PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
items: Do fish get wasted? Assessing the influence of effluents on parasitic infection of wild fish
items: Relationship between vertical and horizontal force-velocity-power profiles in various sports and levels of practice
items: A general pattern of the species abundance distribution
items: Family-based whole-exome sequencing identifies novel loss-of-function mutations of FBN1 for Marfan syndrome
items: MTBseq: a comprehensive pipeline for whole genome sequence analysis of Mycobacterium tuberculosis complex isolates
items: Optimizing the trainable B-COSFIRE filter for retinal blood vessel segmentation
items: The relationship between social rank and spatial learning in pheasants, Phasianus colchicus: cause or consequence?
items: Toxicity of Melaleuca alternifolia essential oil to the mitochondrion and NAD+/NADH dehydrogenase in Tribolium confusum
items: CMTCN: a web tool for investigating cancer-specific microRNA and transcription factor co-regulatory networks
items: A divergence between underlying and final causes of death in selected conditions: an analysis of death registries in Peru

Do fish get wasted? Assessing the influence of effluents on parasitic infection of wild fish
type: item
type: AcademicArticle
description: Many ecosystems are influenced simultaneously by multiple stressors. One important environmental stressor is aquatic pollution via wastewater treatment plant (WWTP) effluents. WWTP effluents may contribute to eutrophication or contain anthropogenic contaminants that directly and/or indirectly influence aquatic wildlife. Both eutrophication and exposure to anthropogenic contaminants may affect the dynamics of fish-parasite systems. With this in mind, we studied the impact of WWTP effluents on infection of brown trout by the parasite Tetracapsuloides bryosalmonae, the causative agent of proliferative kidney disease (PKD). PKD is associated with the long-term decline of wild brown trout (Salmo trutta) populations in Switzerland. We investigated PKD infection of brown trout at two adjacent sites (≈400 m apart) of a Swiss river. The sites are similar in terms of ecology except that one site receives WWTP effluents. We evaluated the hypothesis that fish inhabiting the effluent site will show greater susceptibility to PKD in terms of prevalence and disease outcome. We assessed susceptibility by (i) infection prevalence, (ii) parasite intensity, (iii) host health in terms of pathology, and (iv) estimated apparent survival rate. At different time points during the study, significant differences between sites concerning all measured parameters were found, thus providing evidence of the influence of effluents on parasitic infection of fish in our study system. However, from these findings we cannot determine if the effluent has a direct influence on the fish host via altering its ability to manage the parasite, or indirectly on the parasite or the invertebrate host via increasing bryozoa (the invertebrate host) reproduction. On a final note, the WWTP adhered to all national guidelines and the effluent only resulted in a minor water quality reduction assessed via standardized methods in this study. Thus, we provide evidence that even a subtle decrease in water quality, resultin…
format: application/pdf
format: text/html
creator: Christyn Bailey
creator: Aurélie Rubin
creator: Nicole Strepparava
creator: Helmut Segner
creator: Jean-François Rubin
creator: Thomas Wahli
subject: Aquaculture, Fisheries and Fish Science
subject: Parasitology
subject: Ecotoxicology
subject: Freshwater Biology
description: doi:10.7717/peerj.5956
publisher: PeerJ Inc.
rights: © 2018 Bailey et al.
abstract: Many ecosystems are influenced simultaneously by multiple stressors. One important environmental stressor is aquatic pollution via wastewater treatment plant (WWTP) effluents. WWTP effluents may contribute to eutrophication or contain anthropogenic contaminants that directly and/or indirectly influence aquatic wildlife. Both eutrophication and exposure to anthropogenic contaminants may affect the dynamics of fish-parasite systems. With this in mind, we studied the impact of WWTP effluents on infection of brown trout by the parasite Tetracapsuloides bryosalmonae, the causative agent of proliferative kidney disease (PKD). PKD is associated with the long-term decline of wild brown trout (Salmo trutta) populations in Switzerland. We investigated PKD infection of brown trout at two adjacent sites (≈400 m apart) of a Swiss river. The sites are similar in terms of ecology except that one site receives WWTP effluents. We evaluated the hypothesis that fish inhabiting the effluent site will show greater susceptibility to PKD in terms of prevalence and disease outcome. We assessed susceptibility by (i) infection prevalence, (ii) parasite intensity, (iii) host health in terms of pathology, and (iv) estimated apparent survival rate. At different time points during the study, significant differences between sites concerning all measured parameters were found, thus providing evidence of the influence of effluents on parasitic infection of fish in our study system. However, from these findings we cannot determine if the effluent has a direct influence on the fish host via altering its ability to manage the parasite, or indirectly on the parasite or the invertebrate host via increasing bryozoa (the invertebrate host) reproduction. On a final note, the WWTP adhered to all national guidelines and the effluent only resulted in a minor water quality reduction assessed via standardized methods in this study. Thus, we provide evidence that even a subtle decrease in water quality, resultin…
bibliographic citation: Bailey et al. (2018) Do fish get wasted? Assessing the influence of effluents on parasitic infection of wild fish. PeerJ 6:e5956 https://doi.org/10.7717/peerj.5956
date submitted: 2018-06-07
date accepted: 2018-10-17
issued: 2018-11-13
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Bailey
  given name: Christyn
author list: Agent
  family name: Rubin
  given name: Aurélie
author list: Agent
  family name: Strepparava
  given name: Nicole
author list: Agent
  family name: Segner
  given name: Helmut
author list: Agent
  family name: Rubin
  given name: Jean-François
author list: Agent
  family name: Wahli
  given name: Thomas
doi: 10.7717/peerj.5956
volume: 6
issn: 2167-8359
publication name: PeerJ
publication date: 2018-11-13
copyright: © 2018 Bailey et al.
