Search results for: De Novo programming

Authors: Z. Babic, I. Veza, A. Balic, M. Crnjac

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The linear programming model is sometimes difficult to apply in real business situations due to its assumption of proportionality. This paper shows an example of how to use De Novo programming approach instead of linear programming. In the De Novo programming, resources are not fixed like in linear programming but resource quantities depend only on available budget. Budget is a new, important element of the De Novo approach. Two different production situations are presented: increasing costs and quantity discounts of raw materials. The focus of this paper is on advantages of the De Novo approach in the optimization of production plan for production company which produces souvenirs made from famous stone from the island of Brac, one of the greatest islands from Croatia.

Keywords: business process, De Novo programming, optimizing, production

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Authors: Nasim Nosoudi, Amir Zadeh, Hunter White, Joshua Conrad, Joon W. Shim

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De novo Malignancy has become one of the major causes of death after transplantation, so early cancer diagnosis and detection can drastically improve survival rates post-transplantation. Most previous work focuses on using artificial intelligence (AI) to predict transplant success or failure outcomes. In this work, we focused on predicting de novo malignancy after liver transplantation using AI. We chose the patients that had malignancy after liver transplantation with no history of malignancy pre-transplant. Their donors were cancer-free as well. We analyzed 254,200 patient profiles with post-transplant malignancy from the US Organ Procurement and Transplantation Network (OPTN). Several popular data mining methods were applied to the resultant dataset to build predictive models to characterize de novo malignancy after liver transplantation. Recipient's bilirubin, creatinine, weight, gender, number of days recipient was on the transplant waiting list, Epstein Barr Virus (EBV), International normalized ratio (INR), and ascites are among the most important factors affecting de novo malignancy after liver transplantation

Keywords: De novo malignancy, bilirubin, data mining, transplantation

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Authors: Ivan Stanev, Maria Koleva

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A common platform for automated programming (CPAP) is defined in details. Two versions of CPAP are described: Cloud-based (including the set of components for classic programming, and the set of components for combined programming) and KBASE based (including the set of components for automated programming, and the set of components for ontology programming). Four KBASE products (module for automated programming of robots, intelligent product manual, intelligent document display, and intelligent form generator) are analyzed and CPAP contributions to automated programming are presented.

Keywords: automated programming, cloud computing, knowledge based software engineering, service oriented architecture

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Authors: Ketaki D. Belsare, Nicholas F. Polizzi, Lior Shtayer, William F. DeGrado

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Nature utilizes metalloproteins to perform chemical transformations with activities and selectivities that have long been the inspiration for design principles in synthetic and biological systems. The chemical reactivities of metalloproteins are directly linked to local environment effects produced by the protein matrix around the metal cofactor. A complete understanding of how the protein matrix provides these interactions would allow for the design of functional metalloproteins. The de novo computational design of proteins have been successfully used in design of active sites that bind metals like di-iron, zinc, copper containing cofactors; however, precisely designing active sites that can bind small molecule ligands (e.g., substrates) along with metal cofactors is still a challenge in the field. The de novo computational design of a functional metalloprotein that contains a purposefully designed substrate binding site would allow for precise control of chemical function and reactivity. Our research strategy seeks to elucidate the design features necessary to bind the cofactor protoporphyrin IX (hemin) in close proximity to a substrate binding pocket in a four helix bundle. First- and second-shell interactions are computationally designed to control orientation, electronic structure, and reaction pathway of the cofactor and substrate. The design began with a parameterized helical backbone that positioned a single histidine residue (as an axial ligand) to receive a second-shell H-bond from a Threonine on the neighboring helix. The metallo-cofactor, hemin was then manually placed in the binding site. A structural feature, pi-bulge was introduced to give substrate access to the protoporphyrin IX. These de novo metalloproteins are currently being tested for their activity towards hydroxylation and epoxidation. The de novo designed protein shows hydroxylation of aniline to 4-aminophenol. This study will help provide structural information of utmost importance in understanding de novo computational design variables impacting the functional activities of a protein.

