Search results for: automated glycan assignment

Authors: Ian Walsh, Terry Nguyen-Khuong, Christopher H. Taron, Pauline M. Rudd

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Glycoproteins and their covalently bonded glycans play critical roles in the immune system, cell communication, disease and disease prognosis. Ultra performance liquid chromatography (UPLC) coupled with mass spectrometry is conventionally used to qualitatively and quantitatively characterise glycan structures in a given sample. Exoglycosidases are enzymes that catalyze sequential removal of monosaccharides from the non-reducing end of glycans. They naturally have specificity for a particular type of sugar, its stereochemistry (α or β anomer) and its position of attachment to an adjacent sugar on the glycan. Thus, monitoring the peak movements (both in the UPLC and MS1) after application of exoglycosidases provides a unique and effective way to annotate sugars with high detail - i.e. differentiating positional and linkage isomers. Manual annotation of an exoglycosidase experiment is difficult and time consuming. As such, with increasing sample complexity and the number of exoglycosidases, the analysis could result in manually interpreting hundreds of peak movements. Recently, we have implemented pattern recognition software for automated interpretation of UPLC-MS1 exoglycosidase digestions. In this work, we explain the software, indicate how much time it will save and provide example usage showing the annotation of positional and linkage isomers in Immunoglobulin G, apolipoprotein J, and simple glycan standards.

Keywords: bioinformatics, automated glycan assignment, liquid chromatography, mass spectrometry

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Authors: K. Veluraja

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Glycan of glycolipids and glycoproteins is playing a significant role in living systems particularly in molecular recognition processes. Molecular recognition processes are attributed to their occurrence on the surface of the cell, sequential arrangement and type of sugar molecules present in the oligosaccharide structure and glyosidic linkage diversity (glycoinformatics) and conformational diversity (glycoconformatics). Molecular Dynamics Simulation study is a theoretical-cum-computational tool successfully utilized to establish glycoconformatics of glycan. The study on various oligosaccharides of glycan clearly indicates that oligosaccharides do exist in multiple conformational states and these conformational states arise due to the flexibility associated with a glycosidic torsional angle (φ,ψ) . As an example: a single disaccharide structure NeuNacα(2-3) Gal exists in three different conformational states due to the differences in the preferential value of glycosidic torsional angles (φ,ψ). Hence establishing three dimensional structural and conformational models for glycan (cartesian coordinates of every individual atoms of an oligosaccharide structure in a preferred conformation) is quite crucial to understand various molecular recognition processes such as glycan-toxin interaction and glycan-virus interaction. The gycoconformatics models obtained for various glycan through Molecular Dynamics Simulation stored in our 3DSDSCAR (3DSDSCAR.ORG) a public domain database and its utility value in understanding the molecular recognition processes and in drug design venture will be discussed.

Keywords: glycan, glycoconformatics, molecular dynamics simulation, oligosaccharide

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Authors: Jihene Jlassi, Ahmed Frikha, Wazna Kortli

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The objectives of Nurse-Patient Assignment are the minimization of the overall hospital cost and the maximization of nurses ‘preferences. This paper aims to assess nurses' satisfaction related to the implementation of patient acuity tool-based assignments. So, we used an integer linear program that assigns patients to nurses while balancing nurse workloads. Then, the proposed model is applied to the Paediatrics Department at Kasserine Hospital Tunisia. Where patients need special acuities and high-level nursing skills and care. Hence, numerical results suggested that proposed nurse-patient assignment models can achieve a balanced assignment

Keywords: nurse-patient assignment, mathematical model, logistics, pediatrics department, balanced assignment

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Authors: Pierre-Louis Lucas, Corinne Loutelier-Bourhis, Narimane Mati-Baouche, Philippe Chan Tchi-Song, Patrice Lerouge, Elodie Mathieu-Rivet, Muriel Bardor

