PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
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
items: Levels of detail analysis of microwave scattering from human head models for brain stroke detection
items: Uncovering the relationship and mechanisms of Tartary buckwheat (Fagopyrum tataricum) and Type II diabetes, hypertension, and hyperlipidemia using a network pharmacology approach
items: Transcriptome sequencing reveals high isoform diversity in the ant Formica exsecta
items: The reanalysis of biogeography of the Asian tree frog, Rhacophorus (Anura: Rhacophoridae): geographic shifts and climatic change influenced the dispersal process and diversification

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.

Levels of detail analysis of microwave scattering from human head models for brain stroke detection
type: item
type: AcademicArticle
description: In this paper, we have presented a microwave scattering analysis from multiple human head models. This study incorporates different levels of detail in the human head models and its effect on microwave scattering phenomenon. Two levels of detail are taken into account; (i) Simplified ellipse shaped head model (ii) Anatomically realistic head model, implemented using 2-D geometry. In addition, heterogenic and frequency-dispersive behavior of the brain tissues has also been incorporated in our head models. It is identified during this study that the microwave scattering phenomenon changes significantly once the complexity of head model is increased by incorporating more details using magnetic resonance imaging database. It is also found out that the microwave scattering results match in both types of head model (i.e., geometrically simple and anatomically realistic), once the measurements are made in the structurally simplified regions. However, the results diverge considerably in the complex areas of brain due to the arbitrary shape interface of tissue layers in the anatomically realistic head model. After incorporating various levels of detail, the solution of subject microwave scattering problem and the measurement of transmitted and backscattered signals were obtained using finite element method. Mesh convergence analysis was also performed to achieve error free results with a minimum number of mesh elements and a lesser degree of freedom in the fast computational time. The results were promising and the E-Field values converged for both simple and complex geometrical models. However, the E-Field difference between both types of head model at the same reference point differentiated a lot in terms of magnitude. At complex location, a high difference value of 0.04236 V/m was measured compared to the simple location, where it turned out to be 0.00197 V/m. This study also contributes to provide a comparison analysis between the direct and iterative solvers so as to fi…
format: application/pdf
format: text/html
creator: Awais Munawar Qureshi
creator: Zartasha Mustansar
subject: Bioengineering
subject: Biophysics
subject: Radiology and Medical Imaging
subject: Computational Science
description: doi:10.7717/peerj.4061
publisher: PeerJ Inc.
rights: © 2017 Qureshi and Mustansar
abstract: In this paper, we have presented a microwave scattering analysis from multiple human head models. This study incorporates different levels of detail in the human head models and its effect on microwave scattering phenomenon. Two levels of detail are taken into account; (i) Simplified ellipse shaped head model (ii) Anatomically realistic head model, implemented using 2-D geometry. In addition, heterogenic and frequency-dispersive behavior of the brain tissues has also been incorporated in our head models. It is identified during this study that the microwave scattering phenomenon changes significantly once the complexity of head model is increased by incorporating more details using magnetic resonance imaging database. It is also found out that the microwave scattering results match in both types of head model (i.e., geometrically simple and anatomically realistic), once the measurements are made in the structurally simplified regions. However, the results diverge considerably in the complex areas of brain due to the arbitrary shape interface of tissue layers in the anatomically realistic head model. After incorporating various levels of detail, the solution of subject microwave scattering problem and the measurement of transmitted and backscattered signals were obtained using finite element method. Mesh convergence analysis was also performed to achieve error free results with a minimum number of mesh elements and a lesser degree of freedom in the fast computational time. The results were promising and the E-Field values converged for both simple and complex geometrical models. However, the E-Field difference between both types of head model at the same reference point differentiated a lot in terms of magnitude. At complex location, a high difference value of 0.04236 V/m was measured compared to the simple location, where it turned out to be 0.00197 V/m. This study also contributes to provide a comparison analysis between the direct and iterative solvers so as to fi…
