PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
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)
items: Fungal infection, decline and persistence in the only obligate troglodytic Neotropical salamander
items: Site selection by geese in a suburban landscape
items: Dichocarpum hagiangense—a new species and an updated checklist of Ranunculaceae in Vietnam
items: Flavoured water consumption alters pharmacokinetic parameters and increases exposure of erlotinib and gefitinib in a preclinical study using Wistar rats

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.
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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.

Fungal infection, decline and persistence in the only obligate troglodytic Neotropical salamander
type: item
type: AcademicArticle
description: The fungal pathogen Batrachochytrium dendrobatidis (Bd) is implicated in global mass die-offs and declines in amphibians. In Mesoamerica, the Bd epidemic wave hypothesis is supported by detection of Bd in historic museum specimens collected over the last century, yet the timing and impact of the early stages of the wave remain poorly understood. Chiropterotriton magnipes, the only obligate troglodytic Neotropical salamander, was abundant in its small range in the decade following its description in 1965, but subsequently disappeared from known localities and was not seen for 34 years. Its decline is roughly coincident with that of other populations of Neotropical salamanders associated with the invasion and spread of Bd. To determine the presence and infection intensity of Bd on C. magnipes and sympatric amphibian species (which are also Bd hosts), we used a noninvasive sampling technique and qPCR assay to detect Bd on museum specimens of C. magnipes collected from 1952 to 2012, and from extant populations of C. magnipes and sympatric species of amphibians. We also tested for the presence of the recently discovered Batrachochytrium salamandivorans (Bsal), another fungal chytridiomycete pathogen of salamanders, using a similar technique specific for Bsal. We did not detect Bd in populations of C. magnipes before 1969, while Bd was detected at low to moderate prevalence just prior to and during declines. This pattern is consistent with Bd-caused epizootics followed by host declines and extirpations described in other hosts. We did not detect Bsal in any extant population of C. magnipes. We obtained one of the earliest positive records of the fungus to date in Latin America, providing additional historical evidence consistent with the Bd epidemic wave hypothesis. Genotyping results show that at least one population is currently infected with the Global Panzootic Lineage of Bd, but our genotyping of the historical positive samples was unsuccessful. The lack of large sam…
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creator: Mizraim Olivares-Miranda
creator: Vance T. Vredenburg
creator: Julio C. García-Sánchez
creator: Allison Q. Byrne
creator: Erica B. Rosenblum
creator: Sean M. Rovito
subject: Conservation Biology
subject: Molecular Biology
subject: Mycology
subject: Veterinary Medicine
subject: Zoology
description: doi:10.7717/peerj.9763
publisher: PeerJ Inc.
rights: © 2020 Olivares-Miranda et al.
abstract: The fungal pathogen Batrachochytrium dendrobatidis (Bd) is implicated in global mass die-offs and declines in amphibians. In Mesoamerica, the Bd epidemic wave hypothesis is supported by detection of Bd in historic museum specimens collected over the last century, yet the timing and impact of the early stages of the wave remain poorly understood. Chiropterotriton magnipes, the only obligate troglodytic Neotropical salamander, was abundant in its small range in the decade following its description in 1965, but subsequently disappeared from known localities and was not seen for 34 years. Its decline is roughly coincident with that of other populations of Neotropical salamanders associated with the invasion and spread of Bd. To determine the presence and infection intensity of Bd on C. magnipes and sympatric amphibian species (which are also Bd hosts), we used a noninvasive sampling technique and qPCR assay to detect Bd on museum specimens of C. magnipes collected from 1952 to 2012, and from extant populations of C. magnipes and sympatric species of amphibians. We also tested for the presence of the recently discovered Batrachochytrium salamandivorans (Bsal), another fungal chytridiomycete pathogen of salamanders, using a similar technique specific for Bsal. We did not detect Bd in populations of C. magnipes before 1969, while Bd was detected at low to moderate prevalence just prior to and during declines. This pattern is consistent with Bd-caused epizootics followed by host declines and extirpations described in other hosts. We did not detect Bsal in any extant population of C. magnipes. We obtained one of the earliest positive records of the fungus to date in Latin America, providing additional historical evidence consistent with the Bd epidemic wave hypothesis. Genotyping results show that at least one population is currently infected with the Global Panzootic Lineage of Bd, but our genotyping of the historical positive samples was unsuccessful. The lack of large sam…
bibliographic citation: Olivares-Miranda et al. (2020) Fungal infection, decline and persistence in the only obligate troglodytic Neotropical salamander. PeerJ 8:e9763 https://doi.org/10.7717/peerj.9763
date submitted: 2020-05-20
date accepted: 2020-07-28
issued: 2020-09-22
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Olivares-Miranda
  given name: Mizraim
author list: Agent
  family name: Vredenburg
  given name: Vance T.