attribution name: Bailey et al.

Relationship between vertical and horizontal force-velocity-power profiles in various sports and levels of practice
type: item
type: AcademicArticle
description: This study aimed (i) to explore the relationship between vertical (jumping) and horizontal (sprinting) force–velocity–power (FVP) mechanical profiles in a large range of sports and levels of practice, and (ii) to provide a large database to serve as a reference of the FVP profile for all sports and levels tested. A total of 553 participants (333 men, 220 women) from 14 sport disciplines and all levels of practice participated in this study. Participants performed squat jumps (SJ) against multiple external loads (vertical) and linear 30–40 m sprints (horizontal). The vertical and horizontal FVP profile (i.e., theoretical maximal values of force (F0), velocity (v0), and power (Pmax)) as well as main performance variables (unloaded SJ height in jumping and 20-m sprint time) were measured. Correlations coefficient between the same mechanical variables obtained from the vertical and horizontal modalities ranged from −0.12 to 0.58 for F0, −0.31 to 0.71 for v0, −0.10 to 0.67 for Pmax, and −0.92 to −0.23 for the performance variables (i.e, SJ height and sprint time). Overall, results showed a decrease in the magnitude of the correlations for higher-level athletes. The low correlations generally observed between jumping and sprinting mechanical outputs suggest that both tasks provide distinctive information regarding the FVP profile of lower-body muscles. Therefore, we recommend the assessment of the FVP profile both in jumping and sprinting to gain a deeper insight into the maximal mechanical capacities of lower-body muscles, especially at high and elite levels.
format: application/pdf
format: text/html
creator: Pedro Jiménez-Reyes
creator: Pierre Samozino
creator: Amador García-Ramos
creator: Víctor Cuadrado-Peñafiel
creator: Matt Brughelli
creator: Jean-Benoît Morin
subject: Kinesiology
description: doi:10.7717/peerj.5937
publisher: PeerJ Inc.
rights: © 2018 Jiménez-Reyes et al.
abstract: This study aimed (i) to explore the relationship between vertical (jumping) and horizontal (sprinting) force–velocity–power (FVP) mechanical profiles in a large range of sports and levels of practice, and (ii) to provide a large database to serve as a reference of the FVP profile for all sports and levels tested. A total of 553 participants (333 men, 220 women) from 14 sport disciplines and all levels of practice participated in this study. Participants performed squat jumps (SJ) against multiple external loads (vertical) and linear 30–40 m sprints (horizontal). The vertical and horizontal FVP profile (i.e., theoretical maximal values of force (F0), velocity (v0), and power (Pmax)) as well as main performance variables (unloaded SJ height in jumping and 20-m sprint time) were measured. Correlations coefficient between the same mechanical variables obtained from the vertical and horizontal modalities ranged from −0.12 to 0.58 for F0, −0.31 to 0.71 for v0, −0.10 to 0.67 for Pmax, and −0.92 to −0.23 for the performance variables (i.e, SJ height and sprint time). Overall, results showed a decrease in the magnitude of the correlations for higher-level athletes. The low correlations generally observed between jumping and sprinting mechanical outputs suggest that both tasks provide distinctive information regarding the FVP profile of lower-body muscles. Therefore, we recommend the assessment of the FVP profile both in jumping and sprinting to gain a deeper insight into the maximal mechanical capacities of lower-body muscles, especially at high and elite levels.
bibliographic citation: Jiménez-Reyes et al. (2018) Relationship between vertical and horizontal force-velocity-power profiles in various sports and levels of practice. PeerJ 6:e5937 https://doi.org/10.7717/peerj.5937
date submitted: 2018-08-15
date accepted: 2018-10-16
issued: 2018-11-13
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Jiménez-Reyes
  given name: Pedro
author list: Agent
  family name: Samozino
  given name: Pierre
author list: Agent
  family name: García-Ramos
  given name: Amador
author list: Agent
  family name: Cuadrado-Peñafiel
  given name: Víctor
author list: Agent
  family name: Brughelli
  given name: Matt
author list: Agent
  family name: Morin
  given name: Jean-Benoît
doi: 10.7717/peerj.5937
volume: 6
issn: 2167-8359
publication name: PeerJ
publication date: 2018-11-13
copyright: © 2018 Jiménez-Reyes et al.
attribution name: Jiménez-Reyes et al.

