PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
items: Field and laboratory metabolism and thermoregulation in rhinoceros auklets
items: Microsatellite instability and Epstein-Barr virus combined with PD-L1 could serve as a potential strategy for predicting the prognosis and efficacy of postoperative chemotherapy in gastric cancer
items: An integrative monograph of Carex section Schoenoxiphium (Cyperaceae)
items: Trp-574-Leu mutation in wild mustard (Sinapis arvensis L.) as a result of als inhibiting herbicide applications
items: Group B Streptococcus and the vaginal microbiome among pregnant women: a systematic review
items: Machine learning in dental, oral and craniofacial imaging: a review of recent progress
items: The impact of COVID-19 pandemic on the level of depression among health care workers: cross-sectional study
items: Longer leisure walking time is associated with positive self-rated health among adults and older adults: a Brazilian nationwide study
items: Multi-scale analysis of the characteristics of the changing landscape of the typical mountainous region of Southwest China over the past 40 years
items: Consequences of herbal mixture supplementation on milk performance, ruminal fermentation, and bacterial diversity in water buffaloes

Field and laboratory metabolism and thermoregulation in rhinoceros auklets
type: item
type: AcademicArticle
description: Seabirds spend most of their lives at sea, except when visiting their breeding sites. Since the thermal conductivity of water is 25 times higher than that of air, seabirds resting on water lose heat and expend a considerable amount of energy for thermoregulation. For example, rhinoceros auklet (Cerorhinca monocerata), a medium-sized (480–620 g) alcid, spends most of its time floating on the sea. In order to estimate the cost of this behavior in terms of their daily energy expenditure (DEE), we studied rhinoceros auklets breeding on Teuri Island, Hokkaido Japan. We measured their resting metabolic rate (RMR) in air and on water by respirometry, and estimated their DEE by the doubly labeled water method. While RMR on water did not vary significantly between 10 °C and 15 °C, it was significantly higher at 5 °C. Air temperature (5.0–20.0 °C) had no effect on RMR. The DEE of free-ranging auklets averaged 1,005.5 kJ day−1 (±130.2, n = 3). Our results indicate that RMRs are elevated for auklets resting on water, particularly below their lower critical temperature (LCT), compared with in air. Accordingly, spending time above their LCT on water at any time of year will provide enhanced benefits, particularly to seabirds such as rhinoceros auklets which rest a considerable amount of time on water.
format: application/pdf
format: text/html
creator: Aika Umeyama
creator: Yasuaki Niizuma
creator: Masaki Shirai
subject: Animal Behavior
subject: Ecology
subject: Marine Biology
subject: Zoology
description: doi:10.7717/peerj.11460
publisher: PeerJ Inc.
rights: © 2021 Umeyama et al.
abstract: Seabirds spend most of their lives at sea, except when visiting their breeding sites. Since the thermal conductivity of water is 25 times higher than that of air, seabirds resting on water lose heat and expend a considerable amount of energy for thermoregulation. For example, rhinoceros auklet (Cerorhinca monocerata), a medium-sized (480–620 g) alcid, spends most of its time floating on the sea. In order to estimate the cost of this behavior in terms of their daily energy expenditure (DEE), we studied rhinoceros auklets breeding on Teuri Island, Hokkaido Japan. We measured their resting metabolic rate (RMR) in air and on water by respirometry, and estimated their DEE by the doubly labeled water method. While RMR on water did not vary significantly between 10 °C and 15 °C, it was significantly higher at 5 °C. Air temperature (5.0–20.0 °C) had no effect on RMR. The DEE of free-ranging auklets averaged 1,005.5 kJ day−1 (±130.2, n = 3). Our results indicate that RMRs are elevated for auklets resting on water, particularly below their lower critical temperature (LCT), compared with in air. Accordingly, spending time above their LCT on water at any time of year will provide enhanced benefits, particularly to seabirds such as rhinoceros auklets which rest a considerable amount of time on water.
bibliographic citation: Umeyama et al. (2021) Field and laboratory metabolism and thermoregulation in rhinoceros auklets. PeerJ 9:e11460 https://doi.org/10.7717/peerj.11460
date submitted: 2020-09-22
date accepted: 2021-04-25
issued: 2021-05-18
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Umeyama
  given name: Aika
author list: Agent
  family name: Niizuma
  given name: Yasuaki
author list: Agent
  family name: Shirai
  given name: Masaki
doi: 10.7717/peerj.11460
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-05-18
copyright: ©2021 Umeyama et al.
attribution name: Umeyama et al.

