Category: Statistics

PLoS One. 2021 Apr 16;16(4):e0250321. doi: 10.1371/journal.pone.0250321. eCollection 2021.

ABSTRACT

OBJECTIVE: Obesity is a negative prognostic factor for various clinical conditions. In this observational cohort study, we evaluated a CT-based assessment of the adipose tissue distribution as a potential non-invasive prognostic parameter in critical illness.

METHODS: Routine CT-scans upon admission to the intensive care unit (ICU) were used to analyze the visceral and subcutaneous adipose tissue areas at the 3rd lumbar vertebra in 155 patients. Results were correlated with various prognostic markers and both short-term- and overall survival. Multiple statistical tools were used for data analysis.

RESULTS: We observed a significantly larger visceral adipose tissue area in septic patients compared to non-sepsis patients. Interestingly, patients requiring mechanical ventilation had a significantly higher amount of visceral adipose tissue correlating with the duration of mechanical ventilation. Moreover, both visceral and subcutaneous adipose tissue area significantly correlated with several laboratory markers. While neither the visceral nor the subcutaneous adipose tissue area was predictive for short-term ICU survival, patients with a visceral adipose tissue area above the optimal cut-off (241.4 cm2) had a significantly impaired overall survival compared to patients with a lower visceral adipose tissue area.

CONCLUSIONS: Our study supports a prognostic role of the individual adipose tissue distribution in critically ill patients. However, additional investigations need to confirm our suggestion that routine CT-based assessment of adipose tissue distribution can be used to yield further information on the patients’ clinical course. Moreover, future studies should address functional and metabolic analysis of different adipose tissue compartments in critical illness.

PMID:33861804 | DOI:10.1371/journal.pone.0250321

PLoS One. 2021 Apr 16;16(4):e0249305. doi: 10.1371/journal.pone.0249305. eCollection 2021.

ABSTRACT

Genetic studies have shifted to sequencing-based rare variants discovery after decades of success in identifying common disease variants by Genome-Wide Association Studies using Single Nucleotide Polymorphism chips. Sequencing-based studies require large sample sizes for statistical power and therefore often inadvertently introduce batch effects because samples are typically collected, processed, and sequenced at multiple centers. Conventionally, batch effects are first detected and visualized using Principal Components Analysis and then controlled by including batch covariates in the disease association models. For sequencing-based genetic studies, because all variants included in the association analyses have passed sequencing-related quality control measures, this conventional approach treats every variant as equal and ignores the substantial differences still remaining in variant qualities and characteristics such as genotype quality scores, alternative allele fractions (fraction of reads supporting alternative allele at a variant position) and sequencing depths. In the Alzheimer’s Disease Sequencing Project (ADSP) exome dataset of 9,904 cases and controls, we discovered hidden variant-level differences between sample batches of three sequencing centers and two exome capture kits. Although sequencing centers were included as a covariate in our association models, we observed differences at the variant level in genotype quality and alternative allele fraction between samples processed by different exome capture kits that significantly impacted both the confidence of variant detection and the identification of disease-associated variants. Furthermore, we found that a subset of top disease-risk variants came exclusively from samples processed by one exome capture kit that was more effective at capturing the alternative alleles compared to the other kit. Our findings highlight the importance of additional variant-level quality control for large sequencing-based genetic studies. More importantly, we demonstrate that automatically filtering out variants with batch differences may lead to false negatives if the batch discordances come largely from quality differences and if the batch-specific variants have better quality.

PMID:33861770 | DOI:10.1371/journal.pone.0249305

PLoS One. 2021 Apr 16;16(4):e0250169. doi: 10.1371/journal.pone.0250169. eCollection 2021.

ABSTRACT

OBJECTIVES: To measure the effects of peer influence and peer selection on drinking behavior in adolescence through a rigorous statistical approach designed to unravel these interrelated processes.

METHODS: We conducted systematic searches of electronic databases, thesis collections and conference proceedings to identify studies that used longitudinal network design and stochastic actor-oriented modeling to analyze drinking behavior in adolescents. Parameter estimates collected from individual studies were analyzed using multilevel random-effects models.

RESULTS: We identified 26 articles eligible for meta-analysis. Meta-analyses for different specifications of the peer influence effect were conducted separately. The peer influence effect was positive for every specification: for average similarity (avSim) mean log odds ratio was 1.27 with 95% confidence interval [0.04; 2.49]; for total similarity (totSim) 0.46 (95% CI = [0.44; 0.48]), and for average alter (avAlt) 0.70 (95% CI = [-0.01; 1.41]). The peer selection effect (simX) was also positive: 0.46 (95% CI = [0.28; 0.63]). Conversion log odds ratio values to Cohen’s d gives estimates from 0.25 to 0.70, which is considered as medium to large effect.