A general pattern of the species abundance distribution
type: item
type: AcademicArticle
description: Since the 1970s, species abundance distributions (SADs) have been one of the most fundamental issues in ecology and have frequently been investigated and reviewed. However, there was surprisingly little consensus. This study focuses on three essential questions. (1) Is there a general pattern of SAD that no community can violate it? (2) If it exists, what does it look like? (3) Why is it like this? The frequency distributions of 19,833 SADs from eight datasets (including eleven taxonomic groups from terrestrial, aquatic, and marine ecosystems) suggest that a general pattern of SAD might exist. According to two hypotheses (the finiteness of the total energy and the causality from the entropy to the diversity), this study assumes that the general pattern of SAD is approximately consistent with Zipf’s law, which means that Zipf’s law might be more easily to observe when one investigates any SAD. In the future, this conjecture not only needs to be tested (or supported) by more and more datasets, but also depends on how well it is explained from different angles of theories.
format: application/pdf
format: text/html
creator: Qiang Su
subject: Biodiversity
description: doi:10.7717/peerj.5928
publisher: PeerJ Inc.
rights: © 2018 Su
abstract: Since the 1970s, species abundance distributions (SADs) have been one of the most fundamental issues in ecology and have frequently been investigated and reviewed. However, there was surprisingly little consensus. This study focuses on three essential questions. (1) Is there a general pattern of SAD that no community can violate it? (2) If it exists, what does it look like? (3) Why is it like this? The frequency distributions of 19,833 SADs from eight datasets (including eleven taxonomic groups from terrestrial, aquatic, and marine ecosystems) suggest that a general pattern of SAD might exist. According to two hypotheses (the finiteness of the total energy and the causality from the entropy to the diversity), this study assumes that the general pattern of SAD is approximately consistent with Zipf’s law, which means that Zipf’s law might be more easily to observe when one investigates any SAD. In the future, this conjecture not only needs to be tested (or supported) by more and more datasets, but also depends on how well it is explained from different angles of theories.
bibliographic citation: Su (2018) A general pattern of the species abundance distribution. PeerJ 6:e5928 https://doi.org/10.7717/peerj.5928
date submitted: 2018-07-26
date accepted: 2018-10-13
issued: 2018-11-13
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Su
  given name: Qiang
doi: 10.7717/peerj.5928
volume: 6
issn: 2167-8359
publication name: PeerJ
publication date: 2018-11-13
copyright: ©2018 Su
attribution name: Su

Family-based whole-exome sequencing identifies novel loss-of-function mutations of FBN1 for Marfan syndrome
type: item
type: AcademicArticle
description: Background Marfan syndrome (MFS) is an inherited connective tissue disorder affecting the ocular, skeletal and cardiovascular systems. Previous studies of MFS have demonstrated the association between genetic defects and clinical manifestations. Our purpose was to investigate the role of novel genetic variants in determining MFS clinical phenotypes. Methods We sequenced the whole exome of 19 individuals derived from three Han Chinese families. The sequencing data were analyzed by a standard pipeline. Variants were further filtered against the public database and an in-house database. Then, we performed pedigree analysis under different inheritance patterns according to American College of Medical Genetics guidelines. Results were confirmed by Sanger sequencing. Results Two novel loss-of-function indels (c.5027_5028insTGTCCTCC, p.D1677Vfs*8; c.5856delG, p.S1953Lfs*27) and one nonsense variant (c.8034C>A, p.Y2678*) of FBN1 were identified in Family 1, Family 2 and Family 3, respectively. All affected members carried pathogenic mutations, whereas other unaffected family members or control individuals did not. These different kinds of loss of function (LOF) variants of FBN1 were located in the cbEGF region and a conserved domain across species and were not reported previously. Conclusions Our study extended and strengthened the vital role of FBN1 LOF mutations in the pathogenesis of MFS with an autosomal dominant inheritance pattern. We confirm that genetic testing by next-generation sequencing of blood DNA can be fundamental in helping clinicians conduct mutation-based pre- and postnatal screening, genetic diagnosis and clinical management for MFS.
