Personalized Trust Management in Decision Making: A Dynamic Clustering Approach

This paper presents a personalized approach for distributed trust management by employing the k-means range algorithm, a combination of the partitional k-means clustering algorithm with orthogonal range search concepts. The aim of this approach is to aid the human or computer agent in organizing information from multiple sources into clusters according to its “trust features”. Thus the agent can perform complicated trust assessments in real-time situations and cooperate with decision-making software to assist in purchasing activities. We conclude by discussing the implications and advantages of this approach in trust management in traditional and mobile e-commerce applications

Synthesis Cost-Optimal Targeted Mutant Protein Libraries

Protein variant libraries produced by site-directed mutagenesis are a useful tool utilized by protein engineers to explore variants with potentially improved properties, such as activity and stability. These libraries are commonly built by selecting residue positions and alternative beneficial mutations for each position. All possible combinations are then constructed and screened, by incorporating degenerate codons at mutation sites. These degenerate codons often encode additional unwanted amino acids or even STOP codons. Our study aims to take advantage of annealing based recombination of oligonucleotides during synthesis and utilize multiple degenerate codons per mutation site to produce targeted protein libraries devoid of unwanted variants. Toward this goal we created an algorithm to calculate the minimum number of degenerate codons necessary to specify any given amino acid set, and a dynamic programming method that uses this algorithm to optimally partition a DNA target sequence with degeneracies into overlapping oligonucleotides, such that the total cost of synthesis of the target mutant protein library is minimized. Computational experiments show that, for a modest increase in DNA synthesis costs, beneficial variant yields in produced mutant libraries are increased by orders of magnitude, an effect particularly pronounced in large combinatorial libraries

Medium access control mechanisms for high speed metropolitan area networks

In this dissertation novel Medium Access Control mechanisms for High Speed Metropolitan Area networks are proposed and their performance is investigated under the presence of single and multiple priority classes of traffic. The proposed mechanisms are based on the Distributed Queue Dual Bus network, which has been adopted by the IEEE standardization committee as the 802.6 standard for Metropolitan Area Networks, and address most of its performance limitations. First, the Rotating Slot Generator scheme is introduced which uses the looped bus architecture that has been proposed for the 802.6 network. According to this scheme the responsibility for generating slots moves periodically from station to station around the loop. In this way, the positions of the stations relative to the slot generator change continuously, and therefore, there are no favorable locations on the busses. Then, two variations of a new bandwidth balancing mechanism, the NSW_BWB and ITU_NSW are introduced. Their main advantage is that their operation does not require the wastage of channel slots and for this reason they can converge very fast to the steady state, where the fair bandwidth allocation is achieved. Their performance and their ability to support multiple priority classes of traffic are thoroughly investigated. Analytic estimates for the stations\u27 throughputs and average segment delays are provided. Moreover, a novel, very effective priority mechanism is introduced which can guarantee almost immediate access for high priority traffic, regardless of the presence of lower priority traffic. Its performance is thoroughly investigated and its ability to support real time traffic, such as voice and video, is demonstrated. Finally, the performance under the presence of erasure nodes of the various mechanisms that have been proposed in this dissertation is examined and compared to the corresponding performance of the most prominent existing mechanisms

Outer membrane protein genes and their small non-coding RNA regulator genes in Photorhabdus luminescens

