Hesham H. Ali

Task scheduling in multiprocessing systems

The complex problem of assigning tasks to processing elements in order to optimize a performance measure has resulted in numerous heuristics aimed at approximating an optimal solution. This article addresses the task scheduling problem in many of its variations and surveys the major solutions. The scheduling techniques we discuss might be used by a compiler writer to optimize the code that comes out of a parallelizing compiler. The compiler would produce grains of sequential code, and the optimizer would schedule these grains such that the program runs in the shortest time.

Adaptive radio channel allocation for supporting coexistence of 802.15.4 and 802.11b

As the explosive growth of the ISM band usage continues, there are many scenarios where different systems operate in the same place at the same time. One of growing concerns is the coexistence of wireless systems [18]. For the successful deployment of mission-critical systems such as wireless sensor networks, it is required to provide a solution for the coexistence. In this paper, we propose a new scheme using multiple radio channels for the coexistence of 802.15.4 LRWPAN and 802.11b WLAN. To evaluate the effectiveness of the proposed scheme, measurement and simulation study are conducted. The simulation results show that the proposed scheme is effective in performance improvement for multi-hop largescale network of 802.15.4. Keywords-component; coexistence; interference; ISM band; 802.15.4; 802.11b

Evolutionary conservation suggests a regulatory function of AUG triplets in 5′-UTRs of eukaryotic genes

By comparing sequences of human, mouse and rat orthologous genes, we show that in 5′-untranslated regions (5′-UTRs) of mammalian cDNAs but not in 3′-UTRs or coding sequences, AUG is conserved to a significantly greater extent than any of the other 63 nt triplets. This effect is likely to reflect, primarily, bona fide evolutionary conservation, rather than cDNA annotation artifacts, because the excess of conserved upstream AUGs (uAUGs) is seen in 5′-UTRs containing stop codons in-frame with the start AUG and many of the conserved AUGs are found in different frames, consistent with the location in authentic non-coding sequences. Altogether, conserved uAUGs are present in at least 20–30% of mammalian genes. Qualitatively similar results were obtained by comparison of orthologous genes from different species of the yeast genus Saccharomyces. Together with the observation that mammalian and yeast 5′-UTRs are significantly depleted in overall AUG content, these findings suggest that AUG triplets in 5′-UTRs are subject to the pressure of purifying selection in two opposite directions: the uAUGs that have no specific function tend to be deleterious and get eliminated during evolution, whereas those uAUGs that do serve a function are conserved. Most probably, the principal role of the conserved uAUGs is attenuation of translation at the initiation stage, which is often additionally regulated by alternative splicing in the mammalian 5′-UTRs. Consistent with this hypothesis, we found that open reading frames starting from conserved uAUGs are significantly shorter than those starting from non-conserved uAUGs, possibly, owing to selection for optimization of the level of attenuation.

CD4+ Regulatory and Effector/Memory T Cell Subsets Profile Motor Dysfunction in Parkinson’s Disease

Animal models and clinical studies have linked the innate and adaptive immune system to the pathology of Parkinson’s disease (PD). Despite such progress, the specific immune responses that influence disease progression have eluded investigators. Herein, we assessed relationships between T cell phenotype and function with PD progression. Peripheral blood lymphocytes from two separate cohorts, a discovery cohort and a validation cohort, totaling 113 PD patients and 96 age- and environment-matched caregivers were examined by flow cytometric analysis and T cell proliferation assays. Increased effector/memory T cells (Tem), defined as CD45RO+ and FAS+ CD4+ T cells and decreased CD31+ and α4β7+ CD4+ T cells were associated with progressive Unified Parkinson’s Disease Rating Scale III scores. However, no associations were seen between immune biomarkers and increased age or disease duration. Impaired abilities of regulatory T cells (Treg) from PD patients to suppress effector T cell function was observed. These data support the concept that chronic immune stimulation, notably Tem activation and Treg dysfunction is linked to PD pathobiology and disease severity, but not disease duration. The association of T cell phenotypes with motor symptoms provides fresh avenues for novel biomarkers and therapeutic designs.

Survey and evaluation of real-time fall detection approaches

As we grow old, our desire for independence does not diminish; yet our health increasingly needs to be monitored. Injuries such as falling can be a serious problem for the elderly. If a person falls and is not able to get assistance within an hour, casualties arising from that fall can result in fatalities as early as 6 months later [1]. It would seem then that a choice between safety and independence must be made. Fortunately, as health care technology advances, simple devices can be made to detect or even predict falls in the elderly, which could easily save lives without too much intrusion on their independence. Much research has been done on the topic of fall detection and fall prediction. Some have attempted to detect falls using a variety of sensors such as: cameras, accelerometers, gyroscopes, microphones, or a combination of the like. This paper is aimed at reporting which existing methods have been found effective by others, as well as documenting the findings of our own experiments. The combination of which will assist in the progression towards a safe, unobtrusive monitoring system for independent seniors.

