Category: Nevin Manimala

Microbiome. 2022 Jun 7;10(1):86. doi: 10.1186/s40168-022-01266-3.

ABSTRACT

BACKGROUND: The relationship between host conditions and microbiome profiles, typically characterized by operational taxonomic units (OTUs), contains important information about the microbial role in human health. Traditional association testing frameworks are challenged by the high dimensionality and sparsity of typical microbiome profiles. Phylogenetic information is often incorporated to address these challenges with the assumption that evolutionarily similar taxa tend to behave similarly. However, this assumption may not always be valid due to the complex effects of microbes, and phylogenetic information should be incorporated in a data-supervised fashion.

RESULTS: In this work, we propose a local collapsing test called phylogeny-guided microbiome OTU-specific association test (POST). In POST, whether or not to borrow information and how much information to borrow from the neighboring OTUs in the phylogenetic tree are supervised by phylogenetic distance and the outcome-OTU association. POST is constructed under the kernel machine framework to accommodate complex OTU effects and extends kernel machine microbiome tests from community level to OTU level. Using simulation studies, we show that when the phylogenetic tree is informative, POST has better performance than existing OTU-level association tests. When the phylogenetic tree is not informative, POST achieves similar performance as existing methods. Finally, in real data applications on bacterial vaginosis and on preterm birth, we find that POST can identify similar or more outcome-associated OTUs that are of biological relevance compared to existing methods.

CONCLUSIONS: Using POST, we show that adaptively leveraging the phylogenetic information can enhance the selection performance of associated microbiome features by improving the overall true-positive and false-positive detection. We developed a user friendly R package POSTm which is freely available on CRAN ( https://CRAN.R-project.org/package=POSTm ). Video Abstract.

PMID:35668471 | DOI:10.1186/s40168-022-01266-3

Int J Health Geogr. 2022 Jun 6;21(1):4. doi: 10.1186/s12942-022-00304-5.

ABSTRACT

BACKGROUND: Local policymakers require information about public health, housing and well-being at small geographical areas. A municipality can for example use this information to organize targeted activities with the aim of improving the well-being of their residents. Surveys are often used to gather data, but many neighborhoods can have only few or even zero respondents. In that case, estimating the status of the local population directly from survey responses is prone to be unreliable.

METHODS: Small Area Estimation (SAE) is a technique to provide estimates at small geographical levels with only few or even zero respondents. In classical individual-level SAE, a complex statistical regression model is fitted to the survey responses by using auxiliary administrative data for the population as predictors, the missing responses are then predicted and aggregated to the desired geographical level. In this paper we compare gradient boosted trees (XGBoost), a well-known machine learning technique, to a structured additive regression model (STAR) designed for the specific problem of estimating public health and well-being in the whole population of the Netherlands.

RESULTS: We compare the accuracy and performance of these models using out-of-sample predictions with five-fold Cross Validation (5CV). We do this for three data sets of different sample sizes and outcome types. Compared to the STAR model, gradient boosted trees are able to improve both the accuracy of the predictions and the total time taken to get these predictions. Even though the models appear quite similar in overall accuracy, the small area predictions at neighborhood level sometimes differ significantly. It may therefore make sense to pursue slightly more accurate models for better predictions into small areas. However, one of the biggest benefits is that XGBoost does not require prior knowledge or model specification. Data preparation and modelling is much easier, since the method automatically handles missing data, non-linear responses, interactions and accounts for spatial correlation structures.

CONCLUSIONS: In this paper we provide new nationwide estimates of health, housing and well-being indicators at neighborhood level in the Netherlands, see ‘Online materials’. We demonstrate that machine learning provides a good alternative to complex statistical regression modelling for small area estimation in terms of accuracy, robustness, speed and data preparation. These results can be used to make appropriate policy decisions at a local level and make recommendations about which estimation methods are beneficial in terms of accuracy, time and budget constraints.

PMID:35668432 | DOI:10.1186/s12942-022-00304-5

BMC Med Educ. 2022 Jun 6;22(1):433. doi: 10.1186/s12909-022-03504-6.

ABSTRACT

BACKGROUND: This study aimed to examine the satisfaction, educational linkage, and self-perceived competence of dental students enrolled in either 4 + 4 dental program, comprising an undergraduate degree and Doctor of Dental Surgery degree (DDS), or 3 + 4 program, which is a BS/DDS combined degree program, in the Korean dental education system.

