Prediction of carbon monoxide in fires by conditional moment closure

Carbon monoxide is the chief killer in fires. Dangerous levels of CO can occur when reacting combustion gases are quenched by heat transfer, or by mixing of the fire plume in a cooled under- or overventilated upper layer. In this paper, carbon monoxide predictions for enclosure fires are modeled by the conditional moment closure (CMC) method and are compared with laboratory data. The modeled fire situation is a buoyant, turbulent, diffusion flame burning under a hood. The fire plume entrains fresh air, and the postflame gases are cooled considerably under the hood by conduction and radiation, emulating conditions which occur in enclosure fires and lead to the freezing of CO burnout. Predictions of CO in the cooled layer are presented in the context of a complete computational fluid dynamics solution of velocity, temperature, and major species concentrations. A range of underhood equivalence ratios, from rich to lean, are investigated. The CMC method predicts CO in very good agreement with data. In particular, CMC is able to correctly predict CO concentrations in lean cooled gases, showing its capability in conditions where reaction rates change considerably.

Bioinformatics for characterisation of allergens, allergenicity and allergic crossreactivity

Allergies are a major cause of chronic ill health in industrialised countries with the incidence of reported cases steadily increasing. This Research Focus details how bioinformatics is transforming the field of allergy through providing databases for management of allergen data, algorithms for characterisation of allergic crossreactivity, structural motifs and B- and T-cell epitopes, tools for prediction of allergenicity and techniques for genomic and proteomic analysis of allergens.

Field assessment of thermal after-ripening time for dormancy release prediction in Lolium rigidum seeds

Dormancy release was studied in four populations of annual ryegrass (Lolium rigidum) seeds to determine whether loss of dormancy in the field can be predicted from temperature alone or whether seed water content (WC) must also be considered. Freshly matured seeds were after-ripened at the northern and southern extremes of the Western Australian cereal cropping region and at constant 37degreesC. Seed WC was allowed to fluctuate with prevailing humidity, but full hydration was avoided by excluding rainfall. Dormancy was measured regularly during after-ripening by germinating seeds with 12-hourly light or in darkness. Germination was lower in darkness than in light/dark and dormancy release was slower when germination was tested in darkness. Seeds were consistently drier, and dormancy release was slower, during after-ripening at 37degreesC than under field conditions. However, within each population, the rate of dormancy release in the field (north and south) in terms of thermal time was unaffected by after-ripening site. While low seed WC slowed dormancy release in seeds held at 37degreesC, dormancy release in seeds after-ripened under Western Australian field conditions was adequately described by thermal after-ripening time, without the need to account for changes in WC elicited by fluctuating environmental humidity.

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.

ANNA: A new prediction method for bioassessment programs

1. Cluster analysis of reference sites with similar biota is the initial step in creating River Invertebrate Prediction and Classification System (RIVPACS) and similar river bioassessment models such as Australian River Assessment System (AUSRIVAS). This paper describes and tests an alternative prediction method, Assessment by Nearest Neighbour Analysis (ANNA), based on the same philosophy as RIVPACS and AUSRIVAS but without the grouping step that some people view as artificial. 2. The steps in creating ANNA models are: (i) weighting the predictor variables using a multivariate approach analogous to principal axis correlations, (ii) calculating the weighted Euclidian distance from a test site to the reference sites based on the environmental predictors, (iii) predicting the faunal composition based on the nearest reference sites and (iv) calculating an observed/expected (O/E) analogous to RIVPACS/AUSRIVAS. 3. The paper compares AUSRIVAS and ANNA models on 17 datasets representing a variety of habitats and seasons. First, it examines each model's regressions for Observed versus Expected number of taxa, including the r(2), intercept and slope. Second, the two models' assessments of 79 test sites in New Zealand are compared. Third, the models are compared on test and presumed reference sites along a known trace metal gradient. Fourth, ANNA models are evaluated for western Australia, a geographically distinct region of Australia. The comparisons demonstrate that ANNA and AUSRIVAS are generally equivalent in performance, although ANNA turns out to be potentially more robust for the O versus E regressions and is potentially more accurate on the trace metal gradient sites. 4. The ANNA method is recommended for use in bioassessment of rivers, at least for corroborating the results of the well established AUSRIVAS- and RIVPACS-type models, if not to replace them.

PREDBALB/c: a system for the prediction of peptide binding to H2(d) molecules, a haplotype of the BALB/c mouse

PREDBALB/c is a computational system that predicts peptides binding to the major histocompatibility complex-2 (H2(d)) of the BALB/c mouse, an important laboratory model organism. The predictions include the complete set of H2(d) class I ( H2-K-d, H2-L-d and H2-D-d) and class II (I-E-d and I-A(d)) molecules. The prediction system utilizes quantitative matrices, which were rigorously validated using experimentally determined binders and non-binders and also by in vivo studies using viral proteins. The prediction performance of PREDBALB/c is of very high accuracy. To our knowledge, this is the first online server for the prediction of peptides binding to a complete set of major histocompatibility complex molecules in a model organism (H2(d) haplotype). PREDBALB/c is available at http://antigen.i2r.a-star.edu.sg/predBalbc/.

