Tag: nevin manimala

Bioinformatics. 2024 Jun 17:btae344. doi: 10.1093/bioinformatics/btae344. Online ahead of print.

ABSTRACT

MOTIVATION: Multi-strain infection is a common yet under-investigated phenomenon of many pathogens. Currently, biologists analyzing SNP information sometimes have to discard mixed infection samples as many downstream analyses require monogenomic inputs. Such a protocol impedes our understanding of the underlying genetic diversity, co-infection patterns, and genomic relatedness of pathogens. A scalable tool to learn and resolve the SNP-haplotypes from polygenomic data is an urgent need in molecular epidemiology.

RESULTS: We develop a slice sampling Markov Chain Monte Carlo algorithm, named SNP-Slice, to learn not only the SNP-haplotypes of all strains in the populations but also which strains infect which hosts. Our method reconstructs SNP-haplotypes and individual heterozygosities accurately without reference panels and outperforms the state-of-the-art methods at estimating the multiplicity of infections and allele frequencies. Thus, SNP-Slice introduces a novel approach to address polygenomic data and opens a new avenue for resolving complex infection patterns in molecular surveillance. We illustrate the performance of SNP-Slice on empirical malaria and HIV datasets and provide recommendations for using our method on empirical datasets.

AVAILABILITY AND IMPLEMENTATION: The implementation of the SNP-Slice algorithm, as well as scripts to analyze SNP-Slice outputs, are available at https://github.com/nianqiaoju/snp-slice.

PMID:38885409 | DOI:10.1093/bioinformatics/btae344

Adv Physiol Educ. 2024 Sep 1;48(3):465-473. doi: 10.1152/advan.00036.2024.

ABSTRACT

Student-faculty interaction (SFI) is an important indicator of student engagement that positively associates with academic achievement and retention. Quantitative information regarding the impact of emergency remote teaching (ERT) during COVID-19 on SFI is limited. This retrospective, observational cohort study tests the hypothesis that COVID-19 ERT negatively affected SFI in a gender-dependent manner. Electronic records of office hour (OH) appointments, used to measure SFI, for first-year medical students across three time periods, before, during and after COVID, were obtained and analyzed. A concerning, marked decline in SFI during and after the COVID-19 pandemic is noted. Before COVID, significantly more women (75.20%) made at least one OH appointment compared with men (40.54%). During COVID, the proportion of women making an OH appointment (69.71%) was statistically indistinguishable from women before COVID-19. In contrast, significantly fewer men during COVID (10.34%) than before COVID made an OH appointment. On return to face-to-face teaching, no rebound effect was observed. Compared with before COVID gender-matched peers, fewer men and women after COVID made OH appointments. Discipline-based analyses show that for all three time periods physiology emerged as the content area in which students made most OH appointments. The reduction in SFI observed, combined with the consistency with which the participants in our study indicated a need for assistance with the physiology discipline, emphasizes the importance of active promotion of faculty support and deliberate efforts to reconnect with students in the post-COVID context.NEW & NOTEWORTHY Applying readily available data, we quantify a persistent, negative impact of the shift to emergency remote teaching (ERT) on a measure of student-faculty interaction (SFI) among first-year medical students. A gender-based component to these effects is also discussed. Before, during, and after COVID, physiology emerged as the most engaged-with discipline as measured by office hour (OH) appointment volume.

PMID:38885323 | DOI:10.1152/advan.00036.2024

Diabetes Technol Ther. 2024 Jun 17. doi: 10.1089/dia.2024.0154. Online ahead of print.

ABSTRACT

BACKGROUND: Continuous glucose monitors (CGMs) are increasingly used to provide a detailed quantification of glycemic control and glucose variability. An open-source R package iglu has been developed to assist with automatic CGM metrics computation and data visualization, providing a comprehensive list of implemented CGM metrics. Motivated by the recent international consensus statement on CGM metrics and recommendations from recent reviews of available CGM software, here we present an updated version of iglu with improved accessibility and expanded functionality.

