Accurate prediction of RNA 5-hydroxymethylcytosine modification by utilizing novel position-specific gapped k-mer descriptors.

RNA modification is an essential step towards generation of new RNA structures. Such modification is potentially able to modify RNA function or its stability. Among different modifications, 5-Hydroxymethylcytosine (5hmC) modification of RNA exhibit significant potential for a series of biological processes. Understanding the distribution of 5hmC in RNA is essential to determine its biological functionality. Although conventional sequencing techniques allow broad identification of 5hmC, they are both time-consuming and resource-intensive. In this study, we propose a new computational tool called iRNA5hmC-PS to tackle this problem. To build iRNA5hmC-PS we extract a set of novel sequence-based features called Position-Specific Gapped k-mer (PSG k-mer) to obtain maximum sequential information. Our feature analysis shows that our proposed PSG k-mer features contain vital information for the identification of 5hmC sites. We also use a group-wise feature importance calculation strategy to select a small subset of features containing maximum discriminative information. Our experimental results demonstrate that iRNA5hmC-PS is able to enhance the prediction performance, dramatically. iRNA5hmC-PS achieves 78.3% prediction performance, which is 12.8% better than those reported in the previous studies. iRNA5hmC-PS is publicly available as an online tool at http://103.109.52.8:81/iRNA5hmC-PS. Its benchmark dataset, source codes, and documentation are available at https://github.com/zahid6454/iRNA5hmC-PS.

Knowledge, attitudes, and fear of COVID-19 during the Rapid Rise Period in Bangladesh.

The study aims to determine the level of Knowledge, Attitude, and Practice (KAP) related to COVID-19 preventive health habits and perception of fear towards COVID-19 in subjects living in Bangladesh. DESIGN: Prospective, cross-sectional survey of (n = 2157) male and female subjects, 13-88 years of age, living in Bangladesh. METHODS: Ethical approval and trial registration were obtained before the commencement of the study. Subjects who volunteered to participate and signed the informed consent were enrolled in the study and completed the structured questionnaire on KAP and Fear of COVID-19 scale (FCV-19S). RESULTS: Twenty-eight percent (28.69%) of subjects reported one or more COVID-19 symptoms, and 21.4% of subjects reported one or more co-morbidities. Knowledge scores were slightly higher in males (8.75± 1.58) than females (8.66± 1.70). Knowledge was significantly correlated with age (p < .005), an education level (p < .001), attitude (p < .001), and urban location (p < .001). Knowledge scores showed an inverse correlation with fear scores (p < .001). Eighty-three percent (83.7%) of subjects with COVID-19 symptoms reported wearing a mask in public, and 75.4% of subjects reported staying away from crowded places. Subjects with one or more symptoms reported higher fear compared to subjects without (18.73± 4.6; 18.45± 5.1). CONCLUSION: Bangladeshis reported a high prevalence of self-isolation, positive preventive health behaviors related to COVID-19, and moderate to high fear levels. Higher knowledge and Practice were found in males, higher education levels, older age, and urban location. Fear of COVID-19 was more prevalent in female and elderly subjects. A positive attitude was reported for the majority of subjects, reflecting the belief that COVID-19 was controllable and containable.

Characterisation of persons with lower limb amputation who attended a tertiary rehabilitation centre in Bangladesh.

Objective: We aimed to describe the causes, types, and consequences of lower limb amputation and the demographics of subjects with such amputation who attended a tertiary rehabilitation center in Bangladesh, Centre for the Rehabilitation of the Paralysed.Methods: Cross-sectional data were collected from subjects with lower limb amputation who attended a specialized rehabilitation center between January 2014 and August 2016. Telephone interviews were conducted using a structured questionnaire. Descriptive analysis, paired t-test, and Fisher's exact test were conducted as well as a regression analysis was performed.Results: A total of 332 respondents, aged 5 to 76 years (mean 37.5± SD 13.8), with lower limb amputation participated in the study. Of the respondents, the majority were male (87.7%) and lived in rural areas (64.8%). Road traffic accidents were the leading cause (58.7%) of amputation followed by peripheral vascular diseases (7.5%) and hit by sharp objects (7.2%). Age (odds ratio: 0.9) and driving as occupation (odds ratio: 7.3) were found to be statistically significant covariates for amputation from road traffic accidents. The mean duration between having an amputation and receiving the first prosthetic fitting was 6.4 years (±8.9). Among the study participants, 30.7% lost their jobs after amputation and their mean monthly income reduced significantly (p < 0.01) from US$119.9 (±421.5) to US$45.8 (±63.1).Conclusion: Majority of the lower limb amputations resulted from traumatic road traffic accidents. Younger males and drivers were found to be more prone to amputation from road traffic accidents. Lower limb amputation creates great health and economic disparity in the amputee's lives.Implications for rehabilitationMajority of the lower limb amputation cases in Bangladesh were attributable to road traffic accidents-a largely preventable cause.The mean time between amputation and prosthetic fitting was more than 6 years which implies lack of awareness and inaccessibility of prosthetic management.Policymakers, regulators, law enforcement, and traffic safety advocates should take urgent actions to prevent road traffic accidents and raise awareness about and improve availability of prosthetic rehabilitation in Bangladesh.