author list: Agent
  family name: García-Sánchez
  given name: Julio C.
author list: Agent
  family name: Byrne
  given name: Allison Q.
author list: Agent
  family name: Rosenblum
  given name: Erica B.
author list: Agent
  family name: Rovito
  given name: Sean M.
doi: 10.7717/peerj.9763
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-09-22
copyright: © 2020 Olivares-Miranda et al.
attribution name: Olivares-Miranda et al.

Site selection by geese in a suburban landscape
type: item
type: AcademicArticle
description: Background In European and North American cities geese are among the most common and most visible large herbivores. As such, their presence and behaviour often conflict with the desires of the human residents. Fouling, noise, aggression and health concerns are all cited as reasons that there are “too many”. Lethal control is often used for population management; however, this raises questions about whether this is a sustainable strategy to resolve the conflict between humans and geese when, paradoxically, it is humans that are responsible for creating the habitat and often providing the food and protection of geese at other times. We hypothesise that the landscaping of suburban parks can be improved to decrease its attractiveness to geese and to reduce the opportunity for conflict between geese and humans. Methods Using observations collected over five years from a botanic garden situated in suburban Belgium and data from the whole of Flanders in Belgium, we examined landscape features that attract geese. These included the presence of islands in lakes, the distance from water, barriers to level flight and the size of exploited areas. The birds studied were the tadornine goose Alopochen aegyptiaca (L. 1766) (Egyptian goose) and the anserine geese, Branta canadensis (L. 1758) (Canada goose), Anser anser (L. 1758) (greylag goose) and Branta leucopsis (Bechstein, 1803) (barnacle goose). Landscape modification is a known method for altering goose behaviour, but there is little information on the power of such methods with which to inform managers and planners. Results Our results demonstrate that lakes with islands attract more than twice as many anserine geese than lakes without islands, but make little difference to Egyptian geese. Furthermore, flight barriers between grazing areas and lakes are an effective deterrent to geese using an area for feeding. Keeping grazing areas small and surrounded by trees reduces their attractiveness to geese. Conclusion The results su…
format: application/pdf
format: text/html
creator: Quentin J. Groom
creator: Tim Adriaens
creator: Claire Colsoulle
creator: Pauline Delhez
creator: Iris Van der Beeten
subject: Animal Behavior
subject: Biogeography
subject: Ecology
subject: Natural Resource Management
description: doi:10.7717/peerj.9846
publisher: PeerJ Inc.
rights: © 2020 Groom et al.
abstract: Background In European and North American cities geese are among the most common and most visible large herbivores. As such, their presence and behaviour often conflict with the desires of the human residents. Fouling, noise, aggression and health concerns are all cited as reasons that there are “too many”. Lethal control is often used for population management; however, this raises questions about whether this is a sustainable strategy to resolve the conflict between humans and geese when, paradoxically, it is humans that are responsible for creating the habitat and often providing the food and protection of geese at other times. We hypothesise that the landscaping of suburban parks can be improved to decrease its attractiveness to geese and to reduce the opportunity for conflict between geese and humans. Methods Using observations collected over five years from a botanic garden situated in suburban Belgium and data from the whole of Flanders in Belgium, we examined landscape features that attract geese. These included the presence of islands in lakes, the distance from water, barriers to level flight and the size of exploited areas. The birds studied were the tadornine goose Alopochen aegyptiaca (L. 1766) (Egyptian goose) and the anserine geese, Branta canadensis (L. 1758) (Canada goose), Anser anser (L. 1758) (greylag goose) and Branta leucopsis (Bechstein, 1803) (barnacle goose). Landscape modification is a known method for altering goose behaviour, but there is little information on the power of such methods with which to inform managers and planners. Results Our results demonstrate that lakes with islands attract more than twice as many anserine geese than lakes without islands, but make little difference to Egyptian geese. Furthermore, flight barriers between grazing areas and lakes are an effective deterrent to geese using an area for feeding. Keeping grazing areas small and surrounded by trees reduces their attractiveness to geese. Conclusion The results su…
bibliographic citation: Groom et al. (2020) Site selection by geese in a suburban landscape. PeerJ 8:e9846 https://doi.org/10.7717/peerj.9846
date submitted: 2020-01-21
date accepted: 2020-08-11
issued: 2020-09-22
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Groom
  given name: Quentin J.
author list: Agent
  family name: Adriaens
  given name: Tim
author list: Agent
  family name: Colsoulle
  given name: Claire
author list: Agent
  family name: Delhez
  given name: Pauline
author list: Agent
  family name: Van der Beeten
  given name: Iris
doi: 10.7717/peerj.9846
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-09-22
copyright: ©2020 Groom et al.
attribution name: Groom et al.

