Nevin Manimala

PLoS One. 2022 Jan 6;17(1):e0262182. doi: 10.1371/journal.pone.0262182. eCollection 2022.

ABSTRACT

Mortality prediction for intensive care unit (ICU) patients is crucial for improving outcomes and efficient utilization of resources. Accessibility of electronic health records (EHR) has enabled data-driven predictive modeling using machine learning. However, very few studies rely solely on unstructured clinical notes from the EHR for mortality prediction. In this work, we propose a framework to predict short, mid, and long-term mortality in adult ICU patients using unstructured clinical notes from the MIMIC III database, natural language processing (NLP), and machine learning (ML) models. Depending on the statistical description of the patients’ length of stay, we define the short-term as 48-hour and 4-day period, the mid-term as 7-day and 10-day period, and the long-term as 15-day and 30-day period after admission. We found that by only using clinical notes within the 24 hours of admission, our framework can achieve a high area under the receiver operating characteristics (AU-ROC) score for short, mid and long-term mortality prediction tasks. The test AU-ROC scores are 0.87, 0.83, 0.83, 0.82, 0.82, and 0.82 for 48-hour, 4-day, 7-day, 10-day, 15-day, and 30-day period mortality prediction, respectively. We also provide a comparative study among three types of feature extraction techniques from NLP: frequency-based technique, fixed embedding-based technique, and dynamic embedding-based technique. Lastly, we provide an interpretation of the NLP-based predictive models using feature-importance scores.

PMID:34990485 | DOI:10.1371/journal.pone.0262182

PLoS One. 2022 Jan 6;17(1):e0262361. doi: 10.1371/journal.pone.0262361. eCollection 2022.

ABSTRACT

BACKGROUND: Rwanda is a sub-Saharan country, where intestinal parasite infections, anemia and undernutrition coexist. The purpose of this research is to study the relationship between intestinal parasite infections and undernutrition/anemia to clarify the priorities of intervention in the rural area of Gakenke district in the Northern Province of Rwanda.

MATERIALS AND METHODS: A total of 674 students from Nemba I School, participated in a cross-sectional study, in which their parasitological and nutritional status were analysed. Statistical analysis was performed by χ2 test, univariate analysis and Odds ratios (OR).

RESULTS: A total of 95.3% of children presented intestinal parasitism, most of whom (94.5%) infected by protozoa and 36.1% infected by soil-transmitted helminths (STH), with Trichuris trichiura (27.3%) being the most prevalent. Multiple infections were found to be high (83.8%), with protozoa and STH co-infections in 30.6%. STH infections were mainly of low/moderate intensity. Neither infection nor STH infection of any intensity profile, was significantly related to anemia. In addition, STH infection, regardless of the intensity profile, was not associated with stunting, underweight or thinness. There was no difference between genders nor among ages in odds of anemia and nutritional status in STH-infected schoolchildren.

CONCLUSION: Multiparasitism remains high among Rwandan schoolchildren and is likely to cause nutritional problems. This work emphasizes the importance of keeping up health programs to reduce the prevalence of infection.

PMID:34990483 | DOI:10.1371/journal.pone.0262361

PLoS One. 2022 Jan 6;17(1):e0261518. doi: 10.1371/journal.pone.0261518. eCollection 2022.

ABSTRACT

INTRODUCTION: Non-Communicable Diseases (NCDs) have become the leading public health problems worldwide and the cardiovascular diseases (CVDs) is one of the major NCDs. Female Community Health Volunteers (FCHVs) in Nepal are the key drivers to implementing frontline health services. We explored the potential for engaging FCHVs for CVD risk screening at the community level in Nepal.

METHODS: We used multiple approaches (quantitative and qualitative) for data collection. The trained FCHVs administered CVD risk screening questionnaire among 491 adults in rural and urban areas and calculated the CVD risk scores. To maintain consistency and quality, a registered medical doctor also, using the same risk scoring chart, independently calculated the CVD risk scores. Kappa statistics and concordance coefficient were used to compare these two sets of risk screening results. Sensitivity and specificity analyses were conducted. Two focus group discussions among the FCHVs were conducted to determine their experiences with CVD risk screening and willingness to engage with CVD prevention and control efforts.

