Tag: statistics

PLoS One. 2022 Feb 25;17(2):e0264455. doi: 10.1371/journal.pone.0264455. eCollection 2022.

ABSTRACT

The pandemic of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) took the world by surprise. Following the first outbreak of COVID-19 in December 2019, several models have been developed to study and understand its transmission dynamics. Although the spread of COVID-19 is being slowed down by vaccination and other interventions, there is still a need to have a clear understanding of the evolution of the pandemic across countries, states and communities. To this end, there is a need to have a clearer picture of the initial spread of the disease in different regions. In this project, we used a simple SEIR model and a Bayesian inference framework to estimate the basic reproduction number of COVID-19 across Africa. Our estimates vary between 1.98 (Sudan) and 9.66 (Mauritius), with a median of 3.67 (90% CrI: 3.31-4.12). The estimates provided in this paper will help to inform COVID-19 modeling in the respective countries/regions.

PMID:35213645 | DOI:10.1371/journal.pone.0264455

PLoS One. 2022 Feb 25;17(2):e0264504. doi: 10.1371/journal.pone.0264504. eCollection 2022.

ABSTRACT

BACKGROUND: The predictive role of hematological indexes of mean platelet volume (MPV) and red cell distribution width (RDW) has been demonstrated in cardiovascular disease concomitant with psoriasis. This meta-analysis is intended to assess whether MPV and RDW can also serve as biomarkers for the early diagnosis and disease severity assessment of psoriasis.

MATERIAL AND METHODS: 13 studies which enrolled 1331 psoriasis patients and 919 healthy volunteers were included after screening the search results from PubMed, Embase and the Cochrane Library since inception to Mar 14, 2020. MPV of psoriasis participants and their counterparts was assessed in 10 studies, and RDW was evaluated in 4 studies, while the disease severity was measured by the Psoriasis Area and Severity Index (PASI) in 11 studies. Random-effect model analysis was applied to calculate pooled standard mean difference (SMD) with 95% confidence interval (95% CI).

RESULTS: Associations of MPV and RDW with the presence of psoriasis were demonstrated (MPV: SMD = 0.503, 95% CI: 0.242-0.765; RDW: SMD = 0.522, 95% CI: 0.228-0.817), but no statistically significant correlation of MPV and disease severity of psoriasis was found in meta-regression analysis (p = 0.208). Subgroup analysis revealed that the diagnosis value of MPV and RDW was consistent regardless of PASI and study type. Heterogeneity analysis between studies was implemented by chi-squared test and I2 statistics. Begg’s and Egger’s test were utilized for the evaluation of publication bias. The sensitivity analysis revealed no significant alteration no matter which study was excluded.

CONCLUSION: MPV and RDW could serve as promising predictive diagnostic biomarkers of psoriasis.

PMID:35213665 | DOI:10.1371/journal.pone.0264504

PLoS One. 2022 Feb 25;17(2):e0264410. doi: 10.1371/journal.pone.0264410. eCollection 2022.

ABSTRACT

The economic, environmental and social sustainability of Dutch dairy farms have attracted increasing societal concern in the past decades. In this paper, we propose a recently developed dynamic Luenberger indicator based on the by-production model to measure dynamic productivity growth in the economic, environmental and social dimensions of sustainability of Dutch dairy farms. Subsequently, we investigate the statistical associations between productivity growth and socio-economic factors using the OLS bootstrap regression model. We find that dairy farms have suffered a decline in dynamic sustainable productivity growth, especially in the environmental dimension where it is more pronounced than in the economic and social dimensions. Furthermore, we find that both technical and scale inefficiency change contribute to the decline of environmental productivity growth. Specialization and government support are associated with a higher economic and environmental sustainability productivity growth, and with, a decreased growth of social sustainable productivity. We found no significant association between the age of the oldest entrepreneur, financial structure, farm size or cost of advisory service and dynamic productivity growth in the three sustainability dimensions. The results provide insights into potential pathways towards improving the three pillars of sustainability.

PMID:35213644 | DOI:10.1371/journal.pone.0264410

PLoS One. 2022 Feb 25;17(2):e0264538. doi: 10.1371/journal.pone.0264538. eCollection 2022.

