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Article ; Online: Advancements in bioinformatics and computational biology: 15th annual Polish Bioinformatic Society Symposium.

Zyla, Joanna / Tobiasz, Joanna / Mika, Justyna / Łabaj, Paweł P / Gruca, Aleksandra

Bioinformatics advances

2024 Volume 4, Issue 1, Page(s) vbad187

Abstract: The Polish Bioinformatic Society (PTBI) Symposium convenes annually at leading Polish Universities, and in 2023, the Silesian University of Technology hosted participants from all over the world. The 15th PTBI Symposium, spanning a 3-day duration and ... ...

Abstract	The Polish Bioinformatic Society (PTBI) Symposium convenes annually at leading Polish Universities, and in 2023, the Silesian University of Technology hosted participants from all over the world. The 15th PTBI Symposium, spanning a 3-day duration and divided into four scientific sessions, gathered around 100 participants and centered on research related to machine learning in biomedicine, RNA structure algorithms, next-generation sequencing methods, and microbiome analysis but was not limited to only those topics. The meeting also recognized outstanding research conducted by young scientists by awarding the best poster and best talk. Finally, the awards for the best PhD, MSc, and BSc thesis in bioinformatics defended in Poland were given. This report summarizes the key highlights and outcomes of the meeting.
Language	English
Publishing date	2024-01-13
Publishing country	England
Document type	Journal Article
ISSN	2635-0041
ISSN (online)	2635-0041
DOI	10.1093/bioadv/vbad187
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Article ; Online: Insights from analyses of low complexity regions with canonical methods for protein sequence comparison.

Jarnot, Patryk / Ziemska-Legiecka, Joanna / Grynberg, Marcin / Gruca, Aleksandra

Briefings in bioinformatics

2022 Volume 23, Issue 5

Abstract: Low complexity regions are fragments of protein sequences composed of only a few types of amino acids. These regions frequently occur in proteins and can play an important role in their functions. However, scientists are mainly focused on regions ... ...

Abstract	Low complexity regions are fragments of protein sequences composed of only a few types of amino acids. These regions frequently occur in proteins and can play an important role in their functions. However, scientists are mainly focused on regions characterized by high diversity of amino acid composition. Similarity between regions of protein sequences frequently reflect functional similarity between them. In this article, we discuss strengths and weaknesses of the similarity analysis of low complexity regions using BLAST, HHblits and CD-HIT. These methods are considered to be the gold standard in protein similarity analysis and were designed for comparison of high complexity regions. However, we lack specialized methods that could be used to compare the similarity of low complexity regions. Therefore, we investigated the existing methods in order to understand how they can be applied to compare such regions. Our results are supported by exploratory study, discussion of amino acid composition and biological roles of selected examples. We show that existing methods need improvements to efficiently search for similar low complexity regions. We suggest features that have to be re-designed specifically for comparing low complexity regions: scoring matrix, multiple sequence alignment, e-value, local alignment and clustering based on a set of representative sequences. Results of this analysis can either be used to improve existing methods or to create new methods for the similarity analysis of low complexity regions.
MeSH term(s)	Algorithms ; Amino Acid Sequence ; Amino Acids/genetics ; Cluster Analysis ; Proteins/chemistry ; Proteins/genetics ; Sequence Alignment ; Sequence Analysis, Protein/methods
Chemical Substances	Amino Acids ; Proteins
Language	English
Publishing date	2022-07-29
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2068142-2
ISSN	1477-4054 ; 1467-5463
ISSN (online)	1477-4054
ISSN	1467-5463
DOI	10.1093/bib/bbac299
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Article ; Online: Prawa własności intelektualnej jako składniki majątków małżonków w świetle art. 33 pkt 9 k.r.o.

Błażej Bugajski / Aleksandra Nowak-Gruca

Ruch Prawniczy, Ekonomiczny i Socjologiczny, Vol 82, Iss

2020 Volume 3

Abstract: Motywem podjęcia rozważań na ten temat praw własności intelektualnej jako składników majątków małżonków jest dokonujący się przewrót technologiczny, w wyniku którego zmienia się własność i struktura czynników produkcji a aktywa intelektualne zyskująi ... ...

