Category: Statistics

Brief Bioinform. 2023 Jan 5:bbac567. doi: 10.1093/bib/bbac567. Online ahead of print.

ABSTRACT

Accurate in silico prediction of conformational B-cell epitopes would lead to major improvements in disease diagnostics, drug design and vaccine development. A variety of computational methods, mainly based on machine learning approaches, have been developed in the last decades to tackle this challenging problem. Here, we rigorously benchmarked nine state-of-the-art conformational B-cell epitope prediction webservers, including generic and antibody-specific methods, on a dataset of over 250 antibody-antigen structures. The results of our assessment and statistical analyses show that all the methods achieve very low performances, and some do not perform better than randomly generated patches of surface residues. In addition, we also found that commonly used consensus strategies that combine the results from multiple webservers are at best only marginally better than random. Finally, we applied all the predictors to the SARS-CoV-2 spike protein as an independent case study, and showed that they perform poorly in general, which largely recapitulates our benchmarking conclusions. We hope that these results will lead to greater caution when using these tools until the biases and issues that limit current methods have been addressed, promote the use of state-of-the-art evaluation methodologies in future publications and suggest new strategies to improve the performance of conformational B-cell epitope prediction methods.

PMID:36611255 | DOI:10.1093/bib/bbac567

Nurs Open. 2023 Jan 7. doi: 10.1002/nop2.1596. Online ahead of print.

ABSTRACT

AIM: This study aims to explore the perception of nurses on the use of mobile phone SMS for managing diabetes in rural Ghana.

DESIGN: Exploratory Descriptive Qualitative Design.

METHODS: Purposive sampling was used to recruit (13) participants relative to data saturation after ethical clearance (REDACTED); using a semi-structured interview guide. All interviews were transcribed verbatim and analysed using thematic content analysis.

RESULTS: Participants believe SMS was useful in facilitating interaction between nurses, clients, family and statistically significant others; improving medication adherence and supporting blood glucose monitoring. The use of infographics was preferred to traditional SMS among digitally literate patients and voice calls for those who were illiterate. Participants had limited knowledge of downloadable diabetic applications. Participants were willing to accept and use SMS for the management of diabetes mellitus.

PATIENT OR PUBLIC CONTRIBUTION: Thirteen nurses actively participated in the study.

PMID:36611225 | DOI:10.1002/nop2.1596

Alzheimers Res Ther. 2023 Jan 7;15(1):6. doi: 10.1186/s13195-022-01126-0.

ABSTRACT

BACKGROUND: High continuity of care (COC) is associated with better clinical outcomes among older adults. The impact of amyloid-β PET scan on COC among adults with mild cognitive impairment (MCI) or dementia of uncertain etiology is unknown.

METHODS: We linked data from the CARE-IDEAS study, which assessed the impact of amyloid-β PET scans on outcomes in Medicare beneficiaries with MCI or dementia of uncertain etiology and their care partners, to Medicare claims (2015-2018). We calculated a participant-level COC index using the Bice-Boxerman formula and claims from all ambulatory evaluation and management visits during the year prior to and following the amyloid-β PET scan. We compared baseline characteristics by scan result (elevated or non-elevated) using standardized differences. To evaluate changes in COC, we used multiple regression models adjusting for sociodemographics, cognitive function, general health status, and the Charlson Comorbidity Index.

RESULTS: Among the 1171 cohort members included in our analytic population, the mean age (SD) was 75.2 (5.4) years, 61.5% were male and 93.9% were non-Hispanic white. Over two-thirds (68.1%) had an elevated amyloid-β PET scan. Mean COC for all patients was 0.154 (SD = 0.102; range = 0-0.73) prior to the scan and 0.158 (SD = 0.105; range = 0-1.0) in the year following the scan. Following the scan, the mean COC index score increased (95% CI) by 0.005 (-0.008, 0.019) points more for elevated relative to not elevated scan recipients, but this change was not statistically significant. There was no association between scan result (elevated vs. not elevated) or any other patient covariates and changes in COC score after the scan.

CONCLUSION: COC did not meaningfully change following receipt of amyloid-β PET scan in a population of Medicare beneficiaries with MCI or dementia of uncertain etiology. Future work examining how care continuity varies across marginalized populations with cognitive impairment is needed.

PMID:36611213 | DOI:10.1186/s13195-022-01126-0

Crit Care. 2023 Jan 7;27(1):7. doi: 10.1186/s13054-022-04298-1.