Double valve replacement in a case of dextrocardia and situs inversus totalis.

The incidence of situs inversus totalis is 1/10,000 to 1/50,000 live births. A 43-year-old female patient was incidentally diagnosed to have situs inversus totalis with severe mitral and aortic stenosis. The patient was thoroughly assessed, and the plan of surgery was modified accordingly. Under cardiopulmonary bypass, the mitral valve and aortic valve were replaced with 27-size and 19-size St. Jude medical mechanical valve, respectively, while the operating surgeon stood on left side. The postoperative period was uneventful. Thorough assessment and preoperative planning are essential for success in such cases.

Device and programming abstractions for spatiotemporal control of active micro-particle swarms.

We present a hardware setup and a set of executable commands for spatiotemporal programming and interactive control of a swarm of self-propelled microscopic agents inside a microfluidic chip. In particular, local and global spatiotemporal light stimuli are used to direct the motion of ensembles of Euglena gracilis, a unicellular phototactic organism. We develop three levels of programming abstractions (stimulus space, swarm space, and system space) to create a scripting language for directing swarms. We then implement a multi-level proof-of-concept biotic game using these commands to demonstrate their utility. These device and programming concepts will enhance our capabilities for manipulating natural and synthetic swarms, with future applications for on-chip processing, diagnostics, education, and research on collective behaviors.

The Impact of Interactivity on Comprehending 2D and 3D Visualizations of Movement Data.

GPS, RFID, and other technologies have made it increasingly common to track the positions of people and objects over time as they move through two-dimensional spaces. Visualizing such spatio-temporal movement data is challenging because each person or object involves three variables (two spatial variables as a function of the time variable), and simply plotting the data on a 2D geographic map can result in overplotting and occlusion that hides details. This also makes it difficult to understand correlations between space and time. Software such as GeoTime can display such data with a three-dimensional visualization, where the 3rd dimension is used for time. This allows for the disambiguation of spatially overlapping trajectories, and in theory, should make the data clearer. However, previous experimental comparisons of 2D and 3D visualizations have so far found little advantage in 3D visualizations, possibly due to the increased complexity of navigating and understanding a 3D view. We present a new controlled experimental comparison of 2D and 3D visualizations, involving commonly performed tasks that have not been tested before, and find advantages in 3D visualizations for more complex tasks. In particular, we tease out the effects of various basic interactions and find that the 2D view relies significantly on "scrubbing" the timeline, whereas the 3D view relies mainly on 3D camera navigation. Our work helps to improve understanding of 2D and 3D visualizations of spatio-temporal data, particularly with respect to interactivity.

An exploratory case control study of risk factors for hepatitis E in rural Bangladesh.

