Search results for: car sequencing and operator allocation

Authors: Hui Li, Xueying Zhao, Ke Ma, Yu Cao, Fan Yang, Qingwen Xu, Wenbin Liu

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Soil can often link a person or item to a crime scene, which makes it a valuable evidence in forensic casework. Several techniques have been utilized in forensic soil discrimination in previous studies. Because soil contains a vast number of microbiomes, the analyse of soil microbiomes is expected to be a potential way to characterise soil evidence. In this study, we applied massively parallel sequencing (MPS) to soil bacterial profiling on the Ion Torrent Personal Genome Machine (PGM). Soils from different regions were collected repeatedly. V-region 3 and 4 of Bacterial 16S rRNA gene were detected by MPS. Operational taxonomic units (OTU, 97%) were used to analyse soil bacteria. Several bioinformatics methods (PCoA, NMDS, Metastats, LEfse, and Heatmap) were applied in bacterial profiles. Our results demonstrate that MPS can provide a more detailed picture of the soil microbiomes and the composition of soil bacterial components from different region was individualistic. In conclusion, the utility of soil bacterial profiling via MPS of the 16S rRNA gene has potential value in characterising soil evidences and associating them with their place of origin, which can play an important role in forensic science in the future.

Keywords: bacterial profiling, forensic, massively parallel sequencing, soil evidence

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Authors: Abdessalem Abbassi, Ahlem Dakhlaoui, Lota D. Tamini

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In this paper, we analyze infinite discrete-time games between hydraulic and thermal power operators in the wholesale electricity market under Cournot competition. We consider a deregulated electrical industry where certain demand is satisfied by hydraulic and thermal technologies. The hydraulic operator decides the production in each season of each period that maximizes the sum of expected profits from power generation with respect to the stochastic dynamic constraint on the water stored in the dam, the environmental constraint and the non-negative output constraint. In contrast, the thermal plant is operated with quadratic cost function, with respect to the capacity production constraint and the non-negativity output constraint. We show that under imperfect competition, the hydraulic operator has a strategic storage of water in the peak season. Then, we quantify the strategic inter-annual and intra-annual water transfer and compare the numerical results. Finally, we show that the thermal operator can restrict the hydraulic output without compensation.

Keywords: asymmetric risk aversion, electricity wholesale market, hydropower dams, imperfect competition

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Authors: Ali W. N. Alattabi, Clare B. Harris, Rafid M. Alkhaddar, Montserrat Ortoneda, David A. Phipps, Ali Alzeyadi, Khalid S. Hashim

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This study was performed to optimise the hydraulic retention time (HRT) and study its effects on the sludge characteristics and the effluent quality in an aerobic suspension sequencing batch reactor (ASSBR) treating synthetic wastewater. The results showed that increasing the HRT from 6 h to 12 h significantly improved the COD and Nitrate removal efficiency; it was increased from 78.7% - 75.7% to 94.7% – 97% for COD and Nitrate respectively. However, increasing the HRT from 12 h to 18 h reduced the COD and Nitrate removal efficiency from 94.7% - 97% to 91.1% – 94.4% respectively. Moreover, Increasing the HRT from 18 h to 24 h did not affect the COD and Nitrate removal efficiency. Sludge volume index (SVI) was used to monitor the sludge settling performance. The results showed a direct relationship between the HRT and SVI value. Increasing the HRT from 6 h to 12 h led to decrease the SVI value from 123 ml/g to 82.5 ml/g, and then it remained constant despite of increasing the HRT from 12 h to 18 h and to 24 h. The results obtained from this study showed that the HRT of 12 h was better for COD and Nitrate removal and a good settling performance occurred during that range.

Keywords: COD, hydraulic retention time, nitrate, sequencing batch reactor, sludge characteristics

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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: Jasper Kevin C. Dionisio, Denise Mae M. Unsay

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In a manufacturing firm, controlling the process ensures that optimum efficiency, productivity, and quality in an organization are achieved. An operation with no standardized procedure yields a poor productivity, inefficiency, and an out of control process. This study focuses on controlling the small intestine processing of a chicken dressing plant through the use of Statistical Process Control (SPC). Since the operation does not employ a standard procedure and does not have an established standard time, the process through the assessment of the observed time of the overall operation of small intestine processing, through the use of X-Bar R Control Chart, is found to be out of control. In the solution of this problem, the researchers conduct a motion and time study aiming to establish a standard procedure for the operation. The normal operator was picked through the use of Westinghouse Rating System. Instead of utilizing the traditional motion and time study, the researchers used the X-Bar R Control Chart in determining the process average of the process that is used for establishing the standard time. The observed time of the normal operator was noted and plotted to the X-Bar R Control Chart. Out of control points that are due to assignable cause were removed and the process average, or the average time the normal operator conducted the process, which was already in control and free form any outliers, was obtained. The process average was then used in determining the standard time of small intestine processing. As a recommendation, the researchers suggest the implementation of the standard time established which is with consonance to the standard procedure which was adopted from the normal operator. With that recommendation, the whole operation will induce a 45.54 % increase in their productivity.