ABSTRACT

BACKGROUND AND OBJECTIVE: Most Asian patients with atrial fibrillation (AF) who undergo percutaneous coronary intervention (PCI) receive only dual antiplatelet therapy (DAPT) without oral anticoagulants (vitamin K antagonists [VKA] or non-VKA oral anticoagulants [NOAC]). However, it has not been fully investigated whether the DAPT results in better clinical outcomes in the early period after PCI than the standard triple therapy with VKA or NOAC.

METHODS: We analyzed the claims records of 11,039 Korean AF population who had PCI between 2013 and 2018. Patients were categorized according to the post-PCI antithrombotic therapy as VKA-based triple therapy (VKA-TT), NOAC-based triple therapy (NOAC-TT), and DAPT groups. After baseline adjustment using inverse probability weighting, we compared the risks of ischemic endpoints (ischemic stroke, myocardial infarction, and all-cause mortality) and major bleeding at 3 months post-PCI.

RESULTS: Ischemic stroke, MI, and all-cause mortality occurred in 105, 423, and 379 patients, respectively, and 138 patients experienced major bleeding. The DAPT group was associated with a lower risk of ischemic stroke and major bleeding (hazard ratio [HR] 0.55, 95% confidence interval [CI] 0.37-0.84) compared to the VKA-TT group, despite no significant differences in the risks of MI and all-cause mortality. In contrast, the DAPT group demonstrated no significant difference in the risks for ischemic endpoints compared to the NOAC-TT group. Additionally, the DAPT group had a numerically lower risk of major bleeding than the NOAC-TT group but this was not statistically significant (HR 0.69, 95% CI 0.45-1.07).

CONCLUSIONS: An outcome benefit of DAPT was observed in the early period after PCI compared to the VKA-TT, but not against NOAC-TT users among the Asian AF population. Given the potential long-term benefits of NOACs, greater efforts should be made to increase compliance in clinical practice with proper combination therapy with NOAC after PCI.

PMID:35213632 | DOI:10.1371/journal.pone.0264538

PLoS One. 2022 Feb 25;17(2):e0264269. doi: 10.1371/journal.pone.0264269. eCollection 2022.

ABSTRACT

The sucrose synthase (SS) is an important enzyme family which play a vital role in sugar metabolism to improve the fruit quality of the plants. In many plant species, the members of SS family have been investigated but the detailed information is not available in legumes particularly and Glycine max specifically. In the present study, we found thirteen SS members (GmSS1-GmSS13) in G. max genome. High conserved regions were present in the GmSS sequences that may due to the selection pressure during evolutionary events. The segmental duplication was the major factor to increase the number of GmSS family members. The identified thirteen GmSS genes were divided into Class I, Class II and Class III with variable numbers of genes in each class. The protein interaction of GmSS gave the co-expression of sucrose synthase with glucose-1-phosphate adenylyltransferase while SLAC and REL test found number of positive sites in the coding sequences of SS family members. All the GmSS family members except GmSS7 and few of class III members, were highly expressed in all the soybean tissues. The expression of the class I members decreased during seed development, whireas, the class II members expression increased during the seed developing, may involve in sugar metabolism during seed development. Solexa sequencing libraries of acidic condition (pH 4.2) stress samples showed that the expression of class I GmSS genes increased 1- to 2-folds in treated samples than control. The differential expression pattern was observed between the members of a paralogous. This study provides detailed genome-wide analysis of GmSS family in soybean that will provide new insights for future evolutionary and soybean breeding to improve the plant growth and development.

PMID:35213642 | DOI:10.1371/journal.pone.0264269

PLoS One. 2022 Feb 25;17(2):e0264283. doi: 10.1371/journal.pone.0264283. eCollection 2022.

