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3. Structure of betweenness uniform graphs with low values of betweenness centrality

Author

Ghanbari, Babak, Hartman, David, Jelínek, Vít, Pokorná, Aneta, Šámal, Robert, and Valtr, Pavel

Subjects
Mathematics - Combinatorics, 05C12, 05C75, 05C82
Abstract

This work deals with undirected graphs that have the same betweenness centrality for each vertex, so-called betweenness uniform graphs (or BUGs). The class of these graphs is not trivial and its classification is still an open problem. Recently, Gago, Coroni\v{c}ov\'a-Hurajov\'a and Madaras conjectured that for every rational $\alpha\ge 3/4$ there exists a BUG having betweenness centrality~$\alpha$. We disprove this conjecture, and provide an alternative view of the structure of betweenness-uniform graphs from the point of view of their complement. This allows us to characterise all the BUGs with betweennes centrality at most 9/10, and show that their betweenness centrality is equal to $\frac{\ell}{\ell+1}$ for some integer $\ell\le 9$. We conjecture that this characterization extends to all the BUGs with betweenness centrality smaller than~1.

Published
2023

4. Computing approximate symmetries of complex networks

Author

Pidnebesna, Anna, Hartman, David, Pokorná, Aneta, Straka, Matěj, and Hlinka, Jaroslav

Subjects
Computer Science - Social and Information Networks, Computer Science - Discrete Mathematics, Mathematics - Numerical Analysis, 05C60, 05C82, 68R10, 68W25, G.2.2, F.2.2
Abstract

The symmetry of complex networks is a global property that has recently gained attention since MacArthur et al. 2008 showed that many real-world networks contain a considerable number of symmetries. These authors work with a very strict symmetry definition based on the network's automorphism. The potential problem with this approach is that even a slight change in the graph's structure can remove or create some symmetry. Recently, Liu 2020 proposed to use an approximate automorphism instead of strict automorphism. This method can discover symmetries in the network while accepting some minor imperfections in their structure. The proposed numerical method, however, exhibits some performance problems and has some limitations while it assumes the absence of fixed points. In this work, we exploit alternative approaches recently developed for treating the Graph Matching Problem and propose a method, which we will refer to as Quadratic Symmetry Approximator (QSA), to address the aforementioned shortcomings. To test our method, we propose a set of random graph models suitable for assessing a wide family of approximate symmetry algorithms. The performance of our method is also demonstrated on brain networks.

Published
2023

5. Diagnostic efficacy and clinical utility of whole-exome sequencing in Czech pediatric patients with rare and undiagnosed diseases

Author

Slaba, Katerina, Pokorna, Petra, Jugas, Robin, Palova, Hana, Prochazkova, Dagmar, Aulicka, Stefania, Spanelova, Klara, Danhofer, Pavlina, Horak, Ondrej, Tuckova, Jana, Kleiblova, Petra, Gaillyova, Renata, Hrunka, Matej, Jouza, Martin, Pinkova, Blanka, Papez, Jan, Konecna, Petra, Zidkova, Jana, Stourac, Petr, Sterba, Jaroslav, Demlova, Regina, Demlova, Eva, Jabandziev, Petr, and Slaby, Ondrej

Published
2024
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8. MiDAS 5: Global diversity of bacteria and archaea in anaerobic digesters

Author

Dueholm, Morten Kam Dahl, Andersen, Kasper Skytte, Korntved, Anne-Kirstine C., Rudkjøbing, Vibeke, Alves, Madalena, Bajón-Fernández, Yadira, Batstone, Damien, Butler, Caitlyn, Cruz, Mercedes Cecilia, Davidsson, Åsa, Erijman, Leonardo, Holliger, Christof, Koch, Konrad, Kreuzinger, Norbert, Lee, Changsoo, Lyberatos, Gerasimos, Mutnuri, Srikanth, O’Flaherty, Vincent, Oleskowicz-Popiel, Piotr, Pokorna, Dana, Rajal, Veronica, Recktenwald, Michael, Rodríguez, Jorge, Saikaly, Pascal E., Tooker, Nick, Vierheilig, Julia, De Vrieze, Jo, Wurzbacher, Christian, and Nielsen, Per Halkjær

