PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
items: Identification and expression profiles of candidate chemosensory receptors in Histia rhodope (Lepidoptera: Zygaenidae)
items: Saururus chinensis-controlled allergic pulmonary disease through NF-κB/COX-2 and PGE2 pathways
items: Drought stress strengthens the link between chlorophyll fluorescence parameters and photosynthetic traits
items: A comparison of common metrics used to quantify the effectiveness of conservation interventions
items: The health-related quality of life of Syrian refugee women in their reproductive age
items: Measurements of the gingival papillae architecture using cone-beam computed tomography in young Chinese adults
items: Perception and practices during the COVID-19 pandemic in an urban community in Nigeria: a cross-sectional study
items: Do Centres of Endemism provide a spatial context for predicting and preserving plant phylogeographic patterns in the Cape Floristic Region, South Africa?
items: Coral cover and rubble cryptofauna abundance and diversity at outplanted reefs in Okinawa, Japan
items: Predictive models for stage and risk classification in head and neck squamous cell carcinoma (HNSCC)

Identification and expression profiles of candidate chemosensory receptors in Histia rhodope (Lepidoptera: Zygaenidae)
type: item
type: AcademicArticle
description: Insect olfaction and vision play important roles in survival and reproduction. Diurnal butterflies mainly rely on visual cues whereas nocturnal moths rely on olfactory signals to locate external resources. Histia rhodope Cramer (Lepidoptera: Zygaenidae) is an important pest of the landscape tree Bischofia polycarpa in China and other Southeast Asian regions. As a diurnal moth, H. rhodope represents a suitable model for studying the evolutionary shift from olfactory to visual communication. However, only a few chemosensory soluble proteins have been characterized and information on H. rhodope chemoreceptor genes is currently lacking. In this study, we identified 45 odorant receptors (ORs), nine ionotropic receptors (IRs), eight gustatory receptors (GRs) and two sensory neuron membrane proteins (SNMPs) from our previously acquired H. rhodope antennal transcriptomic data. The number of chemoreceptors of H. rhodope was less compared with that found in many nocturnal moths. Some specific chemoreceptors such as OR co-receptor (ORco), ionotropic receptors co-receptor, CO2 receptors, sugar receptors and bitter receptors were predicted by phylogenetic analysis. Notably, two candidate pheromone receptors (PRs) were identified within a novel PR lineage. qRT-PCR results showed that almost all tested genes (22/24) were predominantly expressed in antennae, indicating that they may be important in olfactory function. Among these antennae-enriched genes, six ORs, five IRs and two GRs displayed female-biased expression, while two ORs displayed male-biased expression. Additionally, HrhoIR75q.2 and HrhoGR67 were more highly expressed in heads and legs. This study enriches the olfactory gene inventory of H. rhodope and provides the foundation for further research of the chemoreception mechanism in diurnal moths.
format: application/pdf
format: text/html
creator: Haibo Yang
creator: Junfeng Dong
creator: Ya-Lan Sun
creator: Zhenjie Hu
creator: Qi-Hui Lyu
creator: Dingxu Li
subject: Bioinformatics
subject: Entomology
subject: Genomics
subject: Molecular Biology
subject: Zoology
description: doi:10.7717/peerj.10035
publisher: PeerJ Inc.
rights: © 2020 Yang et al.
abstract: Insect olfaction and vision play important roles in survival and reproduction. Diurnal butterflies mainly rely on visual cues whereas nocturnal moths rely on olfactory signals to locate external resources. Histia rhodope Cramer (Lepidoptera: Zygaenidae) is an important pest of the landscape tree Bischofia polycarpa in China and other Southeast Asian regions. As a diurnal moth, H. rhodope represents a suitable model for studying the evolutionary shift from olfactory to visual communication. However, only a few chemosensory soluble proteins have been characterized and information on H. rhodope chemoreceptor genes is currently lacking. In this study, we identified 45 odorant receptors (ORs), nine ionotropic receptors (IRs), eight gustatory receptors (GRs) and two sensory neuron membrane proteins (SNMPs) from our previously acquired H. rhodope antennal transcriptomic data. The number of chemoreceptors of H. rhodope was less compared with that found in many nocturnal moths. Some specific chemoreceptors such as OR co-receptor (ORco), ionotropic receptors co-receptor, CO2 receptors, sugar receptors and bitter receptors were predicted by phylogenetic analysis. Notably, two candidate pheromone receptors (PRs) were identified within a novel PR lineage. qRT-PCR results showed that almost all tested genes (22/24) were predominantly expressed in antennae, indicating that they may be important in olfactory function. Among these antennae-enriched genes, six ORs, five IRs and two GRs displayed female-biased expression, while two ORs displayed male-biased expression. Additionally, HrhoIR75q.2 and HrhoGR67 were more highly expressed in heads and legs. This study enriches the olfactory gene inventory of H. rhodope and provides the foundation for further research of the chemoreception mechanism in diurnal moths.
bibliographic citation: Yang et al. (2020) Identification and expression profiles of candidate chemosensory receptors in Histia rhodope (Lepidoptera: Zygaenidae). PeerJ 8:e10035 https://doi.org/10.7717/peerj.10035
date submitted: 2020-05-14
date accepted: 2020-09-03
issued: 2020-09-24
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Yang
  given name: Haibo
author list: Agent
  family name: Dong
  given name: Junfeng
author list: Agent
  family name: Sun
  given name: Ya-Lan
author list: Agent
  family name: Hu
  given name: Zhenjie
author list: Agent
  family name: Lyu
  given name: Qi-Hui
author list: Agent
  family name: Li
  given name: Dingxu
doi: 10.7717/peerj.10035
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-09-24
copyright: ©2020 Yang et al.
attribution name: Yang et al.

