PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
items: Comparative functional analysis of proteins containing low-complexity predicted amyloid regions
items: Uncovering full-length transcript isoforms of sugarcane cultivar Khon Kaen 3 using single-molecule long-read sequencing
items: Adipose tissues of MPC1± mice display altered lipid metabolism-related enzyme expression levels
items: From the cage to the wild: introductions of Psittaciformes to Puerto Rico
items: Using the validated Reflective Functioning Questionnaire to investigate mentalizing in individuals presenting with eating disorders with and without self-harm
items: Confidence in eating disorder knowledge does not predict actual knowledge in collegiate female athletes
items: Ensemble learning for detecting gene-gene interactions in colorectal cancer
items: Don’t worry, be active: how to facilitate the detection of errors in immersive virtual environments
items: Association of urban forest landscape characteristics with biomass and soil carbon stocks in Harbin City, Northeastern China
items: Effects of agricultural management on phyllosphere fungal diversity in vineyards and the association with adjacent native forests

Comparative functional analysis of proteins containing low-complexity predicted amyloid regions
type: item
type: AcademicArticle
description: Background In both prokaryotic and eukaryotic proteins, repeated occurrence of a single or a group of few amino acids are found. These regions are termed as low complexity regions (LCRs). It has been observed that amino acid bias in LCR is directly linked to their uncontrolled expansion and amyloid formation. But a comparative analysis of the behavior of LCR based on their constituent amino acids and their association with amyloidogenic propensity is not available. Methods Firstly we grouped all LCRs on the basis of their composition: homo-polymers, positively charged amino acids, negatively charged amino acids, polar amino acids and hydrophobic amino acids. We analyzed the compositional pattern of LCRs in each group and their propensity to form amyloids. The functional characteristics of proteins containing different groups of LCRs were explored using DAVID. In addition, we also analyzed the classes, pathways and functions of human proteins that form amyloids in LCRs. Results Among homopolymeric LCRs, the most common was Gln repeats. LCRs composed of repeats of Met and aromatic amino acids were amongst the least occurring. The results revealed that LCRs composed of negatively charged and polar amino acids were more common in comparison to LCRs formed by positively charged and hydrophobic amino acids. We also noted that generally proteins with LCRs were involved in transcription but those with Gly repeats were associated to translational activities. Our analysis suggests that proteins in which LCR is composed of hydrophobic residues are more prone toward amyloid formation. We also found that the human proteins with amyloid forming LCRs were generally involved in binding and catalytic activity. Discussion The presented analysis summarizes the most common and least occurring LCRs in proteins. Our results show that though repeats of Gln are the most abundant but Asn repeats make longest stretch of low complexity. The results showed that potential of LCRs to form amyloi…
format: application/pdf
format: text/html
creator: Bandana Kumari
creator: Ravindra Kumar
creator: Vipin Chauhan
creator: Manish Kumar
subject: Bioinformatics
subject: Computational Biology
description: doi:10.7717/peerj.5823
publisher: PeerJ Inc.
rights: © 2018 Kumari et al.
abstract: Background In both prokaryotic and eukaryotic proteins, repeated occurrence of a single or a group of few amino acids are found. These regions are termed as low complexity regions (LCRs). It has been observed that amino acid bias in LCR is directly linked to their uncontrolled expansion and amyloid formation. But a comparative analysis of the behavior of LCR based on their constituent amino acids and their association with amyloidogenic propensity is not available. Methods Firstly we grouped all LCRs on the basis of their composition: homo-polymers, positively charged amino acids, negatively charged amino acids, polar amino acids and hydrophobic amino acids. We analyzed the compositional pattern of LCRs in each group and their propensity to form amyloids. The functional characteristics of proteins containing different groups of LCRs were explored using DAVID. In addition, we also analyzed the classes, pathways and functions of human proteins that form amyloids in LCRs. Results Among homopolymeric LCRs, the most common was Gln repeats. LCRs composed of repeats of Met and aromatic amino acids were amongst the least occurring. The results revealed that LCRs composed of negatively charged and polar amino acids were more common in comparison to LCRs formed by positively charged and hydrophobic amino acids. We also noted that generally proteins with LCRs were involved in transcription but those with Gly repeats were associated to translational activities. Our analysis suggests that proteins in which LCR is composed of hydrophobic residues are more prone toward amyloid formation. We also found that the human proteins with amyloid forming LCRs were generally involved in binding and catalytic activity. Discussion The presented analysis summarizes the most common and least occurring LCRs in proteins. Our results show that though repeats of Gln are the most abundant but Asn repeats make longest stretch of low complexity. The results showed that potential of LCRs to form amyloi…
bibliographic citation: Kumari et al. (2018) Comparative functional analysis of proteins containing low-complexity predicted amyloid regions. PeerJ 6:e5823 https://doi.org/10.7717/peerj.5823
date submitted: 2018-03-31
date accepted: 2018-09-25
issued: 2018-10-30
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Kumari
  given name: Bandana
author list: Agent
  family name: Kumar
  given name: Ravindra
author list: Agent
  family name: Chauhan
  given name: Vipin
author list: Agent
  family name: Kumar
  given name: Manish
doi: 10.7717/peerj.5823
volume: 6
issn: 2167-8359
publication name: PeerJ
publication date: 2018-10-30
copyright: © 2018 Kumari et al.
attribution name: Kumari et al.