Microsatellite instability and Epstein-Barr virus combined with PD-L1 could serve as a potential strategy for predicting the prognosis and efficacy of postoperative chemotherapy in gastric cancer
type: item
type: AcademicArticle
description: Background Microsatellite instability (MSI) and Epstein-Barr virus (EBV)-positive molecular subtypes exhibit complex immune responses in gastric cancer (GC), and PD-L1 has emerged as a prognostic biomarker associated with the cancer immune microenvironment. This study aimed to determine the prognostic value of molecular subtypes and whether the addition of PD-L1 would accurately predict the prognosis and guide postoperative chemotherapy for GC patients. Methods We performed molecular subtyping of tissue microarray slides from 226 GC patients who were treated with radical gastrectomy. The MSI status and PD-L1 expression were evaluated through immunohistochemistry (IHC) and EBV status through situ hybridization. Multiplex polymerase chain reaction (PCR) was also performed on 50 cases to validate the accuracy of IHC in defining MSI status. Differences in overall survival (OS) were assessed using the Kaplan-Meier method, log-rank test and Cox proportional hazards regression model. Results Among the 226 GC patients, 52 (23.2%) patients were classified as the MSI subtype, 11 (4.9%) were EBV+ subtype, and 161 (71.9%) were MSS (Microsatellite stable) /EBV− subtype according to TCGA analysis. Two patients were both positive for MSI and EBV infection. EBV+ cases showed higher PD-L1 positivity than MSI cases and MSS/EBV− cases (81.8% vs. 50.0% vs. 35.4%, P = 0.003). Compared with the non-MSS/EBV− (MSI or EBV+ cases) subgroup, GC patients with MSS/EBV− were associated with the worst outcomes (HR = 1.610, 95% CI [1.046–2.479], P = 0.031). MSS/EBV− GCs alone could benefit from postoperative chemotherapy (HR = 0.452, 95% CI [0.299–0.682], P < 0.001), and PD-L1-positive expression could also predict a better prognosis (HR = 0.612, 95% CI [0.389–0.962], P = 0.033) in this subgroup. Considering both chemotherapy efficacy and PD-L1 expression in the MSS/EBV− subgroup, chemotherapy could improve the prognosis for PD-L1-negative MSS/EBV− GCs (HR = 0.357, 95% CI [0.217–0.587], P < 0.001)…
format: application/pdf
format: text/html
creator: Na Yang
creator: Yanhua Wu
creator: Meishan Jin
creator: Zhifang Jia
creator: Yueqi Wang
creator: Donghui Cao
creator: Lili Qin
creator: Xueying Wang
creator: Min Zheng
creator: Xueyuan Cao
creator: Jing Jiang
subject: Molecular Biology
subject: Gastroenterology and Hepatology
subject: Oncology
subject: Histology
subject: Medical Genetics
description: doi:10.7717/peerj.11481
publisher: PeerJ Inc.
rights: © 2021 Yang et al.
abstract: Background Microsatellite instability (MSI) and Epstein-Barr virus (EBV)-positive molecular subtypes exhibit complex immune responses in gastric cancer (GC), and PD-L1 has emerged as a prognostic biomarker associated with the cancer immune microenvironment. This study aimed to determine the prognostic value of molecular subtypes and whether the addition of PD-L1 would accurately predict the prognosis and guide postoperative chemotherapy for GC patients. Methods We performed molecular subtyping of tissue microarray slides from 226 GC patients who were treated with radical gastrectomy. The MSI status and PD-L1 expression were evaluated through immunohistochemistry (IHC) and EBV status through situ hybridization. Multiplex polymerase chain reaction (PCR) was also performed on 50 cases to validate the accuracy of IHC in defining MSI status. Differences in overall survival (OS) were assessed using the Kaplan-Meier method, log-rank test and Cox proportional hazards regression model. Results Among the 226 GC patients, 52 (23.2%) patients were classified as the MSI subtype, 11 (4.9%) were EBV+ subtype, and 161 (71.9%) were MSS (Microsatellite stable) /EBV− subtype according to TCGA analysis. Two patients were both positive for MSI and EBV infection. EBV+ cases showed higher PD-L1 positivity than MSI cases and MSS/EBV− cases (81.8% vs. 50.0% vs. 35.4%, P = 0.003). Compared with the non-MSS/EBV− (MSI or EBV+ cases) subgroup, GC patients with MSS/EBV− were associated with the worst outcomes (HR = 1.610, 95% CI [1.046–2.479], P = 0.031). MSS/EBV− GCs alone could benefit from postoperative chemotherapy (HR = 0.452, 95% CI [0.299–0.682], P < 0.001), and PD-L1-positive expression could also predict a better prognosis (HR = 0.612, 95% CI [0.389–0.962], P = 0.033) in this subgroup. Considering both chemotherapy efficacy and PD-L1 expression in the MSS/EBV− subgroup, chemotherapy could improve the prognosis for PD-L1-negative MSS/EBV− GCs (HR = 0.357, 95% CI [0.217–0.587], P < 0.001)…
bibliographic citation: Yang et al. (2021) Microsatellite instability and Epstein-Barr virus combined with PD-L1 could serve as a potential strategy for predicting the prognosis and efficacy of postoperative chemotherapy in gastric cancer. PeerJ 9:e11481 https://doi.org/10.7717/peerj.11481
date submitted: 2021-01-04
date accepted: 2021-04-27
issued: 2021-05-18
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Yang
  given name: Na
author list: Agent
  family name: Wu
  given name: Yanhua
author list: Agent
  family name: Jin
  given name: Meishan
author list: Agent
  family name: Jia
  given name: Zhifang
author list: Agent
  family name: Wang
  given name: Yueqi
author list: Agent
  family name: Cao
  given name: Donghui
author list: Agent
  family name: Qin
  given name: Lili
author list: Agent
  family name: Wang
  given name: Xueying
author list: Agent
  family name: Zheng
  given name: Min
author list: Agent
  family name: Cao
  given name: Xueyuan
author list: Agent
  family name: Jiang
  given name: Jing
doi: 10.7717/peerj.11481
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-05-18
copyright: ©2021 Yang et al.
attribution name: Yang et al.

