Showing papers by "Muhammad Younas published in 2013"

Detection and genotyping of restriction fragment associated polymorphisms in polyploid crops with a pseudo-reference sequence: a case study in allotetraploid Brassica napus

Abstract: The presence of homoeologous sequences and absence of a reference genome sequence make discovery and genotyping of single nucleotide polymorphisms (SNPs) more challenging in polyploid crops. To address this challenge, we constructed reduced representation libraries (RRLs) for two Brassica napus inbred lines and their 91 doubled haploid (DH) progenies using a modified ddRADseq technique. A bioinformatics pipeline termed RFAPtools was developed to discover and genotype SNPs and presence/absence variations (PAVs). Using this pipeline, a pseudo-reference sequence (PRF) containing 180,991 sequence tags was constructed. By aligning sequence reads to the pseudo-reference sequence, allelic SNPs as well as PAVs were identified and genotyped with RFAPtools. Two parallel linkage maps, one SNP bin map containing 8,780 SNP loci and one PAV linkage map containing 12,423 dominant loci, were constructed. By aligning marker sequences to B. rapa sequence scaffolds, whose genome is available, we assigned 44 unassembled sequence scaffolds comprising 8.15 Mb onto the B. rapa chromosomes, and also identified 14 instances of misassembly and eight instances of mis-ordering sequence scaffolds. These results indicate that the modified ddRADseq approach is a cost-effective and simple method to genotype tens of thousands SNPs and PAV markers in a polyploidy plant species. The results also demonstrated that RFAPtools developed in this study are powerful to mine allelic SNPs from homoeologous sequences in polyploids, therefore they are generally applicable in either diploid or polyploid species with or without a reference genome sequence.

Performance Evaluation of OLSR and AODV Protocols in a VANET Crossroad Scenario

Abstract: In this paper, we investigate the performance of OLSR and AODV protocols in a VANET crossroad scenario. The mobility patterns of vehicles are generated by means of CAVENET (Cellular Automaton based Vehicular Network) and as communication protocol simulator, is used NS3(Network Simulator 3). For the simulations, we used IEEE802.11p standard, TwoRayGroundPropagationLossModel and sent multiple CBR flows over UDP between ten pairs source-destination. We use Packet Delivery Ratio (PDR), throughput and delay as evaluation metrics. We compared the performance of both protocols and the simulation results shows that for big values of transmission rates, OLSR performs better than AODV. For small transmission rates, the delay is less than 0.1sec and both protocols can be used for real time applications such as safety applications. For big values of transmission rate, the delay is higher than 1 sec and these protocols can be used for applications that tolerate this delay such as streaming and entertainment.

Towards QoS in Internet of Things for Delay Sensitive Information

Abstract: Ensuring QoS for transmission of delay sensitive information is of paramount importance in network of smart devices formally known as Internet of Things (IoTs). The most commonly used Best Effort service model cannot be an attractive mechanism to treat delay sensitive traffic. Heterogeneous smart devices with limited buffer capacity needs effective buffer management scheme and differentiated service priorities to provide preferential treatment to delay sensitive traffic. This paper proposes a cost-effective analytical model for a finite capacity queueing system with pre-emptive resume service priority and push-out buffer management scheme. The analytical model can be used to predict the performance of smart devices under various traffic conditions that meet the required QoS constraints of IoT devices.

Body measurements and body condition scoring as basis for estimation of live weight in Nili-Ravi buffaloes.

Abstract: Received: Revised: Accepted: November 10, 2012 February 10, 2013 March 21, 2013

Mobility Management Scheme for Context-Aware Transactions in Pervasive and Mobile Cyberspace

Abstract: Rapid advances in software systems, wireless networks, and embedded devices have led to the development of a pervasive and mobile cyberspace that provides an infrastructure for anywhere/anytime service provisioning in different domains such as engineering, commerce, education, and entertainment This style of service provisioning enables users to freely move between geographical areas and to continuously access information and conduct online transactions However, such a high mobility may cause performance and reliability problems during the execution of transactions For example, the unavailability of sufficient bandwidth can result in failure of transactions when users move from one area (cell) to another We present a context-aware transaction model that dynamically adapts to the users' needs and execution environments Accordingly, we develop a new mobility management scheme that ensures seamless connectivity and reliable execution of context-aware transactions during mobility of users The proposed scheme is designed and developed using a combination of different queuing models We conduct various experiments in order to show that the proposed scheme optimizes the mobility management process and increases the throughput of context-aware transactions

A Lightweight Architecture for the Web-of-Things

Abstract: The past few years have marked a shift in Web development as users have become accustomed to Web applications with dynamic content and enhanced user experience. New emerging protocols and standards seek to provide increased flexibility by making available new models of interaction to Web applications. One such application is the Web of Things. In this paper, we propose a new lightweight architecture for the Web of Things, based on RESTful approaches. We further show, through a proof of concept application, taking a smart city as its context, how new technologies can be combined to support our proposed architecture and application development for the Web of Things. We argue that the use of protocols and standards such as WebSocket, WebSocket API, Server-Sent Events and JSON, the JavaScript Object Notation, can make the vision of the Web of Things a reality.