RESULTS: The mean level of agreement between two sets of risk screening results was 94.5% (Kappa = 0.77, P<0.05). Sensitivity of FCHV screening was 90.3% (95% CI: 0.801-0.964); and the specificity was 97% (95% CI: 0.948, 0.984). FCHVs who participated in the FGDs expressed a strong enthusiasm and readiness to using the CVD risk screening tools. Despite their busy workload, all FCHVs showed high level of motivation and willingness in using CVD risk screening tools and contribute to the prevention and control efforts of NCDs. The FCHVs recommended needs for providing additional training and capacity building opportunities.

CONCLUSION: We conclude that there is a potential for engaging FCHVs to use simple CVD risk screening tools at the community level. The findings are promising, however, further studies engaging larger number of FCHVs and larger population would warrant feasibility of such tools within the existing healthcare systems in Nepal.

PMID:34990481 | DOI:10.1371/journal.pone.0261518

PLoS One. 2022 Jan 6;17(1):e0262323. doi: 10.1371/journal.pone.0262323. eCollection 2022.

ABSTRACT

INTRODUCTION: Quality antenatal care is a window of opportunity for improving maternal and neonatal outcomes. Numerous studies have shown a positive effect of women empowerment on improved coverage of maternal and reproductive health services, including antenatal care (ANC). However, there is scarce evidence on the association between women’s empowerment and improved ANC services both in terms of coverage and quality. Addressing this gap, this paper examines the relationship between multi-dimensional measures of women empowerment on utilization of quality ANC (service coverage and consultation) in Pakistan.

METHODS: We used Pakistan Demographic and Health Survey 2017-18 (PDHS) data which comprises of 6,602 currently married women aged between 15-49 years who had a live birth in the past five years preceding the survey. Our exposure variables were three-dimensional measures of women empowerment (social independence, decision making, and attitude towards domestic violence), and our outcome variables were quality of antenatal coverage [i.e. a composite binary measure based on skilled ANC (trained professional), timeliness (1st ANC visit during first trimester), sufficiency of ANC visits (4 or more)] and quality of ANC consultation (i.e. receiving at least 7 or more essential antenatal components out of 8). Data were analysed in Stata 16.0 software. Descriptive statistics were used to describe sample characteristics and binary logistic regression was employed to assess the association between empowerment and quality of antenatal care.

RESULTS: We found that 41.4% of the women received quality ANC coverage and 30.6% received quality ANC consultations during pregnancy. After controlling for a number of socio-economic and demographic factors, all three measures of women’s empowerment independently showed a positive relationship with both outcomes. Women with high autonomy (i.e. strongly opposed the notion of violence) in the domain of attitude to violence are 1.66 (95% CI 1.30-2.10) and 1.45 (95% CI 1.19-1.75) and times more likely to receive antenatal coverage and quality ANC consultations respectively, compared with women who ranked low on attitude to violence. Women who enjoy high social independence had 1.87 (95% CI 1.44-2.43) and 2.78 (95% CI 2.04-3.79) higher odds of quality antenatal coverage and consultations respectively, as compared with their counterparts. Similarly, women who had high autonomy in household decision making 1.98 (95% CI 1.60-2.44) and 1.56 (95% CI 2.17-1.91) were more likely to receive quality antenatal coverage and consultation respectively, as compared to women who possess low autonomy in household decision making.

CONCLUSION: The quality of ANC coverage and consultation with service provider is considerably low in Pakistan. Women’s empowerment related to social independence, gendered beliefs about violence, and decision-making have an independent positive association with the utilisation of quality antenatal care. Thus, efforts directed towards empowering women could be an effective strategy to improve utilisation of quality antenatal care in Pakistan.

PMID:34990479 | DOI:10.1371/journal.pone.0262323

PLoS One. 2022 Jan 6;17(1):e0261555. doi: 10.1371/journal.pone.0261555. eCollection 2022.

