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).

Towards the in silico identification of class II restricted T-cell epitopes:a partial least squares iterative self-consistent algorithm for affinity prediction

Motivation: The immunogenicity of peptides depends on their ability to bind to MHC molecules. MHC binding affinity prediction methods can save significant amounts of experimental work. The class II MHC binding site is open at both ends, making epitope prediction difficult because of the multiple binding ability of long peptides. Results: An iterative self-consistent partial least squares (PLS)-based additive method was applied to a set of 66 pep- tides no longer than 16 amino acids, binding to DRB1*0401. A regression equation containing the quantitative contributions of the amino acids at each of the nine positions was generated. Its predictability was tested using two external test sets which gave r pred =0.593 and r pred=0.655, respectively. Furthermore, it was benchmarked using 25 known T-cell epitopes restricted by DRB1*0401 and we compared our results with four other online predictive methods. The additive method showed the best result finding 24 of the 25 T-cell epitopes. Availability: Peptides used in the study are available from http://www.jenner.ac.uk/JenPep. The PLS method is available commercially in the SYBYL molecular modelling software package. The final model for affinity prediction of peptides binding to DRB1*0401 molecule is available at http://www.jenner.ac.uk/MHCPred. Models developed for DRB1*0101 and DRB1*0701 also are available in MHC- Pred

Penalized Least Squares Fitting

* Supported by the Army Research Office under grant DAAD-19-02-10059.

No Royal Road but at Least a Gateway to the Mathematical Knowledge: The EuDML Project

Радослав Павлов - Представен е проектът EuDML – Европейската цифрова библиотека по математика (http://www.eudml.eu), който цели: • да създаде обща инфраструктура за безпроблемна навигация, търсене и взаимодействие в рамките на плътна мрежа от разпределено валидирано многоезично математическо съдържание в цифрова форма, което да е достъпно в цяла Европа, и така да направи математиката лесно достъпна за всички потребители; • да задоволи изискването за надежден и дългосрочен достъп до математическите изследвания. Представен е и българският принос в проекта – BulDML – цифрово хранилище за математическа литература на Института по математика и информатика на БАН (http://sci-gems.math.bas.bg).

A laser induced breakdown spectroscopy quantitative analysis method based on the robust least squares support vector machine regression model

Data fluctuation in multiple measurements of Laser Induced Breakdown Spectroscopy (LIBS) greatly affects the accuracy of quantitative analysis. A new LIBS quantitative analysis method based on the Robust Least Squares Support Vector Machine (RLS-SVM) regression model is proposed. The usual way to enhance the analysis accuracy is to improve the quality and consistency of the emission signal, such as by averaging the spectral signals or spectrum standardization over a number of laser shots. The proposed method focuses more on how to enhance the robustness of the quantitative analysis regression model. The proposed RLS-SVM regression model originates from the Weighted Least Squares Support Vector Machine (WLS-SVM) but has an improved segmented weighting function and residual error calculation according to the statistical distribution of measured spectral data. Through the improved segmented weighting function, the information on the spectral data in the normal distribution will be retained in the regression model while the information on the outliers will be restrained or removed. Copper elemental concentration analysis experiments of 16 certified standard brass samples were carried out. The average value of relative standard deviation obtained from the RLS-SVM model was 3.06% and the root mean square error was 1.537%. The experimental results showed that the proposed method achieved better prediction accuracy and better modeling robustness compared with the quantitative analysis methods based on Partial Least Squares (PLS) regression, standard Support Vector Machine (SVM) and WLS-SVM. It was also demonstrated that the improved weighting function had better comprehensive performance in model robustness and convergence speed, compared with the four known weighting functions.

Strong Consistency of the Conditional Least Squares Estimator for a Nonstationary Process. Example of the Garch Model

2000 Mathematics Subject Classification: Primary: 62M10, 62J02, 62F12, 62M05, 62P05, 62P10; secondary: 60G46, 60F15.

Group Comparisons on Cognitive Attributes Using the Least Squares Distance Model of Cognitive Diagnosis

2010 Mathematics Subject Classification: 62P15.

A simplified implementation of the least squares solution for pairwise comparisons matrices

This is a follow up to "Solution of the least squares method problem of pairwise comparisons matrix" by Bozóki published by this journal in 2008. Familiarity with this paper is essential and assumed. For lower inconsistency and decreased accuracy, our proposed solutions run in seconds instead of days. As such, they may be useful for researchers willing to use the least squares method (LSM) instead of the geometric means (GM) method.

