PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
items: Large-scale gene expression analysis reveals robust gene signatures for prognosis prediction in lung adenocarcinoma
items: Comparison of therapeutic effects of different mesenchymal stem cells on rheumatoid arthritis in mice
items: Associations between cortisol awakening response and resting electroencephalograph asymmetry
items: Spray-dried immobilized lipase from Geobacillus sp. strain ARM in sago
items: A simple model of a growing tumour
items: ConFindr: rapid detection of intraspecies and cross-species contamination in bacterial whole-genome sequence data
items: Recommendations for dietary level of micro-minerals and vitamin D3 to Atlantic salmon (Salmo salar) parr and post-smolt when fed low fish meal diets
items: Prevalence and contributing factors of dental caries of 6-year-old children in four regions of China
items: Funmap2: an R package for QTL mapping using longitudinal phenotypes
items: Integrating species and interactions into similarity metrics: a graph theory-based approach to understanding community similarity

Large-scale gene expression analysis reveals robust gene signatures for prognosis prediction in lung adenocarcinoma
type: item
type: AcademicArticle
description: Lung adenocarcinoma (LUAD) is the leading cause of cancer-related death worldwide. High mortality in LUAD motivates us to stratify the patients into high- and low-risk groups, which is beneficial for the clinicians to design a personalized therapeutic regimen. To robustly predict the risk, we identified a set of robust prognostic gene signatures and critical pathways based on ten gene expression datasets by the meta-analysis-based Cox regression model, 25 of which were selected as predictors of multivariable Cox regression model by MMPC algorithm. Gene set enrichment analysis (GSEA) identified the Aurora-A pathway, the Aurora-B pathway, and the FOXM1 transcription factor network as prognostic pathways in LUAD. Moreover, the three prognostic pathways were also the biological processes of G2-M transition, suggesting that hyperactive G2-M transition in cell cycle was an indicator of poor prognosis in LUAD. The validation in the independent datasets suggested that overall survival differences were observed not only in all LUAD patients, but also in those with a specific TNM stage, gender, and age group. The comprehensive analysis demonstrated that prognostic signatures and the prognostic model by the large-scale gene expression analysis were more robust than models built by single data based gene signatures in LUAD overall survival prediction.
format: application/pdf
format: text/html
creator: Yiyan Songyang
creator: Wei Zhu
creator: Cong Liu
creator: Lin-lin Li
creator: Wei Hu
creator: Qun Zhou
creator: Han Zhang
creator: Wen Li
creator: Dejia Li
subject: Cell Biology
subject: Molecular Biology
subject: Oncology
subject: Data Science
description: doi:10.7717/peerj.6980
publisher: PeerJ Inc.
rights: © 2019 Songyang et al.
abstract: Lung adenocarcinoma (LUAD) is the leading cause of cancer-related death worldwide. High mortality in LUAD motivates us to stratify the patients into high- and low-risk groups, which is beneficial for the clinicians to design a personalized therapeutic regimen. To robustly predict the risk, we identified a set of robust prognostic gene signatures and critical pathways based on ten gene expression datasets by the meta-analysis-based Cox regression model, 25 of which were selected as predictors of multivariable Cox regression model by MMPC algorithm. Gene set enrichment analysis (GSEA) identified the Aurora-A pathway, the Aurora-B pathway, and the FOXM1 transcription factor network as prognostic pathways in LUAD. Moreover, the three prognostic pathways were also the biological processes of G2-M transition, suggesting that hyperactive G2-M transition in cell cycle was an indicator of poor prognosis in LUAD. The validation in the independent datasets suggested that overall survival differences were observed not only in all LUAD patients, but also in those with a specific TNM stage, gender, and age group. The comprehensive analysis demonstrated that prognostic signatures and the prognostic model by the large-scale gene expression analysis were more robust than models built by single data based gene signatures in LUAD overall survival prediction.
bibliographic citation: Songyang et al. (2019) Large-scale gene expression analysis reveals robust gene signatures for prognosis prediction in lung adenocarcinoma. PeerJ 7:e6980 https://doi.org/10.7717/peerj.6980
date submitted: 2019-02-19
date accepted: 2019-04-18
issued: 2019-06-03
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Songyang
  given name: Yiyan
author list: Agent
  family name: Zhu
  given name: Wei
author list: Agent
  family name: Liu
  given name: Cong
author list: Agent
  family name: Li
  given name: Lin-lin
author list: Agent
  family name: Hu
  given name: Wei
author list: Agent
  family name: Zhou
  given name: Qun
author list: Agent
  family name: Zhang
  given name: Han
author list: Agent
  family name: Li
  given name: Wen
author list: Agent
  family name: Li
  given name: Dejia
doi: 10.7717/peerj.6980
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-06-03
copyright: ©2019 Songyang et al.
attribution name: Songyang et al.

