chinese conferences. Conclusions The current MI in China can be characterized as “hot in industry application, and cold in academic research.” Taking into consideration the…
bibliographic citation: Liang et al. (2017) Development of medical informatics in China over the past 30 years from a conference perspective and a Sino-American comparison. PeerJ 5:e4082 https://doi.org/10.7717/peerj.4082
date submitted: 2017-08-21
date accepted: 2017-11-01
issued: 2017-11-21
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Liang
  given name: Jun
author list: Agent
  family name: Wei
  given name: Kunyan
author list: Agent
  family name: Meng
  given name: Qun
author list: Agent
  family name: Chen
  given name: Zhenying
author list: Agent
  family name: Zhang
  given name: Jiajie
author list: Agent
  family name: Lei
  given name: Jianbo
doi: 10.7717/peerj.4082
volume: 5
issn: 2167-8359
publication name: PeerJ
publication date: 2017-11-21
copyright: ©2017 Liang et al.
attribution name: Liang et al.

Genome-wide survey of single-nucleotide polymorphisms reveals fine-scale population structure and signs of selection in the threatened Caribbean elkhorn coral, Acropora palmata
type: item
type: AcademicArticle
description: The advent of next-generation sequencing tools has made it possible to conduct fine-scale surveys of population differentiation and genome-wide scans for signatures of selection in non-model organisms. Such surveys are of particular importance in sharply declining coral species, since knowledge of population boundaries and signs of local adaptation can inform restoration and conservation efforts. Here, we use genome-wide surveys of single-nucleotide polymorphisms in the threatened Caribbean elkhorn coral, Acropora palmata, to reveal fine-scale population structure and infer the major barrier to gene flow that separates the eastern and western Caribbean populations between the Bahamas and Puerto Rico. The exact location of this break had been subject to discussion because two previous studies based on microsatellite data had come to differing conclusions. We investigate this contradiction by analyzing an extended set of 11 microsatellite markers including the five previously employed and discovered that one of the original microsatellite loci is apparently under selection. Exclusion of this locus reconciles the results from the SNP and the microsatellite datasets. Scans for outlier loci in the SNP data detected 13 candidate loci under positive selection, however there was no correlation between available environmental parameters and genetic distance. Together, these results suggest that reef restoration efforts should use local sources and utilize existing functional variation among geographic regions in ex situ crossing experiments to improve stress resistance of this species.
format: application/pdf
format: text/html
creator: Meghann K. Devlin-Durante
creator: Iliana B. Baums
subject: Conservation Biology
subject: Genomics
subject: Marine Biology
subject: Climate Change Biology
description: doi:10.7717/peerj.4077
publisher: PeerJ Inc.
rights: © 2017 Devlin-Durante and Baums
abstract: The advent of next-generation sequencing tools has made it possible to conduct fine-scale surveys of population differentiation and genome-wide scans for signatures of selection in non-model organisms. Such surveys are of particular importance in sharply declining coral species, since knowledge of population boundaries and signs of local adaptation can inform restoration and conservation efforts. Here, we use genome-wide surveys of single-nucleotide polymorphisms in the threatened Caribbean elkhorn coral, Acropora palmata, to reveal fine-scale population structure and infer the major barrier to gene flow that separates the eastern and western Caribbean populations between the Bahamas and Puerto Rico. The exact location of this break had been subject to discussion because two previous studies based on microsatellite data had come to differing conclusions. We investigate this contradiction by analyzing an extended set of 11 microsatellite markers including the five previously employed and discovered that one of the original microsatellite loci is apparently under selection. Exclusion of this locus reconciles the results from the SNP and the microsatellite datasets. Scans for outlier loci in the SNP data detected 13 candidate loci under positive selection, however there was no correlation between available environmental parameters and genetic distance. Together, these results suggest that reef restoration efforts should use local sources and utilize existing functional variation among geographic regions in ex situ crossing experiments to improve stress resistance of this species.
bibliographic citation: Devlin-Durante et al. (2017) Genome-wide survey of single-nucleotide polymorphisms reveals fine-scale population structure and signs of selection in the threatened Caribbean elkhorn coral, Acropora palmata. PeerJ 5:e4077 https://doi.org/10.7717/peerj.4077
date submitted: 2017-06-19
date accepted: 2017-10-31
issued: 2017-11-21
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Devlin-Durante
  given name: Meghann K.
author list: Agent
  family name: Baums
  given name: Iliana B.
doi: 10.7717/peerj.4077
volume: 5
issn: 2167-8359
publication name: PeerJ
publication date: 2017-11-21
copyright: ©2017 Devlin-Durante and Baums
attribution name: Devlin-Durante and Baums