Saururus chinensis-controlled allergic pulmonary disease through NF-κB/COX-2 and PGE2 pathways
type: item
type: AcademicArticle
description: Saururus chinensis is a perennial herb found in the northeastern regions of Asia, including Korea, China, and Japan, and is used in traditional medicine. Studies have identified the four major constituents in Saururus chinensis water extract (LHF618®) as miquelianin (11.75 ± 0.092 mg/g), rutin (1.20 ± 0.008 mg/g), quercitrin (2.38 ± 0.389 mg/g), and quercetin (0.068 ± 0.017 mg/g). Saururus chinensis can improve the symptoms of ovalbumin- or fine dust-induced allergic pulmonary disease by suppressing the effects of WBCs and neutrophils in BALF and IgE in the serum. Saururus chinensis dose-dependently recovered morphological changes such as mucous hyper secretion (from 2.7 ± 0.46 to 0.6 ± 0.65), pulmonary epithelial cell hyperplasia (from 2.4 ± 0.55 to 0.7 ± 0.67), and inflammatory cell infiltration (from 2.3 ± 0.45 to 0.6 ± 0.43), and effectively controlled cDNA levels and protein levels of IL-13. It inhibited NF-κB translocation and COX-2 protein synthesis and suppressed the expression of PGE2. Our results show that Saururus chinensis controlled allergic pulmonary disease via the anti-inflammatory pathways, NF-κB/COX-2 and PGE2. Saururus chinensis may be a promising drug candidate against fine dust-induced allergic pulmonary disease.
format: application/pdf
format: text/html
creator: MiKyung Song
creator: Soon-Young Lee
creator: Minhee Kim
creator: Sangwoug Park
creator: Juyeon Park
creator: Yongbum Kwon
creator: Dae-Hun Park
subject: Biochemistry
subject: Allergy and Clinical Immunology
subject: Drugs and Devices
subject: Respiratory Medicine
description: doi:10.7717/peerj.10043
publisher: PeerJ Inc.
rights: © 2020 Song et al.
abstract: Saururus chinensis is a perennial herb found in the northeastern regions of Asia, including Korea, China, and Japan, and is used in traditional medicine. Studies have identified the four major constituents in Saururus chinensis water extract (LHF618®) as miquelianin (11.75 ± 0.092 mg/g), rutin (1.20 ± 0.008 mg/g), quercitrin (2.38 ± 0.389 mg/g), and quercetin (0.068 ± 0.017 mg/g). Saururus chinensis can improve the symptoms of ovalbumin- or fine dust-induced allergic pulmonary disease by suppressing the effects of WBCs and neutrophils in BALF and IgE in the serum. Saururus chinensis dose-dependently recovered morphological changes such as mucous hyper secretion (from 2.7 ± 0.46 to 0.6 ± 0.65), pulmonary epithelial cell hyperplasia (from 2.4 ± 0.55 to 0.7 ± 0.67), and inflammatory cell infiltration (from 2.3 ± 0.45 to 0.6 ± 0.43), and effectively controlled cDNA levels and protein levels of IL-13. It inhibited NF-κB translocation and COX-2 protein synthesis and suppressed the expression of PGE2. Our results show that Saururus chinensis controlled allergic pulmonary disease via the anti-inflammatory pathways, NF-κB/COX-2 and PGE2. Saururus chinensis may be a promising drug candidate against fine dust-induced allergic pulmonary disease.
bibliographic citation: Song et al. (2020) Saururus chinensis-controlled allergic pulmonary disease through NF-κB/COX-2 and PGE2 pathways. PeerJ 8:e10043 https://doi.org/10.7717/peerj.10043
date submitted: 2020-04-17
date accepted: 2020-09-04
issued: 2020-09-24
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Song
  given name: MiKyung
author list: Agent
  family name: Lee
  given name: Soon-Young
author list: Agent
  family name: Kim
  given name: Minhee
author list: Agent
  family name: Park
  given name: Sangwoug
author list: Agent
  family name: Park
  given name: Juyeon
author list: Agent
  family name: Kwon
  given name: Yongbum
author list: Agent
  family name: Park
  given name: Dae-Hun
doi: 10.7717/peerj.10043
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-09-24
copyright: ©2020 Song et al.
attribution name: Song et al.