Uncovering full-length transcript isoforms of sugarcane cultivar Khon Kaen 3 using single-molecule long-read sequencing
type: item
type: AcademicArticle
description: Background Sugarcane is an important global food crop and energy resource. To facilitate the sugarcane improvement program, genome and gene information are important for studying traits at the molecular level. Most currently available transcriptome data for sugarcane were generated using second-generation sequencing platforms, which provide short reads. The de novo assembled transcripts from these data are limited in length, and hence may be incomplete and inaccurate, especially for long RNAs. Methods We generated a transcriptome dataset of leaf tissue from a commercial Thai sugarcane cultivar Khon Kaen 3 (KK3) using PacBio RS II single-molecule long-read sequencing by the Iso-Seq method. Short-read RNA-Seq data were generated from the same RNA sample using the Ion Proton platform for reducing base calling errors. Results A total of 119,339 error-corrected transcripts were generated with the N50 length of 3,611 bp, which is on average longer than any previously reported sugarcane transcriptome dataset. 110,253 sequences (92.4%) contain an open reading frame (ORF) of at least 300 bp long with ORF N50 of 1,416 bp. The mean lengths of 5′ and 3′ untranslated regions in 73,795 sequences with complete ORFs are 1,249 and 1,187 bp, respectively. 4,774 transcripts are putatively novel full-length transcripts which do not match with a previous Iso-Seq study of sugarcane. We annotated the functions of 68,962 putative full-length transcripts with at least 90% coverage when compared with homologous protein coding sequences in other plants. Discussion The new catalog of transcripts will be useful for genome annotation, identification of splicing variants, SNP identification, and other research pertaining to the sugarcane improvement program. The putatively novel transcripts suggest unique features of KK3, although more data from different tissues and stages of development are needed to establish a reference transcriptome of this cultivar.
format: application/pdf
format: text/html
creator: Jittima Piriyapongsa
creator: Pavita Kaewprommal
creator: Sirintra Vaiwsri
creator: Songtham Anuntakarun
creator: Warodom Wirojsirasak
creator: Prapat Punpee
creator: Peeraya Klomsa-ard
creator: Philip J. Shaw
creator: Wirulda Pootakham
creator: Thippawan Yoocha
creator: Duangjai Sangsrakru
creator: Sithichoke Tangphatsornruang
creator: Sissades Tongsima
creator: Somvong Tragoonrung
subject: Agricultural Science
subject: Bioinformatics
subject: Genomics
subject: Plant Science
description: doi:10.7717/peerj.5818
publisher: PeerJ Inc.
rights: © 2018 Piriyapongsa et al.
abstract: Background Sugarcane is an important global food crop and energy resource. To facilitate the sugarcane improvement program, genome and gene information are important for studying traits at the molecular level. Most currently available transcriptome data for sugarcane were generated using second-generation sequencing platforms, which provide short reads. The de novo assembled transcripts from these data are limited in length, and hence may be incomplete and inaccurate, especially for long RNAs. Methods We generated a transcriptome dataset of leaf tissue from a commercial Thai sugarcane cultivar Khon Kaen 3 (KK3) using PacBio RS II single-molecule long-read sequencing by the Iso-Seq method. Short-read RNA-Seq data were generated from the same RNA sample using the Ion Proton platform for reducing base calling errors. Results A total of 119,339 error-corrected transcripts were generated with the N50 length of 3,611 bp, which is on average longer than any previously reported sugarcane transcriptome dataset. 110,253 sequences (92.4%) contain an open reading frame (ORF) of at least 300 bp long with ORF N50 of 1,416 bp. The mean lengths of 5′ and 3′ untranslated regions in 73,795 sequences with complete ORFs are 1,249 and 1,187 bp, respectively. 4,774 transcripts are putatively novel full-length transcripts which do not match with a previous Iso-Seq study of sugarcane. We annotated the functions of 68,962 putative full-length transcripts with at least 90% coverage when compared with homologous protein coding sequences in other plants. Discussion The new catalog of transcripts will be useful for genome annotation, identification of splicing variants, SNP identification, and other research pertaining to the sugarcane improvement program. The putatively novel transcripts suggest unique features of KK3, although more data from different tissues and stages of development are needed to establish a reference transcriptome of this cultivar.
bibliographic citation: Piriyapongsa et al. (2018) Uncovering full-length transcript isoforms of sugarcane cultivar Khon Kaen 3 using single-molecule long-read sequencing. PeerJ 6:e5818 https://doi.org/10.7717/peerj.5818
date submitted: 2018-07-11
date accepted: 2018-09-23
issued: 2018-10-30
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Piriyapongsa
  given name: Jittima
author list: Agent
  family name: Kaewprommal
  given name: Pavita
author list: Agent
  family name: Vaiwsri
  given name: Sirintra
author list: Agent
  family name: Anuntakarun
  given name: Songtham
author list: Agent
  family name: Wirojsirasak
  given name: Warodom
author list: Agent
  family name: Punpee
  given name: Prapat
author list: Agent
  family name: Klomsa-ard
  given name: Peeraya
author list: Agent
  family name: Shaw
  given name: Philip J.
author list: Agent
  family name: Pootakham
  given name: Wirulda
author list: Agent
  family name: Yoocha
  given name: Thippawan
author list: Agent
  family name: Sangsrakru
  given name: Duangjai
author list: Agent
  family name: Tangphatsornruang
  given name: Sithichoke
author list: Agent
  family name: Tongsima
  given name: Sissades
author list: Agent
  family name: Tragoonrung
  given name: Somvong
doi: 10.7717/peerj.5818
volume: 6
issn: 2167-8359
publication name: PeerJ
publication date: 2018-10-30
copyright: ©2018 Piriyapongsa et al.
attribution name: Piriyapongsa et al.