An integrative monograph of Carex section Schoenoxiphium (Cyperaceae)
type: item
type: AcademicArticle
description: Carex section Schoenoxiphium (Cariceae, Cyperaceae) is endemic to the Afrotropical biogeographic region and is mainly distributed in southern and eastern Africa, with its center of diversity in eastern South Africa. The taxon was formerly recognized as a distinct genus and has a long history of taxonomic controversy. It has also an important morphological and molecular background in particular dealing with the complexity of its inflorescence and the phylogenetic relationships of its species. We here present a fully updated and integrative monograph of Carex section Schoenoxiphium based on morphological, molecular and cytogenetic data. A total of 1,017 herbarium specimens were examined and the majority of the species were studied in the field. Previous molecular phylogenies based on Sanger-sequencing of four nuclear and plastid DNA regions and RAD-seq were expanded. For the first time, chromosome numbers were obtained, with cytogenetic counts on 44 populations from 15 species and one hybrid. Our taxonomic treatment recognizes 21 species, one of them herein newly described (C. gordon-grayae). Our results agree with previous molecular works that have found five main lineages in Schoenoxiphium. We provide detailed morphological descriptions, distribution maps and analytical drawings of all accepted species in section Schoenoxiphium, an identification key, and a thorough nomenclatural survey including 19 new typifications and one nomen novum.
format: application/pdf
format: text/html
creator: Modesto Luceño
creator: Tamara Villaverde
creator: José Ignacio Márquez-Corro
creator: Rogelio Sánchez-Villegas
creator: Enrique Maguilla
creator: Marcial Escudero
creator: Pedro Jiménez-Mejías
creator: Manuel Sánchez-Villegas
creator: Monica Miguez
creator: Carmen Benítez-Benítez
creator: A. Muthama Muasya
creator: Santiago Martín-Bravo
subject: Biodiversity
subject: Conservation Biology
subject: Molecular Biology
subject: Plant Science
subject: Taxonomy
description: doi:10.7717/peerj.11336
publisher: PeerJ Inc.
rights: © 2021 Luceño et al.
abstract: Carex section Schoenoxiphium (Cariceae, Cyperaceae) is endemic to the Afrotropical biogeographic region and is mainly distributed in southern and eastern Africa, with its center of diversity in eastern South Africa. The taxon was formerly recognized as a distinct genus and has a long history of taxonomic controversy. It has also an important morphological and molecular background in particular dealing with the complexity of its inflorescence and the phylogenetic relationships of its species. We here present a fully updated and integrative monograph of Carex section Schoenoxiphium based on morphological, molecular and cytogenetic data. A total of 1,017 herbarium specimens were examined and the majority of the species were studied in the field. Previous molecular phylogenies based on Sanger-sequencing of four nuclear and plastid DNA regions and RAD-seq were expanded. For the first time, chromosome numbers were obtained, with cytogenetic counts on 44 populations from 15 species and one hybrid. Our taxonomic treatment recognizes 21 species, one of them herein newly described (C. gordon-grayae). Our results agree with previous molecular works that have found five main lineages in Schoenoxiphium. We provide detailed morphological descriptions, distribution maps and analytical drawings of all accepted species in section Schoenoxiphium, an identification key, and a thorough nomenclatural survey including 19 new typifications and one nomen novum.
bibliographic citation: Luceño et al. (2021) An integrative monograph of Carex section Schoenoxiphium (Cyperaceae). PeerJ 9:e11336 https://doi.org/10.7717/peerj.11336
date submitted: 2021-02-23
date accepted: 2021-04-01
issued: 2021-05-17
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Luceño
  given name: Modesto
author list: Agent
  family name: Villaverde
  given name: Tamara
author list: Agent
  family name: Márquez-Corro
  given name: José Ignacio
author list: Agent
  family name: Sánchez-Villegas
  given name: Rogelio
author list: Agent
  family name: Maguilla
  given name: Enrique
author list: Agent
  family name: Escudero
  given name: Marcial
author list: Agent
  family name: Jiménez-Mejías
  given name: Pedro
author list: Agent
  family name: Sánchez-Villegas
  given name: Manuel
author list: Agent
  family name: Miguez
  given name: Monica
author list: Agent
  family name: Benítez-Benítez
  given name: Carmen
author list: Agent
  family name: Muasya
  given name: A. Muthama
author list: Agent
  family name: Martín-Bravo
  given name: Santiago
doi: 10.7717/peerj.11336
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-05-17
copyright: © 2021 Luceño et al.
attribution name: Luceño et al.

Trp-574-Leu mutation in wild mustard (Sinapis arvensis L.) as a result of als inhibiting herbicide applications
type: item
type: AcademicArticle
description: Wheat is one of the most important crops grown all around the world. Weeds cause significant yield loss and damage to wheat and their control is generally based on herbicide application. Regular use leads to herbicide resistance in weeds. This study aims to reveal molecular detection of Sinapis arvensis resistance mutation against ALS inhibiting herbicides. For this purpose, survey studies have been carried out in wheat growing areas in Amasya, Çorum, Tokat, and Yozgat provinces and wild mustard seeds have been collected from 310 different fields. According to bioassay tests with tribenuron-methyl, 13 of these populations, have not been affected by the registered dose of herbicide. When survived populations were subjected to dose-effect study and herbicides were applied at 26-fold, the highest and lowest resistance coefficients were determined as 7.2 (A-007) and 1.02 (T-034) respectively. In addition, B domain region from ALS gene was amplified and analyzed in molecular studies to determine point mutation in wild mustard against ALS herbicides. The PCR products were sequenced and target-site mutation to Leucine was observed at Trp-574 amino acide. In the study, point mutation in Trp-574 amino acide and Trp-574 Leu mutation in Sinapis arvensis have been detected for the first time in Turkey.