Keywords: motion and time study, process controlling, statistical process control, X-Bar R Control chart

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Authors: Amin Mojiri, Hamidi Abdul Aziz

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Leachate is created while water penetrates through the waste in a landfill, carrying some forms of pollutants. In literature, for treatment of wastewater and leachate, different ways of biological treatment were used. Sequencing batch reactor (SBR) is a kind of biological treatment. This study investigated the co-treatment of landfill leachate and domestic waste water by SBR and powdered activated carbon augmented (PAC) SBR process. The response surface methodology (RSM) and central composite design (CCD) were employed. The independent variables were aeration rate (L/min), contact time (h), and the ratio of leachate to wastewater mixture (%; v/v)). To perform an adequate analysis of the aerobic process, three dependent parameters, i.e. COD, color, and ammonia-nitrogen (NH3-N or NH4-N) were measured as responses. The findings of the study indicated that the PAC-SBR showed a higher performance in elimination of certain pollutants, in comparison with SBR. With the optimal conditions of aeration rate (0.6 L/min), leachate to waste water ratio (20%), and contact time (10.8 h) for the PAC-SBR, the removal efficiencies for color, NH3-N, and COD were 72.8%, 98.5%, and 65.2%, respectively.

Keywords: co-treatment, landfill Leachate, wastewater, sequencing batch reactor, activate carbon

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Authors: Kenichiro Hida, Shin-Ichi Kuribayashi

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NFV-based network implements a variety of network functions with software on general-purpose servers, and this allows the network operator to select any capabilities and locations of network functions without any physical constraints. In this paper, we evaluate the influence of the maximum tolerable network delay on the virtual routing function deployment guidelines which the authors proposed previously. Our evaluation results have revealed the following: (1) the more the maximum tolerable network delay condition becomes severe, the more the number of areas where the route selection function is installed increases and the total network cost increases, (2) the higher the routing function cost relative to the circuit bandwidth cost, the increase ratio of total network cost becomes larger according to the maximum tolerable network delay condition.

Keywords: NFV (Network Functions Virtualization), resource allocation, virtual routing function, minimum total network cost

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Authors: S. Fahiminiya, J. Nadaf, F. Rauch, L. Jerome-Majewska, J. Majewski

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Background: Sequencing of protein coding regions of human genome (Whole Exome Sequencing; WES), has demonstrated a great success in the identification of causal mutations for several rare genetic disorders in human. Generally, most of WES studies have focused on rare variants in coding exons and splicing-sites where missense substitutions lead to the alternation of protein product. Although focusing on this category of variants has revealed the mystery behind many inherited genetic diseases in recent years, a subset of them remained still inconclusive. Here, we present the result of our WES studies where analyzing only rare variants in coding regions was not conclusive but further investigation revealed the involvement of non-coding variants and copy number variations (CNV) in etiology of the diseases. Methods: Whole exome sequencing was performed using our standard protocols at Genome Quebec Innovation Center, Montreal, Canada. All bioinformatics analyses were done using in-house WES pipeline. Results: To date, we successfully identified several disease causing mutations within gene coding regions (e.g. SCARF2: Van den Ende-Gupta syndrome and SNAP29: 22q11.2 deletion syndrome) by using WES. In addition, we showed that variants in non-coding regions and CNV have also important value and should not be ignored and/or filtered out along the way of bioinformatics analysis on WES data. For instance, in patients with osteogenesis imperfecta type V and in patients with glucocorticoid deficiency, we identified variants in 5'UTR, resulting in the production of longer or truncating non-functional proteins. Furthermore, CNVs were identified as the main cause of the diseases in patients with metaphyseal dysplasia with maxillary hypoplasia and brachydactyly and in patients with osteogenesis imperfecta type VII. Conclusions: Our study highlights the importance of considering non-coding variants and CNVs during interpretation of WES data, as they can be the only cause of disease under investigation.

Keywords: whole exome sequencing data, non-coding variants, copy number variations, rare diseases

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Authors: Chuan-Ming Tung, Jin-Cheng Fu, Chia-En Feng