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N-glycosylation is a post-translational modification taking place in the Endoplasmic Reticulum and the Golgi apparatus where defined glycan features are added on protein in a very specific sequence Asn-X-Thr/Ser/Cys were X can be any amino acid except proline. Because it is well-established that those N-glycans play a critical role in protein biological activity, protein half-life and that a different N-glycan structure may induce an immune response, they are very important in Biopharmaceuticals which are mainly glycoproteins bearing N-glycans. From now, most of the biopharmaceuticals are produced by mammalian cells like Chinese Hamster Ovary cells (CHO) for their N-glycosylation similar to the human, but due to the high production costs, several other species are investigated as the possible alternative system. In this purpose, the green microalgae Chlamydomonas reinhardtii was investigated as the potential production system for Biopharmaceuticals. This choice was influenced by the facts that C. reinhardtii is a well-study microalgae which is growing fast with a lot of molecular biology tools available. This organism is also producing N-glycan on its endogenous proteins. However, the analysis of the N-glycan structure of this microalgae has revealed some differences as compared to the human. Rather than in Human where the glycans are processed by key enzymes called N-acetylglucosaminyltransferase I and II (GnTI and GnTII) adding GlcNAc residue to form a GlcNAc₂Man₃GlcNAc₂ core N-glycan, C. reinhardtii lacks those two enzymes and possess a GnTI independent glycosylation pathway. Moreover, some enzymes like xylosyltransferases and methyltransferases not present in human are supposed to act on the glycans of C. reinhardtii. Furthermore, the recent structural study by mass spectrometry shows that the N-glycosylation precursor supposed to be conserved in almost all eukaryotic cells results in a linear Man₅GlcNAc₂ rather than a branched one in C. reinhardtii. In this work, we will discuss the new released MS information upon C. reinhardtii N-glycan structure and their impact on our attempt to modify the glycan in a Human manner. Two strategies will be discussed. The first one consisted in the study of Xylosyltransferase insertional mutants from the CLIP library in order to remove xyloses from the N-glycans. The second will go further in the humanization by transforming the microalgae with the exogenous gene from Toxoplasma gondii having an activity similar to GnTI and GnTII with the aim to synthesize GlcNAc₂Man₃GlcNAc₂ in C. reinhardtii.

Keywords: Chlamydomonas reinhardtii, N-glycosylation, glycosyltransferase, mass spectrometry, humanization

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Authors: Abigail Tan, Heng Liang Tan, Vanessa Ding, James Hui, Eng Hin Lee, Andre Choo

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Introduction: Comparative oncology investigates the similarities in spontaneous carcinogenesis between humans and animals, in order to identify treatments that can benefit these patients. Companion animals (CA), like canines and felines, are of special interest when it comes to studying human cancers due to their exposure to the same environmental factors and develop tumours with similar features. The purpose of this study is to explore the cross-reactivity of monoclonal antibodies (mAbs) across cancers in humans and CA. Material and Methods: A panel of CA mAbs generated in the lab was screened on multiple human cancer cell lines through flow cytometry to identify for positive binders. Shortlisted candidates were then characterised by biochemical and functional assays e.g., antibody-drug conjugate (ADC) and western blot assays, including glycan studies. Results: Candidate mAb KP52 was generated from whole-cell immunisation using feline mammary carcinoma. KP52 showed strong positive binding to human cancer cells, such as breast cancer and ovarian cancer. Furthermore, KP52 demonstrated strong killing ( > 50%) as an ADC with Saporin as the payload. Western blot results revealed the molecular weight of the antigen targets to be approximately 45kD and 50kD under reduced conditions. Glycan studies suggest that the epitope is glycan in nature, specifically an O-linked glycan. Conclusion: Candidate mAb KP52 has a therapeutic potential as an ADC against feline mammary cancer, human ovarian cancer, human mammary cancer, human pancreatic cancer, and human gastric cancer.

