Improving the performance of the iterative signature algorithm for the identification of relevant patterns

The iterative signature algorithm (ISA) has become very attractive to detect co-regulated genes from microarray data matrices and can be a useful tool for the identification of similar patterns in many other kinds of numerical data matrices. Nevertheless, its algorithmic strategy exhibits some limitations since it is based on statistical behavior of the average and considers averages weighted by scores not necessarily positive. Hence, we propose to take the median instead of the average and to use absolutes scores in ISA's structure. Furthermore, a generalized function is also introduced in the algorithm in order to improve its algorithmic strategy for detecting high value or low value biclusters. The effects of these simple modifications on the performance of the biclustering algorithm are evaluated through an experimental comparative study involving synthetic data sets and real data from the organism Saccharomyces cerevisiae. The experimental results show that the proposed variations of ISA outperform the original version in many situations. Absolute scores in ISA are shown to be essential for the correct interpretation of the biclusters found by the algorithm. The median instead of the average turns the biclustering algorithm more resilient to outliers in the data sets. Copyright © 2011 Wiley Periodicals, Inc

Correlations in interference and diffraction

Quantum formalism of Fraunhofer diffraction is obtained. The state of the diffraction optical field is connected with the state of the incident optical field by a diffraction factor. Based on this formalism, correlations of the diffraction modes are calculated with different kinds of incident optical fields. Influence of correlations of the incident modes on the diffraction pattern is analyzed and an explanation of the ''ghost'' diffraction is proposed.Comment: 16 pages, 2 figures, Latex, to appear in J. Mod. Op

Genetic algorithms for positron lifetime data

Recently, genetic algorithms have been applied for ultrafast optical spectrometry in systems with several convoluted lifetimes. We apply these algorithms and compare the results with POSFIT (by Kirkegaard and Eldrup) and LT programme (by Kansy). The analysis was applied to three types of samples: molybdenum monocrystals, Czochralski-grown silicon with oxygen precipitates, Si with under-surface cavities obtained by He + H ion co- implantation. In all three tests, the genetic algorithm performs very well, in particular for short lifetimes. Further developments to model the resolution function in genetic algorithms are needed

Tytuł prawny do składowiska odpadów

The aim of this article is to analyse the “legal title” of a real property on which a landfill is located. Firstly, it must be established who is under obligation to hold such a title, concerning the phase of landfill’s exploitation. Secondly, it must be examined what kind of a legal title is required for the obliged person. The analysed issue may determine the possibility of execution of the landfill owner’s obligations.Celem opracowania jest analiza „tytułu prawnego” nieruchomości, na której znajduje się składowisko odpadów. Następnie ustalić należy, czy, i jeżeli tak – to jaki, tytuł prawny jest wymagany do prowadzenia składowiska odpadów, począwszy od chwili jego założenia do etapu eksploatacji. Analizowane zagadnienie ma istotne znaczenie dla  problematyki egzekwowania na prowadzącym składowisko odpadów ciążących na nim obowiązków

Ocena czynności śródbłonka naczyniowego - gdzie jesteśmy, dokąd zmierzamy?

Śródbłonek naczyniowy odgrywa niezwykle istotną rolę w organizmie. Pojedyncza warstwa komórek wyścielająca ścianę naczyń wydziela wiele substancji o działaniu wazoaktywnym, wpływającym na procesy krzepnięcia i fibrynolizy, biorących udział w regulacji procesów zapalnych, a także w oddziaływaniach między komórkami i ścianą naczyń. Dysfunkcja śródbłonka naczyniowego wyrażająca się zaburzeniem tych złożonych procesów odgrywa zasadniczą rolę w patogenezie miażdżycy. Obecnie dysponujemy biochemicznymi i fizycznymi metodami umożliwiającymi ocenę czynności śródbłonka naczyniowego. Oznaczenie biodostępności tlenku azotu, stężenia czynnika von Willebranda lub cząstek adhezyjnych koreluje z występowaniem czynników ryzyka chorób sercowo-naczyniowych. Wśród metod fizycznych uznaną metodą oceny funkcji śródbłonka jest określenie stopnia rozszerzenia tętnicy ramiennej po uprzedniej okluzji mankietem manometru tętnic przedramienia lub proksymalnej części ramienia (FMD). Stosuje się również techniki oceniające sztywność naczyń (PWA, PWV). Pośrednią metodą oceny dysfunkcji śródbłonka jest określenie grubości błony środkowej i błony wewnętrznej tętnicy szyjnej (IMT). Zwiększenie grubości tego kompleksu koreluje z dysfunkcją endotelium. Duże nadzieje pokłada się w nowej metodzie oceniającej czynność śródbłonka w odpowiedzi na reaktywne przekrwienie (RH-PAT). Metody fizyczne, zwłaszcza nieinwazyjne, są kluczowe dla wczesnej identyfikacji osób zagrożonych wystąpieniem zdarzeń sercowo-naczyniowych, dlatego konieczny jest dalszy ich rozwój. (Folia Cardiologica Excerpta 2010; 5, 5: 292-297

