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.

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.

Gamma-band oscillations in fronto-central areas during performance of a sensorimotor integration task: A qEEG coherence study

This study aimed to elucidate electrophysiological and cortical mechanisms involved in anticipatory actions when 23 healthy right-handed subjects had to catch a free falling object by qEEG gamma-band (30-100 Hz). It is involved in cognitive processes, memory, spatial/temporal and proprioceptive factors. Our hypothesis is that an increase in gamma coherence in frontal areas will be observed during moment preceding ball drop, due to their involvement in attention, planning, selection of movements, preparation and voluntary control of action and in central areas during moment after ball drop, due to their involvement in motor preparation, perception and execution of movement. However, through a paired t-test, we found an increase in gamma coherence for F3-F4 electrode pair during moment preceding ball drop and confirmed our hypothesis for C3-C4 electrode pair. We conclude that gamma plays an important role in reflecting binding of several brain areas in a complex motor task as observed in our results. Moreover, for selection of movements, preparation and voluntary control of action, motor preparation, perception and execution of movement, the integration of somatosensory and visual information is mandatory. (C) 2010 Elsevier Ireland Ltd. All rights reserved.

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.

Smart Alerts: Development of Software to Optimize Data Monitoring

Dherte PM, Negrao MPG, Mori Neto S, Holzhacker R, Shimada V, Taberner P, Carmona MJC - Smart Alerts: Development of a Software to Optimize Data Monitoring. Background and objectives: Monitoring is useful for vital follow-ups and prevention, diagnosis, and treatment of several events in anesthesia. Although alarms can be useful in monitoring they can cause dangerous user`s desensitization. The objective of this study was to describe the development of specific software to integrate intraoperative monitoring parameters generating ""smart alerts"" that can help decision making, besides indicating possible diagnosis and treatment. Methods: A system that allowed flexibility in the definition of alerts, combining individual alarms of the parameters monitored to generate a more elaborated alert system was designed. After investigating a set of smart alerts, considered relevant in the surgical environment, a prototype was designed and evaluated, and additional suggestions were implemented in the final product. To verify the occurrence of smart alerts, the system underwent testing with data previously obtained during intraoperative monitoring of 64 patients. The system allows continuous analysis of monitored parameters, verifying the occurrence of smart alerts defined in the user interface. Results: With this system a potential 92% reduction in alarms was observed. We observed that in most situations that did not generate alerts individual alarms did not represent risk to the patient. Conclusions: Implementation of software can allow integration of the data monitored and generate information, such as possible diagnosis or interventions. An expressive potential reduction in the amount of alarms during surgery was observed. Information displayed by the system can be oftentimes more useful than analysis of isolated parameters.

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.

Social adaptation of children with mild intellectual disability: Effects of partial integration within primary school classes

is study examined the social adaptation of children with mild intellectual disability who were either (a) partially integrated into regular primary school classes, or (b) full-time in separate classes, All of the children were integrated in sport and play activities with the whole school. Consistent with previous research, children with intellectual disability were less socially accepted than were a matched group of control children. Children in partially integrated classes received more play nominations than those in separate classes, brit there was no greater acceptance as a best friend. On teachers' reports, disabled children had higher levels of inappropriate social behaviours, but there was no significant difference in appropriate behaviours. Self-assessments by integrated children were more negative than those by children in separate classes, and their peer-relationship satisfaction was lower. Ratings by disabled children of their satisfaction with peer relationships were associated with ratings of appropriate social skills by themselves and their teachers, and with self-ratings of negative behaviour. The study confirmed that partial integration can have negative consequences for children with an intellectual disability.

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.

Re-integration into work

This is the first complete textbook designed for physiotherapists and occupational therapists on the topic of pain. It was developed for use in conjunction with the International Association for the Study of Pain's pain curriculum for OTs and PTs. The book addresses the nature of pain, the neuroanatomical and neurophysiological substrates of pain, the psychological... More aspects of pain, the lifespan approach to pain, pain measurement, pain and placebo, modalities for treating pain, and special topics in pain. It provides an overview of the physiological, psychosocial, and environmental aspects of pain experience across the lifespan. Aimed primarily at OTs and PTs the assessment and interventions issues pertaining to the perspectives of each profession are discussed in detail. The book is also relevant to the other health professions involved in pain management or intending to work in this area.

Gamma band oscillations under influence of bromazepam during a sensorimotor integration task: An EEG coherence study

The goal of the present study was to explore the dynamics of the gamma band using the coherence of the quantitative electroencephalography (qEEG) in a sensorimotor integration task and the influence of the neuromodulator bromazepam on the band behavior. Our hypothesis is that the needs of the typewriting task will demand the coupling of different brain areas, and that the gamma band will promote the binding of information. It is also expected that the neuromodulator will modify this coupling. The sample was composed of 39 healthy subjects. We used a randomized double-blind design and divided subjects into three groups: placebo (n = 13), bromazepam 3 mg (n = 13) and bromazepam 6 mg (n = 13). The two-way ANOVA analysis demonstrated a main effect for the factors condition (i.e., C4-CZ electrode pair) and moment (i.e., C3-CZ, C3-C4 and C4-CZ pairs of electrodes). We propose that the gamma band plays an important role in the binding among several brain areas in complex motor tasks and that each hemisphere is influenced in a different manner by the neuromodulator. (C) 2009 Elsevier Ireland Ltd. All rights reserved.