PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
items: IL-6 and TNF-α salivary levels according to the periodontal status in Portuguese pregnant women
items: DNA metabarcoding of littoral hard-bottom communities: high diversity and database gaps revealed by two molecular markers
items: Candidate genes in gastric cancer identified by constructing a weighted gene co-expression network
items: Bioinformatic analysis and identification of potential prognostic microRNAs and mRNAs in thyroid cancer
items: Candidate genes associated with red colour formation revealed by comparative genomic variant analysis of red- and green-skinned fruits of Japanese apricot (Prunus mume)
items: Quantitative estimation of soil salinity by means of different modeling methods and visible-near infrared (VIS–NIR) spectroscopy, Ebinur Lake Wetland, Northwest China
items: Post-traumatic stress symptoms are associated with better performance on a delayed match-to-position task
items: Patterns of genetic structuring at the northern limits of the Australian smelt (Retropinna semoni) cryptic species complex
items: Relationships between parents’ academic backgrounds and incomes and building students’ healthy eating habits
items: Stinging wasps (Hymenoptera: Aculeata), which species have the longest sting?

IL-6 and TNF-α salivary levels according to the periodontal status in Portuguese pregnant women
type: item
type: AcademicArticle
description: Background Periodontitis is associated with increased concentration of inflammatory markers and saliva has been proposed as a non-invasive diagnostic fluid in oral and systemic diseases. The levels of salivary biomarkers, such as cytokines, could potentially be used to distinguish periodontal healthy individuals from subjects with periodontal disease. The purpose of this study was to characterize the salivary levels of two inflammatory biomarkers associated with periodontitis, interleukin-6 (IL-6) and tumour necrosis factor-alpha (TNF-α), in order to assess whether these cytokines salivary levels could potentially be used to complement periodontitis pregnant women diagnose. Methods Forty-four pregnant women were distributed into three groups, according to their periodontal status: healthy, mild/moderate periodontitis and severe periodontitis. Unstimulated saliva was collected and analysis of TNF-α and IL-6 salivary levels were performed with Immulite®. Results Women with periodontitis exhibited significantly higher levels (p = 0.001) of salivary IL-6 and TNF-α compared with the healthy group: 25.1 (±11.2) pg/mL vs. 16.3 (±5.0) pg/mL and 29.7 (±17.2) pg/mL vs. 16.2 (±7.6) pg/mL, approximately 1.5 and 1.8 times more, respectively. Additionally, cytokines were significantly increased (p < 0.05) in severe periodontitis compared to periodontal healthy pregnant women. Conclusions These results revealed that IL-6 and TNF-α salivary biomarkers provide high discriminatory capacity for distinguishing periodontal disease from periodontal health in pregnant women.
format: application/pdf
format: text/html
creator: Vanessa Machado
creator: Maria Fernanda Mesquita
creator: Maria Alexandra Bernardo
creator: Ester Casal
creator: Luís Proença
creator: José João Mendes
subject: Dentistry
subject: Epidemiology
subject: Immunology
subject: Nursing
description: doi:10.7717/peerj.4710
publisher: PeerJ Inc.
rights: © 2018 Machado et al.
abstract: Background Periodontitis is associated with increased concentration of inflammatory markers and saliva has been proposed as a non-invasive diagnostic fluid in oral and systemic diseases. The levels of salivary biomarkers, such as cytokines, could potentially be used to distinguish periodontal healthy individuals from subjects with periodontal disease. The purpose of this study was to characterize the salivary levels of two inflammatory biomarkers associated with periodontitis, interleukin-6 (IL-6) and tumour necrosis factor-alpha (TNF-α), in order to assess whether these cytokines salivary levels could potentially be used to complement periodontitis pregnant women diagnose. Methods Forty-four pregnant women were distributed into three groups, according to their periodontal status: healthy, mild/moderate periodontitis and severe periodontitis. Unstimulated saliva was collected and analysis of TNF-α and IL-6 salivary levels were performed with Immulite®. Results Women with periodontitis exhibited significantly higher levels (p = 0.001) of salivary IL-6 and TNF-α compared with the healthy group: 25.1 (±11.2) pg/mL vs. 16.3 (±5.0) pg/mL and 29.7 (±17.2) pg/mL vs. 16.2 (±7.6) pg/mL, approximately 1.5 and 1.8 times more, respectively. Additionally, cytokines were significantly increased (p < 0.05) in severe periodontitis compared to periodontal healthy pregnant women. Conclusions These results revealed that IL-6 and TNF-α salivary biomarkers provide high discriminatory capacity for distinguishing periodontal disease from periodontal health in pregnant women.
bibliographic citation: Machado et al. (2018) IL-6 and TNF-α salivary levels according to the periodontal status in Portuguese pregnant women. PeerJ 6:e4710 https://doi.org/10.7717/peerj.4710
date submitted: 2018-02-21
date accepted: 2018-04-16
issued: 2018-05-04
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Machado
  given name: Vanessa
author list: Agent
  family name: Mesquita
  given name: Maria Fernanda
author list: Agent
  family name: Bernardo
  given name: Maria Alexandra
author list: Agent
  family name: Casal
  given name: Ester
author list: Agent
  family name: Proença
  given name: Luís
author list: Agent
  family name: Mendes
  given name: José João
doi: 10.7717/peerj.4710
volume: 6
issn: 2167-8359
publication name: PeerJ
publication date: 2018-05-04
copyright: ©2018 Machado et al.
attribution name: Machado et al.