Investigation of AODV Throughput Considering RREQ, RREP and RERR Packets

Abstract: As Mobile Ad hoc Networks (MANETs) are attracting attention for their potential use in several fields such as collaborative computing and multimedia communications, there is an increasing need to minimize the overhead introduced by routing protocols in the network In this paper, we analyze the performance of a MANET by simulations, in terms of RREQ, RREP and RERR, considering Random Waypoint Mobility (RWM) model We consider the cases when all nodes are moving and source and destination nodes are static We evaluate the performance by measuring the throughput and AODV control packets

Pressure driven spin crossover and isostructural phase transition in LaFeO3

Abstract: We have studied the behavior of LaFeO3 under pressure (P) using density functional theory (DFT) and atomistic simulations. Ground state structural properties of LaFeO3 are correctly described by atomistic simulations. The effect of high pressure shows that there is an isotropic compression up to 100 GPa. However, DFT calculations show that within pressure range 0 < P < 32.4 GPa, LaFeO3 retains its ground state electronic structure. On the other hand, at P ∼32.4 GPa high to low spin magnetic phase transition is observed, which is accompanied by 6.9% volume collapse of LaFeO3 unit cell, while retaining the ground state orthorhombic crystal structure, i.e., isostructural phase transition. Furthermore, the band gap is closed leading insulator to metal transition. This differing behavior observed by the two techniques can be attributed to the omission of magnetic effects in static simulations. The simultaneous magnetic, electrical, and structural (volume collapse) phase transitions of LaFeO3 under compression as revealed by DFT calculations corroborate experimental findings. From these results, we can elaborate the mechanism of phase transition in LaFeO3: increasing crystal field induces a high spin to low spin transition, which in turn drives the electrical transitions and volume collapse.

Factors influencing body weights at different ages in thalli sheep

Abstract: Thalli is native sheep breed of Thall area of the Punjab, Pakistan. Data on 17030 birth records of 5421 Thalli sheep maintained at Livestock Experiment S tation, Rakh Ghulaman, district Bhakkar during 1975 -2004 were utilized in the present study with the aimto evaluate the performance of Thalli sheep in Pakistan. The genetic parameter estimation was performedusingREML procedurebyfitting an Individual A nimal Model.Birth weightwith an average of

A Next-Generation Approach to Combating Botnets

Abstract: As part of a defense-in-depth security solution for domain-controlled enterprise networks, a proposed self-healing system architecture is designed to increase resiliency against botnets with minimal disruption to network services.

Context-Aware and Cloud Based Adaptation of the User Experience

Abstract: This paper explores the notion of cross-source integration of cloud-based, context-aware information. The objective is to develop a new solution that incorporates remote, web based configuration of Android phones and advances the research area of context-aware information and web applications. It expands the notion of context-awareness harvesting from web applications, enabling automatic adaptation and behaviour altering of smartphones in accordance with implicit user needs. Results from the conducted experiment show the viability of tailoring contextual information through a web application to provide users with timely, relevant and adapted application behavior and content. Through the developed application suite, we present a remote configurable, adaptive application solution to demonstrate the validity of our proposal. The novelty in this work is the new proposed solution and design whereby context-aware information is harvested from several dimensions to allow web application executions to build rich foundations on which algorithms for context-aware computation can be based.

A fuzzy-based reliability system for knowledge sharing between robots in P2P JXTA-overlay platform

Abstract: The design of an efficient collaborative multi-robot framework that ensures the autonomy and the individual requirements of the involved robots is a very challenging task. This requires designing an efficient platform for inter-robot communication. P2P is a good approach to achieve this goal. P2P aims at making the communication ubiquitous thereby crossing the communication boundary and has many attractive features to use it as a platform for collaborative multi-robot environments. In this paper, we present our implemented P2P system based on JXTA Overlay. We use JXTA Overlay as a platform for robot collaboration and knowledge sharing. We also propose a fuzzy-based peer reliability system for JXTA-Overlay platform considering three parameters: Actual Behavior Criterion (ABC), Mutually Agreed Behavior (MAB) and Reputation (R). We evaluated the knowledge sharing system by many experiments and show that this system has a good performance and can be used successfully for knowledge sharing between robots. Also, we present some simulation results, which show the fuzzy-based peer reliability system has a good behavior and can successfully select the best peer candidate.

