PCA and K-Means decipher genome

In this paper, we aim to give a tutorial for undergraduate students studying statistical methods and/or bioinformatics. The students will learn how data visualization can help in genomic sequence analysis. Students start with a fragment of genetic text of a bacterial genome and analyze its structure. By means of principal component analysis they ``discover'' that the information in the genome is encoded by non-overlapping triplets. Next, they learn how to find gene positions. This exercise on PCA and K-Means clustering enables active study of the basic bioinformatics notions. Appendix 1 contains program listings that go along with this exercise. Appendix 2 includes 2D PCA plots of triplet usage in moving frame for a series of bacterial genomes from GC-poor to GC-rich ones. Animated 3D PCA plots are attached as separate gif files. Topology (cluster structure) and geometry (mutual positions of clusters) of these plots depends clearly on GC-content.Comment: 18 pages, with program listings for MatLab, PCA analysis of genomes and additional animated 3D PCA plot

Vibration based damage identification of a scale-model steel frame structure subjected to bolt connection failures

Large-span steel frame structures prove to be an ideal choice for their speed of construction, relatively low cost, strength, durability and structural design flexibility. For this type of structure, the beam-column connections are critical for its structural integrity and overall stability. This is because a steel frame generally fails first at its connectors, due to the change in stress redistribution with adjacent members and material related failures, caused by various factors such as fire, seismic activity or material deterioration. Since particular attention is required at a steel frame’s connection points, this study explores the applicability of a comprehensive structural health monitoring (SHM) method to identify early damage and prolong the lifespan of connection points of steel frames. An impact hammer test was performed on a scale-model steel frame structure, recording its dynamic response to the hammer strike via an accelerometer. The testing procedure included an intact scenario and two damage scenarios by unfastening four bolt connections in an accumulating order. Based entirely on time-domain experimental data for its calibration, an Auto Regressive Average Exogenous (ARMAX) model is used to create a simple and accurate model for vibration simulation. The calibrated ARMAX model is then used to identify various bolt-connection related damage scenarios via R2 value. The findings in this study suggest that the proposed time-domain approach is capable of identifying structural damage in a parsimonious manner and can be used as a quick or initial solution

Does prophylactic sotalol and magnesium decrease the incidence of atrial fibrillation following coronary artery bypass surgery: a propensity-matched analysis

BACKGROUND: Atrial fibrillation can occur in up to 40% of patients undergoing coronary surgery. METHODS: We retrospectively analysed 103 consecutive coronary surgery patients under the care of one surgeon between April 2003 and September 2003. These patients received 40 mg of sotalol orally twice daily from the first post-operative day for 6 weeks and 2 g of magnesium intravenously immediately post surgery and on the first post-operative day. We developed a propensity score for the probability of receiving sotalol and magnesium after coronary surgery. 89 patients from the sotalol and magnesium group were successfully matched with 89 unique coronary surgery patients who did not receive either sotalol or magnesium with an identical propensity score. RESULTS: Preoperative characteristics were well matched between groups. There was no significant difference with respect to in-hospital mortality between groups (sotalol and magnesium 1.1% versus control 4.5%; p = 0.17). The incidence of atrial fibrillation in the sotalol and magnesium group was 13.5% compared to 27.0% in the controls (p = 0.025). CONCLUSION: The combination of sotalol and magnesium can significantly reduce the incidence of post-operative atrial fibrillation following coronary surgery

Qualitative characterization of healthcare wastes

The biological hazard inherent in the clinical wastes should be considered during the management and treatment process as well as the disposal into the environment. In this chapter, the risks associated with the clinical wastes as well as the management of these wastes are discussed. The chapter focused on reviewing the types of healthcare wastes generated from hospitals and clinics as well as the regulations and management practices used for these wastes. Moreover, the health risk associated with the infectious agents which have the potential to be transmitted into the environment. It has appeared that the clinical wastes represent real hazards for the human health and the environment if they were not managed properly

Optically programmable gate array

The Optically Programmable Gate Array (OPGA), an optical version of a conventional FPGA, benefits from a direct parallel interface between an optical memory and a logic circuit. The OPGA utilizes a holographic memory accessed by an array of VCSELs to program its logic. An active pixel sensor array incorporated into the OPGA chip makes it possible to optically address the logic in a very short time allowing for rapid dynamic reconfiguration. Combining spatial and shift multiplexing to store the configuration pages in the memory, the OPGA module can be made compact. The reconfiguration capability of the OPGA can be applied to solve more efficiently problems in pattern recognition and database search