High sensitivity RNA pseudoknot prediction

Most ab initio pseudoknot predicting methods provide very few folding scenarios for a given RNA sequence and have low sensitivities. RNA researchers, in many cases, would rather sacrifice the specificity for a much higher sensitivity for pseudoknot detection. In this study, we introduce the Pseudoknot Local Motif Model and Dynamic Partner Sequence Stacking (PLMM_DPSS) algorithm which predicts all PLM model pseudoknots within an RNA sequence in a neighboring-region-interference-free fashion. The PLM model is derived from the existing Pseudobase entries. The innovative DPSS approach calculates the optimally lowest stacking energy between two partner sequences. Combined with the Mfold, PLMM_DPSS can also be used in predicting complicated pseudoknots. The test results of PLMM_DPSS, PKNOTS, iterated loop matching, pknotsRG and HotKnots with Pseudobase sequences have shown that PLMM_DPSS is the most sensitive among the five methods. PLMM_DPSS also provides manageable pseudoknot folding scenarios for further structure determination.

Computational Approach Involving Use of the Internal Transcribed Spacer 1 Region for Identification of Mycobacterium Species

ABSTRACT The rapid and reliable identification of clinically significant Mycobacterium species is a challenge for diagnostic laboratories. This study evaluates a unique sequence-dependent identification algorithm called MycoAlign for the differential identification of Mycobacterium species. The MycoAlign system uses pan-Mycobacterium-specific primer amplification in combination with a customized database and algorithm. The results of testing were compared with conventional phenotypic assays and GenBank sequence comparisons using the 16S rRNA target. Discrepant results were retested and evaluated using a third independent database. The custom database was generated using the hypervariable sequences of the internal transcribed spacer 1 (ITS-1) region of the rRNA gene complex from characterized Mycobacterium species. An automated sequence-validation process was used to control quality and specificity of evaluated sequence. A total of 181 Mycobacterium strains (22 reference strains and 159 phenotypically identified clinical isolates) and seven nonmycobacterial clinical isolates were evaluated in a comparative study to validate the accuracy of the MycoAlign algorithm. MycoAlign correctly identified all referenced strains and matched species in 94% of the phenotypically identified Mycobacterium clinical isolates. The ITS-1 sequence target showed a higher degree of specificity in terms of Mycobacterium identification than the 16S rRNA sequence by use of GenBank BLAST. This study showed the MycoAlign algorithm to be a reliable and rapid approach for the identification of Mycobacterium species and confirmed the superiority of the ITS-1 region sequence over the 16S rRNA gene sequence as a target for sequence-based species identification.

An Optimal Algorithm for Scheduling Interval Ordered Tasks with Communication on N Processors

The problem of scheduling task graphs on multiprocessor systems have received considerable attention in recent years. This problem is known to be NP-hard in its general form as well as many restricted cases. Few polynomial algorithms have been developed for solving special cases of the scheduling problem when the communication cost is not considered. For example, Papadimitriou and Yannakakis showed that unit execution time tasks in interval orders can be scheduled in linear time on N processors when communication cost is assumed to be zero. They have also shown that the generalization of this problem to arbitrary execution times is NP-complete. The complexity of the problem arises even more when communication among tasks is considered. Papadimitriou and Yannakakis also showed that the problem of optimally scheduling unit-time task graphs with communication on an unlimited number of processors is NP-complete. They provided a simple way to approximate the optimal schedule length within a factor of two. In this paper, we study the problem of scheduling task graphs with communication on a given number of processors when the task graph is an interval order. We introduce an optimal algorithm for solving the scheduling problem when the execution cost of the system tasks is identical and equal to the communication cost between any pair of processors.

THE TIME COMPLEXITY OF SCHEDULING INTERVAL ORDERS WITH COMMUNICATION IS POLYNOMIAL

Papadimitrjou and Yannakakis showed that unit execution time tasks in interval orders can be scheduled in linear time on N processors when communication cost is ignored. The objective function was to minimize the schedule length. They have also shown that the generalization of this problem to arbitrary execution times is NP-complete. In this paper, we study the problem of scheduling task graphs with communication on N processors when the task graph is an interval order. We prove that this scheduling problem can be solved in polynomial time when the execution cost of the system tasks is identical and equal to the communication cost between any pair of processors. We introduce an algorithm of O(Ne) to minimize the schedule length, where e is the number of arcs in the interval order.

The Role of Social Capital in the Creation of Community Wireless Networks

Community wireless networks (CWNs) offer free or affordable Internet access for the purpose of improving the well-being of the community. Many questions have been raised about the ownership, sustainability, and social and economic implications of CWNs. To address these concerns, we propose a conceptual framework that describes the role of social capital in the creation of CWNs. This framework takes into account a number of collective actions and cooperative activities that contribute to the development of CWNs. These actions and cooperative activities include donating money and hardware, volunteering manpower and technical skills, developing open source software for the network, and sharing wireless nodes with peers. We used the collective actions and cooperation construct of the social capital concept to attribute these types of community contributions. We collected data via a survey to support the proposed framework. The primary implication for practitioners is that mobilizing embedded resources in communities can build a common wireless infrastructure for their digital needs. This study is an important step towards advancing this topic as an intellectual stream.