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Article ; Online: ARA: a flexible pipeline for automated exploration of NCBI SRA datasets.

Maurya, Anand / Szymanski, Maciej / Karlowski, Wojciech M

2023 Volume 12

Abstract: Background: One of the most effective and useful methods to explore the content of biological databases is searching with nucleotide or protein sequences as a query. However, especially in the case of nucleic acids, due to the large volume of data ... ...

Abstract	Background: One of the most effective and useful methods to explore the content of biological databases is searching with nucleotide or protein sequences as a query. However, especially in the case of nucleic acids, due to the large volume of data generated by the next-generation sequencing (NGS) technologies, this approach is often not available. The hierarchical organization of the NGS records is primarily designed for browsing or text-based searches of the information provided in metadata-related keywords, limiting the efficiency of database exploration. Findings: We developed an automated pipeline that incorporates the well-established NGS data-processing tools and procedures to allow easy and effective sampling of the NCBI SRA database records. Given a file with query nucleotide sequences, our tool estimates the matching content of SRA accessions by probing only a user-defined fraction of a record's sequences. Based on the selected parameters, it allows performing a full mapping experiment with records that meet the required criteria. The pipeline is designed to be easy to operate-it offers a fully automatic setup procedure and is fixed on tested supporting tools. The modular design and implemented usage modes allow a user to scale up the analyses into complex computational infrastructure. Conclusions: We present an easy-to-operate and automated tool that expands the way a user can access and explore the information contained within the records deposited in the NCBI SRA database.
MeSH term(s)	Amino Acid Sequence ; Databases, Factual ; High-Throughput Nucleotide Sequencing ; Metadata ; Nucleotides
Chemical Substances	Nucleotides
Language	English
Publishing date	2023-08-17
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2708999-X
ISSN	2047-217X ; 2047-217X
ISSN (online)	2047-217X
ISSN	2047-217X
DOI	10.1093/gigascience/giad067
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Article: The Influence of Surface Texture of Elements Made of PA6-Based Composites on Anti-Graffiti Effect of Paint Coating.

Mróz, Adrian / Szymański, Maciej / Koch, Paweł / Pawlicki, Marek / Meller, Artur / Przekop, Robert Edward

Materials (Basel, Switzerland)

2024 Volume 17, Issue 9

Abstract: The aim of the work was to investigate the influence of the surface texture of composite based on PA6, intended for wet painting, on the stability of the colour and gloss parameters. The stability of the paint coating was required to be maintained ... ...

Abstract	The aim of the work was to investigate the influence of the surface texture of composite based on PA6, intended for wet painting, on the stability of the colour and gloss parameters. The stability of the paint coating was required to be maintained despite exposure to mechanical stress resulting from attempts to manually remove graffiti stains. The study examined the influence of surface texture on the effectiveness of cleaning. In the case of painted surfaces from which graffiti stains were effectively removed, the roughness, colour parameters and gloss of the paint coating were measured. During the research, it was found that roughness after painting decreased to the value of Ra < 2.00 µm meets aesthetic expectations and at the same time ensures the effective removal of graffiti stains. For this surface, there were no negative effects of the mechanical impact on the textures or quality parameters of the coating as a result of manual graffiti removal. As a result of the conducted research, the recommended maximum values of roughness and textures of the surfaces to be painted were determined in order to ensure a sufficiently low amount of work necessary to effectively remove traces of graffiti.
Language	English
Publishing date	2024-04-23
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	2487261-1
ISSN	1996-1944
ISSN	1996-1944
DOI	10.3390/ma17091951
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Article ; Online: tRNA-Cys gene clusters exhibit high variability in Arabidopsis thaliana.

Szymanski, Maciej / Maurya, Anand / Kopec, Piotr / Karlowski, Wojciech M

BMC plant biology

2023 Volume 23, Issue 1, Page(s) 623

Abstract: Although most of the genes encoding tRNAs in plants are dispersed throughout the genome, a fraction of them form tRNA gene clusters. In Arabidopsis thaliana, the smallest of tRNA clusters on chromosome 5 consists of four tRNA-Cys-GCA genes placed within ... ...

