Search results for: sequence alignment problem

Authors: P. Parthiban, Sonu Rajak, R. Dhanalakshmi

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This paper presents an Ant Colony Optimization (ACO) approach, combined with a Speed Optimization Algorithm (SOA) to solve the Vehicle Routing Problem (VRP) with environmental considerations, which is well known as Pollution-Routing Problem (PRP). It consists of routing a number of vehicles to serve a set of customers, and determining fuel consumption, driver wages and their speed on each route segment, while respecting the capacity constraints and time windows. Since VRP is NP-hard problem, so PRP also a NP-hard problem, which requires metaheuristics to solve this type of problems. The proposed solution method consists of two stages. Stage one is to solve a Vehicle Routing Problem with Time Window (VRPTW) using ACO and in the second stage, a SOA is run on the resulting VRPTW solution. Given a vehicle route, the SOA consists of finding the optimal speed on each arc of the route to minimize an objective function comprising fuel consumption costs and driver wages. The proposed algorithm tested on benchmark problem, the preliminary results show that the proposed algorithm can provide good solutions within reasonable computational time.

Keywords: ant colony optimization, CO2 emissions, speed optimization, vehicle routing

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Authors: Dávid Csercsik, Péter Kádár

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In the case of the proposed method, the problem is parallelized by considering multiple possible mode of operation profiles, which determine the range in which the generators operate in each period. For each of these profiles, the optimization is carried out independently, and the best resulting dispatch is chosen. For each such profile, the resulting problem is a quadratic programming (QP) problem with a potentially negative definite Q quadratic term, and constraints depending on the actual operation profile. In this paper we analyze the performance of available MATLAB optimization methods and solvers for the corresponding QP.

Keywords: optimization, MATLAB, quadratic programming, economic dispatch

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Authors: Petr Šimek

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This work deals with the problem of synchronization of bus frames during transmission using USB (Universal Serial Bus). The principles for synchronization between USB and the non-deterministic CAN (Controller Area Network) bus will be described here. Furthermore, the work deals with ensuring the time sequence of communication frames when receiving from multiple communication bus channels. The structure of a general object for storing frames from different types of communication buses, such as CAN and LIN (Local Interconnect Network), will be described here. Finally, an evaluation of the communication throughput of bus frames for USB High speed will be performed. The creation of this architecture was based on the analysis of the communication of control units with a large number of communication buses. For the design of the architecture, a test HW with a USB-HS interface was used, which received previously known messages, which were compared with the received result. The result of this investigation is the block architecture of the control program for test HW ensuring correct data transmission via the USB bus.

Keywords: analysis, CAN, interface, LIN, synchronization, USB

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Authors: David L. Knott, Robert Kingsland, Alistair Hitchon

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The proposed Newcastle Light Rail is a key part of the revitalisation of Newcastle, NSW and will provide a frequent and reliable travel option throughout the city centre, running from Newcastle Interchange at Wickham to Pacific Park in Newcastle East, a total of 2.7 kilometers in length. Approximately one-third of the route, along Hunter and Scott Streets, is subject to potential shallow underground mine workings. The extent of mining and seams mined is unclear. Convicts mined the Yard Seam and overlying Dudley (Dirty) Seam in Newcastle sometime between 1800 and 1830. The Australian Agricultural Company mined the Yard Seam from about 1831 to the 1860s in the alignment area. The Yard Seam was about 3 feet (0.9m) thick, and therefore, known as the Yard Seam. Mine maps do not exist for the workings in the area of interest and it was unclear if both or just one seam was mined. Information from 1830s geological mapping and other data showing shaft locations were used along Scott Street and information from the 1908 Royal Commission was used along Hunter Street to develop an investigation program. In addition, mining was encountered for several sites to the south of the alignment at depths of about 7 m to 25 m. Based on the anticipated depths of mining, it was considered prudent to assess the potential for sinkhole development on the proposed alignment and realigned underground utilities and to obtain approval for the work from Subsidence Advisory NSW (SA NSW). The assessment consisted of a desktop study, followed by a subsurface investigation. Four boreholes were drilled along Scott Street and three boreholes were drilled along Hunter Street using HQ coring techniques in the rock. The placement of boreholes was complicated by the presence of utilities in the roadway and traffic constraints. All the boreholes encountered the Yard Seam, with conditions varying from unmined coal to an open void, indicating the presence of mining. The geotechnical information obtained from the boreholes was expanded by using various downhole techniques including; borehole camera, borehole sonar, and downhole geophysical logging. The camera provided views of the rock and helped to explain zones of no recovery. In addition, timber props within the void were observed. Borehole sonar was performed in the void and provided an indication of room size as well as the presence of timber props within the room. Downhole geophysical logging was performed in the boreholes to measure density, natural gamma, and borehole deviation. The data helped confirm that all the mining was in the Yard Seam and that the overlying Dudley Seam had been eroded in the past over much of the alignment. In summary, the assessment allowed the potential for sinkhole subsidence to be assessed and a mitigation approach developed to allow conditional approval by SA NSW. It also confirmed the presence of mining in the Yard Seam, the depth to the seam and mining conditions, and indicated that subsidence did not appear to have occurred in the past.