DNA metabarcoding of littoral hard-bottom communities: high diversity and database gaps revealed by two molecular markers
type: item
type: AcademicArticle
description: Biodiversity assessment of marine hard-bottom communities is hindered by the high diversity and size-ranges of the organisms present. We developed a DNA metabarcoding protocol for biodiversity characterization of structurally complex natural marine hard-bottom communities. We used two molecular markers: the “Leray fragment” of mitochondrial cytochrome c oxidase (COI), for which a novel primer set was developed, and the V7 region of the nuclear small subunit ribosomal RNA (18S). Eight different shallow marine littoral communities from two National Parks in Spain (one in the Atlantic Ocean and another in the Mediterranean Sea) were studied. Samples were sieved into three size fractions from where DNA was extracted separately. Bayesian clustering was used for delimiting molecular operational taxonomic units (MOTUs) and custom reference databases were constructed for taxonomic assignment. Despite applying stringent filters, we found high values for MOTU richness (2,510 and 9,679 MOTUs with 18S and COI, respectively), suggesting that these communities host a large amount of yet undescribed eukaryotic biodiversity. Significant gaps are still found in sequence reference databases, which currently prevent the complete taxonomic assignment of the detected sequences. In our dataset, 85% of 18S MOTUs and 64% of COI MOTUs could be identified to phylum or lower taxonomic level. Nevertheless, those unassigned were mostly rare MOTUs with low numbers of reads, and assigned MOTUs comprised over 90% of the total sequence reads. The identification rate might be significantly improved in the future, as reference databases are further completed. Our results show that marine metabarcoding, currently applied mostly to plankton or sediments, can be adapted to structurally complex hard bottom samples. Thus, eukaryotic metabarcoding emerges as a robust, fast, objective and affordable method to comprehensively characterize the diversity of marine benthic communities dominated by macroscopic s…
format: application/pdf
format: text/html
creator: Owen S. Wangensteen
creator: Creu Palacín
creator: Magdalena Guardiola
creator: Xavier Turon
subject: Biodiversity
subject: Ecology
subject: Marine Biology
description: doi:10.7717/peerj.4705
publisher: PeerJ Inc.
rights: © 2018 Wangensteen et al.
abstract: Biodiversity assessment of marine hard-bottom communities is hindered by the high diversity and size-ranges of the organisms present. We developed a DNA metabarcoding protocol for biodiversity characterization of structurally complex natural marine hard-bottom communities. We used two molecular markers: the “Leray fragment” of mitochondrial cytochrome c oxidase (COI), for which a novel primer set was developed, and the V7 region of the nuclear small subunit ribosomal RNA (18S). Eight different shallow marine littoral communities from two National Parks in Spain (one in the Atlantic Ocean and another in the Mediterranean Sea) were studied. Samples were sieved into three size fractions from where DNA was extracted separately. Bayesian clustering was used for delimiting molecular operational taxonomic units (MOTUs) and custom reference databases were constructed for taxonomic assignment. Despite applying stringent filters, we found high values for MOTU richness (2,510 and 9,679 MOTUs with 18S and COI, respectively), suggesting that these communities host a large amount of yet undescribed eukaryotic biodiversity. Significant gaps are still found in sequence reference databases, which currently prevent the complete taxonomic assignment of the detected sequences. In our dataset, 85% of 18S MOTUs and 64% of COI MOTUs could be identified to phylum or lower taxonomic level. Nevertheless, those unassigned were mostly rare MOTUs with low numbers of reads, and assigned MOTUs comprised over 90% of the total sequence reads. The identification rate might be significantly improved in the future, as reference databases are further completed. Our results show that marine metabarcoding, currently applied mostly to plankton or sediments, can be adapted to structurally complex hard bottom samples. Thus, eukaryotic metabarcoding emerges as a robust, fast, objective and affordable method to comprehensively characterize the diversity of marine benthic communities dominated by macroscopic s…
bibliographic citation: Wangensteen et al. (2018) DNA metabarcoding of littoral hard-bottom communities: high diversity and database gaps revealed by two molecular markers. PeerJ 6:e4705 https://doi.org/10.7717/peerj.4705
date submitted: 2017-11-22
date accepted: 2018-04-15
issued: 2018-05-04
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Wangensteen
  given name: Owen S.
author list: Agent
  family name: Palacín
  given name: Creu
author list: Agent
  family name: Guardiola
  given name: Magdalena
author list: Agent
  family name: Turon
  given name: Xavier
doi: 10.7717/peerj.4705
volume: 6
issn: 2167-8359
publication name: PeerJ
publication date: 2018-05-04
copyright: ©2018 Wangensteen et al.
attribution name: Wangensteen et al.