ABSTRACT

BACKGROUND: Current guidelines suggest the introduction of early nutrition support within the first 48 h of admission to the intensive care unit (ICU) for patients who cannot eat. In that context, we aimed to describe nutrition practices in the ICU and study the association between the introduction of early nutrition support (< 48 h) in the ICU and patient mortality at day 28 (D28) using data from a multicentre prospective cohort.

METHODS: The ‘French-Speaking ICU Nutritional Survey’ (FRANS) study was conducted in 26 ICUs in France and Belgium over 3 months in 2015. Adult patients with a predicted ICU length of stay > 3 days were consecutively included and followed for 10 days. Their mortality was assessed at D28. We investigated the association between early nutrition (< 48 h) and mortality at D28 using univariate and multivariate propensity-score-weighted logistic regression analyses.

RESULTS: During the study period, 1206 patients were included. Early nutrition support was administered to 718 patients (59.5%), with 504 patients receiving enteral nutrition and 214 parenteral nutrition. Early nutrition was more frequently prescribed in the presence of multiple organ failure and less frequently in overweight and obese patients. Early nutrition was significantly associated with D28 mortality in the univariate analysis (crude odds ratio (OR) 1.69, 95% confidence interval (CI) 1.23-2.34) and propensity-weighted multivariate analysis (adjusted OR (aOR) 1.05, 95% CI 1.00-1.10). In subgroup analyses, this association was stronger in patients ≤ 65 years and with SOFA scores ≤ 8. Compared with no early nutrition, a significant association was found of D28 mortality with early enteral (aOR 1.06, 95% CI 1.01-1.11) but not early parenteral nutrition (aOR 1.04, 95% CI 0.98-1.11).

CONCLUSIONS: In this prospective cohort study, early nutrition support in the ICU was significantly associated with increased mortality at D28, particularly in younger patients with less severe disease. Compared to no early nutrition, only early enteral nutrition appeared to be associated with increased mortality. Such findings are in contrast with current guidelines on the provision of early nutrition support in the ICU and may challenge our current practices, particularly concerning patients at low nutrition risk. Trial registration ClinicalTrials.gov Identifier: NCT02599948. Retrospectively registered on November 5th 2015.

PMID:36611211 | DOI:10.1186/s13054-022-04298-1

Malar J. 2023 Jan 7;22(1):10. doi: 10.1186/s12936-022-04416-y.

ABSTRACT

BACKGROUND: Even though malaria is preventable, it remains the leading cause of under-five morbidity and mortality in low-and middle-income countries. Despite the World Health Organization (WHO) recommendations, its advantage, and its free-of-cost access, the utilization of insecticide-treated nets (ITN) is still low in East Africa. Therefore, this study aimed to assess ITN use and associated factors among households having under-five children in East Africa.

METHODS: The most recent Demographic and Health Survey (DHS) datasets of East African countries were used. A total of 174,411 weighted samples was used for analysis. Given the hierarchical nature of DHS data, a multilevel binary logistic regression model was fitted to identify factors associated with ITN use. Four models were fitted and a model with the lowest deviance value was chosen as the best-fitted model for the data. Variables with a p-value < 0.2 in the bivariable analysis were considered for the multivariable analysis. In the multivariable multilevel binary logistic regression analysis, the Adjusted Odds Ratio (AOR) with the 95% Confidence Interval (CI) was reported to declare the statistical significance and strength of association.

RESULTS: In this study, the proportion of ITN use among households having under-five children in East Africa was 46.32% (95% CI 46.08%, 46.55%), ranging from 11.8% in Zimbabwe to 70.03% in Rwanda. In the multivariable analysis, being in the age group 25-34 years, married, widowed, and divorced, primary and post-primary education, wealthy households, having a lower household size, many under-five children, having media exposure, and male-headed households were associated with higher odds of ITN use. Moreover, respondents from a rural place of residence, communities with a higher level of media exposure, communities with lower poverty levels, and communities with higher education levels had higher odds of ITN use.

CONCLUSION: In this study, the proportion of ITN use was relatively low. Both individual and community-level factors were associated with ITN use. Therefore, giving attention, especially to those who had no formal education, the poor, younger age groups, and households with the large family size is advisable to increase awareness about ITN use. Moreover, media campaigns regarding ITN use should be strengthened.

PMID:36611186 | DOI:10.1186/s12936-022-04416-y

Eur J Med Res. 2023 Jan 7;28(1):12. doi: 10.1186/s40001-022-00966-8.

ABSTRACT

OBJECTIVES: To investigate whether intravenous thrombolysis (IVT) with alteplase (a recombinant tissue plasminogen activator, rt-PA) before endovascular treatment (EVT) is beneficial for acute ischemic stroke (AIS) patients in different periods.

