Remote sensing image processing using MCDF

Modified conjugate directional filtering (MCDF) is a new method proposed by Guo and Watson in 2002 for digital data and image processing. It provides ability in not only integrating directional-filtered results in conjugate directions into one image that shows the maximum linear features in these conjugate directions, but also further manipulating the outcomes using a number of predefined MCDF operations for different purposes. The use of MCDF (add1) to remote sensing image processing with 2D spectral analysis proves that the MCDF operation brings enhanced information integration operated in two different directions, which is the weaknesses of using the conventional methods in image processing. Its adaptive weighting system offers even more choices in combining selectively intensified results together to achieve a balanced presentation, which cannot be achieved using any traditional processing methods

PepMapper: a collaborative web tool for mapping epitopes from affinity-selected peptides

Epitope mapping from affinity-selected peptides has become popular in epitope prediction, and correspondingly many Web-based tools have been developed in recent years. However, the performance of these tools varies in different circumstances. To address this problem, we employed an ensemble approach to incorporate two popular Web tools, MimoPro and Pep-3D-Search, together for taking advantages offered by both methods so as to give users more choices, support and convenience for their specific purposes of epitope-peptide mapping. The combined operation of Union finds as many associated peptides as possible from both methods, which increases sensitivity in finding potential epitopic regions on a given antigen surface. The combined operation of Intersection achieves to some extent the mutual verification by the two methods and hence increases the likelihood of locating the genuine epitopic region on a given antigen in relation to the interacting peptides. The Consistency between Intersection and Union is an indirect sufficient condition to assess the likelihood of successful peptide-epitope mapping. On average from 27 tests, the combined operations of PepMapper outperformed either MimoPro or Pep-3D-Search alone. Therefore, PepMapper is another multipurpose mapping tool for epitope prediction from affinity-selected peptides. The Web server can be freely accessed at: http://informatics.nenu.edu.cn/PepMapper

Intelligent techniques for simulation and modelling

An engineering or a scientific problem is often based on some physical natures. To solve such a problem, we need to formulate the problem as a mathematical model in terms of variables, functions, and equations. The process of creating such a model, solving it, and interpreting the result in physical, chemical, geometric, engineering, or other terms is modelling. Such a model is likely comprised of a number of unknown factors, such as temporal and spatial constraints. By varying one or more of these unknown factors within the limits, different outcomes can be generated from the mathematical model and/or solution. These outcomes correlate to different physical, chemical, geometric, engineering scenarios. This model-based iterative mathematical computation is simulation. Modelling and simulation are two different but closely related approaches in many disciplines

MimoPro : a more efficient Web-based tool for epitope prediction using phage display libraries

Background: A B-cell epitope is a group of residues on the surface of an antigen which stimulates humoral responses. Locating these epitopes on antigens is important for the purpose of effective vaccine design. In recent years, mapping affinity-selected peptides screened from a random phage display library to the native epitope has become popular in epitope prediction. These peptides, also known as mimotopes, share the similar structure and function with the corresponding native epitopes. Great effort has been made in using this similarity between such mimotopes and native epitopes in prediction, which has resulted in better outcomes than statistics-based methods can. However, it cannot maintain a high degree of satisfaction in various circumstances. Results: In this study, we propose a new method that maps a group of mimotopes back to a source antigen so as to locate the interacting epitope on the antigen. The core of this method is a searching algorithm that is incorporated with both dynamic programming (DP) and branch and bound (BB) optimization and operated on a series of overlapping patches on the surface of a protein. These patches are then transformed to a number of graphs using an adaptable distance threshold (ADT) regulated by an appropriate compactness factor (CF), a novel parameter proposed in this study. Compared with both Pep-3D-Search and PepSurf, two leading graph-based search tools, on average from the results of 18 test cases, MimoPro, the Web-based implementation of our proposed method, performed better in sensitivity, precision, and Matthews correlation coefficient (MCC) than both did in epitope prediction. In addition, MimoPro is significantly faster than both Pep-3D-Search and PepSurf inprocessing. Conclusions: Our search algorithm designed for processing well constructed graphs using an ADT regulated by CF is more sensitive and significantly faster than other graph-based approaches in epitope prediction. MimoPro is a viable alternative to both PepSurf and Pep-3D-Search for epitope prediction in the same kind, and freely accessible through the MimoPro server located at http://informatics.nenu.edu.cn/MimoPr

Advanced techniques for computational and information sciences: Editorial

This is the editorial preface to Special Issue on Advanced Techniques for Computational and Information Sciences with Mathematical Problems in Engineering

Engaging village health workers in non-communicable disease (NCD) prevention and control in Vietnam: A qualitative study

The burden of non-communicable diseases (NCDs) continues to grow in Vietnam, and reducing the burden of NCDs is a national priority. This study explored perspective of community health workers (CHWs), known as Village Health Workers (VHWs) in Vietnam, and public health leaders towards potential of expanding VHWs’ role to deliver NCDs prevention and control services, and determined barriers and facilitators. We conducted focus group discussions (FGDs) with VHWs (n = 24) and in-depth interviews (IDIs) with public health administrators (n = 13). The findings show that VHWs in Vietnam deliver multiple public health services, including several NCDs related services. Perceived barriers include lack of policy support, shortages of trained health personnel, lack of training, imbalanced workload and inadequate remuneration. Perceived barriers include lack of policy support, shortages of trained health personnel, lack of training, imbalanced workload and inadequate remuneration. Facilitators include government commitment to NCDs prevention and control, priority on capacity building, professional recognition and provision of incentives with availability of appropriate resources. While additional quantitative studies are needed to supplement the current qualitative findings, the current results inform the policy and intervention development in engaging VHWs in the delivery of community-based NCDs prevention and control initiatives in Vietnam