Candidate genes in gastric cancer identified by constructing a weighted gene co-expression network
type: item
type: AcademicArticle
description: Background Gastric cancer (GC) is one of the most common cancers with high mortality globally. However, the molecular mechanisms of GC are unclear, and the prognosis of GC is poor. Therefore, it is important to explore the underlying mechanisms and screen for novel prognostic markers and treatment targets. Methods The genetic and clinical data of GC patients in The Cancer Genome Atlas (TCGA) was analyzed by weighted gene co-expression network analysis (WGCNA). Modules with clinical significance and preservation were distinguished, and gene ontology and pathway enrichment analysis were performed. Hub genes of these modules were validated in the TCGA dataset and another independent dataset from the Gene Expression Omnibus (GEO) database by t-test. Furthermore, the significance of these genes was confirmed via survival analysis. Results We found a preserved module consisting of 506 genes was associated with clinical traits including pathologic T stage and histologic grade. PDGFRB, COL8A1, EFEMP2, FBN1, EMILIN1, FSTL1 and KIRREL were identified as candidate genes in the module. Their expression levels were correlated with pathologic T stage and histologic grade, also affected overall survival of GC patients. Conclusion These candidate genes may be involved in proliferation and differentiation of GC cells. They may serve as novel prognostic markers and treatment targets. Moreover, most of them were first reported in GC and deserved further research.
format: application/pdf
format: text/html
creator: Jian Chen
creator: Xiuwen Wang
creator: Bing Hu
creator: Yifu He
creator: Xiaojun Qian
creator: Wei Wang
subject: Bioinformatics
subject: Genetics
subject: Oncology
description: doi:10.7717/peerj.4692
publisher: PeerJ Inc.
rights: © 2018 Chen et al.
abstract: Background Gastric cancer (GC) is one of the most common cancers with high mortality globally. However, the molecular mechanisms of GC are unclear, and the prognosis of GC is poor. Therefore, it is important to explore the underlying mechanisms and screen for novel prognostic markers and treatment targets. Methods The genetic and clinical data of GC patients in The Cancer Genome Atlas (TCGA) was analyzed by weighted gene co-expression network analysis (WGCNA). Modules with clinical significance and preservation were distinguished, and gene ontology and pathway enrichment analysis were performed. Hub genes of these modules were validated in the TCGA dataset and another independent dataset from the Gene Expression Omnibus (GEO) database by t-test. Furthermore, the significance of these genes was confirmed via survival analysis. Results We found a preserved module consisting of 506 genes was associated with clinical traits including pathologic T stage and histologic grade. PDGFRB, COL8A1, EFEMP2, FBN1, EMILIN1, FSTL1 and KIRREL were identified as candidate genes in the module. Their expression levels were correlated with pathologic T stage and histologic grade, also affected overall survival of GC patients. Conclusion These candidate genes may be involved in proliferation and differentiation of GC cells. They may serve as novel prognostic markers and treatment targets. Moreover, most of them were first reported in GC and deserved further research.
bibliographic citation: Chen et al. (2018) Candidate genes in gastric cancer identified by constructing a weighted gene co-expression network. PeerJ 6:e4692 https://doi.org/10.7717/peerj.4692
date submitted: 2018-01-23
date accepted: 2018-04-11
issued: 2018-05-04
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Chen
  given name: Jian
author list: Agent
  family name: Wang
  given name: Xiuwen
author list: Agent
  family name: Hu
  given name: Bing
author list: Agent
  family name: He
  given name: Yifu
author list: Agent
  family name: Qian
  given name: Xiaojun
author list: Agent
  family name: Wang
  given name: Wei
doi: 10.7717/peerj.4692
volume: 6
issn: 2167-8359
publication name: PeerJ
publication date: 2018-05-04
copyright: ©2018 Chen et al.
attribution name: Chen et al.

Bioinformatic analysis and identification of potential prognostic microRNAs and mRNAs in thyroid cancer
type: item
type: AcademicArticle
description: Thyroid cancer is one of the most common endocrine malignancies. Multiple evidences revealed that a large number of microRNAs and mRNAs were abnormally expressed in thyroid cancer tissues. These microRNAs and mRNAs play important roles in tumorigenesis. In the present study, we identified 72 microRNAs and 1,766 mRNAs differentially expressed between thyroid cancer tissues and normal thyroid tissues and evaluated their prognostic values using Kaplan-Meier survival curves by log-rank test. Seven microRNAs (miR-146b, miR-184, miR-767, miR-6730, miR-6860, miR-196a-2 and miR-509-3) were associated with the overall survival. Among them, three microRNAs were linked with six differentially expressed mRNAs (miR-767 was predicted to target COL10A1, PLAG1 and PPP1R1C; miR-146b was predicted to target MMP16; miR-196a-2 was predicted to target SYT9). To identify the key genes in the protein-protein interaction network , we screened out the top 10 hub genes (NPY, NMU, KNG1, LPAR5, CCR3, SST, PPY, GABBR2, ADCY8 and SAA1) with higher degrees. Only LPAR5 was associated with the overall survival. Multivariate analysis demonstrated that miR-184, miR-146b, miR-509-3 and LPAR5 were an independent risk factors for prognosis. Our results of the present study identified a series of prognostic microRNAs and mRNAs that have the potential to be the targets for treatment of thyroid cancer.
