Tag: nevin manimala

Life Sci Alliance. 2024 Aug 6;7(10):e202402713. doi: 10.26508/lsa.202402713. Print 2024 Oct.

ABSTRACT

Probabilistic topic modelling has become essential in many types of single-cell data analysis. Based on probabilistic topic assignments in each cell, we identify the latent representation of cellular states. A dictionary matrix, consisting of topic-specific gene frequency vectors, provides interpretable bases to be compared with known cell type-specific marker genes and other pathway annotations. However, fitting a topic model on a large number of cells would require heavy computational resources-specialized computing units, computing time and memory. Here, we present a scalable approximation method customized for single-cell RNA-seq data analysis, termed ASAP, short for Annotating a Single-cell data matrix by Approximate Pseudobulk estimation. Our approach is more accurate than existing methods but requires orders of magnitude less computing time, leaving much lower memory consumption. We also show that our approach is widely applicable for atlas-scale data analysis; our method seamlessly integrates single-cell and bulk data in joint analysis, not requiring additional preprocessing or feature selection steps.

PMID:39107066 | DOI:10.26508/lsa.202402713

BMJ Open Qual. 2024 Aug 5;13(3):e002807. doi: 10.1136/bmjoq-2024-002807.

ABSTRACT

INTRODUCTION: Sequential compression devices (SCDs) are the mainstay of mechanical prophylaxis for venous thromboembolism in perioperative neurosurgical patients and are especially crucial when chemical prophylaxis is contraindicated.

OBJECTIVES: This study aimed to characterise and improve SCD compliance in neurosurgery stepdown patients.

METHODS: SCD compliance in a neurosurgical stepdown unit was tracked across 13 months (August 2022-August 2023). When not properly functioning, the missing element was documented. Compliance was calculated daily in all patients with SCD orders, and then averaged monthly. Most common barriers to compliance were identified. With nursing, we implemented a best practice alert to facilitate nursing education at month 3 and tracked compliance over 9 months, with two breaks in surveillance. At month 12, we implemented a patient-engagement measure through creating and distributing a patient-directed infographic and tracked compliance over 2 months.

RESULTS: Compliance averaged 19.7% (n=95) during August and 38.4% (n=131) in September. After implementing the best practice alert and supply chain upgrades, compliance improved to 48.8% (n=150) in October, 41.2% (n=104) in March and 45.9% (n=76) in April. The infographic improved compliance to 51.4% (n=70) in July and 55.1% (n=34) in August. Compliance was significantly increased from baseline in August to October (z=4.5838, p<0.00001), sustained through March (z=3.2774, p=0.00104) and further improved by August (z=3.9025, p=0.0001).

CONCLUSION: Beyond an initial Hawthorne effect, implementation of the best practice nursing alert facilitated sustained improvement in SCD compliance despite breaks in surveillance. SCD compliance nonetheless remained below 50% until implementation of patient-engagement measures which were dependent on physician involvement.

PMID:39107035 | DOI:10.1136/bmjoq-2024-002807

BMJ Open. 2024 Aug 6;14(8):e084485. doi: 10.1136/bmjopen-2024-084485.

ABSTRACT

OBJECTIVES: Inappropriate prescribing of antibiotics is a key driver of antimicrobial resistance. This study aimed to describe urine sampling rates and antibiotic prescribing for patients with lower urinary tract infections (UTIs) in English general practice.

DESIGN: A retrospective population-based study using administrative data.

SETTING: IQVIA Medical Research Database (IMRD) data from general practices in England, 2015-2022.

PARTICIPANTS: Patients who have consulted with an uncomplicated UTI in England general practices captured in the IMRD.

OUTCOME MEASURES: Trends in UTI episodes (episodes were defined as UTI diagnosis codes occurring within 14 days of each other), testing and antibiotic prescribing on the same day as initial UTI consultation were assessed from January 2015 to December 2022. Associations, using univariate and multivariate logistic regressions, were examined between consultation and demographic factors on the odds of a urine test.