format: application/pdf
format: text/html
creator: Bahadir Sin
creator: İzzet Kadıoglu
subject: Agricultural Science
subject: Plant Science
description: doi:10.7717/peerj.11385
publisher: PeerJ Inc.
rights: © 2021 Sin et al.
abstract: Wheat is one of the most important crops grown all around the world. Weeds cause significant yield loss and damage to wheat and their control is generally based on herbicide application. Regular use leads to herbicide resistance in weeds. This study aims to reveal molecular detection of Sinapis arvensis resistance mutation against ALS inhibiting herbicides. For this purpose, survey studies have been carried out in wheat growing areas in Amasya, Çorum, Tokat, and Yozgat provinces and wild mustard seeds have been collected from 310 different fields. According to bioassay tests with tribenuron-methyl, 13 of these populations, have not been affected by the registered dose of herbicide. When survived populations were subjected to dose-effect study and herbicides were applied at 26-fold, the highest and lowest resistance coefficients were determined as 7.2 (A-007) and 1.02 (T-034) respectively. In addition, B domain region from ALS gene was amplified and analyzed in molecular studies to determine point mutation in wild mustard against ALS herbicides. The PCR products were sequenced and target-site mutation to Leucine was observed at Trp-574 amino acide. In the study, point mutation in Trp-574 amino acide and Trp-574 Leu mutation in Sinapis arvensis have been detected for the first time in Turkey.
bibliographic citation: Sin et al. (2021) Trp-574-Leu mutation in wild mustard (Sinapis arvensis L.) as a result of als inhibiting herbicide applications. PeerJ 9:e11385 https://doi.org/10.7717/peerj.11385
date submitted: 2020-11-27
date accepted: 2021-04-09
issued: 2021-05-17
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Sin
  given name: Bahadir
author list: Agent
  family name: Kadıoglu
  given name: İzzet
doi: 10.7717/peerj.11385
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-05-17
copyright: ©2021 Sin et al.
attribution name: Sin et al.

Group B Streptococcus and the vaginal microbiome among pregnant women: a systematic review
type: item
type: AcademicArticle
description: Background Vaginal microbiome studies frequently report diversity metrics and communities of microbiomes associated with reproductive health outcomes. Reports of Streptococcus agalactiae (also known as Group B Streptococcus or GBS), the leading cause of neonatal infectious morbidity and mortality, are notably lacking from the studies of the vaginal microbiome, despite being a known contributor to preterm birth and other complications. Therefore, the purpose of this systematic review was to explore the frequency of GBS reporting in vaginal microbiome literature pertaining to pregnancy and to examine methodological bias that contributes to differences in species and genus-level microbiome reporting. Lack of identification of GBS via sequencing-based approaches due to methodologic or reporting bias may result incomplete understanding of bacterial composition during pregnancy and subsequent birth outcomes. Methodology A systematic review was conducted following the PRISMA guideline. Three databases (PubMed, CINAHL, and Web of Science) were used to identify papers for review based on the search terms “vaginal microbiome”, “pregnancy”, and “16S rRNA sequencing”. Articles were evaluated for methods of DNA extraction and sequencing, 16S region, taxonomy classification database, number of participants or vaginal specimens, and pregnancy trimester. Results Forty-five research articles reported employing a metagenomic approach or 16S approach for vaginal microbiome analysis during pregnancy that explicitly reported taxonomic composition and were included in this review. Less than 30% of articles reported the presence of GBS (N = 13). No significant differences in methodology were identified between articles that reported versus did not report GBS. However, there was large variability across research methods used for vaginal microbiome analysis and species-level bacterial community reporting. Conclusion Considerable differences in study design and data formatting methods may co…
format: application/pdf
format: text/html
creator: Sungju Lim
creator: Shilpa Rajagopal
creator: Ye Ryn Jeong
creator: Dumebi Nzegwu
creator: Michelle L. Wright
subject: Genomics
subject: Microbiology
subject: Molecular Biology
subject: Taxonomy
subject: Women’s Health
description: doi:10.7717/peerj.11437
publisher: PeerJ Inc.
rights: © 2021 Lim et al.
abstract: Background Vaginal microbiome studies frequently report diversity metrics and communities of microbiomes associated with reproductive health outcomes. Reports of Streptococcus agalactiae (also known as Group B Streptococcus or GBS), the leading cause of neonatal infectious morbidity and mortality, are notably lacking from the studies of the vaginal microbiome, despite being a known contributor to preterm birth and other complications. Therefore, the purpose of this systematic review was to explore the frequency of GBS reporting in vaginal microbiome literature pertaining to pregnancy and to examine methodological bias that contributes to differences in species and genus-level microbiome reporting. Lack of identification of GBS via sequencing-based approaches due to methodologic or reporting bias may result incomplete understanding of bacterial composition during pregnancy and subsequent birth outcomes. Methodology A systematic review was conducted following the PRISMA guideline. Three databases (PubMed, CINAHL, and Web of Science) were used to identify papers for review based on the search terms “vaginal microbiome”, “pregnancy”, and “16S rRNA sequencing”. Articles were evaluated for methods of DNA extraction and sequencing, 16S region, taxonomy classification database, number of participants or vaginal specimens, and pregnancy trimester. Results Forty-five research articles reported employing a metagenomic approach or 16S approach for vaginal microbiome analysis during pregnancy that explicitly reported taxonomic composition and were included in this review. Less than 30% of articles reported the presence of GBS (N = 13). No significant differences in methodology were identified between articles that reported versus did not report GBS. However, there was large variability across research methods used for vaginal microbiome analysis and species-level bacterial community reporting. Conclusion Considerable differences in study design and data formatting methods may co…
bibliographic citation: Lim et al. (2021) Group B Streptococcus and the vaginal microbiome among pregnant women: a systematic review. PeerJ 9:e11437 https://doi.org/10.7717/peerj.11437
date submitted: 2021-01-25
date accepted: 2021-04-20
issued: 2021-05-17
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Lim
  given name: Sungju
author list: Agent
  family name: Rajagopal
  given name: Shilpa
author list: Agent
  family name: Jeong
  given name: Ye Ryn
author list: Agent
  family name: Nzegwu
  given name: Dumebi
author list: Agent
  family name: Wright
  given name: Michelle L.