Keywords: downhole investigation techniques, drilling, mine subsidence, yard seam

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Authors: Kyugneun Lee, Ikjin Lee

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Parameter estimation with inverse problem often suffers from unfavorable conditions in the real world. Useless data and many input parameters make the problem complicated or insoluble. Data refinement and reformulation of the problem can solve that kind of difficulties. In this research, a method to solve the rank deficient inverse problem is suggested. A multi-physics system which has rank deficiency caused by response correlation is treated. Impeditive information is removed and the problem is reformulated to sequential estimations using Bayesian network (BN) and subset groups. At first, subset grouping of the responses is performed. Feature selection with singular value decomposition (SVD) is used for the grouping. Next, BN inference is used for sequential conditional estimation according to the group hierarchy. Directed acyclic graph (DAG) structure is organized to maximize the estimation ability. Variance ratio of response to noise is used to pairing the estimable parameters by each response.

Keywords: Bayesian network, feature selection, rank deficiency, statistical inverse analysis

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Authors: David Chao, John Lai, Alvin Wu, Carl Wang

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For lithium-ion batteries with multiple cell configurations, some use scenarios can cause uneven aging effects to each cell within the battery because of uneven current distribution. Hence the focus of the study is to explore the aging effect(s) on batteries with different construction designs. In order to systematically study the influence of various factors in some key battery configurations, a detailed analysis of three key battery construction factors is conducted. And those key factors are (1) terminal position; (2) cell alignment matrix; and (3) interconnect resistance between cells. In this study, the 2S2P circuitry has been set as a model multi-cell battery to set up different battery samples, and the aging behavior is studied by a cycling test to analyze the current distribution and recoverable capacity. According to the outcome of aging tests, some key findings are: (I) different cells alignment matrices can have an impact on the cycle life of the battery; (II) symmetrical structure has been identified as a critical factor that can influence the battery cycle life, and unbalanced resistance can lead to inconsistent cell aging status; (III) the terminal position has been found to contribute to the uneven current distribution, that can cause an accelerated battery aging effect; and (IV) the internal connection resistance increase can actually result in cycle life increase; however, it is noteworthy that such increase in cycle life is accompanied by a decline in battery performance. In summary, the key findings from the study can help to identify the key aging factor of multi-cell batteries, and it can be useful to effectively improve the accuracy of battery capacity predictions.

Keywords: multiple cells battery, current distribution, battery aging, cell connection

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Authors: Sadegh Lotfieblisofla, Arash Khodabakhshi

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Tissue plasminogen activator (tPA) as a serine protease plays an important role in the fibrinolytic system and the dissolution of fibrin clots in human body. The production of this drug in plants such as tobacco could reduce its production costs. In this study, expression of tPA gene and protein targeting to different plant cell compartments, using various signal peptides has been investigated. For high level of expression, Kozak sequence was used after CaMV35S in the beginning of the gene. In order to design the final construction, Extensin, KDEL (amino acid sequence including Lys-Asp-Glu-Leu) and SP (γ-zein signal peptide coding sequence) were used as leader signals to conduct this protein into apoplast, endoplasmic reticulum and cytosol spaces, respectively. Cloned human tPA gene under the CaMV (Cauliflower mosaic virus) 35S promoter and NOS (Nopaline Synthase) terminator into pBI121 plasmid was transferred into tobacco explants by Agrobacterium tumefaciens strain LBA₄₄₀₄. The presence and copy number of genes in transgenic tobacco was proved by Southern blotting. Enzymatic activity of the rt-PA protein in transgenic plants compared to non-transgenic plants was confirmed by Zymography assay. The presence and amount of rt-PA recombinant protein in plants was estimated by ELISA analysis on crude protein extract of transgenic tobacco using a specific antibody. The yield of recombinant tPA in transgenic tobacco for SP, KDEL, Extensin signals were counted 0.50, 0.68, 0.69 microgram per milligram of total soluble proteins.