RESULTS: There were 743 350 UTI episodes; 50.8% had a urine test. Testing rates fluctuated with an upward trend and large decline in 2020. Same-day UTI antibiotic prescribing occurred in 78.2% of episodes. In multivariate modelling, factors found to decrease odds of a urine test included age ≥85 years (0.83, 95% CI 0.82 to 0.84), consultation type (remote vs face to face, 0.45, 95% CI 0.45 to 0.46), episodes in London compared with the South (0.74, 95% CI 0.72 to 0.75) and increasing practice size (0.77, 95% CI 0.76 to 0.78). Odds of urine tests increased in males (OR 1.11, 95% CI 1.10 to 1.13), for those episodes without a same-day UTI antibiotic (1.10, 95% CI 1.04 to 1.16) for episodes for those with higher deprivation status (Indices of Multiple Deprivation 8 vs 1, 1.51, 95% CI 1.48 to 1.54). Compared with 2015, 2016-2019 saw increased odds of testing while 2020 and 2021 saw decreases, with 2022 showing increased odds.

CONCLUSION: Urine testing for UTI in general practice in England showed an upward trend, with same-day antibiotic prescribing remaining consistent, suggesting greater alignment to national guidelines. The COVID-19 pandemic impacted testing rates, though as of 2022, they began to recover.

PMID:39107033 | DOI:10.1136/bmjopen-2024-084485

BMJ Open. 2024 Aug 6;14(8):e085758. doi: 10.1136/bmjopen-2024-085758.

ABSTRACT

BACKGROUND: The 2018 Nigeria Demographic and Health Survey shows poor maternal health in northern Nigeria. Contraceptive use remains low and maternal mortality high. Studies show that cultural norms related to men’s decision-making role in the family significantly contribute to this phenomenon.

OBJECTIVES: The assessment was designed to identify barriers to service delivery and utilisation of maternal-health and family-planning services in three northern Nigerian states, focusing on aspects of service delivery affected by husband involvement.

DESIGN: Qualitative design included 16 focus group discussions and 12 in-depth interviews with facility clients, and 16 in-depth interviews with healthcare providers, in each of the three states.

SETTING: Primary healthcare facilities in three northern Nigeria states: Bauchi, Kebbi and Sokoto.

PARTICIPANTS: Women who came to the facility for family-planning services (n=233 in 24 focus groups); women who came for antenatal care (n=97 in 12 focus groups); men married to women who either received antenatal care or delivered in a facility (n=96 in 12 focus groups); mothers of newborns who delivered in a facility (n=36) and healthcare providers (n=48).

RESULTS: We found gender barriers to contraceptive use and to obtaining maternal healthcare, with some women requiring their husband’s permission to use services, even in emergencies. Several supply-side barriers exacerbate the situation. Many healthcare providers would not provide women with a family-planning method without their husbands’ presence or approval; some male providers would not admit a woman to deliver in a facility if her husband objected to her being treated by a man and there was no female provider present and some facilities do not have the infrastructure to accommodate men.

CONCLUSION: Despite years of programming, barriers to women’s family-planning and maternal-health service utilisation persist. State governments in northern Nigeria should invest in additional provider training, improving infrastructure and hiring more female healthcare providers.

PMID:39107032 | DOI:10.1136/bmjopen-2024-085758

BMJ Open. 2024 Aug 5;14(8):e083904. doi: 10.1136/bmjopen-2024-083904.

ABSTRACT

OBJECTIVE: Low birth weight (LBW) is an important indicator of newborn health and can have long-term implications for a child’s development. Spatial exploratory analysis provides a toolkit to gain insight into inequalities in LBW. Few studies in Ghana have explored the spatial distribution of LBW to understand the extent of the problem geographically. This study explores individual and cluster-level distributions of LBW using spatial exploration components for common determinants from nationally representative survey data.

