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1

Influence of sprinkler irrigation and nitrogen fertilization on the quality of malt and wort from barley grains

Błażewicz J., Żarski J., Dudek S., Kuśmierek-Tomaszewska R.

Infrastruktura i Ekologia Terenów Wiejskich

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2017

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nr IV/1

1469--1481

EN

The aim of the research was the evaluation of sprinkler irrigation and nitrogen fertilization on some selected features of the quality of malt and wort from ‘Marthe’ and ‘Mauritia’ malting barley grains. The field experiment was carried out in the years 2010-2012 at the Research Station of the University of Science and Technology in Mochełek near Bydgoszcz. As a result of 3-year field experiment and laboratory test of grain, malt and wort, it was found that introducing sprinkler irrigation into the production process of malting barley is a step justified by the obtained quality effects. It was found that in the case of irrigated malting barley cultivations nitrogen fertilization at the rate of 30 kg·ha-1 provides (in relation to control, non-irrigated treatment) the highest values of such parameters as weight of the technical barley crops, content of protein, extractivity of Pilsen type malt, amount of obtained wort and simplified mashing efficiency. The combination of sprinkler irrigation of malting barley plants with their nitrogen fertilization at the increased rates of 60 and 90 kg·ha-1, resulted in the following effect – high mass of the usable grain of crops remained but their quality deteriorated. Malt produced from malting barley fertilized with nitrogen at the rates of 60 and 90 kg·ha-1, in spite of applied sprinkler irrigation, was characterized by unacceptable – from the technological point of view - increased content of protein in malt in the amount of over 11.5% d.m., as well as huge decrease in malt extractivity (even by 2%) and lower, simplified mashing efficiency (below 70%).

2

Zawartość ksantohumolu w polskich piwach

Toboła D., Stompor M., Błażewicz J., Anioł M.

Przemysł Chemiczny

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2014

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T. 93, nr 8

1447-1450

PL

Zbadano zawartość ksantohumolu (XN) w 27 piwach polskich oraz dla porównania w 8 wybranych piwach niemieckich. Do wydzielenia analitu zastosowano ekstrakcję micelarną. Jego zawartość oznaczono za pomocą wysokosprawnej chromatografii cieczowej z detekcją diodową (HPLC-DAD). W celu pełnej charakterystyki piw określono ich właściwości fizykochemiczne i zbadano zależność pomiędzy tymi właściwościami a zawartością XN, która w piwach polskich mieściła się w zakresie 0,006–0,22 mg/L. Największą ilość XN stwierdzono w piwach ciemnych oraz jasnych niefiltrowanych o zawartości ekstraktu powyżej 12,5% mas.

EN

Twenty seven Polish and 8 German beers were studied for xanthohumol content by cloud point extn. with high-performance liq. chromatogr. and diode array detection. The largest amts. of xanthohumol (up to 0.22 mg/L) were found in the dark and unfiltered light beers with an ext. content 12.5% by mass or more.

3

Simplified mashing efficiency. Novel method for optimization of food industry wort production with the use of adjuncts

Szwed Ł. P., Tomaszewska-Ciosk E., Błażewicz J.

Polish Journal of Chemical Technology

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2014

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Vol. 16, nr 3

36--39

EN

Malt extracts and malt concentrates have a broad range of application in food industry. Those products are obtained by methods similar to brewing worts. The possible reduction of cost can be achieved by application of malt substitutes likewise in brewing industry. As the malt concentrates for food industry do not have to fulfill strict norms for Beer production it is possible to produce much cheaper products. It was proved that by means of mathematic optimization it is possible to determine the optimal share of unmalted material for cheap yet effective production of wort.

4

Preprocessing and Storing High - Throughput Sequencing Data

Świercz A., Bosak B., Chłopkowski M., Hoffa A., Kasprzak M., Kurowski M., Piontek T., Błażewicz J.