Hepatitis E virus (HEV) is the major cause of epidemic and sporadic hepatitis globally. Outbreaks are associated with fecal contamination of drinking water, yet the environmental reservoir of HEV between epidemics remains unclear. In contrast to neighboring countries, where epidemics and sporadic disease co-occur, HEV-endemic communities in rural Bangladesh seldom report outbreaks; sporadic hepatitis E is reported from urban and rural areas of the country. Besides typical enteric risk factors, other routes for HEV infection and disease are unclear. We conducted monthly household surveillance of a southern Bangladeshi community of 23,500 people to find incident cases of acute hepatitis E over a 22 month period. An algorithm was used to capture 279 candidate cases, of which 46 were confirmed acute HEV infections. An exploratory case-control study was conducted to identify putative risk factors for disease. Nearly 70% of cases were over 15 years old. Female gender seemed protective (OR:0.34) against hepatitis E in this conservative setting, as was the use of sanitary latrines (OR:0.28). Socioeconomic status or animal exposures were not significant predictors of disease, although outdoor employment and recent urban travel were. Unexpectedly, recent contact with a "jaundiced" patient and a history of injection exposure in the 3 months prior to disease (OR:15.50) were significant. Susceptible individuals from "endemic" communities share similar enteric exposure risks to those commonly associated with tourists from non-endemic countries. This study also raises the novel possibility of parenteral and person-to-person transmission of HEV in non-epidemic, sporadic disease settings.

Baseline comorbidities in a skin cancer prevention trial in Bangladesh.

BACKGROUND: Epidemiologic research suggests that increased cancer risk due to chronic arsenic exposure persists for several decades even after the exposure has terminated. Observational studies suggest that antioxidants exert a protective effect on arsenical skin lesions and cancers among those chronically exposed to arsenic through drinking water. This study reports on the design, methods and baseline analyses from the Bangladesh Vitamin E and Selenium Trial (BEST), a population-based chemoprevention study conducted among adults in Bangladesh with visible arsenic toxicity. MATERIALS AND METHODS: Bangladesh Vitamin E and Selenium Trial is a 2 × 2 full factorial, double-blind, randomized controlled trial of 7000 adults having manifest arsenical skin lesions evaluating the efficacy of 6-year supplementation with alpha-tocopherol (100 mg daily) and L-selenomethionine (200 µg daily) for the prevention of nonmelanoma skin cancer. RESULTS: In cross-sectional analyses, we observed significant associations of skin lesion severity with male gender (female prevalence odds ratio (POR) = 0.87; 95% CI = 0.79-0.96), older age (aged 36-45 years, POR = 1.27; 95% CI = 1.13-1.42; aged 46-55 years, POR = 1.44; 95% CI = 1.27-1.64 and aged 56-65 years, POR = 1.50; 95% CI = 1.26-1.78 compared with aged 25-35 years), hypertension (POR = 1.29; 95% CI = 1.08-1.55), diabetes (POR = 2.13; 95% CI = 1.32-3.46), asthma (POR = 1.55; 95% CI = 1.03-2.32) and peptic ulcer disease (POR = 1.20; 95% CI = 1.07-1.35). CONCLUSIONS: We report novel associations between arsenical skin lesions with several common chronic diseases. With the rapidly increasing burden of preventable cancers in developing countries, efficient and feasible chemoprevention study designs and approaches, such as employed in BEST, may prove both timely and potentially beneficial in conceiving cancer chemoprevention trials in Bangladesh and beyond.

Reinforced tension line suture closure after midline laparotomy in emergency surgery.

Midline laparotomy is an emergency surgical operation frequently performed in cases of intra-abdominal pathology. Closure of the incision is usually done by continuous suturing by mass closure. In an emergency operation the intra-abdominal milieu is usually contaminated leading to gut oedema and, hence, an increase in postoperative intra-abdominal pressure. It is complicated by wound dehiscence, burst abdomen, etc. The cause of this complication is an increase in horizontal tensile forces on the site of the insertion of sutures which cuts the sheath. In this technique of reinforced tension line suture peak tensile forces are distributed from the suture base to the surrounding tissue through a horizontal suture, thereby preventing the suture from cutting through the tissue. From July 2007 to June 2009 patients requiring laparotomy were randomly divided into test and control groups by a 'closed envelope' technique. Their postoperative intra-abdominal pressure was recorded by urinary bladder catheter manometry. The result of this technique was compared with the incidence of burst abdomen in cases where it was closed by continuous suture. A total of 190 patients underwent laparotomy. In 90 the abdomen was closed by reinforced tension line (RTL) and in 100 patients by continuous suturing. None of the RTL group had a burst abdomen. Thirteen who had closure by continuous suture had a burst abdomen. The analysis of the results was done using the chi-square test. On comparing the incidence of burst abdomen in cases operated by continuous suture technique and by RTL, the P value was found to be 0.0026 which is highly significant. On analysis of the incidence of burst abdomen in cases having a grade II intra-abdominal pressure the P value was found to be 0.0009 which is highly significant. Closure of midline incision by RTL reduces the incidence of burst abdomen. Registration No. PROVCTRI/2008/091/000269 (http://www.ctri.in).

