Automated, phylogeny-based genotype delimitation of the Hepatitis Viruses HBV and HCV

Background The classification of hepatitis viruses still predominantly relies on ad hoc criteria, i.e., phenotypic traits and arbitrary genetic distance thresholds. Given the subjectivity of such practices coupled with the constant sequencing of samples and discovery of new strains, this manual approach to virus classification becomes cumbersome and impossible to generalize. Methods Using two well-studied hepatitis virus datasets, HBV and HCV, we assess if computational methods for molecular species delimitation that are typically applied to barcoding biodiversity studies can also be successfully deployed for hepatitis virus classification. For comparison, we also used ABGD, a tool that in contrast to other distance methods attempts to automatically identify the barcoding gap using pairwise genetic distances for a set of aligned input sequences. Results—Discussion We found that the mPTP species delimitation tool identified even without adapting its default parameters taxonomic clusters that either correspond to the currently acknowledged genotypes or to known subdivision of genotypes (subtypes or subgenotypes). In the cases where the delimited cluster corresponded to subtype or subgenotype, there were previous concerns that their status may be underestimated. The clusters obtained from the ABGD analysis differed depending on the parameters used. However, under certain values the results were very similar to the taxonomy and mPTP which indicates the usefulness of distance based methods in virus taxonomy under appropriate parameter settings. The overlap of predicted clusters with taxonomically acknowledged genotypes implies that virus classification can be successfully automated

Experience of stigmatization in children receiving inpatient and outpatient mental health treatment: a longitudinal study.

Mental health-related stigma is poorly understood, and minimal research has focused on the experience of stigma from children's perspectives. We sought to investigate whether children treated as inpatients and outpatients had different experiences of stigma over time and whether stigma is linked to global functioning cross-sectionally and longitudinally. Children, aged 8-12 years, receiving treatment within a national specialist mental health inpatient unit were matched for age, gender and diagnosis with children receiving outpatient treatment (N = 64). Validated measures of stigma, global functioning and symptom severity were collected at the start of treatment and upon discharge from the ward for inpatients, and a similar timeframe for their individually matched outpatients. Latent change score models and partial correlation coefficients were employed to test our hypotheses. No differences in most aspects of stigma between children treated as inpatients and outpatients were observed, except for personal rejection at baseline and self-stigma at follow-up favouring outpatients. A reduction in stigma was observed in societal devaluation, personal rejection and secrecy for inpatients, and self-stigma and secrecy for outpatients between the two assessments. Societal devaluation declined at a higher rate among inpatients compared to outpatients, albeit reductions in stigma were comparable for all remaining measures. No association was found between the change in stigma and change in global functioning. Future research may offer further insights into the development and maintenance of stigma and identify key targets for anti-stigma interventions to reduce its long-term impact

Measuring stigma in children receiving mental health treatment: Validation of the Paediatric Self-Stigmatization Scale (PaedS)

BACKGROUND: Research on the impact of stigma associated with mental illness in children is scarce. Considering the known negative effects of stigma associated with mental illness in adults, it is crucial to explore the stigma experienced by children who access mental health treatment. However, no scale measuring self-stigmatization in younger children is available to date. This study aimed to develop and validate such a scale, the Paediatric Self-Stigmatization Scale (PaedS). METHODS: A total of 156 children (119 receiving outpatient and 37 receiving inpatient treatment), aged 8-12 years, completed the PaedS, the Self-Perception Profile for Children and the Pediatric Quality of Life Inventory (PedsQL - Child Report, ages 8-12). In addition, parents completed the PedsQL (Parent Report for Children, ages 8-12), the Strengths and Difficulties Questionnaire (SDQ) and a modified subscale of the PaedS measuring the children's rejection by others due to their mental health difficulties. RESULTS: A confirmatory factor analysis showed that a four-factor structure, comprising Societal Devaluation, Personal Rejection, Self-Stigma and Secrecy scales, had excellent fit to the data (CFI=0.95; TLI=0.95; RMSEA=0.05). Child-reported PaedS scores were positively correlated with parental-reported PaedS scores and negatively with PedsQL, the SDQ, and 5 out of 6 subscales of the Self-Perception Profile for Children, suggesting adequate convergent validity (all P-values<0.05). CONCLUSIONS: The PaedS is a valid instrument, which is hoped to advance the understanding of self-stigmatization in children with mental health difficulties and contribute to its prevention

Status and perspectives of hospital mortality in a public urban Hellenic hospital, based on a five-year review