format: application/pdf
format: text/html
creator: Jianing Tang
creator: Deguang Kong
creator: Qiuxia Cui
creator: Kun Wang
creator: Dan Zhang
creator: Qianqian Yuan
creator: Xing Liao
creator: Yan Gong
creator: Gaosong Wu
subject: Bioinformatics
description: doi:10.7717/peerj.4674
publisher: PeerJ Inc.
rights: © 2018 Tang et al.
abstract: Thyroid cancer is one of the most common endocrine malignancies. Multiple evidences revealed that a large number of microRNAs and mRNAs were abnormally expressed in thyroid cancer tissues. These microRNAs and mRNAs play important roles in tumorigenesis. In the present study, we identified 72 microRNAs and 1,766 mRNAs differentially expressed between thyroid cancer tissues and normal thyroid tissues and evaluated their prognostic values using Kaplan-Meier survival curves by log-rank test. Seven microRNAs (miR-146b, miR-184, miR-767, miR-6730, miR-6860, miR-196a-2 and miR-509-3) were associated with the overall survival. Among them, three microRNAs were linked with six differentially expressed mRNAs (miR-767 was predicted to target COL10A1, PLAG1 and PPP1R1C; miR-146b was predicted to target MMP16; miR-196a-2 was predicted to target SYT9). To identify the key genes in the protein-protein interaction network , we screened out the top 10 hub genes (NPY, NMU, KNG1, LPAR5, CCR3, SST, PPY, GABBR2, ADCY8 and SAA1) with higher degrees. Only LPAR5 was associated with the overall survival. Multivariate analysis demonstrated that miR-184, miR-146b, miR-509-3 and LPAR5 were an independent risk factors for prognosis. Our results of the present study identified a series of prognostic microRNAs and mRNAs that have the potential to be the targets for treatment of thyroid cancer.
bibliographic citation: Tang et al. (2018) Bioinformatic analysis and identification of potential prognostic microRNAs and mRNAs in thyroid cancer. PeerJ 6:e4674 https://doi.org/10.7717/peerj.4674
date submitted: 2018-02-09
date accepted: 2018-04-06
issued: 2018-05-04
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Tang
  given name: Jianing
author list: Agent
  family name: Kong
  given name: Deguang
author list: Agent
  family name: Cui
  given name: Qiuxia
author list: Agent
  family name: Wang
  given name: Kun
author list: Agent
  family name: Zhang
  given name: Dan
author list: Agent
  family name: Yuan
  given name: Qianqian
author list: Agent
  family name: Liao
  given name: Xing
author list: Agent
  family name: Gong
  given name: Yan
author list: Agent
  family name: Wu
  given name: Gaosong
doi: 10.7717/peerj.4674
volume: 6
issn: 2167-8359
publication name: PeerJ
publication date: 2018-05-04
copyright: ©2018 Tang et al.
attribution name: Tang et al.

Candidate genes associated with red colour formation revealed by comparative genomic variant analysis of red- and green-skinned fruits of Japanese apricot (Prunus mume)
type: item
type: AcademicArticle
description: The red-skinned fruit of Japanese apricot (Prunus mume Sieb. et Zucc) appeals to customers due to its eye-catching pigmentation, while the mechanism related to its colour formation is still unclear. In this study, genome re-sequencing of six Japanese apricot cultivars was carried out with approximately 92.2 Gb of clean bases using next-generation sequencing. A total of 32,004 unigenes were assembled with an average of 83.1% coverage rate relative to reference genome. A wide range of genetic variation was detected, including 7,387,057 single nucleotide polymorphisms, 456,222 insertions or deletions and 129,061 structural variations in all genomes. Comparative sequencing data revealed that 13 candidate genes were involved in biosynthesis of anthocyanin. Significantly higher expression patterns were observed in genes encoding three anthocyanin synthesis structural genes (4CL, F3H and UFGT), five transcription factors (MYB–bHLH–WD40 complexes and NAC) and five anthocyanin accumulation related genes (GST1, RT1, UGT85A2, ABC and MATE transporters) in red-skinned than in green-skinned Japanese apricots using reverse transcription-quantitative polymerase chain reaction. Eight main kinds of anthocyanin s were detected by UPLC/MS, and cyanidin 3-glucoside was identified as the major anthocyanin (124.2 mg/kg) in red-skinned cultivars. The activity of UDP-glucose flavonoid-3-O-glycosyltransferase enzyme determined by UPLC was significantly higher in all red-skinned cultivars, suggesting that it is the potential vital regulatory gene for biosynthesis of anthocyanin in Japanese apricot.
format: application/pdf
format: text/html
creator: Xiaopeng Ni
creator: Song Xue
creator: Shahid Iqbal
creator: Wanxu Wang
creator: Zhaojun Ni
creator: Muhammad Khalil-ur-Rehman
creator: Zhihong Gao
subject: Genomics
subject: Molecular Biology
subject: Plant Science
description: doi:10.7717/peerj.4625
publisher: PeerJ Inc.
rights: © 2018 Ni et al.