MATERIALS AND METHODS: The survey questionnaire using a 5-point Likert scale was developed and validated by four dental education experts, consisting of satisfaction with undergraduate courses, the interconnection of undergraduate courses with the DDS curriculum, and self-assessed core competency for dental graduates. A total of 252 students provided informed consent and voluntarily responded to the survey, among whom 109 students were in the 3 + 4 system and 143 were in the 4 + 4 system. Cronbach’s correlation analysis and independent t-test were conducted for each evaluation item.

RESULTS: Students’ overall satisfaction level with the undergraduate education was higher in the 4 + 4 system than in the 3 + 4 system (P = 0.003). Students enrolled in the 4 + 4 system recognized that natural sciences are more connected to the graduate-level DDS program (P < 0.001), while the 3 + 4 students recognized that studies in medicine are closely interconnected to the DDS program (P = 0.001). There was almost no statistically significant difference in the students’ perception of competency between the two education systems.

DISCUSSION: Even though this study analyzed the case of a single university operating both 3 + 4 and 4 + 4 systems, it can be used as the groundwork for developing new opportunities and models of dental education system.

PMID:35668421 | DOI:10.1186/s12909-022-03504-6

BMC Endocr Disord. 2022 Jun 7;22(1):153. doi: 10.1186/s12902-022-01062-y.

ABSTRACT

BACKGROUND: The aim of this study is to compare muscle strength and architecture between type 1 diabetes patients and healthy volunteers and to assess whether there is an ultrasonographic structural change in this population.

METHODS: Thirty-two patients with T1D (23 female, 9 male) with an age average of 31.3 ± 8.7 years, matched in terms of age, gender, height, weight and physical activity were included in the study. In the T1D and control group, ultrasonographic measurements of quadriceps femoris muscle (RF, VI, VM, VL) and pennate angle (VI, VM, VL) were performed. Muscle strength values were measured using isokinetic dynamometer system at angular velocities of 60º/s and 180º/s in both groups.

RESULTS: Initially, both groups were similar in demographic and clinical characteristics (p > 0.05). In the T1D group, there was a statistically significant difference in flexion/extension peak torque measurements at an angular velocity of 60º/s compared to the control group (p < 0.05). In support of these isokinetic measurements, RF, VI, VM, VL muscle thicknesses and VI, VM pennate angle measurements in T1Ds were significantly lower (p < 0.05). When the T1D group was subgrouped according to HbA1C and diabetes duration, there was no significant difference in ultrasonographic and isokinetic measurements between the two groups (p > 0.05). When the T1D group was subgrouped, in the group that used insulin pump RF, VI, VM muscle thickness measurements were significantly higher (p < 0.05) than the group using subcutaneous insulin.

CONCLUSIONS: This study supports that muscle strength and architecture are adversely affected in the T1D patient group, insulin deficiency is a risk factor for sarcopenia and this can be shown through ultrasonography. It can also be said that insulin pump use has more positive effects in terms of diabetic myopathy than subcutaneous insulin, and diabetic myopathy develops independently of other diabetic complications. As a result, the muscle architecture of T1D people is adversely affected by insulin deprivation, so regular physical activity should be an integral part of diabetes treatment.

PMID:35668406 | DOI:10.1186/s12902-022-01062-y

BMC Med Educ. 2022 Jun 7;22(1):437. doi: 10.1186/s12909-022-03514-4.

ABSTRACT

BACKGROUND: To investigate the effect of the bridge-in, objective, preassessment, participatory learning, post assessment, and summary (BOPPPS) model combined with case-based learning (CBL) on ophthalmology teaching for five-year paediatric undergraduates.

METHODS: The effects of the BOPPPS model combined with CBL (BOPPPS-CBL) and traditional lecture-based learning (LBL) on ophthalmology teaching were compared among students in a five-year programme. The questionnaire surveys of the students were collected and statistically analysed after the class. The final examination scores, including on elementary knowledge and case analysis, in the two groups were analysed.

RESULTS: There were no statistically significant differences between the teachers and students in the baseline data. More students agreed that the BOPPPS-CBL model helped develop their problem-solving skills, analytical skills and motivation for learning better than the LBL model. There was no significant difference in learning pressure between the two groups. The final examination scores of the BOPPPS-CBL group were significantly higher than those of the LBL group. The overall course satisfaction of the BOPPPS-CBL group was obviously higher than that of the LBL group.

CONCLUSIONS: The BOPPPS-CBL model is an effective ophthalmology teaching method for five-year paediatric undergraduates.