Abstract	Motywem podjęcia rozważań na ten temat praw własności intelektualnej jako składników majątków małżonków jest dokonujący się przewrót technologiczny, w wyniku którego zmienia się własność i struktura czynników produkcji a aktywa intelektualne zyskująi będą zyskiwać na znaczeniu. W artykule przedstawiono w pierwszej kolejności kwestie terminologiczne związane z pojęciami „własność intelektualna”, „dobra niematerialne” i „prawo własności intelektualnej”. Dopiero po wyjaśnieniu tego zagadnienia omówiono podstawowe założenia konstrukcyjne majątkowych ustrojów małżeńskich i wynikające z nich zasady przyporządkowywania praw własności intelektualnej, które ustanawia Kodeks rodzinny i opiekuńczy. W uwagach końcowych zaprezentowano ocenę obowiązujących przepisów Kodeksu rodzinnego i opiekuńczego, które dotyczą prawa własności intelektualnej.
Keywords	prawo własności intelektualnej ; Kodeks rodzinny i opiekuńczy ; majątkowy ustrój małżeński ; prawa autorskie ; prawa pokrewne ; prawa własności przemysłowej ; Law ; K ; Social Sciences ; H
Language	English
Publishing date	2020-09-01T00:00:00Z
Publisher	Adam Mickiewicz University, Poznan
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Are the Classical Symptoms of Hypertension in Children Still Sensitive Enough?

Mirecka, Julia / Stańczyk, Małgorzata / Olejniczak, Aleksandra / Zamojska, Justyna / Gruca, Marta / Kowara-Dzik, Karolina / Wosiak, Agnieszka / Szadkowska, Agnieszka / Smolewska, Elżbieta / Tkaczyk, Marcin

Clinical pediatrics

2024 , Page(s) 99228231225318

Abstract: The available literature is scarce on the initial symptoms of arterial hypertension in children. Our study aimed to analyze the initial clinical profile of patients referred to the hospital with suspected hypertension and those diagnosed with ... ...

Abstract	The available literature is scarce on the initial symptoms of arterial hypertension in children. Our study aimed to analyze the initial clinical profile of patients referred to the hospital with suspected hypertension and those diagnosed with hypertension for the first time during a hospitalization for other reasons. This study was a retrospective analysis of medical records in 471 patients. More than half of the patients showed no symptoms. The most common symptom reported was a headache-28% (132) of patients. The diagnosis of elevated blood pressure or hypertension was more frequent in asymptomatic patients (
Language	English
Publishing date	2024-01-23
Publishing country	United States
Document type	Journal Article
ZDB-ID	207678-0
ISSN	1938-2707 ; 0009-9228
ISSN (online)	1938-2707
ISSN	0009-9228
DOI	10.1177/00099228231225318
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Article ; Online: Assessment of Cardiovascular Risk Factors in Patients with Juvenile Idiopathic Arthritis.

Gruca, Marta / Zamojska, Justyna / Niewiadomska-Jarosik, Katarzyna / Wosiak, Agnieszka / Stasiak, Aleksandra / Sikorska, Karolina / Stańczyk, Jerzy / Smolewska, Elżbieta

Nutrients

2023 Volume 15, Issue 7

Abstract: Introduction: The aim of this study was to assess the exposure to cardiovascular disease (CVD) risk factors in patients with juvenile idiopathic arthritis (JIA). Intima-media complex thickness (IMT), selected metabolic parameters and health behaviors ... ...

Abstract	Introduction: The aim of this study was to assess the exposure to cardiovascular disease (CVD) risk factors in patients with juvenile idiopathic arthritis (JIA). Intima-media complex thickness (IMT), selected metabolic parameters and health behaviors were assessed in the course of the study. Methods: The study included study group, which consisted of 45 patients with JIA and 37 healthy age- and sex-matched children in the control group. Analyses in both groups included anthropometric parameters, laboratory tests, IMT and a questionnaire on exposure to modifiable CVD risk factors. Results: The study confirmed that CVD risk factors were present in both groups of patients. Significantly more children with JIA had abnormal BMI ( Conclusions: Patients with JIA are exposed to cardiovascular risk factors equally to their healthy peers. Ideal cardiovascular health should be pursued in the pediatric population with particular attention paid to patients with chronic diseases (i.e., JIA). The application of carotid artery IMT measurement in the assessment of CVD risk requires studies on a larger group of patients.
MeSH term(s)	Humans ; Child ; Cardiovascular Diseases/etiology ; Cardiovascular Diseases/complications ; Arthritis, Juvenile/complications ; Arthritis, Juvenile/metabolism ; Risk Factors ; Carotid Intima-Media Thickness ; Heart Disease Risk Factors ; Risk Assessment
Language	English
Publishing date	2023-03-30
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	2518386-2
ISSN	2072-6643 ; 2072-6643
ISSN (online)	2072-6643
ISSN	2072-6643
DOI	10.3390/nu15071700
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Article ; Online: Intraoperative Hypotension and Its Association with Postoperative Acute Kidney Injury in Patients Undergoing Pancreaticoduodenectomy: A 5-Year, Single-Center, Retrospective Cohort Study.