Toward high-quality gradient estimation on regular lattices.

In this paper, we present two methods for accurate gradient estimation from scalar field data sampled on regular lattices. The first method is based on the multidimensional Taylor series expansion of the convolution sum and allows us to specify design criteria such as compactness and approximation power. The second method is based on a Hilbert space framework and provides a minimum error solution in the form of an orthogonal projection operating between two approximation spaces. Both methods lead to discrete filters, which can be combined with continuous reconstruction kernels to yield highly accurate estimators as compared to the current state of the art. We demonstrate the advantages of our methods in the context of volume rendering of data sampled on Cartesian and Body-Centered Cubic lattices. Our results show significant qualitative and quantitative improvements for both synthetic and real data, while incurring a moderate preprocessing and storage overhead.

Epidemiology and risk factors of incident hepatitis E virus infections in rural Bangladesh.

Hepatitis E virus (HEV) is the most common cause of acute viral hepatitis in the world. Most of South Asia is HEV endemic, with frequent seasonal epidemics of hepatitis E and continuous sporadic cases. This author group's epidemiologic work and clinical reports suggest that Bangladesh is HEV endemic, but there have been few population-based studies of this country's HEV burden. The authors calculated HEV infection rates, over an 18-month interval between 2003 and 2005, by following a randomly selected cohort of 1,134 subjects between the ages of 1 and 88 years, representative of rural communities in southern Bangladesh. Baseline prevalence of antibody to hepatitis E virus (anti-HEV) was 22.5%. Seroincidence was 60.3 per 1,000 person-years during the first 12 months and 72.4 per 1,000 person-years from >12 to 18 months (during the monsoon season), peaking by age 50 years and with low rates during childhood. Few of the seroconverting subjects reported hepatitis-like illness. Overall incidence was calculated to be 64 per 1,000 person-years, with 1,172 person-years followed. No significant associations were found between anti-HEV incidence and demographic or socioeconomic factors for which data were available. This is the first study to document annual HEV infection rates among "healthy" and very young to elderly subjects in a rural Bangladeshi population.

Population seroprevalence of hepatitis E virus antibodies in rural Bangladesh.

Hepatitis E virus (HEV) causes a substantial burden of sporadic and epidemic disease worldwide. HEV infections result in serious morbidity and mortality, especially among pregnant women, and have significant economic costs. Few population-based studies have characterized the epidemiology of HEV. A rural Bangladeshi population was studied to determine the age- and gender- specific population seroprevalence of antibodies to HEV. Of 1,134 specimens tested from a representative, random population sample, 255 (22.5%) were anti-HEV IgG seropositive. Seroprevalence was lower among women (19.7%) than among men (25.8%). We found anti-HBc (hepatitis B core) in 380 of 1080(35.2%) tested, anti-HCV (hepatitis C) in 14 of 917(1.5%) tested, and anti-HAV (hepatitis A) in 116 of 124(93.5%) tested individuals. Our data suggest that viral hepatitis, especially HEV, remains an under-recognized and significant public health problem in rural Bangladeshi populations, warranting further attention.

Flocculant-disinfectant point-of-use water treatment for reducing arsenic exposure in rural Bangladesh.

We introduced flocculant-disinfectant water treatment for 12 weeks in 103 households in Bangladesh to assess if drinking water would be chemically and microbiologically improved and the body burden of arsenic reduced. The median concentration of arsenic in tubewell water decreased by 88% after introduction of the flocculant-disinfectant from 136 microg/l at baseline to 16 (p < 0.001). The median concentration of total urinary arsenic decreased 42% from 385 microg/g creatinine at baseline to 225 microg/g creatinine after intervention (p < 0.001). Among 206 post-intervention drinking water samples that were reportedly treated on the date the sample was collected, 99 (48%) lacked residual free chlorine and 100 (49%) were contaminated with thermotolerant coliforms. The flocculant-disinfectant markedly reduced arsenic in drinking water, but treated drinking water was frequently contaminated with fecal organisms. The lesser reduction in urinary arsenic compared to water arsenic and the health consequences of this reduction require further research.