Keywords: ADC, comparative oncology, mAb, therapeutic

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Authors: Dominika Pihikova, Stefan Belicky, Tomas Bertok, Roman Sokol, Petra Kubanikova, Jan Tkac

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Since aberrant glycosylation is frequently accompanied by both physiological and pathological processes in a human body (cancer, AIDS, inflammatory diseases, etc.), the analysis of tumor-associated glycan patterns have a great potential for the development of novel diagnostic approaches. Moreover, altered glycoforms may assist as a suitable tool for the specificity and sensitivity enhancement in early-stage prostate cancer diagnosis. In this paper we discuss the construction and optimization of ultrasensitive sandwich biosensor platform employing lectin as glycan-binding protein. We focus on the immunoassay development, reduction of non-specific interactions and final glycoprofiling of human serum samples including both prostate cancer (PCa) patients and healthy controls. The fabricated biosensor was measured by label-free electrochemical impedance spectroscopy (EIS) with further lectin microarray verification. Furthermore, we analyzed different biosensor interfaces with atomic force microscopy (AFM) in nanomechanical mapping mode showing a significant differences in the altitude. These preliminary results revealing an elevated content of α-2,3 linked sialic acid in PCa patients comparing with healthy controls. All these experiments are important step towards development of point-of-care devices and discovery of novel glyco-biomarkers applicable in cancer diagnosis.

Keywords: biosensor, glycan, lectin, prostate cancer

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Authors: Mohammed Salem Alzahrani

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In this paper, student admission process is studied to optimize the assignment of vacant seats with three main objectives. Utilizing all vacant seats, satisfying all program of study admission requirements and maintaining fairness among all candidates are the three main objectives of the optimization model. Seat Assignment Method (SAM) is used to build the model and solve the optimization problem with help of Northwest Coroner Method and Least Cost Method. A closed formula is derived for applying the priority of assigning seat to candidate based on SAM.

Keywords: admission process model, assignment problem, Hungarian Method, Least Cost Method, Northwest Corner Method, SAM

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Authors: Elham Kazemi

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Quadratic Assignment Problem (QAP) is one the combinatorial optimization problems about which research has been done in many companies for allocating some facilities to some locations. The issue of particular importance in this process is the costs of this allocation and the attempt in this problem is to minimize this group of costs. Since the QAP’s are from NP-hard problem, they cannot be solved by exact solution methods. Cuckoo Optimization Algorithm is a Meta-heuristicmethod which has higher capability to find the global optimal points. It is an algorithm which is basically raised to search a continuous space. The Quadratic Assignment Problem is the issue which can be solved in the discrete space, thus the standard arithmetic operators of Cuckoo Optimization Algorithm need to be redefined on the discrete space in order to apply the Cuckoo Optimization Algorithm on the discrete searching space. This paper represents the way of discretizing the Cuckoo optimization algorithm for solving the quadratic assignment problem.

Keywords: Quadratic Assignment Problem (QAP), Discrete Cuckoo Optimization Algorithm (DCOA), meta-heuristic algorithms, optimization algorithms

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Authors: Jose Francisco Ferreira Ribeiro, Alexandre Bevilacqua Leoneti, Andre Lucirton Costa

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This paper presents a mathematical model in binary variables 0/1 to make the assignment of surgical procedures to the operating rooms in a hospital. The proposed mathematical model is based on the generalized assignment problem, which maximizes the sum of preferences for the use of the operating rooms by doctors, respecting the time available in each room. The corresponding program was written in Visual Basic of Microsoft Excel, and tested to schedule surgeries at St. Lydia Hospital in Ribeirao Preto, Brazil.

