Identification Of New Types Research Articles

Enhancing the Radiative Rate in III−V Semiconductor Plasmonic Core−Shell Nanowire Resonators

We investigate the radiative properties of plasmonic core-shell nanowire resonators and, using boundary element method calculations, demonstrate enhanced radiative decay rate by up to 3500 times in nanoscale compound semiconductor/metal cavities. Calculation of the local density of optical states enables identification of new types of modes in cavities with mode volumes on the order of 10(-4)(λ/n)(3). These modes dramatically enhance the radiative decay rate and significantly modify the polarization of far-field emission.

A new target for proteasome inhibitors: FoxM1

Importance of the field: The proteasome is responsible for ubiquitin- and ATP-dependent proteolysis of cellular proteins. The latest advances in proteasome studies led to the development of proteasome inhibitors as drugs against human cancer. It has been shown that proteasome inhibitors selectively kill cancer, but not normal cells. However, the exact mechanisms of the anticancer activity of proteasome inhibitors are not well understood. The oncogenic transcription factor Forkhead Box M1 (FoxM1) is overexpressed in a majority of human carcinomas, while its expression is usually low in normal cells. In addition, FoxM1 may also drive tumor invasion, angiogenesis and metastasis. For these reasons, FoxM1 is an attractive target for anticancer drugs.Areas covered in this review: My aim is to discuss recent publications that point out novel mechanism of action of proteasome inhibitors. In addition, I describe the identification of new types of proteasome inhibitors, called thiazole antibiotics. Using a cell-based screening system, the thiazole antibiotics siomycin A and thiostrepton were isolated as inhibitors of FoxM1 transcriptional activity and expression. Paradoxically, it has been shown that these drugs also stabilize the expression of other proteins and act as proteasome inhibitors in vitro. Moreover, it was found that well-known proteasome inhibitors, such as MG115, MG132 and bortezomib, inhibit FoxM1 transcriptional activity and FoxM1 expression.What the reader will gain: It has been shown that proteasome inhibitors suppress FoxM1 expression and simultaneously induce apoptosis in human tumor cell lines. This review describes the correlation between negative regulation of FoxM1 by proteasome inhibitors and apoptosis, and suggests that negative regulation of FoxM1 is a universal feature of these drugs and may contribute to their anticancer activity.Take home message: Oncogenic transcription factor FoxM1 is upregulated in a majority of human cancers, suggesting that growth of cancer cells may depend on FoxM1 activity. A short time ago, it has been shown that proteasome inhibitors simultaneously inhibit FoxM1 expression and induce apoptosis in human cancer cells. This effect may explain specificity of proteasome inhibitors to induce apoptosis in cancer, but not in normal cells. Now, it is critical to determine the role of suppression of FoxM1 in apoptosis induced by proteasome inhibitors and to establish how significant the inhibition of FoxM1 is for the anticancer activity of proteasome inhibitors.

A new measurement of sequence conservation

BackgroundUnderstanding sequence conservation is important for the study of sequence evolution and for the identification of functional regions of the genome. Current studies often measure sequence conservation based on every position in contiguous regions. Therefore, a large number of functional regions that contain conserved segments separated by relatively long divergent segments are ignored. Our goal in this paper is to define a new measurement of sequence conservation such that both contiguously conserved regions and discontiguously conserved regions can be detected based on this new measurement. Here and in the following, conserved regions are those regions that share similarity higher than a pre-specified similarity threshold with their homologous regions in other species. That is, conserved regions are good candidates of functional regions and may not be always functional. Moreover, conserved regions may contain long and divergent segments.ResultsTo identify both discontiguously and contiguously conserved regions, we proposed a new measurement of sequence conservation, which measures sequence similarity based only on the conserved segments within the regions. By defining conserved segments using the local alignment tool CHAOS, under the new measurement, we analyzed the conservation of 1642 experimentally verified human functional non-coding regions in the mouse genome. We found that the conservation in at least 11% of these functional regions could be missed by the current conservation analysis methods. We also found that 72% of the mouse homologous regions identified based on the new measurement are more similar to the human functional sequences than the aligned mouse sequences from the UCSC genome browser. We further compared BLAST and discontiguous MegaBLAST with our method. We found that our method picks up many more conserved segments than BLAST and discontiguous MegaBLAST in these regions.ConclusionsIt is critical to have a new measurement of sequence conservation that is based only on the conserved segments in one region. Such a new measurement can aid the identification of better local "orthologous" regions. It will also shed light on the identification of new types of conserved functional regions in vertebrate genomes [1].

Application-Level Traffic Monitoring and an Analysis on IP Networks

Traditional traffic identification methods based on well-known port numbers are not appropriate for the identification of new types of Internet applications. This paper proposes a new method to identify current Internet traffic, which is a preliminary but essential step toward traffic characterization. We categorized most current network-based applications into several classes according to their traffic patterns. Then, using this categorization, we developed a flow grouping method that determines the application name of traffic flows. We have incorporated our method into NG-MON, a traffic analysis system, to analyze Internet traffic between our enterprise network and the Internet, and characterized all the traffic according to their application types.