PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
items: https://peerj.com/articles/11940
items: Antimicrobial resistance among Enterobacteriaceae, Staphylococcus aureus, and Pseudomonas spp. isolates from clinical specimens from a hospital in Nairobi, Kenya
items: To culture or not to culture: a snapshot of culture-dependent and culture-independent bacterial diversity from peanut rhizosphere
items: https://peerj.com/articles/12062
items: The biomechanical characteristics of the strongman atlas stone lift
items: Predictors of periodontal and caries related perinatal oral healthcare, investigation of dentists’ practices: a cross-sectional study
items: Towards a pragmatic use of statistics in ecology
items: The bioinformatics and experimental analysis of AlkB family for prognosis and immune cell infiltration in hepatocellular carcinoma
items: Geographic disparities and socio-demographic predictors of pertussis risk in Florida
items: Exploring private land conservation non-adopters’ attendance at outreach events in the Chesapeake Bay watershed, USA

https://peerj.com/articles/11940
type: item
type: AcademicArticle
title: Revisiting food-sourced vitamins for consumer diet and health needs: a perspective review, from vitamin classification, metabolic functions, absorption, utilization, to balancing nutritional requirements
description: The significant attention gained by food-sourced vitamins has provided insights into numerous current researches; for instance, the potential reversal of epigenetic age using a diet and lifestyle intervention, the balance between food and dietary supplements in the general population, the role of diet and food intake in age-related macular degeneration, and the association of dietary supplement use, nutrient intake and mortality among adults. As relevant literature about food-sourced vitamin increases, continuous synthesis is warranted. To supplement existing information, this perspective review discussed food-sourced vitamins for consumer diet and health needs, scoping from vitamin absorption, metabolic functions, utilization, to balancing nutritional requirements. Relevant literatures were identified through a search of databases like Google Scholar, Web of Science, the Interscience Online Library, ScienceDirect, and PubMed. We demonstrated that vitamins whether from plant- and animal-based sources are prerequisites for the metabolic functions of the human body. The fat- and water-soluble classification of vitamins remains consistent with their respective absorption and dissolution potentials, underpinned by numerous physiological functions. Vitamins, largely absorbed in the small intestine, have their bioavailability dependent on the food composition, its associated interactions, as well as alignment with their metabolic functions, which involves antioxidants, coenzymes, electron acceptor/donor, and hormones. Moreover, vitamin deficiencies, in every form, pose a serious threat to human health. Vitamin toxicities remain rare, but can still occur mainly from supplementation, although it appears much less in water-soluble vitamins of which some excesses get readily removed by the human body, different from the fat-soluble ones that are stored in tissues and organs. Besides discussions of absorption, transport, and cellular uptake of vitamins, this perspective review…
format: application/pdf
format: text/html
creator: Chigozie E. Ofoedu
creator: Jude O. Iwouno
creator: Ebelechukwu O. Ofoedu
creator: Chika C. Ogueke
creator: Victory S. Igwe
creator: Ijeoma M. Agunwah
creator: Arinze F. Ofoedum
creator: James S. Chacha
creator: Onyinye P. Muobike
creator: Adedoyin O. Agunbiade
creator: Njideka E. Njoku
creator: Angela A. Nwakaudu
creator: Nkiru E. Odimegwu
creator: Onyekachi E. Ndukauba
creator: Chukwuka U. Ogbonna
creator: Joncer Naibaho
creator: Maciej Korus
creator: Charles Odilichukwu R. Okpala
subject: Biochemistry
subject: Food Science and Technology
subject: Nutrition
description: doi:10.7717/peerj.11940
publisher: PeerJ Inc.
rights: © 2021 Ofoedu et al.
abstract: The significant attention gained by food-sourced vitamins has provided insights into numerous current researches; for instance, the potential reversal of epigenetic age using a diet and lifestyle intervention, the balance between food and dietary supplements in the general population, the role of diet and food intake in age-related macular degeneration, and the association of dietary supplement use, nutrient intake and mortality among adults. As relevant literature about food-sourced vitamin increases, continuous synthesis is warranted. To supplement existing information, this perspective review discussed food-sourced vitamins for consumer diet and health needs, scoping from vitamin absorption, metabolic functions, utilization, to balancing nutritional requirements. Relevant literatures were identified through a search of databases like Google Scholar, Web of Science, the Interscience Online Library, ScienceDirect, and PubMed. We demonstrated that vitamins whether from plant- and animal-based sources are prerequisites for the metabolic functions of the human body. The fat- and water-soluble classification of vitamins remains consistent with their respective absorption and dissolution potentials, underpinned by numerous physiological functions. Vitamins, largely absorbed in the small intestine, have their bioavailability dependent on the food composition, its associated interactions, as well as alignment with their metabolic functions, which involves antioxidants, coenzymes, electron acceptor/donor, and hormones. Moreover, vitamin deficiencies, in every form, pose a serious threat to human health. Vitamin toxicities remain rare, but can still occur mainly from supplementation, although it appears much less in water-soluble vitamins of which some excesses get readily removed by the human body, different from the fat-soluble ones that are stored in tissues and organs. Besides discussions of absorption, transport, and cellular uptake of vitamins, this perspective review…
bibliographic citation: Ofoedu et al. (2021) Revisiting food-sourced vitamins for consumer diet and health needs: a perspective review, from vitamin classification, metabolic functions, absorption, utilization, to balancing nutritional requirements. PeerJ 9:e11940 https://doi.org/10.7717/peerj.11940
date submitted: 2021-03-26
date accepted: 2021-07-19
issued: 2021-09-01
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Ofoedu
  given name: Chigozie E.
author list: Agent
  family name: Iwouno
  given name: Jude O.