Keywords: metalloproteins, protein design, de novo protein, biocatalysis

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Authors: Matthew T. Wilson

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This paper covers a selection of research utilizing grammar-based genetic programming, and illustrates how context-free grammar can be used to constrain genetic programming. It focuses heavily on grammatical evolution, one of the most popular variants of grammar-based genetic programming, and the way its operators and terminals are specialized and modified from those in genetic programming. A variety of implementations of grammatical evolution for general use are covered, as well as research each focused on using grammatical evolution or grammar-based genetic programming on a single application, or to solve a specific problem, including some of the classically considered genetic programming problems, such as the Santa Fe Trail.

Keywords: context-free grammar, genetic algorithms, genetic programming, grammatical evolution

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Authors: A. Bari

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Integer programming is a branch of mathematical programming techniques in operations research in which some or all of the variables are required to be integer valued. Various cuts have been used to solve these problems. We have also developed cuts known as NAZ cut & A-T cut to solve the integer programming problems. These cuts are used to reduce the feasible region and then reaching the optimal solution in minimum number of steps.

Keywords: Integer Programming, NAZ cut, A-T cut, Cutting plane method

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Authors: Dalia M. Abouelfadl, Noha N. Yassen, Marwa E. Shabana

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Background: The evolution of immune therapy motivated many to study the relation between immune response and progression of cancer. Little is known about expression of PD-L1 (a newly evolving immunotherapeutic drug) in papillary thyroid carcinoma (PTC) arising de-novo and PTC arising on top of autoimmune thyroiditis (Hashimoto's (HT) and lymphocytic thyroiditis (LT)). The aim of this work is to study the alteration of expression of PD-L1 in PTCs arising from de-novo or on top of HT OR LT using immunohistochemistry and image analyser system. Method: 100 paraffin blocks for PTC cases were collected retrospectively for staining using PD-L1 rabbit monoclonal antibody (BIOCARE-ACI 3171 A, C). The antibody expression is measured digitally using Image Analyzer Leica Qwin 3000, and the membranous and cytoplasmic expression of PD-L1 in tumor cells was considered positive. The results were correlated with tumor grade, size, and LN status. Results: The study samples consisted of 41 cases of PTC arising De novo, 36 cases on top of HT, and 23 on top of LT. Expression of PD-L1 was highest among the PTC-HL group (25 case-69%) followed by PTC-TL group (14 case-60.8%) then de-novo PTC (19 case-46%) with P Value < 0.05. PD-L1 expression correlated with nodal metastasis and was not relevant to tumor size or grade. Conclusion: The severity of the immune response in tumor microenvironment directly influences PTC prognosis. The anti PD-L1 Ab can be a very successful therapeutic agent for PTC arising on top of HT.

Keywords: carcinoma, Hashimoto's, lymphocytic, papillary, PD-L1, thyroiditis

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Authors: Ismael Zamora, Elisabeth Ortega, Tatiana Radchenko, Guillem Plasencia

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The structure elucidation based on Mass Spectra (MS) data of unknown substances is an unresolved problem that affects many different fields of application. The recent overview of software available for structure elucidation of small molecules has shown the demand for efficient computational tool that will be able to perform structure elucidation of unknown small molecules and peptides. We developed an algorithm for De-Novo fragment analysis based on MS data that proposes a set of scored and ranked structures that are compatible with the MS and MSMS spectra. Several different algorithms were developed depending on the initial set of fragments and the structure building processes. Also, in all cases, several scores for the final molecule ranking were computed. They were validated with small and middle databases (DB) with the eleven test set compounds. Similar results were obtained from any of the databases that contained the fragments of the expected compound. We presented an algorithm. Or De-Novo fragment analysis based on only mass spectrometry (MS) data only that proposed a set of scored/ranked structures that was validated on different types of databases and showed good results as proof of concept. Moreover, the solutions proposed by Mass Spectrometry were submitted to the prediction of NMR spectra in order to elucidate which of the proposed structures was compatible with the NMR spectra collected.