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In recent years, the rapid development of urban land in Taiwan has led to the constant increase of the areas of impervious surface, which has increased the risk of waterlogging during heavy rainfall. Therefore, in recent years, promoting runoff allocation responsibilities has often been used as a means of reducing regional flooding. In this study, the single catchment area covering both urban and rural land as the study area is discussed. Based on Storm Water Management Model, urban and rural land in a single catchment area was explored to develop the runoff allocation responsibilities according to their respective control regulation on land use. The impacts of runoff increment and reduction in sub-catchment area were studied to understand the impact of highly developed urban land on the reduction of flood risk of rural land at the back end. The results showed that the rainfall with 1 hour short delay of 2 years, 5 years, 10 years, and 25 years return period. If the study area was fully developed, the peak discharge at the outlet would increase by 24.46% -22.97% without runoff allocation responsibilities. The front-end urban land would increase runoff from back-end of rural land by 76.19% -46.51%. However, if runoff allocation responsibilities were carried out in the study area, the peak discharge could be reduced by 58.38-63.08%, which could make the front-end to reduce 54.05% -23.81% of the peak flow to the back-end. In addition, the researchers found that if it was seen from the perspective of runoff allocation responsibilities of per unit area, the residential area of urban land would benefit from the relevant laws and regulations of the urban system, which would have a better effect of reducing flood than the residential land in rural land. For rural land, the development scale of residential land was generally small, which made the effect of flood reduction better than that of industrial land. Agricultural land requires a large area of land, resulting in the lowest share of the flow per unit area. From the point of the planners, this study suggests that for the rural land around the city, its responsibility should be assigned to share the runoff. And setting up rain water storage facilities in the same way as urban land, can also take stock of agricultural land resources to increase the ridge of field for flood storage, in order to improve regional disaster reduction capacity and resilience.

Keywords: runoff allocation responsibilities, land use, flood mitigation, SWMM

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Authors: Ghita Benayad

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Asset allocation, which affects the long-term profitability of portfolios by distributing assets to fulfill a range of investment objectives, is the cornerstone of investment management in the dynamic and complicated world of financial markets. This paper offers a technique for optimizing strategic asset allocation with the goal of improving portfolio performance by addressing the inherent complexity and uncertainty of the market through the use of Principal Component Analysis (PCA) in a multi-objective modeling framework. The study's first section starts with a critical evaluation of conventional asset allocation techniques, highlighting how poorly they are able to capture the intricate relationships between assets and the volatile nature of the market. In order to overcome these challenges, the project suggests a PCA-driven methodology that isolates important characteristics influencing asset returns by decreasing the dimensionality of the investment universe. This decrease provides a stronger basis for asset allocation decisions by facilitating a clearer understanding of market structures and behaviors. Using a multi-objective optimization model, the project builds on this foundation by taking into account a number of performance metrics at once, including risk minimization, return maximization, and the accomplishment of predetermined investment goals like regulatory compliance or sustainability standards. This model provides a more comprehensive understanding of investor preferences and portfolio performance in comparison to conventional single-objective optimization techniques. While applying the PCA-driven multi-objective optimization model to historical market data, aiming to construct portfolios better under different market situations. As compared to portfolios produced from conventional asset allocation methodologies, the results show that portfolios optimized using the proposed method display improved risk-adjusted returns, more resilience to market downturns, and better alignment with specified investment objectives. The study also looks at the implications of this PCA technique for portfolio management, including the prospect that it might give investors a more advanced framework for navigating financial markets. The findings suggest that by combining PCA with multi-objective optimization, investors may obtain a more strategic and informed asset allocation that is responsive to both market conditions and individual investment preferences. In conclusion, this capstone project improves the field of financial engineering by creating a sophisticated asset allocation optimization model that integrates PCA with multi-objective optimization. In addition to raising concerns about the condition of asset allocation today, the proposed method of portfolio management opens up new avenues for research and application in the area of investment techniques.

Keywords: asset allocation, portfolio optimization, principle component analysis, multi-objective modelling, financial market

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Authors: Ayon Mukherjee

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Covariate-adjusted response-adaptive (CARA) designs use the available responses to skew the treatment allocation in a clinical trial in towards treatment found at an interim stage to be best for a given patient's covariate profile. Extensive research has been done on various aspects of CARA designs with the patient responses assumed to follow a parametric model. However, ranges of application for such designs are limited in real-life clinical trials where the responses infrequently fit a certain parametric form. On the other hand, robust estimates for the covariate-adjusted treatment effects are obtained from the parametric assumption. To balance these two requirements, designs are developed which are free from distributional assumptions about the survival responses, relying only on the assumption of proportional hazards for the two treatment arms. The proposed designs are developed by deriving two types of optimum allocation designs, and also by using a distribution function to link the past allocation, covariate and response histories to the present allocation. The optimal designs are based on biased coin procedures, with a bias towards the better treatment arm. These are the doubly-adaptive biased coin design (DBCD) and the efficient randomized adaptive design (ERADE). The treatment allocation proportions for these designs converge to the expected target values, which are functions of the Cox regression coefficients that are estimated sequentially. These expected target values are derived based on constrained optimization problems and are updated as information accrues with sequential arrival of patients. The design based on the link function is derived using the distribution function of a probit model whose parameters are adjusted based on the covariate profile of the incoming patient. To apply such designs, the treatment allocation probabilities are sequentially modified based on the treatment allocation history, response history, previous patients’ covariates and also the covariates of the incoming patient. Given these information, an expression is obtained for the conditional probability of a patient allocation to a treatment arm. Based on simulation studies, it is found that the ERADE is preferable to the DBCD when the main aim is to minimize the variance of the observed allocation proportion and to maximize the power of the Wald test for a treatment difference. However, the former procedure being discrete tends to be slower in converging towards the expected target allocation proportion. The link function based design achieves the highest skewness of patient allocation to the best treatment arm and thus ethically is the best design. Other comparative merits of the proposed designs have been highlighted and their preferred areas of application are discussed. It is concluded that the proposed CARA designs can be considered as suitable alternatives to the traditional balanced randomization designs in survival trials in terms of the power of the Wald test, provided that response data are available during the recruitment phase of the trial to enable adaptations to the designs. Moreover, the proposed designs enable more patients to get treated with the better treatment during the trial thus making the designs more ethically attractive to the patients. An existing clinical trial has been redesigned using these methods.