ABSTRACT

Non-alcoholic fatty liver disease (NAFLD) and depression are common disorders and have bidirectional contributing relationships to metabolic syndrome. We aimed to determine whether a fasting serum signature of recent, self-reported depressive symptoms could be identified in a heterogeneous NAFLD cohort using nuclear magnetic resonance (NMR)-based metabolomics integrated with clinical chemistry. Serum nuclear magnetic resonance (NMR) metabolite profiles and corresponding clinical chemistry were compared between patients with depressive symptoms in the last 12-months (n = 81) and patients without recent depressive symptoms (n = 137 controls) using multivariate statistics. Orthogonal partial least squares discriminant analysis (OPLS-DA) of the biochemical and metabolomic data identified NAFLD patients with recent depression with a cross-validated accuracy of 61.5%, independent of age, sex, medication, and other comorbidities. This led to the development of a diagnostic algorithm with AUC 0.83 for future testing in larger clinical cohorts. Serum triglycerides, VLDL cholesterol, and the inflammatory biomarker GlycA were key metabolites increased in patients with recent depressive symptoms, while serum glutamine level was reduced. Here, serum NMR metabolite analysis provides a link between disturbed lipid metabolism, inflammation, and active mental health issues in NAFLD, irrespective of disease severity.

PMID:34990473 | DOI:10.1371/journal.pone.0261555

PLoS One. 2022 Jan 6;17(1):e0260543. doi: 10.1371/journal.pone.0260543. eCollection 2022.

ABSTRACT

In Canadian boreal forests, bryophytes represent an essential component of biodiversity and play a significant role in ecosystem functioning. Despite their ecological importance and sensitivity to disturbances, bryophytes are overlooked in conservation strategies due to knowledge gaps on their distribution, which is known as the Wallacean shortfall. Rare species deserve priority attention in conservation as they are at a high risk of extinction. This study aims to elaborate predictive models of rare bryophyte species in Canadian boreal forests using remote sensing-derived predictors in an Ensemble of Small Models (ESMs) framework. We hypothesize that high ESMs-based prediction accuracy can be achieved for rare bryophyte species despite their low number of occurrences. We also assess if there is a spatial correspondence between rare and overall bryophyte richness patterns. The study area is located in western Quebec and covers 72,292 km2. We selected 52 bryophyte species with <30 occurrences from a presence-only database (214 species, 389 plots in total). ESMs were built from Random Forest and Maxent techniques using remote sensing-derived predictors related to topography and vegetation. Lee’s L statistic was used to assess and map the spatial relationship between rare and overall bryophyte richness patterns. ESMs yielded poor to excellent prediction accuracy (AUC > 0.5) for 73% of the modeled species, with AUC values > 0.8 for 19 species, which confirmed our hypothesis. In fact, ESMs provided better predictions for the rarest bryophytes. Likewise, our study revealed a spatial concordance between rare and overall bryophyte richness patterns in different regions of the study area, which have important implications for conservation planning. This study demonstrates the potential of remote sensing for assessing and making predictions on inconspicuous and rare species across the landscape and lays the basis for the eventual inclusion of bryophytes into sustainable development planning.

PMID:34990454 | DOI:10.1371/journal.pone.0260543

MMWR Morb Mortal Wkly Rep. 2022 Jan 7;71(1):14-18. doi: 10.15585/mmwr.mm7101a3.

ABSTRACT

Firearm homicides and suicides represent an ongoing public health concern in the United States. During 2018-2019, a total of 28,372 firearm homicides (including 3,612 [13%] among youths and young adults aged 10-19 years [youths]) and 48,372 firearm suicides (including 2,463 [5%] among youths) occurred among U.S. residents (1). This report is the fourth in a series* that provides statistics on firearm homicides and suicides in major metropolitan areas. As with earlier reports, this report provides a special focus on youth violence, including suicide, recognizing the magnitude of the problem and the importance of early prevention efforts. Firearm homicide and suicide rates were calculated for the 50 most populous U.S. metropolitan statistical areas (MSAs)^† for the periods 2015-2016 and 2018-2019, separated by a transition year (2017), using mortality data from the National Vital Statistics System (NVSS) and population data from the U.S. Census Bureau. Following a period of decreased firearm homicide rates among persons of all ages after 2006-2007 in large metropolitan areas collectively and nationally, by 2015-2016 rates had returned to levels comparable to those observed a decade earlier and remained nearly unchanged as of 2018-2019. Firearm suicide rates among persons aged ≥10 years have continued to increase in large MSAs collectively as well as nationally. Although the youth firearm suicide rate remained much lower than the overall rate, the youth rate nationally also continued to increase, most notably outside of large MSAs. The findings in this report underscore a continued and urgent need for a comprehensive approach to prevention. This includes efforts to prevent firearm homicide and suicide in the first place and support individual persons and communities at increased risk, as well as lessening harms after firearm homicide and suicide have occurred.