Keywords: De Novo, structure elucidation, mass spectrometry, NMR

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Authors: Mustafa Ekici, Sacide Güzin Mazman

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Programming is the one of ability in computer science fields which is generally perceived difficult by students and various individual differences have been implicated in that ability success. Although several factors that affect programming ability have been identified over the years, there is not still a full understanding of why some students learn to program easily and quickly while others find it complex and difficult. Programming self-efficacy and mathematic success are two of those essential individual differences which are handled as having important effect on the programming success. This study aimed to identify the relationship between programming performance, programming self efficacy and mathematics success. The study group is consisted of 96 undergraduates from Department of Econometrics of Uşak University. 38 (39,58%) of the participants are female while 58 (60,41%) of them are male. Study was conducted in the programming-I course during 2014-2015 fall term. Data collection tools are comprised of programming course final grades, programming self efficacy scale and a mathematics achievement test. Data was analyzed through correlation analysis. The result of study will be reported in the full text of the study.

Keywords: programming performance, self efficacy, mathematic success, computer science

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Authors: Sujeet Kumar Singh, Shiv Prasad Yadav

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This paper develops an approach for solving intuitionistic fuzzy linear fractional programming (IFLFP) problem where the cost of the objective function, the resources, and the technological coefficients are triangular intuitionistic fuzzy numbers. Here, the IFLFP problem is transformed into an equivalent crisp multi-objective linear fractional programming (MOLFP) problem. By using fuzzy mathematical programming approach the transformed MOLFP problem is reduced into a single objective linear programming (LP) problem. The proposed procedure is illustrated through a numerical example.

Keywords: triangular intuitionistic fuzzy number, linear programming problem, multi objective linear programming problem, fuzzy mathematical programming, membership function

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Authors: S. H. Nasseri, A. Ebrahimnejad

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Fuzzy set theory has been applied to many fields, such as operations research, control theory, and management sciences. In this paper, we consider two classes of fuzzy linear programming (FLP) problems: Fuzzy number linear programming and linear programming with trapezoidal fuzzy variables problems. We state our recently established results and develop fuzzy primal simplex algorithms for solving these problems. Finally, we give illustrative examples.

Keywords: fuzzy linear programming, fuzzy numbers, duality, sensitivity analysis

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Authors: Mohammad Shokoohi-Yekta, Hamid Mirebrahim

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A body of research has been devoted to investigating the preferences of computer programmers. These researches used various questionnaires to find out what programming language is most popular among programmers. The problem with such research is that the programmers are usually familiar with only a few languages; therefore, disregarding a number of other languages which might have characteristics that match their preferences more closely. To overcome such a problem, we decided to investigate the preferences of programmers in regards to the characteristics of languages, which help us to discover the languages that include the most characteristics preferred by the users. We conducted a user study to measure the preferences of programmers on different characteristics of programming languages and then tried to compare existing languages in the areas of application, Web and system programming. Overall, the results of our study indicated that the Ruby programming language has the highest preference score in the two areas of application and Web, and C++ has the highest score in the system area. The results of our study can also help programming language designers know the characteristics they should consider when developing new programming languages in order to attract more programmers.

Keywords: object orientation, programming language design, programmers' preferences, characteristic

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Authors: Bing Li

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The primitive code-level design patterns (PDP) are the rudimentary programming elements to develop any distributed systems in the generic distributed programming environment, GreatFree. The PDP works with the primitive distributed application programming interfaces (PDA), the distributed modeling, and the distributed concurrency for scaling-up. They not only hide developers from underlying technical details but also support sufficient adaptability to a variety of distributed computing environments. Programming with them, the simplest distributed system, the lightweight messaging two-node client/server (TNCS) system, is constructed rapidly with straightforward and repeatable behaviors, copy-paste-replace (CPR). As any distributed systems are made up of the simplest ones, those PDAs, as well as the PDP, are generic for distributed programming.