Keywords: generalized assignment problem, logistics, optimization, scheduling

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Authors: Kunal Das, Priya Sengupta, Abhishek K. Singh

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Pin assignment, scheduling, routing and error detection for arbitrary biochemical protocols in Digital Microfluidic Biochip have been reported in this paper. The research work is concentrating on pin assignment for 2 or 3 droplets routing in the arbitrary biochemical protocol, scheduling and routing in m × n biochip. The volumetric error arises due to droplet split in the biochip. The volumetric error detection is also addressed using biochip AND logic gate which is known as microfluidic AND or mAND gate. The algorithm for pin assignment for m × n biochip required m+n-1 numbers of pins. The basic principle of this algorithm is that no same pin will be allowed to be placed in the same column, same row and diagonal and adjacent cells. The same pin should be placed a distance apart such that interference becomes less. A case study also reported in this paper.

Keywords: digital microfludic biochip, cross-contamination, pin assignment, microfluidic AND gate

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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: Abdullah Alsheddy

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This paper presents the employment of Pareto optimality as a strategy to help (single-objective) local search escaping local optima. Instead of local search, Pareto local search is applied to solve the quadratic assignment problem which is multi-objectivized by adding a helper objective. The additional objective is defined as a function of the primary one with augmented penalties that are dynamically updated.

Keywords: Pareto optimization, multi-objectivization, quadratic assignment problem, local search

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Authors: Halil Ibrahim Demir, Abdullah Hulusi Kokcam, Fuat Simsir, Özer Uygun

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Traditionally, three important manufacturing functions which are process planning, scheduling and due-date assignment are performed sequentially and separately. Although there are numerous works on the integration of process planning and scheduling and plenty of works focusing on scheduling with due date assignment, there are only a few works on integrated process planning, scheduling and due-date assignment. Although due-dates are determined without taking into account of weights of the customers in the literature, here weighted due-date assignment is employed to get better performance. Jobs are scheduled according to weighted earliest due date dispatching rule and due dates are determined according to some popular due date assignment methods by taking into account of the weights of each job. Simulated Annealing, Evolutionary Strategies, Random Search, hybrid of Random Search and Simulated Annealing, and hybrid of Random Search and Evolutionary Strategies, are applied as solution techniques. Three important manufacturing functions are integrated step-by-step and higher integration levels are found better. Search meta-heuristics are found to be very useful while improving performance measure.

Keywords: process planning, weighted scheduling, weighted due-date assignment, simulated annealing, evolutionary strategies, hybrid searches

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Authors: F. Debbat, F. T. Bendimerad

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The efficient frequency assignment for radio communications becomes more and more crucial when developing new information technologies and their applications. It is consists in defining an assignment of frequencies to radio links, to be established between base stations and mobile transmitters. Separation of the frequencies assigned is necessary to avoid interference. However, unnecessary separation causes an excess requirement for spectrum, the cost of which may be very high. This problem is NP-hard problem which cannot be solved by conventional optimization algorithms. It is therefore necessary to use metaheuristic methods to solve it. This paper proposes Hybrid approach based on simulated annealing (SA) and Tabu Search (TS) methods to solve this problem. Computational results, obtained on a number of standard problem instances, testify the effectiveness of the proposed approach.

Keywords: cellular mobile communication, frequency assignment problem, optimization, tabu search, simulated annealing

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Authors: Halil Ibrahim Demir, Alper Goksu, Onur Canpolat, Caner Erden, Melek Nur

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Traditionally process planning, scheduling and due date assignment are performed sequentially and separately. High interrelation between these functions makes integration very useful. Although there are numerous works on integrated process planning and scheduling and many works on scheduling with due date assignment, there are only a few works on the integration of these three functions. Here we tested the different integration levels of these three functions and found a fully integrated version as the best. We applied genetic search and random search and genetic search was found better compared to the random search. We penalized all earliness, tardiness and due date related costs. Since all these three terms are all undesired, it is better to penalize all of them.