author list: Agent
  family name: Ofoedu
  given name: Ebelechukwu O.
author list: Agent
  family name: Ogueke
  given name: Chika C.
author list: Agent
  family name: Igwe
  given name: Victory S.
author list: Agent
  family name: Agunwah
  given name: Ijeoma M.
author list: Agent
  family name: Ofoedum
  given name: Arinze F.
author list: Agent
  family name: Chacha
  given name: James S.
author list: Agent
  family name: Muobike
  given name: Onyinye P.
author list: Agent
  family name: Agunbiade
  given name: Adedoyin O.
author list: Agent
  family name: Njoku
  given name: Njideka E.
author list: Agent
  family name: Nwakaudu
  given name: Angela A.
author list: Agent
  family name: Odimegwu
  given name: Nkiru E.
author list: Agent
  family name: Ndukauba
  given name: Onyekachi E.
author list: Agent
  family name: Ogbonna
  given name: Chukwuka U.
author list: Agent
  family name: Naibaho
  given name: Joncer
author list: Agent
  family name: Korus
  given name: Maciej
author list: Agent
  family name: Okpala
  given name: Charles Odilichukwu R.
doi: 10.7717/peerj.11940
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-09-01
copyright: © 2021 Ofoedu et al.
attribution name: Ofoedu et al.

Antimicrobial resistance among Enterobacteriaceae, Staphylococcus aureus, and Pseudomonas spp. isolates from clinical specimens from a hospital in Nairobi, Kenya
type: item
type: AcademicArticle
description: Background Antimicrobial resistance among pathogens of public health importance is an emerging problem in sub-Saharan Africa. Unfortunately, published information on the burden and patterns of antimicrobial resistance (AMR) in this region is sparse. There is evidence that the burden and patterns of AMR vary by geography and facility. Knowledge of local epidemiology of AMR is thus important for guiding clinical decisions and mitigation strategies. Therefore, the objective of this study was to determine the burden and predictors of AMR and multidrug resistance (MDR) among bacterial pathogens isolated from specimens submitted to the diagnostic laboratory of a hospital in Nairobi, Kenya. Methods This retrospective study used laboratory records of 1,217 clinical specimens submitted for bacterial culture and sensitivity testing at the diagnostic laboratory of The Karen Hospital in Nairobi, Kenya between 2012 and 2016. Records from specimens positive for Enterobacteriaceae, Staphylococcus aureus, or Pseudomonas spp. isolates were included for analysis. Firth logistic models, which minimize small sample bias, were used to investigate determinants of AMR and MDR of the isolates. Results A total of 222 specimens had bacterial growth. Most Enterobacteriaceae isolates were resistant to commonly used drugs such as penicillin/β-lactamase inhibitor combinations (91.2%) and folate pathway inhibitors (83.7%). Resistance to extended-spectrum cephalosporins was also high (52.9%). Levels of AMR and MDR for Enterobacteriaceae were 88.5% and 51%, respectively. Among S. aureus isolates, 57.1% were AMR, while 16.7% were MDR. As many as 42.1% of the Pseudomonas spp. isolates were aminoglycoside-resistant and 15% were fluoroquinolone-resistant, but none exhibited resistance to antipseudomonal carbapenems. Half of Pseudomonas spp. isolates were AMR but none were MDR. Significant predictors of MDR among Enterobacteriaceae were organism species (p = 0.002) and patient gender (p = 0.024). Conclu…
format: application/pdf
format: text/html
creator: Jennifer Lord
creator: Anthony Gikonyo
creator: Amos Miwa
creator: Agricola Odoi
subject: Microbiology
subject: Epidemiology
subject: Global Health
subject: Infectious Diseases
subject: Public Health
description: doi:10.7717/peerj.11958
publisher: PeerJ Inc.
rights: © 2021 Lord et al.
abstract: Background Antimicrobial resistance among pathogens of public health importance is an emerging problem in sub-Saharan Africa. Unfortunately, published information on the burden and patterns of antimicrobial resistance (AMR) in this region is sparse. There is evidence that the burden and patterns of AMR vary by geography and facility. Knowledge of local epidemiology of AMR is thus important for guiding clinical decisions and mitigation strategies. Therefore, the objective of this study was to determine the burden and predictors of AMR and multidrug resistance (MDR) among bacterial pathogens isolated from specimens submitted to the diagnostic laboratory of a hospital in Nairobi, Kenya. Methods This retrospective study used laboratory records of 1,217 clinical specimens submitted for bacterial culture and sensitivity testing at the diagnostic laboratory of The Karen Hospital in Nairobi, Kenya between 2012 and 2016. Records from specimens positive for Enterobacteriaceae, Staphylococcus aureus, or Pseudomonas spp. isolates were included for analysis. Firth logistic models, which minimize small sample bias, were used to investigate determinants of AMR and MDR of the isolates. Results A total of 222 specimens had bacterial growth. Most Enterobacteriaceae isolates were resistant to commonly used drugs such as penicillin/β-lactamase inhibitor combinations (91.2%) and folate pathway inhibitors (83.7%). Resistance to extended-spectrum cephalosporins was also high (52.9%). Levels of AMR and MDR for Enterobacteriaceae were 88.5% and 51%, respectively. Among S. aureus isolates, 57.1% were AMR, while 16.7% were MDR. As many as 42.1% of the Pseudomonas spp. isolates were aminoglycoside-resistant and 15% were fluoroquinolone-resistant, but none exhibited resistance to antipseudomonal carbapenems. Half of Pseudomonas spp. isolates were AMR but none were MDR. Significant predictors of MDR among Enterobacteriaceae were organism species (p = 0.002) and patient gender (p = 0.024). Conclu…
bibliographic citation: Lord et al. (2021) Antimicrobial resistance among Enterobacteriaceae, Staphylococcus aureus, and Pseudomonas spp. isolates from clinical specimens from a hospital in Nairobi, Kenya. PeerJ 9:e11958 https://doi.org/10.7717/peerj.11958
date submitted: 2021-05-10
date accepted: 2021-07-21
issued: 2021-09-01
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Lord
  given name: Jennifer
author list: Agent
  family name: Gikonyo
  given name: Anthony
author list: Agent
  family name: Miwa
  given name: Amos
author list: Agent
  family name: Odoi
  given name: Agricola
doi: 10.7717/peerj.11958
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-09-01
copyright: ©2021 Lord et al.
attribution name: Lord et al.