<p>Abstract</p> <p>Background</p> <p>Analysis of hospital mortality helps to assess the standards of health-care delivery.</p> <p>Methods</p> <p>This is a retrospective cohort study evaluating the causes of deaths which occurred during the years 1995–1999 in a single hospital. The causes of death were classified according to the International Statistical Classification of Diseases (ICD-10).</p> <p>Results</p> <p>Of the 149,896 patients who were discharged the 5836 (3.4%) died. Males constituted 55% and females 45%. The median age was 75.1 years (1 day – 100 years).</p> <p>The seven most common ICD-10 chapters IX, II, IV, XI, XX, X, XIV included 92% of the total 5836 deaths.</p> <p>The most common contributors of non-neoplasmatic causes of death were cerebrovascular diseases (I60–I69) at 15.8%, ischemic heart disease (I20–I25) at 10.3%, cardiac failure (I50.0–I50.9) at 7.9%, diseases of the digestive system (K00–K93) at 6.7%, diabetes mellitus (E10–E14) at 6.6%, external causes of morbidity and mortality (V01–Y98) at 6.2%, renal failure (N17–N19) at 4.5%, influenza and pneumonia (J10–J18) at 4.1% and certain infectious and parasitic diseases (A00–B99) at 3.2%, accounting for 65.3% of the total 5836 deaths.</p> <p>Neoplasms (C00–D48) caused 17.7% (n = 1027) of the total 5836 deaths, with leading forms being the malignant neoplasms of bronchus and lung (C34) at 3.5% and the malignant neoplasms of large intestine (C18–21.2) at 1.5%. The highest death rates occurred in the intensive care unit (23.3%), general medicine (10.7%), cardiology (6.5%) and nephrology (5.5%).</p> <p>Key problems related to certification of death were identified. Nearly half of the deaths (49.3%: n = 2879) occurred by the completion of the third day, which indicates the time limits for investigation and treatment. On the other hand, 6% (n = 356) died between the 29^thand 262^nddays after admission.</p> <p>Inadequacies of the emergency care service, infection control, medical oncology, rehabilitation, chronic and terminal care facilities, as well as lack of regional targets for reducing mortality related to diabetes, recruitment of organ donors, provision for the aging population and lack of prevention programs were substantiated.</p> <p>Conclusion</p> <p>Several important issues were raised. Disease specific characteristics, as well as functional and infrastructural inadequacies were identified and provided evidence for defining priorities and strategies for improving the standards of care. Effective transformation can promise better prospects.</p

Gastric and intestinal barrier impairment in tropical enteropathy and HIV: limited impact of micronutrient supplementation during a randomised controlled trial

<p>Abstract</p> <p>Background</p> <p>Although micronutrient supplementation can reduce morbidity and mortality due to diarrhoea, nutritional influences on intestinal host defence are poorly understood. We tested the hypothesis that micronutrient supplementation can enhance barrier function of the gut.</p> <p>Methods</p> <p>We carried out two sub-studies nested within a randomised, double-blind placebo-controlled trial of daily micronutrient supplementation in an urban community in Lusaka, Zambia. In the first sub-study, gastric pH was measured in 203 participants. In the second sub-study, mucosal permeability, lipopolysaccharide (LPS) and anti-LPS antibodies, and serum soluble tumour necrosis factor receptor p55 (sTNFR55) concentrations were measured in 87 participants. Up to three stool samples were also analysed microbiologically for detection of asymptomatic intestinal infection. Gastric histology was subsequently analysed in a third subset (n = 37) to assist in interpretation of the pH data. Informed consent was obtained from all participants after a three-stage information and consent process.</p> <p>Results</p> <p>Hypochlorhydria (fasting gastric pH > 4.0) was present in 75 (37%) of participants. In multivariate analysis, HIV infection (OR 4.1; 95%CI 2.2-7.8; <it>P </it>< 0.001) was associated with hypochlorhydria, but taking anti-retroviral treatment (OR 0.16; 0.04-0.67; <it>P </it>= 0.01) and allocation to micronutrient supplementation (OR 0.53; 0.28-0.99; <it>P </it>< 0.05) were protective. Hypochlorhydria was associated with increased risk of salmonellosis. Mild (grade 1) gastric atrophy was found in 5 participants, irrespective of <it>Helicobacter pylori </it>or HIV status. Intestinal permeability, LPS concentrations in serum, anti-LPS IgG, and sTNFR55 concentrations did not differ significantly between micronutrient and placebo groups. Anti-LPS IgM was reduced in the micronutrient recipients (<it>P <</it>0.05).</p> <p>Conclusions</p> <p>We found evidence of a specific effect of HIV on gastric pH which was readily reversed by anti-retroviral therapy and not mediated by gastric atrophy. Micronutrients had a modest impact on gastric pH and one marker of bacterial translocation.</p> <p>Trial Registration</p> <p>Current Controlled Trials ISRCTN31173864</p

A proposal for a new integrated Tsunami intensity scale (ITIS-2012)

The implementation of a new Tsunami Intensity Scale is proposed because a vast amount of data has been collected from the two megatsunamis that took place in the Indian Ocean in 2004 and northeast Japan in 2011. The newly proposed scale is 12-grade and is based on the assessment of a large number of objective criteria that are easily accessible and incorporated into six groups. As a result, it does not saturate as six-grade scales do. More specifically, the estimation of intensity values takes into account: (1) the quantities of the phenomena, (2) the direct impact on humans, (3) the impact on mobile objects, (4) the impact on coastal infrastructure, (5) the impact on the environment, and (6) the impact on structures. The new scale is compatible with the widely used EMS1998 and ESI2007 scales and has a reliable horizontal correspondence throughout the groups of criteria. It is easily and directly applicable to all environments, and particularly useful for the outlining of microzones of different intensities in any tsunami-affected area. It can be implemented for any land use/cover type, such as urban, rural, industrial, touristic, and so on, and at the same time, morphologic diversity of affected areas is not an obstacle to application

Anthropometric, flexibility, strength-power, and sport-specific correlates in elite fencing

This study investigated selected structural correlates of fencing performance. 33 elite fencers were tested on (a) selected anthropometric, flexibility, and strength-power related parameters, and (b) specific lower extremity functional fencing tests. Multiple regression showed that drop jump and thigh cross-sectional area were best predictors of lunge time and distance of squat jump on the shuttle test. When the two performance variables were expressed per Lean Body Mass, lunge time was significantly predicted only by the performance on the arm-driven counter-movement jump, while time on the shuttle test was best predicted by three noncollinear significant predictors: squat jump performance, thigh circumference, and percent body fat. Lunge time and time on the shuttle test were predicted by explosive power, while none of the nontrainable anthropometric measures or years of training seemed to be important in performance of fencing-related skills. © Perceptual and Motor Skills 2010