title: PeerJ description: Articles published in PeerJ link: https://peerj.com/articles/index.rss3?journal=peerj&page=844 creator: info@peerj.com PeerJ errorsTo: info@peerj.com PeerJ language: en title: To culture or not to culture: a snapshot of culture-dependent and culture-independent bacterial diversity from peanut rhizosphere link: https://peerj.com/articles/12035 last-modified: 2021-09-01 description: BackgroundSequencing 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.MethodsIn 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.ResultsIn 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. creator: Ankit Hinsu creator: Ashvin Dumadiya creator: Anjali Joshi creator: Rohitkumar Kotadiya creator: Kavan Andharia creator: Prakash Koringa creator: Ramesh Kothari uri: https://doi.org/10.7717/peerj.12035 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2021 Hinsu et al. 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 link: https://peerj.com/articles/12062 last-modified: 2021-09-01 description: ObjectiveTo 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.MethodsA 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.ResultsA 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.ConclusionThe 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. creator: Alvaro García Pérez creator: Álvaro Edgar González-Aragón Pineda creator: Hilda Gonzalez Olivares uri: https://doi.org/10.7717/peerj.12062 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2021 García Pérez et al. title: The biomechanical characteristics of the strongman atlas stone lift link: https://peerj.com/articles/12066 last-modified: 2021-09-01 description: BackgroundThe 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.MethodsKinematic 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.ResultsThe 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 repetition were identified. Male athletes displayed smaller hip ROM during the second pull phase of the first three repetitions when compared with the final repetition and smaller hip extension at lift completion during the first two repetitions when compared with the final two repetitions. Female athletes did not display these between-repetition differences.ConclusionsSome of the between-sex biomechanical differences observed were suggested to be the result of between-sex anthropometric differences. Between-repetition differences observed may be attributed to the increase in stone mass and acute fatigue. The biomechanical characteristics of the atlas stone lift shared similarities with the previously researched Romanian deadlift and front squat. Strongman athletes, coaches and strength and conditioning coaches are recommended to take advantage of these similarities to achieve greater training adaptations and thus performance in the atlas stone lift and its similar movements. creator: Benjamin Hindle creator: Anna Lorimer creator: Paul Winwood creator: Daniel Brimm creator: Justin W.L. Keogh uri: https://doi.org/10.7717/peerj.12066 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2021 Hindle et al. title: Predictors of periodontal and caries related perinatal oral healthcare, investigation of dentists’ practices: a cross-sectional study link: https://peerj.com/articles/12080 last-modified: 2021-09-01 description: BackgroundThe 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.MethodsA 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.ResultsOverall 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).ConclusionsCollectively 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 patients. Failing to recognize the link between periodontal disease and obstetric complications increases the possibility of hesitance to counsel pregnant patients regarding the same. The appreciation of the evidence for poor perinatal oral health and risk of early childhood caries increases the likelihood of counseling by dentists on caries prevention. creator: Muhammad Qasim Javed creator: Usman Anwer Bhatti creator: Arham Riaz creator: Farooq Ahmad Chaudhary uri: https://doi.org/10.7717/peerj.12080 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2021 Javed et al. title: Towards a pragmatic use of statistics in ecology link: https://peerj.com/articles/12090 last-modified: 2021-09-01 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. creator: Leonardo Braga Castilho creator: Paulo Inácio Prado uri: https://doi.org/10.7717/peerj.12090 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2021 Castilho and Prado title: The bioinformatics and experimental analysis of AlkB family for prognosis and immune cell infiltration in hepatocellular carcinoma link: https://peerj.com/articles/12123 last-modified: 2021-09-01 description: BackgroundServing 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.MethodsSeveral bioinformatics tools and in vitro experiments were used to identify the immune-related profiles and prognostic values of AlkB family in HCC.ResultsIn 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.ConclusionsCollectively, 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. creator: Bi Peng creator: Yuanliang Yan creator: Zhijie Xu uri: https://doi.org/10.7717/peerj.12123 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2021 Peng et al. title: Geographic disparities and socio-demographic predictors of pertussis risk in Florida link: https://peerj.com/articles/11902 last-modified: 2021-08-31 description: BackgroundPertussis 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.MethodsPertussis 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.ResultsCounty-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. Counties