Keywords: tPA, recombinant, transgenic, tobacco

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Authors: Chyong-Ru Liu, Wen-Shiung Huang, Wan-Ching Tang, Shan-Pei Chen

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Two of the biggest challenges companies involved in sports and exercise information services face are how to strengthen participation in virtual sports/exercise communities and how to increase the ongoing participatoriness of those communities. In the past, relatively little research has explored mechanisms for strengthening alignment practice and community response from the perspective of self-construal, and as such this study seeks to explore the self-construal of virtual sports/exercise communities, the role it plays in the emotional commitment of forming communities, and the factor that can strengthen alignment practice. Moreover, which factor of the emotional commitment of forming virtual communities have the effect of strengthening interference in the process of transforming customer citizenship behaviors? This study collected 625 responses from the two leading websites in terms of fan numbers in the provision of information on road race and marathon events in Taiwan, with model testing conducted through linear structural equation modelling and the bootstrapping technique to test the proposed hypotheses. The results proved independent construal had a stronger positive direct effect on affective commitment to fellow customers than did interdependent construal, and the influences of affective commitment to fellow customers in enhancing customer citizenship behavior. Public self-consciousness moderates the relationships among independent self-construal and interdependent self-construal on effective commitment to fellow customers. Perceived playfulness moderates the relationships between effective commitment to fellow customers and customer citizenship behavior. The findings of this study provide significant insights for the researchers and related organizations. From the theoretical perspective, this is empirical research that investigated the self-construal theory and responses (i.e., affective commitment to fellow customers, customer citizenship behavior) in virtual sports/exercise communities. We further explore how to govern virtual sports/exercise community participants’ heterogeneity through public self-consciousness mechanism to align participants’ affective commitment. Moreover, perceived playfulness has the effect of strengthening effective commitment to fellow customers with customer citizenship behaviors. The results of this study can provide a foundation for the construction of future theories and can be provided to related organizations for reference in their planning of virtual communities.

Keywords: self-construal theory, public self-consciousness, affective commitment, customer citizenship behavior

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Authors: Mirjana Ruppel, Rajendra Persad, Amit Bahl, Sanja Dogramadzi, Chris Melhuish, Lyndon Smith

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Multimodal image registration is a profoundly complex task which is why deep learning has been used widely to address it in recent years. However, two main challenges remain: Firstly, the lack of ground truth data calls for an unsupervised learning approach, which leads to the second challenge of defining a feasible loss function that can compare two images of different modalities to judge their level of alignment. To avoid this issue altogether we implement a generative adversarial network consisting of two registration networks GAB, GBA and two discrimination networks DA, DB connected by spatial transformation layers. GAB learns to generate a deformation field which registers an image of the modality B to an image of the modality A. To do that, it uses the feedback of the discriminator DB which is learning to judge the quality of alignment of the registered image B. GBA and DA learn a mapping from modality A to modality B. Additionally, a cycle-consistency loss is implemented. For this, both registration networks are employed twice, therefore resulting in images ˆA, ˆB which were registered to ˜B, ˜A which were registered to the initial image pair A, B. Thus the resulting and initial images of the same modality can be easily compared. A dataset of liver CT and MRI was used to evaluate the quality of our approach and to compare it against learning and non-learning based registration algorithms. Our approach leads to dice scores of up to 0.80 ± 0.01 and is therefore comparable to and slightly more successful than algorithms like SimpleElastix and VoxelMorph.

Keywords: cycle consistency, deformable multimodal image registration, deep learning, GAN

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Authors: Akintunde O. Osibamowo, Abdulrasaq O. Olusanya

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The present study was designed to examine the effect of problem-solving approach as a medium of instruction in teaching and learning of mathematics to improve the achievement of the student. One Hundred (100) students were randomly chosen from five (5) Junior Secondary School in Ijebu-Ode Local Government Area of Ogun State, Nigeria. The data was collected through Mathematics Achievement Test (MAT) on the two groups (experimental and control group). The study confirmed that there is a significant different in the achievement of students exposed to problem-solving approach than those not exposed. The result also indicated that male students, however, had a greater mean-score than the female with no significant difference in their achievement. The result of the study supports the use of problem-solving approach in the teaching and learning of mathematics in secondary schools.

Keywords: problem, achievement, teaching phases, experimental control

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Authors: A. Ferasat, S. Rostampour Yasouri

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Seasonal flu is a highly contagious infection caused by influenza viruses. These viruses undergo genetic changes that result in new epidemics across the globe. Medical attention is crucial in severe cases, particularly for the elderly, frail, and those with chronic illnesses, as their immune systems are often weaker. The purpose of this study was to detect new subtypes of the influenza A virus rapidly using a specific RT-PCR method based on the HA gene (hemagglutinin). In the winter and spring of 2022_2023, 120 embryonated egg samples were cultured, suspected of seasonal influenza. RNA synthesis, followed by cDNA synthesis, was performed. Finally, the PCR technique was applied using a pair of specific primers designed based on the HA gene. The PCR product was identified after purification, and the nucleotide sequence of purified PCR products was compared with the sequences in the gene bank. The results showed a high similarity between the sequence of the positive samples isolated from the patients and the sequence of the new strains isolated in recent years. This RT-PCR technique is entirely specific in this study, enabling the detection and multiplication of influenza and its subspecies from clinical samples. The RT-PCR technique based on the HA gene, along with sequencing, is a fast, specific, and sensitive diagnostic method for those infected with influenza viruses and its new subtypes. Rapid molecular diagnosis of influenza is essential for suspected people to control and prevent the spread of the disease to others. It also prevents the occurrence of secondary (sometimes fatal) pneumonia that results from influenza and pathogenic bacteria. The critical role of rapid diagnosis of new strains of influenza is to prepare a drug vaccine against the latest viruses that did not exist in the community last year and are entirely new viruses.