Computational Methods in Science and Technology

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2014

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Vol. 20, No. 1

9--20

EN

DNA sequencing is a process of recognizing DNA sequences of genomes. The process consists in reading short sequences, that are subsequences of a genome, and merging them into longer sequences, preferably the whole genome. In the first phase even billions of short sequences are read at once. To simplify and speed up the second phase, we develop a pipeline of preprocessing the initial set of short sequences that is removing low quality reads and duplicated reads.We also propose a method for preliminary joining overlapping sequences, which resulted in decreasing the cardinality of initial sets to 13.9% and 27.8%. We also examine possible ways to store the huge amount of experimental data. We compare different compression methods, from which the best appeared to be DSRC, developed for special type of text files containing short sequences and their quality. We test the parameters for TCP data transferring to find the best transfer rate.

5

Internet shopping optimization problem

Błażewicz J., Kovalyov M. Y., Musiał J., Urbański A. P., Wojciechowski A.

International Journal of Applied Mathematics and Computer Science

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2010

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Vol. 20, no 2

385-390

EN

A high number of Internet shops makes it difficult for a customer to review manually all the available offers and select optimal outlets for shopping. A partial solution to the problem is brought by price comparators which produce price rankings from collected offers. However, their possibilities are limited to a comparison of offers for a single product requested by the customer. The issue we investigate in this paper is a multiple-item multiple-shop optimization problem, in which total expenses of a customer to buy a given set of items should be minimized over all available offers. In this paper, the Internet Shopping Optimization Problem (ISOP) is defined in a formal way and a proof of its strong NP-hardness is provided. We also describe polynomial time algorithms for special cases of the problem.

6

Cerberus: A New Information Retrieval Tool for Marine Metagenomics

Radom M., Kottmann R., Rybarczyk A., Formanowicz P., Szachniuk M., Glöckner F. O., Błażewicz J.

Foundations of Computing and Decision Sciences

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2010

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Vol. 35, No. 2

107-126

EN

The number of papers published every year in scientific journals is growing tremendously, especially in biological sciences. Keeping the track of a given branch of science is therefore a difficult task. This was one of the reasons for developing the classification tool we called Cerberus. The classification categories may correspond to some areas of research defined by the user. We have used the tool to classify papers as containing marine metagenomic, terrestrial metagenomic or non-metagenomic information. Cerberus is based on special filters using weighted domain vocabularies. Depending on the number of occurrences of the keywords from the vocabularies in the paper, the program classifies the paper to a predefined category. This classification can precede the information extraction since it can reduce the number of papers to be analyzed. Classification of papers using the method we propose results in an accurate and precise result set of articles that are relevant to the scientist. This can reduce the resources needed to find the data required in ones field of studies.

7

Flexibility of Dicer Studied by Implicit Solvent Molecular Dynamics Simulations

Sarzyńska J., Mickiewicz A., Miłostan M., Łukasiak P., Błażewicz J., Figlerowicz M., Kuliński T.

Computational Methods in Science and Technology

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2010

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Vol. 16, No. 1

97-104

EN

Dicer is an enzyme responsible for processing double-stranded RNAs and plays a key role in an RNAi mechanism. Structural insight into the Dicer is provided by the crystal structure of eukaryotic Dicer from Giardia intestinalis. It has been proposed that the structure has three structurally rigid regions that are connected by the flexible hinges. Flexibility of the Dicer is believed to be a critical feature for its function. Spatial arrangement of the RNA-recognition and the catalytic regions is crucial for producing small RNAs of defined length. It has been suggested that in the Giardia Dicer a Platform domain may help in specific arrangement of these regions. To learn more about the role of the Platform domain in Giardia Dicer, we have performed molecular dynamics (MD) simulations of the whole Dicer (WT Dicer) and the Dicer with a deleted platform domain (delta Plf Dicer). The MD simulations were carried out in an implicit solvent model with two implementations of analytic Generalized Born (GB) solvation model in CHARMM: GBMV (Generalized Born using Molecular Volume) and GBSW (Generalized Born with simple Switching). To detect the key global motions of the Dicer, a principal component analysis (PCA) of the obtained MD trajectories has been used. To further explore the motion of the Dicer, we performed a domain motion analysis with the DYNDOM program. The simulations show that both WT Dicer and delta Plf Dicer display flexibility which can be described as a movement of two or three domains. The removal of the Platform substantially changed the flexibility and arrangement of these domains. During the MD simulations of delta Plf Dicer an large movement of the RNA-recognition domain was observed.

