Nevin Manimala

Bioinformatics. 2021 Jul 16:btab531. doi: 10.1093/bioinformatics/btab531. Online ahead of print.

ABSTRACT

MOTIVATION: The rise in the number of genotyped ancient individuals provides an opportunity to estimate population admixture models for many populations. However, in models describing modern populations as mixtures of ancient ones, it is typically difficult to estimate the model mixing coefficients and to evaluate its fit to the data.

RESULTS: We present LINADMIX, designed to tackle this problem by solving a constrained linear model when both the ancient and the modern genotypes are represented in a low-dimensional space. LINADMIX estimates the mixing coefficients and their standard errors, and computes a p-value for testing the model fit to the data. We quantified the performance of LINADMIX using an extensive set of simulated studies. We show that LINADMIX can accurately estimate admixture coefficients, and is robust to factors such as population size, genetic drift, proportion of missing data, and various types of model misspecification.

AVAILABILITY: LINADMIX is available as a python code at https://github.com/swidler/linadmix.

SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

PMID:34270685 | DOI:10.1093/bioinformatics/btab531

PLoS One. 2021 Jul 16;16(7):e0254475. doi: 10.1371/journal.pone.0254475. eCollection 2021.

ABSTRACT

BACKGROUND: The coverage of long lasting insecticidal nets (LLIN) and intermittent preventive treatment of malaria in pregnancy (IPTp) uptake for the prevention of malaria commonly vary by geography. Many sub-Saharan Africa (SSA) countries, including Nigeria are adopting the use of LLIN and IPTp to fight malaria. Albeit, the coverage of these interventions to prevent malaria across geographical divisions have been understudied in many countries. In this study, we aimed to explore the differentials in LLIN and IPTp uptake across Nigerian geopolitical zones.

METHODS: We analyzed data from Nigeria Multiple Indicator Cluster Survey (MICS) 2016-17. The outcome variables were IPTp and LLIN uptake among women of childbearing age (15-49 years). A total sample of 24,344 women who had given birth were examined for IPTp use and 36,176 women for LLIN use. Percentages, Chi-square test and multivariable logit models plots were used to examine the geopolitical zones differentials in IPTp and LLIN utilization. Data was analyzed at 5% level of significance.

RESULTS: The overall prevalence of IPTp was 76.0% in Nigeria. Moreover, there were differences across geopolitical zones: North Central (71.3%), North East (76.9%), North West (78.2%), South East (76.1%), South South (79.7%) and South West (72.4%) respectively. Furthermore, the prevalence of LLIN was 87.7%% in Nigeria. Also, there were differences across geopolitical zones: North Central (89.1%), North East (91.8%), North West (90.0%), South East (77.3%), South South (81.1%) and South West (69.8%) respectively. Women who have access to media use, married, educated and non-poor were more likely to uptake IPTp. On the other hand, rural dwellers and those with media use were more likely to use LLIN. Conversely, married, educated, non-poor and women aged 25-34 and 35+ were less likely to use LLIN.

CONCLUSION: Though the utilization of IPTp and LLIN was relatively high, full coverage are yet to be achieved. There was geopolitical zones differentials in the prevalence of IPTp and LLIN in Nigeria. Promoting the utilization of IPTp and LLINs across the six geopolitical zones through intensive health education and widespread mass media campaigns will help to achieve the full scale IPTp and LLIN utilization.

PMID:34270607 | DOI:10.1371/journal.pone.0254475

PLoS One. 2021 Jul 16;16(7):e0254832. doi: 10.1371/journal.pone.0254832. eCollection 2021.

ABSTRACT

PURPOSE: To assess the agreement and repeatability of horizontal visible iris diameter (HVID) or white-to-white (WTW) measurements between four imaging modalities; combination slit scanning elevation/Placido tomography, infrared biometry, dual rotating scheimpflug camera/Placido tomography, and swept source anterior segment optical coherence tomography (AS-OCT).

METHODS: A prospective study of 35 right eyes of healthy volunteers were evaluated using the Orbscan IIz, IOL Master 700, Galilei G2, and DRI Triton OCT devices. The inter-device agreement and repeatability of HVID/WTW measurements for each device were analysed.

RESULTS: Mean HVID/WTW values obtained by the Orbscan IIz, IOL Master 700, Galilei G2 and DRI Triton OCT were 11.77 ± 0.40 mm, 12.40 ± 0.43 mm, 12.25 ± 0.42 mm, and 12.42 ± 0.47 mm, respectively. All pairwise comparisons revealed statistically significant differences in mean HVID/WTW measurements (p = <0.01) except for the IOL Master 700-DRI OCT Triton pair (p = 0.56). Mean differences showed that the DRI Triton OCT produced the highest HVID/WTW values, followed by the IOL Master 700, Galilei G2 and Orbscan IIz, respectively. The limits of agreement were large on all device pairs. There was high repeatability for all devices (ICC ≥ 0.980). The highest repeatability was seen in the Galilei G2 (ICC = 0.995) and lowest in the Orbscan IIz (ICC = 0.980).