Drought stress strengthens the link between chlorophyll fluorescence parameters and photosynthetic traits
type: item
type: AcademicArticle
description: Chlorophyll fluorescence (ChlF) has been used to understand photosynthesis and its response to climate change, particularly with satellite-based data. However, it remains unclear how the ChlF ratio and photosynthesis are linked at the leaf level under drought stress. Here, we examined the link between ChlF ratio and photosynthesis at the leaf level by measuring photosynthetic traits, such as net CO2 assimilation rate (An), the maximum carboxylation rate of Rubisco (Vcmax), the maximum rate of electron transport (Jmax), stomatal conductance (gs) and total chlorophyll content (Chlt). The ChlF ratio of the leaf level such as maximum quantum efficiency of PSII (Fv/Fm) is based on fluorescence kinetics. ChlF intensity ratio (LD685/LD740) based on spectrum analysis was obtained. We found that a combination of the stomatal limitation, non-stomatal limitation, and Chlt regulated leaf photosynthesis under drought stress, while Jmax and Chlt governed the ChlF ratio. A significant link between the ChlF ratio and An was found under drought stress while no significant correlation in the control, which indicated that drought stress strengthens the link between the ChlF ratio and photosynthetic traits. These results suggest that the ChlF ratio can be a powerful tool to track photosynthetic traits of terrestrial ecosystems under drought stress.
format: application/pdf
format: text/html
creator: Jie Zhuang
creator: Yonglin Wang
creator: Yonggang Chi
creator: Lei Zhou
creator: Jijing Chen
creator: Wen Zhou
creator: Jun Song
creator: Ning Zhao
creator: Jianxi Ding
subject: Ecology
subject: Ecosystem Science
subject: Plant Science
subject: Climate Change Biology
description: doi:10.7717/peerj.10046
publisher: PeerJ Inc.
rights: © 2020 Zhuang et al.
abstract: Chlorophyll fluorescence (ChlF) has been used to understand photosynthesis and its response to climate change, particularly with satellite-based data. However, it remains unclear how the ChlF ratio and photosynthesis are linked at the leaf level under drought stress. Here, we examined the link between ChlF ratio and photosynthesis at the leaf level by measuring photosynthetic traits, such as net CO2 assimilation rate (An), the maximum carboxylation rate of Rubisco (Vcmax), the maximum rate of electron transport (Jmax), stomatal conductance (gs) and total chlorophyll content (Chlt). The ChlF ratio of the leaf level such as maximum quantum efficiency of PSII (Fv/Fm) is based on fluorescence kinetics. ChlF intensity ratio (LD685/LD740) based on spectrum analysis was obtained. We found that a combination of the stomatal limitation, non-stomatal limitation, and Chlt regulated leaf photosynthesis under drought stress, while Jmax and Chlt governed the ChlF ratio. A significant link between the ChlF ratio and An was found under drought stress while no significant correlation in the control, which indicated that drought stress strengthens the link between the ChlF ratio and photosynthetic traits. These results suggest that the ChlF ratio can be a powerful tool to track photosynthetic traits of terrestrial ecosystems under drought stress.
bibliographic citation: Zhuang et al. (2020) Drought stress strengthens the link between chlorophyll fluorescence parameters and photosynthetic traits. PeerJ 8:e10046 https://doi.org/10.7717/peerj.10046
date submitted: 2020-02-25
date accepted: 2020-09-04
issued: 2020-09-24
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Zhuang
  given name: Jie
author list: Agent
  family name: Wang
  given name: Yonglin
author list: Agent
  family name: Chi
  given name: Yonggang
author list: Agent
  family name: Zhou
  given name: Lei
author list: Agent
  family name: Chen
  given name: Jijing
author list: Agent
  family name: Zhou
  given name: Wen
author list: Agent
  family name: Song
  given name: Jun
author list: Agent
  family name: Zhao
  given name: Ning
author list: Agent
  family name: Ding
  given name: Jianxi
doi: 10.7717/peerj.10046
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-09-24
copyright: ©2020 Zhuang et al.
attribution name: Zhuang et al.

A comparison of common metrics used to quantify the effectiveness of conservation interventions
type: item
type: AcademicArticle
description: Background Evidence-based conservation is urgently needed to identify, apply and promote effective interventions for mitigation of threats and recovery of the natural environment. Estimation of intervention effectiveness is subject to robust study design and statistical analysis, and much progress is documented in these fields. In contrast, little is understood about the accuracy and biases (underestimation and overestimation) of different effectiveness metrics and how they are affected by sample size. Methods In this study, a dataset (n = 500 cases) consisting of random, positive, integer numbers was simulated to produce frequency input data for the 2 × 2 contingency table. For each case, three metrics of the relative risk, odds ratio and the magnitude of change were calculated, their disparity was estimated and the characteristics of treatment (with intervention) and control (without intervention) samples significantly affecting this disparity were studied by means of linear regression. Further, four case studies from different conservation interventions are provided to support the results. Results The study has shown that the relative risk and the magnitude of change produce identical estimates of intervention effectiveness only when treatment and control samples are equal, or when the number of target outcomes (e.g., number of livestock killed by predators) in treatment sample reaches zero. In other situations, the magnitude of change gives overestimates or underestimates, depending on relationships between treatment and control sample sizes. The table summarizing the conditions of equalities and biases between these two metrics is provided. These conditions are valid for both reduction-aimed interventions reducing negative target outcomes (e.g., livestock protection to reduce livestock losses to predators) and for addition-aimed interventions increasing positive target outcomes (e.g., establishment of protected areas to increase species presence). No significan…
format: application/pdf
format: text/html
creator: Igor Khorozyan
subject: Biodiversity
subject: Conservation Biology
subject: Ecology
subject: Zoology
subject: Natural Resource Management
description: doi:10.7717/peerj.9873
publisher: PeerJ Inc.
