Computational methods for prediction of T-cell epitopes - a framework for modelling, testing, and applications

Computational models complement laboratory experimentation for efficient identification of MHC-binding peptides and T-cell epitopes. Methods for prediction of MHC-binding peptides include binding motifs, quantitative matrices, artificial neural networks, hidden Markov models, and molecular modelling. Models derived by these methods have been successfully used for prediction of T-cell epitopes in cancer, autoimmunity, infectious disease, and allergy. For maximum benefit, the use of computer models must be treated as experiments analogous to standard laboratory procedures and performed according to strict standards. This requires careful selection of data for model building, and adequate testing and validation. A range of web-based databases and MHC-binding prediction programs are available. Although some available prediction programs for particular MHC alleles have reasonable accuracy, there is no guarantee that all models produce good quality predictions. In this article, we present and discuss a framework for modelling, testing, and applications of computational methods used in predictions of T-cell epitopes. (C) 2004 Elsevier Inc. All rights reserved.

Electronic medical records may be inadequate for improving population health status through general practice: cervical smears as a case study

Objective: To determine whether routine electronic records are an accurate source of population health data in general practice through reviewing cervical smears rates in four South Australian practices. Methods: The cervical screening rate in a purposive sample of four general practices (three rural and one urban) was obtained using an audit of medical records and a telephone follow-up. Results: The cervical screening rate using only immediately available electronic medical records indicated an overall low rate for the participating practices (44.9%). However, telephone follow-up and adjustments to the denominator indicated the real rate to be 85.7%. The offer of appointments during the telephone follow-up further improved this rate for eligible women (93.8%). Conclusions and implications: Electronic medical records may be inadequate in preventive screening in general practice, without ensuring their accuracy. Updating records by telephone or personal follow-up produces a much more accurate denominator.

HPLC-FLD methods to quantify chloroaluminum phthalocyanine in nanoparticles, plasma and tissue: application in pharmacokinetic and biodistribution studies

Analytical and bioanalytical methods of high-performance liquid chromatography with fluorescence detection (HPLC-FLD) were developed and validated for the determination of chloroaluminum phthalocyanine in different formulations of polymeric nanocapsules, plasma and livers of mice. Plasma and homogenized liver samples were extracted with ethyl acetate, and zinc phthalocyanine was used as internal standard. The results indicated that the methods were linear and selective for all matrices studied. Analysis of accuracy and precision showed adequate values, with variations lower than 10% in biological samples and lower than 2% in analytical samples. The recoveries were as high as 96% and 99% in the plasma and livers, respectively. The quantification limit of the analytical method was 1.12 ng/ml, and the limits of quantification of the bioanalytical method were 15 ng/ml and 75 ng/g for plasma and liver samples, respectively. The bioanalytical method developed was sensitive in the ranges of 15-100 ng/ml in plasma and 75-500 ng/g in liver samples and was applied to studies of biodistribution and pharmacokinetics of AlClPc. (C) 2011 Elsevier B.V. All rights reserved.

Response to Screening for abdominal aortic aneurysm - Screening reduces deaths related to aneurysm

Editor—We reported the study in a transparent fashion and were deliberately cautious in our conclusions. Australia and the United Kingdom are very different with regard to arrangements for primary care, which did not permit us to undertake a preliminary assessment of the eligibility of men for screening before we randomised them and issued half invitations to attend for the ultrasound examination.

Validated spectrophotometric and spectrofluorimetric methods for determination of chloroaluminum phthalocyanine in nanocarriers