METHODS: The functionality was expanded to include automated computation of hypo- and hyperglycemia episodes with corresponding visualizations, composite metrics of glycemic control (Glycemia Risk Index (GRI), Personal Glycemic State (PGS)) and glycemic metrics associated with postprandial excursions. The algorithm for Mean Amplitude of Glycemic Excursions (MAGE) has been updated for improved accuracy, and the corresponding visualization has been added. Automated hierarchical clustering capabilities have been added to facilitate statistical analysis. The accessibility was improved by providing support for the automatic processing of common data formats, expanding the graphical user interface, and providing mirrored functionality in Python.

RESULTS: The updated version of iglu has been released to the Comprehensive R Archive Network (CRAN) as version 4.0.0. The corresponding Python wrapper has been released to the Python Package Index (PyPI) as version 0.1.0. The new functionality has been demonstrated using CGM data from 19 subjects with prediabetes and type 2 diabetes.

CONCLUSIONS: An updated version of iglu provides comprehensive and accessible software for analyses of CGM data that meets the needs of researchers with varying levels of programming experience. It is freely available on CRAN and on GitHub at https://github.com/irinagain/iglu.

PMID:38885321 | DOI:10.1089/dia.2024.0154

Vet Med Sci. 2024 Jul;10(4):e1478. doi: 10.1002/vms3.1478.

ABSTRACT

BACKGROUND/OBJECTIVES: The public perception relating to the welfare of horses involved with equestrian sports is associated with training methods used and the presentation of horses at events. In this context, very tight nosebands, which are intended to prevent the horse from opening its mouth, also attract a lot of attention. Various studies have evaluated the impact of tight nosebands on stress parameters, whereas the effect of tight nosebands on upper airway function is unknown. Therefore, the aim of the study was to use overground endoscopy to evaluate changes in pharyngeal and laryngeal function when a tight noseband is fitted. Moreover, the ridden horse pain ethogram (RHpE) was applied to investigate signs of discomfort (Dyson et al., 2018).

STUDY DESIGN: A randomized, blinded, and prospective study was performed.

METHODS: Sixteen warmblood horses consisting of twelve mares and four geldings with a mean age of 11.63 ± 3.53 years were ridden on 2 consecutive days with either loose or tight nosebands (two fingers or no space between bridge of the nose and noseband, respectively) and inserted endoscope in a random order. Videos were taken in a riding arena during a standardized exercise protocol involving beginner level tasks for 30 min in all gaits. For video analysis, freeze frames were prepared and analyzed at the beginning of the expiration phase. Pharyngeal diameter was measured using the pharynx-epiglottis ratio. Other findings (swallowing, pharyngeal collapse, soft palate movements, and secretion) were also evaluated. Moreover, the RHpE was applied. Descriptive statistics and generalized linear mixed effects models were used. Results with a p-value < 0.05 were considered statistically significant.

RESULTS: While the pharynx-epiglottis ratio did not change significantly in horses ridden with loose versus tight nosebands, there was an increase in mean grade and total counts of parameters assessed in the pharyngeal region, for example, grade of secretion (1.5 [±SD 0.89] vs. 3.13 [±SD 0.96]; p = 0.0001), axial deviation of the aryepiglottic folds (0.29 [±SD 0.73] vs. 1.33 [±SD 1.44]; p = 0.01), and pharyngeal collapse (0.69 [±SD 0.87] vs. 1.88 [±SD 1.54]; p = 0.005) in horses ridden with tight nosebands. There was no RHpE score above 8 indicating musculoskeletal pain, but the RHpE scores were significantly higher in horses ridden with tight nosebands (p < 0.001).

MAIN LIMITATIONS: Video quality was limited when horses showed large amounts of secretion. Another limitation was the small number of horses.