Comparison of therapeutic effects of different mesenchymal stem cells on rheumatoid arthritis in mice
type: item
type: AcademicArticle
description: Background Rheumatoid arthritis (RA) is a chronic and nonspecific autoimmune disease, which leads to joint destruction and deformity. To investigate the potential of human mesenchymal stem cells (MSCs) as a new therapeutic strategy for patients with RA, we compared the therapeutic effects of bone marrow derived MSCs (BMSCs), umbilical cord derived MSCs (UCs), and stem cells derived from human exfoliated deciduous teeth (SHED) on collagen-induced arthritis (CIA) in mice. Methods A total of 24 DBA/1 mice were infused with type II collagen to induce RA in the experimental model. MSC-treated mice were infused with UCs, BMSCs, and SHED, respectively. Bone erosion and joint destruction were measured by micro-computed tomographic (micro-CT) analysis and hematoxylin and eosin staining. The levels of tumor necrosis factor α (TNF-α) and interleukin-1β (IL-1β) were measured by immunohistochemistry and Enzyme-Linked Immunosorbent Assay (ELISA). Results Systemic delivery of MSCs significantly improved the severity of the symptoms related to CIA to greater extent compared with the untreated control group. Micro-CT revealed reduced bone erosions in the metatarsophalangeal joints upon treatment with MSCs. Additionally, according to histologic evaluation, reduced synovitis and articular destruction were observed in MSC-treated groups. The levels of TNF-α and IL-1β in the serum and joints decreased with treatment by MSCs. Conclusion Our findings suggest that systemic infusion of UCs, BMSCs, and SHED may significantly alleviate the effects of RA. The therapeutic effect of BMSCs was greater than that of SHED, while the UCs were shown to have the best therapeutic effect on CIA mice. In conclusion, compared with BMSCs and SHED, UCs may be a more suitable source of MSCs for the treatment of patients with RA.
format: application/pdf
format: text/html
creator: Qing Zhang
creator: Qihong Li
creator: Jun Zhu
creator: Hao Guo
creator: Qiming Zhai
creator: Bei Li
creator: Yan Jin
creator: Xiaoning He
creator: Fang Jin
subject: Cell Biology
subject: Immunology
subject: Rheumatology
subject: Translational Medicine
description: doi:10.7717/peerj.7023
publisher: PeerJ Inc.
rights: © 2019 Zhang et al.
abstract: Background Rheumatoid arthritis (RA) is a chronic and nonspecific autoimmune disease, which leads to joint destruction and deformity. To investigate the potential of human mesenchymal stem cells (MSCs) as a new therapeutic strategy for patients with RA, we compared the therapeutic effects of bone marrow derived MSCs (BMSCs), umbilical cord derived MSCs (UCs), and stem cells derived from human exfoliated deciduous teeth (SHED) on collagen-induced arthritis (CIA) in mice. Methods A total of 24 DBA/1 mice were infused with type II collagen to induce RA in the experimental model. MSC-treated mice were infused with UCs, BMSCs, and SHED, respectively. Bone erosion and joint destruction were measured by micro-computed tomographic (micro-CT) analysis and hematoxylin and eosin staining. The levels of tumor necrosis factor α (TNF-α) and interleukin-1β (IL-1β) were measured by immunohistochemistry and Enzyme-Linked Immunosorbent Assay (ELISA). Results Systemic delivery of MSCs significantly improved the severity of the symptoms related to CIA to greater extent compared with the untreated control group. Micro-CT revealed reduced bone erosions in the metatarsophalangeal joints upon treatment with MSCs. Additionally, according to histologic evaluation, reduced synovitis and articular destruction were observed in MSC-treated groups. The levels of TNF-α and IL-1β in the serum and joints decreased with treatment by MSCs. Conclusion Our findings suggest that systemic infusion of UCs, BMSCs, and SHED may significantly alleviate the effects of RA. The therapeutic effect of BMSCs was greater than that of SHED, while the UCs were shown to have the best therapeutic effect on CIA mice. In conclusion, compared with BMSCs and SHED, UCs may be a more suitable source of MSCs for the treatment of patients with RA.
bibliographic citation: Zhang et al. (2019) Comparison of therapeutic effects of different mesenchymal stem cells on rheumatoid arthritis in mice. PeerJ 7:e7023 https://doi.org/10.7717/peerj.7023
date submitted: 2019-01-21
date accepted: 2019-04-25
issued: 2019-06-03
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Zhang
  given name: Qing
author list: Agent
  family name: Li
  given name: Qihong
author list: Agent
  family name: Zhu
  given name: Jun
author list: Agent
  family name: Guo
  given name: Hao
author list: Agent
  family name: Zhai
  given name: Qiming
author list: Agent
  family name: Li
  given name: Bei
author list: Agent
  family name: Jin
  given name: Yan
author list: Agent
  family name: He
  given name: Xiaoning
author list: Agent
  family name: Jin
  given name: Fang
doi: 10.7717/peerj.7023
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-06-03
copyright: © 2019 Zhang et al.
attribution name: Zhang et al.

