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.

Regulation of conditioned and unconditioned fear in rats by 5-HT1A receptors in the dorsal periaqueductal gray

Studies on the involvement of 5-HT1-mediated mechanisms in the dorsal periaqueductal gray (dPAG) of animals with past stressful experiences have not been conducted so far. We investigated the role of 5-HT1 receptors in the dPAG of rats previously submitted to contextual fear conditioning. Defensive behaviors induced by activation of the dPAG were assessed by measuring the lowest electric current applied to this structure (threshold) able to produce freezing and escape responses during testing sessions of contextual fear conditioning, in which animals were placed in a context previously paired to footshocks. The 5-HT1A function of the dPAG was evaluated by local injections of 8-OH-DPAT (4 and 8 nmol/0.2 mu L) and WAY-100635 (10 nmol/0.2 mu L), selective agonist and antagonist of 5-HT1A receptors, respectively. In accordance with previous studies, 8-OH-DPAT increased aversive thresholds (antiaversive effects) but injections of WAY 100635 into the dPAG did not produce significant effects on the aversive thresholds in naive rats. However, the aversive thresholds of animals exhibiting contextual fear remained unchanged with both treatments. Moreover, 8-OH-DPAT and WAY 100635 did not change the dPAG post-stimulation freezing. The present results suggest that the stressful experience of being fear conditioned has an effect on the role of the 5-HT1A receptors in mediating unconditioned fear. Also, the reduction in the regulation of the defensive behaviors by 5-HT1A-mediated mechanisms in the dPAG of these animals may underlie the stress precipitated psychopathology associated with the neural substrates of aversion of the dPAG. (c) 2007 Elsevier Inc. All rights reserved.

Trigeminal pain and quantitative sensory testing in painful peripheral diabetic neuropathy

Objective: To evaluate patients with Diabetes Mellitus type 2 and painful peripheral neuropathy in order to investigate oral complaints and facial somatosensory findings. Research design and methods: Case-control study; 29 patients (12 women, mean age 57.86 yo) with Diabetes Mellitus type 2 and 31 age-gender-matched controls were evaluated with a standardized protocol for general characteristics, orofacial pain, research diagnostic criteria for temporomandibular disorders, visual analogue scale and McGill Pain questionnaire, and a systematic protocol of quantitative sensory testing for bilateral facial sensitivity at the areas innervated by the trigeminal branches, which included the thermal detection by ThermoSensi 2, tactile evaluation with vonFrey filaments, and superficial pain thresholds with a superficial algometer (Micromar). Statistical analysis was performed with Wilcoxon, chi-square, confidence intervals and Spearman (p < 0.05). Results: Orofacial pain was reported by 55.2% of patients, and the most common descriptor was fatigue (50%); 17.2% had burning mouth. Myofascial temporomandibular disorders were diagnosed in 9(31%) patients. The study group showed higher sensory thresholds of pain at the right maxillary branch (p = 0.017) but sensorial differences were not associated with pain (p = 0.608). Glycemia and HbA(1c) were positively correlated with the quantitative sensory testing results of pain (p < 0.05) and cold (p = 0.044) perceptions. Higher pain thresholds were correlated with higher glycemia and glycated hemoglobin (p = 0.027 and p = 0.026). Conclusions: There was a high prevalence of orofacial pain and burning mouth was the most common complaint. The association of loss of pain sensation and higher glycemia and glycated hemoglobin can be of clinical use for the follow-up of DM complications. (C) 2010 Elsevier Ltd. All rights reserved.

ISPRM`S WAY FORWARD

This paper outlines approaches to developing the International Society of Physical and Rehabilitation Medicine (ISPRM) and addresses many current challenges Most importantly, these approaches provide the basis for ISPRM to develop its leadership role within the field of Physical and Rehabilitation Medicine (PRM) and in relation to the World Health Organization (WHO) and the United Nations (UN) system at large. They also address a number of specific critiques of the current situation. A positioning of ISPRM within the world architecture of the UN and WHO systems, as well as the consideration and fostering of respective emerging regional PRM societies, is central to establishing networking connections at different levels of the world society. Yearly congresses, possibly in co-operation with a regional society, based on a defined regional rotation, are suggested. Thus, frustration with the current bidding system for a biennial congress and an intermediate meeting could be overcome. Yearly congresses are also an important step towards increasing the organization`s funding base, and hence the possibility to expand the functions of ISPRM`s central office. ISPRM`s envisioned leadership role in the context of an international web of PRM journals complementing the formally defined official journal of ISPRM, regional societies and so forth, is an inclusive rather than exclusive approach that contributes to the development of PRM journals worldwide. An important prerequisite for the further development of ISPRM is the expansion and bureaucratization of its Central Office, adding professionalism and systematic allocation of resources to the strengths of the voluntary engagement of individual PRM doctors.