abstract: The red-skinned fruit of Japanese apricot (Prunus mume Sieb. et Zucc) appeals to customers due to its eye-catching pigmentation, while the mechanism related to its colour formation is still unclear. In this study, genome re-sequencing of six Japanese apricot cultivars was carried out with approximately 92.2 Gb of clean bases using next-generation sequencing. A total of 32,004 unigenes were assembled with an average of 83.1% coverage rate relative to reference genome. A wide range of genetic variation was detected, including 7,387,057 single nucleotide polymorphisms, 456,222 insertions or deletions and 129,061 structural variations in all genomes. Comparative sequencing data revealed that 13 candidate genes were involved in biosynthesis of anthocyanin. Significantly higher expression patterns were observed in genes encoding three anthocyanin synthesis structural genes (4CL, F3H and UFGT), five transcription factors (MYB–bHLH–WD40 complexes and NAC) and five anthocyanin accumulation related genes (GST1, RT1, UGT85A2, ABC and MATE transporters) in red-skinned than in green-skinned Japanese apricots using reverse transcription-quantitative polymerase chain reaction. Eight main kinds of anthocyanin s were detected by UPLC/MS, and cyanidin 3-glucoside was identified as the major anthocyanin (124.2 mg/kg) in red-skinned cultivars. The activity of UDP-glucose flavonoid-3-O-glycosyltransferase enzyme determined by UPLC was significantly higher in all red-skinned cultivars, suggesting that it is the potential vital regulatory gene for biosynthesis of anthocyanin in Japanese apricot.
bibliographic citation: Ni et al. (2018) Candidate genes associated with red colour formation revealed by comparative genomic variant analysis of red- and green-skinned fruits of Japanese apricot (Prunus mume). PeerJ 6:e4625 https://doi.org/10.7717/peerj.4625
date submitted: 2017-10-26
date accepted: 2018-03-24
issued: 2018-05-04
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Ni
  given name: Xiaopeng
author list: Agent
  family name: Xue
  given name: Song
author list: Agent
  family name: Iqbal
  given name: Shahid
author list: Agent
  family name: Wang
  given name: Wanxu
author list: Agent
  family name: Ni
  given name: Zhaojun
author list: Agent
  family name: Khalil-ur-Rehman
  given name: Muhammad
author list: Agent
  family name: Gao
  given name: Zhihong
doi: 10.7717/peerj.4625
volume: 6
issn: 2167-8359
publication name: PeerJ
publication date: 2018-05-04
copyright: © 2018 Ni et al.
attribution name: Ni et al.

Quantitative estimation of soil salinity by means of different modeling methods and visible-near infrared (VIS–NIR) spectroscopy, Ebinur Lake Wetland, Northwest China
type: item
type: AcademicArticle
description: Soil salinization is one of the most common forms of land degradation. The detection and assessment of soil salinity is critical for the prevention of environmental deterioration especially in arid and semi-arid areas. This study introduced the fractional derivative in the pretreatment of visible and near infrared (VIS–NIR) spectroscopy. The soil samples (n = 400) collected from the Ebinur Lake Wetland, Xinjiang Uyghur Autonomous Region (XUAR), China, were used as the dataset. After measuring the spectral reflectance and salinity in the laboratory, the raw spectral reflectance was preprocessed by means of the absorbance and the fractional derivative order in the range of 0.0–2.0 order with an interval of 0.1. Two different modeling methods, namely, partial least squares regression (PLSR) and random forest (RF) with preprocessed reflectance were used for quantifying soil salinity. The results showed that more spectral characteristics were refined for the spectrum reflectance treated via fractional derivative. The validation accuracies showed that RF models performed better than those of PLSR. The most effective model was established based on RF with the 1.5 order derivative of absorbance with the optimal values of R2 (0.93), RMSE (4.57 dS m−1), and RPD (2.78 ≥ 2.50). The developed RF model was stable and accurate in the application of spectral reflectance for determining the soil salinity of the Ebinur Lake wetland. The pretreatment of fractional derivative could be useful for monitoring multiple soil parameters with higher accuracy, which could effectively help to analyze the soil salinity.
format: application/pdf
format: text/html
creator: Jingzhe Wang
creator: Jianli Ding
creator: Aerzuna Abulimiti
creator: Lianghong Cai
subject: Soil Science
subject: Data Mining and Machine Learning
subject: Natural Resource Management
subject: Environmental Impacts
subject: Spatial and Geographic Information Science
description: doi:10.7717/peerj.4703
publisher: PeerJ Inc.
rights: © 2018 Wang et al.
abstract: Soil salinization is one of the most common forms of land degradation. The detection and assessment of soil salinity is critical for the prevention of environmental deterioration especially in arid and semi-arid areas. This study introduced the fractional derivative in the pretreatment of visible and near infrared (VIS–NIR) spectroscopy. The soil samples (n = 400) collected from the Ebinur Lake Wetland, Xinjiang Uyghur Autonomous Region (XUAR), China, were used as the dataset. After measuring the spectral reflectance and salinity in the laboratory, the raw spectral reflectance was preprocessed by means of the absorbance and the fractional derivative order in the range of 0.0–2.0 order with an interval of 0.1. Two different modeling methods, namely, partial least squares regression (PLSR) and random forest (RF) with preprocessed reflectance were used for quantifying soil salinity. The results showed that more spectral characteristics were refined for the spectrum reflectance treated via fractional derivative. The validation accuracies showed that RF models performed better than those of PLSR. The most effective model was established based on RF with the 1.5 order derivative of absorbance with the optimal values of R2 (0.93), RMSE (4.57 dS m−1), and RPD (2.78 ≥ 2.50). The developed RF model was stable and accurate in the application of spectral reflectance for determining the soil salinity of the Ebinur Lake wetland. The pretreatment of fractional derivative could be useful for monitoring multiple soil parameters with higher accuracy, which could effectively help to analyze the soil salinity.