Associations between cortisol awakening response and resting electroencephalograph asymmetry
type: item
type: AcademicArticle
description: The cortisol awakening response (CAR), a rapid cortisol rise in the morning after awakening, has been proposed to provide energy to cope with daily demands and suggested to be associated with brain functions. Electroencephalogram (EEG) asymmetry studies have implicated asymmetric cortical activation, especially in frontal cortex, in approach-withdrawal motivation. In this study, we examined the relationship between the CAR and lateralized cortical activity under rest in 55 university male students. Saliva samples were collected at 0, 15, 30 and 60 min after awakening on the two consecutive workdays. The lateralized cortical activity at frontocentral sites was examined by alpha asymmetry score. The results showed that a higher CAR was positively associated with alpha asymmetry score, which indicated that the higher CAR is linked with more left-sided cortical activity at frontocentral sites under resting state. This association still existed even after controlling psychological and sleep quality variables. These results suggested that appropriately mobilizing energy resource storage after awakening revealed as CAR might be associated with goal-directed approach tendencies before any eventual stressful situation, characteristic of more left than right resting-state frontocentral cortical activity.
format: application/pdf
format: text/html
creator: Hongxia Duan
creator: Huihua Fang
creator: Yuling Zhang
creator: Xia Shi
creator: Liang Zhang
subject: Neuroscience
subject: Psychiatry and Psychology
description: doi:10.7717/peerj.7059
publisher: PeerJ Inc.
rights: © 2019 Duan et al.
abstract: The cortisol awakening response (CAR), a rapid cortisol rise in the morning after awakening, has been proposed to provide energy to cope with daily demands and suggested to be associated with brain functions. Electroencephalogram (EEG) asymmetry studies have implicated asymmetric cortical activation, especially in frontal cortex, in approach-withdrawal motivation. In this study, we examined the relationship between the CAR and lateralized cortical activity under rest in 55 university male students. Saliva samples were collected at 0, 15, 30 and 60 min after awakening on the two consecutive workdays. The lateralized cortical activity at frontocentral sites was examined by alpha asymmetry score. The results showed that a higher CAR was positively associated with alpha asymmetry score, which indicated that the higher CAR is linked with more left-sided cortical activity at frontocentral sites under resting state. This association still existed even after controlling psychological and sleep quality variables. These results suggested that appropriately mobilizing energy resource storage after awakening revealed as CAR might be associated with goal-directed approach tendencies before any eventual stressful situation, characteristic of more left than right resting-state frontocentral cortical activity.
bibliographic citation: Duan et al. (2019) Associations between cortisol awakening response and resting electroencephalograph asymmetry. PeerJ 7:e7059 https://doi.org/10.7717/peerj.7059
date submitted: 2019-03-21
date accepted: 2019-05-03
issued: 2019-06-03
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Duan
  given name: Hongxia
author list: Agent
  family name: Fang
  given name: Huihua
author list: Agent
  family name: Zhang
  given name: Yuling
author list: Agent
  family name: Shi
  given name: Xia
author list: Agent
  family name: Zhang
  given name: Liang
doi: 10.7717/peerj.7059
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-06-03
copyright: © 2019 Duan et al.
attribution name: Duan et al.

Spray-dried immobilized lipase from Geobacillus sp. strain ARM in sago
type: item
type: AcademicArticle
description: Sago starch is traditionally used as food especially in Southeast Asia. Generally, sago is safe for consumption, biodegradable, easily available and inexpensive. Therefore, this research was done to expand the potential of sago by using it as a support for enzyme immobilization. In this study, ARM lipase, which was isolated from Geobacillus sp. strain ARM, was overexpressed in Escherichia coli system and then purified using affinity chromatography. The specific activity of the pure enzyme was 650 U/mg, increased 7 folds from the cell lysate. The purified enzyme was immobilized in gelatinized sago and spray-dried by entrapment technique in order to enhance the enzyme operational stability for handling at high temperature and also for storage. The morphology of the gelatinized sago and immobilized enzyme was studied by scanning electron microscopy. The results showed that the spray-dried gelatinized sago was shrunken and became irregular in structure as compared to untreated sago powder. The surface areas and porosities of spray-dried gelatinized sago with and without the enzyme were analyzed using BET and BJH method and have shown an increase in surface area and decrease in pore size. The immobilized ARM lipase showed good performance at 60–80 °C, with a half-life of 4 h and in a pH range 6–9. The immobilized enzyme could be stored at 10 °C with the half-life for 9 months. Collectively, the spray-dried immobilized lipase shows promising capability for industrial uses, especially in food processing.