Influence of deep-freezing on the autofluorescent properties of human plasma proteins

Background. Fluorescence-based techniques are powerful and valuable tools for studying biological materials. Fluorescence spectroscopy is one of these techniques which measures autofluorescence from a sample containing components such as proteins. The aim of this study was to evaluate the influence of deep freezing on spectroscopic properties of human plasma using fluorescence spectroscopy.Patients, materials and methods. The study group consisted of patients admitted to the Department of Cardiology and Internal Medicine at the University Hospital in Bydgoszcz, due to a preliminary diagnosis of acute coronary syndrome. The overall group comprised 27 patients. From each patient, 4 ml of blood was taken to obtainplasma that was used for further examination. In order to measure plasma spectroscopic properties, a Hitachi F-7000 spectrofluorimeter was used. The received results were analysed and evaluated with Origin 9.0 (OriginLab).Results. Spectroscopic analysis of human plasma before and after freezing allowed us to divide plasma samples into three different subgroups, depending on their fluorescent properties. The first subgroup consisted of plasma samples, which showed entirely differently in spectroscopic analysis after one week of deep-freezing. The second subgroup of plasma samples showed partial changes in the measurements of autofluorescence, and in the third subgroup freezing-resistant plasma samples were included.Conclusions. It seems that the process of deep-freezing could affect the autofluorescent properties of human plasma proteins. The explanation of the specific mechanisms responsible for the change of plasma fluorescent properties during the process of deep-freezing requires further elucidation

Efficient analysis in planet transit surveys

With the growing number of projects dedicated to the search for extrasolar planets via transits, there is a need to develop fast, automatic, robust methods with a statistical background in order to efficiently do the analysis. We propose a modified analysis of variance (AoV) test particularly suitable for the detection of planetary transits in stellar light curves. We show how savings of labor by a factor of over 10 could be achieved by the careful organization of computations. Basing on solid analytical statistical formulation, we discuss performance of our and other methods for different signal-to-noise and number of observations.Comment: 7 pages, to be published in MNRAS, downloadable software from http://www.camk.edu.pl/~alex/#softwar

Information management in DNA replication modeled by directional, stochastic chains with memory

[EN] Stochastic chains represent a key variety of phenomena in many branches of science within the context of information theory and thermodynamics. They are typically approached by a sequence of independent events or by a memoryless Markov process. Stochastic chains are of special significance to molecular biology, where genes are conveyed by linear polymers made up of molecular subunits and transferred from DNA to proteins by specialized molecular motors in the presence of errors. Here, we demonstrate that when memory is introduced, the statistics of the chain depends on the mechanism by which objects or symbols are assembled, even in the slow dynamics limit wherein friction can be neglected. To analyze these systems, we introduce a sequence-dependent partition function, investigate its properties, and compare it to the standard normalization defined by the statistical physics of ensembles. We then apply this theory to characterize the enzyme-mediated information transfer involved in DNA replication under the real, non-equilibrium conditions, reproducing measured error rates and explaining the typical 100-fold increase in fidelity that is experimentally found when proofreading and edition take place. Our model further predicts that approximately 1 kT has to be consumed to elevate fidelity in one order of magnitude. We anticipate that our results are necessary to interpret configurational order and information management in many molecular systems within biophysics, materials science, communication, and engineering. Published by AIP Publishing.It is a pleasure to thank J. M. R. Parrondo and D. G. Aleja for fruitful discussion. This work was supported the Spanish Ministry of Economy and Competitiveness (Grant Nos. MAT2013-49455-EXP and MAT2015-71806-R).Arias-Gonzalez, JR. (2016). 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Statistics of the Microwave Background Anisotropies Caused by the Squeezed Cosmological Perturbations

It is likely that the observed large-angular-scale anisotropies in the microwave background radiation are induced by the cosmological perturbations of quantum-mechanical origin. Such perturbations are now placed in squeezed vacuum quantum states and, hence, are characterized by large variances of their amplitude. The statistical properties of the anisotropies should reflect the underlying statistics of the squeezed vacuum quantum states. The theoretical variances for the temperature angular correlation function are derived and described quantitatively. It is shown that they are indeed large. Unfortunately, these large theoretical statistical uncertainties will make the extraction of cosmological information from the measured anisotropies a much more difficult problem than we wanted it to be.Comment: 33 pages REVTEX 3.0, Direct all correspondence to L. P. Grishchuk, [email protected]