Adipose tissues of MPC1± mice display altered lipid metabolism-related enzyme expression levels
type: item
type: AcademicArticle
description: Mitochondrial pyruvate carrier 1 (MPC1) is a component of the MPC1/MPC2 heterodimer that facilitates the transport of pyruvate into mitochondria. Pyruvate plays a central role in carbohydrate, fatty, and amino acid catabolism. The present study examined epididymal white adipose tissue (eWAT) and intrascapular brown adipose tissue (iBAT) from MPC1± mice following 24 weeks of feeding, which indicated low energy accumulation as evidenced by low body and eWAT weight and adipocyte volume. To characterize molecular changes in energy metabolism, we analyzed the transcriptomes of the adipose tissues using RNA-Sequencing (RNA-Seq). The results showed that the fatty acid oxidation pathway was activated and several genes involved in this pathway were upregulated. Furthermore, qPCR and western blotting indicated that numerous genes and proteins that participate in lipolysis were also upregulated. Based on these findings, we propose that the energy deficiency caused by reduced MPC1 activity can be alleviated by activating the lipolytic pathway.
format: application/pdf
format: text/html
creator: Shiying Zou
creator: Liye Zhu
creator: Kunlun Huang
creator: Haoshu Luo
creator: Wentao Xu
creator: Xiaoyun He
subject: Cell Biology
subject: Developmental Biology
subject: Molecular Biology
description: doi:10.7717/peerj.5799
publisher: PeerJ Inc.
rights: © 2018 Zou et al.
abstract: Mitochondrial pyruvate carrier 1 (MPC1) is a component of the MPC1/MPC2 heterodimer that facilitates the transport of pyruvate into mitochondria. Pyruvate plays a central role in carbohydrate, fatty, and amino acid catabolism. The present study examined epididymal white adipose tissue (eWAT) and intrascapular brown adipose tissue (iBAT) from MPC1± mice following 24 weeks of feeding, which indicated low energy accumulation as evidenced by low body and eWAT weight and adipocyte volume. To characterize molecular changes in energy metabolism, we analyzed the transcriptomes of the adipose tissues using RNA-Sequencing (RNA-Seq). The results showed that the fatty acid oxidation pathway was activated and several genes involved in this pathway were upregulated. Furthermore, qPCR and western blotting indicated that numerous genes and proteins that participate in lipolysis were also upregulated. Based on these findings, we propose that the energy deficiency caused by reduced MPC1 activity can be alleviated by activating the lipolytic pathway.
bibliographic citation: Zou et al. (2018) Adipose tissues of MPC1± mice display altered lipid metabolism-related enzyme expression levels. PeerJ 6:e5799 https://doi.org/10.7717/peerj.5799
date submitted: 2018-04-11
date accepted: 2018-09-20
issued: 2018-10-30
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Zou
  given name: Shiying
author list: Agent
  family name: Zhu
  given name: Liye
author list: Agent
  family name: Huang
  given name: Kunlun
author list: Agent
  family name: Luo
  given name: Haoshu
author list: Agent
  family name: Xu
  given name: Wentao
author list: Agent
  family name: He
  given name: Xiaoyun
doi: 10.7717/peerj.5799
volume: 6
issn: 2167-8359
publication name: PeerJ
publication date: 2018-10-30
copyright: ©2018 Zou et al.
attribution name: Zou et al.

From the cage to the wild: introductions of Psittaciformes to Puerto Rico
type: item
type: AcademicArticle
description: Introduced psittacine birds can become highly invasive. In this study, we assessed invasions of Psittaciformes in Puerto Rico. We reviewed the literature, public databases, citizen science records, and performed in situ population surveys across the island to determine the historical and current status and distribution of psittacine species. We used count data from Ebird to determine population trends. For species whose populations were increasing, we modelled their potential distribution using niche modeling techniques. We found 46 Psittaciformes in Puerto Rico, of which 26% are only present as pets, at least 29 species have been reported in the wild, and of those, there is evidence that at least 12 species are breeding. Our results indicate that most introduced species which have been detected as established still persist, although mostly in localized areas and small populations. Clear evidence of invasiveness was found for Brotogeris versicolurus and Myiopsitta monachus, which have greatly expanded their range in recent years. Psittacara erythrogenys and Eupsittacula canicularis also showed population increases, although to a lesser degree. The niche models predicted suitable areas for the four species, and also indicate the potential for range expansion. We discuss the factors leading to invasion success, assess the potential impacts, and we discuss possible management strategies and research prospects.
format: application/pdf
format: text/html
creator: Wilfredo Falcón
creator: Raymond L. Tremblay
subject: Ecology
subject: Zoology
description: doi:10.7717/peerj.5669
publisher: PeerJ Inc.