Keywords: influenza, molecular diagnosis, patients, RT-PCR technique

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Authors: Sven Tackenberg, Sönke Duckwitz, Andreas Petz, Christopher M. Schlick

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This paper introduces an extension to the well-established Resource-Constrained Project Scheduling Problem (RCPSP) to apply it to complex maintenance problems. The problem is to assign technicians to a team which has to process several tasks with multi-level skill requirements during a work shift. Here, several alternative activities for a task allow both, the temporal shift of activities or the reallocation of technicians and tools. As a result, switches from one valid work process variant to another can be considered and may be selected by the developed evolutionary algorithm based on the present skill level of technicians or the available tools. An additional complication of the observed scheduling problem is that the locations of the construction sites are only temporarily accessible during a day. Due to intensive rail traffic, the available time slots for maintenance and repair works are extremely short and are often distributed throughout the day. To identify efficient working periods, a first concept of a Bayesian network is introduced and is integrated into the extended RCPSP with pre-emptive and non-pre-emptive tasks. Thereby, the Bayesian network is used to calculate the probability of a maintenance task to be processed during a specific period of the shift. Focusing on the domain of maintenance of the railway infrastructure in metropolitan areas as the most unproductive implementation process at construction site, the paper illustrates how the extended RCPSP can be applied for maintenance planning support. A multi-criteria evolutionary algorithm with a problem representation is introduced which is capable of revising technician-task allocations, whereas the duration of the task may be stochastic. The approach uses a novel activity list representation to ensure easily describable and modifiable elements which can be converted into detailed shift schedules. Thereby, the main objective is to develop a shift plan which maximizes the utilization of each technician due to a minimization of the waiting times caused by rail traffic. The results of the already implemented core algorithm illustrate a fast convergence towards an optimal team composition for a shift, an efficient sequence of tasks and a high probability of the subsequent implementation due to the stochastic durations of the tasks. In the paper, the algorithm for the extended RCPSP is analyzed in experimental evaluation using real-world example problems with various size, resource complexity, tightness and so forth.

Keywords: maintenance management, scheduling, resource constrained project scheduling problem, genetic algorithms

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Authors: Imad H. Hameed, Mohammad A. Jebor, Ammera J. Omer

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The aim of this research is to study the mitochonderial coding region by using the Sanger sequencing technique and establish the degree of variation characteristic of a fragment. FTA® Technology (FTA™ paper DNA extraction) utilized to extract DNA. Portion of coding region encompassing positions 11719 –12384 amplified in accordance with the Anderson reference sequence. PCR products purified by EZ-10 spin column then sequenced and Detected by using the ABI 3730xL DNA Analyzer. Five new polymorphic positions 11741, 11756, 11878, 11887 and 12133 are described may be suitable sources for identification purpose in future. The calculated value D= 0.95 and RMP=0.048 of the genetic diversity should be understood as high in the context of coding function of the analysed DNA fragment. The relatively high gene diversity and a relatively low random match probability were observed in Iraq population. The obtained data can be used to identify the variable nucleotide positions characterized by frequent occurrence which is most promising for various identifications.

Keywords: coding region, Iraq, mitochondrial DNA, polymorphic positions, sanger technique

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Authors: Alisa Kazarina, Guntis Gerhards, Elina Petersone-Gordina, Ilva Pole, Viktorija Igumnova, Janis Kimsis, Valentina Capligina, Renate Ranka

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Human body is inhabited by a vast number of microorganisms, collectively known as the human microbiome, and there is a tremendous interest in evolutionary changes in human microbial ecology, diversity and function. The field of paleomicrobiology, study of ancient human microbiome, is powered by modern techniques of Next Generation Sequencing (NGS), which allows extracting microbial genomic data directly from archaeological sample of interest. One of the major techniques is 16S rRNA gene sequencing, by which certain 16S rRNA gene hypervariable regions are being amplified and sequenced. However, some limitations of this method exist including the taxonomic precision and efficacy of different regions used. The aim of this study was to evaluate the phylogenetic sensitivity of different 16S rRNA gene hypervariable regions for microbiome studies in the archaeological samples. Towards this aim, archaeological bone samples and corresponding soil samples from each burial environment were collected in Medieval cemeteries in Latvia. The Ion 16S™ Metagenomics Kit targeting different 16S rRNA gene hypervariable regions was used for library construction (Ion Torrent technologies). Sequenced data were analysed by using appropriate bioinformatic techniques; alignment and taxonomic representation was done using Mothur program. Sequences of most abundant genus were further aligned to E. coli 16S rRNA gene reference sequence using MEGA7 in order to identify the hypervariable region of the segment of interest. Our results showed that different hypervariable regions had different discriminatory power depending on the groups of microbes, as well as the nature of samples. On the basis of our results, we suggest that wider range of primers used can provide more accurate recapitulation of microbial communities in archaeological samples. Acknowledgements. This work was supported by the ERAF grant Nr. 1.1.1.1/16/A/101.