8

Some remarks on evaluating the quality of the multiple sequence alignment based on the BAliBASE benchmark

Błażewicz J., Formanowicz P., Wojciechowski P.

International Journal of Applied Mathematics and Computer Science

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2009

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Vol. 19, no 4

675-678

EN

BAliBASE is one of the most widely used benchmarks for multiple sequence alignment programs. The accuracy of alignment methods is measured by bali score-an application provided together with the database. The standard accuracy measures are the Sum of Pairs (SP) and the Total Column (TC). We have found that, for non-core block columns, results calculated by bali score are different from those obtained on the basis of the formal definitions of the measures. We do not claim that one of these measures is better than the other, but they are definitely different. Such a situation can be the source of confusion when alignments obtained using various methods are compared. Therefore, we propose a new nomenclature for the measures of the quality of multiple sequence alignments to distinguish which one was actually calculated. Moreover, we have found that the occurrence of a gap in some column in the first sequence of the reference alignment causes column discarding.

9

The Knapsack-Lightening problem and its application to scheduling HRT tasks

Nawrocki J.R., Complak W., Błażewicz J., Kopczyńska S., Maćkowiak M.

Bulletin of the Polish Academy of Sciences. Technical Sciences

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2009

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Vol. 57, nr 1

71-77

EN

In hard real-time systems timeliness is as important as functional correctness. Such systems contain so called hard real-time tasks (HRT tasks) which must be finished by a given deadline. One of the methods of scheduling of HRT tasks is periodic loading introduced by Schweitzer, Dror, and Trudeau. The paper presents an extension to that method which allows for deterministic utilization of cache memory in hard real-time systems. It is based on a new version of the Knapsack problem named Knapsack-Lightening. In the paper the Knapsack-Lightening problem is defined, its complexity is analyzed, and an exact algorithm along with two heuristics are presented. More-over the application of the Knapsack-Lightening problem to scheduling HRT tasks is described.

10

Graph reduction and its application to DNA sequence assembly

Błażewicz J., Kasprzak M.

Bulletin of the Polish Academy of Sciences. Technical Sciences

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2008

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Vol. 56, nr 1

65-70

EN

The results presented here are twofold. First, a heuristic algorithm is proposed which, through removing some unnecessary arcs from a digraph, tends to reduce it into an ad joint and thus simplifies the search for a Hamiltonian cycle. Second, a heuristic algorithm for DNA sequence assembly is proposed, which uses a graph model of the problem instance, and incorporates two independent procedures of reducing the set of arcs - one of them being the former algorithm. Finally, results of tests of the assembly algorithm on parts of chromosome arm 2R of Drosophila melanogaster are presented.

11

On the computational complexity of designing DNA randomizations in a combinatorial protein experiment

Błażewicz J., Dziurdza B., Markiewicz W. T., Oguz C.

Foundations of Computing and Decision Sciences

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2007

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Vol. 32, No. 3

185-197

EN

In combinatorial protein experiments based on phage display and similar methods, protein libraries are constructed by expressing a partially randomized DNA (gene) libraries. Since the distribution of proteins in the output library depends on nucleotides frequencies in DNA library one has to adjust them carefully taking into account diversity-completeness trade-off and results from possible previous cycles of experiments (i.e. knowledge about sequences that have been already obtained and tested). The approach considered in this paper allows to maximize the number of new amino acid sequences physically generated in each cycle of the experiment. The mathematical model of the described approach is presented and its computational complexity is analyzed.

12

3D-Judge : a metaserver approach to protein structure prediction

Jaśkowski W., Błażewicz J., Łukasiak P., Miłostan M., Krasnogor N.