ABSTRACT

The CUSUM control chart is suitable for detecting small to moderate parameter shifts for processes involving autocorrelated data. The average run length (ARL) can be used to assess the ability of a CUSUM control chart to detect changes in a long-memory seasonal autoregressive fractionally integrated moving average with exogenous variable (SARFIMAX) process with underlying exponential white noise. Herein, new ARLs via an analytical integral equation (IE) solution as an analytical IE and a numerical IE method to test a CUSUM control chart’s ability to detect a wide range of shifts in the mean of a SARFIMAX(P, D, Q, r)s process with underlying exponential white noise are presented. The analytical IE formulas were derived by using the Fredholm integral equation of the second type while the numerical IE method for the approximate ARL is based on quadrature rules. After applying Banach’s fixed-point theorem to guarantee its existence and uniqueness, the precision of the proposed analytical IE ARL was the same as the numerical IE method. The sensitivity and accuracy of the ARLs based on both methods were assessed on a CUSUM control chart running a SARFIMAX(P, D, Q, r)s process with underlying exponential white noise. The results of an extensive numerical study comprising the examination of a wide variety of out-of-control situations and computational schemes reveal that none of the methods outperformed the IE. Specifically, the computational scheme is easier and can be completed in one step. Hence, it is recommended for use in this situation. An illustrative example based on real data is also provided, the results of which were found to be in accordance with the research results.

PMID:35213619 | DOI:10.1371/journal.pone.0264283

PLoS One. 2022 Feb 25;17(2):e0264393. doi: 10.1371/journal.pone.0264393. eCollection 2022.

ABSTRACT

Chronic kidney disease (CKD) is a major public health problem in low- and middle-income countries (LMICs). Although CKD prevalence has been rapidly increasing in LMICs, particularly in Asia, quantitative studies on the current epidemiology of CKD in this region are limited. This study aimed to identify the prevalence of CKD stages 3-5 in LMICs in Asia, by subregion, country economy classification, identification of CKD, traditional and non-traditional risk factors. A systematic review and meta-analysis of observational studies was conducted through a literature search of seven electronic databases and grey literature search published until November 2021. The Newcastle-Ottawa quality assessment scale (NOS) was used to assess the risk of bias of each study. A random-effects model was used to estimate pooled prevalence. The protocol is registered in the International Prospective Register of Systematic Reviews (PROSPERO CRD42019120519). Of 4,548 potentially relevant records, 110 studies with moderate and high quality were included with 4,760,147 subjects. The average prevalence (95% CI) of CKD stages 3-5 in 14 LMICs in Asia was 11.2% (9.3-13.2%). The prevalence of CKD stages 3-5 was varied among subregions and country economic classification. CKD prevalence was 8.6% (7.2-10.2%) in east Asia, 12.0% (7.7-17.0%) in south-east Asia, 13.1% (8.7-18.2%) in western Asia, and 13.5% (9.5-18.0%) in south Asia. CKD prevalence was 9.8% (8.3-11.5%) in upper-middle-income countries and 13.8% (9.9-18.3%) in lower-middle-income countries. Prevalence of CKD stage 3-5 in LMICs in Asia is comparable to global prevalence. High level of heterogeneity was observed. Study of factors and interventions that lead to the delay of CKD progression is needed.

PMID:35213610 | DOI:10.1371/journal.pone.0264393

PLoS One. 2022 Feb 25;17(2):e0264343. doi: 10.1371/journal.pone.0264343. eCollection 2022.

ABSTRACT

OBJECTIVE: After stratifying for age, sex and multimorbidity at baseline, our aim is to analyse time trends in incident multimorbidity and polypharmacy in the 15-year clinical trajectories of individual patients in a family medicine setting.

METHODS: This study was carried out using data from the Registration Network Family Medicine in the South of the Netherlands. The clinical trajectories of 10037 subjects during the 15-year period (2000-2014) were analyzed in a repeated measurement of using a generalized estimating equations model as well as a multilevel random intercept model with repeated measurements to determine patterns of incident multimorbidity and polypharmacy. Hierarchical age-period-cohort models were used to generate age and cohort trajectories for comparison with prevalence trends in multimorbidity literature.

RESULTS: Multimorbidity was more common in females than in males throughout the duration of the 15-year trajectory (females: 39.6%; males: 33.5%). With respective ratios of 11.7 and 5.9 between the end and the beginning of the 15-year period, the youngest female and male groups showed a substantial increase in multimorbidity prevalence. Ratios in the oldest female and male groups were 2.2 and 1.9 respectively. Females had higher levels of multimorbidity than males in the 0-24-year and 25-44-year age groups, but the levels converged to a prevalence of 92.2% in the oldest male and 90.7% in the oldest female group. Similar, albeit, moderate differences were found in polypharmacy patterns.