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creator: Zhening Pu
creator: Haoliang Sun
creator: Junjie Du
creator: Yue Cheng
creator: Keshuai He
creator: Buqing Ni
creator: Weidong Gu
creator: Juncheng Dai
creator: Yongfeng Shao
subject: Genetics
subject: Genomics
subject: Molecular Biology
subject: Cardiology
subject: Medical Genetics
description: doi:10.7717/peerj.5927
publisher: PeerJ Inc.
rights: © 2018 Pu et al.
abstract: Background Marfan syndrome (MFS) is an inherited connective tissue disorder affecting the ocular, skeletal and cardiovascular systems. Previous studies of MFS have demonstrated the association between genetic defects and clinical manifestations. Our purpose was to investigate the role of novel genetic variants in determining MFS clinical phenotypes. Methods We sequenced the whole exome of 19 individuals derived from three Han Chinese families. The sequencing data were analyzed by a standard pipeline. Variants were further filtered against the public database and an in-house database. Then, we performed pedigree analysis under different inheritance patterns according to American College of Medical Genetics guidelines. Results were confirmed by Sanger sequencing. Results Two novel loss-of-function indels (c.5027_5028insTGTCCTCC, p.D1677Vfs*8; c.5856delG, p.S1953Lfs*27) and one nonsense variant (c.8034C>A, p.Y2678*) of FBN1 were identified in Family 1, Family 2 and Family 3, respectively. All affected members carried pathogenic mutations, whereas other unaffected family members or control individuals did not. These different kinds of loss of function (LOF) variants of FBN1 were located in the cbEGF region and a conserved domain across species and were not reported previously. Conclusions Our study extended and strengthened the vital role of FBN1 LOF mutations in the pathogenesis of MFS with an autosomal dominant inheritance pattern. We confirm that genetic testing by next-generation sequencing of blood DNA can be fundamental in helping clinicians conduct mutation-based pre- and postnatal screening, genetic diagnosis and clinical management for MFS.
bibliographic citation: Pu et al. (2018) Family-based whole-exome sequencing identifies novel loss-of-function mutations of FBN1 for Marfan syndrome. PeerJ 6:e5927 https://doi.org/10.7717/peerj.5927
date submitted: 2018-05-03
date accepted: 2018-10-13
issued: 2018-11-13
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Pu
  given name: Zhening
author list: Agent
  family name: Sun
  given name: Haoliang
author list: Agent
  family name: Du
  given name: Junjie
author list: Agent
  family name: Cheng
  given name: Yue
author list: Agent
  family name: He
  given name: Keshuai
author list: Agent
  family name: Ni
  given name: Buqing
author list: Agent
  family name: Gu
  given name: Weidong
author list: Agent
  family name: Dai
  given name: Juncheng
author list: Agent
  family name: Shao
  given name: Yongfeng
doi: 10.7717/peerj.5927
volume: 6
issn: 2167-8359
publication name: PeerJ
publication date: 2018-11-13
copyright: © 2018 Pu et al.
attribution name: Pu et al.

MTBseq: a comprehensive pipeline for whole genome sequence analysis of Mycobacterium tuberculosis complex isolates
type: item
type: AcademicArticle
description: Analyzing whole-genome sequencing data of Mycobacterium tuberculosis complex (MTBC) isolates in a standardized workflow enables both comprehensive antibiotic resistance profiling and outbreak surveillance with highest resolution up to the identification of recent transmission chains. Here, we present MTBseq, a bioinformatics pipeline for next-generation genome sequence data analysis of MTBC isolates. Employing a reference mapping based workflow, MTBseq reports detected variant positions annotated with known association to antibiotic resistance and performs a lineage classification based on phylogenetic single nucleotide polymorphisms (SNPs). When comparing multiple datasets, MTBseq provides a joint list of variants and a FASTA alignment of SNP positions for use in phylogenomic analysis, and identifies groups of related isolates. The pipeline is customizable, expandable and can be used on a desktop computer or laptop without any internet connection, ensuring mobile usage and data security. MTBseq and accompanying documentation is available from https://github.com/ngs-fzb/MTBseq_source.
format: application/pdf
format: text/html
creator: Thomas Andreas Kohl
creator: Christian Utpatel
creator: Viola Schleusener
creator: Maria Rosaria De Filippo
creator: Patrick Beckert
creator: Daniela Maria Cirillo
creator: Stefan Niemann
subject: Molecular Biology
subject: Infectious Diseases
subject: Public Health
subject: Population Biology
description: doi:10.7717/peerj.5895
publisher: PeerJ Inc.
rights: © 2018 Kohl et al.
abstract: Analyzing whole-genome sequencing data of Mycobacterium tuberculosis complex (MTBC) isolates in a standardized workflow enables both comprehensive antibiotic resistance profiling and outbreak surveillance with highest resolution up to the identification of recent transmission chains. Here, we present MTBseq, a bioinformatics pipeline for next-generation genome sequence data analysis of MTBC isolates. Employing a reference mapping based workflow, MTBseq reports detected variant positions annotated with known association to antibiotic resistance and performs a lineage classification based on phylogenetic single nucleotide polymorphisms (SNPs). When comparing multiple datasets, MTBseq provides a joint list of variants and a FASTA alignment of SNP positions for use in phylogenomic analysis, and identifies groups of related isolates. The pipeline is customizable, expandable and can be used on a desktop computer or laptop without any internet connection, ensuring mobile usage and data security. MTBseq and accompanying documentation is available from https://github.com/ngs-fzb/MTBseq_source.
