Characterisation of a Composite Exonic Regulatory Element of Splicing (CERES) in <i>CFTR</i> Exon 12: Functional Properties and Evolutionary Constraints

Genotype screening in human disease frequently results in the identification of exon/intron sequence variations whose direct connection with occurrence of disease is often unclear, especially if they occur within exons but do not alter the amino acid coding sequence. However, it is now clear that many of these seemingly harmless changes very often can exert flaws in the splicing process by affecting splicing regulatory elements (SREs). Usually, SREs are classified based on their mode of action with regards to exon inclusion, either positive (enhancer) or negative (silencer). In addition to these clear cut definitions, using systematic site directed mutagenesis experiments in previous analyses from our lab we have identified a novel type of splicing controlling element that we called CERES (for Composite Exonic Regulatory Element of Splicing). The distinguishing feature of CERES elements resides in the fact that they represent an extreme physical overlap of enhancer and silencer sequence. As a result, the functional effect at the level of exon inclusion/skipping of a single nucleotide change in a CERES element is hard to predict. In this study I have addressed both issues in the context of the functional CERES2 element in CFTR exon 12. The result show that CERES2 can bind to a number of SR (SF2/ASF and SRp55) and hnRNP (A1, A2, C2, U, DAZAP1) factors in a small stretch of RNA in close proximity to each other. In particular, one of the disease causing mutations, G48C and a synonymous substitution next to it (A49G) showed reduced binding with SF2/ASF, whereas another natural mutation, A51T showed that the SF2/ASF interaction was increased compared to the wild type exon 12 sequences. Functional assays confirmed the potential regulatory role of the SF2/ASF and hnRNP Al interactions. Two synonymous mouse substitutions (T40C and C52T) near the CERES2 region were observed to cause skipping in human exon 12 but had no effect if the exon was truncated in a reduced context. Restoration of the truncated sequences restored skipping of the exon. However, if these flanking sequences were replaced with mouse sequences then no skipping occurred. This observation suggested that the human exon 12 sequences have ESS regions in both flanks of the exon whereas in the mouse sequence the flanking exon sequences contain ESE elements. Affinity purification of these flanking sequence showed that both of the mouse flanking sequences bind to SR proteins (SF/ASF, SRp 75, SRp 55 and SRp 40) but not in human. The consequences of this situation were then checked at the evolutionary level by comparing the distribution of SREs in different species. Altogether, our results suggest that in several species other than human the entire sequence of CFTR exon 12 is involved in its definition

Analysis of Bulk Power System Resilience Using Vulnerability Graph

Critical infrastructure such as a Bulk Power System (BPS) should have some quantifiable measure of resiliency and definite rule-sets to achieve a certain resilience value. Industrial Control System (ICS) and Supervisory Control and Data Acquisition (SCADA) networks are integral parts of BPS. BPS or ICS are themselves not vulnerable because of their proprietary technology, but when the control network and the corporate network need to have communications for performance measurements and reporting, the ICS or BPS become vulnerable to cyber-attacks. Thus, a systematic way of quantifying resiliency and identifying crucial nodes in the network is critical for addressing the cyber resiliency measurement process. This can help security analysts and power system operators in the decision-making process. This thesis focuses on the resilience analysis of BPS and proposes a ranking algorithm to identify critical nodes in the network. Although there are some ranking algorithms already in place, but they lack comprehensive inclusion of the factors that are critical in the cyber domain. This thesis has analyzed a range of factors which are critical from the point of view of cyber-attacks and come up with a MADM (Multi-Attribute Decision Making) based ranking method. The node ranking process will not only help improve the resilience but also facilitate hardening the network from vulnerabilities and threats. The proposed method is called MVNRank which stands for Multiple Vulnerability Node Rank. MVNRank algorithm takes into account the asset value of the hosts, the exploitability and impact scores of vulnerabilities as quantified by CVSS (Common Vulnerability Scoring System). It also considers the total number of vulnerabilities and severity level of each vulnerability, degree centrality of the nodes in vulnerability graph and the attacker’s distance from the target node. We are using a multi-layered directed acyclic graph (DAG) model and ranking the critical nodes in the corporate and control network which falls in the paths to the target ICS. We don\u27t rank the ICS nodes but use them to calculate the potential power loss capability of the control center nodes using the assumed ICS connectivity to BPS. Unlike most of the works, we have considered multiple vulnerabilities for each node in the network while generating the rank by using a weighted average method. The resilience computation is highly time consuming as it considers all the possible attack paths from the source to the target node which increases in a multiplicative manner based on the number of nodes and vulnerabilities. Thus, one of the goals of this thesis is to reduce the simulation time to compute resilience which is achieved as illustrated in the simulation results

