Balance of Polarization in a Hybrid Fiber Optic Sensor

This paper presents the eect of light polarization in a hybrid ber optic sensor. The hybrid sensor is dened as a combination of interferometer sensor and modalmetric sensor. Hybrid sensor system is based on the eect of outputting interferometric sensor of interference as a result of changes made by the modalmetric system. Balance of polarization in the arms of classical interferometer sensor leads to improvement of contrast of interference pattern at the output of the interferometer. Aim of this study is to present a balance light polarization eects in a hybrid system

Dynamic resolution of functionally related gene sets in response to acute heat stress

<p>Abstract</p> <p>Background</p> <p>Using a gene clustering strategy we determined intracellular pathway relationships within skeletal myotubes in response to an acute heat stress stimuli. Following heat shock, the transcriptome was analyzed by microarray in a temporal fashion to characterize the dynamic relationship of signaling pathways.</p> <p>Results</p> <p>Bioinformatics analyses exposed coordination of functionally-related gene sets, depicting mechanism-based responses to heat shock. Protein turnover-related pathways were significantly affected including protein folding, pre-mRNA processing, mRNA splicing, proteolysis and proteasome-related pathways. Many responses were transient, tending to normalize within 24 hours.</p> <p>Conclusion</p> <p>In summary, we show that the transcriptional response to acute cell stress is largely transient and proteosome-centric.</p

Uncovering mechanisms of transcriptional regulations by systematic mining of cis regulatory elements with gene expression profiles

<p>Abstract</p> <p>Background</p> <p>Contrary to the traditional biology approach, where the expression patterns of a handful of genes are studied at a time, microarray experiments enable biologists to study the expression patterns of many genes simultaneously from gene expression profile data and decipher the underlying hidden biological mechanism from the observed gene expression changes. While the statistical significance of the gene expression data can be deduced by various methods, the biological interpretation of the data presents a challenge.</p> <p>Results</p> <p>A method, called CisTransMine, is proposed to help infer the underlying biological mechanisms for the observed gene expression changes in microarray experiments. Specifically, this method will predict potential cis-regulatory elements in promoter regions which could regulate gene expression changes. This approach builds on the MotifADE method published in 2004 and extends it with two modifications: up-regulated genes and down-regulated genes are tested separately and in addition, tests have been implemented to identify combinations of transcription factors that work synergistically. The method has been applied to a genome wide expression dataset intended to study myogenesis in a mouse C2C12 cell differentiation model. The results shown here both confirm the prior biological knowledge and facilitate the discovery of new biological insights.</p> <p>Conclusion</p> <p>The results validate that the CisTransMine approach is a robust method to uncover the hidden transcriptional regulatory mechanisms that can facilitate the discovery of mechanisms of transcriptional regulation.</p

Mutations in TRAF3IP1/IFT54 reveal a new role for IFT proteins in microtubule stabilization

Ciliopathies are a large group of clinically and genetically heterogeneous disorders caused by defects in primary cilia. Here we identified mutations in TRAF3IP1 (TNF Receptor-Associated Factor Interacting Protein 1) in eight patients from five families with nephronophthisis (NPH) and retinal degeneration, two of the most common manifestations of ciliopathies. TRAF3IP1 encodes IFT54, a subunit of the IFT-B complex required for ciliogenesis. The identified mutations result in mild ciliary defects in patients but also reveal an unexpected role of IFT54 as a negative regulator of microtubule stability via MAP4 (microtubule-associated protein 4). Microtubule defects are associated with altered epithelialization/polarity in renal cells and with pronephric cysts and microphthalmia in zebrafish embryos. Our findings highlight the regulation of cytoplasmic microtubule dynamics as a role of the IFT54 protein beyond the cilium, contributing to the development of NPH-related ciliopathies

Identification of Novel Genes and Pathways Regulating SREBP Transcriptional Activity

BACKGROUND: Lipid metabolism in mammals is orchestrated by a family of transcription factors called sterol regulatory element-binding proteins (SREBPs) that control the expression of genes required for the uptake and synthesis of cholesterol, fatty acids, and triglycerides. SREBPs are thus essential for insulin-induced lipogenesis and for cellular membrane homeostasis and biogenesis. Although multiple players have been identified that control the expression and activation of SREBPs, gaps remain in our understanding of how SREBPs are coordinated with other physiological pathways. METHODOLOGY: To identify novel regulators of SREBPs, we performed a genome-wide cDNA over-expression screen to identify proteins that might modulate the transcription of a luciferase gene driven from an SREBP-specific promoter. The results were verified through secondary biological assays and expression data were analyzed by a novel application of the Gene Set Enrichment Analysis (GSEA) method. CONCLUSIONS/SIGNIFICANCE: We screened 10,000 different cDNAs and identified a number of genes and pathways that have previously not been implicated in SREBP control and cellular cholesterol homeostasis. These findings further our understanding of lipid biology and should lead to new insights into lipid associated disorders

Cross-Over between Discrete and Continuous Protein Structure Space: Insights into Automatic Classification and Networks of Protein Structures