bibliographic citation: Wang et al. (2018) Quantitative estimation of soil salinity by means of different modeling methods and visible-near infrared (VIS–NIR) spectroscopy, Ebinur Lake Wetland, Northwest China. PeerJ 6:e4703 https://doi.org/10.7717/peerj.4703
date submitted: 2018-02-12
date accepted: 2018-04-14
issued: 2018-05-03
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Wang
  given name: Jingzhe
author list: Agent
  family name: Ding
  given name: Jianli
author list: Agent
  family name: Abulimiti
  given name: Aerzuna
author list: Agent
  family name: Cai
  given name: Lianghong
doi: 10.7717/peerj.4703
volume: 6
issn: 2167-8359
publication name: PeerJ
publication date: 2018-05-03
copyright: ©2018 Wang et al.
attribution name: Wang et al.

Post-traumatic stress symptoms are associated with better performance on a delayed match-to-position task
type: item
type: AcademicArticle
description: Many individuals with posttraumatic stress disorder (PTSD) report experiencing frequent intrusive memories of the original traumatic event (e.g., flashbacks). These memories can be triggered by situations or stimuli that reflect aspects of the trauma and may reflect basic processes in learning and memory, such as generalization. It is possible that, through increased generalization, non-threatening stimuli that once evoked normal memories become associated with traumatic memories. Previous research has reported increased generalization in PTSD, but the role of visual discrimination processes has not been examined. To investigate visual discrimination in PTSD, 143 participants (Veterans and civilians) self-assessed for symptom severity were grouped according to the presence of severe PTSD symptoms (PTSS) vs. few/no symptoms (noPTSS). Participants were given a visual match-to-sample pattern separation task that varied trials by spatial separation (Low, Medium, High) and temporal delays (5, 10, 20, 30 s). Unexpectedly, the PTSS group demonstrated better discrimination performance than the noPTSS group at the most difficult spatial trials (Low spatial separation). Further assessment of accuracy and reaction time using diffusion drift modeling indicated that the better performance by the PTSS group on the hardest trials was not explained by slower reaction times, but rather a faster accumulation of evidence during decision making in conjunction with a reduced threshold, indicating a tendency in the PTSS group to decide quickly rather than waiting for additional evidence to support the decision. This result supports the need for future studies examining the precise role of discrimination and generalization in PTSD, and how these cognitive processes might contribute to expression and maintenance of PTSD symptoms.
format: application/pdf
format: text/html
creator: Meghan D. Caulfield
creator: Catherine E. Myers
subject: Neuroscience
subject: Psychiatry and Psychology
subject: Computational Science
description: doi:10.7717/peerj.4701
publisher: PeerJ Inc.
rights: © 2018 Caulfield and Myers
abstract: Many individuals with posttraumatic stress disorder (PTSD) report experiencing frequent intrusive memories of the original traumatic event (e.g., flashbacks). These memories can be triggered by situations or stimuli that reflect aspects of the trauma and may reflect basic processes in learning and memory, such as generalization. It is possible that, through increased generalization, non-threatening stimuli that once evoked normal memories become associated with traumatic memories. Previous research has reported increased generalization in PTSD, but the role of visual discrimination processes has not been examined. To investigate visual discrimination in PTSD, 143 participants (Veterans and civilians) self-assessed for symptom severity were grouped according to the presence of severe PTSD symptoms (PTSS) vs. few/no symptoms (noPTSS). Participants were given a visual match-to-sample pattern separation task that varied trials by spatial separation (Low, Medium, High) and temporal delays (5, 10, 20, 30 s). Unexpectedly, the PTSS group demonstrated better discrimination performance than the noPTSS group at the most difficult spatial trials (Low spatial separation). Further assessment of accuracy and reaction time using diffusion drift modeling indicated that the better performance by the PTSS group on the hardest trials was not explained by slower reaction times, but rather a faster accumulation of evidence during decision making in conjunction with a reduced threshold, indicating a tendency in the PTSS group to decide quickly rather than waiting for additional evidence to support the decision. This result supports the need for future studies examining the precise role of discrimination and generalization in PTSD, and how these cognitive processes might contribute to expression and maintenance of PTSD symptoms.
bibliographic citation: Caulfield et al. (2018) Post-traumatic stress symptoms are associated with better performance on a delayed match-to-position task. PeerJ 6:e4701 https://doi.org/10.7717/peerj.4701
date submitted: 2017-08-18
date accepted: 2018-04-13
issued: 2018-05-03
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Caulfield
  given name: Meghan D.
author list: Agent
  family name: Myers
  given name: Catherine E.