Foundations of Computing and Decision Sciences

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2007

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Vol. 32, No. 1

3-14

EN

Analysing arid predicting the detailed three dimensional conformation of protein structures is a critical and important task within structural bioinformatics with impact on other fields, e.g.. drug design and delivery, sensing technologies, etc. Unfortunately, it is hard to identify one methodology that will give the best prediction of the three-dimensional structure for any sequence. That is, some predictors are best suited for some sequences and not for others. In trying to address this drawback of current prediction algorithms the research community introduced the concept of protein prediction metaservers. In this paper we propose a new metaserver method called 3D-Judge that uses an artificial neural network (ANN) to select the best model from among models produced by individual servers. The fundamental innovation we introduce is that the AXN is not only used to decide which models and servers to use as good predictions but, crucially, it is also used to analyse and "remember" the past performances of the servers it has access to. Thus, our method acts as both a kind of majority voting algorithm, by selecting models arising from different servers based on their mutual similarity, and also a reinforced learning method that takes cues from historical data of previously solved structures. We train and evaluate our metaserver based on previous GASP results and we compare SD-Judge with a popular and effective metaserver, namely. 3D-Jury. The obtained results indicate that 3D-Judge is competitive with 3D-Jury, outperforming it on many cases. We also present a discussion on future extensions to 3D-Judge.

13

New machine learning methods for prediction of protein secondary structures

Błażewicz J., Łukasiak P., Wilk S.

Control and Cybernetics

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2007

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Vol. 36, no 1

183-201

EN

The first and probably the most important step in predicting the tertiary structure of proteins from its primary structure is to predict as many as possible secondary structures in a protein chain. Secondary structure prediction problem has been known for almost a quarter of century. In this paper, new machine learning methods such as LAD, LEM2, and MODLEM have been used for secondary protein structure prediction with the aim to choose the best among them which will be later parallelized in order to handle a huge amount of data sets.

14

On graph theoretical models for peptide sequence assembly

Błażewicz J., Borowski M., Formanowicz P., Głowacki T.

Foundations of Computing and Decision Sciences

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2005

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Vol. 30, No. 3

183-191

EN

The amino acid sequences of proteins determine their structure and functionality, hence methods for reading such sequences are crucial for many areas of biological sciences. Obviously, the genetic information encoding proteins is written in DNA however, knowing gene sequences is not always sufficient for determining the corresponding amino acid sequences. Since direct methods for reading amino acid seqeunces allow for determination of only very short fragments, some methods for assembly of these fragments are required. In this paper, we show and analyze some graph theoretic models of the peptide sequence assembly process.

15

Computational methods in diagnostics of chronic hepatitis C

Kędziora P., Figlerowicz M., Formanowicz P., Alejska M., Jackowiak P., Malinowska N., Frątczak A., Błażewicz J.

Bulletin of the Polish Academy of Sciences. Technical Sciences

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2005

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Vol. 53, nr 3

273-281

EN

Despite the considerable progress that has recently been made in medicine, the treatment of viral infections is still a problem remaining to be solved. This especially concerns infections caused by newly emerging patogenes such as: human immunodeficiency virus, hepatitis C virus or SARS-coronavirus. There are several lines of evidence that the unusual genetic polymorphism of these viruses is responsible for the observed therapeutic difficulties. In order to determine whether some parameters describing a very complex and variable viral population can be used as prognostic factors during antiviral treatment computational methods were applied. To this end, the structure of the viral population and virus evolution in the organisms of two patients suffering from chronic hepatitis C were analyzed. Here we demonstrated that phylogenetic trees and Hamming distances best reflect the differences between virus populations present in the organisms of patients who responded positively and negatively to the applied therapy. Interestingly, the obtained results suggest that based on the elaborated method df virus population analysis one can predict the final outcome of the treatment even before it has started.

16

On the complexity of the Double Digest Problem

Błażewicz J., Burke E., Jaroszewski M., Kasprzak M., Paliswiat B., Pryputniewicz P.

Control and Cybernetics

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2004

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Vol. 33, no 1

133-140

EN

The problem of genome mapping is considered. It is showed that the Double Digest Problem (DDP) is NP-hard in its search version, while its decision version is trivially easy.

17

A tabu search strategy for finding low energy structures of proteins in HP - model

Błażewicz J., Łukasiak P., Miłostan M., Dill K.