Dichocarpum hagiangense—a new species and an updated checklist of Ranunculaceae in Vietnam
type: item
type: AcademicArticle
description: Dichocarpum hagiangense from Ha Giang province, northern Vietnam is described and illustrated. Diagnostic features of the new species are a short rhizomatous stem, (2–)3-foliolate or simple leaves, and pink-purple flowers. The described species is distinct from closely allied D. trifoliolatum in having longer sepals, shape and obcordate apex of petal limbs, shorter flower stem, number and tooth shape of basal leaves; it differs from D. basilare and D. carinatum in having stem leaf, retuse apex and longer of central leaflet, number and (2–)3-foliated (or simple) of leaf. With the support of molecular data, the new species was clearly distinguished from other species in the Dichocarpum group by eight autapomorphic characters in nrITS sequence. A key to all species of Dichocarpum is provided. We suggest the IUCN conservation status of D. hagiangense to be “Critically Endangered”. A newest checklist of the family Ranunculaceae in Vietnam is updated.
format: application/pdf
format: text/html
creator: Minh Ty Nguyen
creator: Ngoc Bon Trinh
creator: Thanh Thi Viet Tran
creator: Tran Duc Thanh
creator: Long Ke Phan
creator: Van The Pham
subject: Biodiversity
subject: Plant Science
subject: Taxonomy
description: doi:10.7717/peerj.9874
publisher: PeerJ Inc.
rights: © 2020 Nguyen et al.
abstract: Dichocarpum hagiangense from Ha Giang province, northern Vietnam is described and illustrated. Diagnostic features of the new species are a short rhizomatous stem, (2–)3-foliolate or simple leaves, and pink-purple flowers. The described species is distinct from closely allied D. trifoliolatum in having longer sepals, shape and obcordate apex of petal limbs, shorter flower stem, number and tooth shape of basal leaves; it differs from D. basilare and D. carinatum in having stem leaf, retuse apex and longer of central leaflet, number and (2–)3-foliated (or simple) of leaf. With the support of molecular data, the new species was clearly distinguished from other species in the Dichocarpum group by eight autapomorphic characters in nrITS sequence. A key to all species of Dichocarpum is provided. We suggest the IUCN conservation status of D. hagiangense to be “Critically Endangered”. A newest checklist of the family Ranunculaceae in Vietnam is updated.
bibliographic citation: Nguyen et al. (2020) Dichocarpum hagiangense—a new species and an updated checklist of Ranunculaceae in Vietnam. PeerJ 8:e9874 https://doi.org/10.7717/peerj.9874
date submitted: 2020-02-14
date accepted: 2020-08-14
issued: 2020-09-22
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Nguyen
  given name: Minh Ty
author list: Agent
  family name: Trinh
  given name: Ngoc Bon
author list: Agent
  family name: Tran
  given name: Thanh Thi Viet
author list: Agent
  family name: Thanh
  given name: Tran Duc
author list: Agent
  family name: Phan
  given name: Long Ke
author list: Agent
  family name: Pham
  given name: Van The
doi: 10.7717/peerj.9874
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-09-22
copyright: ©2020 Nguyen et al.
attribution name: Nguyen et al.