Keywords: censored response, Cox regression, efficiency, ethics, optimal allocation, power, variability

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Authors: Shilpa Vasavada

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One of the 17 SustainableDevelopmentGoals focuses on gender equality. The paper is based on the learning derived from working with two Corporate Social Responsibility cases in India: one, CSR of an International Corporate and the other, CSR of a multi state national level corporate -on their efforts to integrate gender perspective in their agriculture and livestock based rural livelihood programs. The author tries to dissect how ‘gender equality’ is seen by these two CSRs, where the goals are different. The implications of a CSR’sunderstandingon ‘gender equality’ as a goal; versus CSR’s understanding of working 'with women for enhancing quantity or quality of production’ gets reflected in their orientation to staff, resource allocation, strategic level and in processes followed at the rural grassroots level. The paper comes up with examples of changes made at programmatic front when CSR understands and works with the focus on gender equality as a goal. On the other hand, the paper also explores the differential, at times, the negative impact on women and the programmes;- when the goals differ. The paper concludes with recommendations for CSRs to take up at their resource allocation and strategic level if gender equality is the goal- which has direct implication at their grassroots programmatic work. The author argues that if gender equality has to be implemented actually in spirit by a CSR, it requires change in mindset and thus an openness to changes in strategies and resource allocation pattern of the CSR and not simply adding on women in the way intervention has been going on.

Keywords: gender equality, approaches, differential impact, resource allocation

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Authors: Rabiatu Bonku, Faisal Alkaabneh

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Inspired by a food banks distribution operation for non-profit organization, we study a variant synchronized vehicle routing problem for equitable resource allocation. This research paper introduces a Mixed Integer Programming (MIP) model aimed at addressing the complex challenge of efficiently distributing vital resources, particularly for food banks serving vulnerable populations in urban areas. Our optimization approach places a strong emphasis on social equity, ensuring a fair allocation of food to partner agencies while minimizing wastage. The primary objective is to enhance operational efficiency while guaranteeing fair distribution and timely deliveries to prevent food spoilage. Furthermore, we assess four distinct models that consider various aspects of sustainability, including social and economic factors. We conduct a comprehensive numerical analysis using real-world data to gain insights into the trade-offs that arise, while also demonstrating the models’ performance in terms of fairness, effectiveness, and the percentage of food waste. This provides valuable managerial insights for food bank managers. We show that our proposed approach makes a significant contribution to the field of logistics optimization and social responsibility, offering valuable insights for improving the operations of food banks.

Keywords: food banks, humanitarian logistics, equitable resource allocation, synchronized vehicle routing

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Authors: M. Nageswara Rao, V. S. N. K. Chaitanya, K. Amarendranath

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This paper presents an optimal allocation and sizing of Distributed Generation (DG) in Radial Distribution Network (RDN) for total power loss minimization and enhances the voltage profile of the system. The two main important part of this study first is to find optimal allocation and second is optimum size of DG. The locations of DGs are identified by Analytical expressions and crow search algorithm has been employed to determine the optimum size of DG. In this study, the DG has been placed on single and multiple allocations.CSA is a meta-heuristic algorithm inspired by the intelligent behavior of the crows. Crows stores their excess food in different locations and memorizes those locations to retrieve it when it is needed. They follow each other to do thievery to obtain better food source. This analysis is tested on IEEE 33 bus and IEEE 69 bus under MATLAB environment and the results are compared with existing methods.

Keywords: analytical expression, distributed generation, crow search algorithm, power loss, voltage profile

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Authors: Lien Gysens, Bert Vanmechelen, Maarten Haspeslagh, Piet Maes, Ann Martens