rights: © 2020 Khorozyan
abstract: Background Evidence-based conservation is urgently needed to identify, apply and promote effective interventions for mitigation of threats and recovery of the natural environment. Estimation of intervention effectiveness is subject to robust study design and statistical analysis, and much progress is documented in these fields. In contrast, little is understood about the accuracy and biases (underestimation and overestimation) of different effectiveness metrics and how they are affected by sample size. Methods In this study, a dataset (n = 500 cases) consisting of random, positive, integer numbers was simulated to produce frequency input data for the 2 × 2 contingency table. For each case, three metrics of the relative risk, odds ratio and the magnitude of change were calculated, their disparity was estimated and the characteristics of treatment (with intervention) and control (without intervention) samples significantly affecting this disparity were studied by means of linear regression. Further, four case studies from different conservation interventions are provided to support the results. Results The study has shown that the relative risk and the magnitude of change produce identical estimates of intervention effectiveness only when treatment and control samples are equal, or when the number of target outcomes (e.g., number of livestock killed by predators) in treatment sample reaches zero. In other situations, the magnitude of change gives overestimates or underestimates, depending on relationships between treatment and control sample sizes. The table summarizing the conditions of equalities and biases between these two metrics is provided. These conditions are valid for both reduction-aimed interventions reducing negative target outcomes (e.g., livestock protection to reduce livestock losses to predators) and for addition-aimed interventions increasing positive target outcomes (e.g., establishment of protected areas to increase species presence). No significan…
bibliographic citation: Khorozyan (2020) A comparison of common metrics used to quantify the effectiveness of conservation interventions. PeerJ 8:e9873 https://doi.org/10.7717/peerj.9873
date submitted: 2020-07-03
date accepted: 2020-08-14
issued: 2020-09-23
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Khorozyan
  given name: Igor
doi: 10.7717/peerj.9873
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-09-23
copyright: © 2020 Khorozyan
attribution name: Khorozyan

The health-related quality of life of Syrian refugee women in their reproductive age
type: item
type: AcademicArticle
description: Background Health-Related Quality of Life (HRQoL) for refugee women in reproductive age is highly affected by physical, political, psychosocial and environmental conditions in countries of asylum. HRQoL is enormously affected by the satisfaction of this vulnerable group with the physical, psychological, emotional and social care services provided in this critical time. Therefore, this study aimed toassess the HRQoL among Syrian refugee women of reproductive age living outside camps in Jordan. Methods A cross-sectional correlational study was conducted with a convenience sample of 523 Syrian refugee women in the host communities in Jordan.Health-related quality of life (HRQOL) was measured using the short-form 36 (SF-36) questionnaire. Results Significant negative correlations were found between SF-36 individual subscales score and the length of marriage, the number of children, parity and family income. The strongest correlations were between pain scale and length of marriage (r = − .21), and between Energy/Fatigue and ‘number of children’ (r = − .21). Conversely, antenatal care was positively correlated with physical, role emotional, pain, and general health. Physical functioning and general health were predicted significantly with less years of marriage, younger age at marriage, less violence and by higher family income. Conclusion This study suggests low HRQoL scores for women of reproductive age across all domains. Several factors such as years of marriage, age at marriage, the number of children, violence, antenatal care and family income affected the women’s general health. The provision of appropriate and accessible reproductive and maternal healthcare services in antenatal visits is critical for ensuring the immediate and long-term health and wellbeing of refugee women and their families.
format: application/pdf
format: text/html
creator: Manar Nabolsi
creator: Reema Safadi
creator: Carolyn Sun
creator: Muayyad Ahmad
creator: Du’a Al-Maharma
creator: Suhaila Halasa
creator: Mohammad Saleh
creator: Jennifer Dohrn
subject: Global Health
subject: Nursing
subject: Public Health
subject: Women’s Health
description: doi:10.7717/peerj.9990
publisher: PeerJ Inc.
rights: © 2020 Nabolsi et al.
abstract: Background Health-Related Quality of Life (HRQoL) for refugee women in reproductive age is highly affected by physical, political, psychosocial and environmental conditions in countries of asylum. HRQoL is enormously affected by the satisfaction of this vulnerable group with the physical, psychological, emotional and social care services provided in this critical time. Therefore, this study aimed toassess the HRQoL among Syrian refugee women of reproductive age living outside camps in Jordan. Methods A cross-sectional correlational study was conducted with a convenience sample of 523 Syrian refugee women in the host communities in Jordan.Health-related quality of life (HRQOL) was measured using the short-form 36 (SF-36) questionnaire. Results Significant negative correlations were found between SF-36 individual subscales score and the length of marriage, the number of children, parity and family income. The strongest correlations were between pain scale and length of marriage (r = − .21), and between Energy/Fatigue and ‘number of children’ (r = − .21). Conversely, antenatal care was positively correlated with physical, role emotional, pain, and general health. Physical functioning and general health were predicted significantly with less years of marriage, younger age at marriage, less violence and by higher family income. Conclusion This study suggests low HRQoL scores for women of reproductive age across all domains. Several factors such as years of marriage, age at marriage, the number of children, violence, antenatal care and family income affected the women’s general health. The provision of appropriate and accessible reproductive and maternal healthcare services in antenatal visits is critical for ensuring the immediate and long-term health and wellbeing of refugee women and their families.
bibliographic citation: Nabolsi et al. (2020) The health-related quality of life of Syrian refugee women in their reproductive age. PeerJ 8:e9990 https://doi.org/10.7717/peerj.9990
date submitted: 2020-05-15
date accepted: 2020-08-28
issued: 2020-09-23
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Nabolsi
  given name: Manar
author list: Agent
  family name: Safadi
  given name: Reema
author list: Agent
  family name: Sun
  given name: Carolyn
author list: Agent
  family name: Ahmad
  given name: Muayyad
author list: Agent
  family name: Al-Maharma
  given name: Du’a
author list: Agent
  family name: Halasa
  given name: Suhaila
author list: Agent
  family name: Saleh
  given name: Mohammad
author list: Agent
  family name: Dohrn
  given name: Jennifer
doi: 10.7717/peerj.9990
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-09-23
copyright: ©2020 Nabolsi et al.
attribution name: Nabolsi et al.