CONCLUSIONS: Advances in methodology for social network analysis have made it possible to accurately estimate peer influence effects free from peer selection effects. More research is necessary to clarify the roles of age, gender, and individual susceptibility on the changing behavior of adolescents under the influence of their peers. Understanding the effects of peer influence should inform practitioners and policy makers to design and deliver more effective prevention programs.

PMID:33861781 | DOI:10.1371/journal.pone.0250169

PLoS One. 2021 Apr 16;16(4):e0250174. doi: 10.1371/journal.pone.0250174. eCollection 2021.

ABSTRACT

INTRODUCTION: Post cesarean section surgical site infection increases both the duration of a patient’s hospital stay and unplanned hospital costs. It can delays recovery, prolongs hospitalization, necessitates readmission, and adds to hospital bills and other morbidities as well as mortalities.

METHOD: Facility-based case-control study was conducted from 1st March to 20th April, 2019 among all the mother records enrolled from 1st January to 31st December, 2018 at Public hospitals in Dire Dawa administration. The records of the mothers’ who had post-cesarean section surgical site infection (119) was extracted by a census and every three consecutive controls (357) for each case were collected by trained data collectors using a structured data extraction tool. Variables which had p-value <0.25 in bivariate analysis were considered as candidates for multivariable analysis. Statistical significance was declared at P-value ≤0.05 with adjusted odd ratio and 95% confidence interval in the multivariable logistic regression model.

RESULT: Age 20-34 years (AOR:5.4; 95%CI:2.35,12.7), age >35 years (AOR:8.9; 95%CI:1.8,43.9), ≥4 per vaginal examinations (AOR: 4.2; 95%CI:2.16,8.22), current history of Chorioamnionitis (AOR:5; 95%CI:1.05,23.9), previous history of cesarean section (AOR:6.2; 95%CI: 2.72,14.36), provision of antibiotics prophylaxis (AOR:3.2; 95%CI:1.81,5.62), perioperative HCT level <30% (AOR:6.9; 95%CI:3.45,14.1) and duration of rupture of membrane >12 hours (AOR:5.4; 95%CI:1.84,15.87) were the independent determinants of post-cesarean section surgical site infection.

CONCLUSION: Increased in age of the mother, higher number of per vaginal examination, having a history of chorioamnionitis, having previous history of cesarean section, not receiving antibiotics prophylaxis, lower perioperative hematocrit level and longer duration of rupture of membrane were statistically significant in multivariable analysis. Therefore; emphasis should be given for mothers who have higher age category, previous cesarean scar and history of choriamnionitis. In addition; provision of antibiotics should be comprehensive for all mothers undergoing cesarean section.

PMID:33861783 | DOI:10.1371/journal.pone.0250174

PLoS One. 2021 Apr 16;16(4):e0248821. doi: 10.1371/journal.pone.0248821. eCollection 2021.

ABSTRACT

BACKGROUND: COVID-19 is the novel coronavirus responsible for the ongoing global outbreak of acute respiratory disease and viral pneumonia. In order to tackle the devastating condition of the virus, countries need to attack the virus with aggressive and targeted tactics. Thus, to strengthen the COVID-19 mitigation measures and to give rapid response, there is an urgent need to understand the public’s knowledge and attitude about of the pandemic at this critical moment.

OBJECTIVE: This study was aimed to assess the knowledge and attitude of communities about COVID-19 and associated factors among Gondar City residents.

METHODS: A community based cross-sectional study was done among 623 respondents in Gondar city from April 20-27/2020. Data were collected using a structured questionnaire adapted from different literatures. The data were entered using Epi data version 3.1 and then exported into STATA version 14 for analysis. Bi-variable and multivariable binary logistic regression were performed. Adjusted odds ratio with 95% CI was used to declare statistically significant variables on the basis of p value less than 0.05 in the multivariable binary logistic regression model.