bibliographic citation: Kohl et al. (2018) MTBseq: a comprehensive pipeline for whole genome sequence analysis of Mycobacterium tuberculosis complex isolates. PeerJ 6:e5895 https://doi.org/10.7717/peerj.5895
date submitted: 2018-04-23
date accepted: 2018-10-09
issued: 2018-11-13
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Kohl
  given name: Thomas Andreas
author list: Agent
  family name: Utpatel
  given name: Christian
author list: Agent
  family name: Schleusener
  given name: Viola
author list: Agent
  family name: De Filippo
  given name: Maria Rosaria
author list: Agent
  family name: Beckert
  given name: Patrick
author list: Agent
  family name: Cirillo
  given name: Daniela Maria
author list: Agent
  family name: Niemann
  given name: Stefan
doi: 10.7717/peerj.5895
volume: 6
issn: 2167-8359
publication name: PeerJ
publication date: 2018-11-13
copyright: © 2018 Kohl et al.
attribution name: Kohl et al.

Optimizing the trainable B-COSFIRE filter for retinal blood vessel segmentation
type: item
type: AcademicArticle
description: Segmentation of the retinal blood vessels using filtering techniques is a widely used step in the development of an automated system for diagnostic retinal image analysis. This paper optimized the blood vessel segmentation, by extending the trainable B-COSFIRE filter via identification of more optimal parameters. The filter parameters are introduced using an optimization procedure to three public datasets (STARE, DRIVE, and CHASE-DB1). The suggested approach considers analyzing thresholding parameters selection followed by application of background artifacts removal techniques. The approach results are better than the other state of the art methods used for vessel segmentation. ANOVA analysis technique is also used to identify the most significant parameters that are impacting the performance results (p-value ¡ 0.05). The proposed enhancement has improved the vessel segmentation accuracy in DRIVE, STARE and CHASE-DB1 to 95.47, 95.30 and 95.30, respectively.
format: application/pdf
format: text/html
creator: Sufian A. Badawi
creator: Muhammad Moazam Fraz
subject: Ophthalmology
subject: Radiology and Medical Imaging
subject: Human-Computer Interaction
subject: Computational Science
description: doi:10.7717/peerj.5855
publisher: PeerJ Inc.
rights: © 2018 Badawi and Fraz
abstract: Segmentation of the retinal blood vessels using filtering techniques is a widely used step in the development of an automated system for diagnostic retinal image analysis. This paper optimized the blood vessel segmentation, by extending the trainable B-COSFIRE filter via identification of more optimal parameters. The filter parameters are introduced using an optimization procedure to three public datasets (STARE, DRIVE, and CHASE-DB1). The suggested approach considers analyzing thresholding parameters selection followed by application of background artifacts removal techniques. The approach results are better than the other state of the art methods used for vessel segmentation. ANOVA analysis technique is also used to identify the most significant parameters that are impacting the performance results (p-value ¡ 0.05). The proposed enhancement has improved the vessel segmentation accuracy in DRIVE, STARE and CHASE-DB1 to 95.47, 95.30 and 95.30, respectively.
bibliographic citation: Badawi et al. (2018) Optimizing the trainable B-COSFIRE filter for retinal blood vessel segmentation. PeerJ 6:e5855 https://doi.org/10.7717/peerj.5855
date submitted: 2018-03-20
date accepted: 2018-09-28
issued: 2018-11-13
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Badawi
  given name: Sufian A.
author list: Agent
  family name: Fraz
  given name: Muhammad Moazam
doi: 10.7717/peerj.5855
volume: 6
issn: 2167-8359
publication name: PeerJ
publication date: 2018-11-13
copyright: ©2018 Badawi and Fraz
attribution name: Badawi and Fraz

The relationship between social rank and spatial learning in pheasants, Phasianus colchicus: cause or consequence?