Application of SmartBox end-device for medical care using JXTA-Overlay P2P system

Abstract: During last decade more and more old people live alone and the number of old people that need medical care is increased. The lack of doctors and the increase of the medical cost is becoming a big problem. Therefore, IT-based information systems should be implemented to help solve this problem. In this paper, we present the experimental results and evaluation of the SmartBox stimulation device for medical applications using a P2P system which is based on JXTA-Overlay. The SmartBox is integrated with our P2P system as a useful tool for monitoring and controlling patients activities. We found by experimental results that by SmartBox we can check the patient's situation. We carried out experiments with a patient in the bed and changed the temperature of the room. From the experimental results, we conclude that the use of SmartBox is an effective way for medical applications.

RP-Match: A Framework for Automatic Mapping of Regulations with Organizational Processes

Abstract: Mapping organizational processes with applicable regulatory guidelines is an important step in Regulatory Compliance Management. The Automation of the mapping process can help the overall compliance process. Though existing approaches compute mapping between different entities (e.g., ontology mapping, sentence similarity, semantic similarity and regulation-requirement mapping), the automation of the mapping process between regulation and processes has not been fully investigated yet. In this paper, we present RP-Match framework and propose a cascading-priority algorithm in order to compute similarity between regulation and processes. The framework also takes account of the structures of the regulation ontology and organizational process ontology for the similarity measures. The framework is tested using a Pharmaceutical industry case study. Results obtained show significant improvement in the mapping process.

Genic microsatellite markers for genetic diversity of rust resistant wheat genotypes

Abstract: The genetic diversity and molecular characterization of 10 wheat genotypes was investigated using 27 polymorphic microsatellite screened primers including Simple Sequence Repeats (SSR). About twenty one loci were found. Bioinformatics tools were applied for constructing dendogram. Lr-19 gene was present in all ten wheat genotypes and Sr-15 gene is present in nine genotypes except Uqab- 2000 that cause resistance against wheat rust. Highest genetic diversity was observed between Shalimar-86 and Pak-81 genotypes and showed the similarity of about 95.34%. Distantly related Uqab- 2000 showed minimum genetic diversity and 65.64% dissimilarity with Kohistan-97. Uqab-2000 rust resistant genes may have an insertion or deletion and examined as distantly related to rest of nine genotypes. The current research found that SSR makers identified rust resistant genes in numerous wheat genotypes. Present work also characterized the wheat genotypes at molecular level and found genetic diversity between different wheat genotypes. SSR markers could distinguish and characterize wheat genotypes, more screened primers could be used for saturation of different regions in further research. Bioinformatics also play a vital role in retrieving, analyzing and interpreting the data for further studies.

Test case design for transactional flows using a dependency-based approach

Abstract: Transactions are a key issue to develop reliable web service based applications. The advanced models used to manage this kind of transactions rely on the dependencies between the involved activities (subtransactions). Dependencies are constraints on the processing produced by the concurrent execution of interdependent activities. Existing work uses formal approaches to verify the consistency and correctness of dependencies in web service transactions, but there is no work on testing their implementation. This paper identifies and defines a set of possible dependencies using logical expressions. These expressions define the preconditions necessary for executing the subtransactions primitive tasks. By using those conditions, we propose a family of test criteria based on control-flow for checking the dependencies between subtransactions. The test criteria provide guidance for test case generation in order to specifically test the implementation of web service subtransactions dependencies.

Prospects and limitations of dairying in Gujranwala district (Punjab-Pakistan).

Abstract: A study involving survey of 120 respondents of different categories from district Gujranwala (Punjab-Pakistan) was conducted to investigate the trends in dairying Average milk production of cows and buffaloes was found to be 4.50 and 6.53 lit./day respectively. Milk is mostly (98.3 %) consumed as fresh processed and marketed to milk collectors in raw form. Combined animal feeding was the common practice with no special dietary allowance for high yielders. Average green fodder offered to lactating cows and buffaloes was found to be 43.49 ±2.67 and 59.03 ±1.39 kg/head/day, whereas corresponding values for dry cows and buffaloes were 26.46 ±2.13 and 39.48 ±1.58 kg/day, respectively. Lactating animals were preferred for concentrate feeding. Animals were vaccinated mainly against foot and mouth disease (FMD) and haemorrhagic septicaemia (HS). Adoption level of disinfection of the navel cord, dehorning (in cows), natural breeding, teat dipping, washing of udder and culling was 8.3, 25.8, 51.7, 20.8, 74 and 61.70 % respectively. Special feeding of dairy animals before calving was also reported by 41.7 % respondents. Record keeping was utterly lacking (91.7 %). Age at first breeding, age at first calving, lactation length, dry period, intercalving interval and productive life in case of buffaloes was 40.87±0.43, 52.48±0.48, 10.66±0.085, 4.35±0.051, 15.13±0.18 months and 9.22 ± 0.18 years respectively while in case of cattle the corresponding values were 29.11±1.280, 43.20±6.33, 9.12±0.37, 2.56±0.11, 12.50±0.50 months and 8.36 ±0.42 years, respectively. It may be inferred from these results that adoption of modern husbandry practices is still grossly lacking with a variable degree leading to low productivity and low profitability of the