UV-VIS-Spectrophotometric and spectrofluorimetric methods have been developed and validated allowing the quantification of chloroaluminum phthalocyanine (CIAIPc) in nanocarriers. In order to validate the methods, the linearity, limit of detection (LOD), limit of quantification (LOQ), precision, accuracy, and selectivity were examined according to USP 30 and ICH guidelines. Linearities range were found between 0.50-3.00 mu g.mL(-1) (Y=0.3829 X [CIAIPc, mu g.mL(-1)] + 0.0126; r=0.9992) for spectrophotometry, and 0.05-1.00 mu g.mL(-1) (Y=2.24 x 10(6) X [CIAIPc, mu g.L(-1)] + 9.74 x 10(4); r=0.9978) for spectrofluorimetry. In addition, ANOVA and Lack-of-fit tests demonstrated that the regression equations were statistically significant (p<0.05), and the resulting linear model is fully adequate for both analytical methods. The LOD values were 0.09 and 0.01 mu g.mL(-1), while the LOCI were 0.27 and 0.04 mu g.mL(-1) for spectrophotometric and spectrofluorimetric methods, respectively. Repeatability and intermediate precision for proposed methods showed relative standard deviation (RSD) between 0.58% to 4.80%. The percent recovery ranged from 98.9% to 102.7% for spectrophotometric analyses and from 94.2% to 101.2% for spectrofluorimetry. No interferences from common excipients were detected and both methods were considered specific. Therefore, the methods are accurate, precise, specific, and reproducible and hence can be applied for quantification of CIAIPc in nanoemulsions (NE) and nanocapsules (NC).

Gestational diabetes mellitus: From consensus to action on screening and treatment

The 1998 consensus guidelines on the management of gestational diabetes mellitus from the Australasian Diabetes in Pregnancy Society emphasised that, “due to a lack of good quality randomised controlled clinical trials in the area of [gestational diabetes mellitus], these guidelines are based on what is a reasonable consensus of informed opinion in Australasia”.1 The clear benefits of treating women with gestational diabetes according to these guidelines have now been demonstrated by the Australian Carbohydrate Intolerance Study in Pregnant Women (ACHOIS).2 This study randomised 1000 women with gestational diabetes to either routine antenatal care or to an intervention that comprised home glucose monitoring, review by a diabetes educator, dietitian and physician, and insulin therapy if glycaemic targets were not met. Serious adverse perinatal outcomes occurred in 1% of the intervention group versus 4% of the routine-care group (adjusted relative risk, 0.33 [95% CI, 0.14–0.75]). The percentage of infants who were large for gestational age was lower in the intervention group (13% v 22%), with no increase in those who were small for gestational age. Although induction of labour was more common in the intervention group (39% v 29%), rates of caesarean delivery were similar (around 31%). Measures of maternal quality of life were more favourable in the intervention group. To prevent one serious perinatal outcome, 34 women needed to be treated. The 1998 guidelines were equivocal in regard to screening for gestational diabetes, allowing either for universal screening or for selective screening based on clinical risk factors in relatively lowrisk populations. In the light of the findings of ACHOIS, we believe that universal screening should now be accepted and implemented.

The impact of simple donor education on donor behavioral deferral and infectious disease rates in Sao Paulo, Brazil

BACKGROUND: Studies have shown that human immunodeficiency virus (HIV) residual risk is higher in Brazilian than in US and European blood donors, probably due to failure to defer at-risk individuals in Brazil. This study assessed the impact of an educational brochure in enhancing blood donors` knowledge about screening test window phase and reducing at-risk individuals from donating. STUDY DESIGN AND METHODS: This trial compared an educational intervention with a blood center`s usual practice. The brochure was distributed in alternating months to all donors. After donating, sampled participants completed two questions about their HIV window period knowledge. The impact on HIV risk deferral, leaving without donation, confidential unit exclusion (CUE) use, and test positivity was also analyzed. RESULTS: From August to November 2007 we evaluated 33,940 donations in the main collection center of Fundacao Pro-Sangue/Hemocentro de Sao Paulo in Sao Paulo, Brazil. A significant (p < 0.001) pamphlet effect was found on correct responses to both questions assessing HIV window phase knowledge (68.1% vs. 52.9%) and transfusion risk (91.1% vs. 87.2%). After adjusting for sex and age, the pamphlet effect was strongest for people with more than 8 years of education. There was no significant pamphlet effect on HIV risk deferral rate, leaving without donation, use of CUE, or infectious disease rates. CONCLUSION: While the educational pamphlet increased window period knowledge, contrary to expectations this information alone was not enough to make donors self-defer or acknowledge their behavioral risk.