Keywords: primitive APIs, primitive code-level design patterns, generic distributed programming, distributed systems, highly patterned development environment, messaging

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Authors: Mazura Mokhtar, Adibah Shuib, Daud Mohamad

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Portfolio optimization problem has received a lot of attention from both researchers and practitioners over the last six decades. This paper provides an overview of the current state of research in portfolio optimization with the support of mathematical programming techniques. On top of that, this paper also surveys the solution algorithms for solving portfolio optimization models classifying them according to their nature in heuristic and exact methods. To serve these purposes, 40 related articles appearing in the international journal from 2003 to 2013 have been gathered and analyzed. Based on the literature review, it has been observed that stochastic programming and goal programming constitute the highest number of mathematical programming techniques employed to tackle the portfolio optimization problem. It is hoped that the paper can meet the needs of researchers and practitioners for easy references of portfolio optimization.

Keywords: portfolio optimization, mathematical programming, multi-objective programming, solution approaches

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Authors: M. Al-Jepoori, D. Bennett

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Teaching Object-Oriented Programming (OOP) as part of a Computing-related university degree is a very difficult task; the road to ensuring that students are actually learning object oriented concepts is unclear, as students often find it difficult to understand the concept of objects and their behavior. This problem is especially obvious in advanced programming modules where Design Pattern and advanced programming features such as Multi-threading and animated GUI are introduced. Looking at the students’ performance at their final year on a university course, it was obvious that the level of students’ understanding of OOP varies to a high degree from one student to another. Students who aim at the production of Games do very well in the advanced programming module. However, the students’ assessment results of the last few years were relatively low; for example, in 2016-2017, the first quartile of marks were as low as 24.5 and the third quartile was 63.5. It is obvious that many students were not confident or competent enough in their programming skills. In this paper, the reasons behind poor performance in Advanced OOP modules are investigated, and a suggested practice for teaching OOP based on a complex case study is described and evaluated.

Keywords: complex programming case study, design pattern, learning advanced programming, object oriented programming

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Authors: Nadia Selene Molina-Moreno, Maria Susana Avila-Garcia, Marco Bianchetti, Marcelina Pantoja-Flores

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Visual Programming Tools available are a great tool for introducing children to programming and to develop a skill set for algorithmic thinking. On the other hand, collaborative learning and pair programming within the context of programming activities, has demonstrated to have social and learning benefits. However, some of the online tools available for programming for children are not designed to allow simultaneous and equitable participation of the team members since they allow only for a single control point. In this paper, a report the work conducted with children playing a user role is presented. A preliminary study to cull ideas, insights, and design considerations for a formal programming course for children aged 8-10 using collaborative learning as a pedagogical approach was conducted. Three setups were provided: 1) lo-fi prototype, 2) PC, 3) a 46' multi-touch single display groupware limited by the application to a single touch entry. Children were interviewed at the end of the sessions in order to know their opinions about teamwork and the different setups defined. Results are mixed regarding the setup, but they agree to like teamwork.

Keywords: children, collaborative programming, visual programming, multi-touch tabletop, lo-fi prototype

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Authors: Debjani Chakraborty, Abhijit Chatterjee, Aishwaryaprajna

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Posynomials, a special type of polynomials, having singularities, pose difficulties while solving geometric programming problems. In this paper, a methodology has been proposed and used to obtain extreme values for geometric programming problems by nth degree polynomial interpolation technique. Here the main idea to optimise the posynomial is to fit a best polynomial which has continuous gradient values throughout the range of the function. The approximating polynomial is smoothened to remove the discontinuities present in the feasible region and the objective function. This spatial interpolation method is capable to optimise univariate and multivariate geometric programming problems. An example is solved to explain the robustness of the methodology by considering a bivariate nonlinear geometric programming problem. This method is also applicable for signomial programming problem.

Keywords: geometric programming problem, multivariate optimisation technique, posynomial, spatial interpolation

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Authors: B. Güney, Ç. Teke

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In recent years, rapid and correct decision making is crucial for both people and enterprises. However, uncertainty makes decision-making difficult. Fuzzy logic is used for coping with this situation. Thus, fuzzy linear programming models are developed in order to handle uncertainty in objective function and the constraints. In this study, a problem of a factory in food industry is investigated, required data is obtained and the problem is figured out as a fuzzy linear programming model. The model is solved using Zimmerman approach which is one of the approaches for fuzzy linear programming. As a result, the solution gives the amount of production for each product type in order to gain maximum profit.