Measurements of the gingival papillae architecture using cone-beam computed tomography in young Chinese adults
type: item
type: AcademicArticle
description: Background The aim of this study was to measure the morphology of interdental papillae (IP) in maxillary anterior teeth using cone-beam computed tomography (CBCT). Methods Twenty-seven periodontally healthy subjects with 135 IP were evaluated by means of periodontal examination and a CBCT scan with an elastomeric matrix containing radiopaque material in position. According to the status of tooth contact and presence of IP, subjects were categorized into three groups: open contact point, complete papillae, and deficient papillae group. The papillae height (PH), facial-lingual thickness (FLT), and interdental distance (IDD) were measured. Data was analyzed with the significance level at α = 0.05. Results The mean PH values were 4.17 ± 0.51 mm, 3.99 ± 0.61 mm, and 3.99 ± 0.62 mm, for the open contact group, complete papilla, and deficient papilla group, respectively. The PH values of the recorded sites among central incisors, lateral incisors, and canine were 4.13 ± 0.56 mm, 3.87 ± 0. 63 mm, and 4.07 ± 0.58 mm, respectively. No statistically significant differences of the PH values were determined between the above three tested groups as well as between the different sites (p > 0.05). The IDD values obtained from the complete papilla group were significantly lower than the other tested groups (p < 0.05). Conclusion The contact point condition of upper anterior sextants may not influence the presence and dimension of the IP in periodontally healthy subjects.
format: application/pdf
format: text/html
creator: Gang Yang
creator: Jie Cao
creator: Wenjie Hu
creator: Kwok-Hung Chung
subject: Dentistry
subject: Radiology and Medical Imaging
description: doi:10.7717/peerj.10006
publisher: PeerJ Inc.
rights: © 2020 Yang et al.
abstract: Background The aim of this study was to measure the morphology of interdental papillae (IP) in maxillary anterior teeth using cone-beam computed tomography (CBCT). Methods Twenty-seven periodontally healthy subjects with 135 IP were evaluated by means of periodontal examination and a CBCT scan with an elastomeric matrix containing radiopaque material in position. According to the status of tooth contact and presence of IP, subjects were categorized into three groups: open contact point, complete papillae, and deficient papillae group. The papillae height (PH), facial-lingual thickness (FLT), and interdental distance (IDD) were measured. Data was analyzed with the significance level at α = 0.05. Results The mean PH values were 4.17 ± 0.51 mm, 3.99 ± 0.61 mm, and 3.99 ± 0.62 mm, for the open contact group, complete papilla, and deficient papilla group, respectively. The PH values of the recorded sites among central incisors, lateral incisors, and canine were 4.13 ± 0.56 mm, 3.87 ± 0. 63 mm, and 4.07 ± 0.58 mm, respectively. No statistically significant differences of the PH values were determined between the above three tested groups as well as between the different sites (p > 0.05). The IDD values obtained from the complete papilla group were significantly lower than the other tested groups (p < 0.05). Conclusion The contact point condition of upper anterior sextants may not influence the presence and dimension of the IP in periodontally healthy subjects.
bibliographic citation: Yang et al. (2020) Measurements of the gingival papillae architecture using cone-beam computed tomography in young Chinese adults. PeerJ 8:e10006 https://doi.org/10.7717/peerj.10006
date submitted: 2020-03-05
date accepted: 2020-08-31
issued: 2020-09-23
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Yang
  given name: Gang
author list: Agent
  family name: Cao
  given name: Jie
author list: Agent
  family name: Hu
  given name: Wenjie
author list: Agent
  family name: Chung
  given name: Kwok-Hung
doi: 10.7717/peerj.10006
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-09-23
copyright: ©2020 Yang et al.
attribution name: Yang et al.

Perception and practices during the COVID-19 pandemic in an urban community in Nigeria: a cross-sectional study
type: item
type: AcademicArticle
description: Background Various perceptions and practices have been associated with the COVID-19 pandemic. In this study, we assessed the perception and practices regarding COVID-19 among residents in selected urban communities of Ibadan, Oyo State, Nigeria. Methods A descriptive cross-sectional study design using a multi-stage sampling technique was used to recruit 360 respondents (Mean age: 33.2 ± 10.6 years; 62.5% females) from households in Ibadan. Data were collected using an interviewer-administered questionnaire from 3rd to 6th June 2020. Those who demonstrated washing of the palm, back of the hand, spaces between the fingers, fingernails, wrist, and thumbs had six points and were categorized to have had a good practice of handwashing. Descriptive statistics were conducted. Bivariate analyses of sociodemographic characteristics and good handwashing practices were conducted using Chi-square test. Logistic regression was conducted to identify the determinants of good handwashing practices. P-values < 0.05 were statistically significant. Results Going to the hospital (95%) and calling the COVID-19 help number (58.3%) were the frequently reported practices among respondents following the development of COVID-19 symptoms. Also, 89 (26%) knew they could contract COVID-19, while 41 (12%) perceived it as an exaggerated event. The effects most frequently reported by respondents were hunger/low income (48.8%) and academic delay (8.8%). Use of face masks by 64.5% and social distancing (48%) were the most frequently reported practices for prevention. Only 71 (20.8%) demonstrated good handwashing practices. The perception of the likelihood to contract COVID-19 and practices to prevent COVID-19 had a weak correlation of 0.239 (p < 0.001). Conclusion Gaps exist in the practices that prevent COVID-19. There is a need to improve handwashing, use of face masks and other practices that prevent COVID-19. Implications across public health communication and policies were stated.