doi: 10.7717/peerj.11437
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-05-17
copyright: ©2021 Lim et al.
attribution name: Lim et al.

Machine learning in dental, oral and craniofacial imaging: a review of recent progress
type: item
type: AcademicArticle
description: Artificial intelligence has been emerging as an increasingly important aspect of our daily lives and is widely applied in medical science. One major application of artificial intelligence in medical science is medical imaging. As a major component of artificial intelligence, many machine learning models are applied in medical diagnosis and treatment with the advancement of technology and medical imaging facilities. The popularity of convolutional neural network in dental, oral and craniofacial imaging is heightening, as it has been continually applied to a broader spectrum of scientific studies. Our manuscript reviews the fundamental principles and rationales behind machine learning, and summarizes its research progress and its recent applications specifically in dental, oral and craniofacial imaging. It also reviews the problems that remain to be resolved and evaluates the prospect of the future development of this field of scientific study.
format: application/pdf
format: text/html
creator: Ruiyang Ren
creator: Haozhe Luo
creator: Chongying Su
creator: Yang Yao
creator: Wen Liao
subject: Dentistry
subject: Orthopedics
subject: Otorhinolaryngology
subject: Radiology and Medical Imaging
subject: Computational Science
description: doi:10.7717/peerj.11451
publisher: PeerJ Inc.
rights: © 2021 Ren et al.
abstract: Artificial intelligence has been emerging as an increasingly important aspect of our daily lives and is widely applied in medical science. One major application of artificial intelligence in medical science is medical imaging. As a major component of artificial intelligence, many machine learning models are applied in medical diagnosis and treatment with the advancement of technology and medical imaging facilities. The popularity of convolutional neural network in dental, oral and craniofacial imaging is heightening, as it has been continually applied to a broader spectrum of scientific studies. Our manuscript reviews the fundamental principles and rationales behind machine learning, and summarizes its research progress and its recent applications specifically in dental, oral and craniofacial imaging. It also reviews the problems that remain to be resolved and evaluates the prospect of the future development of this field of scientific study.
bibliographic citation: Ren et al. (2021) Machine learning in dental, oral and craniofacial imaging: a review of recent progress. PeerJ 9:e11451 https://doi.org/10.7717/peerj.11451
date submitted: 2020-10-02
date accepted: 2021-04-22
issued: 2021-05-17
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Ren
  given name: Ruiyang
author list: Agent
  family name: Luo
  given name: Haozhe
author list: Agent
  family name: Su
  given name: Chongying
author list: Agent
  family name: Yao
  given name: Yang
author list: Agent
  family name: Liao
  given name: Wen
doi: 10.7717/peerj.11451
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-05-17
copyright: © 2021 Ren et al.
attribution name: Ren et al.

The impact of COVID-19 pandemic on the level of depression among health care workers: cross-sectional study
type: item
type: AcademicArticle
description: Background The outbreak of the novel Corona Virus Infectious Disease 2019 (COVID-19) has spread rapidly to many countries leading to thousands of deaths globally. The burden of this pandemic has affected the physical and mental health of the frontline health care workers (HCWs) who are exposed to high risk of infection and psychological stressors. Aims The aim is to measure the level of depression among healthcare workers in Saudi Arabia during COVID-19 pandemic to establish interventional strategies. Method A descriptive cross-sectional study was used to conduct the current study. The data of this study was recruited between 15 June and 15 July 2020 from healthcare providers who work in both public and private healthcare sectors in Riyadh and Eastern province in Saudi Arabia utilizing a self-administered questionnaire. The study was approved by the Institutional Review Board at Dr. Sulaiman Al Habib Medical Group (IRB Log No. RC20.06.88-2). Data were collected by using The Zung Self-Rating Depression Scale SDS. A total of 900 healthcare providers working in the healthcare setting during COVID-19 pandemic were invited to participate in the study. A total of 650 healthcare providers participated in the study by completing and submitting the survey. Results Almost 30% suffered from depression which can be divided into three categories; mild depression (26.2%), moderate/major (2.5%) and severe/extreme (0.8%). The finding shows that the level of depression among respondents at the age range of 31–40 years old was significantly higher than the level of depression among respondents with the age above 50 years old. Non-Saudi healthcare workers experienced more depression than Saudi workers. It also shows how nurses suffered from depression compared to their physician colleagues. Those who did not suffer from sleeping disorder perceived more depression as compared to those who are having sleeping disorder. Conclusion It is recommended that health care facilities should impl…
format: application/pdf
format: text/html
creator: Abbas Al Mutair
creator: Alya Al Mutairi
creator: Zainab Ambani
creator: Abbas Shamsan
creator: Sana AlMahmoud
creator: Saad Alhumaid
subject: Evidence Based Medicine
subject: Global Health
subject: Psychiatry and Psychology
subject: Public Health
description: doi:10.7717/peerj.11469
publisher: PeerJ Inc.