Keywords: food industry, fuzzy linear programming, fuzzy logic, linear programming

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Authors: Jiaqi Yin, Baofeng Liang

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The rapid development in the fields of computer science and information technology presents new challenges and opportunities for foundational programming education. Traditional programming courses often focus heavily on theoretical knowledge while neglecting students’ practical programming and problem-solving abilities. This paper delves into the significance of programming education based on application abilities and provides a detailed explanation of a reform approach that incorporates project-driven teaching to nurture students with more comprehensive computer science skills.

Keywords: fundamentals of programming, application abilities, pedagogical reform, program design

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Authors: Naser Shagerdi Esmaeli, Mohsen Hamidpour, Parisa Hasankhani Tehrani

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Background: The TP53 mutation is frequently detected in acute myeloid leukemia (AML) patients with complex karyotype (CK), but the stability of this mutation during the clinical course remains unclear. Material and Methods: In this study, TP53 mutations were identified in 7% of 500 patients with de novo AML and 58.8% of patients with CK in Tabriz, Iran. TP53 mutations were closely associated with older age, lower white blood cell (WBC) and platelet counts, FAB M6 subtype, unfavorable-risk cytogenetics, and CK, but negatively associated with NPM1 mutation, FLT3/ITD and DNMT3A mutation. Result: Multivariate analysis demonstrated that TP53 mutation was an independent poor prognostic factor for overall survival and disease-free survival among the total cohort and the subgroup of patients with CK. A scoring system incorporating TP53 mutation and nine other prognostic factors, including age, WBC counts, cytogenetics, and gene mutations, into survival analysis proved to be very useful to stratify AML patients. Sequential study of 420 samples showed that TP53 mutations were stable during AML evolution, whereas the mutation was acquired only in 1 of the 126 TP53 wild-type patients when therapy-related AML originated from different clone emerged. Conclusion: In conclusion, TP53 mutations are associated with distinct clinic-biological features and poor prognosis in de novo AML patients and are rather stable during disease progression.

Keywords: acute myloblastic leukemia, TP53, FLT3/ITD, Iran

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Authors: Li-Zhi Liao

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The central path has played the key role in the interior point method. However, the convergence of the central path may not be true even in some convex programming problems with linear constraints. In this paper, the generalized central paths are introduced for convex programming. One advantage of the generalized central paths is that the paths will always converge to some optimal solutions of the convex programming problem for any initial interior point. Some additional theoretical properties for the generalized central paths will be also reported.

Keywords: central path, convex programming, generalized central path, interior point method

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Authors: Qasim M. Kriri

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Few Saudi Arabia production companies face financial profit issues until this moment. This work presents a linear integer programming model that solves a production problem of a Saudi Food Company in Saudi Arabia. An optimal solution to the above-mentioned problem is a Linear Programming solution. In this regard, the main purpose of this project is to maximize profit. Linear Programming Technique has been used to derive the maximum profit from production of natural juice at Saudi Food Co. The operations of production of the company were formulated and optimal results are found out by using Lindo Software that employed Sensitivity Analysis and Parametric linear programming in order develop Linear Programming. In addition, the parameter values are increased, then the values of the objective function will be increased.

Keywords: parameter linear programming, objective function, sensitivity analysis, optimize profit

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Authors: Sanam Haseen, Abdul Bari

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In this paper a three stage multivariate programming problem with random survey cost and variances as random variables has been formulated as a non-linear stochastic programming problem. The problem has been converted into an equivalent deterministic form using chance constraint programming and modified E-modeling. An empirical study of the problem has been done at the end of the paper using R-simulation.

Keywords: chance constraint programming, modified E-model, stochastic programming, stratified sample surveys, three stage sample surveys

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Authors: Tunjo Perić, Franjo Bratić

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In this paper the goal programming methodology for solving multiple objective problem of the technological variants and production plan optimization has been applied. The optimization criteria are determined and the multiple objective linear programming model for solving a problem of the technological variants and production plan optimization is formed and solved. Then the obtained results are analysed. The obtained results point out to the possibility of efficient application of the goal programming methodology in solving the problem of the technological variants and production plan optimization. The paper points out on the advantages of the application of the goal programming methodolohy compare to the Surrogat Worth Trade-off method in solving this problem.