format: application/pdf
format: text/html
creator: Olayinka Ilesanmi
creator: Aanuoluwapo Afolabi
subject: Virology
subject: Epidemiology
subject: Global Health
subject: Infectious Diseases
subject: Public Health
description: doi:10.7717/peerj.10038
publisher: PeerJ Inc.
rights: © 2020 Ilesanmi and Afolabi
abstract: Background Various perceptions and practices have been associated with the COVID-19 pandemic. In this study, we assessed the perception and practices regarding COVID-19 among residents in selected urban communities of Ibadan, Oyo State, Nigeria. Methods A descriptive cross-sectional study design using a multi-stage sampling technique was used to recruit 360 respondents (Mean age: 33.2 ± 10.6 years; 62.5% females) from households in Ibadan. Data were collected using an interviewer-administered questionnaire from 3rd to 6th June 2020. Those who demonstrated washing of the palm, back of the hand, spaces between the fingers, fingernails, wrist, and thumbs had six points and were categorized to have had a good practice of handwashing. Descriptive statistics were conducted. Bivariate analyses of sociodemographic characteristics and good handwashing practices were conducted using Chi-square test. Logistic regression was conducted to identify the determinants of good handwashing practices. P-values < 0.05 were statistically significant. Results Going to the hospital (95%) and calling the COVID-19 help number (58.3%) were the frequently reported practices among respondents following the development of COVID-19 symptoms. Also, 89 (26%) knew they could contract COVID-19, while 41 (12%) perceived it as an exaggerated event. The effects most frequently reported by respondents were hunger/low income (48.8%) and academic delay (8.8%). Use of face masks by 64.5% and social distancing (48%) were the most frequently reported practices for prevention. Only 71 (20.8%) demonstrated good handwashing practices. The perception of the likelihood to contract COVID-19 and practices to prevent COVID-19 had a weak correlation of 0.239 (p < 0.001). Conclusion Gaps exist in the practices that prevent COVID-19. There is a need to improve handwashing, use of face masks and other practices that prevent COVID-19. Implications across public health communication and policies were stated.
bibliographic citation: Ilesanmi et al. (2020) Perception and practices during the COVID-19 pandemic in an urban community in Nigeria: a cross-sectional study. PeerJ 8:e10038 https://doi.org/10.7717/peerj.10038
date submitted: 2020-07-08
date accepted: 2020-09-04
issued: 2020-09-23
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Ilesanmi
  given name: Olayinka
author list: Agent
  family name: Afolabi
  given name: Aanuoluwapo
doi: 10.7717/peerj.10038
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-09-23
copyright: © 2020 Ilesanmi and Afolabi
attribution name: Ilesanmi and Afolabi

Do Centres of Endemism provide a spatial context for predicting and preserving plant phylogeographic patterns in the Cape Floristic Region, South Africa?
type: item
type: AcademicArticle
description: Aim The evolutionary forces that gave rise to the exceptional plant species richness of the Cape Floristic Region (CFR) have also likely played a role at the intraspecific level (i.e. plant populations)—and thereby generating shared phylogeographic patterns among taxa. Here we test whether plant populations in the CFR exhibit phylogeographic breaks across the boundaries between Centres of Endemism (CoEs). The boundaries between CoEs (derived from the distribution ranges of endemic taxa and currently mapped at a coarse, Quarter Degree Square scale) represent a spatial proxy for the evolutionary diversifying drivers acting on plant taxa in the CFR. Location The CFR, located along the southern Cape of South Africa. Methods Published phylogeographic literature were compiled and spatial patterns of genetic divergence re-analysed to assess the frequency at which CFR plant taxa exhibit phylogeographic breaks either (1) across or (2) within CoE boundaries. Population pairs from each study were compared across and within CoEs and scored as either exhibiting a phylogeographic break or not. Results Phylogeographic breaks in Cape plants were found to occur across the boundaries of CoEs more often than not. Significantly more population pairs exhibited phylogeographic breaks across CoE boundaries (506 of the 540, χ2 = 886, p < 0.001) and fewer breaks within CoEs (94 of 619, χ2 = 300, p < 0.001) than would be expected if there was equal probability of a genetic break occurring across CoE boundaries. Main conclusions The evolutionary forces that have produced and maintained the exceptional plant diversity in the CFR appear to have operated at the population level, producing similar patterns of phylogeographic structuring of plant lineages regardless of life history or taxonomy. This tendency for Cape plants to exhibit shared patterns of spatially structured genetic diversity that match the distribution of endemic taxa may assist CFR phylogeographers to streamline sampling efforts …
format: application/pdf
format: text/html
creator: Nicholas C. Galuszynski
creator: Alastair J. Potts
subject: Biodiversity
subject: Biogeography
subject: Conservation Biology
subject: Genetics
subject: Plant Science
description: doi:10.7717/peerj.10045
publisher: PeerJ Inc.