PMID:34990441 | DOI:10.15585/mmwr.mm7101a3

Dis Colon Rectum. 2022 Feb 1;65(2):276-283. doi: 10.1097/DCR.0000000000002146.

ABSTRACT

BACKGROUND: The American Statistical Association, among others, has called for the use of statistical methods beyond p ≤ 0.05. The fragility index is a statistical metric defined as the minimum number of patients for whom if an event rather than a nonevent occurred, then the p value would increase to ≥0.05. Previous reviews have demonstrated that many randomized controlled trials have a low fragility index, suggesting they may not be robust.

OBJECTIVE: The purpose of this study was to review the fragility indices of randomized controlled trials in colorectal surgery.

DATA SOURCES: A PubMed search was performed.

STUDY SELECTION: Colorectal surgery randomized controlled trials with a dichotomous primary outcome p ≤ 0.05 and publication between 2016 and 2018 were systematically identified.

INTERVENTIONS: All procedural interventions related to colorectal surgery were included.

MAIN OUTCOME MEASURES: The main measures were the fragility index and the number of patients lost to follow-up for each trial. The percentage of trials with the number of patients lost to follow-up greater than the fragility index was calculated.

RESULTS: In total, 712 abstracts were reviewed, with 90 trials meeting the inclusion criteria. The median fragility index was 3 (interquartile range of 1 to 10). In 51 of the 90 trials (57%), the number of patients lost to follow-up was greater than the fragility index.

LIMITATIONS: The fragility index is only one measure of the robustness of a randomized clinical trial.

CONCLUSIONS: Most colorectal surgery randomized controlled trials have a low fragility index. In 57% of trials, more patients were lost to follow-up than would be required to change the outcome of the trial from “significant” to “nonsignificant” based on the p value. This emphasizes the importance of assessing the robustness of clinical trials when considering their clinical application, rather than relying solely on the p value. See Video Abstract at http://links.lww.com/DCR/B741.CUANDO EL VALOR-P ES INSUFICIENTE: ÍNDICE DE FRAGILIDAD APLICADO EN ESTUDIOS ALEATORIOS CONTROLADOS EN CIRUGÍA COLORECTAL.

ANTECEDENTES: La Sociedad Estadounidense de Estadística, entre otros, ha pedido el uso de métodos estadísticos más allá de p <0,05. El índice de fragilidad es una medida estadística definida como el número de desenlaces que podrían cambiar para revertir, o conseguir, la significación estadística, así el valor p aumentaría a ≥ 0,05. Las revisiones anteriores han demostrado que muchos estudios aleatorios controlados tienen un índice de fragilidad bajo, lo que sugiere que pueden poco sólidos.

OBJETIVO: El propósito de la présente investigación fué de revisar los índices de fragilidad de los estudios aleatorios controlados en cirugía colorrectal.

FUENTES DE DATOS: PubMed.

SELECCIN DE ESTUDIOS: Se identificaron sistemáticamente estudios aleatorios controlados de cirugía colorrectal con un resultado primario dicotómico, valor de p ≤ 0,05 y publicados entre 2016-2018.

INTERVENCIONES: Se incluyeron todas aquellas intervenciones con procedimientos relacionados con la cirugía colorrectal.

PRINCIPALES MEDIDAS DE RESULTADO: Las principales medidas fueron: el índice de fragilidad y el número de pacientes perdidos durante el seguimiento en cada estudio. Se calculó el el índice de fragilidad en porcentaje de estudios con el mayor número de pacientes perdidos durante el seguimiento mas prolongado.

RESULTADOS: En total, se revisaron 712 resúmenes con 90 ensayos que cumplieron con los criterios de inclusión. La mediana del índice de fragilidad fue de 3 (rango intercuartíl de 1 a 10). En 51 de los 90 estudios (57%), el número de pacientes perdidos durante el seguimiento fue mayor que el índice de fragilidad.