format: application/pdf
format: text/html
creator: Nur Syazwani Mohtar
creator: Mohd Basyaruddin Abdul Rahman
creator: Shuhaimi Mustafa
creator: Mohd Shukuri Mohamad Ali
creator: Raja Noor Zaliha Raja Abd. Rahman
subject: Biotechnology
subject: Food Science and Technology
subject: Microbiology
subject: Molecular Biology
description: doi:10.7717/peerj.6880
publisher: PeerJ Inc.
rights: © 2019 Mohtar et al.
abstract: Sago starch is traditionally used as food especially in Southeast Asia. Generally, sago is safe for consumption, biodegradable, easily available and inexpensive. Therefore, this research was done to expand the potential of sago by using it as a support for enzyme immobilization. In this study, ARM lipase, which was isolated from Geobacillus sp. strain ARM, was overexpressed in Escherichia coli system and then purified using affinity chromatography. The specific activity of the pure enzyme was 650 U/mg, increased 7 folds from the cell lysate. The purified enzyme was immobilized in gelatinized sago and spray-dried by entrapment technique in order to enhance the enzyme operational stability for handling at high temperature and also for storage. The morphology of the gelatinized sago and immobilized enzyme was studied by scanning electron microscopy. The results showed that the spray-dried gelatinized sago was shrunken and became irregular in structure as compared to untreated sago powder. The surface areas and porosities of spray-dried gelatinized sago with and without the enzyme were analyzed using BET and BJH method and have shown an increase in surface area and decrease in pore size. The immobilized ARM lipase showed good performance at 60–80 °C, with a half-life of 4 h and in a pH range 6–9. The immobilized enzyme could be stored at 10 °C with the half-life for 9 months. Collectively, the spray-dried immobilized lipase shows promising capability for industrial uses, especially in food processing.
bibliographic citation: Mohtar et al. (2019) Spray-dried immobilized lipase from Geobacillus sp. strain ARM in sago. PeerJ 7:e6880 https://doi.org/10.7717/peerj.6880
date submitted: 2018-10-04
date accepted: 2019-03-29
issued: 2019-05-31
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Mohtar
  given name: Nur Syazwani
author list: Agent
  family name: Abdul Rahman
  given name: Mohd Basyaruddin
author list: Agent
  family name: Mustafa
  given name: Shuhaimi
author list: Agent
  family name: Mohamad Ali
  given name: Mohd Shukuri
author list: Agent
  family name: Raja Abd. Rahman
  given name: Raja Noor Zaliha
doi: 10.7717/peerj.6880
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-05-31
copyright: ©2019 Mohtar et al.
attribution name: Mohtar et al.

A simple model of a growing tumour
type: item
type: AcademicArticle
description: This paper presents the CellCycler, a model of a growing tumour which aims to simulate and predict the effect of treatment on xenograft studies or in the clinic. The model, which is freely available as a web application, uses ordinary differential equations (ODEs) to simulate cells as they pass through the phases of the cell cycle. However the guiding philosophy of the model is that it should only use parameters that can be observed or reasonably well approximated. There is no representation of the complex internal dynamics of each cell; instead the level of analysis is limited to cell state observables such as cell phase, apoptosis, and damage. We show that this approach, while limited in many respects, still naturally accounts for a heteregenous cell population with varying doubling time, and closely captures the dynamics of a growing tumour as it is exposed to treatment. The program is demonstrated using three case studies.
format: application/pdf
format: text/html
creator: David Orrell
creator: Hitesh B. Mistry
subject: Computational Biology
subject: Mathematical Biology
subject: Oncology
subject: Pharmacology
description: doi:10.7717/peerj.6983
publisher: PeerJ Inc.
rights: © 2019 Orrell and Mistry
abstract: This paper presents the CellCycler, a model of a growing tumour which aims to simulate and predict the effect of treatment on xenograft studies or in the clinic. The model, which is freely available as a web application, uses ordinary differential equations (ODEs) to simulate cells as they pass through the phases of the cell cycle. However the guiding philosophy of the model is that it should only use parameters that can be observed or reasonably well approximated. There is no representation of the complex internal dynamics of each cell; instead the level of analysis is limited to cell state observables such as cell phase, apoptosis, and damage. We show that this approach, while limited in many respects, still naturally accounts for a heteregenous cell population with varying doubling time, and closely captures the dynamics of a growing tumour as it is exposed to treatment. The program is demonstrated using three case studies.
bibliographic citation: Orrell et al. (2019) A simple model of a growing tumour. PeerJ 7:e6983 https://doi.org/10.7717/peerj.6983
date submitted: 2018-11-26
date accepted: 2019-04-17
issued: 2019-05-31
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Orrell
  given name: David
author list: Agent
  family name: Mistry
  given name: Hitesh B.