Computational Methods in Science and Technology

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2004

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Vol. 10, nr 1

7-19

EN

HP-model is one of the most successful and well-studied simplified lattice models of protein folding. It uses mathematical abstraction of proteins for hiding many aspects of the folding process and works as hypothesis generator. Due to the NP-hardness results of the protein folding problem many approximation algorithms, have been used to solve it. In the paper, the method for finding low energy conformations of proteins, based on the tabu search strategy, has been proposed. The algorithm has been extensively tested and the tests showed its very good performance.

18

Evolutionary algorithm for a reconstruction of NOE paths in NMR spectra of RNA chains

Błażewicz J., Szachniuk M., Wojtowicz A.

Bulletin of the Polish Academy of Sciences. Technical Sciences

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2004

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Vol. 52, nr 3

221-230

EN

Resonance-assignment remains one of the hardest stages in RNA tertiary structure determination with the use of Nuclear Magnetic Resonanse spectroscopy. We propose an evolutionary algorithm being a tool for an automatization of the procedure. NOE pathway, which determines the assignments, is constructed during an analysis of possible connections between resonances within aromatic and anomeric region of 2D-NOESY spectra resulting from appropriate NMR experiments. Computational tests demonstrate the performance of the evolutionary algorithm as compared with the exact branch-and-cut procedure applied for the experimental and simulated spectral data for RNA molecules.

19

Artificial evolution. An algorithm for an exploration of the amino acid sequences space

Błażewicz J., Dziurdza B., Markiewicz W. T.

Foundations of Computing and Decision Sciences

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2003

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Vol. 28, No. 4

195-209

EN

Artifical evolution methods are useful tools in designing of drugs and proteins with the desired properties. One of the applications is searching for new proteins which have the required features. Due to some disadvantages of known artificial evolution methods, such as phage display or SELEX, the new approach to artificial evolution experiment is being studied. The mathematical model for this approach is introduced and the interesting classes of efficient randomization patterns are defined The corresponding algorithm to find them is also presented. The model allows to plan an artificial evolution experiment and makes this new approach efficient. The introduced model has led to the new optimization problem: Efficient Randomization one, for which an exact algorithm is described.

20

Szeregowanie zadań elastycznych

Błażewicz J., Kovalyov M., Machowiak M., Trystram D., Węglarz J.

Zeszyty Naukowe. Automatyka / Politechnika Śląska

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2002

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z. 134

67-79

PL

Przedstawiono tutaj problem szeregowania n niezależnych zadań w systemie procesorów równoległych. Zadania są elastyczne, tj. zadanie może być wykonywane przez kilka procesorów jednocześnie oraz prędkość wykonywania zadania jest nieliniową funkcją od ilości procesorów przydzielonych do niego. Całkowita liczba procesorów w systemie wynosi m i jest to górna granica liczby procesorów, które mogą być używane przez wszystkie zadania w tym samym czasie. Dodatkowym założeniem jest podzielność zadań oraz możliwość zmiany liczby procesorów przydzielonych do zadania w trakcie jego wykonywania. Celem jest znalezienie uszeregowania, dla którego czas zakończenia wszystkich zadań jest najkrótszy z możliwych. Prezentowany jest prosty algorytm o złożoności 0(n), rozwiązujący ten problem w przypadku, kiedy wszystkie funkcje prędkości wykonywania są wypukłe. Jeżeli funkcje te są wszystkie wklęsłe, przedstawiono algorytm pakowania prostokątów (PACK), który rozwiązuje ten problem w czasie wielomianowym.

EN

The problem of optimal scheduling n independent tasks on a parallel processor system is studied. The tasks are malleable, i.e. a task may be executed by several processors simultaneously and the processing speed of a task is a non-linear function of the number of processors allotted to it. The total number of processors is m and it is an upper bound on the number of processors that can be used by all the tasks simultaneously. It is assumed that the tasks are preemptable and the number of processors allotted to one task may change during its execution. The objective is to find a schedule for which the makespan, is minimized. An 0(n) algorithm is presented to solve this problem when all the processing speed functions are convex. If these functions are all concave the rectangles packing (PACK) algorithm is presented, which solves the problem in polynomial time.