To culture or not to culture: a snapshot of culture-dependent and culture-independent bacterial diversity from peanut rhizosphere
type: item
type: AcademicArticle
description: Background Sequencing driven metagenomics studies have been instrumental in various aspects of microbiology including identification of newer taxa. While this culture-independent approach has its own merits and demerits, several studies have focussed on comparing it with traditional culture-dependent (CD) approach. However, most of these comparative studies rely on Sanger sequencing of complete 16S rRNA gene from pure culture colonies to determine the culturable bacterial diversity. This approach undercounts culturable diversity as only fewer isolates are selected, sequenced, and identified. Methods In this study, we have used an Illumina based partial 16S sequencing to identify all the microbes growing on the media and directly comparing with its culture-independent (CI) counterpart. Eight different media were used to target different organisms from soil. Diversity on these media were compared with their CI counterpart. The NGS data was analysed using DADA2 to provide more resolution to the data. Results In line with studies of similar nature, current study presented higher bacterial diversity in CI approach. However, the current study reflected that a greater number of sequence variants were missed out in CI approach as compared to number of sequence variants shared with CD approach. We observed around 322 (5.98%) ASVs (Amplicon Sequence Variants) exclusively present in CD samples while, 234 (4.35%) ASVs were shared between both approaches. Most of these 322 CD exclusive ASVs were classified as Enterobacteriaceae family and Bacillus genus, with several ASVs annotated at the species level as well, and these organisms are more commonly observed in soil and were also detected in CI approach. Furthermore, 22 genera were exclusively detected in CD samples, most of which were reported from soil and water.
format: application/pdf
format: text/html
creator: Ankit Hinsu
creator: Ashvin Dumadiya
creator: Anjali Joshi
creator: Rohitkumar Kotadiya
creator: Kavan Andharia
creator: Prakash Koringa
creator: Ramesh Kothari
subject: Agricultural Science
subject: Bioinformatics
subject: Microbiology
subject: Molecular Biology
subject: Soil Science
description: doi:10.7717/peerj.12035
publisher: PeerJ Inc.
rights: © 2021 Hinsu et al.
abstract: Background Sequencing driven metagenomics studies have been instrumental in various aspects of microbiology including identification of newer taxa. While this culture-independent approach has its own merits and demerits, several studies have focussed on comparing it with traditional culture-dependent (CD) approach. However, most of these comparative studies rely on Sanger sequencing of complete 16S rRNA gene from pure culture colonies to determine the culturable bacterial diversity. This approach undercounts culturable diversity as only fewer isolates are selected, sequenced, and identified. Methods In this study, we have used an Illumina based partial 16S sequencing to identify all the microbes growing on the media and directly comparing with its culture-independent (CI) counterpart. Eight different media were used to target different organisms from soil. Diversity on these media were compared with their CI counterpart. The NGS data was analysed using DADA2 to provide more resolution to the data. Results In line with studies of similar nature, current study presented higher bacterial diversity in CI approach. However, the current study reflected that a greater number of sequence variants were missed out in CI approach as compared to number of sequence variants shared with CD approach. We observed around 322 (5.98%) ASVs (Amplicon Sequence Variants) exclusively present in CD samples while, 234 (4.35%) ASVs were shared between both approaches. Most of these 322 CD exclusive ASVs were classified as Enterobacteriaceae family and Bacillus genus, with several ASVs annotated at the species level as well, and these organisms are more commonly observed in soil and were also detected in CI approach. Furthermore, 22 genera were exclusively detected in CD samples, most of which were reported from soil and water.
bibliographic citation: Hinsu et al. (2021) To culture or not to culture: a snapshot of culture-dependent and culture-independent bacterial diversity from peanut rhizosphere. PeerJ 9:e12035 https://doi.org/10.7717/peerj.12035
date submitted: 2021-06-03
date accepted: 2021-08-01
issued: 2021-09-01
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Hinsu
  given name: Ankit
author list: Agent
  family name: Dumadiya
  given name: Ashvin
author list: Agent
  family name: Joshi
  given name: Anjali
author list: Agent
  family name: Kotadiya
  given name: Rohitkumar
author list: Agent
  family name: Andharia
  given name: Kavan
author list: Agent
  family name: Koringa
  given name: Prakash
author list: Agent
  family name: Kothari
  given name: Ramesh
doi: 10.7717/peerj.12035
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-09-01
copyright: © 2021 Hinsu et al.
attribution name: Hinsu et al.

