Toward prediction of class II mouse major histocompatibility complex peptide binding affinity:in silico bioinformatic evaluation using partial least squares, a robust multivariate statistical technique

The accurate identification of T-cell epitopes remains a principal goal of bioinformatics within immunology. As the immunogenicity of peptide epitopes is dependent on their binding to major histocompatibility complex (MHC) molecules, the prediction of binding affinity is a prerequisite to the reliable prediction of epitopes. The iterative self-consistent (ISC) partial-least-squares (PLS)-based additive method is a recently developed bioinformatic approach for predicting class II peptide−MHC binding affinity. The ISC−PLS method overcomes many of the conceptual difficulties inherent in the prediction of class II peptide−MHC affinity, such as the binding of a mixed population of peptide lengths due to the open-ended class II binding site. The method has applications in both the accurate prediction of class II epitopes and the manipulation of affinity for heteroclitic and competitor peptides. The method is applied here to six class II mouse alleles (I-Ab, I-Ad, I-Ak, I-As, I-Ed, and I-Ek) and included peptides up to 25 amino acids in length. A series of regression equations highlighting the quantitative contributions of individual amino acids at each peptide position was established. The initial model for each allele exhibited only moderate predictivity. Once the set of selected peptide subsequences had converged, the final models exhibited a satisfactory predictive power. Convergence was reached between the 4th and 17th iterations, and the leave-one-out cross-validation statistical terms - q2, SEP, and NC - ranged between 0.732 and 0.925, 0.418 and 0.816, and 1 and 6, respectively. The non-cross-validated statistical terms r2 and SEE ranged between 0.98 and 0.995 and 0.089 and 0.180, respectively. The peptides used in this study are available from the AntiJen database (http://www.jenner.ac.uk/AntiJen). The PLS method is available commercially in the SYBYL molecular modeling software package. The resulting models, which can be used for accurate T-cell epitope prediction, will be made freely available online (http://www.jenner.ac.uk/MHCPred).

Budget participation in Malaysian local authorites

This study examines the effect of budgetary participation on departmental performance via budget adequacy, organisational commitment and role ambiguity. The responses of 108 budget preparers and budget users drawn from a cross-section of Malaysian local authorities, to a questionnaire survey were analysed by using mediation analysis, path analysis and Pearson Product-Moment Correlation technique. The results suggest that budget adequacy, organisational commitment, and role ambiguity are important links in the process. The results of this study suggest that the relationship between budget participation and departmental performance is statistically, significantly, positively and marginally correlated. Of more interest was the finding that budget adequacy, organisational commitment, and role ambiguity are important intervening variables in the relationship between budget participation and departmental performance. The test for mediation effect, demonstrated that budget adequacy, organisational commitment, and role ambiguity had partially mediated the relationship of budget participation and departmental performance. These three variables act as partial mediators when they significantly reduced or decreased the path coefficient of budget participation and departmental performance rather than eliminating the relationship. Furthermore, the test for direct and indirect effect of budget participation on departmental performance, suggests that budget participation predicted or affected departmental performance more strongly in the indirect way than it did in a direct way. This suggests that, even though the correlation between budget participation and departmental performance was significant, the path interpretation suggests that the correlation arose because budget participation was correlated with other variables that have direct effect upon departmental performance not budget participation itself directly predicted departmental performance. Therefore, there is enough evidence to suggest that budget participation of budget preparers and budget users affects departmental performance of Malaysian local authorities indirectly via budget adequacy, organisational commitment and role ambiguity. Among the indirect effects, the link between budget participation, budget adequacy, organisational commitment, role ambiguity and departmental performance may be the most important in term of this study’s contribution. The decomposition of the observed correlation between budget participation, budget adequacy, organisational commitment and role ambiguity showed that budget 3 participation of budget preparers and budget users of Malaysian local authorities in the budget setting has direct effect on budget adequacy, organisational commitment and role ambiguity. Budget adequacy and organisational commitment was directly related. However, the relationship of role ambiguity and organisational commitment in this study was indirectly related. This suggests that participation of budget preparers and budget users in the budget setting of Malaysian local authorities lead to decrease role ambiguity that provide adequate budgetary supports, which lead to increase organisational commitment and thus enhance departmental performance. In relation to the strength of the relationships of the variables undertaken for the study, the overall relationships between variables are significant and positively related except that of role ambiguity relationship. The relationships of role ambiguity with budget participation, budget adequacy, organisational performance and departmental performance are negatively related.