CONCLUSIONS: We sought to specify the progression of multimorbidity from an early age. As a result, our study adds to the multimorbidity literature by specifying changes in chronic disease accumulation with relation to polypharmacy, and by tracking differences in patient trajectories according to age and sex. Multimorbidity and polypharmacy are common and their prevalence is accelerating, with a relatively rapid increase in younger groups. From the point of view of family medicine, this underlines the need for a longitudinal approach and a life course perspective in patient care.

PMID:35213615 | DOI:10.1371/journal.pone.0264343

PLoS One. 2022 Feb 25;17(2):e0264131. doi: 10.1371/journal.pone.0264131. eCollection 2022.

ABSTRACT

The integrity of peer review is essential for modern science. Numerous studies have therefore focused on identifying, quantifying, and mitigating biases in peer review. One of these better-known biases is prestige bias, where the recognition of a famous author or affiliation leads reviewers to subconsciously treat their submissions preferentially. A common mitigation approach for prestige bias is double-blind reviewing, where the identify of authors is hidden from reviewers. However, studies on the effectivness of this mitigation are mixed and are rarely directly comparable to each other, leading to difficulty in generalization of their results. In this paper, we explore the design space for such studies in an attempt to reach common ground. Using an observational approach with a large dataset of peer-reviewed papers in computer systems, we systematically evaluate the effects of different prestige metrics, aggregation methods, control variables, and outlier treatments. We show that depending on these choices, the data can lead to contradictory conclusions with high statistical significance. For example, authors with higher h-index often preferred to publish in competitive conferences which are also typically double-blind, whereas authors with higher paper counts often preferred the single-blind conferences. The main practical implication of our analyses is that a narrow evaluation may lead to unreliable results. A thorough evaluation of prestige bias requires a careful inventory of assumptions, metrics, and methodology, often requiring a more detailed sensitivity analysis than is normally undertaken. Importantly, two of the most commonly used metrics for prestige evaluation, past publication count and h-index, are not independent from the choice of publishing venue, which must be accounted for when comparing authors prestige across conferences.

PMID:35213600 | DOI:10.1371/journal.pone.0264131

PLoS One. 2022 Feb 25;17(2):e0264004. doi: 10.1371/journal.pone.0264004. eCollection 2022.

ABSTRACT

BACKGROUND: Childhood immunization is one of the most cost-effective prevention measures for children’s mortality and morbidity, saving 2-3 million lives per year. In Ethiopia, under-five mortality rates, about 190,000 children die each year. Different research conducted in Ethiopia on childhood vaccination have focused on either vaccination coverage of individual vaccine or complete and incomplete vaccination. As far as my literature searching, studies separated the vaccination status into non-vaccinated, partially vaccinated and full vaccinated and assorted factors among children age 12-23 month in Ethiopia were limited. Therefore, the aim of this study was to identify factors associated with vaccination status among children 12-23 months of age in Ethiopia.

METHOD: A secondary data analysis was done based on the 2016 Ethiopian Demographic and Health Survey (EDHS). A total weighted sample of 1911 children age 12-23 months of age were included in the study. Logit based Multinomial logistic regression analysis was computed to distinguish factors associated with routine vaccination of children aged 12-23 months. P-value less than 0.05 was used to declare statistical significance of each independent variables, and adjusted odd ratio (AOR) with 95% confidence interval were used to present the result and STATA 14 was utilized for data management and analysis.

RESULT: Overall the prevalence of full vaccinated children was 35%, while 49% of children were partially vaccinated and 16% were non-vaccinated. In multinomial analysis, having focused ANC (at least four visits) contrasted to no ANC visits at all had 9.7 higher odd of being fully vaccinated than not vaccinated [AOR = 9.74, 95% CI = 3.52-26.94], and 5 times higher odd of being partially vaccinated than not vaccinated [AOR = 4.97, 95% CI = 2.00-12.33].

CONCLUSION: The present study found that childhood full vaccination status was low compared with the World Health Organization targets. Frequency of ANC visit and visited by field worker were significantly associated both partially and full vaccination whereas, visited health facility last 12 months and wealth status were significantly associated with childhood full vaccination.

PMID:35213589 | DOI:10.1371/journal.pone.0264004