Genetic Threading

The biological function of proteins is dependent, to a large extent, on their native three dimensional conformation. Thus, it is important to know the structure of as many proteins as possible. Since experimental methods for structure determination are very tedious, there is a significant effort to calculate the structure of a protein from its linear sequence. Direct methods of calculating structure from sequence are not available yet. Thus, an indirect approach to predict the conformation of protein, called threading, is discussed. In this approach, known structures are used as constraints, to restrict the search for the native conformation. Threading requires finding good alignments between a sequence and a structure, which is a major computational challenge and a practical bottleneck in applying threading procedures. The Genetic Algorithm paradigm, an efficient search method that is based on evolutionary ideas, is used to perform sequence to structure alignments. A proper representation is discussed in which genetic operators can be effectively implemented. The algorithm performance is tested for a set of six sequence/structure pairs. The effects of changing operators and parameters are explored and analyzed.     

Resource-efficient routing and scheduling of time-constrained streaming communication on networks-on-chip

Network-on-chip-based multiprocessor systems-on-chip are considered as future embedded systems platforms. One of the steps in mapping an application onto such a parallel platform involves scheduling the communication on the network-on-chip. This paper presents different scheduling strategies that minimize resource usage by exploiting all scheduling freedom offered by networks-on-chip. It also introduces a technique to take the dynamism in applications into account when scheduling the communication of an application on the network-on-chip while minimizing the resource usage. Our experiments show that resource-utilization is improved when compared to existing techniques.     

Efficient Regular Data Structures and Algorithms for Dilation, Location, and Proximity Problems

In this paper we investigate data structures obtained by a recursive partitioning of the multi- dimensional input domain into regions of equal size. One of the best known examples of such a structure is the quadtree . It is used here as a basis for more complex data structures. We also provide multidimensional versions of the stratified tree by van Emde Boas [vEB]. We show that under the assumption that the input points have limited precision (i.e., are drawn from the integer grid of size u ) these data structures yield efficient solutions to many important problems. In particular, they allow us to achieve O(log log u) time per operation for dynamic approximate nearest neighbor (under insertions and deletions) and exact on-line closest pair (under insertions only) in any constant number of dimensions. They allow O(log log u) point location in a given planar shape or in its expansion (dilation by a ball of a given radius). Finally, we provide a linear time (optimal) algorithm for computing the expansion of a shape represented by a region quadtree. This result shows that the spatial order imposed by this regular data structure is sufficient to optimize the operation of dilation by a ball. Received January 19, 1999; revised November 4, 1999.     

Efficient matching of nonrectangular shapes

Most known two-dimensional matching algorithms have a rectangular text (image) and rectangular pattern (template) as their input. These matching algorithms perform a row by row analysis followed by some column processing. These techniques are only efficient if all the rows are of equal length, hence the necessity for rectangular patterns.We present a novel method for analysing patterns with rows of different lengths. This enables finding all occurrences of a nonrectangular figure of heightm in ann×n text in time . We make use of thesmaller matching problem.The smaller matching problem is that of finding all appearances of a numerical one dimensional pattern in a numerical one-dimensional text, where every element of the pattern is no greater than the corresponding text element.Partially supported by NSF grant CCR-88-03641 and a University of Maryland full year research award.Supported by a University of Maryland Graduate Fellowship, an ACM Samuel M. Alexander Fellowship and NSF grant CCR-88-03641.     

Optimum loading of machines in a flexible manufacturing system using a mixed-integer linear mathematical programming model and genetic algorithm

Machine loading problem in a flexible manufacturing system (FMS) encompasses various types of flexibility aspects pertaining to part selection and operation assignments. The evolution of flexible manufacturing systems offers great potential for increasing flexibility by ensuring both cost-effectiveness and customized manufacturing at the same time. This paper proposes a linear mathematical programming model with both continuous and zero-one variables for job selection and operation allocation problems in an FMS to maximize profitability and utilization of system. The proposed model assigns operations to different machines considering capacity of machines, batch-sizes, processing time of operations, machine costs, tool requirements, and capacity of tool magazine. A genetic algorithm (GA) is then proposed to solve the formulated problem. Performance of the proposed GA is evaluated based on some benchmark problems adopted from the literature. A statistical test is conducted which implies that the proposed algorithm is robust in finding near-optimal solutions. Comparison of the results with those published in the literature indicates supremacy of the solutions obtained by the proposed algorithm for attempted model.     

Maintaining awareness using policies; Enabling agents to identify relevance of information

The field of computer supported cooperative work aims at providing information technology models, methods, and tools that assist individuals to cooperate. The presented paper is based on three main observations from literature. First, one of the problems in utilizing information technology for cooperation is to identify the relevance of information, called awareness. Second, research in computer supported cooperative work proposes the use of agent technologies to aid individuals to maintain their awareness. Third, literature lacks the formalized methods on how software agents can identify awareness. This paper addresses the problem of awareness identification. The main contribution of this paper is to propose and evaluate a formalized structure, called Policy-based Awareness Management (PAM). PAM extends the logic of general awareness in order to identify relevance of information. PAM formalizes existing policies into Directory Enabled Networks-next generation structure and uses them as a source for awareness identification. The formalism is demonstrated by applying PAM to the space shuttle Columbia disaster occurred in 2003. The paper also argues that efficacy and cost-efficiency of the logic of general awareness will be increased by PAM. This is evaluated by simulation of hypothetical scenarios as well as a case study.     