Keywords: 16S rRNA gene, ancient human microbiome, archaeology, bioinformatics, genomics, microbiome, molecular biology, next-generation sequencing

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Authors: R. Sulakshana, R. Lakshmi

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Clustered Regularly Interspaced Short Palindromic Repeats, CRISPR associate (CRISPR/Cas) is an adaptive immunity system found in bacteria and archaea. It has been modified to serve as a potent gene editing tool. Moreover, it has found widespread use in the field of genome research because of its accessibility and low cost. Several bioinformatics methods have been created to aid in the construction of specific single guide RNA (sgRNA), which is highly active and crucial to CRISPR/Cas performance. Various Cas proteins, including Cas1, Cas2, Cas9, and Cas12, have been used to create genome engineering tools because of their programmable sequence specificity. Class 1 and 2 CRISPR/Cas systems, as well as the processes of all known Cas proteins (including Cas9 and Cas12), are discussed in this review paper. In addition, the various CRISPR methodologies and their tools so far discovered are discussed. Finally, the challenges and issues in the CRISPR system along with future works, are presented.

Keywords: gene editing tool, Cas proteins, CRISPR, guideRNA, programmable sequence

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Authors: Eun-Ji Lee, Hye-Sung Park, Chan-Jung Lee, Won-Sik Kong

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We analyzed the DNA sequence of the ITS (Internal Transcribed Spacer) region of the 18S ribosomal gene and compared it with the gene sequence of T. fuciformis and Hypoxylon sp. in the BLAST database. The sequences of collected T. fuciformis and Hypoxylon sp. have over 99% homology in the T. fuciformis and Hypoxylon sp. sequence BLAST database. In order to select the optimal medium for T. fuciformis, five kinds of a medium such as Potato Dextrose Agar (PDA), Mushroom Complete Medium (MCM), Malt Extract Agar (MEA), Yeast extract (YM), and Compost Extract Dextrose Agar (CDA) were used. T. fuciformis showed the best growth on PDA medium, and Hypoxylon sp. showed the best growth on MCM. So as to investigate the optimum pH and temperature, the pH range was set to pH4 to pH8 and the temperature range was set to 15℃ to 35℃ (5℃ degree intervals). Optimum culture conditions for the T. fuciformis growth were pH5 at 25℃. Hypoxylon sp. were pH6 at 25°C. In order to confirm the most suitable carbon source, we used fructose, galactose, saccharose, soluble starch, inositol, glycerol, xylose, dextrose, lactose, dextrin, Na-CMC, adonitol. Mannitol, mannose, maltose, raffinose, cellobiose, ethanol, salicine, glucose, arabinose. In the optimum carbon source, T. fuciformis is xylose and Hypoxylon sp. is arabinose. Using the column test, we confirmed sawdust a suitable for T. fuciformis, since the composition of sawdust affects the growth of fruiting bodies of T. fuciformis. The sawdust we used is oak tree, pine tree, poplar, birch, cottonseed meal, cottonseed hull. In artificial cultivation of T. fuciformis with sawdust medium, T. fuciformis and Hypoxylon sp. showed fast mycelial growth on mixture of oak tree sawdust, cottonseed hull, and wheat bran.

Keywords: cultivation, optimal condition, tremella fuciformis, nutritional source

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Authors: Çağrı Özgün Kibiroğlu, Zeynep Turgut

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This paper considers a hub location problem where the network service area partitioned into predetermined zones (represented by node clusters is given) and potential hub nodes capacity levels are determined a priori as a selection criteria of hub to investigate congestion effect on network. The objective is to design hub network by determining all required hub locations in the node clusters and also allocate non-hub nodes to hubs such that the total cost including transportation cost, opening cost of hubs and penalty cost for exceed of capacity level at hubs is minimized. A mixed integer linear programming model is developed introducing additional constraints to the traditional model of capacitated multiple allocation hub location problem and empirically tested.

