Commenced in January 2007
Frequency: Monthly
Edition: International
Paper Count: 4


4 Survival Model for Partly Interval-Censored Data with Application to Anti D in Rhesus D Negative Studies

Authors: F. A. M. Elfaki, Amar Abobakar, M. Azram, M. Usman


This paper discusses regression analysis of partly interval-censored failure time data, which is occur in many fields including demographical, epidemiological, financial, medical and sociological studies. For the problem, we focus on the situation where the survival time of interest can be described by the additive hazards model in the present of partly interval-censored. A major advantage of the approach is its simplicity and it can be easily implemented by using R software. Simulation studies are conducted which indicate that the approach performs well for practical situations and comparable to the existing methods. The methodology is applied to a set of partly interval-censored failure time data arising from anti D in Rhesus D negative studies.

Keywords: Anti D in Rhesus D negative, Cox’s model, EM algorithm.

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3 Use of GIS for the Performance Evaluation of Canal Irrigation System in Rice Wheat Cropping Zone

Authors: Umm-e- Kalsoom, M. Arshad, Sadia Iqbal, M. Usman, M. Adnan


The research study evaluated the performance of irrigation system by using special scientific tools like Remote Sensing and GIS technology, so that proper measurements could be taken for the sustainable agriculture and water management. Different performance evaluation parameters had been calculated for the purposed data was gathered from field investigation and different government and private organizations. According to the calculations, organic matter ranges from 0.19% (low value) to 0.76% (high value). In flat irrigation system for wheat yield ranges from 3347.16 to 5260.39 kg/ha, while the total water applied to wheat crop ranges from 252.94 to 279.19 mm and WUE ranges from 13.07 to 18.37 kg/ha/mm. For rice yield ranges from 3347.47 to 5433.07 kg/ha with total water supplied to rice crop ranges from 764.71 to 978.15 mm and WUE ranges from 3.49 to 5.71 kg/ha/mm. Similarly, in raised bed system wheat yield ranges from 4569.13 to 6008.60 kg/ha, total water supplied ranges from 158.87 to 185.09 mm and WUE ranges from 27.20 to 33.54 kg/ha/mm while in rice crop, yield ranges from 5285.04 to 6716.69 kg/ha, total water supplied ranges from 600.72 to 755.06 mm and WUE ranges from 6.41 to 10.05 kg/ha/mm. Almost 51.3% water saving is observed in bed irrigation system as compared to flat system. Less water supplied to beds is more affective as its WUE value is higher than flat system where more water is supplied in both the seasons. Similarly, RWS values show that maximum water deficit while minimum area is getting adequate water supply. Greater yield is recorded in bed system as plant per square meter is more in bed system in comparison of flat system Thus, the integration of GIS tools to regularly compute performance indices could provide irrigation managers with the means for managing efficiently the irrigation system.

Keywords: Field survey, Relative Water Supply (RWS), Remote sensing maps, Water Use Efficiency (WUE).

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2 Fabless Prototyping Methodology for the Development of SOI based MEMS Microgripper

Authors: H. M. Usman Sani, Shafaat A. Bazaz, Nisar Ahmed


In this paper, Fabless Prototyping Methodology is introduced for the design and analysis of MEMS devices. Conventionally Finite Element Analysis (FEA) is performed before system level simulation. In our proposed methodology, system level simulation is performed earlier than FEA as it is computationally less extensive and low cost. System level simulations are based on equivalent behavioral models of MEMS device. Electrostatic actuation based MEMS Microgripper is chosen as case study to implement this methodology. This paper addresses the behavioral model development and simulation of actuator part of an electrostatically actuated Microgripper. Simulation results show that the actuator part of Microgripper works efficiently for a voltage range of 0-45V with the corresponding jaw displacement of 0-4.5425μm. With some minor changes in design, this range can be enhanced to 15μm at 85V.

Keywords: MEMS Actuator, Behavioral Model, CoventorWare, Microgripper, SOIMUMPs, System Level Simulation

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1 Bioinformatic Analysis of Retroelement-Associated Sequences in Human and Mouse Promoters

Authors: Nadezhda M. Usmanova, Nikolai V. Tomilin


Mammalian genomes contain large number of retroelements (SINEs, LINEs and LTRs) which could affect expression of protein coding genes through associated transcription factor binding sites (TFBS). Activity of the retroelement-associated TFBS in many genes is confirmed experimentally but their global functional impact remains unclear. Human SINEs (Alu repeats) and mouse SINEs (B1 and B2 repeats) are known to be clustered in GCrich gene rich genome segments consistent with the view that they can contribute to regulation of gene expression. We have shown earlier that Alu are involved in formation of cis-regulatory modules (clusters of TFBS) in human promoters, and other authors reported that Alu located near promoter CpG islands have an increased frequency of CpG dinucleotides suggesting that these Alu are undermethylated. Human Alu and mouse B1/B2 elements have an internal bipartite promoter for RNA polymerase III containing conserved sequence motif called B-box which can bind basal transcription complex TFIIIC. It has been recently shown that TFIIIC binding to B-box leads to formation of a boundary which limits spread of repressive chromatin modifications in S. pombe. SINEassociated B-boxes may have similar function but conservation of TFIIIC binding sites in SINEs located near mammalian promoters has not been studied earlier. Here we analysed abundance and distribution of retroelements (SINEs, LINEs and LTRs) in annotated sequences of the Database of mammalian transcription start sites (DBTSS). Fractions of SINEs in human and mouse promoters are slightly lower than in all genome but >40% of human and mouse promoters contain Alu or B1/B2 elements within -1000 to +200 bp interval relative to transcription start site (TSS). Most of these SINEs is associated with distal segments of promoters (-1000 to -200 bp relative to TSS) indicating that their insertion at distances >200 bp upstream of TSS is tolerated during evolution. Distribution of SINEs in promoters correlates negatively with the distribution of CpG sequences. Using analysis of abundance of 12-mer motifs from the B1 and Alu consensus sequences in genome and DBTSS it has been confirmed that some subsegments of Alu and B1 elements are poorly conserved which depends in part on the presence of CpG dinucleotides. One of these CpG-containing subsegments in B1 elements overlaps with SINE-associated B-box and it shows better conservation in DBTSS compared to genomic sequences. It has been also studied conservation in DBTSS and genome of the B-box containing segments of old (AluJ, AluS) and young (AluY) Alu repeats and found that CpG sequence of the B-box of old Alu is better conserved in DBTSS than in genome. This indicates that Bbox- associated CpGs in promoters are better protected from methylation and mutation than B-box-associated CpGs in genomic SINEs. These results are consistent with the view that potential TFIIIC binding motifs in SINEs associated with human and mouse promoters may be functionally important. These motifs may protect promoters from repressive histone modifications which spread from adjacent sequences. This can potentially explain well known clustering of SINEs in GC-rich gene rich genome compartments and existence of unmethylated CpG islands.

Keywords: Retroelement, promoter, CpG island, DNAmethylation.

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