Abstract	Although most of the genes encoding tRNAs in plants are dispersed throughout the genome, a fraction of them form tRNA gene clusters. In Arabidopsis thaliana, the smallest of tRNA clusters on chromosome 5 consists of four tRNA-Cys-GCA genes placed within repeating units of 0.4 kbp. A systematic analysis of the genomic sequences of syntenic regions from various ecotypes of A. thaliana showed that the general structure of the cluster, consisting of a tRNA-Cys pseudogene followed by repeating units containing tRNA-Cys genes, is well conserved. However, there is significant heterogeneity in the number of repeating units between different ecotypes. A unique feature of this cluster is the presence of putative transposable elements (Helitron). In addition, two further tRNA-Cys gene mini-clusters (gene pairs) in A. thaliana were identified. RNA-seq-based evaluation of expression of tRNA-Cys-GCA genes showed a positive signal for 11 out of 13 unique transcripts. An analysis of the conservation of the tRNA-Cys clusters from A. thaliana with the corresponding regions from four other Arabidopsis species suggests a sequence of events that led to the divergence of these regions.
MeSH term(s)	Arabidopsis/genetics ; Base Sequence ; Genome ; RNA, Transfer/genetics ; Multigene Family
Chemical Substances	RNA, Transfer (9014-25-9)
Language	English
Publishing date	2023-12-07
Publishing country	England
Document type	Journal Article
ZDB-ID	2059868-3
ISSN	1471-2229 ; 1471-2229
ISSN (online)	1471-2229
ISSN	1471-2229
DOI	10.1186/s12870-023-04632-x
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Article: Blood Pressure Changes During Mechanical Thrombectomy for Acute Ischemic Stroke Are Associated With Serious Early Treatment Complications: Symptomatic Intracerebral Hemorrhage and Malignant Brain Edema.

Wiącek, Marcin / Szymański, Maciej / Walewska, Klaudia / Bartosik-Psujek, Halina

Frontiers in neurology

2022 Volume 13, Page(s) 884519

Abstract: Background: Symptomatic intracranial hemorrhage (sICH) and malignant brain edema (MBE) are well-known deleterious endovascular treatment (EVT) complications that some studies found to be associated with postprocedural blood pressure (BP) variability. We ...

Abstract	Background: Symptomatic intracranial hemorrhage (sICH) and malignant brain edema (MBE) are well-known deleterious endovascular treatment (EVT) complications that some studies found to be associated with postprocedural blood pressure (BP) variability. We aimed to evaluate their association with periprocedural BP changes, including its intraprocedural decrease. Methods: We retrospectively analyzed the data of 132 consecutive patients that underwent EVT between 1 December 2018 and 31 December 2019, for anterior circulation ischemic stroke. Analyzed predictors of sICH and MBE included non-invasively obtained BP before and 5-min after treatment, intraprocedural relative decreases of BP from baseline, and its post-treatment increases. SICH was defined in accordance with the Safe Implementation of Thrombolysis in Stroke-Monitoring Study (SITS-MOST) criteria and MBE as brain edema with midline shift on the follow-up imaging. We used binary logistic regression analysis to investigate the association of BP parameters and the incidence of sICH and MBE. Results: Among the included patients, 11 (8.3%) developed sICH and 31 (23.5%) MBE. The intraprocedural decrease of mean arterial blood pressure (MAP) was independently associated with MBE occurrence (aOR per 10 mmHg drop from baseline 1.27; 95% CI 1.01-1.60; P = 0.040). Over 40% MAP drop was associated with a higher risk of sICH in the entire cohort (aOR 4.24; 95% CI 1.33-13.51; P = 0.015), but not in the subgroup with successful reperfusion (aOR 2.81; 95% CI 0.64-12.23; P = 0.169). Post-treatment systolic blood pressure (SBP) and MAP elevation above their minimal values during MT are significantly associated with the development of sICH (aOR per 10 mmHg SBP increase 1.78; 95% CI 1.15-2.76; P = 0.010 and aOR per 10 mmHg MAP increase 1.78; 95% CI 1.04-3.03; P = 0.035). Conclusions: In the anterior circulation ischemic stroke patients relative MAP decrease during EVT is associated with a higher risk of MBE occurrence, and over 40% MAP drop with a higher incidence of both MBE and sICH. Post-treatment elevation of SBP and MAP increased the risk of sICH.
Language	English
Publishing date	2022-07-05
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	2564214-5
ISSN	1664-2295
ISSN	1664-2295
DOI	10.3389/fneur.2022.884519
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Article ; Online: Baryon femtoscopy in heavy-ion collisions at ALICE

Szymański Maciej Paweł

EPJ Web of Conferences, Vol 71, p

2014 Volume 00130

Abstract: In this report, femtoscopic measurements with pp, p¯p¯${\rm{\bar p\bar p}}$, pp¯${\rm{p\bar p}}$, pΛ¯${\rm{p}}\bar \Lambda $, p¯Λ${\rm{\bar p}}\Lambda $ and ΛΛ¯$\Lambda \bar \Lambda $ pairs in Pb–Pb collisions at √sNN = 2:76 TeV registered by ALICE at ... ...