doi: 10.7717/peerj.6983
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-05-31
copyright: ©2019 Orrell and Mistry
attribution name: Orrell and Mistry

ConFindr: rapid detection of intraspecies and cross-species contamination in bacterial whole-genome sequence data
type: item
type: AcademicArticle
description: Whole-genome sequencing (WGS) of bacterial pathogens is currently widely used to support public-health investigations. The ability to assess WGS data quality is critical to underpin the reliability of downstream analyses. Sequence contamination is a quality issue that could potentially impact WGS-based findings; however, existing tools do not readily identify contamination from closely-related organisms. To address this gap, we have developed a computational pipeline, ConFindr, for detection of intraspecies contamination. ConFindr determines the presence of contaminating sequences based on the identification of multiple alleles of core, single-copy, ribosomal-protein genes in raw sequencing reads. The performance of this tool was assessed using simulated and lab-generated Illumina short-read WGS data with varying levels of contamination (0–20% of reads) and varying genetic distance between the designated target and contaminant strains. Intraspecies and cross-species contamination was reliably detected in datasets containing 5% or more reads from a second, unrelated strain. ConFindr detected intraspecies contamination with higher sensitivity than existing tools, while also being able to automatically detect cross-species contamination with similar sensitivity. The implementation of ConFindr in quality-control pipelines will help to improve the reliability of WGS databases as well as the accuracy of downstream analyses. ConFindr is written in Python, and is freely available under the MIT License at github.com/OLC-Bioinformatics/ConFindr.
format: application/pdf
format: text/html
creator: Andrew J. Low
creator: Adam G. Koziol
creator: Paul A. Manninger
creator: Burton Blais
creator: Catherine D. Carrillo
subject: Bioinformatics
subject: Genomics
subject: Microbiology
subject: Public Health
description: doi:10.7717/peerj.6995
publisher: PeerJ Inc.
rights: © 2019 Low et al.
abstract: Whole-genome sequencing (WGS) of bacterial pathogens is currently widely used to support public-health investigations. The ability to assess WGS data quality is critical to underpin the reliability of downstream analyses. Sequence contamination is a quality issue that could potentially impact WGS-based findings; however, existing tools do not readily identify contamination from closely-related organisms. To address this gap, we have developed a computational pipeline, ConFindr, for detection of intraspecies contamination. ConFindr determines the presence of contaminating sequences based on the identification of multiple alleles of core, single-copy, ribosomal-protein genes in raw sequencing reads. The performance of this tool was assessed using simulated and lab-generated Illumina short-read WGS data with varying levels of contamination (0–20% of reads) and varying genetic distance between the designated target and contaminant strains. Intraspecies and cross-species contamination was reliably detected in datasets containing 5% or more reads from a second, unrelated strain. ConFindr detected intraspecies contamination with higher sensitivity than existing tools, while also being able to automatically detect cross-species contamination with similar sensitivity. The implementation of ConFindr in quality-control pipelines will help to improve the reliability of WGS databases as well as the accuracy of downstream analyses. ConFindr is written in Python, and is freely available under the MIT License at github.com/OLC-Bioinformatics/ConFindr.
bibliographic citation: Low et al. (2019) ConFindr: rapid detection of intraspecies and cross-species contamination in bacterial whole-genome sequence data. PeerJ 7:e6995 https://doi.org/10.7717/peerj.6995
date submitted: 2019-01-22
date accepted: 2019-04-20
issued: 2019-05-31
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Low
  given name: Andrew J.
author list: Agent
  family name: Koziol
  given name: Adam G.
author list: Agent
  family name: Manninger
  given name: Paul A.
author list: Agent
  family name: Blais
  given name: Burton
author list: Agent
  family name: Carrillo
  given name: Catherine D.
doi: 10.7717/peerj.6995
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-05-31
copyright: ©2019 Low et al.
attribution name: Low et al.