Putowski, Zbigniew / Majewska, Karolina / Gruca, Karol / Zimnoch, Aleksandra / Szczepańska, Anna / Krzych, Łukasz J / Jabłońska, Beata / Mrowiec, Sławomir

Medical science monitor : international medical journal of experimental and clinical research

2023 Volume 29, Page(s) e938945

Abstract: BACKGROUND Intraoperative hypotension (IOH) is a common phenomenon in high-risk surgery and is often linked to postoperative acute kidney injury (AKI). Pancreaticoduodenectomy (PD), or Whipple's procedure, is a lengthy and complex surgical procedure to ... ...

Abstract	BACKGROUND Intraoperative hypotension (IOH) is a common phenomenon in high-risk surgery and is often linked to postoperative acute kidney injury (AKI). Pancreaticoduodenectomy (PD), or Whipple's procedure, is a lengthy and complex surgical procedure to remove the head of the pancreas, gallbladder and bile duct, and the first part of the duodenum. This retrospective 5-year study from a single center in Poland included 303 patients who underwent PD and evaluated IOH as a factor associated with AKI. MATERIAL AND METHODS We analyzed perioperative data to assess how various IOH thresholds can predict AKI (according to KDIGO criteria). Several IOH definitions were applied, including absolute and relative thresholds, based on the mean arterial pressure (MAP). Statistically significant IOH thresholds were inserted into multivariable logistic regression models with previously established independent variables. RESULTS We included 303 patients over a 5-year period (2016-2021). There were 58 (19.1%) cases of postoperative AKI. MAP <55 mmHg and a maximal% drop from preinduction MAP were the only IOH definitions associated with AKI. Multivariable analysis revealed that max% drop from preinduction MAP (per 10%, OR=1.65; AUROC=0.70) was the IOH definition best suited for AKI prediction in patients undergoing PD. CONCLUSIONS In patients undergoing PD, it is important to prevent excessive blood pressure drops in regards to preinduction blood pressure values. In this cohort, relative IOH thresholds were better suited for prediction of AKI than the absolute IOH thresholds.
MeSH term(s)	Humans ; Retrospective Studies ; Cohort Studies ; Pancreaticoduodenectomy/adverse effects ; Intraoperative Complications ; Postoperative Complications/etiology ; Hypotension ; Acute Kidney Injury/complications ; Risk Factors
Language	English
Publishing date	2023-04-11
Publishing country	United States
Document type	Journal Article
ZDB-ID	1439041-3
ISSN	1643-3750 ; 1234-1010
ISSN (online)	1643-3750
ISSN	1234-1010
DOI	10.12659/MSM.938945
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Article ; Online: Data- and expert-driven rule induction and filtering framework for functional interpretation and description of gene sets.

Gruca, Aleksandra / Sikora, Marek

Journal of biomedical semantics

2017 Volume 8, Issue 1, Page(s) 23

Abstract: Background: High-throughput methods in molecular biology provided researchers with abundance of experimental data that need to be interpreted in order to understand the experimental results. Manual methods of functional gene/protein group interpretation ...