rights: © 2021 Al Mutair et al.
abstract: Background The outbreak of the novel Corona Virus Infectious Disease 2019 (COVID-19) has spread rapidly to many countries leading to thousands of deaths globally. The burden of this pandemic has affected the physical and mental health of the frontline health care workers (HCWs) who are exposed to high risk of infection and psychological stressors. Aims The aim is to measure the level of depression among healthcare workers in Saudi Arabia during COVID-19 pandemic to establish interventional strategies. Method A descriptive cross-sectional study was used to conduct the current study. The data of this study was recruited between 15 June and 15 July 2020 from healthcare providers who work in both public and private healthcare sectors in Riyadh and Eastern province in Saudi Arabia utilizing a self-administered questionnaire. The study was approved by the Institutional Review Board at Dr. Sulaiman Al Habib Medical Group (IRB Log No. RC20.06.88-2). Data were collected by using The Zung Self-Rating Depression Scale SDS. A total of 900 healthcare providers working in the healthcare setting during COVID-19 pandemic were invited to participate in the study. A total of 650 healthcare providers participated in the study by completing and submitting the survey. Results Almost 30% suffered from depression which can be divided into three categories; mild depression (26.2%), moderate/major (2.5%) and severe/extreme (0.8%). The finding shows that the level of depression among respondents at the age range of 31–40 years old was significantly higher than the level of depression among respondents with the age above 50 years old. Non-Saudi healthcare workers experienced more depression than Saudi workers. It also shows how nurses suffered from depression compared to their physician colleagues. Those who did not suffer from sleeping disorder perceived more depression as compared to those who are having sleeping disorder. Conclusion It is recommended that health care facilities should impl…
bibliographic citation: Al Mutair et al. (2021) The impact of COVID-19 pandemic on the level of depression among health care workers: cross-sectional study. PeerJ 9:e11469 https://doi.org/10.7717/peerj.11469
date submitted: 2021-02-17
date accepted: 2021-04-26
issued: 2021-05-17
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Al Mutair
  given name: Abbas
author list: Agent
  family name: Al Mutairi
  given name: Alya
author list: Agent
  family name: Ambani
  given name: Zainab
author list: Agent
  family name: Shamsan
  given name: Abbas
author list: Agent
  family name: AlMahmoud
  given name: Sana
author list: Agent
  family name: Alhumaid
  given name: Saad
doi: 10.7717/peerj.11469
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-05-17
copyright: © 2021 Al Mutair et al.
attribution name: Al Mutair et al.

Longer leisure walking time is associated with positive self-rated health among adults and older adults: a Brazilian nationwide study
type: item
type: AcademicArticle
description: Background To verify the association between weekly leisure walking time and positive self-rated health in the Brazilian adult and elderly population. Methods This cross-sectional study used information collected in 2019 across all regions of Brazil. This study included 25,785 people aged ≥ 18 years (mean = 51.6; standard deviation = 18.0) from all capitals of the Brazilian states who reported practicing walking as physical activity during leisure time. Self-rated health was the dependent variable (positive or negative). The leisure walking time/week was the main exposure and it was categorized in “150 minutes/week”, “150–299 minutes/week” and “≥ 300 minutes/week”. We used binary logistic regression to estimate odds ratio (OR) and 95% confidence intervals (95% CI) that was adjusted for relevant covariates. Results We found that individuals who reported leisure walking for a period from 150 to 299 minutes/week and those who reported walking for a period ≥ 300 minutes/week were respectively 28% (OR = 1.28. 95% CI [1.10–1.48]) and 52% (OR = 1.52. 95% CI [1.27–1.82]) more likely of perceiving their health positively compared to those who reported walking for a period < 150 minutes/week. Individuals who reported leisure walking time <150 minutes/week had 72.3% (95% CI [70.4–74.1]) probability of perceiving their health positively. Individuals who reported leisure walking time from 150 to 299 minutes/week had 76.6% (95% CI [75.0 –78.3) probability of perceiving their health positively. On the other hand, individuals who reported leisure walking time ≥ 300 minutes/week had 79.2% probability (95% CI [77.1–81.4]) of perceiving their health positively. Conclusion Longer leisure walking time was associated with positive self-rated health among adults and older adults in Brazil.
format: application/pdf
format: text/html
creator: Diego Augusto Santos Silva
subject: Epidemiology
subject: Kinesiology
subject: Psychiatry and Psychology
subject: Public Health
description: doi:10.7717/peerj.11471
publisher: PeerJ Inc.