Axial Young's modulus prediction of single-walled carbon nanotube arrays with diameters from nanometer to meter scales

Based on a self-similar array model, we systematically investigated the axial Young's modulus (Y-axis) of single-walled carbon nanotube (SWNT) arrays with diameters from nanometer to meter scales by an analytical approach. The results show that the Y-axis of SWNT arrays decreases dramatically with the increases of their hierarchy number (s) and is not sensitive to the specific size and constitution when s is the same, and the specific Young's modulus Y-axis(s) is independent of the packing configuration of SWNTs. Our calculations also show that the Y-axis of SWNT arrays with diameters of several micrometers is close to that of commercial high performance carbon fibers (CFs), but the Y-axis(s) of SWNT arrays is much better than that of high performance CFs. (C) 2005 American Institute of Physics.

The role of CD4 T help in multiple vaccinations when using minimal CD8 T cell epitope peptides

Background: The fact that some cancers and viral infections can be controlled by effector CD8 T cells led to the possibility of utilising minimal CD8 T cell epitope peptides as vaccines. However using minimal CD8 T cell epitope peptide immunisations and a tumour protection model in mice, we have previously shown that functional memory CD8 T cells are not generated unless CD4 T help is provided at the time of CD8 T cell priming. Short-lived effector cells nevertheless are generated in the absence of T help. Aim: To determine the role of CD4 T help in multiple immunisations. Method: Minimal CD8 T cell peptides of HPV16 E7 protein and Ovalbumin were used (with adjuvants Quil-A or IFA) as immunogens in C57BL mice. The presence of effector CD8 T cells were determined by tumour protection assays and was quantified by IFN-gamma ELISPOT assays. Results: In the present study we show that unless T help is provided at the time CD8 T cells are primed, no CD8 effector cells are generated when boosted with the vaccine again in the absence of T help. Our results further show that this failure could be prevented by the inclusion of a T helper peptide during the primary or booster immunisations.

Prediction of impact forces in a vibratory ball mill using an inverse technique

To understand the dynamic mechanisms of the mechanical milling process in a vibratory mill, it is necessary to determine the characteristics of the impact forces associated with the collision events. However, it is difficult to directly measure the impact force in an operating mill. This paper describes an inverse technique for the prediction of impact forces from acceleration measurements on a vibratory ball mill. The characteristics of the vibratory mill have been investigated by the modal testing technique, and its system modes have been identified. In the modelling of the system vibration response to the impact forces, two modal equations have been used to describe the modal responses. The superposition of the modal responses gives rise to the total response of the system. A method based on an optimisation approach has been developed to predict the impact forces by minimising the difference between the measured acceleration of the vibratory ball mill and the predicted acceleration from the solution of the modal equations. The predicted and measured impact forces are in good agreement. Copyright (C) 1996 Elsevier Science Ltd.

Encephalitogenicity of murine, but not bovine, DM20 in SJL mice is due to a single amino acid difference in the immunodominant encephalitogenic epitope

Myelin proteolipid protein (PLP) contains 2 immunodominant encephalitogenic epitopes in SJL mice, namely PLP residues 139-151 and 178-191. DM20, a minor isoform of PLP, lacks residues 116-150 and consequently contains only the single major encephalitogenic epitope 178-191. However, it has been found previously that bovine DM20 is not encephalitogenic in SJL mice. Since residue 188 within peptide 178-191 is phenylalanine (F) in murine DM20 and alanine (A) in bovine DM20, we tested the effect of this difference on the immune responses and induction of EAE. SJL mice were immunized with either highly purified murine or bovine DM20. Residues 178-191 were found to be immunodominant for each, but only murine and not bovine DM20 was encephalitogenic. A synthetic peptide corresponding to the murine 178-191 sequence (F188) was also encephalitogenic, whereas the peptide corresponding to the bovine sequence (A188) was not. Both F188 and A188 bind with high affinity to I-A(s) and both are recognized by the SJL T cell repertoire. A188-specific T cell lines reacted to both A188 and F188, but F188-specific T cell lines were not stimulated by A188. F188-specific T cell lines produced mRNA for the Th1 cytokines IL2 and IFN gamma and, in passive transfer experiments, were encephalitogenic upon stimulation with F188, but not A188. In contrast, A188-specific T cell lines produced mRNA for IL4, IL5 and IL10, in addition to IL2 and IFN gamma, and were not encephalitogenic after stimulation with either F188 or A188. Cotransfer of A188-specific T cell lines with F188-specific T cell lines resulted in protection from EAE. Thus, A188 induces a functionally different phenotype of T cells from that induced by F188. Taken together these data suggest that the failure of bovine DM20 to induce EAE may be attributable to induction of protective rather than pathogenic T cells by the immunodominant epitope.

Prediction of psychological adjustment to multiple sclerosis

This study examined the utility of self-efficacy as a predictor of social activity and mood control in multiple sclerosis (MS). Seventy-one subjects with MS were recruited from people attending an MS centre or from a mailing list and were examined on two occasions that were two months apart. Clinic patients were more disabled than patients who completed assessments by post, but they were of higher socioeconomic status and were less dysphoric; We attempted to predict self-reported performance of mood control and social activity at two months, from self-efficacy or performance on these tasks at pretest. Demographic variables, disorder status, disability, self-esteem and depression were also allowed to compete for entry into multiple regressions. Substantial stability in mood, performance and disability was observed over the two months. In both mood control and social activity, past performance was the strongest predictor of later performance, but self-efficacy also contributed significantly to the prediction. The disability level entered a prediction of social activity; but no other variables predicted either type of performance. A secondary analysis predicting self-esteem at two months also included self-efficacy for social activity, illustrating the contribution of perceived capability to later assessments of self-worth. The study provided support for self-efficacy as a predictor of later behavioural outcomes and self-esteem in multiple sclerosis. (C) 1997 Elsevier Science Ltd.