Commenced in January 2007
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Edition: International
Paper Count: 4

Search results for: Rafał Adamczak

4 Dimensionality Reduction of PSSM Matrix and its Influence on Secondary Structure and Relative Solvent Accessibility Predictions

Authors: Rafał Adamczak

Abstract:

State-of-the-art methods for secondary structure (Porter, Psi-PRED, SAM-T99sec, Sable) and solvent accessibility (Sable, ACCpro) predictions use evolutionary profiles represented by the position specific scoring matrix (PSSM). It has been demonstrated that evolutionary profiles are the most important features in the feature space for these predictions. Unfortunately applying PSSM matrix leads to high dimensional feature spaces that may create problems with parameter optimization and generalization. Several recently published suggested that applying feature extraction for the PSSM matrix may result in improvements in secondary structure predictions. However, none of the top performing methods considered here utilizes dimensionality reduction to improve generalization. In the present study, we used simple and fast methods for features selection (t-statistics, information gain) that allow us to decrease the dimensionality of PSSM matrix by 75% and improve generalization in the case of secondary structure prediction compared to the Sable server.

Keywords: Secondary structure prediction, feature selection, position specific scoring matrix.

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3 Finding Approximate Tandem Repeats with the Burrows-Wheeler Transform

Authors: Agnieszka Danek, Rafał Pokrzywa

Abstract:

Approximate tandem repeats in a genomic sequence are two or more contiguous, similar copies of a pattern of nucleotides. They are used in DNA mapping, studying molecular evolution mechanisms, forensic analysis and research in diagnosis of inherited diseases. All their functions are still investigated and not well defined, but increasing biological databases together with tools for identification of these repeats may lead to discovery of their specific role or correlation with particular features. This paper presents a new approach for finding approximate tandem repeats in a given sequence, where the similarity between consecutive repeats is measured using the Hamming distance. It is an enhancement of a method for finding exact tandem repeats in DNA sequences based on the Burrows- Wheeler transform.

Keywords: approximate tandem repeats, Burrows-Wheeler transform, Hamming distance, suffix array

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2 Climate Change and Food Security: The Legal Aspects with Special Focus on the European Union

Authors: M. Adamczak-Retecka, O. Hołub-Śniadach

Abstract:

Dangerous of climate change is now global problem and as such has a strategic priority also for the European Union. Europe and European citizens try to do their best to cut greenhouse gas emissions, moreover they substantially encourage other nations and regions to follow the same way. The European Commission and a number of Member States have developed adaptation strategies in order to help strengthen EU's resilience to the inevitable impacts of climate change. The EU has long been a driving force in international negotiations on climate change and was instrumental in the development of the UN Framework Convention on Climate Change. As the world's leading donor of development aid, the EU also provides substantial funding to help developing countries tackle climate change problem. Global warming influences human health, biodiversity, ecosystems but also many social and economic sectors. The aim of this paper is to focus on impact of claimant change on for food security. Food security challenges are directly related to globalization, climate change. It means that current and future food policy is exposed to all cross-cutting and that must be linked with environmental and climate targets, which supposed to be achieved. In the 7th EAP —The new general Union Environment Action Program to 2020, called “Living well, within the limits of our planet” EU has agreed to step up its efforts to protect natural capital, stimulate resource efficient, low carbon growth and innovation, and safeguard people’s health and wellbeing– while respecting the Earth’s natural limits.

Keywords: Climate change, EU law, food policy, food security.

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1 Study on Carbon Nanostructures Influence on Changes in Static Friction Forces

Authors: Rafał Urbaniak, Robert Kłosowiak, Michał Ciałkowski, Jarosław Bartoszewicz

Abstract:

The Chair of Thermal Engineering at Poznan University of Technology has been conducted research works on the possibilities of using carbon nanostructures in energy and mechanics applications for a couple of years. Those studies have provided results in a form of co-operation with foreign research centres, numerous publications and patent applications. Authors of this paper have studied the influence of multi-walled carbon nanostructures on changes in static friction arising when steel surfaces were moved. Tests were made using the original test stand consisting of automatically controlled inclined plane driven by precise stepper motors. Computer program created in the LabView environment was responsible for monitoring of the stand operation, accuracy of measurements and archiving the obtained results. Such a solution enabled to obtain high accuracy and repeatability of all conducted experiments. Tests and analysis of the obtained results allowed us to determine how additional layers of carbon nanostructures influenced on changes of static friction coefficients. At the same time, we analyzed the potential possibilities of applying nanostructures under consideration in mechanics.

Keywords: Carbon nanotubes, static friction, dynamic friction.

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