RESULTS: The overall knowledge and attitude of the community towards COVID19 was 51.85% [95% CI (47.91%-55.78%)] and 53.13% [95% CI (49.20, 57.06%)], respectively. In this study, being married [AOR = 0.60 at 95% CI: (0.42, 0.86)], educational level; primary [AOR = 3.14 at 95% CI: (1.78,5.54)], secondary [AOR = 2.81 at 95% CI: (1.70,4.63)], college and above [AOR = 4.49 at 95% CI: 7.92, 13.98)], and family size [AOR = 1.80, at 95% CI: (1.05, 3.08)] were emerged as statistically significant factors impacting the knowledge of the community about COVID-19. Besides, educational level; primary [AOR = 1.76 at 95% CI: (1.03, 3.01)], secondary [AOR = 1.69 at 95% CI: (1.07, 2.68)], and college & above [AOR = 2.38 at 95% CI: (1.50, 3.79)], and family size; four to six members [AOR = 1.84 at 95% CI (1.27, 2.67)], above seven members [AOR = 1.79 at 95% CI (1.08, 2.96)] were factors identified as significantly attribute for positive attitude of the communities towards COVID-19.

CONCLUSION: More than half of the respondents had better knowledge and attitude regarding COVID-19. Higher educational level and larger family size were significant factors predominantly affecting the knowledge and attitude of the communities towards COVID-19.

PMID:33861758 | DOI:10.1371/journal.pone.0248821

PLoS One. 2021 Apr 16;16(4):e0249811. doi: 10.1371/journal.pone.0249811. eCollection 2021.

ABSTRACT

In Appalachia, La Crosse virus (LACV) is a leading pediatric arbovirus and public health concern for children under 16 years. LACV is transmitted via the bite of an infected Aedes mosquito. Thus, it is imperative to understand the dynamics of the local vector population in order to assess risk and transmission. Using entomological data collected from Knox County, Tennessee in 2013, we formulate an environmentally-driven system of ordinary differential equations to model mosquito population dynamics over a single season. Further, we include infected compartments to represent LACV transmission within the mosquito population. Findings suggest that the model, with dependence on degree days and accumulated precipitation, can closely describe field data. This model confirms the need to include these environmental variables when planning control strategies.

PMID:33861763 | DOI:10.1371/journal.pone.0249811

PLoS Negl Trop Dis. 2021 Apr 16;15(4):e0008813. doi: 10.1371/journal.pntd.0008813. Online ahead of print.

ABSTRACT

The control of arboviruses carried by Aedes aegypti (Linnaeus) and Aedes albopictus (Skuse) can be performed with tools that monitor and reduce the circulation of these vectors. Therefore, the efficiency of four types of traps in capturing A. aegypti and A. albopictus eggs and adults, with the biological product Vectobac WG, was evaluated in the field. For this, 20 traps were installed in two locations, which were in the South (Londrina, Paraná) and North (Manaus, Amazonas) Regions of Brazil, from March to April 2017 and January to February 2018, respectively. The UELtrap-E (standard trap) and UELtrap-EA traps captured A. aegypti and A. albopictus eggs: 1703/1866 eggs in Londrina, and 10268/2149 eggs in Manaus, respectively, and presented high ovitraps positivity index (OPI) values (averages: 100%/100% in Londrina, and 100%/96% in Manaus, respectively); and high egg density index (EDI) values (averages: 68/75 in Londrina, and 411/89 in Manaus, respectively), so they had statistically superior efficiency to that of the CRtrap-E and CRtrap-EA traps in both regions, that captured less eggs and adults: 96/69 eggs in Londrina, and 1091/510 eggs in Manaus, respectively. Also presented lower OPI values (averages: 28%/4% in Londrina, and 88%/60% in Manaus, respectively); and lower EDI values (averages: 10.5/9 in Londrina, and 47/30 in Manaus, respectively). The capture ratios of Aedes adults in the UELtrap-EA and CRtrap-EA traps in Londrina and Manaus were 53.3%/29.5% and 0%/9.8%, respectively. UELtrap-EA can be adopted as efficient tool for Aedes monitoring due to their high sensitivity, low cost and ease of use.

PMID:33861744 | DOI:10.1371/journal.pntd.0008813

PLoS Comput Biol. 2021 Apr 16;17(4):e1008580. doi: 10.1371/journal.pcbi.1008580. Online ahead of print.