Recommendations for dietary level of micro-minerals and vitamin D3 to Atlantic salmon (Salmo salar) parr and post-smolt when fed low fish meal diets
type: item
type: AcademicArticle
description: Atlantic salmon (Salmo salar) feeds have changed drastically in their composition from being predominantly marine-based to plant-based. This has altered the dietary supply and availability of micro-nutrients to Atlantic salmon. The impact of graded inclusion levels of a nutrient package (NP) comprising of 25 different micro-nutrients were studied in Atlantic salmon parr in freshwater (Trial 1) and post-smolts in seawater (Trial 2). In brief, the NP was included from 0 to 400%, where 100% corresponded to the recommendation by the National Research Council, 2011. Micro-nutrients, namely Zn, Mn, Se, Cu, Fe, Co, I and vitamin D3 were included in the NP with the objective of (re)evaluating the dietary need to meet the requirement of Atlantic salmon parr and post-smolt, when fed low fish meal, plant ingredient-based diets. Responses in apparent availability coefficient (AAC), whole body and vertebrae mineral concentrations, and retention were analysed. AAC of Cu, Mn, Se and Zn responded in a quadratic fashion with an increase in NP from 0 to 400% in freshwater parr; AAC could not be measured in post-smolt salmon. The whole-body concentration of Zn, Se, Co and I in Atlantic salmon parr were significantly affected by increasing NP inclusion; the same was observed for Zn, Se and Co in post-smolt Atlantic salmon. Vertebrae mineral concentration as the response criterion was non-responsive in parr; whereas, in post-smolt, Co had a linear increase, while Zn and Se showed a non-linear increase upon 0 to 400 NP inclusion. Zinc concentration and activities of alkaline phosphatase (ALP) and tartrate-resistant acid phosphatase (TRAP) in vertebrae indicated increased bone resorption in post-smolt Atlantic salmon; TRAP activity increased linearly with NP inclusion in post-smolt, but not in parr. Significant correlations between Zn and Se were observed in AAC and vertebral concentrations, indicating an interaction in intestinal uptake and vertebral deposition. Overall, Atlantic salmon …
format: application/pdf
format: text/html
creator: P. Antony Jesu Prabhu
creator: Erik-Jan Lock
creator: Gro-Ingunn Hemre
creator: Kristin Hamre
creator: Marit Espe
creator: Pål A. Olsvik
creator: Joana Silva
creator: Ann-Cecilie Hansen
creator: Johan Johansen
creator: Nini H. Sissener
creator: Rune Waagbø
subject: Agricultural Science
subject: Aquaculture, Fisheries and Fish Science
subject: Marine Biology
subject: Nutrition
subject: Freshwater Biology
description: doi:10.7717/peerj.6996
publisher: PeerJ Inc.
rights: © 2019 Antony Jesu Prabhu et al.
abstract: Atlantic salmon (Salmo salar) feeds have changed drastically in their composition from being predominantly marine-based to plant-based. This has altered the dietary supply and availability of micro-nutrients to Atlantic salmon. The impact of graded inclusion levels of a nutrient package (NP) comprising of 25 different micro-nutrients were studied in Atlantic salmon parr in freshwater (Trial 1) and post-smolts in seawater (Trial 2). In brief, the NP was included from 0 to 400%, where 100% corresponded to the recommendation by the National Research Council, 2011. Micro-nutrients, namely Zn, Mn, Se, Cu, Fe, Co, I and vitamin D3 were included in the NP with the objective of (re)evaluating the dietary need to meet the requirement of Atlantic salmon parr and post-smolt, when fed low fish meal, plant ingredient-based diets. Responses in apparent availability coefficient (AAC), whole body and vertebrae mineral concentrations, and retention were analysed. AAC of Cu, Mn, Se and Zn responded in a quadratic fashion with an increase in NP from 0 to 400% in freshwater parr; AAC could not be measured in post-smolt salmon. The whole-body concentration of Zn, Se, Co and I in Atlantic salmon parr were significantly affected by increasing NP inclusion; the same was observed for Zn, Se and Co in post-smolt Atlantic salmon. Vertebrae mineral concentration as the response criterion was non-responsive in parr; whereas, in post-smolt, Co had a linear increase, while Zn and Se showed a non-linear increase upon 0 to 400 NP inclusion. Zinc concentration and activities of alkaline phosphatase (ALP) and tartrate-resistant acid phosphatase (TRAP) in vertebrae indicated increased bone resorption in post-smolt Atlantic salmon; TRAP activity increased linearly with NP inclusion in post-smolt, but not in parr. Significant correlations between Zn and Se were observed in AAC and vertebral concentrations, indicating an interaction in intestinal uptake and vertebral deposition. Overall, Atlantic salmon …
bibliographic citation: Antony Jesu Prabhu et al. (2019) Recommendations for dietary level of micro-minerals and vitamin D3 to Atlantic salmon (Salmo salar) parr and post-smolt when fed low fish meal diets. PeerJ 7:e6996 https://doi.org/10.7717/peerj.6996
date submitted: 2019-03-05
date accepted: 2019-04-20
issued: 2019-05-31
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Antony Jesu Prabhu
  given name: P.
author list: Agent
  family name: Lock
  given name: Erik-Jan
author list: Agent
  family name: Hemre
  given name: Gro-Ingunn
author list: Agent
  family name: Hamre
  given name: Kristin
author list: Agent
  family name: Espe
  given name: Marit
author list: Agent
  family name: Olsvik
  given name: Pål A.
author list: Agent
  family name: Silva
  given name: Joana
author list: Agent
  family name: Hansen
  given name: Ann-Cecilie
author list: Agent
  family name: Johansen
  given name: Johan
author list: Agent
  family name: Sissener
  given name: Nini H.
author list: Agent
  family name: Waagbø
  given name: Rune
doi: 10.7717/peerj.6996
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-05-31
copyright: ©2019 Antony Jesu Prabhu et al.
attribution name: Antony Jesu Prabhu et al.