rights: © 2018 Falcón and Tremblay
abstract: Introduced psittacine birds can become highly invasive. In this study, we assessed invasions of Psittaciformes in Puerto Rico. We reviewed the literature, public databases, citizen science records, and performed in situ population surveys across the island to determine the historical and current status and distribution of psittacine species. We used count data from Ebird to determine population trends. For species whose populations were increasing, we modelled their potential distribution using niche modeling techniques. We found 46 Psittaciformes in Puerto Rico, of which 26% are only present as pets, at least 29 species have been reported in the wild, and of those, there is evidence that at least 12 species are breeding. Our results indicate that most introduced species which have been detected as established still persist, although mostly in localized areas and small populations. Clear evidence of invasiveness was found for Brotogeris versicolurus and Myiopsitta monachus, which have greatly expanded their range in recent years. Psittacara erythrogenys and Eupsittacula canicularis also showed population increases, although to a lesser degree. The niche models predicted suitable areas for the four species, and also indicate the potential for range expansion. We discuss the factors leading to invasion success, assess the potential impacts, and we discuss possible management strategies and research prospects.
bibliographic citation: Falcón et al. (2018) From the cage to the wild: introductions of Psittaciformes to Puerto Rico. PeerJ 6:e5669 https://doi.org/10.7717/peerj.5669
date submitted: 2018-02-28
date accepted: 2018-08-28
issued: 2018-10-30
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Falcón
  given name: Wilfredo
author list: Agent
  family name: Tremblay
  given name: Raymond L.
doi: 10.7717/peerj.5669
volume: 6
issn: 2167-8359
publication name: PeerJ
publication date: 2018-10-30
copyright: ©2018 Falcón and Tremblay
attribution name: Falcón and Tremblay

Using the validated Reflective Functioning Questionnaire to investigate mentalizing in individuals presenting with eating disorders with and without self-harm
type: item
type: AcademicArticle
description: Background The present study builds on previous research which explored the relationship between mentalizing and eating disorders (ED) in a subgroup of patients with comorbid self-harm (SH). Whereas previous literature had linked this comorbidity to impulse-control difficulties, more recent advances have suggested that a lack of a mentalizing stance might be responsible for a more treatment-resistant and severe symptomatology in this subgroup of clients. Methods A cross-sectional, quasi-experimental, questionnaire-based, between-groups design was employed and a measure of mentalizing was compared in individuals presenting with ED only, individuals presenting with ED and concurrent SH and a control group. Results Individuals with ED with concurrent SH reported significantly more mentalizing ability impairment than individuals without concurrent SH. In addition, both groups differed significantly from the control group. Opposite scoring patterns were identified in hypo- and hypermentalizing with the comorbid group reporting the lowest scores in hypermentalizing and the highest scores in hypomentalizing. Conclusions The current findings confirm that individuals with concurrent ED and SH report more severe impairments in mentalizing ability. Such impairments entail difficulties in symbolic capacity and abstract thinking and a concretisation of inner life, exemplified by a rigid, often inflexible focus on the physical world. The clinical implications that a lack of a mentalizing stance can have on individuals’ ability to engage with the therapeutic process and to initiate change are reflected upon.
format: application/pdf
format: text/html
creator: Angie Cucchi
creator: James A. Hampton
creator: Alesia Moulton-Perkins
subject: Clinical Trials
subject: Cognitive Disorders
subject: Evidence Based Medicine
subject: Nutrition
subject: Psychiatry and Psychology
description: doi:10.7717/peerj.5756
publisher: PeerJ Inc.
rights: © 2018 Cucchi et al.
abstract: Background The present study builds on previous research which explored the relationship between mentalizing and eating disorders (ED) in a subgroup of patients with comorbid self-harm (SH). Whereas previous literature had linked this comorbidity to impulse-control difficulties, more recent advances have suggested that a lack of a mentalizing stance might be responsible for a more treatment-resistant and severe symptomatology in this subgroup of clients. Methods A cross-sectional, quasi-experimental, questionnaire-based, between-groups design was employed and a measure of mentalizing was compared in individuals presenting with ED only, individuals presenting with ED and concurrent SH and a control group. Results Individuals with ED with concurrent SH reported significantly more mentalizing ability impairment than individuals without concurrent SH. In addition, both groups differed significantly from the control group. Opposite scoring patterns were identified in hypo- and hypermentalizing with the comorbid group reporting the lowest scores in hypermentalizing and the highest scores in hypomentalizing. Conclusions The current findings confirm that individuals with concurrent ED and SH report more severe impairments in mentalizing ability. Such impairments entail difficulties in symbolic capacity and abstract thinking and a concretisation of inner life, exemplified by a rigid, often inflexible focus on the physical world. The clinical implications that a lack of a mentalizing stance can have on individuals’ ability to engage with the therapeutic process and to initiate change are reflected upon.
bibliographic citation: Cucchi et al. (2018) Using the validated Reflective Functioning Questionnaire to investigate mentalizing in individuals presenting with eating disorders with and without self-harm. PeerJ 6:e5756 https://doi.org/10.7717/peerj.5756
date submitted: 2018-05-07
date accepted: 2018-09-14
issued: 2018-10-29
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Cucchi
  given name: Angie
author list: Agent
  family name: Hampton
  given name: James A.
author list: Agent
  family name: Moulton-Perkins
  given name: Alesia
doi: 10.7717/peerj.5756
volume: 6
issn: 2167-8359
publication name: PeerJ
publication date: 2018-10-29
copyright: ©2018 Cucchi et al.
attribution name: Cucchi et al.