Keywords: process planning, scheduling, due-date assignment, genetic algorithm, random search

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Authors: Halil Ibrahim Demir, Tarık Cakar, Ibrahim Cil, Muharrem Dugenci, Caner Erden

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Conventionally, process planning, scheduling, and due-date assignment functions are performed separately and sequentially. The interdependence of these functions requires integration. Although integrated process planning and scheduling, and scheduling with due date assignment problems are popular research topics, only a few works address the integration of these three functions. This work focuses on the integration of process planning, WMS scheduling, and WPPW due date assignment. Another novelty of this work is the use of a weighted due date assignment. In the literature, due dates are generally assigned without considering the importance of customers. However, in this study, more important customers get closer due dates. Typically, only tardiness is punished, but the JIT philosophy punishes both earliness and tardiness. In this study, all weighted earliness, tardiness, and due date related costs are penalized. As no customer desires distant due dates, such distant due dates should be penalized. In this study, various levels of integration of these three functions are tested and genetic search and random search are compared both with each other and with ordinary solutions. Higher integration levels are superior, while search is always useful. Genetic searches outperformed random searches.

Keywords: process planning, weighted scheduling, weighted due-date assignment, genetic algorithm, random search

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Authors: Jahanshah Ashkani, Kevin J. Naidoo

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Glycosylation is the major posttranslational modification (PTM) process in cellular development. In tumour development, it is marked by structural alteration of carbohydrates (glycans) that is the result of aberrant glycosylation. Altered glycan structures affect cell surface ligand-receptor interactions that interfere with the regulation of cell adhesion, migration, and proliferation. The resulting changes in glycan biosynthesis pathways originate from altered expression of glycosyltransferases and glycosidases. While the alteration in glycosylation patterns is a recognized “hallmark of cancer”, the influential overview of the biology of cancer proposes eight hallmarks with no explicit suggestion to connectivity with glycosylation. Recently, we have discovered a connection between the glycosyltransferase gene expression and cancer type and subtype. Here we present an association between aberrant glycosylation and the biological hallmarks of breast cancer by exploring the common regulatory mechanisms at the genomic scale. The result of this study bridges the glycobiological and biological pathways that are accepted hallmarks of cancer by connecting their common regulatory pathways. This is an impetus for further investigation as target therapies of breast cancer are very likely to be uncovered from this.

Keywords: aberrant glycosylation, biological hallmarks, breast cancer, regulatory mechanism

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Authors: Qing Lyu, Hang Zhu

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Various flows in the network require to go through different types of middlebox. The improper placement of network middlebox and path assignment for flows could greatly increase the network latency and also decrease the performance of network. Minimizing the total end to end latency of all the ows requires to assign path for the incoming flows. In this paper, the flow path assignment problem in regard to the placement of various kinds of middlebox is studied. The flow path assignment problem is formulated to a linear programming problem, which is very time consuming. On the other hand, a naive greedy algorithm is studied. Which is very fast but causes much more latency than the linear programming algorithm. At last, the paper presents a heuristic algorithm named FPA, which takes bottleneck link information and estimated bandwidth occupancy into consideration, and achieves near optimal latency in much less time. Evaluation results validate the effectiveness of the proposed algorithm.

Keywords: flow path, latency, middlebox, network

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Authors: Ivan Stanev, Maria Koleva

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Automated software development issues are addressed in this paper. Layers and packages of a Common Platform for Automated Programming (CPAP) are defined based on Service Oriented Architecture, Cloud computing, Knowledge based automated software engineering (KBASE) and Method of automated programming. Tools of seven leading companies (AWS of Amazon, Azure of Microsoft, App Engine of Google, vCloud of VMWare, Bluemix of IBM, Helion of HP, OCPaaS of Oracle) are analyzed in the context of CPAP. Based on the results of the analysis CPAP requirements are formulated

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

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Authors: Ivan Belik

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In terms of social networks split graphs correspond to the variety of interpersonal and intergroup relations. In this paper we analyse the interaction between the cliques (socially strong and trusty groups) and the independent sets (fragmented and non-connected groups of people) as the basic components of any split graph. Based on the Semi-Lagrangean relaxation for the k-cardinality assignment problem we show the way of how to minimize the socially risky interactions between the cliques and the independent sets within the social network.