CONCLUSIONS: The four devices exhibit high repeatability, but should not be used interchangeably for HVID/WTW measurements in clinical practice.

PMID:34270605 | DOI:10.1371/journal.pone.0254832

PLoS One. 2021 Jul 16;16(7):e0254579. doi: 10.1371/journal.pone.0254579. eCollection 2021.

ABSTRACT

BACKGROUND: Although Diabetes Self-Management Education (DSME) programs are recommended to help reduce the burden of diabetes and diabetes-related complications, Florida is one of the states with the lowest DSME participation rates. Moreover, there is evidence of geographic disparities of not only DSME participation rates but the burden of diabetes as well. Understanding these disparities is critical for guiding control programs geared at improving participation rates and diabetes outcomes. Therefore, the objectives of this study were to: (a) investigate geographic disparities of diabetes prevalence and DSME participation rates; and (b) identify predictors of the observed disparities in DSME participation rates.

METHODS: Behavioral Risk Factor Surveillance System (BRFSS) data for 2007 and 2010 were obtained from the Florida Department of Health. Age-adjusted diabetes prevalence and DSME participation rates were computed at the county level and their geographic distributions visualized using choropleth maps. Significant changes in diabetes prevalence and DSME participation rates between 2007 and 2010 were assessed and counties showing significant changes were mapped. Clusters of high diabetes prevalence before and after adjusting for common risk factors and DSME participation rates were identified, using Tango’s flexible spatial scan statistics, and their geographic distribution displayed in maps. Determinants of the geographic distribution of DSME participation rates and predictors of the identified high rate clusters were identified using ordinary least squares and logistic regression models, respectively.

RESULTS: County level age-adjusted diabetes prevalence varied from 4.7% to 17.8% while DSME participation rates varied from 26.6% to 81.2%. There were significant (p≤0.05) increases in both overall age-adjusted diabetes prevalence and DSME participation rates from 2007 to 2010 with diabetes prevalence increasing from 7.7% in 2007 to 8.6% in 2010 while DSME participation rates increased from 51.4% in 2007 to 55.1% in 2010. Generally, DSME participation rates decreased in rural areas while they increased in urban areas. High prevalence clusters of diabetes (both adjusted and unadjusted) were identified in northern and central Florida, while clusters of high DSME participation rates were identified in central Florida. Rural counties and those with high proportion of Hispanics tended to have low DSME participation rates.

CONCLUSIONS: The findings confirm that geographic disparities in both diabetes prevalence and DSME participation rates exist. Specific attention is required to address these disparities especially in areas that have high diabetes prevalence but low DSME participation rates. Study findings are useful for guiding resource allocation geared at reducing disparities and improving diabetes outcomes.

PMID:34270601 | DOI:10.1371/journal.pone.0254579

PLoS One. 2021 Jul 16;16(7):e0254369. doi: 10.1371/journal.pone.0254369. eCollection 2021.

ABSTRACT

BACKGROUND: Dengue has emerged as a major public health problem in Bhutan, with increasing incidence and widening geographic spread over recent years. This study aimed to investigate the knowledge and clinical management of dengue among medical practitioners in Bhutan.

METHODS: We administered a survey questionnaire to all practitioners currently registered under the Bhutan Medical and Health Council. The questionnaire contained items on four domains including transmission, clinical course and presentation, diagnosis and management, and surveillance and prevention of dengue. Participants were able to respond using an online Qualtrics survey, with the invitation and link distributed via email.

RESULTS: A total of 97 respondents were included in the study (response rate: 12.7%), of which 61.86% were Health Assistants/Clinical Officers (HAs/COs) and 38.14% were medical doctors. The afternoon feeding behaviour of Aedes mosquito was correctly identified by only 24.7% of the respondents, and ~66.0% of them failed to identify lethargy as a warning sign for severe dengue. Knowledge on diagnosis using NS1 antigen and the clinical significance of elevated haematocrit for initial fluid replacement was strikingly low at 47.4% and 27.8% respectively. Despite dengue being a nationally notifiable disease, ~60% of respondents were not knowledgeable on the timing and type of cases to be reported. Respondent’s median score was higher for the surveillance and reporting domain, followed by their knowledge on transmission of dengue. Statistically significant factors associated with higher knowledge included respondents being a medical doctor, working in a hospital and experience of having diagnosed dengue.