https://peerj.com/articles/12062
type: item
type: AcademicArticle
title: Oral health-related quality-of-life scores differ by socioeconomic status, mother’s level of education, dental visits and severity of malocclusion in mixed dentition of eight-to-ten-year-old schoolchildren
description: Objective To determinate the association among socioeconomic status subject’s mother’s level of educational attainment, dental visits, and malocclusion in mixed dentition with on the OHRQoL of eight-to-ten-year-old children. Methods A cross-sectional study conducted, in 2019, on Mexican children from households of different socioeconomic status (SES). The prevalence of malocclusion was evaluated using the Dental Aesthetic Index (DAI), while the SES of the participants’ households was evaluated using the three categories (corresponding to a high, middle, or low-income household) stipulated by the Consejo Nacional de Población (CONAPO or National Population Council). Oral Health-related Quality of Life (OHRQoL) was evaluated using the Child Perceptions Questionnaire (CPQ8-10). Poisson regression models were performed for the analysis of the data obtained. Results A total of 79.4% of the subjects presented some type of malocclusion in mixed dentition, which was, by severity, as follows: definite (31.3%); severe (25.6%); and, very severe (22.5%). The Poisson regression model revealed a greater negative impact on the following four CPQ8-10domains for children with severe/very severe malocclusion [RR]: oral symptoms [2.78]; functional limitations [2.72]; emotional well-being [2.59]; and, social well-being [3.99]. A greater impact on the four CPQ8-10domains was found for children from a low-income household than for children from a high-income (p < 0.001) household. Furthermore, poor oral hygiene, lack of dental visits, and the mother’s level of educational attainment (<9 years) were found to have a negative impact on OHRQoL. Conclusion The findings of the present study demonstrated that the severity of malocclusion was associated with a greater negative impact on the OHRQoL of children, while those children who face greater health inequalities are likely to report a greater negative impact on their OHRQoL.
format: application/pdf
format: text/html
creator: Alvaro García Pérez
creator: Álvaro Edgar González-Aragón Pineda
creator: Hilda Gonzalez Olivares
subject: Dentistry
subject: Epidemiology
subject: Pediatrics
subject: Public Health
description: doi:10.7717/peerj.12062
publisher: PeerJ Inc.
rights: © 2021 García Pérez et al.
abstract: Objective To determinate the association among socioeconomic status subject’s mother’s level of educational attainment, dental visits, and malocclusion in mixed dentition with on the OHRQoL of eight-to-ten-year-old children. Methods A cross-sectional study conducted, in 2019, on Mexican children from households of different socioeconomic status (SES). The prevalence of malocclusion was evaluated using the Dental Aesthetic Index (DAI), while the SES of the participants’ households was evaluated using the three categories (corresponding to a high, middle, or low-income household) stipulated by the Consejo Nacional de Población (CONAPO or National Population Council). Oral Health-related Quality of Life (OHRQoL) was evaluated using the Child Perceptions Questionnaire (CPQ8-10). Poisson regression models were performed for the analysis of the data obtained. Results A total of 79.4% of the subjects presented some type of malocclusion in mixed dentition, which was, by severity, as follows: definite (31.3%); severe (25.6%); and, very severe (22.5%). The Poisson regression model revealed a greater negative impact on the following four CPQ8-10domains for children with severe/very severe malocclusion [RR]: oral symptoms [2.78]; functional limitations [2.72]; emotional well-being [2.59]; and, social well-being [3.99]. A greater impact on the four CPQ8-10domains was found for children from a low-income household than for children from a high-income (p < 0.001) household. Furthermore, poor oral hygiene, lack of dental visits, and the mother’s level of educational attainment (<9 years) were found to have a negative impact on OHRQoL. Conclusion The findings of the present study demonstrated that the severity of malocclusion was associated with a greater negative impact on the OHRQoL of children, while those children who face greater health inequalities are likely to report a greater negative impact on their OHRQoL.
bibliographic citation: García Pérez et al. (2021) Oral health-related quality-of-life scores differ by socioeconomic status, mother’s level of education, dental visits and severity of malocclusion in mixed dentition of eight-to-ten-year-old schoolchildren. PeerJ 9:e12062 https://doi.org/10.7717/peerj.12062
date submitted: 2021-03-04
date accepted: 2021-08-04
issued: 2021-09-01
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: García Pérez
  given name: Alvaro
author list: Agent
  family name: González-Aragón Pineda
  given name: Álvaro Edgar
author list: Agent
  family name: Gonzalez Olivares
  given name: Hilda
doi: 10.7717/peerj.12062
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-09-01
copyright: ©2021 García Pérez et al.
attribution name: García Pérez et al.

The biomechanical characteristics of the strongman atlas stone lift
type: item
type: AcademicArticle
description: Background The atlas stone lift is a popular strongman exercise where athletes are required to pick up a large, spherical, concrete stone and pass it over a bar or place it on to a ledge. The aim of this study was to use ecologically realistic training loads and set formats to (1) establish the preliminary biomechanical characteristics of athletes performing the atlas stone lift; (2) identify any biomechanical differences between male and female athletes performing the atlas stone lift; and (3) determine temporal and kinematic differences between repetitions of a set of atlas stones of incremental mass. Methods Kinematic measures of hip, knee and ankle joint angle, and temporal measures of phase and repetition duration were collected whilst 20 experienced strongman athletes (female: n = 8, male: n = 12) performed three sets of four stone lifts of incremental mass (up to 85% one repetition maximum) over a fixed-height bar. Results The atlas stone lift was categorised in to five phases: the recovery, initial grip, first pull, lap and second pull phase. The atlas stone lift could be biomechanically characterised by maximal hip and moderate knee flexion and ankle dorsiflexion at the beginning of the first pull; moderate hip and knee flexion and moderate ankle plantarflexion at the beginning of the lap phase; moderate hip and maximal knee flexion and ankle dorsiflexion at the beginning of the second pull phase; and maximal hip, knee extension and ankle plantarflexion at lift completion. When compared with male athletes, female athletes most notably exhibited: greater hip flexion at the beginning of the first pull, lap and second pull phase and at lift completion; and a shorter second pull phase duration. Independent of sex, first pull and lap phase hip and ankle range of motion (ROM) were generally smaller in repetition one than the final three repetitions, while phase and total repetition duration increased throughout the set. Two-way interactions between sex and repeti…
format: application/pdf
format: text/html
creator: Benjamin Hindle
creator: Anna Lorimer
creator: Paul Winwood
creator: Daniel Brimm
creator: Justin W.L. Keogh
subject: Anatomy and Physiology
subject: Kinesiology
description: doi:10.7717/peerj.12066
publisher: PeerJ Inc.