Keywords: cliques, independent sets, k-cardinality assignment, social networks, split graphs

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Authors: Ekta Jain, Kalpana Dahiya, Vanita Verma

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This paper discusses a priority based imbalanced time minimization assignment problem dealing with the allocation of n jobs to m < n persons in which the project is carried out in two stages, viz. Stage-I and Stage-II. Stage-I consists of n1 ( < m) primary jobs and Stage-II consists of remaining (n-n1) secondary jobs which are commenced only after primary jobs are finished. Each job is to be allocated to exactly one person, and each person has to do at least one job. It is assumed that nature of the Stage-I jobs is such that one person can do exactly one primary job whereas a person can do more than one secondary job in Stage-II. In a particular stage, all persons start doing the jobs simultaneously, but if a person is doing more than one job, he does them one after the other in any order. The aim of the proposed study is to find the feasible assignment which minimizes the total time for the two stage execution of the project. For this, an iterative algorithm is proposed, which at each iteration, solves a constrained imbalanced time minimization assignment problem to generate a pair of Stage-I and Stage-II times. For solving this constrained problem, an algorithm is developed in the current paper. Later, alternate combinations based method to solve the priority based imbalanced problem is also discussed and a comparative study is carried out. Numerical illustrations are provided in support of the theory.

Keywords: assignment, imbalanced, priority, time minimization

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Authors: Abdelfetah Laouzai, Rachid Ouafi

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In a traffic network, users usually choose their way so that it reduces their travel time between pairs origin-destination. This behavior might seem selfish as it produces congestions in different parts of the network. The traffic assignment problem (TAP) models the interactions between congestion and user travel decisions to obtain vehicles flows over each axis of the traffic network. The resolution methods of TAP serve as a tool allows predicting users’ distribution, identifying congesting points and affecting the travelers’ behavior in the choice of their route in the network following dynamic data. In this article, we will present a review about specific resolution approach of TAP. A comparative analysis is carried out on those approaches so that it highlights the characteristics, advantages and disadvantages of each.

Keywords: network traffic, travel decisions, approaches, traffic assignment, flows

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Authors: Hoi-Lam Ma, Sai-Ho Chung

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In traditional integrated berth allocation with quay crane assignment models, time dimension is usually assumed in hourly based. However, nowadays, transshipment becomes the main business to many container terminals, especially in Southeast Asia (e.g. Hong Kong and Singapore). In these terminals, vessel arrivals are usually very frequent with small handling volume and very short staying time. Therefore, the traditional hourly-based modeling approach may cause significant berth and quay crane idling, and consequently cannot meet their practical needs. In this connection, a 15-minute-based modeling approach is requested by industrial practitioners. Accordingly, a Three-level Genetic Algorithm (3LGA) with Quay Crane (QC) shifting heuristics is designed to fulfill the research gap. The objective function here is to minimize the total service time. Preliminary numerical results show that the proposed 15-minute-based approach can reduce the berth and QC idling significantly.

Keywords: transshipment, integrated berth allocation, variable-in-time quay crane assignment, quay crane assignment

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Authors: Qusay Alghazali, Tibor Cinkler, Abdulhalim Fayad

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In modern optical networks, the flex grid spectrum usage is most widespread, where higher bit rate streams get larger spectrum slices while lower bit rate traffic streams get smaller spectrum slices. To our practice, under the ITU-T recommendation, G.694.1, spectrum slices of 50, 75, and 100 GHz are being used with central frequency at 193.1 THz. However, when these spectrum slices are not sufficient, multiple spectrum slices can use either one next to another or anywhere in the optical wavelength. In this paper, we propose the analysis of the wavelength assignment problem. We compare different algorithms for this spectrum assignment with and without protection. As a reference for comparisons, we concluded that the Integer Linear Programming (ILP) provides the global optimum for all cases. The most scalable algorithm is the greedy one, which yields results in subsequent ranges even for more significant network instances. The algorithms’ benchmark implemented using the LEMON C++ optimization library and simulation runs based on a minimum number of spectrum slices assigned to lightpaths and their execution time.