ABSTRACT

An important question in neuroscience is whether or not we can interpret spontaneous variations in the pattern of correlation between brain areas, which we refer to as functional connectivity or FC, as an index of dynamic neuronal communication in fMRI. That is, can we measure time-varying FC reliably? And, if so, can FC reflect information transfer between brain regions at relatively fast-time scales? Answering these questions in practice requires dealing with the statistical challenge of having high-dimensional data and a comparatively lower number of time points or volumes. A common strategy is to use PCA to reduce the dimensionality of the data, and then apply some model, such as the hidden Markov model (HMM) or a mixture model of Gaussian distributions, to find a set of distinct FC patterns or states. The distinct spatial properties of these FC states together with the time-resolved switching between them offer a flexible description of time-varying FC. In this work, I show that in this context PCA can suffer from systematic biases and loss of sensitivity for the purposes of finding time-varying FC. To get around these issues, I propose a novel variety of the HMM, named HMM-PCA, where the states are themselves PCA decompositions. Since PCA is based on the data covariance, the state-specific PCA decompositions reflect distinct patterns of FC. I show, theoretically and empirically, that fusing dimensionality reduction and time-varying FC estimation in one single step can avoid these problems and outperform alternative approaches, facilitating the quantification of transient communication in the brain.

PMID:33861733 | DOI:10.1371/journal.pcbi.1008580

PLoS Negl Trop Dis. 2021 Apr 16;15(4):e0009298. doi: 10.1371/journal.pntd.0009298. Online ahead of print.

ABSTRACT

BACKGROUND: Snakebite envenoming is a medical emergency which is common in many tropical lower- and middle-income countries. Traditional healers are frequently consulted as primary care-givers for snakebite victims in distress. Traditional healers therefore present a valuable source of information about how snakebite is perceived and handled at the community level, an understanding of which is critical to improve and extend snakebite-related healthcare.

METHOD: The study was approached from the interpretive paradigm with phenomenology as a methodology. Semi-structured interviews were conducted with 19 traditional healers who treat snakebite patients in two rural settings in Ghana. From the Ashanti and Upper West regions respectively, 11 and 8 healers were purposively sampled. Interview data was coded, collated and analysed thematically using ATLAS.ti 8 software. Demographic statistics were analysed using IBM SPSS Statistics version 26.

FINDINGS: Snakebite was reportedly a frequent occurrence, perceived as dangerous and often deadly by healers. Healers felt optimistic in establishing a diagnosis of snakebite using a multitude of methods, ranging from herbal applications to spiritual consultations. They were equally confident about their therapies; encompassing the administration of plant and animal-based concoctions and manipulations of bite wounds. Traditional healers were consulted for both physical and spiritual manifestations of snakebite or after insufficient pain control and lack of antivenom at hospitals; referrals by healers to hospitals were primarily done to receive antivenom and care for wound complications. Most healers welcomed opportunities to engage more productively with hospitals and clinical staff.

CONCLUSIONS: The fact that traditional healers did sometimes refer victims to hospitals indicates that improvement of antivenom stocks, pain management and wound care can potentially improve health seeking at hospitals. Our results emphasize the need to explore future avenues for communication and collaboration with traditional healers to improve health seeking behaviour and the delivery of much-needed healthcare to snakebite victims.

PMID:33861735 | DOI:10.1371/journal.pntd.0009298

PLoS One. 2021 Apr 16;16(4):e0246118. doi: 10.1371/journal.pone.0246118. eCollection 2021.

ABSTRACT

BACKGROUND: Cytomegalovirus (CMV) infection is amongst the most important factors complicating solid organ transplantation. In a large prospective randomized clinical trial, valganciclovir prophylaxis reduced the occurrence of CMV infection and disease compared with preemptive therapy in CMV-positive renal allograft recipients (VIPP study; NCT00372229). Here, we present a subanalysis of the VIPP study, investigating single nucleotide polymorphisms (SNPs) in immune-response-related genes and their association with active CMV infection, CMV disease, graft loss or death, rejection, infections, and leukopenia.

METHODS: Based on literature research ten SNPs were analyzed for TLR4, three for IFN-γ, six for IL10, nine for IL37, and two for TNF-α. An asymptotic independence test (Cochran-Armitage trend test) was used to examine associations between SNPs and the occurrence of CMV infection or other negative outcomes. Statistical significance was defined as p<0.05 and Bonferroni correction for multiple testing was performed.

RESULTS: SNPs were analyzed on 116 blood samples. No associations were found between the analyzed SNPs and the occurrence of CMV infection, rejection and leukopenia in all patients. For IL37 rs2723186, an association with CMV disease (p = 0.0499), for IL10 rs1800872, with graft loss or death (p = 0.0207) and for IL10 rs3024496, with infections (p = 0.0258) was observed in all patients, however did not hold true after correction for multiple testing.

CONCLUSION: The study did not reveal significant associations between the analyzed SNPs and the occurrence of negative outcomes in CMV-positive renal transplant recipients after correction for multiple testing. The results of this association analysis may be of use in guiding future research efforts.

PMID:33861738 | DOI:10.1371/journal.pone.0246118