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Bovine papillomavirus (BPV) types 1 and 2 play a central role in the etiology of the most common neoplasm in horses, the equine sarcoid. The unknown mechanism behind the unique variety in a clinical presentation on the one hand and the host-dependent clinical outcome of BPV-1 infection, on the other hand, indicate the involvement of additional factors. Earlier studies have reported the potential functional significance of intratypic sequence variants, along with the existence of sarcoid-sourced BPV variants. Therefore, intratypic sequence variation seems to be an important emerging viral factor. This study aimed to give a broad insight in sarcoid-sourced BPV variation and explore its potential association with disease presentation. In order to do this, a nanopore sequencing approach was successfully optimized for screening a wide spectrum of clinical samples. Specimens of each tumour were initially screened for BPV-1/-2 by quantitative real-time PCR. A custom-designed primer set was used on BPV-positive samples to amplify the complete viral genome in two multiplex PCR reactions, resulting in a set of overlapping amplicons. For phylogenetic analysis, separate alignments were made of all available complete genome sequences for BPV-1/-2. The resulting alignments were used to infer Bayesian phylogenetic trees. We found substantial genetic variation among sarcoid-derived BPV-1, although this variation could not be linked to disease severity. Several of the BPV-1 genomes had multiple major deletions. Remarkably, the majority of the cluster within the region coding for late viral genes. Together with the extensiveness (up to 603 nucleotides) of the described deletions, this suggests an altered function of L1/L2 in disease pathogenesis. By generating a significant amount of complete-length BPV genomes, we succeeded in introducing next-generation sequencing into veterinary research focusing on the equine sarcoid, thus facilitating the first report of both nanopore-based sequencing of complete sarcoid-sourced BPV-1/-2 and the simultaneous nanopore sequencing of multiple complete genomes originating from a single clinical sample.

Keywords: Bovine papillomavirus, equine sarcoid, horse, nanopore sequencing, phylogenetic analysis

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Authors: Sunil Dutta

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Synchronization is defined as ‘the sequencing and re-sequencing of all relative and absolute activities in time and space and continuous alignment of those actions with purposeful objective in a complex and dynamic atmosphere. In a complex and dynamic production / maintenance setup, no single group can work in isolation for long. In addition, many activities in projects take place simultaneously at the same time. Work of every section / group is interwoven with work of others. The various activities / interactions which take place in production / overhaul workshops are interlinked because of physical requirements (information, material, workforces, equipment, and space) and dependencies. The activity sequencing is determined by physical dependencies of various department / sections / units (e.g., inventory availability must be ensured before stripping and disassembling of equipment), whereas resource dependencies do not. Theory of constraint facilitates identification, analyses and exploitation of the constraint in methodical manner. These constraints (equipment, manpower, policies etc.) prevent the department / sections / units from getting optimum exploitation of available resources. The significance of theory of constraints for achieving synchronization at overhaul workshop is illustrated in this paper.

Keywords: synchronization, overhaul, throughput, obsolescence, uncertainty

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Authors: Phumelele Kubheka, Pius Owolawi, Gbolahan Aiyetoro

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Twitter is one of the most popular social media platforms where users can share their opinions on different subjects. As of 2010, The Twitter platform generates more than 12 Terabytes of data daily, ~ 4.3 petabytes in a single year. For this reason, Twitter is a great source for big mining data. Many industries such as Telecommunication companies can leverage the availability of Twitter data to better understand their markets and make an appropriate business decision. This study performs topic modeling on Twitter data using Latent Dirichlet Allocation (LDA). The obtained results are benchmarked with another topic modeling technique, Latent Semantic Indexing (LSI). The study aims to retrieve topics on a Twitter dataset containing user tweets on South African Telcos. Results from this study show that LSI is much faster than LDA. However, LDA yields better results with higher topic coherence by 8% for the best-performing model represented in Table 1. A higher topic coherence score indicates better performance of the model.

Keywords: big data, latent Dirichlet allocation, latent semantic indexing, telco, topic modeling, twitter

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Authors: Qingqing Gai, Junxing Shen, Yu Luo

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Due to the hardware architecture characteristics, some operators tend to acquire better performance if the input/output tensor dimensions are aligned to a certain minimum granularity, such as convolution and deconvolution commonly used in deep learning. Furthermore, if the requirements are not met, the general strategy is to pad with 0 to satisfy the requirements, potentially leading to the under-utilization of the hardware resources. Therefore, for the convolution and deconvolution whose input and output channels do not meet the minimum granularity alignment, we propose to transfer the W-dimensional data to the C-dimension for computation (W2C) to enable the C-dimension to meet the hardware requirements. This scheme also reduces the number of computations in the W-dimension. Although this scheme substantially increases computation, the operator’s speed can improve significantly. It achieves remarkable speedups on multiple hardware accelerators, including Nvidia Tensor cores, Qualcomm digital signal processors (DSPs), and Huawei neural processing units (NPUs). All you need to do is modify the network structure and rearrange the operator weights offline without retraining. At the same time, for some operators, such as the Reducemax, we observe that transferring the Cdimensional data to the W-dimension(C2W) and replacing the Reducemax with the Maxpool can accomplish acceleration under certain circumstances.