PMID:35668389 | DOI:10.1186/s12909-022-03514-4

BMC Public Health. 2022 Jun 6;22(1):1127. doi: 10.1186/s12889-022-12655-6.

ABSTRACT

PURPOSE: Despite a maturing literature on the association between subjective wellbeing (SWB) and mental condition, little is known regarding the happiness-physical health relation in China, among middle-aged and elderly women (MAEW) in particular. This study aimed to understand the effect of physical health on the SWB of MAEW in China.

METHODS: Data from the 2014 and 2018 China Family Panel Study were used to analyse the SWB of women over the age of 45 years. In addition, descriptive statistics was used to describe the population distribution and panel ordered logit regression for regression analysis.

RESULTS: Majority of the respondents reported satisfactory SWB, and the proportion of the respondents who were very happy and happy was more than 68%. In terms of health factors, self-rated health, 2-week morbidity and BMI were significantly related to the SWB of MAEW (all P-values < 0.05). Physical exercise (P-value < 0.01) was positively associated with SWB, whereas smoking status and drinking status were not related to SWB. In addition, demographic indicators, such as registered residence (P-value < 0.01), income (P-value < 0.01) and social status (P-value < 0.01), significantly affected the SWB of MAEW.

CONCLUSION: This study showed that MAEW’s physical health could affect their SWB. Increased attention should be paid to the physical health of MAEW to improve their SWB. Policy mechanisms could be designed to motivate MAEW to take the initiative to engage in regular physical activity to improve their SWB. In addition, increased attention be paid to groups with low socioeconomic status and high stress, especially those who are employed, to improve residents’ happiness.

PMID:35668385 | DOI:10.1186/s12889-022-12655-6

BMC Musculoskelet Disord. 2022 Jun 6;23(1):544. doi: 10.1186/s12891-022-05486-4.

ABSTRACT

BACKGROUND: Osteoarthritis (OA) is a common degenerative joint disease leading to significant pain, mobility limitation, economic burden, reduced quality of life, and disability among adults globally. Psychological factors related to pain intensity (PI), kinesiophobia, fall self-efficacy (FSE), and balance may lead to a poor OA prognosis. This study was designed to explore the association between PI, kinesiophobia, FSE, balance, and age, gender, marital status, site of OA, duration, symmetry, comorbidity, and adaptive behaviours among patients with knee or hip OA.

METHODS: This cross-sectional study involved 70 purposively selected participants aged 59.91 ± 11.12 years. Numeric pain rating scale, Tampa scale for kinesiophobia, fall-efficacy scale, and timed up and go test were used to measure PI, kinesiophobia, FSE, and balance, respectively. Statistical analyses were completed with the Pearson correlation test, independent samples t-test, and multiple linear regression.

RESULTS: The participants were mainly women (n = 59, 84.3%). However, there was no gender difference in the reported PI, kinesiophobia, FSE, and balance. There was a significant correlation between FSE and balance (r = 0.422, p<0.001). Kinesiophobia was significantly associated with the presence of comorbidity (β = 0.240, p = 0.001) and knee OA (β = 0.208, p<0.042). There was an association between FSE and the use of a walking aid (β = -0.442, p<0.042), stop-for-rest during walking (β = -0.292, p = 0.002), presence of comorbidity (β = 0.209, p = 0.014), and bilateral lower limb OA (β = 0.167, p = 0.057). Balance was associated with the use of a walking aid (β = -0.421, p<0.001) and stop-for-rest during walking (β = – 0.294, p = 0.006).

CONCLUSION: Osteoarthritis-related psychological distress affects both men and women. This study support integration of psychological outcomes in the assessment, management, and follow-up of people with lower limb osteoarthritis. Moreover, comorbidity worsened psychological distress among people with osteoarthritis. Therefore, the traditional biomedical management of osteoarthritis can be optimised by timely diagnosis and treatment of comorbidities, and the inclusion of psychotherapy.

PMID:35668383 | DOI:10.1186/s12891-022-05486-4

BMC Infect Dis. 2022 Jun 6;22(1):521. doi: 10.1186/s12879-022-07501-4.

ABSTRACT

BACKGROUND: Women of reproductive age group have greater predilection to urinary tract infections (UTI). Various risk factors increase the prevalence in women. Emergence of multidrug resistant uropathogens make clinical management of UTI challenging. Here we assess holding of urine as risk factor of UTI in women and reasons for delayed voiding. We also investigate the relationship between frequency of UTIs and overall behavioural features, menstrual hygiene and attitude of women towards their own health issues.