CONCLUSIONS: Results add to the evidence obtained in other studies that tight nosebands do not only cause adverse reactions based on the RHpE score such as head behind the vertical or intense staring but also contribute to changes in the pharyngeal region, such as increased secretion and collapse of pharyngeal structures. This may provide further support for future decisions regarding regulations on nosebands.

PMID:38885311 | DOI:10.1002/vms3.1478

Europace. 2024 Jun 17:euae170. doi: 10.1093/europace/euae170. Online ahead of print.

ABSTRACT

AIMS AND BACKGROUND: Subcutaneous implantable cardioverter-defibrillators (S-ICD) have become established in preventing sudden cardiac death, with some advantages over transvenous defibrillator systems, including a lower incidence of lead failures. Despite technological advancements, S-ICD carriers may suffer from significant complications, such as premature battery depletion (PBD) which led to an advisory for nearly 40,000 patients. This multicenter study evaluated the incidence of PBD in a large set of S-ICD patients.

METHODS: Data from patients implanted with S-ICD models A209 and A219 between October 2012 and July 2023 across 9 centers in Europe and the USA was reviewed. Incidence and implications of PBD, defined as clinically observed sudden drop in battery longevity were analyzed and compared to PBD with the definition of battery depletion within 60 months. Prospectively collected clinical data was obtained retrospectively from medical records, device telemetry, and manufacturer reports. This registry is listed on clinicaltrials.gov (NCT05713708).

RESULTS: Of the 1,112 S-ICD devices analyzed, 547 (49.2%) were equipped with a potentially affected capacitor linked to PBD occurrence, currently under FDA advisory. The median follow-up time for all patients was 46 (IQR 24-63) months. Clinically suspected PBD was observed in 159 (29.1%) of cases, with a median time to generator removal or replacement of 65 (IQR 55-72) months, indicative of significant deviations from expected battery lifespan. Manufacturer confirmation of PBD was made in 91.7% of devices returned for analysis. No cases of PBD were observed in devices that were not under advisory.

CONCLUSION: This manufacturer-independent analysis highlights a notable incidence of PBD in patients equipped with S-ICD models under advisory and the rate of PBD in this study corresponds to the rate currently estimated by the manufacturer. To the best of our knowledge this provides the largest contemporary peer-reviewed study cohort investigating the actual incidence of PBD in S-ICD patients. These findings emphasize the importance of post-market registries in collaboration between clinicians and the manufacturer to optimize safety and efficacy in S-ICD treatment.

PMID:38885309 | DOI:10.1093/europace/euae170

PLoS One. 2024 Jun 17;19(6):e0303526. doi: 10.1371/journal.pone.0303526. eCollection 2024.

ABSTRACT

With the escalating demand for energy, there is a growing focus on decentralized, small-scale energy infrastructure. The success of new turbines in this context is notable. However, many of these turbines do not follow many of the basic ideas established to evaluate their performance, leaving no precise technique or mathematical model. This research developed a Ducted Horizontal-axis Helical Wind Turbine (DHAHWT). The DHAHWT is a duct-mounted helical savonius turbine with a venturi and diffuser to improve flow. Unlike a vertical axis helical savonius turbine, DHAHWT revolves roughly parallel to the wind, making it a horizontal turbine. This complicates mathematical and theoretical analysis. This study created a DHAHWT mathematical model. COMSOL simulations utilizing Menter’s Shear Stress Transport model (SST) across an incoming velocity range of 1m/s to 4m/s were used to evaluate the turbine’s interaction with the wind. MATLAB was used to train an artificial neural network (ANN) utilizing COMSOL data to obtain greater velocity data. The Mean Average Percentage Error (MAPE) and Root Mean Square Error (RMSE) of ANN data were found to be 3%, indicating high accuracy. Further, using advanced statistical methods the Pearson’s correlation coefficient was calculated resulting in a better understanding of the relationship of between incoming velocity and velocity at different sections of the wind turbine. This study will shed light on the aerodynamics and working of DHAHWT.