A framework for specification-based testing

Test templates and a test template framework are introduced as useful concepts in specification-based testing. The framework can be defined using any model-based specification notation and used to derive tests from model-based specifications-in this paper, it is demonstrated using the Z notation. The framework formally defines test data sets and their relation to the operations in a specification and to other test data sets, providing structure to the testing process. Flexibility is preserved, so that many testing strategies can be used. Important application areas of the framework are discussed, including refinement of test data, regression testing, and test oracles.

Human immunodeficiency virus test-seeking blood donors in a large blood bank in Sao Paulo, Brazil

BACKGROUND: Persons with human immunodeficiency virus (HIV) risk behaviors are excluded from donation to reduce the risk of transfusion-transmitted infection. Persons donating to be tested for HIV may therefore deny risk behaviors. STUDY DESIGN AND METHODS: A random sample of donors completed a survey on motivations, knowledge, and attitudes on the screening process. Donors were considered test seekers if they agreed with two statements ""I think that blood donation is a good, fast, and anonymous way to get my blood tested"" and ""I donate to get my test results."" This study was conducted from June to November 2006 at the largest blood bank in Sao Paulo, Brazil. RESULTS: Of 3061 participants, 208 (7%) were test seekers. They tended to be male and had a lower educational level. They were more likely to have incorrect knowledge about blood safety (e.g., not knowing that a unit can test antibody negative and still transmit infection, 60% vs. 42%, p = 0.02), express dissatisfaction with screening questions (e.g., feeling that important questions were not asked, 14% vs. 5%, p < 0.01), and concur that donors do not answer questions truthfully (e.g., donors have more sexual partners than they admit, 29% vs. 18%, p < 0.01). Test seekers were more likely to believe that it is acceptable to donate blood to get tested for HIV (41% vs. 10%, p < 0.01). CONCLUSIONS: Test-seeking motivation, coupled with low knowledge of window period risk, is counter to improving blood safety and to donor prevention needs. Donor education needs to be improved along with availability of appropriate HIV counseling and testing.

Laboratory wear testing of polyurethane elastomers

A dry sand-rubber wheel abrasion test was used to investigate the wear behaviour of polyurethanes. The dry sand-rubber wheel abrasion test (DSRW test) is an approved ASTM test designed primarily for testing metals, therefore, in this study the set of test conditions was optimized for use with polyurethane elastomers. The wear performance of polyurethanes was assessed for the range of Shore hardness 85A to 65D, and a correlation was identified between the wear rate and the sample hardness. Polyurethane elastomers can be separated into three classes according to their hardness and wear performance, and each class shows a different dependence on the specimen temperature. This work has implications for use of the DSRW test for the prediction of field performance of polyurethanes. (C) Elsevier Science S.A.

Testing market efficiency: Evidence from the NFL sports betting market

This article examines the efficiency of the National Football League (NFL) betting market. The standard ordinary least squares (OLS) regression methodology is replaced by a probit model. This circumvents potential econometric problems, and allows us to implement more sophisticated betting strategies where bets are placed only when there is a relatively high probability of success. In-sample tests indicate that probit-based betting strategies generate statistically significant profits. Whereas the profitability of a number of these betting strategies is confirmed by out-of-sample testing, there is some inconsistency among the remaining out-of-sample predictions. Our results also suggest that widely documented inefficiencies in this market tend to dissipate over time.

Lymphocyte proliferation testing in chromium allergic contact dermatitis

Background. Lymphocyte proliferation testing (LPT) has some advantages over patch testing to diagnose allergic contact dermatitis. It is harmless, objective and can be used in clinical situations where patch testing is not recommended. Unfortunately, significant success has only been achieved with nickel. There are few studies on chromium LPT and they were performed with different methods, leading to inconsistent results. Methods. To determine the best parameters for chromium LPT, we tested 20 patients with allergic contact dermatitis to the metal and 20 controls, using various protocols. Results. The best sensitivity and specificity ratios were achieved with 6-day cultures stimulated with a range from 7.5 x 10(-4) to 5 x 10(-3) mol/L of nonfiltered chromium chloride solutions. The sensitivity, specificity and accuracy values found within this range were 65%, 95% and 80%, respectively. Conclusion. Further investigation is necessary to achieve better sensitivity values.