rights: © 2021 Silva
abstract: Background To verify the association between weekly leisure walking time and positive self-rated health in the Brazilian adult and elderly population. Methods This cross-sectional study used information collected in 2019 across all regions of Brazil. This study included 25,785 people aged ≥ 18 years (mean = 51.6; standard deviation = 18.0) from all capitals of the Brazilian states who reported practicing walking as physical activity during leisure time. Self-rated health was the dependent variable (positive or negative). The leisure walking time/week was the main exposure and it was categorized in “150 minutes/week”, “150–299 minutes/week” and “≥ 300 minutes/week”. We used binary logistic regression to estimate odds ratio (OR) and 95% confidence intervals (95% CI) that was adjusted for relevant covariates. Results We found that individuals who reported leisure walking for a period from 150 to 299 minutes/week and those who reported walking for a period ≥ 300 minutes/week were respectively 28% (OR = 1.28. 95% CI [1.10–1.48]) and 52% (OR = 1.52. 95% CI [1.27–1.82]) more likely of perceiving their health positively compared to those who reported walking for a period < 150 minutes/week. Individuals who reported leisure walking time <150 minutes/week had 72.3% (95% CI [70.4–74.1]) probability of perceiving their health positively. Individuals who reported leisure walking time from 150 to 299 minutes/week had 76.6% (95% CI [75.0 –78.3) probability of perceiving their health positively. On the other hand, individuals who reported leisure walking time ≥ 300 minutes/week had 79.2% probability (95% CI [77.1–81.4]) of perceiving their health positively. Conclusion Longer leisure walking time was associated with positive self-rated health among adults and older adults in Brazil.
bibliographic citation: Silva (2021) Longer leisure walking time is associated with positive self-rated health among adults and older adults: a Brazilian nationwide study. PeerJ 9:e11471 https://doi.org/10.7717/peerj.11471
date submitted: 2020-12-17
date accepted: 2021-04-26
issued: 2021-05-17
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Silva
  given name: Diego Augusto Santos
doi: 10.7717/peerj.11471
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-05-17
copyright: ©2021 Silva
attribution name: Silva

Multi-scale analysis of the characteristics of the changing landscape of the typical mountainous region of Southwest China over the past 40 years
type: item
type: AcademicArticle
description: Context Yunnan Province is an important ecological security barrier in China. This study investigated the temporal and spatial changes to landscape ecology and is of great significance for guiding landscape protection and future socio-economic development. Objectives To analyze the temporal and spatial changes of the landscape patterns at the county, river basin, and provincial levels, and clarify and describe the temporal and spatial differentiation characteristics of the landscape patterns in Yunnan Province. Methods Based on landscape ecology, GIS spatial analysis, and spatio-temporal change analysis, nine landscape pattern indices, and spatial autocorrelation for different years, were calculated. Results The landscape of Yunnan Province has evolved as a whole toward isolation. The indices of separation and fragmentation changed significantly from 2010 to 2015. From 2015 to 2018 the rate of fragmentation decreased. Fragmentation in the Nu Jiang and Irrawaddy River basins was less than in other basins. The landscape patterns of the Jinsha and Pearl River basins were relatively fragmented due to human activity, socioeconomic development, and utilization. The differences between the Lancang and Red River Basins were relatively small and at an intermediate level. Conclusions Spatial autocorrelation analysis indicated that there are three areas with typical clusters, namely the Hengduan Mountains where the degree of fragmentation of the landscape was low, while landscape connectivity and aggregation were high. The subtropical region of Southern Yunnan displayed high landscape heterogeneity, a complex shape index, and high connectivity and sprawl. Central Yunnan exhibited a fragmented landscape with poor connectivity and aggregation. These three regions correspond with “the three screens and two belts” in the Main Functional Planning Area of Yunnan Province.
format: application/pdf
format: text/html
creator: Fang Liu
creator: Wanbin Wang
creator: Jinliang Wang
creator: Xingzi Zhang
creator: Jing Ren
creator: Yuexiong Liu
subject: Ecology
subject: Spatial and Geographic Information Science
description: doi:10.7717/peerj.10923
publisher: PeerJ Inc.
rights: © 2021 Liu et al.
abstract: Context Yunnan Province is an important ecological security barrier in China. This study investigated the temporal and spatial changes to landscape ecology and is of great significance for guiding landscape protection and future socio-economic development. Objectives To analyze the temporal and spatial changes of the landscape patterns at the county, river basin, and provincial levels, and clarify and describe the temporal and spatial differentiation characteristics of the landscape patterns in Yunnan Province. Methods Based on landscape ecology, GIS spatial analysis, and spatio-temporal change analysis, nine landscape pattern indices, and spatial autocorrelation for different years, were calculated. Results The landscape of Yunnan Province has evolved as a whole toward isolation. The indices of separation and fragmentation changed significantly from 2010 to 2015. From 2015 to 2018 the rate of fragmentation decreased. Fragmentation in the Nu Jiang and Irrawaddy River basins was less than in other basins. The landscape patterns of the Jinsha and Pearl River basins were relatively fragmented due to human activity, socioeconomic development, and utilization. The differences between the Lancang and Red River Basins were relatively small and at an intermediate level. Conclusions Spatial autocorrelation analysis indicated that there are three areas with typical clusters, namely the Hengduan Mountains where the degree of fragmentation of the landscape was low, while landscape connectivity and aggregation were high. The subtropical region of Southern Yunnan displayed high landscape heterogeneity, a complex shape index, and high connectivity and sprawl. Central Yunnan exhibited a fragmented landscape with poor connectivity and aggregation. These three regions correspond with “the three screens and two belts” in the Main Functional Planning Area of Yunnan Province.
bibliographic citation: Liu et al. (2021) Multi-scale analysis of the characteristics of the changing landscape of the typical mountainous region of Southwest China over the past 40 years. PeerJ 9:e10923 https://doi.org/10.7717/peerj.10923
date submitted: 2020-09-08
date accepted: 2021-01-19
issued: 2021-05-14
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Liu
  given name: Fang
author list: Agent
  family name: Wang
  given name: Wanbin
author list: Agent
  family name: Wang
  given name: Jinliang
author list: Agent
  family name: Zhang
  given name: Xingzi
author list: Agent
  family name: Ren
  given name: Jing
author list: Agent
  family name: Liu
  given name: Yuexiong
doi: 10.7717/peerj.10923
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-05-14
copyright: ©2021 Liu et al.
attribution name: Liu et al.