Keywords: convolution, deconvolution, W2C, C2W, alignment, hardware accelerator

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Authors: Abu S. Mustafa, Mohammad W. Khan, Faraz Shaheed Khan, Nazima Habibi

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Brucellosis is a zoonotic disease of worldwide prevalence. There are at least four species and several strains of Brucella that cause human disease. Brucella genomes have very limited variation across strains, which hinder strain identification using classical molecular techniques, including PCR and 16 S rDNA sequencing. The aim of this study was to perform whole genome sequencing of clinical isolates of Brucella and perform bioinformatics and comparative genomics analyses to determine the existence of genetic differences across the isolates of a single Brucella species and strain. The draft sequence data were generated from 15 clinical isolates of Brucella melitensis (biovar 2 strain 63/9) using MiSeq next generation sequencing platform. The generated reads were used for further assembly and analysis. All the analysis was performed using Bioinformatics work station (8 core i7 processor, 8GB RAM with Bio-Linux operating system). FastQC was used to determine the quality of reads and low quality reads were trimmed or eliminated using Fastx_trimmer. Assembly was done by using Velvet and ABySS softwares. The ordering of assembled contigs was performed by Mauve. An online server RAST was employed to annotate the contigs assembly. Annotated genomes were compared using Mauve and ACT tools. The QC score for DNA sequence data, generated by MiSeq, was higher than 30 for 80% of reads with more than 100x coverage, which suggested that data could be utilized for further analysis. However when analyzed by FastQC, quality of four reads was not good enough for creating a complete genome draft so remaining 11 samples were used for further analysis. The comparative genome analyses showed that despite sharing same gene sets, single nucleotide polymorphisms and insertions/deletions existed across different genomes, which provided a variable extent of diversity to these bacteria. In conclusion, the next generation sequencing, bioinformatics, and comparative genome analysis can be utilized to find variations (point mutations, insertions and deletions) across different genomes of Brucella within a single strain. This information could be useful in surveillance and epidemiological studies supported by Kuwait University Research Sector grants MI04/15 and SRUL02/13.

Keywords: brucella, bioinformatics, comparative genomics, whole genome sequencing

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Authors: Sonia Sonia

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This paper presents a family of iterative scheme for solving nonlinear systems of equations which have wide application in sciences and engineering. The proposed iterative family is based upon some parameters which generates many different iterative schemes. This family is completely derivative free and uses first of divided difference operator. Moreover some numerical experiments are performed and compared with existing methods. Analysis of convergence shows that the presented family has fourth-order of convergence. The dynamical behaviour of proposed family and local convergence have also been discussed. The numerical performance and convergence region comparison demonstrates that proposed family is efficient.

Keywords: convergence, divided difference operator, nonlinear system, Newton's method

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Authors: Parvaneh Mahmoudi, Ahmad Moeni, Seyed Mojtaba Khayam Nekoei, Mohsen Mardi, Mehrshad Zeinolabedini, Ghasem Hosseini Salekdeh

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Saffron (Crocus sativus L.) is one of the most important spice and medicinal plants. The three-branch style of C. sativus flowers are the most important economic part of the plant and known as saffron, which has several medicinal properties. Despite the economic and biological significance of this plant, knowledge about its molecular characteristics is very limited. In the present study, we, for the first time, constructed a comprehensive dataset for C. sativus stigma through de novo transcriptome sequencing. We performed de novo transcriptome sequencing of C. sativus stigma using the Illumina paired-end sequencing technology. A total of 52075128 reads were generated and assembled into 118075 unigenes, with an average length of 629 bp and an N50 of 951 bp. A total of 66171unigenes were identified, among them, 66171 (56%) were annotated in the non-redundant National Center for Biotechnology Information (NCBI) database, 30938 (26%) were annotated in the Swiss-Prot database, 10273 (8.7%) unigenes were mapped to 141 Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway database, while 52560 (44%) and 40756 (34%) unigenes were assigned to Gen Ontology (GO) categories and Eukaryotic Orthologous Groups of proteins (KOG), respectively. In addition, 65 candidate genes involved in three stages of crocin biosynthesis were identified. Finally, transcriptome sequencing of saffron stigma was used to identify 6779 potential microsatellites (SSRs) molecular markers. High-throughput de novo transcriptome sequencing provided a valuable resource of transcript sequences of C. sativus in public databases. In addition, most of candidate genes potentially involved in crocin biosynthesis were identified which could be further utilized in functional genomics studies. Furthermore, numerous obtained SSRs might contribute to address open questions about the origin of this amphiploid spices with probable little genetic diversity.

Keywords: saffron, transcriptome, NGS, bioinformatic

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Authors: Amir Ghasem Norouzi, Mahdi Zowghi

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This study propose a framework based on the fuzzy T-Norms, T-conorm, a novel operator, and multi-expert approach to help organizations build awareness of the critical influential factors on the success of knowledge management (KM) implementation, analysis the failure of knowledge management. This study considers the complex uncertainty concept that is in knowledge management implementing capability (KMIC) and it is used by fuzzy logic for this reason. The contribution of our paper is shown with an empirical study in a nonprofit educational organization evaluation.