Keywords: spectrum assignment, integer linear programming, greedy algorithm, international telecommunication union, library for efficient modeling and optimization in networks

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Authors: Sharon Hovav, Ilya Levner, Oren Nahum, Istvan Szabo

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In modern large-scale logistic centers (e.g., big automated warehouses), complex logistic operations performed by human staff (pickers) need to be coordinated with the operations of automated facilities (robots, conveyors, cranes, lifts, flow racks, etc.). The efficiency of advanced logistic centers strongly depends on optimizing picking technologies in synch with the facility/product layout, as well as on optimal distribution of material flows (products) in the system. The challenge is to develop a mathematical operations research (OR) tool that will optimize system cost-effectiveness. In this work, we propose a model that describes an automatic logistic center consisting of a set of workstations located at several galleries (floors), with each station containing a known number of flow racks. The requirements of each product and the working capacity of stations served by a given set of workers (pickers) are assumed as predetermined. The goal of the model is to maximize system efficiency. The proposed model includes two echelons. The first is the setting of the (optimal) number of workstations needed to create the total processing/logistic system, subject to picker capacities. The second echelon deals with the assignment of the products to the workstations and flow racks, aimed to achieve maximal throughputs of picked products over the entire system given picker capacities and budget constraints. The solutions to the problems at the two echelons interact to balance the overall load in the flow racks and maximize overall efficiency. We have developed an operations research model within each echelon. In the first echelon, the problem of calculating the optimal number of workstations is formulated as a non-standard bin-packing problem with capacity constraints for each bin. The problem arising in the second echelon is presented as a constrained product-workstation-flow rack assignment problem with non-standard mini-max criteria in which the workload maximum is calculated across all workstations in the center and the exterior minimum is calculated across all possible product-workstation-flow rack assignments. The OR problems arising in each echelon are proved to be NP-hard. Consequently, we find and develop heuristic and approximation solution algorithms based on exploiting and improving local optimums. The LC model considered in this work is highly dynamic and is recalculated periodically based on updated demand forecasts that reflect market trends, technological changes, seasonality, and the introduction of new items. The suggested two-echelon approach and the min-max balancing scheme are shown to work effectively on illustrative examples and real-life logistic data.

Keywords: logistics center, product-workstation, assignment, maximum performance, load balancing, fast algorithm

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Authors: Abhijeet Ostawal, Parmjit Lall

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The run times for a large strategic model that we were managing had become too long leading to delays in project delivery, increased costs and loss in productivity. Software developers are continuously working towards developing more efficient tools by changing their algorithms and processes. The issue faced by our team was how do you apply the latest technologies on validated existing models which are based on much older versions of software that do not have the latest software capabilities. The multi-model transport model that we had could only be run in sequential assignment order. Recent upgrades to the software now allowed the assignment to be run in parallel, a concept called parallelization. Parallelization is a Python script working only within the latest version of the software. A full model transfer to the latest version was not possible due to time, budget and the potential changes in trip assignment. This article is to show the method to adapt and update the Python script in such a way that it can be used in older software versions by calling the latest version and then recalling the old version for assignment model without affecting the results. Through a process of trial-and-error run time savings of up to 30-40% have been achieved. Assignment results were maintained within the older version and through this learning process we’ve applied this methodology to other even older versions of the software resulting in huge time savings, more productivity and efficiency for both client and consultant.