PMID:38885289 | DOI:10.1371/journal.pone.0303526

J Med Philos. 2024 Jun 17:jhae017. doi: 10.1093/jmp/jhae017. Online ahead of print.

ABSTRACT

Jerome Wakefield criticizes my biostatistical analysis of the pathological-as statistically subnormal biological part-functional ability relative to species, sex, and age-for its lack of a harm clause. He first charges me with ignoring two general distinctions: biological versus medical pathology, and disease of a part versus disease of a whole organism. He then offers 10 counterexamples that, he says, are harmless dysfunctions but not medical disorders. Wakefield ends by arguing that we need a harm clause to explain American psychiatry’s 1973 decision to declassify homosexuality. I reply, first, that his two distinctions are philosophic fantasies alien to medical usage, invented only to save his own harmful-dysfunction analysis (HDA) from a host of obvious counterexamples. In any case, they do not coincide with the harmless/harmful distinction. In reality, medicine admits countless chronic diseases that are, contrary to Wakefield, subclinical for most of their course, as well as many kinds of typically harmless skin pathology. As for his 10 counterexamples, no medical source he cites describes them as he does. I argue that none of his examples contradicts the biostatistical analysis: all either are not part-dysfunctions (situs inversus, incompetent sperm, normal-flora infection) or are indeed classified as medical disorders (donated kidney, Typhoid Mary’s carrier status, latent tuberculosis or HIV, cherry angiomas). And if Wakefield’s HDA fits psychiatry, the fact that it does not fit medicine casts doubt on psychiatry’s status as a medical specialty.

PMID:38885259 | DOI:10.1093/jmp/jhae017

PLoS One. 2024 Jun 17;19(6):e0303898. doi: 10.1371/journal.pone.0303898. eCollection 2024.

ABSTRACT

Non-traumatic orthopedic conditions are pathological conditions involving musculoskeletal system that includes muscles, tendons, bone and joints and associated with frequent medical and surgical care and high treatment costs. There is paucity of information on the pattern of non-traumatic orthopedic conditions in low and middle income countries. The purpose of this study was to determine the epidemiology of non-traumatic orthopedic conditions among inpatients at the Kenyatta National Hospital in Kenya. This was a cross-sectional study with a sample of 175 charts reviewed. Approximately, 70.3% of the inpatients were aged between 25 to 64 years of age with the mean age of 39.97 years (STD 18.78). Ever married tended to be older 53.5 (95% CI: 46.8-60.2) years than other marital statuses. Approximately, 60.6% were males, 38.9% had comorbidities and 49.1% were casuals or unemployed. All inpatients were Kenyans with Nairobi County comprising 52.6% of all inpatients. Approximately, 77.7% were self-referrals. The commonest non-trauma orthopaedic conditions were infection and non-union (35.4%) and spinal degenerative diseases (20.60%) and the least was limb deformities (1.70%). Compared to females, males were 3.703 (p<0.001) times more likely to have infection and non-union. Patients with primary, secondary and tertiary education were 88.2% (p<0.001), 75.6% (p<0.001) and 68.1% (p = 0.016) less likely to have infection and non-union compared to those with no or preschool education. Widows were 8.500 (p = 0.028) times more likely to have spinal degenerative disease than married. Males were 70.8% (p = 0.031) less likely to have osteoarthritis than females. Inpatients with secondary education were 5.250 (p = 0.040) times more likely to have osteoarthritis than those with no or preschool education. In conclusion, majority of inpatients were young and middle aged adults. Infection and non-union and spinal degenerative diseases were the most common non-trauma orthopedic conditions. While males and those with low education were more likely to have infection and non-union, married were more likely to have spinal degenerative disease. Osteoarthritis was more likely among female admissions.

PMID:38885257 | DOI:10.1371/journal.pone.0303898

JMIR Public Health Surveill. 2024 Jun 17;10:e56064. doi: 10.2196/56064.

ABSTRACT

BACKGROUND: Predicting vaccination behaviors accurately could provide insights for health care professionals to develop targeted interventions.