LIMITACIONES: El índice de fragilidad es solo una medida de la robustez de un estúdio clínico aleatorio.

CONCLUSIONES: La mayoría de los estudios aleatorios y controlados en cirugía colorrectal tienen un índice de fragilidad bajo. En el 57% de los estudios, se perdieron más pacientes durante el seguimiento de los que se necesitarían para cambiar el resultado del estudios de grado “significativo” a un grado “no significativo” según el valor-p. Este concepto enfatiza la importancia de evaluar la robustez de los estudios clínicos al considerar su aplicación verdadera aplicación clínica, en lugar de depender únicamente del valor-p. Consulte Video Resumen en http://links.lww.com/DCR/B741. (Traducción-Dr. Xavier Delgadillo).

PMID:34990426 | DOI:10.1097/DCR.0000000000002146

Dis Colon Rectum. 2022 Feb 1;65(2):228-237. doi: 10.1097/DCR.0000000000002084.

ABSTRACT

BACKGROUND: Self-expanding metal stents as a bridge to surgery in acute malignant large-bowel obstruction has gained popularity. However, long-term oncologic outcomes have not been well established.

OBJECTIVE: To investigate long-term oncologic outcomes of patients undergoing curative resection after the placement of a colonic stent compared with emergency surgery for acute malignant large-bowel obstruction.

DESIGN: This is a retrospective study.

SETTING: All patients presenting at 3 tertiary care centers between April 2002 and December 2012 with a diagnosis of complete malignant large-bowel obstruction were reviewed. Patients with disease distal to the hepatic flexure were selected for analysis.

PATIENTS: One hundred twenty-two patients who underwent either emergency surgery or placement of a colonic stent with curative intent were included.

INTERVENTIONS: Patients receiving emergency surgery within 24 hours of presenting with obstructive symptoms, including those with failed stents, were included in the emergency surgery group. All patients with clinically successful stent deployment before surgery were included in the stent group.

MAIN OUTCOME MEASURES: Overall survival and disease-free survival were calculated using the Kaplan-Meier method.

RESULTS: Sixty-four patients underwent emergency surgery, and 58 patients underwent placement of a self-expanding metal stent. Groups were similar in terms of sex, tumor stage and grade, and Charlson and Charlson-Age Comorbidity Index scores. Patients in the surgery group were older than patients in the stent group. There were no differences in the number of lymph nodes harvested, positive nodes, rates of vascular and perineural invasion, or utilization of chemotherapy. Thirty-day mortality after resection was similar between groups (7.41% vs 4.41%; p > 0.05). Patients who underwent colonic stenting as a bridge to surgery had similar 10-year overall survival (40.5% vs 32.7%; p = 0.13) and 10-year disease-free survival (40.2% vs 33.8%; p = 0.26) compared with those who underwent emergency surgery. Similar results were seen on intention-to-treat analysis.

LIMITATIONS: This was a small retrospective study.

CONCLUSIONS: Stent insertion followed by oncologic resection is associated with similar overall survival and disease-free survival compared with emergency resection. Stent insertion as a bridge to surgery should be considered in patients presenting with malignant colorectal obstruction. See Video Abstract at http://links.lww.com/DCR/B714Los Stents Metálicos Autoexpandibles No Afectan Negativamente Los Resultados A Largo Plazo En La Obstrucción Maligna Aguda Del Colon: Un Análisis Retrospectivo.

ANTECEDENTES: Los stents metálicos autoexpandibles como puente a una cirugía en la obstrucción maligna aguda del colon han ganado popularidad. Sin embargo, no se han establecido bien los resultados oncológicos a largo plazo.

OBJETIVO: Investigar los resultados oncológicos a largo plazo de los pacientes sometidos a resección curativa después de la colocación de un stent colónico en comparación con la cirugía de urgencia para la obstrucción maligna aguda del colon.

DISEO: Estudio retrospectivo.

MBITO: Entre abril de 2002 y diciembre de 2012, se revisaron todos los pacientes que acudieron a tres centros de tercer nivel con un diagnóstico de obstrucción maligna completa del colon. Se seleccionaron para el análisis los pacientes con enfermedad distal al ángulo hepático.