Application of Nonlinear Site Response Analysis in Coastal Plain South Carolina

The 1933 Long Beach, 1957 San Francisco, 1967 Caracas, 1985 Mexico City, 1989 Loma Prieta, and 1994 Northridge earthquake events left evidences of how the local site condition can affect the characteristics of propagating earthquake wave from the bedrock through the top soil. The ground motion amplitude, frequency content or the duration can be affected by the local site condition and thus can cause significant amplification or de-amplification to the original bedrock motion which can seriously affect the structures. Quantification of such site effect on ground motions is a challenging task. This dissertation is dedicated to improve the existing ground response quantification techniques and the related knowledge base. The first major attempt towards ground response quantification was the development of the 1994 NEHRP (BSSC, 1995) seismic site factor provision. Since the development of the NEHRP provisions, several studies have found these factors to produce inadequate predictions for the state of South Carolina. In an attempt to generate seismic site factors based on conditions specific to South Carolina Coastal Plain (SCCP), a series of nonlinear one-dimensional ground response analyses are performed by this author as part of a research team considering appropriate soil profiles and location specific ground excitations. After the generation of this new site factor model, a systematic repercussions study is performed by applying earthquake loads, considering both NEHRP and the new site factors, on typical highway bridge structures

Novel Approaches and Architecture for Survivable Optical Internet

Any unexpected disruption to WDM (Wavelength Division Multiplexing) based optical networks which carry data traffic at tera-bit per second may result in a huge loss to its end-users and the carrier itself. Thus survivability has been well-recognized as one of the most important objectives in the design of optical Internet. This thesis proposes a novel survivable routing architecture for the optical Internet. We focus on a number of key issues that are essential to achieve the desired service scenarios, including the tasks of (a) minimizing the total number of wavelengths used for establishing working and protection paths in WDM networks; (b) minimizing the number of affected working paths in case of a link failure; (c) handling large scale WDM mesh networks; and (d) supporting both Quality of Service (QoS) and best-effort based working lightpaths. To implement the above objectives, a novel path based shared protection framework namely Group Shared protection (GSP) is proposed where the traffic matrix can be divided into multiple protection groups (PGs) based on specific grouping policy, and optimization is performed on these PGs. To the best of our knowledge this is the first work done in the area of group based WDM survivable routing approaches where not only the resource sharing is conducted among the PGs to achieve the best possible capacity efficiency, but also an integrated survivable routing framework is provided by incorporating the above objectives. Simulation results show the effectiveness of the proposed schemes

Regular graph-based logical topology design in multi-hop optical networks.

Existing approaches for logical topology design and routing for multi-hop optical networks become intractable for large networks. One approach which has been used is to treat the logical topology design problem separately from the routing problem which can be solved as a LP problem. The straightforward formulation of the LP problem has been reported but this is also feasible only for relatively smaller networks since the basis size for the simplex method is O(n3) where n is the number of nodes in the network. In this paper, by exploiting the special structure of the routing problem, we present an efficient column generation scheme embedded into the revised simplex method. This approach makes it feasible to handle networks with relatively large number of nodes. To study the approach experimentally we have used a number of traffic based heuristics for generating the logical topologies. These include a variation of the well known HLDA heuristic and two simple traffic based heuristics to generate logical topologies based on regular graphs. Many researchers feel that regular graphs are not well suited for wide area optical networks. The interesting result is that logical topologies based on regular graphs perform quite well compared to others. This suggests that it is useful to consider regular graphs as possible topologies for wide area networks and should be included as potential candidates for large wide area networks. Paper copy at Leddy Library: Theses & Major Papers - Basement, West Bldg. / Call Number: Thesis2001 .H36. Source: Masters Abstracts International, Volume: 40-03, page: 0722. Advisers: Arunita Jaekel; Yash P. Aneja. Thesis (M.Sc.)--University of Windsor (Canada), 2001

The effectiveness of micro-credit programmes focusing on household income, expenditure and savings: Evidence from Bangladesh

This paper assesses the effectiveness of microfinance on household income, expenditure and savings. The survey examined those borrowers who had successfully completed at least three cycles of a loan. A household level survey (N=3000) was carried out to collect information about individuals receiving microcredit from one of the largest NGOs, ASA. The authors employed a multiple regression and discovered that the microcredit programme of ASA has a significant positive impact on household income, expenditures and savings. Moreover, the paper reveals that the level of education plays an important and statistically significant role in increasing the household income, expenditure and savings. Hence, the ASA microcredit programme has a positive impact on reducing poverty in Bangladesh and enhancing the competitiveness of deprived rural and urban households in improving their standard of living.Internal Grant Agency of FaME TBU [IGA/FaME/2017/010