Prevalence and contributing factors of dental caries of 6-year-old children in four regions of China
type: item
type: AcademicArticle
description: Background From 2005 to 2015, the prevalence of dental caries in both primary and permanent dentitions was significantly increased in China. Previous studies have shown that the prevalence of permanent dental caries in school-aged children had already reached 19.7%–54.0%, 97.5% affecting first permanent molars. This study aimed to investigate the prevalence and contributing factors of dental caries in 6-year-old children in four regions of China to provide information for oral health promotion programs. Methods A randomized cluster sampling method was employed in the study. All 6-year-old first grade children from the selected schools were invited to receive a clinical oral examination. Dental caries were diagnosed according to the World Health Organization criteria. The erupting first permanent molars were recorded using the modified International Caries Detection Assessment System. Questionnaires assessing children’s oral health-related behaviors and their caretakers’ oral health awareness and attitudes were completed by the children’s parents or guardians. Results Overall, 4,936 6-year-old school children participated in the survey. The prevalence of caries among these children was 87.7%, with a mean number of decayed, missing and filled teeth of 6.04 (SD, 4.24). In primary dentition, the caries prevalence was 87.7%, and the mean dmft score was 6.01 (SD, 4.22). In permanent dentition, the caries prevalence was 2.0%, the mean DFS score was 0.04 (SD, 0.31). All permanent dental caries occurred on the first permanent molars. Carious tooth surfaces were identified as modified ICDAS code “A” to indicate initial caries and distinct visual change in enamel. The mean DAS score of non-cavitated caries in the first permanent molars was 0.18 (SD, 0.67). Logistic regression analysis showed that regional and gender factors were significantly related to the caries experience of these children. Conclusions The 6-year-old children from four regions of China had sever primary den…
format: application/pdf
format: text/html
creator: Zhaoyou Wang
creator: Wensheng Rong
creator: Ying Zhang
creator: Xiaojuan Zeng
creator: Zhiqiang Li
creator: Zhiwen Liu
subject: Dentistry
subject: Pediatrics
subject: Public Health
description: doi:10.7717/peerj.6997
publisher: PeerJ Inc.
rights: © 2019 Wang et al.
abstract: Background From 2005 to 2015, the prevalence of dental caries in both primary and permanent dentitions was significantly increased in China. Previous studies have shown that the prevalence of permanent dental caries in school-aged children had already reached 19.7%–54.0%, 97.5% affecting first permanent molars. This study aimed to investigate the prevalence and contributing factors of dental caries in 6-year-old children in four regions of China to provide information for oral health promotion programs. Methods A randomized cluster sampling method was employed in the study. All 6-year-old first grade children from the selected schools were invited to receive a clinical oral examination. Dental caries were diagnosed according to the World Health Organization criteria. The erupting first permanent molars were recorded using the modified International Caries Detection Assessment System. Questionnaires assessing children’s oral health-related behaviors and their caretakers’ oral health awareness and attitudes were completed by the children’s parents or guardians. Results Overall, 4,936 6-year-old school children participated in the survey. The prevalence of caries among these children was 87.7%, with a mean number of decayed, missing and filled teeth of 6.04 (SD, 4.24). In primary dentition, the caries prevalence was 87.7%, and the mean dmft score was 6.01 (SD, 4.22). In permanent dentition, the caries prevalence was 2.0%, the mean DFS score was 0.04 (SD, 0.31). All permanent dental caries occurred on the first permanent molars. Carious tooth surfaces were identified as modified ICDAS code “A” to indicate initial caries and distinct visual change in enamel. The mean DAS score of non-cavitated caries in the first permanent molars was 0.18 (SD, 0.67). Logistic regression analysis showed that regional and gender factors were significantly related to the caries experience of these children. Conclusions The 6-year-old children from four regions of China had sever primary den…
bibliographic citation: Wang et al. (2019) Prevalence and contributing factors of dental caries of 6-year-old children in four regions of China. PeerJ 7:e6997 https://doi.org/10.7717/peerj.6997
date submitted: 2018-12-11
date accepted: 2019-04-22
issued: 2019-05-31
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Wang
  given name: Zhaoyou
author list: Agent
  family name: Rong
  given name: Wensheng
author list: Agent
  family name: Zhang
  given name: Ying
author list: Agent
  family name: Zeng
  given name: Xiaojuan
author list: Agent
  family name: Li
  given name: Zhiqiang
author list: Agent
  family name: Liu
  given name: Zhiwen
doi: 10.7717/peerj.6997
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-05-31
copyright: ©2019 Wang et al.
attribution name: Wang et al.