Keywords: hub location problem, p-hub median problem, clustering, congestion

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Authors: Geetha Baskaran, Andrzej Barjiela, Rong Qu

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Motivation: Nurse scheduling is a complex combinatorial optimization problem. It is also known as NP-hard. It needs an efficient re-scheduling to minimize some trade-off of the measures of violation by reducing selected constraints to soft constraints with measurements of their violations. Problem Statement: In this paper, we extend our novel approach to solve the nurse scheduling problem by transforming it through Information Granulation. Approach: This approach satisfies the rules of a typical hospital environment based on a standard benchmark problem. Generating good work schedules has a great influence on nurses' working conditions which are strongly related to the level of a quality health care. Domain transformation that combines the strengths of operation research and artificial intelligence was proposed for the solution of the problem. Compared to conventional methods, our approach involves judicious grouping (information granulation) of shifts types’ that transforms the original problem into a smaller solution domain. Later these schedules from the smaller problem domain are converted back into the original problem domain by taking into account the constraints that could not be represented in the smaller domain. An Integer Programming (IP) package is used to solve the transformed scheduling problem by expending the branch and bound algorithm. We have used the GNU Octave for Windows to solve this problem. Results: The scheduling problem has been solved in the proposed formalism resulting in a high quality schedule. Conclusion: Domain transformation represents departure from a conventional one-shift-at-a-time scheduling approach. It offers an advantage of efficient and easily understandable solutions as well as offering deterministic reproducibility of the results. We note, however, that it does not guarantee the global optimum.

Keywords: domain transformation, nurse scheduling, information granulation, artificial intelligence, simulation

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Authors: Leyla Esfandiari

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Rapid, sensitive detection of nucleic acid (NA) molecules of specific sequence is of interest for a range of diverse health-related applications such as screening for genetic diseases, detecting pathogenic microbes in food and water, and identifying biological warfare agents in homeland security. Sequence-specific nucleic acid detection platforms rely on base pairing interaction between two complementary single stranded NAs, which can be detected by the optical, mechanical, or electrochemical readout. However, many of the existing platforms require amplification by polymerase chain reaction (PCR), fluorescent or enzymatic labels, and expensive or bulky instrumentation. In an effort to address these shortcomings, our research is focused on utilizing the cutting edge nanotechnology and microfluidics along with resistive pulse electrical measurements to design and develop a cost-effective, handheld and highly-sensitive nanopore-based sensor for point-of-care medical diagnostics.

Keywords: diagnostics, nanopore, nucleic acids, sensor

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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: Abu Hashan Md Mashud, M. Sharif Uddin, Aminur Rahman Khan

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In this paper, we formulate a new problem as a linear programming and Integer Programming problem and maximize profit within the limited budget and limited resources based on the construction of a tea garden problem. It describes a new idea about how to optimize profit and focuses on the practical aspects of modeling and the challenges of providing a solution to a complex real life problem. Finally, a comparative study is carried out among Graphical method, Simplex method and Branch and bound method.

Keywords: integer programming, tea garden, graphical method, simplex method, branch and bound method

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Authors: Pavan K. Rallabandi, Kailash C. Patidar

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In this paper, we present an optimization technique or a learning algorithm using the hybrid architecture by combining the most popular sequence recognition models such as Recurrent Neural Networks (RNNs) and Hidden Markov models (HMMs). In order to improve the sequence or pattern recognition/ classification performance by applying a hybrid/neural symbolic approach, a gradient descent learning algorithm is developed using the Real Time Recurrent Learning of Recurrent Neural Network for processing the knowledge represented in trained Hidden Markov Models. The developed hybrid algorithm is implemented on automata theory as a sample test beds and the performance of the designed algorithm is demonstrated and evaluated on learning the deterministic finite state automata.

Keywords: hybrid systems, hidden markov models, recurrent neural networks, deterministic finite state automata

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Authors: Glenn Auld Knierim

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Automated robotic winding of high-temperature superconductors (HTS) addresses precision, efficiency, and reliability critical to the commercialization of products. Today’s HTS materials are mature and commercially promising but require manufacturing attention. In particular to the exaggerated rectangular cross-section (very thin by very wide), winding precision is critical to address the stress that can crack the fragile ceramic superconductor (SC) layer and destroy the SC properties. Damage potential is highest during peak operations, where winding stress magnifies operational stress. Another challenge is operational parameters such as magnetic field alignment affecting design performance. Winding process performance, including precision, capability for geometric complexity, and efficient repeatability, are required for commercial production of current HTS. Due to winding limitations, current HTS magnets focus on simple pancake configurations. HTS motors, generators, MRI/NMR, fusion, and other projects are awaiting robotic wound solenoid, planar, and spherical magnet configurations. As with conventional power cables, full transposition winding is required for long length alternating current (AC) and pulsed power cables. Robotic production is required for transposition, periodic swapping of cable conductors, and placing into precise positions, which allows power utility required minimized reactance. A full transposition SC cable, in theory, has no transmission length limits for AC and variable transient operation due to no resistance (a problem with conventional cables), negligible reactance (a problem for helical wound HTS cables), and no long length manufacturing issues (a problem with both stamped and twisted stacked HTS cables). The Infinity Physics team is solving manufacturing problems by developing automated manufacturing to produce the first-ever reliable and utility-grade commercial SC cables and magnets. Robotic winding machines combine mechanical and process design, specialized sense and observer, and state-of-the-art optimization and control sequencing to carefully manipulate individual fragile SCs, especially HTS, to shape previously unattainable, complex geometries with electrical geometry equivalent to commercially available conventional conductor devices.