Keywords: fuzzy logic, knowledge management, multi expert analysis, consensus oriented average operator

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Authors: Rohalla Moghimi, Sirus Mohammadi

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Batteries for storage of electricity from solar and wind generation farms are a key element in the success of sustainability. In recent years, due to large integration of Renewable Energy Sources (RESs) like wind turbine and photovoltaic unit into the Micro-Grid (MG), the necessity of Battery Energy Storage (BES) has increased dramatically. The BES has several benefits and advantages in the MG-based applications such as short term power supply, power quality improvement, facilitating integration of RES, ancillary service and arbitrage. This paper presents the cost-based formulation to determine the optimal size of the BES in the operation management of MG. Also, some restrictions, i.e. power capacity of Distributed Generators (DGs), power and energy capacity of BES, charge/discharge efficiency of BES, operating reserve and load demand satisfaction should be considered as well. In this paper, a methodology is proposed for the optimal allocation and economic analysis of ESS in MGs on the basis of net present value (NPV). As the optimal operation of an MG strongly depends on the arrangement and allocation of its ESS, economic operation strategies and optimal allocation methods of the ESS devices are required for the MG.

Keywords: microgrid, energy storage system, optimal sizing, net present value

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Authors: N. Borjalilu, P. Rabiei, A. Enjoo

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Flight Data Monitoring (FDM) program assists an operator in aviation industries to identify, quantify, assess and address operational safety risks, in order to improve safety of flight operations. FDM is a powerful tool for an aircraft operator integrated into the operator’s Safety Management System (SMS), allowing to detect, confirm, and assess safety issues and to check the effectiveness of corrective actions, associated with human errors. This article proposes a model for safety risk assessment level of flight data in a different aspect of event focus based on fuzzy set values. It permits to evaluate the operational safety level from the point of view of flight activities. The main advantages of this method are proposed qualitative safety analysis of flight data. This research applies the opinions of the aviation experts through a number of questionnaires Related to flight data in four categories of occurrence that can take place during an accident or an incident such as: Runway Excursions (RE), Controlled Flight Into Terrain (CFIT), Mid-Air Collision (MAC), Loss of Control in Flight (LOC-I). By weighting each one (by F-TOPSIS) and applying it to the number of risks of the event, the safety risk of each related events can be obtained.

Keywords: F-topsis, fuzzy set, flight data monitoring (FDM), flight safety

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Authors: Christina Killian, Katie Wall, Séamus Fanning, Guerrino Macori

Abstract:

Deep-level metagenomics offers a useful technical approach to explore the three dynamic One Health axes: healthcare, domiciliary and veterinary. There is currently limited understanding of the composition of complex biofilms, natural abundance of AMR genes and gene transfer occurrence in these ecological niches. By using a newly established small-scale complex biofilm model, COMBAT has the potential to provide new information on microbial diversity, antimicrobial resistance (AMR)-encoding gene abundance, and their transfer in complex biofilms of importance to these three One Health axes. Shotgun metagenomics has been used to sample the genomes of all microbes comprising the complex communities found in each biofilm source. A comparative analysis between untreated and biocide-treated biofilms is described. The basic steps include the purification of genomic DNA, followed by library preparation, sequencing, and finally, data analysis. The use of long-read sequencing facilitates the completion of metagenome-assembled genomes (MAG). Samples were sequenced using a PromethION platform, and following quality checks, binning methods, and bespoke bioinformatics pipelines, we describe the recovery of individual MAGs to identify mobile gene elements (MGE) and the corresponding AMR genotypes that map to these structures. High-throughput sequencing strategies have been deployed to characterize these communities. Accurately defining the profiles of these niches is an essential step towards elucidating the impact of the microbiota on each niche biofilm environment and their evolution.

Keywords: COMBAT, biofilm, metagenomics, high-throughput sequencing

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Authors: Francis O. Nwawuru

Abstract:

The convergence analysis of split monotone inclusion problems and fixed point problems of certain nonlinear mappings are investigated in the setting of real Hilbert spaces. Inertial extrapolation term in the spirit of Polyak is incorporated to speed up the rate of convergence. Under standard assumptions, a strong convergence of the proposed algorithm is established without computing the resolvent operator or involving Yosida approximation method. The stepsize involved in the algorithm does not depend on the spectral radius of the linear operator. Furthermore, applications of the proposed algorithm in solving some related optimization problems are also considered. Our result complements and extends numerous results in the literature.

Keywords: fixedpoint, hilbertspace, monotonemapping, resolventoperators

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Authors: Pouya Karimi, Ramin Gasemi Shayan, Parsa Sheykhzade

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Ease shotgun DNA sequencing is changing the microbial sciences. Sequencing instruments are compelling to the point that example planning is currently the key constraining element. Here, we present a microfluidic test readiness stage that incorporates the key strides in cells to grouping library test groundwork for up to 96 examples and decreases DNA input prerequisites 100-overlay while keeping up or improving information quality. The universally useful microarchitecture we show bolsters work processes with subjective quantities of response and tidy up or catch steps. By decreasing the example amount necessities, we empowered low-input (∼10,000 cells) entire genome shotgun (WGS) sequencing of Mycobacterium tuberculosis and soil miniaturized scale settlements with prevalent outcomes. We additionally utilized the upgraded throughput to succession ∼400 clinical Pseudomonas aeruginosa libraries and exhibit magnificent single-nucleotide polymorphism discovery execution that clarified phenotypically watched anti-toxin opposition. Completely coordinated lab-on-chip test arrangement beats specialized boundaries to empower more extensive organization of genomics across numerous fundamental research and translational applications.