Abstract	Background: High-throughput methods in molecular biology provided researchers with abundance of experimental data that need to be interpreted in order to understand the experimental results. Manual methods of functional gene/protein group interpretation are expensive and time-consuming; therefore, there is a need to develop new efficient data mining methods and bioinformatics tools that could support the expert in the process of functional analysis of experimental results. Results: In this study, we propose a comprehensive framework for the induction of logical rules in the form of combinations of Gene Ontology (GO) terms for functional interpretation of gene sets. Within the framework, we present four approaches: the fully automated method of rule induction without filtering, rule induction method with filtering, expert-driven rule filtering method based on additive utility functions, and expert-driven rule induction method based on the so-called seed or expert terms - the GO terms of special interest which should be included into the description. These GO terms usually describe some processes or pathways of particular interest, which are related to the experiment that is being performed. During the rule induction and filtering processes such seed terms are used as a base on which the description is build. Conclusion: We compare the descriptions obtained with different algorithms of rule induction and filtering and show that a filtering step is required to reduce the number of rules in the output set so that they could be analyzed by a human expert. However, filtering may remove information from the output rule set which is potentially interesting for the expert. Therefore, in the study, we present two methods that involve interaction with the expert during the process of rule induction. Both of them are able to reduce the number of rules, but only in the case of the method based on seed terms, each of the created rule includes expert terms in combination with the other terms. Further analysis of such combinations may provide new knowledge about biological processes and their combination with other pathways related to genes described by the rules. A suite of Matlab scripts that provide the functionality of a comprehensive framework for the rule induction and filtering presented in this study is available free of charge at: http://rulego.polsl.pl/framework .
Language	English
Publishing date	2017-06-26
Publishing country	England
Document type	Journal Article
ZDB-ID	2548651-2
ISSN	2041-1480 ; 2041-1480
ISSN (online)	2041-1480
ISSN	2041-1480
DOI	10.1186/s13326-017-0129-x
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Article ; Online: MAINE: a web tool for multi-omics feature selection and rule-based data exploration.

Gruca, Aleksandra / Henzel, Joanna / Kostorz, Iwona / Stęclik, Tomasz / Wróbel, Łukasz / Sikora, Marek

Bioinformatics (Oxford, England)

2021 Volume 38, Issue 6, Page(s) 1773–1775

Abstract: Summary: Patient multi-omics datasets are often characterized by a high dimensionality; however, usually only a small fraction of the features is informative, that is change in their value is directly related to the disease outcome or patient survival. ... ...

Abstract	Summary: Patient multi-omics datasets are often characterized by a high dimensionality; however, usually only a small fraction of the features is informative, that is change in their value is directly related to the disease outcome or patient survival. In medical sciences, in addition to a robust feature selection procedure, the ability to discover human-readable patterns in the analyzed data is also desirable. To address this need, we created MAINE-Multi-omics Analysis and Exploration. The unique functionality of MAINE is the ability to discover multidimensional dependencies between the selected multi-omics features and event outcome prediction as well as patient survival probability. Learned patterns are visualized in the form of interpretable decision/survival trees and rules. Availability and implementation: MAINE is freely available at maine.ibemag.pl as an online web application. Supplementary information: Supplementary data are available at Bioinformatics online.
MeSH term(s)	Humans ; Multiomics ; Maine ; Software
Language	English
Publishing date	2021-12-23
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	1422668-6
ISSN	1367-4811 ; 1367-4803
ISSN (online)	1367-4811
ISSN	1367-4803
DOI	10.1093/bioinformatics/btab862
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Article ; Online: Konieczne cechy utworu. Uwagi po 20 latach obowiązywania ustawy o prawie autorskim i prawach pokrewnych

Aleksandra Nowak-Gruca

Ruch Prawniczy, Ekonomiczny i Socjologiczny, Vol 77, Iss

2015 Volume 2

Abstract: W artykule przedstawiono nowe spojrzenie na centralny i najpoważniejszy problem, przed którym stoi dziś prawo autorskie, a jest nim stwierdzanie istnienia koniecznych cech utworu. Na tle krótkiej charakterystyki przedmiotu ochrony prawa autorskiego oraz ... ...