rights: © 2020 Galuszynski and Potts
abstract: Aim The evolutionary forces that gave rise to the exceptional plant species richness of the Cape Floristic Region (CFR) have also likely played a role at the intraspecific level (i.e. plant populations)—and thereby generating shared phylogeographic patterns among taxa. Here we test whether plant populations in the CFR exhibit phylogeographic breaks across the boundaries between Centres of Endemism (CoEs). The boundaries between CoEs (derived from the distribution ranges of endemic taxa and currently mapped at a coarse, Quarter Degree Square scale) represent a spatial proxy for the evolutionary diversifying drivers acting on plant taxa in the CFR. Location The CFR, located along the southern Cape of South Africa. Methods Published phylogeographic literature were compiled and spatial patterns of genetic divergence re-analysed to assess the frequency at which CFR plant taxa exhibit phylogeographic breaks either (1) across or (2) within CoE boundaries. Population pairs from each study were compared across and within CoEs and scored as either exhibiting a phylogeographic break or not. Results Phylogeographic breaks in Cape plants were found to occur across the boundaries of CoEs more often than not. Significantly more population pairs exhibited phylogeographic breaks across CoE boundaries (506 of the 540, χ2 = 886, p < 0.001) and fewer breaks within CoEs (94 of 619, χ2 = 300, p < 0.001) than would be expected if there was equal probability of a genetic break occurring across CoE boundaries. Main conclusions The evolutionary forces that have produced and maintained the exceptional plant diversity in the CFR appear to have operated at the population level, producing similar patterns of phylogeographic structuring of plant lineages regardless of life history or taxonomy. This tendency for Cape plants to exhibit shared patterns of spatially structured genetic diversity that match the distribution of endemic taxa may assist CFR phylogeographers to streamline sampling efforts …
bibliographic citation: Galuszynski et al. (2020) Do Centres of Endemism provide a spatial context for predicting and preserving plant phylogeographic patterns in the Cape Floristic Region, South Africa?. PeerJ 8:e10045 https://doi.org/10.7717/peerj.10045
date submitted: 2020-06-29
date accepted: 2020-09-04
issued: 2020-09-23
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Galuszynski
  given name: Nicholas C.
author list: Agent
  family name: Potts
  given name: Alastair J.
doi: 10.7717/peerj.10045
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-09-23
copyright: © 2020 Galuszynski and Potts
attribution name: Galuszynski and Potts

Coral cover and rubble cryptofauna abundance and diversity at outplanted reefs in Okinawa, Japan
type: item
type: AcademicArticle
description: Global climate change is leading to damage and loss of coral reef ecosystems. On subtropical Okinawa Island in southwestern Japan, the prefectural government is working on coral reef restoration by outplanting coral colonies from family Acroporidae back to reefs after initially farming colonies inside protected nurseries. In order to establish a baseline for future comparisons, in this study we documented the current status of reefs undergoing outplanting at Okinawa Island, and nearby locations where no human manipulation has occurred. We examined three sites on the coast of Onna Village on the west coast of the island; each site included an outplanted and control location. We used (1) coral rubble sampling to measure and compare abundance and diversity of rubble cryptofauna; and (2) coral reef monitoring using Line Intercept Transects to track live coral coverage. Results showed that rubble shape had a positive correlation with the numbers of animals found within rubble themselves and may therefore constitute a reliable abundance predictor. Each outplanted location did not show differences with the corresponding control location in terms of rubble cryptofauna abundance, but outplanted locations had significantly lower coral coverage. Overall, differences between sites (Maeganeku1, Maeganeku2 and Manza, each including both outplanted and control locations) were significant, for both rubble cryptofauna and coral coverage. We recommend (1) to outplant colonies from more stress-resistant genera in place of Acropora, and (2) to conduct regular surveys to monitor the situation closely. With a lack of baseline data preceding impacts, rigorous monitoring over time can highlight trends towards increases or decreases in evaluated variables, allowing to obtain a clearer idea of the effects of transplants and on the trajectory of impacts due to climate change and local stressors . Finally, we also recommend (3) to establish conservation and sustainable practices that could aid…
format: application/pdf
format: text/html
creator: Piera Biondi
creator: Giovanni Diego Masucci
creator: James Davis Reimer
subject: Conservation Biology
subject: Ecology
subject: Marine Biology
description: doi:10.7717/peerj.9185
publisher: PeerJ Inc.
rights: © 2020 Biondi et al.