INTRODUCTION: Three major outer membrane protein genes of Escherichia coli, ompF, ompC, and ompA respond to stress factors. Transcripts from these genes are regulated by the small non-coding RNAs micF, micC, and micA, respectively. Here we examine Photorhabdus luminescens, an organism that has a different habitat from E. coli for outer membrane protein genes and their regulatory RNA genes. RESULTS: By bioinformatics analysis of conserved genetic loci, mRNA 5'UTR sequences, RNA secondary structure motifs, upstream promoter regions and protein sequence homologies, an ompF -like porin gene in P. luminescens as well as a duplication of this gene have been predicted. Gene loci for micF RNA, as well as OmpC protein and its associated regulatory micC RNA, were not found. Significantly, a sequence bearing the appropriate signatures of the E. coli micA RNA was located. The ompA homolog was previously annotated in P. luminescens. CONCLUSION: Presence of an ompF-like porin in P. luminescens is in keeping with the necessity to allow for passage of small molecules into the cell. The apparent lack of ompC, micC and micF suggests that these genes are not essential to P. luminescens and ompC and micF in particular may have been lost when the organism entered its defined life cycle and partially protected habitat. Control of porin gene expression by RNA may be more prevalent in free- living cells where survival is dependent on the ability to make rapid adjustments in response to environmental stress. Regulation of ompA by micA may have been retained due to a necessity for ompA control during one or both stages of the P. luminescens life cycle. REVIEWERS: This article was reviewed by Tal Dagan (nominated by Dan Graur), Mikhail Gelfand and Anna Gerasimova (nominated by Mikhail Gelfand) and J Peter Gogarten. OPEN PEER REVIEW: Reviewed by Tal Dagan (nominated by Dan Graur), Mikhail Gelfand and Anna Gerasimova (nominated by Mikhail Gelfand) and J Peter Gogarten. For the full reviews, please go to the Reviewers' comments section

Improved Algorithms for Approximate String Matching (Extended Abstract)

The problem of approximate string matching is important in many different areas such as computational biology, text processing and pattern recognition. A great effort has been made to design efficient algorithms addressing several variants of the problem, including comparison of two strings, approximate pattern identification in a string or calculation of the longest common subsequence that two strings share. We designed an output sensitive algorithm solving the edit distance problem between two strings of lengths n and m respectively in time O((s-|n-m|)min(m,n,s)+m+n) and linear space, where s is the edit distance between the two strings. This worst-case time bound sets the quadratic factor of the algorithm independent of the longest string length and improves existing theoretical bounds for this problem. The implementation of our algorithm excels also in practice, especially in cases where the two strings compared differ significantly in length. Source code of our algorithm is available at http://www.cs.miami.edu/\~dimitris/edit_distanceComment: 10 page

“I want my mum to know that I am a good guy...”: A thematic analysis of the accounts of adolescents who exhibit Child-to-Parent Violence in the UK

This qualitative study explores child-to-parent violence (CPV) in the UK based on the accounts of adolescents who exhibit this type of family violence. The key areas of interest concern the familial relationships and contexts within which adolescents are embedded, and their perceptions about their emotional states and how these interplay with CPV. Eight participants were recruited in total from a community sample from two different intervention programmes aiming to tackle CPV in England. Methods included participant-observation, face-to-face interviews and hand-written interviews; all data were analysed thematically. Results suggest that CPV is linked with adverse childhood experiences (ACEs), unsatisfactory relationships with parents, perceived emotional rejection from parents, and emotional dysregulation in young people. In this study, violent behaviour was directed not only against mothers but in all cases against siblings and stepfathers. The findings address the complexity of the subject and the need for tailored, evidence-based interventions in the field of CPV

Statistical and trend analysis of water quality and quantity data for the Strymon River in Greece

Strymon is a transboundary river of Greece, Bulgaria and Former Yugoslav Republic of Macedonia (FYROM) in southeastern Europe. Water quality parameters and the discharge have been monitored each month just 10 km downstream of the river’s entry into Greece. The data of nine water quality variables (T, ECw, DO, SO₄^2-, Na⁺+K⁺, Mg²⁺ , Ca²⁺, NO₃^&#8254;, TP) and the discharge for the period 1980-1997 were selected for this analysis. In this paper a) the time series of monthly values of water quality parameters and the discharge were analysed using statistical methods, b) the existence of trends and the evaluation of the best fitted models were performed and c) the relationships between concentration and loads of constituents both with the discharge were also examined. Boxplots for summarising the distribution of a data set were used. The &#967²-test and the Kolmogorov-Smirnov test were used to select the theoretical distribution which best fitted the data. Simple regression was used to examine the concentration-discharge and the load-discharge relationships. According to the correlation coefficient (r) values the relation between concentrations and discharge is weak (r< 0.592) while the relation between loads and discharge is very strong (r > 0.902). Trends were detected using the nonparametric Spearman’s criterion upon the data for the variables: Q, ECw, DO, SO₄^2-, Na⁺+K⁺ and NO₃^&#8254; on which temporal trend analysis was performed.</p> <p style='line-height: 20px;'><b>Keywords: </b>Strymon river, water quality, discharge, concentration, load, statistics, trend