College of Information Science & Technology

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.

With the rapid accumulation of gene expression data in publicly accessible databases, computational study of gene regulation has become an obtainable goal. Intrinsic to this task will be data mining tools for inferring knowledge from biological data. In this project, we have developed a ...

In this paper we introduce a new formal approach for mining biological data sets. The proposed grammar based approach provides a flexible and powerful tool for advanced sequence comparison and data mining. The approach benefits from the power of regular ...

Groundwater is a very important resource, particularly in arid regions. In Makkah, which is the religious capital of the kingdom, water supply is provided from the aquifers of many valleys inside and around it and from the desalination plant in Jeddah. In this paper, the chemical and bacteriological water qualities of different resources of groundwater in Makkah were evaluated. The results of the chemical and bacteriological parameters were compared with the Saudi Arabian Specifications and Measurements Agency and with the United State Environmental Protection Agency (USEPA) standard in order to determine the suitability of these water resources for drinking. The paper depicted the contamination sources of each location and studied the quality of each well by periodic examinations and described the deviation in the quality of groundwater with time.

Sequencing of large fragments of genomic DNA makes it possible to perform comparisons of genomic sequences for identification of protein-coding regions. We have conducted a comparative analysis of homologous genomic sequences of organisms with different evolutionary ...

Reverse-engineering of gene networks using linear models often results in an underdetermined system because of excessive unknown parameters. In addition, the practical utility of linear models has remained unclear. We address these problems by developing an improved method, EXpression Array MINing Engine (EXAMINE), to infer gene regulatory networks from time-series gene expression data sets. EXAMINE takes advantage of sparse graph theory to overcome the excessive-parameter problem with an adaptive-connectivity model and fitting algorithm. EXAMINE also guarantees that the most parsimonious network structure will be found with its incremental adaptive fitting process. Compared to previous linear models, where a fully connected model is used, EXAMINE reduces the number of parameters by O(N), thereby increasing the chance of recovering the underlying regulatory network. The fitting algorithm increments the connectivity during the fitting process until a satisfactory fit is obtained. We performed a systematic study to explore the data mining ability of linear models. A guideline for using linear models is provided: If the system is small (3-20 elements), more than 90% of the regulation pathways can be determined correctly. For a large-scale system, either clustering is needed or it is necessary to integrate information in addition to expression profile. Coupled with the clustering method, we applied EXAMINE to rat central nervous system development (CNS) data with 112 genes. We were able to efficiently generate regulatory networks with statistically significant pathways that have been predicted previously.

In recent years, substantial effort has been applied to de novo regulatory motif discovery. At this time, more than 150 software tools exist to detect regulatory binding sites given a set of genomic sequences. As the number of software packages increases, it becomes more important to identify the tools with the best performance characteristics for specific problem domains. Identifying the correct tool is difficult because of the great variability in motif detection software. Consequently, many labs spend considerable effort testing methods to find one that works well in their problem of interest.

Background: Comparative Genomic Hybridization (CGH) is a molecular approach for detecting DNA Copy Number Alterations (CNAs) in tumor, which are among the key causes of tumorigenesis. However in the post-genomic era, most studies in cancer biology have been focusing on Gene Expression Profiling (GEP) but not CGH, and as a result, an enormous amount of GEP data had been accumulated in public databases for a wide variety of tumor types. We exploited this resource of GEP data to define possible recurrent CNAs in tumor. In addition, the CNAs identified by GEP would be more functionally relevant CNAs in the disease pathogenesis since the functional effects of CNAs can be reflected by altered gene expression.

This paper introduces a package, BioDatabase, a web-based application allowing for genetic sequence identification via the creation of custom databases. These custom databases contain a relatively small set of genetic data, specific to a species or a subset for a species. Each custom database sequence contains genetic regions with a highly conserved start and end sequence, along with other specific characteristics defined by an administrator. The package addresses issues regarding GenBank, whose information is valuable, yet difficult to properly utilize due to its size and quality. GenBank's size also prohibits optimal alignment algorithms from being used when identifying sequences against it. BioDatabase integrates this information, allowing optimal alignment algorithms to be run against local data obtained from GenBank or input manually by a researcher. This maximizes application performance with minimal impact on the speed results are returned to researchers. The BioDatabase package allows researchers to formulate sequence identification concepts and test their ideas against a validated database. Our concluding case study highlights this capability. The case study involves Mycobacterium identification using the 16S and ITS genetic regions. In the case study, researchers were able to correctly identify 72 of 78 Mycobacterium isolates through new sequence identification techniques using the BioDatabase package. These results proved to provide better identification of Mycobacterium in most cases than existing techniques.