doi: 10.7717/peerj.4701
volume: 6
issn: 2167-8359
publication name: PeerJ
publication date: 2018-05-03
copyright: ©2018 Caulfield and Myers
attribution name: Caulfield and Myers

Patterns of genetic structuring at the northern limits of the Australian smelt (Retropinna semoni) cryptic species complex
type: item
type: AcademicArticle
description: Freshwater fishes often exhibit high genetic population structure due to the prevalence of dispersal barriers (e.g., waterfalls) whereas population structure in diadromous fishes tends to be weaker and driven by natal homing behaviour and/or isolation by distance. The Australian smelt (Retropinnidae: Retropinna semoni) is a native fish with a broad distribution spanning inland and coastal drainages of south-eastern Australia. Previous studies have demonstrated variability in population genetic structure and movement behaviour (potamodromy, facultative diadromy, estuarine residence) across the southern part of its geographic range. Some of this variability may be explained by the existence of multiple cryptic species. Here, we examined genetic structure of populations towards the northern extent of the species’ distribution, using ten microsatellite loci and sequences of the mitochondrial cyt b gene. We tested the hypothesis that genetic connectivity among rivers should be low due to a lack of dispersal via the marine environment, but high within rivers due to dispersal. We investigated populations corresponding with two putative cryptic species, SEQ-North (SEQ-N), and SEQ-South (SEQ-S) lineages occurring in south east Queensland drainages. These two groups formed monophyletic clades in the mtDNA gene tree and among river phylogeographic structure was also evident within each clade. In agreement with our hypothesis, highly significant overall FST values suggested that both groups exhibit very low dispersal among rivers (SEQ-S FST = 0.13; SEQ-N FST= 0.27). Microsatellite data indicated that connectivity among sites within rivers was also limited, suggesting dispersal may not homogenise populations at the within-river scale. Northern groups in the Australian smelt cryptic species complex exhibit comparatively higher among-river population structure and smaller geographic ranges than southern groups. These properties make northern Australian smelt populations potentiall…
format: application/pdf
format: text/html
creator: Md Rakeb-Ul Islam
creator: Daniel J. Schmidt
creator: David A. Crook
creator: Jane M. Hughes
subject: Aquaculture, Fisheries and Fish Science
subject: Conservation Biology
subject: Ecology
subject: Genetics
subject: Zoology
description: doi:10.7717/peerj.4654
publisher: PeerJ Inc.
rights: © 2018 Islam et al.
abstract: Freshwater fishes often exhibit high genetic population structure due to the prevalence of dispersal barriers (e.g., waterfalls) whereas population structure in diadromous fishes tends to be weaker and driven by natal homing behaviour and/or isolation by distance. The Australian smelt (Retropinnidae: Retropinna semoni) is a native fish with a broad distribution spanning inland and coastal drainages of south-eastern Australia. Previous studies have demonstrated variability in population genetic structure and movement behaviour (potamodromy, facultative diadromy, estuarine residence) across the southern part of its geographic range. Some of this variability may be explained by the existence of multiple cryptic species. Here, we examined genetic structure of populations towards the northern extent of the species’ distribution, using ten microsatellite loci and sequences of the mitochondrial cyt b gene. We tested the hypothesis that genetic connectivity among rivers should be low due to a lack of dispersal via the marine environment, but high within rivers due to dispersal. We investigated populations corresponding with two putative cryptic species, SEQ-North (SEQ-N), and SEQ-South (SEQ-S) lineages occurring in south east Queensland drainages. These two groups formed monophyletic clades in the mtDNA gene tree and among river phylogeographic structure was also evident within each clade. In agreement with our hypothesis, highly significant overall FST values suggested that both groups exhibit very low dispersal among rivers (SEQ-S FST = 0.13; SEQ-N FST= 0.27). Microsatellite data indicated that connectivity among sites within rivers was also limited, suggesting dispersal may not homogenise populations at the within-river scale. Northern groups in the Australian smelt cryptic species complex exhibit comparatively higher among-river population structure and smaller geographic ranges than southern groups. These properties make northern Australian smelt populations potentiall…
bibliographic citation: Islam et al. (2018) Patterns of genetic structuring at the northern limits of the Australian smelt (Retropinna semoni) cryptic species complex. PeerJ 6:e4654 https://doi.org/10.7717/peerj.4654
date submitted: 2017-09-25
date accepted: 2018-03-31
issued: 2018-05-03
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Islam
  given name: Md Rakeb-Ul
author list: Agent
  family name: Schmidt
  given name: Daniel J.
author list: Agent
  family name: Crook
  given name: David A.
author list: Agent
  family name: Hughes
  given name: Jane M.
doi: 10.7717/peerj.4654
volume: 6
issn: 2167-8359
publication name: PeerJ
publication date: 2018-05-03
copyright: ©2018 Islam et al.
attribution name: Islam et al.

