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.

Highly integrated and automated high-speed grinding system for printer heads constructed by combination materials

The fabrication of heavy-duty printer heads involves a great deal of grinding work. Previously in the printer manufacturing industry, four grinding procedures were manually conducted in four grinding machines, respectively. The productivity of the whole grinding process was low due to the long loading time. Also, the machine floor space occupation was large because of the four separate grinding machines. The manual operation also caused inconsistent quality. This paper reports the system and process development of a highly integrated and automated high-speed grinding system for printer heads. The developed system, which is believed to be the first of its kind, not only produces printer heads of consistently good quality, but also significantly reduces the cycle time and machine floor space occupation.

Material influence on the stress corrosion cracking of rock bolts

Rock bolt stress corrosion cracking (SCC) has been investigated using the linearly increasing stress test (LIST). One series of experiments determined the threshold stress of various bolt metallurgies (900 MPa for 1355AXRC, and 800 MPa for MAC and MA840B steels). The high values of threshold stress suggest that SCC begins in rock bolts when they are sheared by moving rock strata. SCC only occurred for environmental conditions which produce hydrogen on the sample surface, leading to hydrogen embrittlement and SCC. Different threshold potentials were determined for a range of metallurgies. Cold work was shown to increase the resistance of the steel to SCC. Rock bolt rib geometry does not have a direct impact on the SCC resistance properties of the bolt, although the process by which the ribs are produced can introduce tensile stresses into the bolt which lower its resistance to SCC. (C) 2004 Elsevier Ltd. All rights reserved.

Effects of Self-Assembled Materials Prepared from V(2)O(5) for Lithium Ion Electroinsertion

Self-assembled materials consisting of V(2)O(5), polyallylamine (PAR) and silver nanoparticles (AgNPs) were obtained by the layer-by-layer (LbL) method, aiming at their application as electrodes for lithium-ion batteries and electrochromic devices. The method employed herein allowed for linear growth of visually homogeneous films composed of V(2)O(5), V(2)O(5)/PAH, and V(2)O(5)/PAH/AgNP with 15 bilayers. According to the Fourier transform infrared spectra, interaction between the oxygen atom of the vanadyl group and the amino group should be responsible for the growth of these films. This interaction also enabled establishment of an electrostatic shield between the lithium ions and the sites with higher negative charge, thereby raising the ionic mobility and consequently increasing the energy storage capacity and reducing the response time. According to the site-saturation model and the electrochemical and spectroelectrochemical results, the presence of PAH in the self-assembled host matrix decreased the number of V(2)O(5) electroactive sites. Thus, AgNPs were stabilized in PAR and inserted into the nanoarchitecture, so as to enhance the specific capacity. This should provide new conducting pathways and connect isolated V(2)O(5) particles in the host matrix. Therefore, new nanoarchitectures for specific interactions were formed spontaneously and chosen as examples in this work, aiming to demonstrate the potentiality of the adopted self-assembled method for enhancing the charge transport rate into the host matrices. The obtained materials displayed suitable properties for use as electrodes in lithium batteries and electrochromic devices.

A study on stress corrosion cracking and hydrogen embrittlement of AZ31 magnesium alloy

The stress corrosion cracking (SCC) behavior and pre-exposure embrittlement of AZ31 magnesium alloy have been studied by slow strain rate tensile (SSRT) tests in this paper. It is showed that AZ31 sheet material is susceptible to SCC in distilled water, ASTM D1.387 solution, 0.01 M NaCl and 0.1 M NaCl solution. The AZ31 magnesium alloy also becomes embrittled if pre-exposed to 0.01 M NaCl solution prior to tensile testing. The degree of embrittlement increased with increasing the pre-exposure time, It is proposed that both the pre-exposure embrittlement and SCC were due to hydrogen which reduces the cohesive strength. i,e,. hydrogen embrittlement, (c) 2005 Elsevier B.V. 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.

Dynamic strain measurement using piezoelectric polymer film

Piezoelectric polymers have been used to form the basis of dynamic strain gauges for the detection of stress waves. The linearity of response was tested using a split Hopkinson pressure bar arrangement. The results obtained illustrate the effectiveness of piezoelectric film strain gauges in the measurement of axial stress waves.