Abstract	W artykule przedstawiono nowe spojrzenie na centralny i najpoważniejszy problem, przed którym stoi dziś prawo autorskie, a jest nim stwierdzanie istnienia koniecznych cech utworu. Na tle krótkiej charakterystyki przedmiotu ochrony prawa autorskiego oraz koncepcji doktrynalnych i orzeczeń sądowych dotykających kwestii istnienia cechy „twórczości o indywidualnym charakterze”, zwrócono uwagę na bezsilność nauki i praktyki w zakresie definiowania przedmiotu ochrony prawa autorskiego. W artykule zaakcentowano potrzebę poszerzania perspektywy badawczej o dorobek innych nauk, w tym nie tylko takich, jak filozofia i psychologia, ale także o zdobycze rozwijającej się ostatnio dynamicznie nowej dyscypliny, jaką jest neuroestetyka. Artykuł w założeniu ma stanowić głos w dyskusji i punkt wyjścia do dalszych studiów nad tematem w kontekście poszukiwania rozwiązań problemu ustalania tzw. granicznego poziomu twórczości.
Keywords	prawo autorskie ; przedmiot prawa autorskiego ; pojęcie utworu ; cecha twórczości w prawie autorskim ; oryginalność i indywidualność dzieła w prawie autorskim ; kryzys pojęcia utworu ; Law ; K ; Social Sciences ; H
Language	English
Publishing date	2015-01-01T00:00:00Z
Publisher	Adam Mickiewicz University, Poznan
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Common low complexity regions for SARS-CoV-2 and human proteomes as potential multidirectional risk factor in vaccine development.

Gruca, Aleksandra / Ziemska-Legiecka, Joanna / Jarnot, Patryk / Sarnowska, Elzbieta / Sarnowski, Tomasz J / Grynberg, Marcin

BMC bioinformatics

2021 Volume 22, Issue 1, Page(s) 182

Abstract: Background: The rapid spread of the COVID-19 demands immediate response from the scientific communities. Appropriate countermeasures mean thoughtful and educated choice of viral targets (epitopes). There are several articles that discuss such choices in ...

Abstract	Background: The rapid spread of the COVID-19 demands immediate response from the scientific communities. Appropriate countermeasures mean thoughtful and educated choice of viral targets (epitopes). There are several articles that discuss such choices in the SARS-CoV-2 proteome, other focus on phylogenetic traits and history of the Coronaviridae genome/proteome. However none consider viral protein low complexity regions (LCRs). Recently we created the first methods that are able to compare such fragments. Results: We show that five low complexity regions (LCRs) in three proteins (nsp3, S and N) encoded by the SARS-CoV-2 genome are highly similar to regions from human proteome. As many as 21 predicted T-cell epitopes and 27 predicted B-cell epitopes overlap with the five SARS-CoV-2 LCRs similar to human proteins. Interestingly, replication proteins encoded in the central part of viral RNA are devoid of LCRs. Conclusions: Similarity of SARS-CoV-2 LCRs to human proteins may have implications on the ability of the virus to counteract immune defenses. The vaccine targeted LCRs may potentially be ineffective or alternatively lead to autoimmune diseases development. These findings are crucial to the process of selection of new epitopes for drugs or vaccines which should omit such regions.
MeSH term(s)	COVID-19 Vaccines ; Coronavirus Nucleocapsid Proteins/immunology ; Epitopes, B-Lymphocyte/immunology ; Epitopes, T-Lymphocyte/immunology ; Humans ; Phosphoproteins/immunology ; Phylogeny ; Proteome ; RNA-Dependent RNA Polymerase/immunology ; Risk Factors ; SARS-CoV-2/genetics ; Sequence Homology ; Spike Glycoprotein, Coronavirus/immunology ; Viral Nonstructural Proteins/immunology
Chemical Substances	COVID-19 Vaccines ; Coronavirus Nucleocapsid Proteins ; Epitopes, B-Lymphocyte ; Epitopes, T-Lymphocyte ; Phosphoproteins ; Proteome ; Spike Glycoprotein, Coronavirus ; Viral Nonstructural Proteins ; nucleocapsid phosphoprotein, SARS-CoV-2 ; spike protein, SARS-CoV-2 ; Nsp3 protein, SARS-CoV (EC 2.7.7.48) ; RNA-Dependent RNA Polymerase (EC 2.7.7.48)
Language	English
Publishing date	2021-04-08
Publishing country	England
Document type	Journal Article
ZDB-ID	2041484-5
ISSN	1471-2105 ; 1471-2105
ISSN (online)	1471-2105
ISSN	1471-2105
DOI	10.1186/s12859-021-04017-7
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