PDDRA: A new pre-fetching based dynamic data replication algorithm in data grids

In recent years, grid technology has had such a fast growth that it has been used in many scientific experiments and research centers. A large number of storage elements and computational resources are combined to generate a grid which gives us shared access to extra computing power. In particular, data grid deals with data intensive applications and provides intensive resources across widely distributed communities. Data replication is an efficient way for distributing replicas among the data grids, making it possible to access similar data in different locations of the data grid. Replication reduces data access time and improves the performance of the system. In this paper, we propose a new dynamic data replication algorithm named PDDRA that optimizes the traditional algorithms. Our proposed algorithm is based on an assumption: members in a VO (Virtual Organization) have similar interests in files. Based on this assumption and also file access history, PDDRA predicts future needs of grid sites and pre-fetches a sequence of files to the requester grid site, so the next time that this site needs a file, it will be locally available. This will considerably reduce access latency, response time and bandwidth consumption. PDDRA consists of three phases: storing file access patterns, requesting a file and performing replication and pre-fetching and replacement. The algorithm was tested using a grid simulator, OptorSim developed by European Data Grid projects. The simulation results show that our proposed algorithm has better performance in comparison with other algorithms in terms of job execution time, effective network usage, total number of replications, hit ratio and percentage of storage filled.     

Graph Pangenomes Track Genetic Variants for Crop Improvement

Global climate change and the urgency to transform crops require an exhaustive genetic evaluation. The large polyploid genomes of food crops, such as cereals, make it difficult to identify candidate genes with confirmed hereditary. Although genome-wide association studies (GWAS) have been proficient in identifying genetic variants that are associated with complex traits, the resolution of acquired heritability faces several significant bottlenecks such as incomplete detection of structural variants (SV), genetic heterogeneity, and/or locus heterogeneity. Consequently, a biased estimate is generated with respect to agronomically complex traits. The graph pangenomes have resolved this missing heritability and provide significant details in terms of specific loci segregating among individuals and evolving to variations. The graph pangenome approach facilitates crop improvements through genome-linked fast breeding.     

The Effect of Intensity-Modulated Radiotherapy to the Head and Neck Region on the Oral Innate Immune Response and Oral Microbiome: A Prospective Cohort Study of Head and Neck Tumour Patients

Neutrophils, also known as polymorphonuclear leukocytes (PMNs), form a significant component of the innate host response, and the consequence of the interaction between the oral microbiota and PMNs is a crucial determinant of oral health status. The impact of radiation therapy (RT) for head and neck tumour (HNT) treatment on the oral innate immune system, neutrophils in particular, and the oral microbiome has not been thoroughly investigated. Therefore, the objective of this study was to characterize RT-mediated changes in oral neutrophils (oPMNs) and the oral microbiome in patients undergoing RT to treat HNTs. Oral rinse samples were collected prior to, during and post-RT from HNT patients receiving RT at Dental Oncology at Princess Margaret Cancer Centre. The oPMNs counts and activation states were analysed using flow cytometry, and the oral microbiome was analysed using 16S rRNA gene sequencing. Statistically significant (p < 0.05) drops in oPMN counts and the activation states of the CD11b, CD16, CD18, CD64 and H3Cit markers from pre-RT to post-RT were observed. Moreover, exposure to RT caused a significant reduction in the relative abundance of commensal Gram-negative bacteria and increased the commensal Gram-positive microbes. Ionizing radiation for the treatment of HNTs simultaneously decreased the recruitment of oPMNs into the oral cavity and suppressed their activation state. The oral microbiome composition post-RT was altered significantly due to RT which may favour the colonization of specific microbial communities unfavourable for the long-term development of a balanced oral microbiome.     

Bi-level fuzzy based advanced reservation of Cloud workflow applications on distributed Grid resources

The increasing demand on execution of large-scale Cloud workflow applications which need a robust and elastic computing infrastructure usually lead to the use of high-performance Grid computing clusters. As the owners of Cloud applications expect to fulfill the requested Quality of Services (QoS) by the Grid environment, an adaptive scheduling mechanism is needed which enables to distribute a large number of related tasks with different computational and communication demands on multi-cluster Grid computing environments. Addressing the problem of scheduling large-scale Cloud workflow applications onto multi-cluster Grid environment regarding the QoS constraints declared by application’s owner is the main contribution of this paper. Heterogeneity of resource types (service type) is one of the most important issues which significantly affect workflow scheduling in Grid environment. On the other hand, a Cloud application workflow is usually consisting of different tasks with the need for different resource types to complete which we call it heterogeneity in workflow. The main idea which forms the soul of all the algorithms and techniques introduced in this paper is to match the heterogeneity in Cloud application’s workflow to the heterogeneity in Grid clusters. To obtain this objective a new bi-level advanced reservation strategy is introduced, which is based upon the idea of first performing global scheduling and then conducting local scheduling. Global-scheduling is responsible to dynamically partition the received DAG into multiple sub-workflows that is realized by two collaborating algorithms: (1) The Critical Path Extraction algorithm (CPE) which proposes a new dynamic task overall critically value strategy based on DAG’s specification and requested resource type QoS status to determine the criticality of each task; and (2) The DAG Partitioning algorithm (DAGP) which introduces a novel dynamic score-based approach to extract sub-workflows based on critical paths by using a new Fuzzy Qualitative Value Calculation System to evaluate the environment. Local-scheduling is responsible for scheduling tasks on suitable resources by utilizing a new Multi-Criteria Advance Reservation algorithm (MCAR) which simultaneously meets high reliability and QoS expectations for scheduling distributed Cloud-base applications. We used the simulation to evaluate the performance of the proposed mechanism in comparison with four well-known approaches. The results show that the proposed algorithm outperforms other approaches in different QoS related terms.