Abstract	In this report, femtoscopic measurements with pp, p¯p¯${\rm{\bar p\bar p}}$, pp¯${\rm{p\bar p}}$, pΛ¯${\rm{p}}\bar \Lambda $, p¯Λ${\rm{\bar p}}\Lambda $ and ΛΛ¯$\Lambda \bar \Lambda $ pairs in Pb–Pb collisions at √sNN = 2:76 TeV registered by ALICE at the LHC are presented. Emission source sizes extracted from the correlation analysis with (anti)protons grow with the event multiplicity, as expected. A method to extract the interaction potentials (e.g. for pΛ¯${\rm{p}}\bar \Lambda $ and p¯Λ${\rm{\bar p}}\Lambda $ pairs) based on femtoscopy analysis is discussed. The importance of taking into account the so-called residual correlations induced by pairs contaminated by secondary particles is emphasized for all analyses mentioned above.
Keywords	Physics ; QC1-999 ; Science ; Q
Language	English
Publishing date	2014-04-01T00:00:00Z
Publisher	EDP Sciences
Document type	Article ; Online
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Article: The path to the genetic code.

Szymanski, Maciej / Barciszewski, Jan

Biochimica et biophysica acta. General subjects

2017 Volume 1861, Issue 11 Pt A, Page(s) 2674–2679

Abstract: In December of 1966 the last nucleotide triplet in the genetic code has been assigned (Brenner et al., 1967 [1]) thus completing years of studies aimed at deciphering the nature of the relationship between the sequences of genes and proteins. The end ... ...

Abstract	In December of 1966 the last nucleotide triplet in the genetic code has been assigned (Brenner et al., 1967 [1]) thus completing years of studies aimed at deciphering the nature of the relationship between the sequences of genes and proteins. The end product, the table of the genetic code, was a crowning achievement of the quest to unravel the basic mechanisms underlying functioning of all living organisms on the molecular level.
MeSH term(s)	Amino Acid Sequence/genetics ; Genetic Code/genetics ; Genetics/history ; History, 20th Century ; Humans ; Proteins/genetics
Chemical Substances	Proteins
Language	English
Publishing date	2017-07-14
Publishing country	Netherlands
Document type	Historical Article ; Journal Article ; Research Support, Non-U.S. Gov't ; Review
ZDB-ID	60-7
ISSN	1879-2596 ; 1879-260X ; 1872-8006 ; 1879-2642 ; 1879-2618 ; 1879-2650 ; 0304-4165 ; 0006-3002 ; 0005-2728 ; 0005-2736 ; 0167-4838 ; 1388-1981 ; 0167-4889 ; 0167-4781 ; 0304-419X ; 1570-9639 ; 0925-4439 ; 1874-9399
ISSN (online)	1879-2596 ; 1879-260X ; 1872-8006 ; 1879-2642 ; 1879-2618 ; 1879-2650
ISSN	0304-4165 ; 0006-3002 ; 0005-2728 ; 0005-2736 ; 0167-4838 ; 1388-1981 ; 0167-4889 ; 0167-4781 ; 0304-419X ; 1570-9639 ; 0925-4439 ; 1874-9399
DOI	10.1016/j.bbagen.2017.07.009
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Article: The path to the genetic code

Szymanski, Maciej / Jan Barciszewski

Biochimica et biophysica acta. 2017 Nov., v. 1861, no. 11

2017

Abstract	In December of 1966 the last nucleotide triplet in the genetic code has been assigned (Brenner et al., 1967 [1]) thus completing years of studies aimed at deciphering the nature of the relationship between the sequences of genes and proteins. The end product, the table of the genetic code, was a crowning achievement of the quest to unravel the basic mechanisms underlying functioning of all living organisms on the molecular level.
Keywords	genes ; genetic code ; proteins
Language	English
Dates of publication	2017-11
Size	p. 2674-2679.
Publishing place	Elsevier B.V.
Document type	Article
ZDB-ID	840755-1
ISSN	0304-4165
ISSN	0304-4165
DOI	10.1016/j.bbagen.2017.07.009
Database	NAL-Catalogue (AGRICOLA)

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Article ; Online: The use of modern measurement techniques for designing pro ecological constructions

Wieczorowski Michał / Gapiński Bartosz / Szymański Maciej / Rękas Artur

E3S Web of Conferences, Vol 19, p

2017 Volume 03013

Abstract: In the paper some possibilities of application modern length and angle metrology techniques to design constructions that support ecology were presented. The paper is based on a project where a lighter bus and train car seat was developed. Different ... ...