DESIGN: We used data from the 2017 Ghana Maternal Health Survey and conducted individual-level and cluster-level analyses of LBW with place and zone of residence in both bivariate and multivariate analyses. By incorporating spatial and survey designs methodology, logistic and Poisson regression models were used to model LBW.

SETTING: Ghana.

PARTICIPANTS: A total of 4127 women aged between 15 and 49 years were included in the individual-level analysis and 864 clusters corresponding to birth weight.

PRIMARY AND SECONDARY OUTCOME MEASURES: Individual and cluster-level distribution for LBW using spatial components for common determinants.

RESULTS: In the individual-level analysis, place and zone of residence were significantly associated with LBW in the bivariate model but not in a multivariate model. Hotspot analysis indicated the presence of LBW clusters in the middle and northern zones of Ghana. Compared with rural areas, clusters in urban areas had significantly lower LBW (p=0.017). Clusters in the northern zone were significantly associated with higher LBW (p=0.018) compared with the coastal zones.

CONCLUSION: Our findings from choropleth hotspot maps suggest LBW clusters in Ghana’s northern and middle zones. Disparities between the rural and urban continuum require specific attention to bridge the healthcare system gap for Ghana’s northern and middle zones.

PMID:39107031 | DOI:10.1136/bmjopen-2024-083904

BMJ Open. 2024 Aug 6;14(8):e080831. doi: 10.1136/bmjopen-2023-080831.

ABSTRACT

OBJECTIVE: To perform a detailed characterisation of diabetes burden and pre-diabetes risk in a rural county with previously documented poor health outcomes in order to understand the local within-county distribution of diabetes in rural areas of America.

DESIGN, SETTING, AND PARTICIPANTS: In 2021, we prospectively mailed health surveys to all households in Sullivan County, a rural county with the second-worst health outcomes of all counties in New York State. Our survey included questions on demographics, medical history and the American Diabetes Association’s Pre-diabetes Risk Test.

PRIMARY OUTCOME AND METHODS: Our primary outcome was an assessment of diabetes burden within this rural county. To help mitigate non-response bias in our survey, raking adjustments were performed across strata of age, sex, race/ethnicity and health insurance. We analysed diabetes prevalence by demographic characteristics and used geospatial analysis to assess for clustering of diagnosed diabetes cases.

RESULTS: After applying raking procedures for the 4725 survey responses, our adjusted diagnosed diabetes prevalence for Sullivan County was 12.9% compared with the 2019 Behavioural Risk Factor Surveillance System (BRFSS) estimate of 8.6%. In this rural area, diagnosed diabetes prevalence was notably higher among non-Hispanic Black (21%) and Hispanic (15%) residents compared with non-Hispanic White (12%) residents. 53% of respondents without a known history of pre-diabetes or diabetes scored as high risk for pre-diabetes. Nearest neighbour analyses revealed that hotspots of diagnosed diabetes were primarily located in the more densely populated areas of this rural county.

CONCLUSIONS: Our mailed health survey to all residents in Sullivan County demonstrated higher diabetes prevalence compared with modelled BRFSS estimates that were based on small telephone samples. Our results suggest the need for better diabetes surveillance in rural communities, which may benefit from interventions specifically tailored for improving glycaemic control among rural residents.

PMID:39107030 | DOI:10.1136/bmjopen-2023-080831

BMJ Open. 2024 Aug 6;14(8):e085513. doi: 10.1136/bmjopen-2024-085513.

ABSTRACT

INTRODUCTION: Ultrasound-guided quadratus lumborum blocks are commonly used for postoperative analgesia during caesarean section. Ultrasound-guided quadratus lumborum blocks can be performed through four approaches, including lateral, posterior, anterior, and intramuscular quadratus lumborum blocks. This systematic review and meta-analysis aims to determine the optimal approach to ultrasound-guided quadratus lumborum blocks for postoperative analgesia in elective caesarean section.