type: item
type: AcademicArticle
description: Individual differences in performances on cognitive tasks have been found to differ according to social rank across multiple species. However, it is not clear whether an individual’s cognitive performance is flexible and the result of their current social rank, modulated by social interactions (social state dependent hypothesis), or if it is determined prior to the formation of the social hierarchy and indeed influences an individual’s rank (prior attributes hypothesis). We separated these two hypotheses by measuring learning performance of male pheasants, Phasianus colchicus, on a spatial discrimination task as chicks and again as adults. We inferred adult male social rank from observing agonistic interactions while housed in captive multi-male multi-female groups. Learning performance of adult males was assayed after social rank had been standardised; by housing single males with two or four females. We predicted that if cognitive abilities determine social rank formation we would observe: consistency between chick and adult performances on the cognitive task and chick performance would predict adult social rank. We found that learning performances were consistent from chicks to adults for task accuracy, but not for speed of learning and chick learning performances were not related to adult social rank. Therefore, we could not support the prior attributes hypothesis of cognitive abilities aiding social rank formation. Instead, we found that individual differences in learning performances of adults were predicted by the number of females a male was housed with; males housed with four females had higher levels of learning performance than males housed with two females; and their most recent recording of captive social rank, even though learning performance was assayed while males were in a standardized, non-competitive environment. This does not support the hypothesis that direct social pressures are causing the inter-individual variation in learning performances th…
format: application/pdf
format: text/html
creator: Ellis J.G. Langley
creator: Jayden O. van Horik
creator: Mark A. Whiteside
creator: Christine E. Beardsworth
creator: Joah R. Madden
subject: Animal Behavior
subject: Developmental Biology
subject: Zoology
description: doi:10.7717/peerj.5738
publisher: PeerJ Inc.
rights: © 2018 Langley et al.
abstract: Individual differences in performances on cognitive tasks have been found to differ according to social rank across multiple species. However, it is not clear whether an individual’s cognitive performance is flexible and the result of their current social rank, modulated by social interactions (social state dependent hypothesis), or if it is determined prior to the formation of the social hierarchy and indeed influences an individual’s rank (prior attributes hypothesis). We separated these two hypotheses by measuring learning performance of male pheasants, Phasianus colchicus, on a spatial discrimination task as chicks and again as adults. We inferred adult male social rank from observing agonistic interactions while housed in captive multi-male multi-female groups. Learning performance of adult males was assayed after social rank had been standardised; by housing single males with two or four females. We predicted that if cognitive abilities determine social rank formation we would observe: consistency between chick and adult performances on the cognitive task and chick performance would predict adult social rank. We found that learning performances were consistent from chicks to adults for task accuracy, but not for speed of learning and chick learning performances were not related to adult social rank. Therefore, we could not support the prior attributes hypothesis of cognitive abilities aiding social rank formation. Instead, we found that individual differences in learning performances of adults were predicted by the number of females a male was housed with; males housed with four females had higher levels of learning performance than males housed with two females; and their most recent recording of captive social rank, even though learning performance was assayed while males were in a standardized, non-competitive environment. This does not support the hypothesis that direct social pressures are causing the inter-individual variation in learning performances th…
bibliographic citation: Langley et al. (2018) The relationship between social rank and spatial learning in pheasants, Phasianus colchicus: cause or consequence?. PeerJ 6:e5738 https://doi.org/10.7717/peerj.5738
date submitted: 2018-03-09
date accepted: 2018-09-11
issued: 2018-11-13
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Langley
  given name: Ellis J.G.
author list: Agent
  family name: van Horik
  given name: Jayden O.
author list: Agent
  family name: Whiteside
  given name: Mark A.
author list: Agent
  family name: Beardsworth
  given name: Christine E.
author list: Agent
  family name: Madden
  given name: Joah R.
doi: 10.7717/peerj.5738
volume: 6
issn: 2167-8359
publication name: PeerJ
publication date: 2018-11-13
copyright: ©2018 Langley et al.
attribution name: Langley et al.

Toxicity of Melaleuca alternifolia essential oil to the mitochondrion and NAD+/NADH dehydrogenase in Tribolium confusum
type: item
type: AcademicArticle
description: Background In our previous study, Melaleuca alternifolia essential oil (EO) was considered to have an insecticidal effect by acting on the mitochondrial respiratory chain in insects. However, the mode of action is not fully understood. Methods In this study, we investigated the insecticidal efficacy of the M. alternifolia EO against another major stored-product pest, Tribolium confusum Jacquelin du Val. Rarefaction and vacuolization of the mitochondrial matrix were evident in oil-fumigated T. confusum adults. Results Alterations to the mitochondria confirmed the insecticidal effect of the M. alternifolia EO. Furthermore, comparative transcriptome analysis of T. confusum using RNA-seq indicated that most of the differentially expressed genes were involved in insecticide detoxification and mitochondrial function. The biochemical analysis showed that the intracellular NAD+/NADH ratio is involved in the differential effect of the M. alternifolia EO. Discussion These results led us to conclude that NAD+/NADH dehydrogenase may be the prime target site for the M. alternifolia EO in insects, leading to blocking of the mitochondrial respiratory chain.
format: application/pdf
format: text/html
creator: Min Liao
creator: Qian-Qian Yang
creator: Jin-Jing Xiao
creator: Yong Huang
creator: Li-Jun Zhou
creator: Ri-Mao Hua
creator: Hai-Qun Cao
subject: Bioinformatics
subject: Entomology
subject: Toxicology
description: doi:10.7717/peerj.5693
publisher: PeerJ Inc.