bibliographic citation: Qureshi et al. (2017) Levels of detail analysis of microwave scattering from human head models for brain stroke detection. PeerJ 5:e4061 https://doi.org/10.7717/peerj.4061
date submitted: 2017-06-08
date accepted: 2017-10-28
issued: 2017-11-21
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Qureshi
  given name: Awais Munawar
author list: Agent
  family name: Mustansar
  given name: Zartasha
doi: 10.7717/peerj.4061
volume: 5
issn: 2167-8359
publication name: PeerJ
publication date: 2017-11-21
copyright: © 2017 Qureshi and Mustansar
attribution name: Qureshi and Mustansar

Uncovering the relationship and mechanisms of Tartary buckwheat (Fagopyrum tataricum) and Type II diabetes, hypertension, and hyperlipidemia using a network pharmacology approach
type: item
type: AcademicArticle
description: Background Tartary buckwheat (TB), a crop rich in protein, dietary fiber, and flavonoids, has been reported to have an effect on Type II diabetes (T2D), hypertension (HT), and hyperlipidemia (HL). However, limited information is available about the relationship between Tartary buckwheat and these three diseases. The mechanisms of how TB impacts these diseases are still unclear. Methods In this study, network pharmacology was used to investigate the relationship between the herb as well as the diseases and the mechanisms of how TB might impact these diseases. Results A total of 97 putative targets of 20 compounds found in TB were obtained. Then, an interaction network of 97 putative targets for these compounds and known therapeutic targets for the treatment of the three diseases was constructed. Based on the constructed network, 28 major nodes were identified as the key targets of TB due to their importance in network topology. The targets of ATK2, IKBKB, RAF1, CHUK, TNF, JUN, and PRKCA were mainly involved in fluid shear stress and the atherosclerosis and PI3K-Akt signaling pathways. Finally, molecular docking simulation showed that 174 pairs of chemical components and the corresponding key targets had strong binding efficiencies. Conclusion For the first time, a comprehensive systemic approach integrating drug target prediction, network analysis, and molecular docking simulation was developed to reveal the relationships and mechanisms between the putative targets in TB and T2D, HT, and HL.
format: application/pdf
format: text/html
creator: Chao-Long Lu
creator: Qi Zheng
creator: Qi Shen
creator: Chi Song
creator: Zhi-Ming Zhang
subject: Bioinformatics
subject: Diabetes and Endocrinology
description: doi:10.7717/peerj.4042
publisher: PeerJ Inc.
rights: © 2017 Lu et al.
abstract: Background Tartary buckwheat (TB), a crop rich in protein, dietary fiber, and flavonoids, has been reported to have an effect on Type II diabetes (T2D), hypertension (HT), and hyperlipidemia (HL). However, limited information is available about the relationship between Tartary buckwheat and these three diseases. The mechanisms of how TB impacts these diseases are still unclear. Methods In this study, network pharmacology was used to investigate the relationship between the herb as well as the diseases and the mechanisms of how TB might impact these diseases. Results A total of 97 putative targets of 20 compounds found in TB were obtained. Then, an interaction network of 97 putative targets for these compounds and known therapeutic targets for the treatment of the three diseases was constructed. Based on the constructed network, 28 major nodes were identified as the key targets of TB due to their importance in network topology. The targets of ATK2, IKBKB, RAF1, CHUK, TNF, JUN, and PRKCA were mainly involved in fluid shear stress and the atherosclerosis and PI3K-Akt signaling pathways. Finally, molecular docking simulation showed that 174 pairs of chemical components and the corresponding key targets had strong binding efficiencies. Conclusion For the first time, a comprehensive systemic approach integrating drug target prediction, network analysis, and molecular docking simulation was developed to reveal the relationships and mechanisms between the putative targets in TB and T2D, HT, and HL.
bibliographic citation: Lu et al. (2017) Uncovering the relationship and mechanisms of Tartary buckwheat (Fagopyrum tataricum) and Type II diabetes, hypertension, and hyperlipidemia using a network pharmacology approach. PeerJ 5:e4042 https://doi.org/10.7717/peerj.4042
date submitted: 2017-07-21
date accepted: 2017-10-25
issued: 2017-11-21
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Lu
  given name: Chao-Long
author list: Agent
  family name: Zheng
  given name: Qi
author list: Agent
  family name: Shen
  given name: Qi
author list: Agent
  family name: Song
  given name: Chi
author list: Agent
  family name: Zhang
  given name: Zhi-Ming
doi: 10.7717/peerj.4042
volume: 5
issn: 2167-8359
publication name: PeerJ
publication date: 2017-11-21
copyright: ©2017 Lu et al.
attribution name: Lu et al.