PACIENTES: Se incluyeron 122 pacientes que fueron operados de urgencia o a una colocación de un stent colónico con intención curativa.

PROCEDIMIENTOS: Los pacientes que se sometieron a cirugía de urgencia dentro de las 24 horas posteriores a la presentación de síntomas obstructivos; se incluyeron aquellos con stents fallidos en el grupo de cirugía de urgencia. Todos los pacientes con colocación clínicamente exitosa del stent antes de la cirugía se incluyeron en el grupo de stent.

PRINCIPALES VARIABLES ANALIZADAS: La sobrevida global y la sobrevida libre de enfermedad se calcularon mediante el método de Kaplan-Meier.

RESULTADOS: Sesenta y cuatro pacientes fueron llevados a cirugía urgente y en 58 pacientes se colocó de un stent metálico autoexpandible. Los grupos fueron similares en relación a sexo, estadio y grado del tumor, puntuación de comorbilidad de Charlson y Charlson-Age. Los pacientes del grupo de cirugía eran mayores que los del grupo de stents. No hubo diferencias en el número de ganglios linfáticos recolectados, ganglios positivos, tasas de invasión vascular y perineural o utilización de quimioterapia. La mortalidad a los 30 días después de la resección fue similar entre los grupos (7,41% frente a 4,41%; p> 0,05). Los pacientes que se sometieron a la colocación de un stent colónico como puente a la cirugía tuvieron una sobrevida general a diez años similar (40,5% vs 32,7%; p = 0,13) y una sobrevida libre de enfermedad a diez años (40,2% vs 33,8%, respectivamente; p = 0,26) en comparación a los operados de urgencia. Se observaron resultados similares en el análisis por intención de tratamiento.

LIMITACIONES: Estudio retrospectivo reducido.

CONCLUSIONES: La utilización de un stent y posteriormente la resección oncológica se asocia a una sobrevida general y una sobrevida libre de enfermedad similar en comparación con la resección de urgencia. La utilización de un stent como puente a la cirugía debe considerarse en pacientes que presentan obstrucción colorrectal maligna. Consulte Video Resumen en http://links.lww.com/DCR/B714. (Traducción-Dr. Lisbeth Alarcon-Bernes).

PMID:34990424 | DOI:10.1097/DCR.0000000000002084

Br J Gen Pract. 2021 Oct 22:BJGP.2021.0311. doi: 10.3399/BJGP.2021.0311. Online ahead of print.

ABSTRACT

BACKGROUND: Numbers of GP locums in the NHS have grown in recent years, yet evidence on the scale and scope of the locum workforce in general practice is sparse.

AIM: To identify characteristics, geographical patterns and drivers of GP locum use.

DESIGN AND SETTING: Observational study of routine data from general practices in England.

METHODS: Descriptive analyses of national GP workforce data betwen December 2017-September 2020, to determine the volume and geographical distribution of locum use and examine the characteristics of locums compared to other GP types. We modelled locum FTE using negative binomial regressions and estimated Incidence Rate Ratios (IRRs) for the association between the outcome and practice and population characteristics.

RESULTS: In December 2019, locums made up 1,217.9 (3.3%) of 33,996.6 total GP FTE which was fewer than other GP types. Median locum age was 42 years (IQR, 36-51), and the majority were UK qualified (660 of 1,034 total locum FTE), were male (642.6 of 1,178.9 locum FTE), and had long-term employment (834.1 of 1,127.9 total locum FTE). Rurality (IRR=1.250; 95%CI 1.095-1.428), inadequate CQC ratings (IRR=2.108; 95%CI 1.370-3.246) and single-handed practice (IRR=4.611; 95%CI 4.101-5.184), were strong predictors of locum use. There was substantial variation in locum use between regions.

CONCLUSION: GP locum use remained stable over time. Compared to other GPs, locums are younger male GPs, a substantial percentage of whom did not qualify in the UK, who serve underperforming practices in rural areas. This is likely to reflect recruitment or high turnover challenges in these practices/areas.

PMID:34990386 | DOI:10.3399/BJGP.2021.0311