Relationships between parents’ academic backgrounds and incomes and building students’ healthy eating habits
type: item
type: AcademicArticle
description: Background Building healthy eating habit is essential for all people. School and family are the prime institutions to instill this habit during early age. This study is aimed at understanding the impact of family such as parents’ educations and incomes on building students’ healthy eating habits. Methods A survey on building students’ eating habits was conducted among primary school students of grade 4 (11 years) and 5 (12 years) from Kulim district, Malaysia. Data from 318 respondents were analysed. Descriptive statistics were used to find the present scenario of their knowledge, attitude and practices towards their eating habits while one-way ANOVA and independent sample t-test were used to find the differences between their practices based on students’ gender, parents’ educations and incomes. Results The study finds that the students have a good knowledge of types of healthy food but yet their preferences are towards the unhealthy food. Though the students’ gender and parents’ educations are not found significantly related to students’ knowledge, attitude and practices towards healthy eating habits, parents’ incomes have significant influence on promoting the healthy eating habit. Discussion Findings of this study can be useful to guide parents in healthy food choices and suggest them to be models to their children in building healthy eating habits.
format: application/pdf
format: text/html
creator: Kazi Enamul Hoque
creator: Kazi Fardinul Hoque
creator: Revethy A/P Thanabalan
subject: Nutrition
subject: Public Health
description: doi:10.7717/peerj.4563
publisher: PeerJ Inc.
rights: © 2018 Hoque et al.
abstract: Background Building healthy eating habit is essential for all people. School and family are the prime institutions to instill this habit during early age. This study is aimed at understanding the impact of family such as parents’ educations and incomes on building students’ healthy eating habits. Methods A survey on building students’ eating habits was conducted among primary school students of grade 4 (11 years) and 5 (12 years) from Kulim district, Malaysia. Data from 318 respondents were analysed. Descriptive statistics were used to find the present scenario of their knowledge, attitude and practices towards their eating habits while one-way ANOVA and independent sample t-test were used to find the differences between their practices based on students’ gender, parents’ educations and incomes. Results The study finds that the students have a good knowledge of types of healthy food but yet their preferences are towards the unhealthy food. Though the students’ gender and parents’ educations are not found significantly related to students’ knowledge, attitude and practices towards healthy eating habits, parents’ incomes have significant influence on promoting the healthy eating habit. Discussion Findings of this study can be useful to guide parents in healthy food choices and suggest them to be models to their children in building healthy eating habits.
bibliographic citation: Hoque et al. (2018) Relationships between parents’ academic backgrounds and incomes and building students’ healthy eating habits. PeerJ 6:e4563 https://doi.org/10.7717/peerj.4563
date submitted: 2017-08-01
date accepted: 2018-03-12
issued: 2018-05-03
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Hoque
  given name: Kazi Enamul
author list: Agent
  family name: Hoque
  given name: Kazi Fardinul
author list: Agent
  family name: A/P Thanabalan
  given name: Revethy
doi: 10.7717/peerj.4563
volume: 6
issn: 2167-8359
publication name: PeerJ
publication date: 2018-05-03
copyright: © 2018 Hoque et al.
attribution name: Hoque et al.

Stinging wasps (Hymenoptera: Aculeata), which species have the longest sting?
type: item
type: AcademicArticle
description: The stings of bees, wasps, and ants are something that catches the attention of anyone that experiences them. While many recent studies have focused on the pain inflicted by the stings of various stinging wasps, bees, or ants (Hymenoptera: Aculeata), little is known about how the length of the sting itself varies between species. Here, we investigate the sting length of a variety of aculeate wasps, and compare that to reported pain and toxicity values. We find that velvet ants (Hymenoptera: Mutillidae) have the longest sting compared to their body size out of any bee, wasp, or ant species. We also find that there is no link between relative sting length and pain; however, we did find an inverse relationship between relative sting length and toxicity with taxa having shorter relative stings being more toxic. While we found a significant relationship between host use and relative sting length, we suggest that the long sting length of the velvet ants is also related to their suite of defenses to avoid predation.
format: application/pdf
format: text/html
creator: Emily A. Sadler
creator: James P. Pitts
creator: Joseph S. Wilson
subject: Ecology
subject: Entomology
description: doi:10.7717/peerj.4743
publisher: PeerJ Inc.
rights: © 2018 Sadler et al.
abstract: The stings of bees, wasps, and ants are something that catches the attention of anyone that experiences them. While many recent studies have focused on the pain inflicted by the stings of various stinging wasps, bees, or ants (Hymenoptera: Aculeata), little is known about how the length of the sting itself varies between species. Here, we investigate the sting length of a variety of aculeate wasps, and compare that to reported pain and toxicity values. We find that velvet ants (Hymenoptera: Mutillidae) have the longest sting compared to their body size out of any bee, wasp, or ant species. We also find that there is no link between relative sting length and pain; however, we did find an inverse relationship between relative sting length and toxicity with taxa having shorter relative stings being more toxic. While we found a significant relationship between host use and relative sting length, we suggest that the long sting length of the velvet ants is also related to their suite of defenses to avoid predation.
bibliographic citation: Sadler et al. (2018) Stinging wasps (Hymenoptera: Aculeata), which species have the longest sting?. PeerJ 6:e4743 https://doi.org/10.7717/peerj.4743
date submitted: 2018-03-08
date accepted: 2018-04-19
issued: 2018-05-02
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Sadler
  given name: Emily A.
author list: Agent
  family name: Pitts
  given name: James P.
author list: Agent
  family name: Wilson
  given name: Joseph S.
doi: 10.7717/peerj.4743
volume: 6
issn: 2167-8359
publication name: PeerJ
publication date: 2018-05-02
copyright: © 2018 Sadler et al.
attribution name: Sadler et al.

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