rights: © 2021 Hindle et al.
abstract: Background The atlas stone lift is a popular strongman exercise where athletes are required to pick up a large, spherical, concrete stone and pass it over a bar or place it on to a ledge. The aim of this study was to use ecologically realistic training loads and set formats to (1) establish the preliminary biomechanical characteristics of athletes performing the atlas stone lift; (2) identify any biomechanical differences between male and female athletes performing the atlas stone lift; and (3) determine temporal and kinematic differences between repetitions of a set of atlas stones of incremental mass. Methods Kinematic measures of hip, knee and ankle joint angle, and temporal measures of phase and repetition duration were collected whilst 20 experienced strongman athletes (female: n = 8, male: n = 12) performed three sets of four stone lifts of incremental mass (up to 85% one repetition maximum) over a fixed-height bar. Results The atlas stone lift was categorised in to five phases: the recovery, initial grip, first pull, lap and second pull phase. The atlas stone lift could be biomechanically characterised by maximal hip and moderate knee flexion and ankle dorsiflexion at the beginning of the first pull; moderate hip and knee flexion and moderate ankle plantarflexion at the beginning of the lap phase; moderate hip and maximal knee flexion and ankle dorsiflexion at the beginning of the second pull phase; and maximal hip, knee extension and ankle plantarflexion at lift completion. When compared with male athletes, female athletes most notably exhibited: greater hip flexion at the beginning of the first pull, lap and second pull phase and at lift completion; and a shorter second pull phase duration. Independent of sex, first pull and lap phase hip and ankle range of motion (ROM) were generally smaller in repetition one than the final three repetitions, while phase and total repetition duration increased throughout the set. Two-way interactions between sex and repeti…
bibliographic citation: Hindle et al. (2021) The biomechanical characteristics of the strongman atlas stone lift. PeerJ 9:e12066 https://doi.org/10.7717/peerj.12066
date submitted: 2021-04-08
date accepted: 2021-08-05
issued: 2021-09-01
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Hindle
  given name: Benjamin
author list: Agent
  family name: Lorimer
  given name: Anna
author list: Agent
  family name: Winwood
  given name: Paul
author list: Agent
  family name: Brimm
  given name: Daniel
author list: Agent
  family name: Keogh
  given name: Justin W.L.
doi: 10.7717/peerj.12066
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-09-01
copyright: © 2021 Hindle et al.
attribution name: Hindle et al.

Predictors of periodontal and caries related perinatal oral healthcare, investigation of dentists’ practices: a cross-sectional study
type: item
type: AcademicArticle
description: Background The objectives of the study were to assess the knowledge, attitude, and practice of dentists towards providing oral health care to pregnant women and to identify barriers and predictors of periodontal and caries related perinatal oral healthcare practices. Methods A cross-sectional analytical survey was conducted on dentists by using a random sampling technique, and a pre-validated questionnaire was delivered to 350 dentists from May 2018 to October 2018. Data were analyzed by utilizing SPSS software. Frequencies and percentages were recorded for descriptive variables. Binary logistic regression was used to analyze the probability of predicting group membership to the dependent variable using different independent variables determined from contingency tables. Results Overall response rate was 41%. The mean knowledge score of respondents was 15.86 ± 3.34. The lowest correct responses were noted in the questions related to periodontal health. It was found that the advice to delay dental visits until after pregnancy was eight times more likely to be observed among dentists who lacked the knowledge of importance of oral health during pregnancy (P = 0.04, OR = 8.75). Dentists were more likely to consult obstetricians regarding dental procedures when they fear a risk of labor in the dental practice (P < 0.05, OR = 3.72). Dentists who had the knowledge of periodontal disease association with preterm delivery were about four times more likely to treat periodontal disease during pregnancy (P = 0.01, OR = 3.95). Dentists knowing the association between maternal oral health and childhood decay were more likely to counsel pregnant patients regarding caries prevention (P > 0.05, OR = 3.75). Conclusions Collectively the results indicated few gaps in knowledge among some dentists and a need to improve existing attitudes towards perinatal oral health. Dentists failing to recognize the importance of perinatal oral health are more likely to be hesitant in treating pregnant…
format: application/pdf
format: text/html
creator: Muhammad Qasim Javed
creator: Usman Anwer Bhatti
creator: Arham Riaz
creator: Farooq Ahmad Chaudhary
subject: Dentistry
subject: Gynecology and Obstetrics
subject: Public Health
subject: Women’s Health
description: doi:10.7717/peerj.12080
publisher: PeerJ Inc.
rights: © 2021 Javed et al.