Confidence in eating disorder knowledge does not predict actual knowledge in collegiate female athletes
type: item
type: AcademicArticle
description: Background Eating disorders are serious psychological disorders with long term health impacts. Athletic populations, tend to have higher incidences of eating disorders compared to the general population. Yet there is little known about athletes’ eating disorder knowledge and how it relates to their confidence in their knowledge. Therefore, the purpose of our study was to evaluate collegiate female athletes’ eating disorder (ED) knowledge and confidence in their knowledge. 51 participants were recruited from a National Association of Intercollegiate Athletics (NAIA) university in the mid-west and asked to complete a 30-question exam assessing one’s knowledge of five different categories related to eating disorders. Confidence in the correctness of answers was assessed with a 5-point Likert-scale (1 = very unconfident, 5 = very confident). A one-way ANOVA was used to determine differences between scores on different categories and overall scores. A simple regression analysis was used to determine if confidence or age was predictive in knowledge scores. Results The average score of participants was 69.1%, SD = 10.8% with an average confidence of 3.69/5, SD = 0.33. Athletes scored lowest with regards to Identifying Signs and Symptoms of EDs compared to other sub-scores (p < 0.05). There was no relationship between knowledge and confidence scores. Discussion There is limited ED knowledge among collegiate female athletes. This may be problematic as many athletes appear confident in the correctness of their answers despite these low scores. Coaches should be aware of this lack of knowledge and work with clinical practitioners, such as dieticians, team physicians and athletic trainers to educate and monitor their athletes on eating disorders, specifically signs and symptoms.
format: application/pdf
format: text/html
creator: Megan E. Rosa-Caldwell
creator: Christopher Todden
creator: Aaron R. Caldwell
creator: Lauren E. Breithaupt
subject: Kinesiology
subject: Nutrition
subject: Women’s Health
subject: Science and Medical Education
description: doi:10.7717/peerj.5868
publisher: PeerJ Inc.
rights: © 2018 Rosa-Caldwell et al.
abstract: Background Eating disorders are serious psychological disorders with long term health impacts. Athletic populations, tend to have higher incidences of eating disorders compared to the general population. Yet there is little known about athletes’ eating disorder knowledge and how it relates to their confidence in their knowledge. Therefore, the purpose of our study was to evaluate collegiate female athletes’ eating disorder (ED) knowledge and confidence in their knowledge. 51 participants were recruited from a National Association of Intercollegiate Athletics (NAIA) university in the mid-west and asked to complete a 30-question exam assessing one’s knowledge of five different categories related to eating disorders. Confidence in the correctness of answers was assessed with a 5-point Likert-scale (1 = very unconfident, 5 = very confident). A one-way ANOVA was used to determine differences between scores on different categories and overall scores. A simple regression analysis was used to determine if confidence or age was predictive in knowledge scores. Results The average score of participants was 69.1%, SD = 10.8% with an average confidence of 3.69/5, SD = 0.33. Athletes scored lowest with regards to Identifying Signs and Symptoms of EDs compared to other sub-scores (p < 0.05). There was no relationship between knowledge and confidence scores. Discussion There is limited ED knowledge among collegiate female athletes. This may be problematic as many athletes appear confident in the correctness of their answers despite these low scores. Coaches should be aware of this lack of knowledge and work with clinical practitioners, such as dieticians, team physicians and athletic trainers to educate and monitor their athletes on eating disorders, specifically signs and symptoms.
bibliographic citation: Rosa-Caldwell et al. (2018) Confidence in eating disorder knowledge does not predict actual knowledge in collegiate female athletes. PeerJ 6:e5868 https://doi.org/10.7717/peerj.5868
date submitted: 2018-03-01
date accepted: 2018-10-03
issued: 2018-10-29
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Rosa-Caldwell
  given name: Megan E.
author list: Agent
  family name: Todden
  given name: Christopher
author list: Agent
  family name: Caldwell
  given name: Aaron R.
author list: Agent
  family name: Breithaupt
  given name: Lauren E.
doi: 10.7717/peerj.5868
volume: 6
issn: 2167-8359
publication name: PeerJ
publication date: 2018-10-29
copyright: ©2018 Rosa-Caldwell et al.
attribution name: Rosa-Caldwell et al.