METHODS: This study enrolled a total of 140 patients hospitalized between 2019 and 2022 with AIS from large vessel occlusion (LVO) in the anterior circulation. Those patients were divided into the EVT alone group and IVT + EVT group, in which EVT was preceded by intravenous rt-PA. According to the time from onset to femoral artery puncture, the above two groups were divided into the following subgroups: < 4.5 h, between 4.5 and 6 h, between 6 and 8 h, and between 8 and 10 h. There were 78 patients in the EVT alone group and 62 patients in the IVT + EVT group.

RESULTS: There was no statistically significant difference in functional independence, recanalization rate, favorable outcome rate, or mortality between the EVT and IVT + EVT groups (P > 0.05). After adjusting for confounding factors, a lower incidence of intracerebral hemorrhage was observed in the EVT group (P < 0.05). A comparison of time-dependent efficacy between the two groups showed that within 6-8 h, there were statistically significant differences between admission and postoperation in the National Institutes of Health Stroke Scale scores at 24 h (P = 0.01) or 7 days (P = 0.02).

CONCLUSIONS: Although there was no difference in clinical efficacy and safety between the abovementioned two groups, treatment with IVT + EVT could increase the risk of bleeding compared to EVT. Moreover, in the 6-8 h subgroup, the efficacy of EVT alone was better than that of IVT + EVT.

PMID:36611184 | DOI:10.1186/s40001-022-00966-8

BMC Public Health. 2023 Jan 7;23(1):54. doi: 10.1186/s12889-022-14911-1.

ABSTRACT

BACKGROUND: Hepatitis C Virus (HCV) is a public health threat which contributes substantially to the global burden of liver disease. There is much debate about effective approaches to scaling up diagnosis of HCV among risk groups. Tayside, a region in the East of Scotland, developed low-threshold community pathways for HCV to lay the foundations of an elimination strategy. In this retrospective study, we sought to: quantify the contribution of community pathways to increasing HCV diagnosis; understand if shifting diagnosis to community settings led to a higher proportion of individuals tested for HCV being actively infected; and describe functional characteristics of the care pathways.

METHODS: Descriptive statistics were used to for analysis of routinely-collected HCV testing data from 1999 to 2017, and a review of the development of the care pathways was undertaken. Community-based testing was offered through general practices (GP); nurse outreach clinics; prisons; drug treatment services; needle and syringe provision (NSP) sites; community pharmacies; and mosques.

RESULTS: Anti-HCV screening was undertaken on 109,430 samples, of which 5176 (4.7%) were reactive. Of all samples, 77,885 (71.2%) were taken in secondary care; 25,044 (22.9%) in GPs; 2970 (2.7%) in prisons; 2415 (2.2%) in drug services; 753 (0.7%) in NSPs; 193 (0.2%) pharmacies; and 170 (0.1%) in mosques. The highest prevalence of HCV infection among those tested was in NSP sites (26%), prisons (14%), and drug treatment centres (12%).

CONCLUSIONS: Decentralised care pathways, particularly in harm reduction and other drug service settings, were key to increasing diagnosis of HCV in the region, but primary and secondary care remain central to elimination efforts.

PMID:36611156 | DOI:10.1186/s12889-022-14911-1

BMC Public Health. 2023 Jan 7;23(1):51. doi: 10.1186/s12889-022-14900-4.

ABSTRACT

BACKGROUND: Undernutrition in under-five children remains a worldwide health issue and is considered one of the leading causes of increased morbidity and mortality. This study aims to assess the impact of home-based nutritional intervention on the nutritional status of preschool children living in rural areas of South India.

METHODS: A single-blinded cluster randomized controlled trial evaluated the impact of the intervention, with weight gain as the primary outcome. A cluster of 12 villages was randomized to intervention or control arms. A total of 253 underweight preschool children from 12 clusters (villages) were randomized to intervention (n = 127) and control arm (n = 126). The intervention was composed of a health-teaching program and a demonstration of nutritious food preparation in addition to the regular services provided at the Anganwadi centers. The control arm received only standard routine care provided in the Anganwadi centre. The anthropometric assessment was carried out at the baseline and every month for a year.