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.

A numerical study of effect of grain boundaries on elastic and plastic properties in nanocomposite materials

Nanocomposite materials have received considerable attention in recent years due to their novel properties. Grain boundaries are considered to play an important role in nanostructured materials. This work focuses on the finite element analysis of the effect of grain boundaries on the overall mechanical properties of aluminium/alumina composites. A grain boundary is incorporated into the commonly used unit cell model to investigate its effect on material properties. By combining the unit cell model with an indentation model, coupled with experimental indentation measurements, the ''effective'' plastic property of the grain boundary is estimated. In addition, the strengthening mechanism is also discussed based on the Estrin-Mecking model.

Effects of magnesium intake deficiency on bone metabolism and bone tissue around osseointegrated implants

Objectives: This study evaluated the effect of magnesium dietary deficiency on bone metabolism and bone tissue around implants with established osseointegration. Materials and methods: For this, 30 rats received an implant in the right tibial metaphysis. After 60 days for healing of the implants, the animals were divided into groups according to the diet received Control group (CTL) received a standard diet with adequate magnesium content, while test group (Mg) received the same diet except for a 90% reduction of magnesium. The animals were sacrificed after 90 days for evaluation of calcium, magnesium, osteocalcin and parathyroid hormone (PTH) serum levels and the deoxypyridinoline (DPD) level in the urine. The effect of magnesium deficiency on skeletal bone tissue was evaluated by densitometry of the lumbar vertebrae, while the effect of bone tissue around titanium implants was evaluated by radiographic measurement of cortical bone thickness and bone density. The effect on biomechanical characteristics was verified by implant removal torque testing. Results: Magnesium dietary deficiency resulted in a decrease of the magnesium serum level and an increase of PTH and DPD levels (P <= 0.05). The Mg group also presented a loss of systemic bone mass decreased cortical bone thickness and lower values of removal torque of the implants (P <= 0.01). Conclusions: The present study concluded that magnesium-deficient diet had a negative influence on bone metabolism as well as on the bone tissue around the implants.

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.

Immunophenotyping and remodeling process in small airways of idiopathic interstitial pneumonias: functional and prognostic significance

Background and Aims: To test whether different degrees of immunologic and fibrotic airway remodeling processes occur in idiopathic interstitial pneumonias (IIPs), with impact on functional tests and survival, we studied the collagen/elastic system and immune cell density in the bronchiolar interstitium of lungs with the major types of IIPs. Materials and Methods: Histochemistry, immunohistochemistry and morphometric analysis were used to evaluate collagen/elastic fibers and immune cells in the bronchiolar interstitium of open lung biopsies of patients with cryptogenic organizing pneumonia [COP/organizing pneumonia (OP) = 10], acute interstitial pneumonia [AIP/diffuse alveolar damage (DAD) = 20], nonspecific interstitial pneumonia (NSIP/NSIP = 20) and idiopathic pulmonary fibrosis/usual interstitial pneumonia (UIP) = 20. Results: OP lungs presented a significant increase in collagenous/elastic fibers and in the total density of immune cells in the bronchiolar interstitium compared to controls, DAD, NSIP and UIP. We observed a significant increase in CD4, CD8 and CD20 lymphocytes, as well as in neutrophils, macrophages and plasma cells in OP. The increased amount of elastic fibers in the bronchiolar interstitium from OP lungs has a direct association with forced vital capacity (FVC) (r(s) = 0.99, P = 0.03). The most important survival predictor was CD20+ lymphocytes in the bronchiolar interstitium. In decreasing order, patients with UIP [Odds Ratio (OR) = 35.01], high forced expiratory volume in 1 s (FEV1)/FVC FVC (OR = 7.01), increased CD20+ lymphocytes (OR = 4.44) and collagenous/elastic fiber densities (OR = 2.03 and OR = 1.49, respectively) in the bronchiolar interstitium were those who had the greatest risk of death, followed by those with AIP, NSIP and COP. Conclusion: Different degrees of immunologic and fibroelastotic airway remodeling processes occur in the major types of IIPs with impact on physiological tests and survival.