Ensemble learning for detecting gene-gene interactions in colorectal cancer
type: item
type: AcademicArticle
description: Colorectal cancer (CRC) has a high incident rate in both men and women and is affecting millions of people every year. Genome-wide association studies (GWAS) on CRC have successfully revealed common single-nucleotide polymorphisms (SNPs) associated with CRC risk. However, they can only explain a very limited fraction of the disease heritability. One reason may be the common uni-variable analyses in GWAS where genetic variants are examined one at a time. Given the complexity of cancers, the non-additive interaction effects among multiple genetic variants have a potential of explaining the missing heritability. In this study, we employed two powerful ensemble learning algorithms, random forests and gradient boosting machine (GBM), to search for SNPs that contribute to the disease risk through non-additive gene-gene interactions. We were able to find 44 possible susceptibility SNPs that were ranked most significant by both algorithms. Out of those 44 SNPs, 29 are in coding regions. The 29 genes include ARRDC5, DCC, ALK, and ITGA1, which have been found previously associated with CRC, and E2F3 and NID2, which are potentially related to CRC since they have known associations with other types of cancer. We performed pairwise and three-way interaction analysis on the 44 SNPs using information theoretical techniques and found 17 pairwise (p < 0.02) and 16 three-way (p ≤ 0.001) interactions among them. Moreover, functional enrichment analysis suggested 16 functional terms or biological pathways that may help us better understand the etiology of the disease.
format: application/pdf
format: text/html
creator: Faramarz Dorani
creator: Ting Hu
creator: Michael O. Woods
creator: Guangju Zhai
subject: Bioinformatics
subject: Computational Biology
subject: Genetics
subject: Epidemiology
subject: Data Mining and Machine Learning
description: doi:10.7717/peerj.5854
publisher: PeerJ Inc.
rights: © 2018 Dorani et al.
abstract: Colorectal cancer (CRC) has a high incident rate in both men and women and is affecting millions of people every year. Genome-wide association studies (GWAS) on CRC have successfully revealed common single-nucleotide polymorphisms (SNPs) associated with CRC risk. However, they can only explain a very limited fraction of the disease heritability. One reason may be the common uni-variable analyses in GWAS where genetic variants are examined one at a time. Given the complexity of cancers, the non-additive interaction effects among multiple genetic variants have a potential of explaining the missing heritability. In this study, we employed two powerful ensemble learning algorithms, random forests and gradient boosting machine (GBM), to search for SNPs that contribute to the disease risk through non-additive gene-gene interactions. We were able to find 44 possible susceptibility SNPs that were ranked most significant by both algorithms. Out of those 44 SNPs, 29 are in coding regions. The 29 genes include ARRDC5, DCC, ALK, and ITGA1, which have been found previously associated with CRC, and E2F3 and NID2, which are potentially related to CRC since they have known associations with other types of cancer. We performed pairwise and three-way interaction analysis on the 44 SNPs using information theoretical techniques and found 17 pairwise (p < 0.02) and 16 three-way (p ≤ 0.001) interactions among them. Moreover, functional enrichment analysis suggested 16 functional terms or biological pathways that may help us better understand the etiology of the disease.
bibliographic citation: Dorani et al. (2018) Ensemble learning for detecting gene-gene interactions in colorectal cancer. PeerJ 6:e5854 https://doi.org/10.7717/peerj.5854
date submitted: 2018-06-05
date accepted: 2018-09-28
issued: 2018-10-29
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Dorani
  given name: Faramarz
author list: Agent
  family name: Hu
  given name: Ting
author list: Agent
  family name: Woods
  given name: Michael O.
author list: Agent
  family name: Zhai
  given name: Guangju
doi: 10.7717/peerj.5854
volume: 6
issn: 2167-8359
publication name: PeerJ
publication date: 2018-10-29
copyright: © 2018 Dorani et al.
attribution name: Dorani et al.

Don’t worry, be active: how to facilitate the detection of errors in immersive virtual environments
type: item
type: AcademicArticle
description: The current research aims to study the link between the type of vision experienced in a collaborative immersive virtual environment (active vs. multiple passive), the type of error one looks for during a cooperative multi-user exploration of a design project (affordance vs. perceptual violations), and the type of setting in which multi-user perform (field in Experiment 1 vs. laboratory in Experiment 2). The relevance of this link is backed by the lack of conclusive evidence on an active vs. passive vision advantage in cooperative search tasks within software based on immersive virtual reality (IVR). Using a yoking paradigm based on the mixed usage of simultaneous active and multiple passive viewings, we found that the likelihood of error detection in a complex 3D environment was characterized by an active vs. multi-passive viewing advantage depending on: (1) the degree of knowledge dependence of the type of error the passive/active observers were looking for (low for perceptual violations, vs. high for affordance violations), as the advantage tended to manifest itself irrespectively from the setting for affordance, but not for perceptual violations; and (2) the degree of social desirability possibly induced by the setting in which the task was performed, as the advantage occurred irrespectively from the type of error in the laboratory (Experiment 2) but not in the field (Experiment 1) setting. Results are relevant to future development of cooperative software based on IVR used for supporting the design review. A multi-user design review experience in which designers, engineers and end-users all cooperate actively within the IVR wearing their own head mounted display, seems more suitable for the detection of relevant errors than standard systems characterized by a mixed usage of active and passive viewing.
format: application/pdf
format: text/html
creator: Sara Rigutti
creator: Marta Stragà
creator: Marco Jez
creator: Giulio Baldassi
creator: Andrea Carnaghi
creator: Piero Miceu
creator: Carlo Fantoni
subject: Neuroscience
subject: Psychiatry and Psychology
subject: Human–Computer Interaction
description: doi:10.7717/peerj.5844
publisher: PeerJ Inc.
rights: © 2018 Rigutti et al.