CONCLUSION: The study revealed major gaps on knowledge and clinical management practices related to dengue in Bhutan. Physicians and health workers working in Basic Health Units need training and regular supervision to improve their knowledge on the care of dengue patients.

PMID:34270594 | DOI:10.1371/journal.pone.0254369

PLoS Med. 2021 Jul 16;18(7):e1003704. doi: 10.1371/journal.pmed.1003704. eCollection 2021 Jul.

ABSTRACT

BACKGROUND: One in 10 people in the United Kingdom will need a total knee replacement (TKR) during their lifetime. Access to this life-changing operation has recently been restricted based on body mass index (BMI) due to belief that high BMI may lead to poorer outcomes. We investigated the associations between BMI and revision surgery, mortality, and pain/function using what we believe to be the world’s largest joint replacement registry.

METHODS AND FINDINGS: We analysed 493,710 TKRs in the National Joint Registry (NJR) for England, Wales, Northern Ireland, and the Isle of Man from 2005 to 2016 to investigate 90-day mortality and 10-year cumulative revision. Hospital Episodes Statistics (HES) and Patient Reported Outcome Measures (PROMs) databases were linked to the NJR to investigate change in Oxford Knee Score (OKS) 6 months postoperatively. After adjustment for age, sex, American Society of Anaesthesiologists (ASA) grade, indication for operation, year of primary TKR, and fixation type, patients with high BMI were more likely to undergo revision surgery within 10 years compared to those with “normal” BMI (obese class II hazard ratio (HR) 1.21, 95% CI: 1.10, 1.32 (p < 0.001) and obese class III HR 1.13, 95% CI: 1.02, 1.26 (p = 0.026)). All BMI classes had revision estimates within the recognised 10-year benchmark of 5%. Overweight and obese class I patients had lower mortality than patients with “normal” BMI (HR 0.76, 95% CI: 0.65, 0.90 (p = 0.001) and HR 0.69, 95% CI: 0.58, 0.82 (p < 0.001)). All BMI categories saw absolute increases in OKS after 6 months (range 18-20 points). The relative improvement in OKS was lower in overweight and obese patients than those with “normal” BMI, but the difference was below the minimal detectable change (MDC; 4 points). The main limitations were missing BMI particularly in the early years of data collection and a potential selection bias effect of surgeons selecting the fitter patients with raised BMI for surgery.

CONCLUSIONS: Given revision estimates in all BMI groups below the recognised threshold, no evidence of increased mortality, and difference in change in OKS below the MDC, this large national registry shows no evidence of poorer outcomes in patients with high BMI. This study does not support rationing of TKR based on increased BMI.

PMID:34270557 | DOI:10.1371/journal.pmed.1003704

PLoS One. 2021 Jul 16;16(7):e0254443. doi: 10.1371/journal.pone.0254443. eCollection 2021.

ABSTRACT

INTRODUCTION: Regulations of the sale of tobacco products to minors have been effective at reducing adolescent tobacco use overall. However, these efforts may not be uniformly enforced in all areas, creating uneven protection against adolescent smoking. Knowledge regarding factors associated with tobacco retail outlet (TRO) violations could help inform better enforcement strategies.

METHODS: In this study, we used Bayesian index regression models to determine if tobacco sales to minors violations across Virginia (2012-2021) were related to store characteristics and neighborhood deprivation and identify geographic areas at significantly elevated risk for violations after adjusting for these factors.

RESULTS: Results show that there were multiple factors associated with a higher likelihood of tobacco sales violations. Store type was an important factor, as grocery stores and pharmacies had significantly lowered likelihood of violations compared with convenience stores. Being located near another TRO was significantly associated with increased risk of sales to a minor. Neighborhood deprivation was also positively associated with TRO sales violations. Further, there were statistically higher likelihood of sales violations occurring in specific areas (e.g., southwest and southeast) of the state that were not explained by neighborhood deprivation and store attributes.

CONCLUSIONS: Together, results highlight the need to better understand where and why TRO sales violations are occurring in order to improve efforts aimed at monitoring and remediating TRO sales violations.

PMID:34270555 | DOI:10.1371/journal.pone.0254443

Gac Med Mex. 2021;157(2):127-132. doi: 10.24875/GMM.M21000537.

ABSTRACT

BACKGROUND: The literature refers that falls are of multifactorial origin, and some authors have proposed to classify risk factors as intrinsic and extrinsic.

OBJECTIVE: To estimate the risk of falls and their association with some intrinsic and extrinsic factors in older adults who receive medical care at the Mexican Institute of Social Security.