Flavoured water consumption alters pharmacokinetic parameters and increases exposure of erlotinib and gefitinib in a preclinical study using Wistar rats
type: item
type: AcademicArticle
description: Background Erlotinib (ERL) and Gefitinib (GEF) are considered first line therapy for the management of non-small cell lung carcinoma (NSCLC). Like other tyrosine kinase inhibitors (TKIs), ERL and GEF are mainly metabolized by the cytochrome P450 (CYP450) CYP3A4 isoform and are substrates for transporter proteins with marked inter-/intra-individual pharmacokinetic (PK) variability. Therefore, ERL and GEF are candidates for drug-drug and food-drug interactions with a consequent effect on drug exposure and/or drug-related toxicities. In recent years, the consumption of flavoured water (FW) has gained in popularity. Among multiple ingredients, fruit extracts, which might constitute bioactive flavonoids, can possess an inhibitory effect on the CYP450 enzymes or transporter proteins. Therefore, in this study we investigated the effects of different types of FW on the PK parameters of ERL and GEF in Wistar rats. Methods ERL and GEF PK parameters in different groups of rats after four weeks consumption of different flavours of FW, namely berry, peach, lime, and pineapple, were determined from plasma drug concentrations using ultra-performance liquid chromatography–tandem mass spectrometry (UPLC-MS/MS). Results Data indicated that tested FWs altered the PK parameters of both ERL and GEF differently. Lime water had the highest impact on most of ERL and GEF PK parameters, with a significant increase in Cmax (95% for ERL, 58% for GEF), AUC0–48 (111% for ERL, 203% for GEF), and AUC0–∞ (200% for ERL, 203% for GEF), along with a significant decrease in the apparent oral clearance of both drugs (65% for ERL, 67% for GEF). The order by which FW affected the PK parameters for ERL and GEF was as follows: lime > pineapple > berry > peach. Conclusion The present study indicates that drinking FW could be of significance in rats receiving ERL or GEF. Our results indicate that the alteration in PKs was mostly recorded with lime, resulting in an enhanced bioavailability, and reduced apparen…
format: application/pdf
format: text/html
creator: Aliyah Almomen
creator: Hadir M. Maher
creator: Nourah Z. Alzoman
creator: Shereen M. Shehata
creator: Amal Alsubaie
subject: Toxicology
subject: Drugs and Devices
subject: Pharmacology
description: doi:10.7717/peerj.9881
publisher: PeerJ Inc.
rights: © 2020 Almomen et al.
abstract: Background Erlotinib (ERL) and Gefitinib (GEF) are considered first line therapy for the management of non-small cell lung carcinoma (NSCLC). Like other tyrosine kinase inhibitors (TKIs), ERL and GEF are mainly metabolized by the cytochrome P450 (CYP450) CYP3A4 isoform and are substrates for transporter proteins with marked inter-/intra-individual pharmacokinetic (PK) variability. Therefore, ERL and GEF are candidates for drug-drug and food-drug interactions with a consequent effect on drug exposure and/or drug-related toxicities. In recent years, the consumption of flavoured water (FW) has gained in popularity. Among multiple ingredients, fruit extracts, which might constitute bioactive flavonoids, can possess an inhibitory effect on the CYP450 enzymes or transporter proteins. Therefore, in this study we investigated the effects of different types of FW on the PK parameters of ERL and GEF in Wistar rats. Methods ERL and GEF PK parameters in different groups of rats after four weeks consumption of different flavours of FW, namely berry, peach, lime, and pineapple, were determined from plasma drug concentrations using ultra-performance liquid chromatography–tandem mass spectrometry (UPLC-MS/MS). Results Data indicated that tested FWs altered the PK parameters of both ERL and GEF differently. Lime water had the highest impact on most of ERL and GEF PK parameters, with a significant increase in Cmax (95% for ERL, 58% for GEF), AUC0–48 (111% for ERL, 203% for GEF), and AUC0–∞ (200% for ERL, 203% for GEF), along with a significant decrease in the apparent oral clearance of both drugs (65% for ERL, 67% for GEF). The order by which FW affected the PK parameters for ERL and GEF was as follows: lime > pineapple > berry > peach. Conclusion The present study indicates that drinking FW could be of significance in rats receiving ERL or GEF. Our results indicate that the alteration in PKs was mostly recorded with lime, resulting in an enhanced bioavailability, and reduced apparen…
bibliographic citation: Almomen et al. (2020) Flavoured water consumption alters pharmacokinetic parameters and increases exposure of erlotinib and gefitinib in a preclinical study using Wistar rats. PeerJ 8:e9881 https://doi.org/10.7717/peerj.9881
date submitted: 2019-11-18
date accepted: 2020-08-15
issued: 2020-09-22
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Almomen
  given name: Aliyah
author list: Agent
  family name: Maher
  given name: Hadir M.
author list: Agent
  family name: Alzoman
  given name: Nourah Z.
author list: Agent
  family name: Shehata
  given name: Shereen M.
author list: Agent
  family name: Alsubaie
  given name: Amal
doi: 10.7717/peerj.9881
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-09-22
copyright: ©2020 Almomen et al.
attribution name: Almomen et al.

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