abstract: Background The objectives of the study were to assess the knowledge, attitude, and practice of dentists towards providing oral health care to pregnant women and to identify barriers and predictors of periodontal and caries related perinatal oral healthcare practices. Methods A cross-sectional analytical survey was conducted on dentists by using a random sampling technique, and a pre-validated questionnaire was delivered to 350 dentists from May 2018 to October 2018. Data were analyzed by utilizing SPSS software. Frequencies and percentages were recorded for descriptive variables. Binary logistic regression was used to analyze the probability of predicting group membership to the dependent variable using different independent variables determined from contingency tables. Results Overall response rate was 41%. The mean knowledge score of respondents was 15.86 ± 3.34. The lowest correct responses were noted in the questions related to periodontal health. It was found that the advice to delay dental visits until after pregnancy was eight times more likely to be observed among dentists who lacked the knowledge of importance of oral health during pregnancy (P = 0.04, OR = 8.75). Dentists were more likely to consult obstetricians regarding dental procedures when they fear a risk of labor in the dental practice (P < 0.05, OR = 3.72). Dentists who had the knowledge of periodontal disease association with preterm delivery were about four times more likely to treat periodontal disease during pregnancy (P = 0.01, OR = 3.95). Dentists knowing the association between maternal oral health and childhood decay were more likely to counsel pregnant patients regarding caries prevention (P > 0.05, OR = 3.75). Conclusions Collectively the results indicated few gaps in knowledge among some dentists and a need to improve existing attitudes towards perinatal oral health. Dentists failing to recognize the importance of perinatal oral health are more likely to be hesitant in treating pregnant…
bibliographic citation: Javed et al. (2021) Predictors of periodontal and caries related perinatal oral healthcare, investigation of dentists’ practices: a cross-sectional study. PeerJ 9:e12080 https://doi.org/10.7717/peerj.12080
date submitted: 2021-01-28
date accepted: 2021-08-06
issued: 2021-09-01
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Javed
  given name: Muhammad Qasim
author list: Agent
  family name: Bhatti
  given name: Usman Anwer
author list: Agent
  family name: Riaz
  given name: Arham
author list: Agent
  family name: Chaudhary
  given name: Farooq Ahmad
doi: 10.7717/peerj.12080
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-09-01
copyright: © 2021 Javed et al.
attribution name: Javed et al.

Towards a pragmatic use of statistics in ecology
type: item
type: AcademicArticle
description: Although null hypothesis testing (NHT) is the primary method for analyzing data in many natural sciences, it has been increasingly criticized. Recently, approaches based on information theory (IT) have become popular and were held by many to be superior because it enables researchers to properly assess the strength of the evidence that data provide for competing hypotheses. Many studies have compared IT and NHT in the context of model selection and stepwise regression, but a systematic comparison of the most basic uses of statistics by ecologists is still lacking. We used computer simulations to compare how both approaches perform in four basic test designs (t-test, ANOVA, correlation tests, and multiple linear regression). Performance was measured by the proportion of simulated samples for which each method provided the correct conclusion (power), the proportion of detected effects with a wrong sign (S-error), and the mean ratio of the estimated effect to the true effect (M-error). We also checked if the p-value from significance tests correlated to a measure of strength of evidence, the Akaike weight. In general both methods performed equally well. The concordance is explained by the monotonic relationship between p-values and evidence weights in simple designs, which agree with analytic results. Our results show that researchers can agree on the conclusions drawn from a data set even when they are using different statistical approaches. By focusing on the practical consequences of inferences, such a pragmatic view of statistics can promote insightful dialogue among researchers on how to find a common ground from different pieces of evidence. A less dogmatic view of statistical inference can also help to broaden the debate about the role of statistics in science to the entire path that leads from a research hypothesis to a statistical hypothesis.
format: application/pdf
format: text/html
creator: Leonardo Braga Castilho
creator: Paulo Inácio Prado
subject: Ecology
subject: Statistics
description: doi:10.7717/peerj.12090
publisher: PeerJ Inc.
rights: © 2021 Castilho and Prado
abstract: Although null hypothesis testing (NHT) is the primary method for analyzing data in many natural sciences, it has been increasingly criticized. Recently, approaches based on information theory (IT) have become popular and were held by many to be superior because it enables researchers to properly assess the strength of the evidence that data provide for competing hypotheses. Many studies have compared IT and NHT in the context of model selection and stepwise regression, but a systematic comparison of the most basic uses of statistics by ecologists is still lacking. We used computer simulations to compare how both approaches perform in four basic test designs (t-test, ANOVA, correlation tests, and multiple linear regression). Performance was measured by the proportion of simulated samples for which each method provided the correct conclusion (power), the proportion of detected effects with a wrong sign (S-error), and the mean ratio of the estimated effect to the true effect (M-error). We also checked if the p-value from significance tests correlated to a measure of strength of evidence, the Akaike weight. In general both methods performed equally well. The concordance is explained by the monotonic relationship between p-values and evidence weights in simple designs, which agree with analytic results. Our results show that researchers can agree on the conclusions drawn from a data set even when they are using different statistical approaches. By focusing on the practical consequences of inferences, such a pragmatic view of statistics can promote insightful dialogue among researchers on how to find a common ground from different pieces of evidence. A less dogmatic view of statistical inference can also help to broaden the debate about the role of statistics in science to the entire path that leads from a research hypothesis to a statistical hypothesis.