METHODS: Case-control study that included individuals of both genders aged ≥ 60 years. Cases were patients who were admitted to the emergency department of a secondary care hospital diagnosed with injury or fracture secondary to a fall; the controls were patients who attended family medicine units. Descriptive, bivariate and multivariate statistical analysis was carried out. The SPSS program, version 22.0, was used.

RESULTS: Three-hundred and forty-two patients were included (171 cases and 171 controls). Mean age was 76.1 ± 8.8 years, 66 % were women and 97.1 % had self-reported chronic diseases. Differences were observed in body mass index, in the proportion of cases with cognitive impairment, use of walking devices and dependence to perform basic and instrumental activities of daily living. Adjusted multivariate analysis revealed an association between the fall event and cognitive impairment and dependence to perform instrumental activities of daily living.

CONCLUSIONS: Cognitive impairment and dependence to perform instrumental activities of daily living were associated with the risk of falling.

PMID:34270533 | DOI:10.24875/GMM.M21000537

Gac Med Mex. 2021;157(2):167-173. doi: 10.24875/GMM.M21000541.

ABSTRACT

INTRODUCTION: Promoting breast cancer (BC) detection in women by means of mammography is a viable strategy to reduce the number of diagnoses at clinically advanced stages and mortality.

OBJECTIVES: To describe the results reported by mammography studies in women, carried out nationally during 2013-2017, and to analyze the spatiotemporal trend of Breast Imaging Reporting and Data System (BIRADS) categories suggestive of malignancy by State.

METHOD: Longitudinal, analytical design that included information on mammography studies of women according to age group (< 40 and ≥ 40), evaluated in units of the Ministry of Health of Mexico during 2013-2017. The frequency of BIRADS categories and a standardized rate suggestive of malignancy (categories 4 and 5) were estimated in women aged ≥ 40 years, and spatial statistics were used to analyze the trend by State.

RESULTS: A total of 3,659,151 mammograms were analyzed, 98.5 % in women aged ≥ 40 years. The malignancy-suggestive rate decreased from 38.3 (2013) to 31 (2017) per 100,000 women aged ≥ 40 years; however, the risk of detection increased up to 13 times in ten States.

CONCLUSIONS: Although the risk of detection in categories suggestive of malignancy decreased at the national level, some States need to reinforce the application of BC detection programs through mammography and increase the participation of the target population.

PMID:34270528 | DOI:10.24875/GMM.M21000541

J Comput Assist Tomogr. 2021 Jul 13. doi: 10.1097/RCT.0000000000001189. Online ahead of print.

ABSTRACT

OBJECTIVE: To investigate the feasibility of quantitative intravoxel incoherent motion (IVIM) and diffusion kurtosis imaging (DKI) analyses in the upper abdominal organs by simultaneous multislice diffusion-weighted imaging (SMS-DWI).

SUBJECTS AND METHODS: In this prospective study, a total of 32 participants underwent conventional DWI (C-DWI) and SMS-DWI sequences with acceleration factors of 2 and 3 (SMS2-DWI and SMS3-DWI, respectively) in the upper abdomen with multiple b-values (0, 10, 20, 50, 80, 100, 150, 200, 500, 800, 1000, 1500, and 2000 seconds/mm2) on a 3 T system (MAGNETOM Prisma; Siemens Healthcare, Erlangen, Germany). Image quality and quantitatively measurements of apparent diffusion coefficient (ADC), true diffusion coefficient (D), pseudodiffusion coefficient (D*), perfusion fraction (f), mean kurtosis (MK), and mean apparent diffusivity (MD) for the liver, pancreas, kidney cortex and medulla, spleen, and erector spine muscle were compared between the 3 sequences.

RESULTS: The acquisition times for C-DWI, SMS2-DWI, and SMS3-DWI were 10 minutes 57 seconds, 5 minutes 9 seconds, and 3 minutes 54 seconds. For image quality parameters, C-DWI and SMS2-DWI yielded better results than SMS3-DWI (P < 0.05). SMS2-DWI had equivalent IVIM and DKI parameters compared with that of C-DWI (P > 0.05). No statistically significant differences in the ADC, D, f, and MD values between the 3 sequences (P > 0.05) were observed. The D* and MK values of the liver (P = 0.005 and P = 0.012) and pancreas (P = 0.019) between SMS3-DWI and C-DWI were significantly different.

CONCLUSIONS: SMS2-DWI can substantially reduce the scan time while maintaining equivalent IVIM and DKI parameters in the abdominal organs compared with C-DWI.

PMID:34270482 | DOI:10.1097/RCT.0000000000001189