Funmap2: an R package for QTL mapping using longitudinal phenotypes
type: item
type: AcademicArticle
description: Quantitative trait locus (QTL) mapping has been used as a powerful tool for inferring the complexity of the genetic architecture that underlies phenotypic traits. This approach has shown its unique power to map the developmental genetic architecture of complex traits by implementing longitudinal data analysis. Here, we introduce the R package Funmap2 based on the functional mapping framework, which integrates prior biological knowledge into the statistical model. Specifically, the functional mapping framework is engineered to include longitudinal curves that describe the genetic effects and the covariance matrix of the trait of interest. Funmap2 chooses the type of longitudinal curve and covariance matrix automatically using information criteria. Funmap2 is available for download at https://github.com/wzhy2000/Funmap2.
format: application/pdf
format: text/html
creator: Nating Wang
creator: Tinyi Chu
creator: Jiangtao Luo
creator: Rongling Wu
creator: Zhong Wang
subject: Bioinformatics
subject: Computational Biology
subject: Genetics
description: doi:10.7717/peerj.7008
publisher: PeerJ Inc.
rights: © 2019 Wang et al.
abstract: Quantitative trait locus (QTL) mapping has been used as a powerful tool for inferring the complexity of the genetic architecture that underlies phenotypic traits. This approach has shown its unique power to map the developmental genetic architecture of complex traits by implementing longitudinal data analysis. Here, we introduce the R package Funmap2 based on the functional mapping framework, which integrates prior biological knowledge into the statistical model. Specifically, the functional mapping framework is engineered to include longitudinal curves that describe the genetic effects and the covariance matrix of the trait of interest. Funmap2 chooses the type of longitudinal curve and covariance matrix automatically using information criteria. Funmap2 is available for download at https://github.com/wzhy2000/Funmap2.
bibliographic citation: Wang et al. (2019) Funmap2: an R package for QTL mapping using longitudinal phenotypes. PeerJ 7:e7008 https://doi.org/10.7717/peerj.7008
date submitted: 2018-10-26
date accepted: 2019-04-23
issued: 2019-05-31
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Wang
  given name: Nating
author list: Agent
  family name: Chu
  given name: Tinyi
author list: Agent
  family name: Luo
  given name: Jiangtao
author list: Agent
  family name: Wu
  given name: Rongling
author list: Agent
  family name: Wang
  given name: Zhong
doi: 10.7717/peerj.7008
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-05-31
copyright: ©2019 Wang et al.
attribution name: Wang et al.

Integrating species and interactions into similarity metrics: a graph theory-based approach to understanding community similarity
type: item
type: AcademicArticle
description: Community similarity is often assessed through similarities in species occurrences and abundances (i.e., compositional similarity) or through the distribution of species interactions (i.e., interaction similarity). Unfortunately, the joint empirical evaluation of both is still a challenge. Here, we analyze community similarity in ecological systems in order to evaluate the extent to which indices based exclusively on species composition differ from those that incorporate species interactions. Borrowing tools from graph theory, we compared the classic Jaccard index with the graph edit distance (GED), a metric that allowed us to combine species composition and interactions. We found that similarity measures computed using only taxonomic composition could differ strongly from those that include composition and interactions. We conclude that new indices that incorporate community features beyond composition will be more robust for assessing similitude between natural systems than those purely based on species occurrences. Our results have therefore important conceptual and practical consequences for the analysis of ecological communities.
format: application/pdf
format: text/html
creator: Daniela N. López
creator: Patricio A. Camus
creator: Nelson Valdivia
creator: Sergio A. Estay
subject: Biodiversity
subject: Ecology
description: doi:10.7717/peerj.7013
publisher: PeerJ Inc.
rights: © 2019 López et al.
abstract: Community similarity is often assessed through similarities in species occurrences and abundances (i.e., compositional similarity) or through the distribution of species interactions (i.e., interaction similarity). Unfortunately, the joint empirical evaluation of both is still a challenge. Here, we analyze community similarity in ecological systems in order to evaluate the extent to which indices based exclusively on species composition differ from those that incorporate species interactions. Borrowing tools from graph theory, we compared the classic Jaccard index with the graph edit distance (GED), a metric that allowed us to combine species composition and interactions. We found that similarity measures computed using only taxonomic composition could differ strongly from those that include composition and interactions. We conclude that new indices that incorporate community features beyond composition will be more robust for assessing similitude between natural systems than those purely based on species occurrences. Our results have therefore important conceptual and practical consequences for the analysis of ecological communities.
bibliographic citation: López et al. (2019) Integrating species and interactions into similarity metrics: a graph theory-based approach to understanding community similarity. PeerJ 7:e7013 https://doi.org/10.7717/peerj.7013
date submitted: 2018-08-10
date accepted: 2019-04-25
issued: 2019-05-31
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: López
  given name: Daniela N.
author list: Agent
  family name: Camus
  given name: Patricio A.
author list: Agent
  family name: Valdivia
  given name: Nelson
author list: Agent
  family name: Estay
  given name: Sergio A.
doi: 10.7717/peerj.7013
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-05-31
copyright: ©2019 López et al.
attribution name: López et al.

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