abstract: The current research aims to study the link between the type of vision experienced in a collaborative immersive virtual environment (active vs. multiple passive), the type of error one looks for during a cooperative multi-user exploration of a design project (affordance vs. perceptual violations), and the type of setting in which multi-user perform (field in Experiment 1 vs. laboratory in Experiment 2). The relevance of this link is backed by the lack of conclusive evidence on an active vs. passive vision advantage in cooperative search tasks within software based on immersive virtual reality (IVR). Using a yoking paradigm based on the mixed usage of simultaneous active and multiple passive viewings, we found that the likelihood of error detection in a complex 3D environment was characterized by an active vs. multi-passive viewing advantage depending on: (1) the degree of knowledge dependence of the type of error the passive/active observers were looking for (low for perceptual violations, vs. high for affordance violations), as the advantage tended to manifest itself irrespectively from the setting for affordance, but not for perceptual violations; and (2) the degree of social desirability possibly induced by the setting in which the task was performed, as the advantage occurred irrespectively from the type of error in the laboratory (Experiment 2) but not in the field (Experiment 1) setting. Results are relevant to future development of cooperative software based on IVR used for supporting the design review. A multi-user design review experience in which designers, engineers and end-users all cooperate actively within the IVR wearing their own head mounted display, seems more suitable for the detection of relevant errors than standard systems characterized by a mixed usage of active and passive viewing.
bibliographic citation: Rigutti et al. (2018) Don’t worry, be active: how to facilitate the detection of errors in immersive virtual environments. PeerJ 6:e5844 https://doi.org/10.7717/peerj.5844
date submitted: 2018-03-07
date accepted: 2018-09-26
issued: 2018-10-29
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Rigutti
  given name: Sara
author list: Agent
  family name: Stragà
  given name: Marta
author list: Agent
  family name: Jez
  given name: Marco
author list: Agent
  family name: Baldassi
  given name: Giulio
author list: Agent
  family name: Carnaghi
  given name: Andrea
author list: Agent
  family name: Miceu
  given name: Piero
author list: Agent
  family name: Fantoni
  given name: Carlo
doi: 10.7717/peerj.5844
volume: 6
issn: 2167-8359
publication name: PeerJ
publication date: 2018-10-29
copyright: © 2018 Rigutti et al.
attribution name: Rigutti et al.

Association of urban forest landscape characteristics with biomass and soil carbon stocks in Harbin City, Northeastern China
type: item
type: AcademicArticle
description: Background Urban forests help in mitigating carbon emissions; however, their associations with landscape patterns are unclear. Understanding the associations would help us to evaluate urban forest ecological services and favor urban forest management via landscape regulations. We used Harbin, capital city of the northernmost province in China, as an example and hypothesized that the urban forests had different landscape metrics among different forest types, administrative districts, and urban–rural gradients, and these differences were closely associated with forest carbon sequestration in the biomass and soils. Methods We extracted the urban forest tree coverage area on the basis of 2 GF-1 remote sensing images and object-oriented based classification method. The analysis of forest landscape patterns and estimation of carbon storage were based on tree coverage data and 199 plots. We also examined the relationships between forest landscape metrics and carbon storage on the basis of forest types, administrative districts, ring roads, and history of urban settlements by using statistical methods. Results The small patches covering an area of less than 0.5 ha accounted for 72.6% of all patches (average patch size, 0.31 ha). The mean patch size (AREA_MN) and largest patch index (LPI) were the highest in the landscape and relaxation forest and Songbei District. The landscape shape index (LSI) and number of patches linearly decreased along rural-urban gradients (p < 0.05). The tree biomass carbon storage varied from less than 10 thousand tons in the urban center (first ring road region and 100-year regions) to more than 100 thousand tons in the rural regions (fourth ring road and newly urbanized regions). In the same urban–rural gradients, soil carbon storage varied from less than five thousand tons in the urban centers to 73–103 thousand tons in the rural regions. The association analysis indicated that the total forest area was the key factor that regulates total carbon…
format: application/pdf
format: text/html
creator: Hailiang Lv
creator: Wenjie Wang
creator: Xingyuan He
creator: Chenhui Wei
creator: Lu Xiao
creator: Bo Zhang
creator: Wei Zhou
subject: Ecology
subject: Forestry
subject: Spatial and Geographic Information Science
description: doi:10.7717/peerj.5825
publisher: PeerJ Inc.
rights: © 2018 Lv et al.