A Bayesian approach to fuzzy hypotheses testing for the estimation of optimal age for vaccination against measles

Fuzzy Bayesian tests were performed to evaluate whether the mother`s seroprevalence and children`s seroconversion to measles vaccine could be considered as ""high"" or ""low"". The results of the tests were aggregated into a fuzzy rule-based model structure, which would allow an expert to influence the model results. The linguistic model was developed considering four input variables. As the model output, we obtain the recommended age-specific vaccine coverage. The inputs of the fuzzy rules are fuzzy sets and the outputs are constant functions, performing the simplest Takagi-Sugeno-Kang model. This fuzzy approach is compared to a classical one, where the classical Bayes test was performed. Although the fuzzy and classical performances were similar, the fuzzy approach was more detailed and revealed important differences. In addition to taking into account subjective information in the form of fuzzy hypotheses it can be intuitively grasped by the decision maker. Finally, we show that the Bayesian test of fuzzy hypotheses is an interesting approach from the theoretical point of view, in the sense that it combines two complementary areas of investigation, normally seen as competitive. (C) 2007 IMACS. Published by Elsevier B.V. All rights reserved.

Application of Real-Time PCR Stool Assay for Helicobacter pylori Detection and Clarithromycin Susceptibility Testing in Brazilian Children

Background: Helicobacter pylori ClariRes assay is a novel commercially available real-time PCR assay allowing H. pylori detection and clarithromycin susceptibility testing in either gastric biopsy or stool specimens. Objective: The aim of this study was to validate the novel biprobe real-time assay in stool specimens from 217 dyspeptic children. Methods: DNA from gastric biopsies and stool specimens were obtained and submitted to the biprobe real time assay for H. pylori detection and clarithromycin susceptibility testing. Results: The sensitivity, specificity, and test accuracy were 69, 100 and 93.9% for the detection of H. pylori infection and 83.3, 100 and 95.6%, for detection of clarithromycin resistance. Conclusion: This assay proved to be appropriate for H. pylori clarithromycin susceptibility testing, particularly in children populations where a high prevalence of clarithromycin-resistant strains is suspected.

HER2 Testing in Breast Carcinoma Very Low Concordance Rate Between Reference and Local Laboratories in Brazil

Breast cancer accounts for approximately one quarter of all cancers in females. HER2 gene amplification or HER2 protein overexpression, detected in about 20% of breast carcinomas, predicts a more aggressive clinical course and determines eligibility for targeted therapy with trastuzumab. HER2 testing has become an essential part of the clinical evaluation of all breast carcinoma patients, and accurate HER2 results are critical in identifying patients who may be benefited from targeted therapy. This study investigated the concordance in the results of HER2 immunohistochemistry assays performed in 500 invasive breast carcinomas between a reference laboratory and 149 local laboratories from all geographic regions of Brazil. Our results showed an overall poor concordance (171 of 500 cases, 34.2%) regarding HER2 results between local and reference laboratories, which may be related to the low-volume load of HER2 assays, inexperience with HER2 scoring system, and/or technical issues related to immunohistochemistry in local laboratories. Standardization of HER2 testing with rigorous quality control measures by local laboratories is highly recommended to avoid erroneous treatment of breast cancer patients.

Integrating toxicity testing in the wastewater management of chemical storage terminals - A proposal based on a ten-year study

Wastewater control at storage terminals of liquid chemical products in bulk is very difficult because of the variety of products handled in the facilities generating effluents of variable composition. The main objective of this work was to verify if the Vibrio fischeri acute toxicity test could be routinely included in the wastewater management of those facilities along with physical and chemical analysis in order to evaluate and improve the quality of the generated effluents. The study was performed in two phases before and after the implementation of better operational practices/treatment technologies. Chemical oxygen demand (COD) and toxicity of treated effluents did not correlate showing that effluents with low COD contain toxic substances and non-biodegradable organic matter, which may be not degraded when discharged into the aquatic environment. Segregation of influents or pre-treatment based on toxicity results and biodegradability index were implemented in the facilities generating significant improvements in the quality of final effluents with reduction of Biochemical oxygen demand (BOD) and toxicity. The integration of physical and chemical analysis with the V.fischeri toxicity test turned out to be an excellent tool for wastewater management in chemical terminals allowing rapid decision making for pollution control and prevention measures. Reuse of rain water was also proposed and when implemented by the facilities resulted in economical and environmental benefits. (C) 2010 Elsevier B.V. All rights reserved.