rights: © 2018 Liao et al.
abstract: Background In our previous study, Melaleuca alternifolia essential oil (EO) was considered to have an insecticidal effect by acting on the mitochondrial respiratory chain in insects. However, the mode of action is not fully understood. Methods In this study, we investigated the insecticidal efficacy of the M. alternifolia EO against another major stored-product pest, Tribolium confusum Jacquelin du Val. Rarefaction and vacuolization of the mitochondrial matrix were evident in oil-fumigated T. confusum adults. Results Alterations to the mitochondria confirmed the insecticidal effect of the M. alternifolia EO. Furthermore, comparative transcriptome analysis of T. confusum using RNA-seq indicated that most of the differentially expressed genes were involved in insecticide detoxification and mitochondrial function. The biochemical analysis showed that the intracellular NAD+/NADH ratio is involved in the differential effect of the M. alternifolia EO. Discussion These results led us to conclude that NAD+/NADH dehydrogenase may be the prime target site for the M. alternifolia EO in insects, leading to blocking of the mitochondrial respiratory chain.
bibliographic citation: Liao et al. (2018) Toxicity of Melaleuca alternifolia essential oil to the mitochondrion and NAD+/NADH dehydrogenase in Tribolium confusum. PeerJ 6:e5693 https://doi.org/10.7717/peerj.5693
date submitted: 2018-05-02
date accepted: 2018-09-05
issued: 2018-11-13
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Liao
  given name: Min
author list: Agent
  family name: Yang
  given name: Qian-Qian
author list: Agent
  family name: Xiao
  given name: Jin-Jing
author list: Agent
  family name: Huang
  given name: Yong
author list: Agent
  family name: Zhou
  given name: Li-Jun
author list: Agent
  family name: Hua
  given name: Ri-Mao
author list: Agent
  family name: Cao
  given name: Hai-Qun
doi: 10.7717/peerj.5693
volume: 6
issn: 2167-8359
publication name: PeerJ
publication date: 2018-11-13
copyright: © 2018 Liao et al.
attribution name: Liao et al.

CMTCN: a web tool for investigating cancer-specific microRNA and transcription factor co-regulatory networks
type: item
type: AcademicArticle
description: Transcription factors (TFs) and microRNAs (miRNAs) are well-characterized trans-acting essential players in gene expression regulation. Growing evidence indicates that TFs and miRNAs can work cooperatively, and their dysregulation has been associated with many diseases including cancer. A unified picture of regulatory interactions of these regulators and their joint target genes would shed light on cancer studies. Although online resources developed to support probing of TF-gene and miRNA-gene interactions are available, online applications for miRNA-TF co-regulatory analysis, especially with a focus on cancers, are lacking. In light of this, we developed a web tool, namely CMTCN (freely available at http://www.cbportal.org/CMTCN), which constructs miRNA-TF co-regulatory networks and conducts comprehensive analyses within the context of particular cancer types. With its user-friendly provision of topological and functional analyses, CMTCN promises to be a reliable and indispensable web tool for biomedical studies.
format: application/pdf
format: text/html
creator: Ruijiang Li
creator: Hebing Chen
creator: Shuai Jiang
creator: Wanying Li
creator: Hao Li
creator: Zhuo Zhang
creator: Hao Hong
creator: Xin Huang
creator: Chenghui Zhao
creator: Yiming Lu
creator: Xiaochen Bo
subject: Bioinformatics
subject: Computational Biology
subject: Genomics
subject: Computational Science
description: doi:10.7717/peerj.5951
publisher: PeerJ Inc.
rights: © 2018 Li et al.
abstract: Transcription factors (TFs) and microRNAs (miRNAs) are well-characterized trans-acting essential players in gene expression regulation. Growing evidence indicates that TFs and miRNAs can work cooperatively, and their dysregulation has been associated with many diseases including cancer. A unified picture of regulatory interactions of these regulators and their joint target genes would shed light on cancer studies. Although online resources developed to support probing of TF-gene and miRNA-gene interactions are available, online applications for miRNA-TF co-regulatory analysis, especially with a focus on cancers, are lacking. In light of this, we developed a web tool, namely CMTCN (freely available at http://www.cbportal.org/CMTCN), which constructs miRNA-TF co-regulatory networks and conducts comprehensive analyses within the context of particular cancer types. With its user-friendly provision of topological and functional analyses, CMTCN promises to be a reliable and indispensable web tool for biomedical studies.