abstract: Global climate change is leading to damage and loss of coral reef ecosystems. On subtropical Okinawa Island in southwestern Japan, the prefectural government is working on coral reef restoration by outplanting coral colonies from family Acroporidae back to reefs after initially farming colonies inside protected nurseries. In order to establish a baseline for future comparisons, in this study we documented the current status of reefs undergoing outplanting at Okinawa Island, and nearby locations where no human manipulation has occurred. We examined three sites on the coast of Onna Village on the west coast of the island; each site included an outplanted and control location. We used (1) coral rubble sampling to measure and compare abundance and diversity of rubble cryptofauna; and (2) coral reef monitoring using Line Intercept Transects to track live coral coverage. Results showed that rubble shape had a positive correlation with the numbers of animals found within rubble themselves and may therefore constitute a reliable abundance predictor. Each outplanted location did not show differences with the corresponding control location in terms of rubble cryptofauna abundance, but outplanted locations had significantly lower coral coverage. Overall, differences between sites (Maeganeku1, Maeganeku2 and Manza, each including both outplanted and control locations) were significant, for both rubble cryptofauna and coral coverage. We recommend (1) to outplant colonies from more stress-resistant genera in place of Acropora, and (2) to conduct regular surveys to monitor the situation closely. With a lack of baseline data preceding impacts, rigorous monitoring over time can highlight trends towards increases or decreases in evaluated variables, allowing to obtain a clearer idea of the effects of transplants and on the trajectory of impacts due to climate change and local stressors . Finally, we also recommend (3) to establish conservation and sustainable practices that could aid…
bibliographic citation: Biondi et al. (2020) Coral cover and rubble cryptofauna abundance and diversity at outplanted reefs in Okinawa, Japan. PeerJ 8:e9185 https://doi.org/10.7717/peerj.9185
date submitted: 2019-08-15
date accepted: 2020-04-23
issued: 2020-09-22
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Biondi
  given name: Piera
author list: Agent
  family name: Masucci
  given name: Giovanni Diego
author list: Agent
  family name: Reimer
  given name: James Davis
doi: 10.7717/peerj.9185
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-09-22
copyright: © 2020 Biondi et al.
attribution name: Biondi et al.

Predictive models for stage and risk classification in head and neck squamous cell carcinoma (HNSCC)
type: item
type: AcademicArticle
description: Machine learning techniques are increasingly used in the analysis of high throughput genome sequencing data to better understand the disease process and design of therapeutic modalities. In the current study, we have applied state of the art machine learning (ML) algorithms (Random Forest (RF), Support Vector Machine Radial Kernel (svmR), Adaptive Boost (AdaBoost), averaged Neural Network (avNNet), and Gradient Boosting Machine (GBM)) to stratify the HNSCC patients in early and late clinical stages (TNM) and to predict the risk using miRNAs expression profiles. A six miRNA signature was identified that can stratify patients in the early and late stages. The mean accuracy, sensitivity, specificity, and area under the curve (AUC) was found to be 0.84, 0.87, 0.78, and 0.82, respectively indicating the robust performance of the generated model. The prognostic signature of eight miRNAs was identified using LASSO (least absolute shrinkage and selection operator) penalized regression. These miRNAs were found to be significantly associated with overall survival of the patients. The pathway and functional enrichment analysis of the identified biomarkers revealed their involvement in important cancer pathways such as GP6 signalling, Wnt signalling, p53 signalling, granulocyte adhesion, and dipedesis. To the best of our knowledge, this is the first such study and we hope that these signature miRNAs will be useful for the risk stratification of patients and the design of therapeutic modalities.
format: application/pdf
format: text/html
creator: Sugandh Kumar
creator: Srinivas Patnaik
creator: Anshuman Dixit
subject: Bioinformatics
subject: Computational Biology
subject: Mathematical Biology
subject: Oncology
subject: Data Mining and Machine Learning
description: doi:10.7717/peerj.9656
publisher: PeerJ Inc.
rights: © 2020 Kumar et al.
abstract: Machine learning techniques are increasingly used in the analysis of high throughput genome sequencing data to better understand the disease process and design of therapeutic modalities. In the current study, we have applied state of the art machine learning (ML) algorithms (Random Forest (RF), Support Vector Machine Radial Kernel (svmR), Adaptive Boost (AdaBoost), averaged Neural Network (avNNet), and Gradient Boosting Machine (GBM)) to stratify the HNSCC patients in early and late clinical stages (TNM) and to predict the risk using miRNAs expression profiles. A six miRNA signature was identified that can stratify patients in the early and late stages. The mean accuracy, sensitivity, specificity, and area under the curve (AUC) was found to be 0.84, 0.87, 0.78, and 0.82, respectively indicating the robust performance of the generated model. The prognostic signature of eight miRNAs was identified using LASSO (least absolute shrinkage and selection operator) penalized regression. These miRNAs were found to be significantly associated with overall survival of the patients. The pathway and functional enrichment analysis of the identified biomarkers revealed their involvement in important cancer pathways such as GP6 signalling, Wnt signalling, p53 signalling, granulocyte adhesion, and dipedesis. To the best of our knowledge, this is the first such study and we hope that these signature miRNAs will be useful for the risk stratification of patients and the design of therapeutic modalities.
bibliographic citation: Kumar et al. (2020) Predictive models for stage and risk classification in head and neck squamous cell carcinoma (HNSCC). PeerJ 8:e9656 https://doi.org/10.7717/peerj.9656
date submitted: 2020-03-12
date accepted: 2020-07-14
issued: 2020-09-22
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Kumar
  given name: Sugandh
author list: Agent
  family name: Patnaik
  given name: Srinivas
author list: Agent
  family name: Dixit
  given name: Anshuman
doi: 10.7717/peerj.9656
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-09-22
copyright: ©2020 Kumar et al.
attribution name: Kumar et al.

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