OBJECTIVE: The aim of this study was to develop predictive models for influenza vaccination behavior among children in China.

METHODS: We obtained data from a prospective observational study in Wuxi, eastern China. The predicted outcome was individual-level vaccine uptake and covariates included sociodemographics of the child and parent, parental vaccine hesitancy, perceptions of convenience to the clinic, satisfaction with clinic services, and willingness to vaccinate. Bayesian networks, logistic regression, least absolute shrinkage and selection operator (LASSO) regression, support vector machine (SVM), naive Bayes (NB), random forest (RF), and decision tree classifiers were used to construct prediction models. Various performance metrics, including area under the receiver operating characteristic curve (AUC), were used to evaluate the predictive performance of the different models. Receiver operating characteristic curves and calibration plots were used to assess model performance.

RESULTS: A total of 2383 participants were included in the study; 83.2% of these children (n=1982) were <5 years old and 6.6% (n=158) had previously received an influenza vaccine. More than half (1356/2383, 56.9%) the parents indicated a willingness to vaccinate their child against influenza. Among the 2383 children, 26.3% (n=627) received influenza vaccination during the 2020-2021 season. Within the training set, the RF model showed the best performance across all metrics. In the validation set, the logistic regression model and NB model had the highest AUC values; the SVM model had the highest precision; the NB model had the highest recall; and the logistic regression model had the highest accuracy, F1 score, and Cohen κ value. The LASSO and logistic regression models were well-calibrated.

CONCLUSIONS: The developed prediction model can be used to quantify the uptake of seasonal influenza vaccination for children in China. The stepwise logistic regression model may be better suited for prediction purposes.

PMID:38885032 | DOI:10.2196/56064

JMIR Form Res. 2024 Jun 17;8:e51292. doi: 10.2196/51292.

ABSTRACT

BACKGROUND: The start of the COVID-19 pandemic resulted in the implementation of nonpharmaceutical interventions by US institutions of higher education at an unprecedented level. During the backdrop of an emerging pandemic, younger adults (eg, college students) had an overall lower risk for severe outcomes for SARS-CoV-2, making this population a potential source of transmission for age groups with high susceptibility and negative health outcomes. We examine how college students’ level of concern for COVID-19 was influenced by different sources of information, their living status, income level, and other demographic identifiers and its association with prevention behavior change.

OBJECTIVE: We sought to examine the level of concern, defined as the extent to which the participant would take corrective action to mitigate contracting or spreading the virus (to family or friends) by using personal protective equipment such as a face mask, practicing social distancing, and following other public health recommendations, among college students during the COVID-19 pandemic.

METHODS: A cross-sectional, web-based survey was conducted in 2021 among 185 college students aged 18-41 years, with most living in New York City and the United States (n=134, 72.4%). Out of 185 college students, 94 provided their zip codes, with 51 of those college students indicating they lived in New York City areas. The participants completed the survey via a QR code. Study participants who did not complete the full survey or were not college students in any US college or university were excluded. Analyses were conducted using R (version 4.2.2; R Foundation for Statistical Computing).

RESULTS: Of 185 respondents participated in the study, 25 (13.5.%) used emails from their schools, 51 (27.6%) used mainstream media, and 109 (58.9%) used social media and other sources to obtain information about COVID-19. Of the 109 participants who learned about the pandemic from social media, 91 (83.5%) were concerned; however, only 63% (32/51) and 60% (15/25) of the participants who sourced information from mainstream media and their schools’ email, respectively, were concerned. Further, the participants who received information from social media and other sources were about 3 times more likely to be concerned about COVID-19 than participants who received information from the university via email (P=.036; OR=3.07, 95% CI: 1.06-8.83)..

CONCLUSIONS: College students who received information from social media and other sources were more likely to be concerned about COVID-19 than students who received information from their school via emails.

PMID:38885019 | DOI:10.2196/51292