PCA Beyond The Concept of Manifolds: Principal Trees, Metro Maps, and Elastic Cubic Complexes

Multidimensional data distributions can have complex topologies and variable local dimensions. To approximate complex data, we propose a new type of low-dimensional ``principal object'': a principal cubic complex. This complex is a generalization of linear and non-linear principal manifolds and includes them as a particular case. To construct such an object, we combine a method of topological grammars with the minimization of an elastic energy defined for its embedment into multidimensional data space. The whole complex is presented as a system of nodes and springs and as a product of one-dimensional continua (represented by graphs), and the grammars describe how these continua transform during the process of optimal complex construction. The simplest case of a topological grammar (``add a node'', ``bisect an edge'') is equivalent to the construction of ``principal trees'', an object useful in many practical applications. We demonstrate how it can be applied to the analysis of bacterial genomes and for visualization of cDNA microarray data using the ``metro map'' representation. The preprint is supplemented by animation: ``How the topological grammar constructs branching principal components (AnimatedBranchingPCA.gif)''.Comment: 19 pages, 8 figure

Elastic Maps and Nets for Approximating Principal Manifolds and Their Application to Microarray Data Visualization

Principal manifolds are defined as lines or surfaces passing through ``the middle'' of data distribution. Linear principal manifolds (Principal Components Analysis) are routinely used for dimension reduction, noise filtering and data visualization. Recently, methods for constructing non-linear principal manifolds were proposed, including our elastic maps approach which is based on a physical analogy with elastic membranes. We have developed a general geometric framework for constructing ``principal objects'' of various dimensions and topologies with the simplest quadratic form of the smoothness penalty which allows very effective parallel implementations. Our approach is implemented in three programming languages (C++, Java and Delphi) with two graphical user interfaces (VidaExpert http://bioinfo.curie.fr/projects/vidaexpert and ViMiDa http://bioinfo-out.curie.fr/projects/vimida applications). In this paper we overview the method of elastic maps and present in detail one of its major applications: the visualization of microarray data in bioinformatics. We show that the method of elastic maps outperforms linear PCA in terms of data approximation, representation of between-point distance structure, preservation of local point neighborhood and representing point classes in low-dimensional spaces.Comment: 35 pages 10 figure

Речеповеденческие стратегии межкультурной коммуникации

Данное исследование посвящено изучению речеповеденческих стратегий в контексте межкультурной коммуникации в методике преподавания английского языка с помощью аутентичных видеороликов. Исследование затрагивает значимые источники образовательных ценностей старшеклассников. Целью исследования является разработка методики обучения студентов. Исследование позволяет сделать вывод: есть некоторые стратегии, которым следует обучать на уроках английского языка для успешной межкультурной коммуникации.This research deals with a study of speech-behavioral strategies in the context of intercultural communication in the methodology of teaching English through authentic videos. The study touches upon the significant sources of educational values of high school students. The purpose of the study is to develop a methodology for teaching students. The research arrives at a conclusion: there are some strategies should be taught at the lessons of English for successful intercultural communication

Phenotypic biomonitoring using multivariate £ow cytometric analysis of multi-stained microorganisms

Abstract A new method for monitoring phenotypic profiles of pure cultures and complex microbial communities was evaluated. The approach was to stain microorganisms with a battery of fluorescent dyes prior to flow cytometry analysis (FCM) and to analyse the data using multivariate methods, including principal component analysis and partial least squares. The FCM method was quantitatively evaluated using different mixtures of pure cultures as well as microbial communities. The results showed that the method could quantitatively and reproducibly resolve both populations and communities of microorganisms with 5% abundance in a diverse microbial background. The feasibility of monitoring complex microbial communities over time during the biodegradation of naphthalene using the FCM method was demonstrated. The biodegradation of naphthalene occurred to differing extents in microcosms representing three different types of aromatic-contaminated groundwater and a sample of bio-basin water. The FCM method distinguished each of these four microbial communities. The phenotypic profiles were compared with genotypic profiles generated by random-amplified polymorphic DNA analysis. The genotypic profiles of the microbial communities described only the microbial composition, and not their functional change, whereas the phenotypic profiles seemed to contain information on both the composition and the functional change of the microorganisms. Furthermore, event analysis of the FCM data showed that microbial communities with initially differing compositions could converge towards a similar composition if they had a capacity for high levels of degradation, whereas microbial communities with similar initial compositions could diverge if they differed in biodegrading ability.

The underpotential deposition that should not be : Cu(1x1) on Au(111)

Peer reviewedPostprin