Keywords: goal programming, multi objective programming, production plan, SWT method, technological variants

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Authors: Lidia N. Hernández-Piña, Carlos R. Jaimez-González

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Interoperability in distributed systems is an important feature that refers to the communication of two applications written in different programming languages. This paper presents a serializer and a de-serializer of PHP objects to and from XML, which is an independent library written in the PHP programming language. The XML generated by this serializer is independent of the programming language, and can be used by other existing Web Objects in XML (WOX) serializers and de-serializers, which allow interoperability with other object-oriented programming languages.

Keywords: interoperability, PHP object serialization, PHP to XML, web objects in XML, WOX

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Authors: Ritu Sharma, Haifeng Shen

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Teaching introductory programming is a challenging task in tertiary education and various factors are believed to have influence on students’ learning of programming. However, these factors were largely studied independently in a chosen context. This paper aims to investigate whether interrelationships exist among the factors and whether the interrelationships are context-dependent. In this empirical study, two universities were chosen from two continents, which represent different cultures, teaching methodologies, assessment criteria and languages used to teach programming in west and east worlds respectively. The results reveal that some interrelationships are common across the two different contexts, while others appear context-dependent.

Keywords: introductory programming, tertiary education, factors, interrelationships, context, empirical study

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Authors: Tlou J. Ramabu

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Programming is one of the challenging subjects in the field of computing. In the higher education sphere, some programming novices’ performance, retention rate, and success rate are not improving. Most of the time, the problem is caused by the slow pace of learning, difficulty in grasping the syntax of the programming language and poor logical skills. More importantly, programming forms part of major subjects within the field of computing. As a result, specialized pedagogical methods and innovation are highly recommended. Little research has been done on the potential productivity of the WhatsApp platform as part of a blended learning model. In this article, the authors discuss the WhatsApp group as a part of blended learning model incorporated for a group of programming novices. We discuss possible administrative activities for productive utilisation of the WhatsApp group on the blended learning overview. The aim is to take advantage of the popularity of WhatsApp and the time students spend on it for their educational purpose. We believe that blended learning featuring a WhatsApp group may ease novices’ cognitive load and strengthen their foundational programming knowledge and skills. This is a work in progress as the proposed blended learning model with WhatsApp incorporated is yet to be implemented.

Keywords: blended learning, higher education, WhatsApp, programming, novices, lecturers

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Authors: M. G. M. Khan, V. D. Prasad, D. K. Rao

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In this manuscript, we discuss the problem of determining the optimum stratification of a study (or main) variable based on the auxiliary variable that follows a uniform distribution. If the stratification of survey variable is made using the auxiliary variable it may lead to substantial gains in precision of the estimates. This problem is formulated as a Nonlinear Programming Problem (NLPP), which turn out to multistage decision problem and is solved using dynamic programming technique.

Keywords: auxiliary variable, dynamic programming technique, nonlinear programming problem, optimum stratification, uniform distribution

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Authors: Meraj Ali Khan, Falleh R. Al-Solamy

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In the present paper, second order duality for multiobjective nonlinear programming are investigated under the second order generalized (F, b, φ, ρ, θ)− univex functions. The weak, strong and converse duality theorems are proved. Further, we also illustrated an example of (F, b, φ, ρ, θ)− univex functions. Results obtained in this paper extend some previously known results of multiobjective nonlinear programming in the literature.

Keywords: duality, multiobjective programming, univex functions, univex

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Authors: Sanaa Rashed Abdallah, Yasser F. Hassan

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The paper will introduce an approach where a rough sets, gene expression programming and rough neural networks are used cooperatively for learning and classification support. The Objective of gene expression programming rough neural networks (GEP-RNN) approach is to obtain new classified data with minimum error in training and testing process. Starting point of gene expression programming rough neural networks (GEP-RNN) approach is an information system and the output from this approach is a structure of rough neural networks which is including the weights and thresholds with minimum classification error.

Keywords: rough sets, gene expression programming, rough neural networks, classification

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