Transcriptome sequencing reveals high isoform diversity in the ant Formica exsecta
type: item
type: AcademicArticle
description: Transcriptome resources for social insects have the potential to provide new insight into polyphenism, i.e., how divergent phenotypes arise from the same genome. Here we present a transcriptome based on paired-end RNA sequencing data for the ant Formica exsecta (Formicidae, Hymenoptera). The RNA sequencing libraries were constructed from samples of several life stages of both sexes and female castes of queens and workers, in order to maximize representation of expressed genes. We first compare the performance of common assembly and scaffolding software (Trinity, Velvet-Oases, and SOAPdenovo-trans), in producing de novo assemblies. Second, we annotate the resulting expressed contigs to the currently published genomes of ants, and other insects, including the honeybee, to filter genes that have annotation evidence of being true genes. Our pipeline resulted in a final assembly of altogether 39,262 mRNA transcripts, with an average coverage of >300X, belonging to 17,496 unique genes with annotation in the related ant species. From these genes, 536 genes were unique to one caste or sex only, highlighting the importance of comprehensive sampling. Our final assembly also showed expression of several splice variants in 6,975 genes, and we show that accounting for splice variants affects the outcome of downstream analyses such as gene ontologies. Our transcriptome provides an outstanding resource for future genetic studies on F. exsecta and other ant species, and the presented transcriptome assembly can be adapted to any non-model species that has genomic resources available from a related taxon.
format: application/pdf
format: text/html
creator: Kishor Dhaygude
creator: Kalevi Trontti
creator: Jenni Paviala
creator: Claire Morandin
creator: Christopher Wheat
creator: Liselotte Sundström
creator: Heikki Helanterä
subject: Bioinformatics
subject: Computational Biology
subject: Entomology
subject: Evolutionary Studies
subject: Genomics
description: doi:10.7717/peerj.3998
publisher: PeerJ Inc.
rights: © 2017 Dhaygude et al.
abstract: Transcriptome resources for social insects have the potential to provide new insight into polyphenism, i.e., how divergent phenotypes arise from the same genome. Here we present a transcriptome based on paired-end RNA sequencing data for the ant Formica exsecta (Formicidae, Hymenoptera). The RNA sequencing libraries were constructed from samples of several life stages of both sexes and female castes of queens and workers, in order to maximize representation of expressed genes. We first compare the performance of common assembly and scaffolding software (Trinity, Velvet-Oases, and SOAPdenovo-trans), in producing de novo assemblies. Second, we annotate the resulting expressed contigs to the currently published genomes of ants, and other insects, including the honeybee, to filter genes that have annotation evidence of being true genes. Our pipeline resulted in a final assembly of altogether 39,262 mRNA transcripts, with an average coverage of >300X, belonging to 17,496 unique genes with annotation in the related ant species. From these genes, 536 genes were unique to one caste or sex only, highlighting the importance of comprehensive sampling. Our final assembly also showed expression of several splice variants in 6,975 genes, and we show that accounting for splice variants affects the outcome of downstream analyses such as gene ontologies. Our transcriptome provides an outstanding resource for future genetic studies on F. exsecta and other ant species, and the presented transcriptome assembly can be adapted to any non-model species that has genomic resources available from a related taxon.
bibliographic citation: Dhaygude et al. (2017) Transcriptome sequencing reveals high isoform diversity in the ant Formica exsecta. PeerJ 5:e3998 https://doi.org/10.7717/peerj.3998
date submitted: 2017-04-14
date accepted: 2017-10-17
issued: 2017-11-21
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Dhaygude
  given name: Kishor
author list: Agent
  family name: Trontti
  given name: Kalevi
author list: Agent
  family name: Paviala
  given name: Jenni
author list: Agent
  family name: Morandin
  given name: Claire
author list: Agent
  family name: Wheat
  given name: Christopher
author list: Agent
  family name: Sundström
  given name: Liselotte
author list: Agent
  family name: Helanterä
  given name: Heikki
doi: 10.7717/peerj.3998
volume: 5
issn: 2167-8359
publication name: PeerJ
publication date: 2017-11-21
copyright: ©2017 Dhaygude et al.
attribution name: Dhaygude et al.