METHODS: A questionnaire based cross-sectional study was performed with 816 hostel residents with written consent. Self-reported data was statistically analysed using SPSS software. Urinalysis and urine culture were done for 50 women by random sampling to obtain the information on leading causative agents of UTI in the study population and their antimicrobial resistance profile.

RESULTS: The prevalence of UTI among the participants without risk factors was found to be 27.5 (95% CI: 24.4-30.7). Attitude of women towards their own personal health issues and use of public toilets showed a correlation with prevalence of infection. Delay in urination on habitual basis was found to be associated with UTI. Uropathogens isolated by random sampling were resistant to multiple drugs that are generally used to treat UTI.

CONCLUSIONS: Holding urine for long time had proven to be an important risk factor and amongst different reasons of holding urine, holding due to poor sanitary condition of public toilets was the most common. Higher frequency of self-reported UTIs is related to holding of urine, behavioural features and attitude of women.

PMID:35668379 | DOI:10.1186/s12879-022-07501-4

BMC Bioinformatics. 2022 Jun 6;23(1):213. doi: 10.1186/s12859-022-04744-5.

ABSTRACT

BACKGROUND: Modern sequencing technologies have generated low-cost microbiome survey datasets, across sample sites, conditions, and treatments, on an unprecedented scale and throughput. These datasets often come with a phylogenetic tree that provides a unique opportunity to examine how shared evolutionary history affects the different patterns in host-associated microbial communities.

RESULTS: In this paper, we describe an R package, phyloMDA, for phylogeny-aware microbiome data analysis. It includes the Dirichlet-tree multinomial model for multivariate abundance data, tree-guided empirical Bayes estimation of microbial compositions, and tree-based multiscale regression methods with relative abundances as predictors.

CONCLUSION: phyloMDA is a versatile and user-friendly tool to analyze microbiome data while incorporating the phylogenetic information and addressing some of the challenges posed by the data.

PMID:35668363 | DOI:10.1186/s12859-022-04744-5

BMC Public Health. 2022 Jun 6;22(1):1130. doi: 10.1186/s12889-022-13507-z.

ABSTRACT

BACKGROUND: Nigeria has one of the highest under-five mortality rates in the world. Identifying the causes of these deaths is crucial to inform changes in policy documents, design and implementation of appropriate interventions to reduce these deaths. This study aimed to provide national and zonal-level estimates of the causes of under-five death in Nigeria in the 2013-2018 periods.

METHODS: We conducted retrospective inquiries into the cause of deaths of 948 neonates and 2,127 children aged 1-59 months as identified in the 2018 Nigeria Demographic and Health Survey (NDHS). The verbal autopsy asked about signs and symptoms during the final illness. The Physician Coded Verbal Autopsy (PCVA) and Expert Algorithm Verbal Autopsy (EAVA) methods were employed to assign the immediate and underlying cause of deaths to all cases.

RESULT: For the analysis, sampling weights were applied to accommodate non-proportional allocation. Boys accounted for 56 percent of neonatal deaths and 51.5 percent of the 1-59-months old deaths. About one-quarter of under-5 mortality was attributed to neonatal deaths, and 50 percent of these neonatal deaths were recorded within 48 h of delivery. Overall, 84 percent of the under-5 deaths were in the northern geopolitical zones. Based on the two methods for case analysis, neonatal infections (sepsis, pneumonia, and meningitis) were responsible for 44 percent of the neonatal deaths, followed by intrapartum injury (PCVA: 21 percent vs. EAVA: 29 percent). The three main causes of death in children aged 1-59 months were malaria (PCVA: 23 percent vs. EAVA: 35 percent), diarrhoea (PCVA: 17 percent vs. EAVA: 23 percent), and pneumonia (PCVA: 10 percent vs. EAVA: 12 percent). In the North West, where the majority of under-5 (1-59 months) deaths were recorded, diarrhoea was the main cause of death (PCVA: 24.3 percent vs. EAVA: 30 percent).

CONCLUSION: The causes of neonatal and children aged 1-59 months deaths vary across the northern and southern regions. By homing on the specific causes of mortality by region, the study provides crucial information that may be useful in planning appropriately tailored interventions to significantly reduce under-five deaths in Nigeria.

PMID:35668378 | DOI:10.1186/s12889-022-13507-z