Solving the Least Squares Method problem in the AHP for 3 X 3 and 4 X 4 matrices

The Analytic Hierarchy Process (AHP) is one of the most popular methods used in Multi-Attribute Decision Making. The Eigenvector Method (EM) and some distance minimizing methods such as the Least Squares Method (LSM) are of the possible tools for computing the priorities of the alternatives. A method for generating all the solutions of the LSM problem for 3 × 3 and 4 × 4 matrices is discussed in the paper. Our algorithms are based on the theory of resultants.

Solution of the Least Squares Method problem of pairwise comparison matrices

The aim of the paper is to present a new global optimization method for determining all the optima of the Least Squares Method (LSM) problem of pairwise comparison matrices. Such matrices are used, e.g., in the Analytic Hierarchy Process (AHP). Unlike some other distance minimizing methods, LSM is usually hard to solve because of the corresponding nonlinear and non-convex objective function. It is found that the optimization problem can be reduced to solve a system of polynomial equations. Homotopy method is applied which is an efficient technique for solving nonlinear systems. The paper ends by two numerical example having multiple global and local minima.

The kernel is in the least core for permutation games

Permutation games are totally balanced transferable utility cooperative games arising from certain sequencing and re-assignment optimization problems. It is known that for permutation games the bargaining set and the core coincide, consequently, the kernel is a subset of the core. We prove that for permutation games the kernel is contained in the least core, even if the latter is a lower dimensional subset of the core. By means of a 5-player permutation game we demonstrate that, in sense of the lexicographic center procedure leading to the nucleolus, this inclusion result can not be strengthened. Our 5-player permutation game is also an example (of minimum size) for a game with a non-convex kernel.

Percepção de cuidadores de crianças acerca da prevenção de acidentes domésticos infantis: análise à luz do modelo de crenças em saúde

This study aimed to analyze the perception of home caregivers of children from zero to five years-old on child domestic accidents and their influence in preventing these events. Exploratory and descriptive study with a qualitative approach, conducted with 20 caregivers attended at the Family Health Unit of Cidade Nova in Natal/Rio Grande do Norte, Brazil. The participants should have age less than 18 years-old, being a caregiver of at least a five year-old child and living in the area ascribed of Family Health Unit in the neighborhood Cidade Nova. Data collection occurred between March and April 2013 and a semistructured interview script was used. This stage was preceded by the acquiescence of the director of health institution where the research was developed, the Health Department of the Municipality of Natal as well as the Ethics Committee in Research of Universidade Federal do Rio Grande do Norte under Opinion nº 219 872 and CAAE nº 12236013.7.0000.5537. It is noted that respondents were asked to formal authorization by the Term of Consent. The data were treated according to the technique of the Collective Subject Discourse and analyzed based on three dimensions of the Health Belief Model, relating to perceptions of susceptibility to infant domestic accidents, self-efficacy to prevent infant and indicia domestic accidents for action of preventing domestic accidents in childhood. The results revealed that all the respondents were women, who, in their majority, they are mothers of the children they care, and predominantly they are aged between 18 and 30 years-old, full high school education and unemployed. Concerning the perception of susceptibility, it was unveiled understanding of deponents on various types of accidents, which are considered preventable. For this purpose, it was highlighted that the constant surveillance of the children is essential, keeping in view their high degree of curiosity and immaturity. On the perceived selfefficacy, the participants reported adopting preventive measures; however, they reported experiencing falls, burns, electric shocks and dog bites. In regard to the meaning attributed to experienced accidents they highlighted their feelings of guilt and despair, particularly about the cases understood as serious. Regarding the last dimension analyzed, related to indications for action, family, friends and television were the main source of information about household accidents and their prevention methods; however, health professionals were rarely cited as issuers of such knowledge. It is concluded that there is a widespread perception of women about prevention of domestic accidents and the weakness in the view of health professionals, including nurses, as disseminators of this information. This suggests the need to strengthen the dialogue on the issue and encouraging the participation of caregivers actively in the prevention of child domestic accidents