Keywords: clinical microbiology, DNA, microbiology, microbial genomics

Procedia PDF Downloads 99

Authors: Khalda Amr, Noha Eltaweel, Sherif Ismail, Hala Raslan

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Introduction: Osteoarthritis is the most common form of arthritis that involves the wearing away of the cartilage that caps the bones in the joints. While rheumatoid arthritis is an autoimmune disease in which the immune system attacks the joints, beginning with the lining of joints. In this study, we aimed to study the top deregulated miRNAs that might be the cause of pathogenesis in both diseases. Methods: Eight cases were recruited in this study: 4 rheumatoid arthritis (RA), 2 osteoarthritis (OA) patients, as well as 2 healthy controls. Total RNA was isolated from plasma to be subjected to miRNA profiling by NGS. Sequencing libraries were constructed and generated using the NEBNextR UltraTM small RNA Sample Prep Kit for Illumina R (NEB, USA), according to the manufacturer’s instructions. The quality of samples were checked using fastqc and multiQC. Results were compared RA vs Controls and OA vs. Controls. Target gene prediction and functional annotation of the deregulated miRNAs were done using Mienturnet. The top deregulated miRNAs in each disease were selected for further validation using qRT-PCR. Results: The average number of sequencing reads per sample exceeded 2.2 million, of which approximately 57% were mapped to the human reference genome. The top DEMs in RA vs controls were miR-6724-5p, miR-1469, miR-194-3p (up), miR-1468-5p, miR-486-3p (down). In comparison, the top DEMs in OA vs controls were miR-1908-3p, miR-122b-3p, miR-3960 (up), miR-1468-5p, miR-15b-3p (down). The functional enrichment of the selected top deregulated miRNAs revealed the highly enriched KEGG pathways and GO terms. Six of the deregulated miRNAs (miR-15b, -128, -194, -328, -542 and -3180) had multiple target genes in the RA pathway, so they are more likely to affect the RA pathogenesis. Conclusion: Six of our studied deregulated miRNAs (miR-15b, -128, -194, -328, -542 and -3180) might be highly involved in the disease pathogenesis. Further functional studies are crucial to assess their functions and actual target genes.

Keywords: next generation sequencing, mirnas, rheumatoid arthritis, osteoarthritis

Procedia PDF Downloads 50

Authors: Habib Onsori, Somayeh Akrami, Mohammad Rahmati

Abstract:

Deafness is the most common sensory disorder with the frequency of 1/1000 in many populations. Mutations in the GJB2 (CX26) gene at the DFNB1 locus on chromosome 13q12 are associated with congenital hearing loss. Approximately 80% of congenital hearing loss cases are recessively inherited and 15% dominantly inherited. Mutations of the GJB2 gene, encoding gap junction protein Connexin 26 (Cx26), are the most common cause of hereditary congenital hearing loss in many countries. This report presents two cases of different mutations from Iranian patients with bilateral hearing loss. DNA studies were performed for the GJB2 gene by PCR and sequencing methods. In one of them, direct sequencing of the gene showed a heterozygous T→C transition at nucleotide 604 resulting in a cysteine to arginine amino acid substitution at codon 202 (C202R) in the fourth extracellular domain (TM4) of the protein. The analyses indicate that the C202R mutation appeared de novo in the proband with a possible dominant effect (GenBank: KF 638275). In the other one, DNA sequencing revealed a compound heterozygous mutation (35delG, 363delC) in the Cx26 gene that is strongly associated with congenital non-syndromic hearing loss (NSHL). So screening the mutations for hearing loss individuals referring to genetics counseling centers before marriage and or pregnancy is recommended.

Keywords: CX26, deafness, GJB2, mutation

Procedia PDF Downloads 458

Authors: Adeolu O. Dairo

Abstract:

Getting the consumer marketing strategy right is a crucial and complex task for firms with a large customer base such as mobile operators in a competitive mobile market. While empirical studies have made efforts to identify key constructs, no geospatial model has been developed to comprehensively assess the viability and interdependency of ground realities regarding the customer, competition, channel and the network quality of mobile operators. With this research, a geo-analytic framework is proposed for strategy formulation and allocation for mobile operators. Firstly, a fuzzy analytic network using a self-organizing feature map clustering technique based on inputs from managers and literature, which depicts the interrelationships amongst ground realities is developed. The model is tested with a mobile operator in the Nigeria mobile market. As a result, a customer-centric geospatial and visualization solution is developed. This provides a consolidated and integrated insight that serves as a transparent, logical and practical guide for strategic, tactical and operational decision making.

Keywords: geospatial, geo-analytics, self-organizing map, customer-centric

Procedia PDF Downloads 147