RESULT: A significant increase in the mean weight kilograms was noted in the intervention group (11.9 ± 0.98 to 13.78 ± 0.89) compared to the control group (11.8 ± 1.03 to 12.96 ± 0.88). In the intervention group, at the baseline, 41.5% were moderately malnourished (> – 2SD-3SD), which decreased to 24% at the end of the year. Similarly, severe malnutrition decreased from 8.69 to 3.16%, while 20.5% of malnourished children achieved normal nutritional status. In the control group, undernourished children demonstrated minimal changes in nutritional status. Analysis of repeated measures of ANOVA results between the intervention and control groups on weight measurements (F (1, 251) = 15.42, p .001) and height measurements (F (2, 1258) = 1.540, p .001) revealed statistical significance.

CONCLUSION: The nutritional status of preschool children is found to be improved by home-based intervention, which includes training mothers or caregivers in planning and preparing healthy nutritious diets, providing timely care, and gaining an understanding and knowledge of the nutritional status along with regular home-based diet preparation.

TRIAL REGISTRATION: [email protected] CTRI/2017/03/008273 [Registered on: 31/03/2017].

PMID:36611154 | DOI:10.1186/s12889-022-14900-4

BMC Womens Health. 2023 Jan 7;23(1):7. doi: 10.1186/s12905-022-02147-5.

ABSTRACT

BACKGROUND: Screening for breast cancer results in early diagnosis of the disease and improves survival. However, increasing participation of women in screening programs is challenging since it is influenced by socioeconomic and cultural factors. This study explores the relationship of socioeconomic and women empowerment factors with breast cancer screening uptakes in the states and union territories of India.

METHODS: We used summary reports of secondary data from all the states and union territories based on the fifth wave of the National Family Health Survey in India. This ecological study compares the uptake of breast cancer screening across states of India. We considered socioeconomic status (SES) and women empowerment status (WES) indicators from the survey as independent variables and state-wise breast cancer screening uptake as dependent variables for studying their association. The determinants of breast cancer screening were calculated using a simple linear regression model.

RESULTS: We found that socioeconomic status and women empowerment status moderately correlated with breast cancer screening uptake (correlation coefficient 0.34 and 0.38, respectively). States with higher rates of literacy among women and of women who had their own bank accounts that they decided how to use reported higher uptake of breast cancer screening (p = 0.01 and 0.03, respectively). However, the correlation was not uniform across all the states. The states of Chandigarh, Delhi, Telangana, and Karnataka showed lower participation despite a higher percentage of literate women and women with their own bank accounts.

CONCLUSION: This study indicates that women’s literacy and having their own bank account may moderately improve their participation in cancer screening. However, higher SES and WES did not translate into better screening in many of the states. More research is needed, especially for states which had low screening uptake despite relatively higher rates of women empowerment.

PMID:36611149 | DOI:10.1186/s12905-022-02147-5

BMC Med Res Methodol. 2023 Jan 7;23(1):5. doi: 10.1186/s12874-022-01828-x.

ABSTRACT

BACKGROUND: In the development of prediction models for a clinical event, it is common to use the static prediction modeling (SPM), a regression model that relates baseline predictors to the time to event. In many situations, the data used in training and validation are from longitudinal studies, where predictor variables are time-varying and measured at clinical visits. But these data are not used in SPM. The landmark analysis (LA), previously proposed for dynamic prediction with longitudinal data, has interpretational difficulty when the baseline is not a risk-changing clinical milestone, as is often the case in observational studies of chronic disease without intervention.

METHODS: This paper studies the generalized landmark analysis (GLA), a statistical framework to develop prediction models for longitudinal data. The GLA includes the LA as a special case, and generalizes it to situations where the baseline is not a risk-changing clinical milestone with a more useful interpretation. Unlike the LA, the landmark variable does not have to be time since baseline in the GLA, but can be any time-varying prognostic variable. The GLA can also be viewed as a longitudinal generalization of localized prediction, which has been studied in the context of low-dimensional cross-sectional data. We studied the GLA using data from the Chronic Renal Insufficiency Cohort (CRIC) Study and the Wisconsin Allograft Replacement Database (WisARD) and compared the prediction performance of SPM and GLA.

RESULTS: In various validation populations from longitudinal data, the GLA generally had similarly or better predictive performance than SPM, with notable improvement being seen when the validation population deviated from the baseline population. The GLA also demonstrated similar or better predictive performance than LA, due to its more general model specification.

CONCLUSIONS: GLA is a generalization of the LA such that the landmark variable does not have to be the time since baseline. It has better interpretation when the baseline is not a risk-changing clinical milestone. The GLA is more adaptive to the validation population than SPM and is more flexible than LA, which may help produce more accurate prediction.

PMID:36611147 | DOI:10.1186/s12874-022-01828-x