Prevalence of Alcohol-Related Problems in an Elderly Population and Their Association With Cognitive Impairment and Dementia

Background: Studies investigating the association between alcohol use and cognitive disorders in the elderly population have produced divergent results. Moreover, the role of alcohol in cognitive dysfunction is not clear. The aims of this study were to estimate the prevalence of alcohol-related problems in an elderly population from Brazil and to investigate their association with cognitive and functional impairment (CFI) and dementia. Methods: A community-based cross-sectional study was performed. A sample of 1,145 elderly people was examined in 2 phases. Several instruments were utilized in the first phase: the CAGE questionnaire was used to identify potential cases of alcohol-related problems, and a screening test for dementia was used to estimate CFI. The CAMDEX interview (Cambridge Examination) and DSM-IV (Diagnostic and Statistical Manual of Mental Disorders, 4th edition) criteria were used for the clinical diagnosis of dementia in the second phase. Results: ""Heavy alcohol use"" (CAGE >= 2) was found in 92 subjects (prevalence: 8.2%). It was associated with gender (males, p < 0.001), low education (only in females, p = 0.002), and low socioeconomic level (p = 0.001, in females; p = 0.002, in males). The Mini Mental State Examination exhibited a nonlinear relationship with alcohol-related problems in females; ""mild-moderate alcohol use"" (CAGE < 2) presented the highest score. A significant association between alcohol-related problems and cognitive dysfunction was found only in females. ""Heavy alcohol use"" was associated with higher CFI and dementia rates compared to ""mild-moderate alcohol use"" (p = 0.003 and p < 0.001, respectively). ""Mild-moderate alcohol use"" had a tendency of association with lower CFI and dementia rates when compared to ""no alcohol use"" (p = 0.063 and 0.050, respectively). Conclusion: Our findings suggest that alcohol use does not have a linear relationship with cognitive decline.

Molecular analysis of CYP21A2 can optimize the follow-up of positive results in newborn screening for congenital adrenal hyperplasia

Neonatal screening for congenital adrenal hyperplasia (CAH) is useful in diagnosing salt wasting form (SW). However, there are difficulties in interpreting positive results in asymptomatic newborns. The main objective is to analyze genotyping as a confirmatory test in children with neonatal positive results. Patients comprised 23 CAH children and 19 asymptomatic infants with persistently elevated 17-hydroxyprogesterone (17OHP) levels. CYP21A2 gene was sequenced and genotypes were grouped according to the enzymatic activity of the less severe allele: A1 null, A2 < 2%, B 3-7%, C > 20%. Twenty-one children with neonatal symptoms and/or 17OHP levels > 80 ng/ml carried A genotypes, except two virilized girls (17OHP < 50 ng/ml) without CAH genotypes. Patients carrying SW genotypes (A1, A2) and low serum sodium levels presented with neonatal 17OHP > 200 ng/ml. Three asymptomatic boys carried simple virilizing genotypes (A2 and B): in two, the symptoms began at 18 months; another two asymptomatic boys had nonclassical genotypes (C). The remaining 14 patients did not present CAH genotypes, and their 17OHP levels were normalized by 14 months of age. Molecular analysis is useful as a confirmatory test of CAH, mainly in boys. It can predict clinical course, identify false-positives and help distinguish between clinical forms of CAH.

Population-based mammography screening and breast cancer incidence in New South Wales, Australia

To analyse breast cancer incidence trends in New South Wales (NSW), Australia, in relation to population-based mammography screening targeting women aged 50 to 69 years. Trends in age-specific incidence of invasive breast cancers in NSW women aged >= 40 years were examined in relation to mammography screening rates and screening cancer detection rates. Incidence of invasive breast cancer in NSW women increased in all age-groups over 1972 to 2002. The incidence trend for women aged 50 to 69 years showed that the steepest rise was associated with increased participation in population-based mammography screening, which was implemented from 1988 and achieved state-wide coverage in 1995. The elevated incidence of invasive cancer significantly exceeded pre-screening levels, and persisted after rates of initial screens declined. This elevated incidence was sustained by the contribution of cancers diagnosed through subsequent screening, and resulted from increased cancer detection rates in subsequent screens. The recent increase in invasive breast cancer incidence in NSW is associated with mammography screening, and occurred mostly in the target age-group women. Persistence of higher incidence after 1994 was not explicable by inflation of cancer incidence due to detection of prevalent screen cases, but was associated with a trend of increased cancer detection rates in subsequent screening rounds, probably consequent to quality improvements in mammography screening diagnosis.