bibliographic citation: Castilho et al. (2021) Towards a pragmatic use of statistics in ecology. PeerJ 9:e12090 https://doi.org/10.7717/peerj.12090
date submitted: 2021-04-29
date accepted: 2021-08-08
issued: 2021-09-01
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Castilho
  given name: Leonardo Braga
author list: Agent
  family name: Prado
  given name: Paulo Inácio
doi: 10.7717/peerj.12090
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-09-01
copyright: © 2021 Castilho and Prado
attribution name: Castilho and Prado

The bioinformatics and experimental analysis of AlkB family for prognosis and immune cell infiltration in hepatocellular carcinoma
type: item
type: AcademicArticle
description: Background Serving as N6-methyladenosine demethylases, the AlkB family is involved in the tumorigenesis of hepatocellular carcinoma (HCC). However, the molecular profiles and clinical values of the AlkB family in HCC are not well known. Methods Several bioinformatics tools and in vitro experiments were used to identify the immune-related profiles and prognostic values of AlkB family in HCC. Results In this study expression levels of ALKBH1/2/3/4/7 were all remarkably increased in HCC tissues when compared with normal tissues. Quantitative PCR (qPCR) and immunohistochemistry were used to validate the expression of AlkB family members in HCC tissues and normal liver tissues. In addition, high expression levels of ALKBH4 were negatively correlated with overall survival (OS) and disease-free survival (DFS) in patients with HCC. Increased ALKBH4 was also associated with pathological stage in HCC patients. The molecular profiles of AlkB family in HCC were mainly associated with peptidyl-serine modification, peptidyl-tyrosine modification, regulation of metal ion transport, etc. Furthermore, tumor-infiltrating immune cell analysis indicated that ALKBH1/2/3/4/5/6/7/8 and FTO were related to the infiltration of different immune cell, such as CD8+ T cells, macrophages, neutrophils, dendritic cells and CD4+ T cells. We also discovered that the methylation levels of ALKBH1/2/4/5/6/8 and FTO were remarkably reduced in HCC tissues. Conclusions Collectively, our findings may deepen the understanding of specific molecular profiles of the AlkB family in HCC pathology. In particular, ALKBH4 could serve as a promising prognostic candidate for treating HCC, and these results might potentiate the development of more reliable therapeutic strategies for patients with HCC.
format: application/pdf
format: text/html
creator: Bi Peng
creator: Yuanliang Yan
creator: Zhijie Xu
subject: Bioinformatics
subject: Molecular Biology
subject: Gastroenterology and Hepatology
subject: Oncology
subject: Medical Genetics
description: doi:10.7717/peerj.12123
publisher: PeerJ Inc.
rights: © 2021 Peng et al.
abstract: Background Serving as N6-methyladenosine demethylases, the AlkB family is involved in the tumorigenesis of hepatocellular carcinoma (HCC). However, the molecular profiles and clinical values of the AlkB family in HCC are not well known. Methods Several bioinformatics tools and in vitro experiments were used to identify the immune-related profiles and prognostic values of AlkB family in HCC. Results In this study expression levels of ALKBH1/2/3/4/7 were all remarkably increased in HCC tissues when compared with normal tissues. Quantitative PCR (qPCR) and immunohistochemistry were used to validate the expression of AlkB family members in HCC tissues and normal liver tissues. In addition, high expression levels of ALKBH4 were negatively correlated with overall survival (OS) and disease-free survival (DFS) in patients with HCC. Increased ALKBH4 was also associated with pathological stage in HCC patients. The molecular profiles of AlkB family in HCC were mainly associated with peptidyl-serine modification, peptidyl-tyrosine modification, regulation of metal ion transport, etc. Furthermore, tumor-infiltrating immune cell analysis indicated that ALKBH1/2/3/4/5/6/7/8 and FTO were related to the infiltration of different immune cell, such as CD8+ T cells, macrophages, neutrophils, dendritic cells and CD4+ T cells. We also discovered that the methylation levels of ALKBH1/2/4/5/6/8 and FTO were remarkably reduced in HCC tissues. Conclusions Collectively, our findings may deepen the understanding of specific molecular profiles of the AlkB family in HCC pathology. In particular, ALKBH4 could serve as a promising prognostic candidate for treating HCC, and these results might potentiate the development of more reliable therapeutic strategies for patients with HCC.
bibliographic citation: Peng et al. (2021) The bioinformatics and experimental analysis of AlkB family for prognosis and immune cell infiltration in hepatocellular carcinoma. PeerJ 9:e12123 https://doi.org/10.7717/peerj.12123
date submitted: 2021-07-09
date accepted: 2021-08-16
issued: 2021-09-01
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Peng
  given name: Bi
author list: Agent
  family name: Yan
  given name: Yuanliang
author list: Agent
  family name: Xu
  given name: Zhijie
doi: 10.7717/peerj.12123
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-09-01
copyright: ©2021 Peng et al.
attribution name: Peng et al.

Geographic disparities and socio-demographic predictors of pertussis risk in Florida
type: item
type: AcademicArticle
description: Background Pertussis is a toxin-mediated respiratory illness caused by Bordetella pertussis that can result in severe complications and death, particularly in infants. Between 2008 and 2011, children less than 3 months old accounted for 83% of the pertussis deaths in the United States. Understanding the geographic disparities in the distribution of pertussis risk and identifying high risk geographic areas is necessary for guiding resource allocation and public health control strategies. Therefore, this study investigated geographic disparities and temporal changes in pertussis risk in Florida from 2010 to 2018. It also investigated socioeconomic and demographic predictors of the identified disparities. Methods Pertussis data covering the time period 2010–2018 were obtained from Florida HealthCHARTS web interface. Spatial patterns and temporal changes in geographic distribution of pertussis risk were assessed using county-level choropleth maps for the time periods 2010–2012, 2013–2015, 2016–2018 and 2010–2018. Tango’s flexible spatial scan statistics were used to identify high-risk spatial clusters which were displayed in maps. Ordinary least squares (OLS) regression was used to identify significant predictors of county-level risk. Residuals of the OLS model were assessed for model assumptions including spatial autocorrelation. Results County-level pertussis risk varied from 0 to 116.31 cases per 100,000 people during the study period. A total of 11 significant (p < 0.05) spatial clusters were identified with risk ratios ranging from 1.5 to 5.8. Geographic distribution remained relatively consistent over time with areas of high risk persisting in the western panhandle, northeastern coast, and along the western coast. Although county level pertussis risks generally increased from 2010–2012 to 2013–2015, risk tended to be lower during the 2016–2018 time period. Significant predictors of county-level pertussis risk were rurality, percentage of females, and median income…
format: application/pdf
format: text/html
creator: Corinne B. Tandy
creator: Agricola Odoi
subject: Epidemiology
subject: Global Health
subject: Infectious Diseases
subject: Public Health
subject: Respiratory Medicine
description: doi:10.7717/peerj.11902
publisher: PeerJ Inc.