Structural classifications of proteins assume the existence of the fold, which is an intrinsic equivalence class of protein domains. Here, we test in which conditions such an equivalence class is compatible with objective similarity measures. We base our analysis on the transitive property of the equivalence relationship, requiring that similarity of A with B and B with C implies that A and C are also similar. Divergent gene evolution leads us to expect that the transitive property should approximately hold. However, if protein domains are a combination of recurrent short polypeptide fragments, as proposed by several authors, then similarity of partial fragments may violate the transitive property, favouring the continuous view of the protein structure space. We propose a measure to quantify the violations of the transitive property when a clustering algorithm joins elements into clusters, and we find out that such violations present a well defined and detectable cross-over point, from an approximately transitive regime at high structure similarity to a regime with large transitivity violations and large differences in length at low similarity. We argue that protein structure space is discrete and hierarchic classification is justified up to this cross-over point, whereas at lower similarities the structure space is continuous and it should be represented as a network. We have tested the qualitative behaviour of this measure, varying all the choices involved in the automatic classification procedure, i.e., domain decomposition, alignment algorithm, similarity score, and clustering algorithm, and we have found out that this behaviour is quite robust. The final classification depends on the chosen algorithms. We used the values of the clustering coefficient and the transitivity violations to select the optimal choices among those that we tested. Interestingly, this criterion also favours the agreement between automatic and expert classifications. As a domain set, we have selected a consensus set of 2,890 domains decomposed very similarly in SCOP and CATH. As an alignment algorithm, we used a global version of MAMMOTH developed in our group, which is both rapid and accurate. As a similarity measure, we used the size-normalized contact overlap, and as a clustering algorithm, we used average linkage. The resulting automatic classification at the cross-over point was more consistent than expert ones with respect to the structure similarity measure, with 86% of the clusters corresponding to subsets of either SCOP or CATH superfamilies and fewer than 5% containing domains in distinct folds according to both SCOP and CATH. Almost 15% of SCOP superfamilies and 10% of CATH superfamilies were split, consistent with the notion of fold change in protein evolution. These results were qualitatively robust for all choices that we tested, although we did not try to use alignment algorithms developed by other groups. Folds defined in SCOP and CATH would be completely joined in the regime of large transitivity violations where clustering is more arbitrary. Consistently, the agreement between SCOP and CATH at fold level was lower than their agreement with the automatic classification obtained using as a clustering algorithm, respectively, average linkage (for SCOP) or single linkage (for CATH). The networks representing significant evolutionary and structural relationships between clusters beyond the cross-over point may allow us to perform evolutionary, structural, or functional analyses beyond the limits of classification schemes. These networks and the underlying clusters are available at http://ub.cbm.uam.es/research/ProtNet.ph

Elongation sensitivity of photonic crystal fibers

We determined theoretically a phase elongation sensitivity of the Photonic Crystal Fibers by means of the Multipole Method. The sensitivity was confirmed experimentally with good agreement for LMA-8 PCF

Elements of Augmented Reality for Vision Systems

The purpose of this article is a discussion about the ongoing research at the Institute of Optoelectronics, Military University of Technology. The aim of the research is obtaining the introduction augmented reality elements in vision systems. Technology of augmented reality in connecting with applied sensor sets can strengthen and expand our sensory modalities. The process of data acquisition and processing can be implemented using variable technologies, appropriate for application. At the conclusion we briefly presented two applications currently under tests

Identification of explosives by matching method in statistical well-chosen measuring points in THz range

Wzrastająca w ostatnim czasie liczba zamachów terrorystycznych z ofiarami śmiertelnymi, którymi są przypadkowi świadkowie zdarzenia, wymusza prace badawcze nad coraz skuteczniejszymi metodami i rozwiązaniami technicznymi usprawniającymi procedury wykrywania zagrożeń związanych z zamachami. Zadanie to jest szczególnie pilne, gdyż terroryści coraz częściej na miejsce potencjalnych zamachów wybierają sytuacje i miejsca, gdzie występuje duże skupisko ludzi i jednocześnie utrudnione są możliwości kontroli osób pod kątem wykrycia niebezpieczeństwa. Celem pracy jest zaprezentowanie metody analizy danych, opartej na wnioskowaniu statystycznym, wspomagającej opracowanie i implementację algorytmu identyfikacji materiałów niebezpiecznych metodą dopasowania właściwości spektralnych w paśmie terahercowym.The increasing interest in the development of identification methods of explosives in THz region over the past few years has been observed because of potential terrorist threats. To determine specific spectra properties of materials, both possible spectroscopic methods — Time Domain Spectroscopy (TDS) and Fourier Transform-Infrared Spectroscopy (FT-IR) are used to analyze different classes of compounds. Results of a single compound separated from the mixture of other natural products have already been published [16, 17]. This paper deals with an identification problem of more than one compound. This task was solved mathematically by means of the following methods: Monte Carlo including principal components analysis (PCA) methods and analytic methods. Investigations were limited to a detector, which is based on a single-frequency Quantum Dot matrix in 0.2-1.3 THz range. The mathematical analysis also includes the atmosphere influence on propagation of THz waves. By means of the presented methods, we indicated fourteen optimal frequency points and next we managed to identify one explosive from a set of ten explosives