The ability of laying pullets to negotiate two ramp designs as measured by bird preference and behaviour
type: item
type: AcademicArticle
description: Background Laying hens are often kept in barn or free-range systems where they must negotiate level changes in the house to access resources. However, collisions and resultant keel fractures are commonplace. Producers sometimes add ramps to make raised areas more accessible but designs vary and very little research has investigated bird preference or behaviour when using different ramp designs, or the effect of ramp design on falls and collisions. Methods Two ramp designs were studied in an experimental setting—a ramp made of plastic poultry slats (grid ramp, GR) and a ramp made of wooden rungs (ladder ramp, LR). Sixty-four young female hens were trained to move to a food reward and this was used to test their behavioural responses when first negotiating the two different ramps during individual tests. Both upward and downward transitions were studied. Ramp preference was also tested using a room that replicated a commercial single-tier system with both types of ramp available. Birds were placed in this room in groups of 16 for three days and their use of the ramps studied. Results A greater percentage of birds successfully completed (reached the reward bowl) on the GR than the LR during both upward (58% vs 37%) and downward (83% vs 73%) transitions, and a smaller percentage of birds made zero attempts to use the GR than the LR (upwards: 13% vs 56%, downwards: 8% vs 26%). When making a downward transition, more hesitation behaviours were seen (head orientations, stepping on the spot, moving away) for the LR. However, more head orientations were seen for the GR during the upward transition. Birds were more likely to abort attempts (an attempt began when a bird placed both feet on the ramp) to move up the GR than the LR. Birds took longer to negotiate the LR than the GR in both directions, and more pauses were seen during a successful upward transition on the LR. Birds were more likely to move down the GR by walking/running whereas birds tended to jump over the entire…
format: application/pdf
format: text/html
creator: Isabelle C. Pettersson
creator: Claire A. Weeks
creator: Kate I. Norman
creator: Christine J. Nicol
subject: Animal Behavior
subject: Zoology
description: doi:10.7717/peerj.4069
publisher: PeerJ Inc.
rights: © 2017 Pettersson et al.
abstract: Background Laying hens are often kept in barn or free-range systems where they must negotiate level changes in the house to access resources. However, collisions and resultant keel fractures are commonplace. Producers sometimes add ramps to make raised areas more accessible but designs vary and very little research has investigated bird preference or behaviour when using different ramp designs, or the effect of ramp design on falls and collisions. Methods Two ramp designs were studied in an experimental setting—a ramp made of plastic poultry slats (grid ramp, GR) and a ramp made of wooden rungs (ladder ramp, LR). Sixty-four young female hens were trained to move to a food reward and this was used to test their behavioural responses when first negotiating the two different ramps during individual tests. Both upward and downward transitions were studied. Ramp preference was also tested using a room that replicated a commercial single-tier system with both types of ramp available. Birds were placed in this room in groups of 16 for three days and their use of the ramps studied. Results A greater percentage of birds successfully completed (reached the reward bowl) on the GR than the LR during both upward (58% vs 37%) and downward (83% vs 73%) transitions, and a smaller percentage of birds made zero attempts to use the GR than the LR (upwards: 13% vs 56%, downwards: 8% vs 26%). When making a downward transition, more hesitation behaviours were seen (head orientations, stepping on the spot, moving away) for the LR. However, more head orientations were seen for the GR during the upward transition. Birds were more likely to abort attempts (an attempt began when a bird placed both feet on the ramp) to move up the GR than the LR. Birds took longer to negotiate the LR than the GR in both directions, and more pauses were seen during a successful upward transition on the LR. Birds were more likely to move down the GR by walking/running whereas birds tended to jump over the entire…
bibliographic citation: Pettersson et al. (2017) The ability of laying pullets to negotiate two ramp designs as measured by bird preference and behaviour. PeerJ 5:e4069 https://doi.org/10.7717/peerj.4069
date submitted: 2017-09-11
date accepted: 2017-10-30
issued: 2017-11-21
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Pettersson
  given name: Isabelle C.
author list: Agent
  family name: Weeks
  given name: Claire A.
author list: Agent
  family name: Norman
  given name: Kate I.
author list: Agent
  family name: Nicol
  given name: Christine J.
doi: 10.7717/peerj.4069
volume: 5
issn: 2167-8359
publication name: PeerJ
publication date: 2017-11-21
copyright: ©2017 Pettersson et al.
attribution name: Pettersson et al.

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