Hypercoiling and hydrophobically associating polymers : interfacial synthesis, surface properties and pharmaceutical applications

The objective of the work described was to identify and synthesize a range of biodegradable hypercoiling or hydrophobically associating polymers to mimic natural apoproteins, such as those found in lung surfactant or plasma apolipoproteins. Stirred interfacial polymerization was used to synthesize potentially biodegradable aromatic polyamides (Mw of 12,000-26,000) based on L-Iysine, L-Iysine ethyl ester, L-ornithine and DL-diaminopropionic acid, by reaction with isophthaloyl chloride. A similar technique was used to synthesize aliphatic polyamides based on L-Iysine ethyl ester and either adipoyl chloride or glutaryl chloride resulting in the synthesis of poly(lysine ethyl ester adipamide) [PLETESA] or poly(lysine ethyl ester glutaramide) (Mw of 126,000 and 26,000, respectively). PLETESA was found to be soluble in both polar and non-polar solvents and the hydrophobic/hydrophilic balance could be modified by partial saponification (66-75%) of the ethyl ester side chains. Surface or interfacial tension/pH profiles were used to assess the conformation of both the poly(isophthalamides) and partially saponified PLETESA in aqueous solution. The results demonstrated that a loss of charge from the polymer was accompanied by an initial fall in surface activity, followed by a rise in activity, and ultimately, by polymer precipitation. These observations were explained by a collapse of the polymer chains into non-surface active intramolecular coils, followed by a transition to an amphipathic conformation, and finally to a collapsed hydrophobe. 2-Dimensional NMR analysis of polymer conformation in polar and non-polar solvents revealed intramolecular associations between the hydrophobic groups within partially saponified PLETESA. Unsaponified PLETESA appeared to form a coiled structure in polar solvents where the ethyl ester side chains were contained within the polymer coil. The implications of the secondary structure of PLETESA and potential biomedical applications are discussed.

All-optical TDM to WDM signal conversion and partial regeneration using XPM with triangular pulses

We propose a new all-optical, all-fibre scheme for conversion of time-division multiplexed to wavelength-division multiplexed signals using cross-phase modulation with triangular pulses. Partial signal regeneration using this technique is also demonstrated.

Full and partial privatization in China:the labor consequences

This paper is the first paper to present findings evaluating the consequences for employees of full and partial privatization using difference-in-differences combined with propensity score matching. We find: (1) partial privatization causes job creation in contrast to full privatization, which destroys jobs, (2) full privatization causes higher labor productivity improvement than partial privatization, (3) wage increases occur only in partially privatized firms and (4) there are small increases in labor quality investment in both cases. The results suggest partial privatization exploits market discipline to induce labor productivity whilst simultaneously providing welfare improvements for labor. This is the ‘win-win’ outcome predicted by the ‘helping hand’ theory of government. Our results suggest that governments are likely to gain wider support for a program of partial privatization rather than full privatization.

All-optical TDM to WDM signal conversion and partial regeneration using XPM with triangular pulses

We propose a new all-optical, all-fibre scheme for conversion of time-division multiplexed to wavelength-division multiplexed signals using cross-phase modulation with triangular pulses. Partial signal regeneration using this technique is also demonstrated.

Improving the performance of FBG sensors in a WDM network using a simulated annealing technique

Simulated annealing technique is used to improve the performance of fiber Bragg grating (FBG) sensors in a wavelength-division-multiplexed network. Experiments demonstrated strain detection accuracy of ̃2.5 με when the spectrums of FBGs are fully or partially overlapped.

Stochasticity, periodicity and localized light structures in partially mode-locked fibre lasers

Physical systems with co-existence and interplay of processes featuring distinct spatio-temporal scales are found in various research areas ranging from studies of brain activity to astrophysics. The complexity of such systems makes their theoretical and experimental analysis technically and conceptually challenging. Here, we discovered that while radiation of partially mode-locked fibre lasers is stochastic and intermittent on a short time scale, it exhibits non-trivial periodicity and long-scale correlations over slow evolution from one round-trip to another. A new technique for evolution mapping of intensity autocorrelation function has enabled us to reveal a variety of localized spatio-temporal structures and to experimentally study their symbiotic co-existence with stochastic radiation. Real-time characterization of dynamical spatio-temporal regimes of laser operation is set to bring new insights into rich underlying nonlinear physics of practical active- and passive-cavity photonic systems.