Consequences of herbal mixture supplementation on milk performance, ruminal fermentation, and bacterial diversity in water buffaloes
type: item
type: AcademicArticle
description: This study was aimed to evaluate the potential of a herbal mixture (HM) to improve production performance, rumen fermentation, and milk fatty acid profile in water buffaloes. Sixteen Murrah buffaloes (in four groups) were fed for 10 weeks with the same basal diet supplemented with 0 (control); 20 (HM20), 30 (HM30), and 40 (HM40) g/buffalo per day. The herbal mixture contained an equal quantity of black pepper (fruit), ginger (tubers), cinnamon (bark), peppermint (leaves), ajwain (seeds) and garlic (bulbs). After two weeks of adaptation, daily milk yield, and weekly milk composition were recorded. On the last day of the experiment, rumen contents were collected to determine rumen fermentation parameters and bacterial diversity through 16S rRNA sequencing. Results revealed no effect of treatment on dry matter intake (DMI), rumen fermentation parameters, and daily milk yield. However, milk fat (%) showed a tendency to increase (p = 0.07) in HM20 as compared with the control group. A significant increase in mono and polyunsaturated fatty acids (C14:1, C16:1, C18:2n6 and C18:3) whereas a decrease in saturated fatty acids (C18:0) in milk was observed in HM20 as compared with the control group. No significant change in bacterial diversity parameters (alpha and beta diversity) was observed in response to the treatment. Despite the substantial variation observed in the relative abundance of bacteria among treatment groups, no significant effect of treatment was observed when compared with the control group. Correlation analysis revealed several positive and negative correlations of rumen bacteria with rumen volatile fatty acids (VFA) and milk yield traits. Bacterial genera including Succinivibrionaceae, Butyrivibrio, Pseudobutyrivibrio, and Lachnospiraceae showed a positive correlation with VFA and milk yield traits. Overall, we observed 52 positive and 10 negative correlations of rumen bacteria with milk fatty acid contents. Our study revealed the potential of the herbal mi…
format: application/pdf
format: text/html
creator: Faizul Hassan
creator: Zhenhua Tang
creator: Hossam M. Ebeid
creator: Mengwei Li
creator: Kaiping Peng
creator: Xin Liang
creator: Chengjian Yang
subject: Agricultural Science
subject: Microbiology
subject: Veterinary Medicine
subject: Zoology
description: doi:10.7717/peerj.11241
publisher: PeerJ Inc.
rights: © 2021 Hassan et al.
abstract: This study was aimed to evaluate the potential of a herbal mixture (HM) to improve production performance, rumen fermentation, and milk fatty acid profile in water buffaloes. Sixteen Murrah buffaloes (in four groups) were fed for 10 weeks with the same basal diet supplemented with 0 (control); 20 (HM20), 30 (HM30), and 40 (HM40) g/buffalo per day. The herbal mixture contained an equal quantity of black pepper (fruit), ginger (tubers), cinnamon (bark), peppermint (leaves), ajwain (seeds) and garlic (bulbs). After two weeks of adaptation, daily milk yield, and weekly milk composition were recorded. On the last day of the experiment, rumen contents were collected to determine rumen fermentation parameters and bacterial diversity through 16S rRNA sequencing. Results revealed no effect of treatment on dry matter intake (DMI), rumen fermentation parameters, and daily milk yield. However, milk fat (%) showed a tendency to increase (p = 0.07) in HM20 as compared with the control group. A significant increase in mono and polyunsaturated fatty acids (C14:1, C16:1, C18:2n6 and C18:3) whereas a decrease in saturated fatty acids (C18:0) in milk was observed in HM20 as compared with the control group. No significant change in bacterial diversity parameters (alpha and beta diversity) was observed in response to the treatment. Despite the substantial variation observed in the relative abundance of bacteria among treatment groups, no significant effect of treatment was observed when compared with the control group. Correlation analysis revealed several positive and negative correlations of rumen bacteria with rumen volatile fatty acids (VFA) and milk yield traits. Bacterial genera including Succinivibrionaceae, Butyrivibrio, Pseudobutyrivibrio, and Lachnospiraceae showed a positive correlation with VFA and milk yield traits. Overall, we observed 52 positive and 10 negative correlations of rumen bacteria with milk fatty acid contents. Our study revealed the potential of the herbal mi…
bibliographic citation: Hassan et al. (2021) Consequences of herbal mixture supplementation on milk performance, ruminal fermentation, and bacterial diversity in water buffaloes. PeerJ 9:e11241 https://doi.org/10.7717/peerj.11241
date submitted: 2020-09-14
date accepted: 2021-03-17
issued: 2021-05-14
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Hassan
  given name: Faizul
author list: Agent
  family name: Tang
  given name: Zhenhua
author list: Agent
  family name: Ebeid
  given name: Hossam M.
author list: Agent
  family name: Li
  given name: Mengwei
author list: Agent
  family name: Peng
  given name: Kaiping
author list: Agent
  family name: Liang
  given name: Xin
author list: Agent
  family name: Yang
  given name: Chengjian
doi: 10.7717/peerj.11241
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-05-14
copyright: ©2021 Hassan et al.
attribution name: Hassan et al.

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