The reanalysis of biogeography of the Asian tree frog, Rhacophorus (Anura: Rhacophoridae): geographic shifts and climatic change influenced the dispersal process and diversification
type: item
type: AcademicArticle
description: Rapid uplifts of the Tibetan Plateau and climate change in Asia are thought to have profoundly modulated the diversification of most of the species distributed throughout Asia. The ranoid tree frog genus Rhacophorus, the largest genus in the Rhacophoridae, is widely distributed in Asia and especially speciose in the areas south and east of the Tibetan Plateau. Here, we infer phylogenetic relationships among species and estimate divergence times, asking whether the spatiotemporal characteristics of diversification within Rhacophorus were related to rapid uplifts of the Tibetan Plateau and concomitant climate change. Phylogenetic analysis recovered distinct lineage structures in Rhacophorus, which indicated a clear distribution pattern from Southeast Asia toward East Asia and India. Molecular dating suggests that the first split within the genus date back to the Middle Oligocene (approx. 30 Ma). The Rhacophorus lineage through time (LTT) showed that there were periods of increased speciation rate: 14–12 Ma and 10–4 Ma. In addition, ancestral area reconstructions supported Southeast Asia as the ancestral area of Rhacophorus. According to the results of molecular dating, ancestral area reconstructions and LTT we think the geographic shifts, the staged rapid rises of the Tibetan Plateau with parallel climatic changes and reinforcement of the Asian monsoons (15 Ma, 8 Ma and 4–3 Ma), possibly prompted a burst of diversification in Rhacophorus.
format: application/pdf
format: text/html
creator: Tao Pan
creator: Yanan Zhang
creator: Hui Wang
creator: Jun Wu
creator: Xing Kang
creator: Lifu Qian
creator: Jinyun Chen
creator: Dingqi Rao
creator: Jianping Jiang
creator: Baowei Zhang
subject: Biodiversity
subject: Biogeography
description: doi:10.7717/peerj.3995
publisher: PeerJ Inc.
rights: © 2017 Pan et al.
abstract: Rapid uplifts of the Tibetan Plateau and climate change in Asia are thought to have profoundly modulated the diversification of most of the species distributed throughout Asia. The ranoid tree frog genus Rhacophorus, the largest genus in the Rhacophoridae, is widely distributed in Asia and especially speciose in the areas south and east of the Tibetan Plateau. Here, we infer phylogenetic relationships among species and estimate divergence times, asking whether the spatiotemporal characteristics of diversification within Rhacophorus were related to rapid uplifts of the Tibetan Plateau and concomitant climate change. Phylogenetic analysis recovered distinct lineage structures in Rhacophorus, which indicated a clear distribution pattern from Southeast Asia toward East Asia and India. Molecular dating suggests that the first split within the genus date back to the Middle Oligocene (approx. 30 Ma). The Rhacophorus lineage through time (LTT) showed that there were periods of increased speciation rate: 14–12 Ma and 10–4 Ma. In addition, ancestral area reconstructions supported Southeast Asia as the ancestral area of Rhacophorus. According to the results of molecular dating, ancestral area reconstructions and LTT we think the geographic shifts, the staged rapid rises of the Tibetan Plateau with parallel climatic changes and reinforcement of the Asian monsoons (15 Ma, 8 Ma and 4–3 Ma), possibly prompted a burst of diversification in Rhacophorus.
bibliographic citation: Pan et al. (2017) The reanalysis of biogeography of the Asian tree frog, Rhacophorus (Anura: Rhacophoridae): geographic shifts and climatic change influenced the dispersal process and diversification. PeerJ 5:e3995 https://doi.org/10.7717/peerj.3995
date submitted: 2017-08-15
date accepted: 2017-10-16
issued: 2017-11-21
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Pan
  given name: Tao
author list: Agent
  family name: Zhang
  given name: Yanan
author list: Agent
  family name: Wang
  given name: Hui
author list: Agent
  family name: Wu
  given name: Jun
author list: Agent
  family name: Kang
  given name: Xing
author list: Agent
  family name: Qian
  given name: Lifu
author list: Agent
  family name: Chen
  given name: Jinyun
author list: Agent
  family name: Rao
  given name: Dingqi
author list: Agent
  family name: Jiang
  given name: Jianping
author list: Agent
  family name: Zhang
  given name: Baowei
doi: 10.7717/peerj.3995
volume: 5
issn: 2167-8359
publication name: PeerJ
publication date: 2017-11-21
copyright: ©2017 Pan et al.
attribution name: Pan et al.

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