We present a new method, link-test, to select prostate cancer biomarkers from SELDI mass spectrometry and microarray data sets. Biomarkers selected by link-test are supported by data sets from both mRNA and protein levels, and therefore results in improved robustness. Link-test determines the level of significance of the association between a microarray marker and a specific mass spectrum marker by constructing background mass spectra distributions estimated by all human protein sequences in the SWISS-PROT database. The data set consist of both microarray and mass spectrometry data from prostate cancer patients and healthy controls. A list of statistically justified prostate cancer biomarkers is reported by link-test. Cross-validation results show high prediction accuracy using the identified biomarker panel. We also employ text mining approach with OMIM database to validate the cancer biomarkers. The study with link-test represents one of the first crossplatform studies of cancer biomarkers.

Abstract. Data mining techniques are important to sift through the huge amount of gene expression values in microarrays resulting in valuable biological knowledge. An important example is classifying cancer samples, which is crucial to biologists for cancer diagnosis ...

This study presents the effects of the changing in color due to aging, thickness and the new color of polyethylene films on the radiative properties. Also, the influences of the radiative properties on the performance of the nocturnal cooling unit used to cool flowing water were studied. The measured data of the transmittance of the polyethylene films having a thickness of 50/~m and having changes in its color by 5, 30 and 100 days aging and also new film data were used to study its effects on the performance of the cooling unit theoretically. Also, two films of thickness 25 and 50/~m and two films having a thickness of 25 #m, with colors of light blue and colorless, were used to examine their effects on the performance of the cooling unit experimentally. The results showed that aging of the polyethylene films leads to substantial degradation in its transmissivity from average values of 0.72, 0.69, 0.57 and 0.42 corresponding to a new one, 5, 30 and 100 days aging in the wavelength range of 8-13 ~m. Also, neither thickness of the films nor their new colors have significant effects on the transmittance. It has been found that the effects of aging of the polyethylene film by 100 days led to the reduction in performance of night cooling by 33.3%. The decrease in thickness of the polyethylene films from 50 to 25 #m leads to an increase in its radiative properties (transmittance) and the performance of the night sky radiation unit by 8.6%. approximately. ~ 1997 Elsevier Science Ltd.

Due to the changing business environment, the need arises to integrate the pre-existing database system in federated way. A great effort had been done to enhance the performance of the Multidatabase management system (MDBMS). The most critical issue considered in this area is the query optimization that can be considered as the backbone of any successful database. Reviewing the most recent related work developed in the query optimization show that, a major challenge for global query optimization in a Multidatabase system is that some required local information about local database components (DBCs) such as local cost model may not be available at the global level due to local autonomy. The main objective of this paper is to introduce a framework that manages a communication between the MDBMS and the DBCs which will be the base to achieving its main goal of solving Query optimization problem.

Due to the rapidly increasing usage of the mobile devices attached to the internet, a lot of researches are being conducted to manage and maximize the benefit of such integration. Accordingly, the innovation of this research is to enhance the performance of the scheduling mechanism of the mobile computing environment by distributing some of the functions of the access point among the available attached mobile devices. Therefore, the first step to reach this aim is to point out how the mobile devices will be ranked and evaluated as a resource. The proposed mechanism is based on the investigation of "self ranking algorithm (SRA)" which provides a lifetime opportunity to reach a proper solution. This mechanism depends on event-based programming approach to start its execution in a pervasive computing environment. Using such mechanism will simplify the scheduling process by grouping the mobile devices according to their selfranking value and assign tasks to these groups. Moreover, it will maximize the benefit of the mobile devices integrated with the already existing grid systems by using their computational power as a subordinate value to the overall power of the system. Finally, the paper evaluates the performance of the investigated algorithm extensively, to show how it overcomes the connection stability problem of the mobile devices depending on the experimental results which emphasized that, the proposed SRA has a great impact compared with the traditional mechanism.

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.