METHODS AND ANALYSIS: The PubMed, EMBASE, Cochrane Library and Web of Science databases will be systematically searched from their inception to 30 July 2024. Randomised controlled trials that compared the analgesic effects of different ultrasound-guided quadratus lumborum block approaches in elective caesarean section will be included. Only publications in English will be eligible for inclusion. The total postoperative analgesic consumption over 24 hours will be the primary outcome. The time to first analgesic request, postoperative pain scores at rest and during movement, and incidence of adverse effects will be secondary outcomes. RevMan V.5.4 will be used for the statistical analysis. Network meta-analysis will be used for indirect comparisons between different approaches across studies. The Grading of Recommendations Assessment, Development and Evaluation approach will be used to assess the quality of evidence for each outcome.

ETHICS AND DISSEMINATION: Ethical approval was not required. The results of this study will be submitted to peer-reviewed journals.

PROSPERO REGISTRATION NUMBER: CRD42024503694.

PMID:39107029 | DOI:10.1136/bmjopen-2024-085513

BMJ Open. 2024 Aug 6;14(8):e081663. doi: 10.1136/bmjopen-2023-081663.

ABSTRACT

INTRODUCTION: Sexual violence is a significant public health concern with severe physical, social and psychological consequences, which can be mitigated by health service utilisation. However, in Uganda and much of sub-Saharan Africa, these services are significantly underused, with 9 out of 10 survivors not seeking care due to a range of psychological, cultural, economic and logistical factors. Thus, there is a strong need for research to improve health service utilisation for survivors of sexual violence.

METHODS AND ANALYSIS: The proposed study seeks to address the underutilization of health services for female survivors of sexual violence using a discrete choice experiment (DCE). The study will be conducted in the greater Masaka region of southwestern Uganda and target adult female survivors of sexual violence. We will first undertake qualitative interviews with 56 survivors of sexual violence to identify the key attributes and levels of the DCE. In order to ensure a sufficiently powered sample, 312 women who meet inclusion criteria will be interviewed. Our primary analysis will employ a mixed (random parameters) logit model. We will also model the role of individual-specific characteristics through latent class models.

ETHICS AND DISSEMINATION: The study protocol was reviewed and approved by the following ethics review boards in Uganda and the USA: the Uganda Virus Research Institute (UVRI), the Uganda National Council for Science and Technology (HS2364ES), Washington University in St Louis and the University of Michigan. Our methods conform to established guidelines for the protection of human subjects involved in research. Our dissemination plan targets a broad audience, ranging from policymakers and government agencies to healthcare providers, academic communities and survivors themselves.

PMID:39107025 | DOI:10.1136/bmjopen-2023-081663

BMJ Open. 2024 Aug 6;14(8):e078582. doi: 10.1136/bmjopen-2023-078582.

ABSTRACT

OBJECTIVE: To determine the prevalence and factors associated with anxiety and depression and the care-seeking behaviour among Nepalese population.

DESIGN AND SETTINGS: Secondary analysis of the data from nationally representative Nepal Demographic and Health Survey 2022.

PARTICIPANTS: Analysed data of 12 355 participants (7442 females and 4913 males) aged 15-49 years.

OUTCOME MEASURES: Depression and anxiety were assessed using Patient Health Questionnaire-9 (PHQ-9) and Generalised Anxiety Disorder Assessment (GAD-7) tools, respectively.

STATISTICAL ANALYSIS: We performed weighted analysis to account for the complex survey design. We presented categorical variables as frequency, per cent and 95% confidence interval (CI), whereas numerical variables were presented as median, inter-quartile range (IQR) and 95% CI. We performed univariate and multivariable logistic regression to determine factors associated with anxiety and depression, and results were presented as crude OR (COR), adjusted OR (AOR) and their 95% CI.