Keywords: model run time, demand model, parallelisation, python scripting

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Authors: Ashish Kumar Agrahari, Amit Kumar

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Paroxysmal nocturnal hemoglobinuria (PNH) is an acquired clonal blood disorder that manifests with hemolytic anemia, thrombosis, and peripheral blood cytopenias. The disease is caused by the deficiency of two glycosylphosphatidylinositols (GPI)-anchored proteins (CD55 and CD59) in the hemopoietic stem cells. The deficiency of GPI-anchored proteins has been associated with the somatic mutations in phosphatidylinositol glycan class A (PIGA). However, the mutations that do not cause PNH is associated with the multiple congenital anomalies-hypotonia-seizures syndrome 2 (MCAHS2). To best of our knowledge, no computational study has been performed to explore the atomistic level impact of PIGA mutations on the structure and dynamics of the protein. In the current work, we are mainly interested to get insights into the molecular mechanism of PIGA mutations. In the initial step, we screened the most pathogenic mutations from the pool of publicly available mutations. Further, to get a better understanding, pathogenic mutations were mapped to the modeled structure and subjected to 50ns molecular dynamics simulation. Our computational study suggests that four mutations are highly vulnerable to altering the structural conformation and stability of the PIGA protein, which illustrates its association with PNH and MCAHS2 phenotype.

Keywords: homology modeling, molecular dynamics simulation, missense mutations PNH, MCAHS2, PIGA

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Authors: Hans Marquez Ramos, Cesar Hernandez, Ingrid Páez

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This paper develops a multiple channel assignment model, which allows to take advantage in most efficient way, spectrum opportunities in cognitive radio networks. Developed scheme allows make several available and frequency adjacent channel assignments, which require a bigger wide band, under an equality environment. The hybrid assignment model it is made by to algorithms, one who makes the ranking and select available frequency channels and the other one in charge of establishing an equality criteria, in order to not restrict spectrum opportunities for all other secondary users who wish to make transmissions. Measurements made were done for average bandwidth, average delay, as well fairness computation for several channel assignment. Reached results were evaluated with experimental spectrum occupational data from GSM frequency band captured. Developed model, shows evidence of improvement in spectrum opportunity use and a wider average transmit bandwidth for each secondary user, maintaining equality criteria in channel assignment.

Keywords: bandwidth, fairness, multichannel, secondary users

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Authors: Halil Ibrahim Demir, Caner Erden, Mumtaz Ipek, Ozer Uygun

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Traditionally, the three important manufacturing functions, which are process planning, scheduling and due-date assignment, are performed separately and sequentially. For couple of decades, hundreds of studies are done on integrated process planning and scheduling problems and numerous researches are performed on scheduling with due date assignment problem, but unfortunately the integration of these three important functions are not adequately addressed. Here, the integration of these three important functions is studied by using genetic, random-genetic hybrid, simulated annealing, random-simulated annealing hybrid and random search techniques. As well, the importance of the integration of these three functions and the power of meta-heuristics and of hybrid heuristics are studied.

Keywords: process planning, weighted scheduling, weighted due-date assignment, genetic search, simulated annealing, hybrid meta-heuristics

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Authors: Lydia Wahid, Mona F. Ahmed, Nevin Darwish

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The vehicle routing problem (VRP) consists of a group of customers that needs to be served. Each customer has a certain demand of goods. A central depot having a fleet of vehicles is responsible for supplying the customers with their demands. The problem is composed of two subproblems: The first subproblem is an assignment problem where the number of vehicles that will be used as well as the customers assigned to each vehicle are determined. The second subproblem is the routing problem in which for each vehicle having a number of customers assigned to it, the order of visits of the customers is determined. Optimal number of vehicles, as well as optimal total distance, should be achieved. In this paper, an approach for solving the first subproblem (the assignment problem) is presented. In the approach, a clustering algorithm is proposed for finding the optimal number of vehicles by grouping the customers into clusters where each cluster is visited by one vehicle. Finding the optimal number of clusters is NP-hard. This work presents a polynomial time clustering algorithm for finding the optimal number of clusters and solving the assignment problem.

Keywords: vehicle routing problems, clustering algorithms, Clarke and Wright Saving Method, agglomerative hierarchical clustering

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