rights: © 2021 Tandy and Odoi
abstract: Background Pertussis is a toxin-mediated respiratory illness caused by Bordetella pertussis that can result in severe complications and death, particularly in infants. Between 2008 and 2011, children less than 3 months old accounted for 83% of the pertussis deaths in the United States. Understanding the geographic disparities in the distribution of pertussis risk and identifying high risk geographic areas is necessary for guiding resource allocation and public health control strategies. Therefore, this study investigated geographic disparities and temporal changes in pertussis risk in Florida from 2010 to 2018. It also investigated socioeconomic and demographic predictors of the identified disparities. Methods Pertussis data covering the time period 2010–2018 were obtained from Florida HealthCHARTS web interface. Spatial patterns and temporal changes in geographic distribution of pertussis risk were assessed using county-level choropleth maps for the time periods 2010–2012, 2013–2015, 2016–2018 and 2010–2018. Tango’s flexible spatial scan statistics were used to identify high-risk spatial clusters which were displayed in maps. Ordinary least squares (OLS) regression was used to identify significant predictors of county-level risk. Residuals of the OLS model were assessed for model assumptions including spatial autocorrelation. Results County-level pertussis risk varied from 0 to 116.31 cases per 100,000 people during the study period. A total of 11 significant (p < 0.05) spatial clusters were identified with risk ratios ranging from 1.5 to 5.8. Geographic distribution remained relatively consistent over time with areas of high risk persisting in the western panhandle, northeastern coast, and along the western coast. Although county level pertussis risks generally increased from 2010–2012 to 2013–2015, risk tended to be lower during the 2016–2018 time period. Significant predictors of county-level pertussis risk were rurality, percentage of females, and median income…
bibliographic citation: Tandy et al. (2021) Geographic disparities and socio-demographic predictors of pertussis risk in Florida. PeerJ 9:e11902 https://doi.org/10.7717/peerj.11902
date submitted: 2021-03-25
date accepted: 2021-07-13
issued: 2021-08-31
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Tandy
  given name: Corinne B.
author list: Agent
  family name: Odoi
  given name: Agricola
doi: 10.7717/peerj.11902
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-08-31
copyright: © 2021 Tandy and Odoi
attribution name: Tandy and Odoi

Exploring private land conservation non-adopters’ attendance at outreach events in the Chesapeake Bay watershed, USA
type: item
type: AcademicArticle
description: Background Outreach events such as trainings, demonstrations, and workshops are important opportunities for encouraging private land operators to adopt voluntary conservation practices. However, the ability to understand the effectiveness of such events at influencing conservation behavior is confounded by the likelihood that attendees are already interested in conservation and may already be adopters. Understanding characteristics of events that draw non-adopters can aid in designing events and messaging that are better able to reach beyond those already interested in conservation. Methods For this study, we interviewed 101 operators of private agricultural lands in Maryland, USA, and used descriptive statistics and qualitative comparative analysis to investigate differences between the kinds of outreach events that adopters and non-adopters attended. Results Our results suggested that non-adopters, as compared to adopters, attended events that provided production-relevant information and were logistically easy to attend. Further, non-adopters were more selective when reading advertisements, generally preferring simplicity. Future research and outreach can build on these findings by experimentally testing the effectiveness of messages that are simple and relevant to farmers’ production priorities.
format: application/pdf
format: text/html
creator: Daniel J. Read
creator: Alexandra Carroll
creator: Lisa A. Wainger
subject: Conservation Biology
subject: Science and Medical Education
subject: Science Policy
subject: Coupled Natural and Human Systems
subject: Natural Resource Management
description: doi:10.7717/peerj.11959
publisher: PeerJ Inc.
rights: © 2021 Read et al.
abstract: Background Outreach events such as trainings, demonstrations, and workshops are important opportunities for encouraging private land operators to adopt voluntary conservation practices. However, the ability to understand the effectiveness of such events at influencing conservation behavior is confounded by the likelihood that attendees are already interested in conservation and may already be adopters. Understanding characteristics of events that draw non-adopters can aid in designing events and messaging that are better able to reach beyond those already interested in conservation. Methods For this study, we interviewed 101 operators of private agricultural lands in Maryland, USA, and used descriptive statistics and qualitative comparative analysis to investigate differences between the kinds of outreach events that adopters and non-adopters attended. Results Our results suggested that non-adopters, as compared to adopters, attended events that provided production-relevant information and were logistically easy to attend. Further, non-adopters were more selective when reading advertisements, generally preferring simplicity. Future research and outreach can build on these findings by experimentally testing the effectiveness of messages that are simple and relevant to farmers’ production priorities.
bibliographic citation: Read et al. (2021) Exploring private land conservation non-adopters’ attendance at outreach events in the Chesapeake Bay watershed, USA. PeerJ 9:e11959 https://doi.org/10.7717/peerj.11959
date submitted: 2021-05-24
date accepted: 2021-07-21
issued: 2021-08-31
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Read
  given name: Daniel J.
author list: Agent
  family name: Carroll
  given name: Alexandra
author list: Agent
  family name: Wainger
  given name: Lisa A.
doi: 10.7717/peerj.11959
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-08-31
copyright: ©2021 Read et al.
attribution name: Read et al.

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