abstract: Background Urban forests help in mitigating carbon emissions; however, their associations with landscape patterns are unclear. Understanding the associations would help us to evaluate urban forest ecological services and favor urban forest management via landscape regulations. We used Harbin, capital city of the northernmost province in China, as an example and hypothesized that the urban forests had different landscape metrics among different forest types, administrative districts, and urban–rural gradients, and these differences were closely associated with forest carbon sequestration in the biomass and soils. Methods We extracted the urban forest tree coverage area on the basis of 2 GF-1 remote sensing images and object-oriented based classification method. The analysis of forest landscape patterns and estimation of carbon storage were based on tree coverage data and 199 plots. We also examined the relationships between forest landscape metrics and carbon storage on the basis of forest types, administrative districts, ring roads, and history of urban settlements by using statistical methods. Results The small patches covering an area of less than 0.5 ha accounted for 72.6% of all patches (average patch size, 0.31 ha). The mean patch size (AREA_MN) and largest patch index (LPI) were the highest in the landscape and relaxation forest and Songbei District. The landscape shape index (LSI) and number of patches linearly decreased along rural-urban gradients (p < 0.05). The tree biomass carbon storage varied from less than 10 thousand tons in the urban center (first ring road region and 100-year regions) to more than 100 thousand tons in the rural regions (fourth ring road and newly urbanized regions). In the same urban–rural gradients, soil carbon storage varied from less than five thousand tons in the urban centers to 73–103 thousand tons in the rural regions. The association analysis indicated that the total forest area was the key factor that regulates total carbon…
bibliographic citation: Lv et al. (2018) Association of urban forest landscape characteristics with biomass and soil carbon stocks in Harbin City, Northeastern China. PeerJ 6:e5825 https://doi.org/10.7717/peerj.5825
date submitted: 2017-12-07
date accepted: 2018-09-25
issued: 2018-10-29
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Lv
  given name: Hailiang
author list: Agent
  family name: Wang
  given name: Wenjie
author list: Agent
  family name: He
  given name: Xingyuan
author list: Agent
  family name: Wei
  given name: Chenhui
author list: Agent
  family name: Xiao
  given name: Lu
author list: Agent
  family name: Zhang
  given name: Bo
author list: Agent
  family name: Zhou
  given name: Wei
doi: 10.7717/peerj.5825
volume: 6
issn: 2167-8359
publication name: PeerJ
publication date: 2018-10-29
copyright: ©2018 Lv et al.
attribution name: Lv et al.

Effects of agricultural management on phyllosphere fungal diversity in vineyards and the association with adjacent native forests
type: item
type: AcademicArticle
description: Agriculture is one of the main drivers of land conversion, and agriculture practices can impact on microbial diversity. Here we characterized the phyllosphere fungal diversity associated with Carménère grapevines under conventional and organic agricultural management. We also explored the fungal diversity present in the adjacent sclerophyllous forests to explore the potential role of native forest on vineyard phyllosphere. After conducting D2 and ITS2 amplicon sequencing, we found that fungal diversity indices did not change between conventional and organic vineyards, but community structure was sensitive to the agricultural management. On the other hand, we found a high proportion of shared fungal OTUs between vineyards and native forests. In addition, both habitats had similar levels of fungal diversity despite forest samples were derived from multiple plant species. In contrast, the community structure was different in both habitats. Interestingly, the native forest had more unidentified species and unique OTUs than vineyards. Forest dominant species were Aureobasidium pullulans and Endoconidioma populi, whereas Davidiella tassiana, Didymella sp., and Alternaria eichhorniae were more abundant in vineyards. Overall, this study argues that a better understanding of the relationship native forests and agroecosystems is needed for maintaining and enhancing ecosystem services provided by natural ecosystems. Finally, knowledge of microbial communities living in the Chilean Mediterranean biome is needed for appropriate conservation management of these biomes and their classification as biodiversity hotspots.
format: application/pdf
format: text/html
creator: Luis E. Castañeda
creator: Toshiko Miura
creator: Roland Sánchez
creator: Olga Barbosa
subject: Agricultural Science
subject: Biodiversity
subject: Conservation Biology
subject: Mycology
description: doi:10.7717/peerj.5715
publisher: PeerJ Inc.
rights: © 2018 Castañeda et al.
abstract: Agriculture is one of the main drivers of land conversion, and agriculture practices can impact on microbial diversity. Here we characterized the phyllosphere fungal diversity associated with Carménère grapevines under conventional and organic agricultural management. We also explored the fungal diversity present in the adjacent sclerophyllous forests to explore the potential role of native forest on vineyard phyllosphere. After conducting D2 and ITS2 amplicon sequencing, we found that fungal diversity indices did not change between conventional and organic vineyards, but community structure was sensitive to the agricultural management. On the other hand, we found a high proportion of shared fungal OTUs between vineyards and native forests. In addition, both habitats had similar levels of fungal diversity despite forest samples were derived from multiple plant species. In contrast, the community structure was different in both habitats. Interestingly, the native forest had more unidentified species and unique OTUs than vineyards. Forest dominant species were Aureobasidium pullulans and Endoconidioma populi, whereas Davidiella tassiana, Didymella sp., and Alternaria eichhorniae were more abundant in vineyards. Overall, this study argues that a better understanding of the relationship native forests and agroecosystems is needed for maintaining and enhancing ecosystem services provided by natural ecosystems. Finally, knowledge of microbial communities living in the Chilean Mediterranean biome is needed for appropriate conservation management of these biomes and their classification as biodiversity hotspots.
bibliographic citation: Castañeda et al. (2018) Effects of agricultural management on phyllosphere fungal diversity in vineyards and the association with adjacent native forests. PeerJ 6:e5715 https://doi.org/10.7717/peerj.5715
date submitted: 2018-05-11
date accepted: 2018-09-10
issued: 2018-10-29
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Castañeda
  given name: Luis E.
author list: Agent
  family name: Miura
  given name: Toshiko
author list: Agent
  family name: Sánchez
  given name: Roland
author list: Agent
  family name: Barbosa
  given name: Olga
doi: 10.7717/peerj.5715
volume: 6
issn: 2167-8359
publication name: PeerJ
publication date: 2018-10-29
copyright: ©2018 Castañeda et al.
attribution name: Castañeda et al.

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