RESULTS: The prevalence of depression and anxiety were 4.0% (95% CI 3.5 to 4.5) and 17.7% (95% CI 16.5 to 18.9), respectively. Divorced or separated participants were found to have higher odds of developing anxiety (AOR 2.40, 95% CI 1.74 to 3.31) and depression (AOR 3.16, 95% CI 1.84 to 5.42). Among ethnic groups, Janajati had lower odds of developing anxiety (AOR 0.77, 95% CI 0.65 to 0.92) and depression (AOR 0.67, 95% CI 0.49 to 0.93) compared with Brahmin/Chhetri. Regarding disability, participants with some difficulty had higher odds of developing anxiety (AOR 1.81, 95% CI 1.56 to 2.10) and depression (AOR 1.94, 95% CI 1.51 to 2.49), and those with a lot of difficulty had higher odds of anxiety (AOR 2.09, 95% CI 1.48 to 2.96) and depression (AOR 2.04, 95% CI 1.06 to 3.90) compared with those without any disability. Among those who had symptoms of anxiety or depression, only 32.9% (95% CI 30.4 to 34.4) sought help for the conditions.

CONCLUSIONS: Marital status and disability status were positively associated with anxiety and depression, whereas Janajati ethnicity had relatively lower odds of experiencing anxiety and depression. It is essential to develop interventions and policies targeting females and divorced individuals to help reduce the burden of anxiety and depression in Nepal.

PMID:39107021 | DOI:10.1136/bmjopen-2023-078582

BMJ Open. 2024 Aug 6;14(8):e083855. doi: 10.1136/bmjopen-2023-083855.

ABSTRACT

OBJECTIVE: This study aims to assess the survival status and predictors of mortality among under-5 children with severe acute malnutrition in Addis Ababa, Ethiopia.

DESIGN: A retrospective cohort study was employed on randomly selected 422 medical records of children under the age of 5 admitted to stabilisation centres in Addis Ababa, Ethiopia. Survival analysis and Cox regression analysis were conducted to determine time spent before the outcome and predictors of desired outcome.

SETTINGS: The stabilisation centres in four governmental hospitals in Addis Ababa, Ethiopia: Tikur Anbessa Specialised Hospital, Zewditu Memorial Hospital, Yekatit 12 Hospital and Tirunesh Beijing Hospital PARTICIPANTS: Of 435 severely malnourished children under the age of 5 admitted to four governmental hospitals in Addis Ababa, Ethiopia, from January 2020 to December 2022, we were able to trace 422 complete records. The remaining 13 medical records were found to be incomplete due to missing medical history information for those children.

PRIMARY AND SECONDARY OUTCOME MEASURES: The primary outcome is the survival status of under-5 children with severe acute malnutrition after admission to the stabilisation centres. The secondary outcome is predictors of survival among these children.

RESULTS: Of 422 children, 44 (10.4%) died, with an incidence rate of 10.3 per 1000 person-days. The median hospital stay was 8 days. Full vaccination (adjusted HR (AHR) 0.2, 95% CI 0.088 to 0.583, p<0.05), feeding practices (F-75) (AHR 0.2, 95% CI 0.062 to 0.651, p<0.01), intravenous fluid administration (AHR 3.7, 95% CI 1.525 to 8.743, p<0.01), presence of HIV (AHR 2.2, 95% CI 1.001 to 4.650, p<0.05), pneumonia (AHR 2.2, 95% CI 1.001 to 4.650, p<0.01) and occurrence of shock (AHR3.5, 95% CI 1.451 to 8.321, p<0.01) were identified as significant predictors of mortality.

CONCLUSION: The study identified a survival rate slightly higher than the acceptable range set by the social and public health economics study group. Factors like vaccination status, HIV, pneumonia, shock, intravenous fluid and the absence of feeding F-75 predicted mortality.

PMID:39107018 | DOI:10.1136/bmjopen-2023-083855