with high pertussis risk tended to be rural (p = 0.021), those with high median incomes (p = 0.039), and those with high percentages of females (p < 0.001).ConclusionThere is evidence that geographic disparities exist and have persisted over time in Florida. This study highlights the application and importance of Geographic Information Systems (GIS) technology and spatial statistical/epidemiological tools in identifying areas of highest disease risk so as to guide resource allocation to reduce health disparities and improve health for all. creator: Corinne B. Tandy creator: Agricola Odoi uri: https://doi.org/10.7717/peerj.11902 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2021 Tandy and Odoi title: Exploring private land conservation non-adopters’ attendance at outreach events in the Chesapeake Bay watershed, USA link: https://peerj.com/articles/11959 last-modified: 2021-08-31 description: BackgroundOutreach 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.MethodsFor 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.ResultsOur 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. creator: Daniel J. Read creator: Alexandra Carroll creator: Lisa A. Wainger uri: https://doi.org/10.7717/peerj.11959 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2021 Read et al. title: Impact of dietary level and ratio of n-6 and n-3 fatty acids on disease progression and mRNA expression of immune and inflammatory markers in Atlantic salmon (Salmo salar) challenged with Paramoeba perurans link: https://peerj.com/articles/12028 last-modified: 2021-08-31 description: The aim of the study was to investigate the influence of dietary level and ratio of n-6/n-3 fatty acids (FA) on growth, disease progression and expression of immune and inflammatory markers in Atlantic salmon (Salmo salar) following challenge with Paramoeba perurans. Fish (80 g) were fed four different diets with different ratios of n-6/n-3 FA; at 1.3, 2.4 and 6.0 and one diet with ratio of 1.3 combined with a higher level of n-3 FA and n-6 FA. The diet with the n-6/n-3 FA ratio of 6.0 was included to ensure potential n-6 FA effects were revealed, while the three other diets were more commercially relevant n-6/n-3 FA ratios and levels. After a pre-feeding period of 3 months, fish from each diet regime were challenged with a standardized laboratory challenge using a clonal culture of P. perurans at the concentration of 1,000 cells L−1. The subsequent development of the disease was monitored (by gross gill score), and sampling conducted before challenge and at weekly sampling points for 5 weeks post-challenge. Challenge with P. perurans did not have a significant impact on the growth of the fish during the challenge period, but fish given the feed with the highest n-6/n-3 FA ratio had reduced growth compared to the other groups. Total gill score for all surfaces showed a significant increase with time, reaching a maximum at 21 days post-challenge and declined thereafter, irrespective of diet groups. Challenge with P. perurans influenced the mRNA expression of examined genes involved in immune and inflammatory response (TNF-α, iNOS, IL4-13b, GATA-3, IL-1β, p53, COX2 and PGE2-EP4), but diet did not influence the gene expression. In conclusion, an increase in dietary n-6/n-3 FA ratio influenced the growth of Atlantic salmon challenged with P. perurans; however, it did not alter the mRNA expression of immune genes or progression of the disease. creator: Chandrasekar Selvam creator: Mark D. Powell creator: Nina S. Liland creator: Grethe Rosenlund creator: Nini H. Sissener uri: https://doi.org/10.7717/peerj.12028 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2021 Selvam et al. title: COVID-19 and regional differences in the timeliness of hip-fracture surgery: an interrupted time-series analysis link: https://peerj.com/articles/12046 last-modified: 2021-08-31 description: BackgroundIt is of great importance to examine the impact of the healthcare reorganization adopted to confront the COVID-19 pandemic on the quality of care provided to non-COVID-19 patients. The aim of this study is to assess the impact of the COVID-19 national lockdown (March 9, 2020) on the quality of care provided to patients with hip fracture (HF) in Piedmont and Emilia-Romagna, two large regions of northern Italy severely hit by the pandemic.MethodsWe calculated the percentage of HF patients undergoing surgery within 2 days of hospital admission. An interrupted time-series analysis was performed on weekly data from December 11, 2019 to June 9, 2020 (≈6 months), interrupting the series in the 2nd week of March. The same data observed the year before were included as a control time series with no “intervention” (lockdown) in the middle of the observation period.ResultsBefore the lockdown, 2-day surgery was 69.9% in Piedmont and 79.2% in Emilia-Romagna; after the lockdown, these proportions were equal to 69.8% (–0.1%) and 69.3% (–9.9%), respectively. While Piedmont did not experience any drop in the amount of surgery, Emilia-Romagna exhibited a significant decline at a weekly rate of –1.29% (95% CI [−1.71 to −0.88]). Divergent trend patterns in the two study regions reflect local differences in pandemic timing as well as in healthcare services capacity, management, and emergency preparedness. creator: Davide Golinelli creator: Jacopo Lenzi creator: Emanuele Adorno creator: Maria Michela Gianino creator: Maria Pia Fantini uri: https://doi.org/10.7717/peerj.12046 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2021 Golinelli et al.