Abstract	In the paper some possibilities of application modern length and angle metrology techniques to design constructions that support ecology were presented. The paper is based on a project where a lighter bus and train car seat was developed. Different options were presented including static and dynamic photogrammetry, computed tomography and thermography. Research related with dynamic behaviour of designed structures gave input to determine deformation of a seat and passengers sitting on it during communication accidents. Works connected to strength of construction elements made it possible to optimize its dimensions maintaining proper durability. Metrological actions taken in relation to production machines and equipment enabled to better recognize phenomena that take place during manufacturing process and to correct its parameters, what in turns also contributed to slim down the construction.
Keywords	Environmental sciences ; GE1-350
Subject code	670
Language	English
Publishing date	2017-01-01T00:00:00Z
Publisher	EDP Sciences
Document type	Article ; Online
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Article ; Online: Assessing the 5S ribosomal RNA heterogeneity in Arabidopsis thaliana using short RNA next generation sequencing data.

Szymanski, Maciej / Karlowski, Wojciech M

Acta biochimica Polonica

2016 Volume 63, Issue 4, Page(s) 841–844

Abstract: In eukaryotes, ribosomal 5S rRNAs are products of multigene families organized within clusters of tandemly repeated units. Accumulation of genomic data obtained from a variety of organisms demonstrated that the potential 5S rRNA coding sequences show a ... ...

Abstract	In eukaryotes, ribosomal 5S rRNAs are products of multigene families organized within clusters of tandemly repeated units. Accumulation of genomic data obtained from a variety of organisms demonstrated that the potential 5S rRNA coding sequences show a large number of variants, often incompatible with folding into a correct secondary structure. Here, we present results of an analysis of a large set of short RNA sequences generated by the next generation sequencing techniques, to address the problem of heterogeneity of the 5S rRNA transcripts in Arabidopsis and identification of potentially functional rRNA-derived fragments.
MeSH term(s)	Arabidopsis/genetics ; Base Sequence ; Gene Expression ; High-Throughput Nucleotide Sequencing ; Inverted Repeat Sequences ; RNA, Plant/genetics ; RNA, Ribosomal, 5S/genetics ; Sequence Analysis, RNA ; Sequence Homology, Nucleic Acid
Chemical Substances	RNA, Plant ; RNA, Ribosomal, 5S
Language	English
Publishing date	2016-11-22
Publishing country	Poland
Document type	Journal Article
ZDB-ID	595762-x
ISSN	1734-154X ; 0001-527X
ISSN (online)	1734-154X
ISSN	0001-527X
DOI	10.18388/abp.2016_1367
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Article ; Online: Baryon femtoscopy considering residual correlations as a tool to extract strong interaction potentials

Szymański Maciej / Kisiel Adam / Zbroszczyk Hanna

EPJ Web of Conferences, Vol 95, p

2015 Volume 04064

Abstract: In this article, the analysis of baryon-antibaryon femtoscopic correlations is presented. In particular, it is shown that taking into account residual correlations is crucial for the description of pΛ¯$\bar \Lambda $ and p̄Λ correlation functions ... ...

Abstract	In this article, the analysis of baryon-antibaryon femtoscopic correlations is presented. In particular, it is shown that taking into account residual correlations is crucial for the description of pΛ¯$\bar \Lambda $ and p̄Λ correlation functions measured by the STAR experiment in Au–Au collisions at the centre-of-mass energy per nucleon pair √sNN = 200 GeV. This approach enables to obtain pΛ¯$\bar \Lambda $ (p̄Λ) source size consistent with the sizes extracted from correlations in pΛ (p̄Λ¯$\bar \Lambda $) and lighter pair systems as well as with model predictions. Moreover, with this analysis it is possible to derive the unknown parameters of the strong interaction potential for baryon-antibaryon pairs under several assumptions.
Keywords	Science ; Q ; Physics ; QC1-999
Publishing date	2015-01-01T00:00:00Z
Publisher	EDP Sciences
Document type	Article ; Online
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