Keywords: automated winding manufacturing, high temperature superconductor, magnet, power cable

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Authors: Eylem Tas

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This empirical study aims to explore the development of students' entrepreneurial skills through problem-based learning within the context of university-industry collaborations (UICs) in curriculum co-design and co-delivery (CDD). The research question guiding this study is: "How do problem-based learning and university-industry collaborations influence the development of students' entrepreneurial skills in the context of curriculum co-design and co-delivery?” To address this question, the study was conducted in a big city in Germany and involved interviews with stakeholders from various industries, including the private sector, government agencies (govt), and non-governmental organizations (NGOs). These stakeholders had established collaborative partnerships with the targeted university for projects encompassing entrepreneurial development aspects in CDD. The study sought to gain insights into the intricacies and subtleties of UIC dynamics and their impact on fostering entrepreneurial skills. Qualitative content analysis, based on Mayring's guidelines, was employed to analyze the interview transcriptions. Through an iterative process of manual coding, 442 codes were generated, resulting in two main sections: "the role of problem-based learning and UIC in fostering entrepreneurship" and "challenges and requirements of problem-based learning within UIC for systematical entrepreneurship development.” The chosen experimental approach of semi-structured interviews was justified by its capacity to provide in-depth perspectives and rich data from stakeholders with firsthand experience in UICs in CDD. By enlisting participants with diverse backgrounds, industries, and company sizes, the study ensured a comprehensive and heterogeneous sample, enhancing the credibility of the findings. The first section of the analysis delved into problem-based learning and entrepreneurial self-confidence to gain a deeper understanding of UIC dynamics from an industry standpoint. It explored factors influencing problem-based learning, alignment of students' learning styles and preferences with the experiential learning approach, specific activities and strategies, and the role of mentorship from industry professionals in fostering entrepreneurial self-confidence. The second section focused on various interactions within UICs, including communication, knowledge exchange, and collaboration. It identified key elements, patterns, and dynamics of interaction, highlighting challenges and limitations. Additionally, the section emphasized success stories and notable outcomes related to UICs' positive impact on students' entrepreneurial journeys. Overall, this research contributes valuable insights into the dynamics of UICs and their role in fostering students' entrepreneurial skills. UICs face challenges in communication and establishing a common language. Transparency, adaptability, and regular communication are vital for successful collaboration. Realistic expectation management and clearly defined frameworks are crucial. Responsible data handling requires data assurance and confidentiality agreements, emphasizing the importance of trust-based relationships when dealing with data sharing and handling issues. The identified key factors and challenges provide a foundation for universities and industrial partners to develop more effective UIC strategies for enhancing students' entrepreneurial capabilities and preparing them for success in today's digital age labor market. The study underscores the significance of collaborative learning and transparent communication in UICs for entrepreneurial development in CDD.

Keywords: collaborative learning, curriculum co-design and co-delivery, entrepreneurial skills, problem-based learning, university-industry collaborations

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Authors: Abdolsalam Ghaderi

Abstract:

In this paper, the single-depot capacitated location-routing problem under uncertainty is presented. The problem aims to find the optimal location of a single depot and the routing of vehicles to serve the customers when the parameters may change under different circumstances. This problem has many applications, especially in the area of supply chain management and distribution systems. To get closer to real-world situations, travel time of vehicles, the fixed cost of vehicles usage and customers’ demand are considered as a source of uncertainty. A combined approach including robust optimization and stochastic programming was presented to deal with the uncertainty in the problem at hand. For this purpose, a mixed integer programming model is developed and a heuristic algorithm based on Variable Neighborhood Search(VNS) is presented to solve the model. Finally, the computational results are presented and future research directions are discussed.

Keywords: location-routing problem, robust optimization, stochastic programming, variable neighborhood search

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Authors: Liudmila A.Guzikova

Abstract:

Being federative state Russia includes more than 80 subjects which are widely diverse by climatic conditions, demographic characteristics, cultural traditions, intensity of migration, economic development and investment attraction and other parameters. Now, in the regions of the country all forms of housing problem are present - housing mismatch to sanitary and hygienic standards, overcrowding, forced residence in financially burdensome housing, homelessness, -although the extent of these symptoms varies widely. Heterogeneity of regional conditions in combination with specifics of regional housing situation requires to concentrate the study of housing problem on the regional level. Traditionally housing market and mortgage are considered as the instruments of housing problem solving. The question arises how the housing market and mortgage market contribute to solving the housing problem in the regions of Russia. Though the purchase of dwelling in ownership should not be regarded as a universal method of the housing problem solving, the purchase of dwelling both by own funds or by use of mortgage can reduce the problem and enhance public satisfaction of living conditions. The aim of the study is to identify differences and similarities in the development of regional housing markets and mortgage lending in the regions of Russia and to evaluate their impact on the status of the housing problem. To achieve the aim of the study the methods of correlation and regression analysis are used. The data of federal statistics constitutes the information base of research. The results of the study contribute to better understanding of the interrelations in housing sphere and can be used to work out social and economic development programs in the regions.