bibliographic citation: Li et al. (2018) CMTCN: a web tool for investigating cancer-specific microRNA and transcription factor co-regulatory networks. PeerJ 6:e5951 https://doi.org/10.7717/peerj.5951
date submitted: 2018-08-22
date accepted: 2018-10-14
issued: 2018-11-12
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Li
  given name: Ruijiang
author list: Agent
  family name: Chen
  given name: Hebing
author list: Agent
  family name: Jiang
  given name: Shuai
author list: Agent
  family name: Li
  given name: Wanying
author list: Agent
  family name: Li
  given name: Hao
author list: Agent
  family name: Zhang
  given name: Zhuo
author list: Agent
  family name: Hong
  given name: Hao
author list: Agent
  family name: Huang
  given name: Xin
author list: Agent
  family name: Zhao
  given name: Chenghui
author list: Agent
  family name: Lu
  given name: Yiming
author list: Agent
  family name: Bo
  given name: Xiaochen
doi: 10.7717/peerj.5951
volume: 6
issn: 2167-8359
publication name: PeerJ
publication date: 2018-11-12
copyright: ©2018 Li et al.
attribution name: Li et al.

A divergence between underlying and final causes of death in selected conditions: an analysis of death registries in Peru
type: item
type: AcademicArticle
description: Background The underlying cause of death is used to study country and global mortality trends and profiles. The final cause of death could also inform the ultimately cause of death in individuals with underlying conditions. Whether there is a pattern between the underlying and final cause of death has not been explored using national death registries. We studied what final causes of death were most common among selected underlying causes using national death registries in Peru, 2015. Methods Underlying and final causes of death were classified according to their ICD-10 codes. Underlying causes included chronic kidney disease (CKD), chronic obstructive pulmonary disease (COPD), hypertension (HTN), diabetes, and selected cancers (cervix, breast, stomach, prostate, and lung). Final causes were categorized as: communicable, cardiovascular, and cancers. Descriptive statistics were used. Results A total of 77,065 death registries were analyzed; cases had a mean age of 69.4 (SD: 19.3) years at death and were mostly men (53.9%). When the underlying cause was HTN, the most frequent final cause was cardiovascular diseases (82.3%). For all the other underlying causes, the most frequent final cause was communicable diseases: COPD (86.4%), CKD (79.3%), cancer (76.5%), and diabetes (68.3%). Conclusions In four selected underlying causes of death there was a divergence with respect to the final cause, suggesting there was a shift from non-communicable to communicable causes. Although efforts should be deployed to prevent underlying non-communicable diseases, potential communicable complications should not be neglected.
format: application/pdf
format: text/html
creator: Rodrigo M. Carrillo-Larco
creator: Antonio Bernabe-Ortiz
subject: Epidemiology
subject: Evidence Based Medicine
subject: Global Health
description: doi:10.7717/peerj.5948
publisher: PeerJ Inc.
rights: © 2018 Carrillo-Larco and Bernabe-Ortiz
abstract: Background The underlying cause of death is used to study country and global mortality trends and profiles. The final cause of death could also inform the ultimately cause of death in individuals with underlying conditions. Whether there is a pattern between the underlying and final cause of death has not been explored using national death registries. We studied what final causes of death were most common among selected underlying causes using national death registries in Peru, 2015. Methods Underlying and final causes of death were classified according to their ICD-10 codes. Underlying causes included chronic kidney disease (CKD), chronic obstructive pulmonary disease (COPD), hypertension (HTN), diabetes, and selected cancers (cervix, breast, stomach, prostate, and lung). Final causes were categorized as: communicable, cardiovascular, and cancers. Descriptive statistics were used. Results A total of 77,065 death registries were analyzed; cases had a mean age of 69.4 (SD: 19.3) years at death and were mostly men (53.9%). When the underlying cause was HTN, the most frequent final cause was cardiovascular diseases (82.3%). For all the other underlying causes, the most frequent final cause was communicable diseases: COPD (86.4%), CKD (79.3%), cancer (76.5%), and diabetes (68.3%). Conclusions In four selected underlying causes of death there was a divergence with respect to the final cause, suggesting there was a shift from non-communicable to communicable causes. Although efforts should be deployed to prevent underlying non-communicable diseases, potential communicable complications should not be neglected.
bibliographic citation: Carrillo-Larco et al. (2018) A divergence between underlying and final causes of death in selected conditions: an analysis of death registries in Peru. PeerJ 6:e5948 https://doi.org/10.7717/peerj.5948
date submitted: 2018-08-14
date accepted: 2018-10-17
issued: 2018-11-12
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Carrillo-Larco
  given name: Rodrigo M.
author list: Agent
  family name: Bernabe-Ortiz
  given name: Antonio
doi: 10.7717/peerj.5948
volume: 6
issn: 2167-8359
publication name: PeerJ
publication date: 2018-11-12
copyright: © 2018 Carrillo-Larco and Bernabe-Ortiz
attribution name: Carrillo-Larco and Bernabe-Ortiz

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