Keywords: housing market, housing problem, mortgage, regional economy

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Authors: Taehan Lee

Abstract:

We consider a network design problem which has shortest routing restriction based on the values determined by the installed facilities on each arc. In conventional multicommodity network design problem, a commodity can be routed through any possible path when the capacity is available. But, we consider a problem in which the commodity between two nodes must be routed on a path which has shortest metric value and the link metric value is determined by the installed facilities on the link. By this routing restriction, the problem has a distinct characteristic. We present an integer programming formulation containing the primal-dual optimality conditions to the shortest path routing. We give some computational results for the model.

Keywords: integer programming, multicommodity network design, routing, shortest path

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Authors: Busaba Phurksaphanrat

Abstract:

This research proposes a pre-emptive fuzzy goal programming model for multi-objective multi-mode resource constrained project scheduling problem. The objectives of the problem are minimization of the total time and the total cost of the project. Objective in a multi-mode resource-constrained project scheduling problem is often a minimization of make-span. However, both time and cost should be considered at the same time with different level of important priorities. Moreover, all elements of cost functions in a project are not included in the conventional cost objective function. Incomplete total project cost causes an error in finding the project scheduling time. In this research, pre-emptive fuzzy goal programming is presented to solve the multi-objective multi-mode resource constrained project scheduling problem. It can find the compromise solution of the problem. Moreover, it is also flexible in adjusting to find a variety of alternative solutions.

Keywords: multi-mode resource constrained project scheduling problem, fuzzy set, goal programming, pre-emptive fuzzy goal programming

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Authors: Danny Barash

Abstract:

Riboswitches are RNA genetic control elements that were originally discovered in bacteria and provide a unique mechanism of gene regulation. They work without the participation of proteins and are believed to represent ancient regulatory systems in the evolutionary timescale. One of the biggest challenges in riboswitch research is that many are found in prokaryotes but only a small percentage of known riboswitches have been found in certain eukaryotic organisms. The few examples of eukaryotic riboswitches were identified using sequence-based bioinformatics search methods that include some slight structural considerations. These pattern-matching methods were the first ones to be applied for the purpose of riboswitch detection and they can also be programmed very efficiently using a data structure called affix arrays, making them suitable for genome-wide searches of riboswitch patterns. However, they are limited by their ability to detect harder to find riboswitches that deviate from the known patterns. Several methods have been developed since then to tackle this problem. The most commonly used by practitioners is Infernal that relies on Hidden Markov Models (HMMs) and Covariance Models (CMs). Profile Hidden Markov Models were also carried out in the pHMM Riboswitch Scanner web application, independently from Infernal. Other computational approaches that have been developed include RMDetect by the use of 3D structural modules and RNAbor that utilizes Boltzmann probability of structural neighbors. We have tried to incorporate more sophisticated secondary structure considerations based on RNA folding prediction using several strategies. The first idea was to utilize window-based methods in conjunction with folding predictions by energy minimization. The moving window approach is heavily geared towards secondary structure consideration relative to sequence that is treated as a constraint. However, the method cannot be used genome-wide due to its high cost because each folding prediction by energy minimization in the moving window is computationally expensive, enabling to scan only at the vicinity of genes of interest. The second idea was to remedy the inefficiency of the previous approach by constructing a pipeline that consists of inverse RNA folding considering RNA secondary structure, followed by a BLAST search that is sequence-based and highly efficient. This approach, which relies on inverse RNA folding in general and our own in-house fragment-based inverse RNA folding program called RNAfbinv in particular, shows capability to find attractive candidates that are missed by Infernal and other standard methods being used for riboswitch detection. We demonstrate attractive candidates found by both the moving-window approach and the inverse RNA folding approach performed together with BLAST. We conclude that structure-based methods like the two strategies outlined above hold considerable promise in detecting riboswitches and other conserved RNAs of functional importance in a variety of organisms.

Keywords: riboswitches, RNA folding prediction, RNA structure, structure-based methods

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Authors: Sharon-Yasotha Veerayah-Mcgregor, Valipuram Manoranjan

Abstract:

A backward or inverse problem is known to be an ill-posed problem due to its instability that easily emerges with any slight change within the conditions of the problem. Therefore, only a limited number of numerical approaches are available to solve a backward problem. This paper considers the Nagumo equation, an equation that describes impulse propagation in nerve axons, which also models population growth with the Allee effect. A creative operator splitting numerical scheme is constructed to solve the inverse Nagumo equation. Computational simulations are used to verify that this scheme is stable, accurate, and efficient.

Keywords: inverse/backward equation, operator-splitting, Nagumo equation, ill-posed, finite-difference

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