Published
2024
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9. Precision immuno-oncology approach for four malignant tumors in siblings with constitutional mismatch repair deficiency syndrome

Author

Palova, Hana, Das, Anirban, Pokorna, Petra, Bajciova, Viera, Pavelka, Zdenek, Jezova, Marta, Pal, Karol, Dimayacyac, Jose R., Negm, Logine, Stengs, Lucie, Bianchi, Vanessa, Vejmelkova, Klara, Noskova, Kristyna, Jarosova, Marie, Mejstrikova, Sona, Mudry, Peter, Kyr, Michal, Merta, Tomas, Tinka, Pavel, Drabova, Klara, Aulicka, Stefania, Jugas, Robin, Tabori, Uri, Slaby, Ondrej, and Sterba, Jaroslav

Published
2024
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10. Cyclin dependent kinase 4/6 inhibitor palbociclib synergizes with BCL2 inhibitor venetoclax in experimental models of mantle cell lymphoma without RB1 deletion

Author

Malarikova, Diana, Jorda, Radek, Kupcova, Kristyna, Senavova, Jana, Dolnikova, Alexandra, Pokorna, Eva, Kazantsev, Dmitry, Nozickova, Kristina, Sovilj, Dana, Bellanger, Celine, Chiron, David, Andera, Ladislav, Krystof, Vladimir, Strnad, Miroslav, Helman, Karel, Klanova, Magdalena, Trneny, Marek, Havranek, Ondrej, and Klener, Pavel

Published
2024
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11. Analysis of mutations in precision oncology using the automated, accurate, and user-friendly web tool PredictONCO

Author

Rayyan Tariq Khan, Petra Pokorna, Jan Stourac, Simeon Borko, Adam Dobias, Joan Planas-Iglesias, Stanislav Mazurenko, Ihor Arefiev, Gaspar Pinto, Veronika Szotkowska, Jaroslav Sterba, Jiri Damborsky, Ondrej Slaby, and David Bednar

Subjects
Precision oncology, Webserver, Mutation, Prediction, Treatment, Next-generation sequencing, Biotechnology, TP248.13-248.65
Abstract

Next-generation sequencing technology has created many new opportunities for clinical diagnostics, but it faces the challenge of functional annotation of identified mutations. Various algorithms have been developed to predict the impact of missense variants that influence oncogenic drivers. However, computational pipelines that handle biological data must integrate multiple software tools, which can add complexity and hinder non-specialist users from accessing the pipeline. Here, we have developed an online user-friendly web server tool PredictONCO that is fully automated and has a low barrier to access. The tool models the structure of the mutant protein in the first step. Next, it calculates the protein stability change, pocket level information, evolutionary conservation, and changes in ionisation of catalytic amino acid residues, and uses them as the features in the machine-learning predictor. The XGBoost-based predictor was validated on an independent subset of held-out data, demonstrating areas under the receiver operating characteristic curve (ROC) of 0.97 and 0.94, and the average precision from the precision-recall curve of 0.99 and 0.94 for structure-based and sequence-based predictions, respectively. Finally, PredictONCO calculates the docking results of small molecules approved by regulatory authorities. We demonstrate the applicability of the tool by presenting its usage for variants in two cancer-associated proteins, cellular tumour antigen p53 and fibroblast growth factor receptor FGFR1. Our free web tool will assist with the interpretation of data from next-generation sequencing and navigate treatment strategies in clinical oncology: https://loschmidt.chemi.muni.cz/predictonco/.

Published
2024
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13. Virtual reality-based neuroproprioceptive physiotherapy in multiple sclerosis: a protocol for a double-arm randomised assessor-blinded controlled trial on upper extremity function, postural function and quality of life, with molecular and functional MRI assessment

Author

Marie Cerna, Ivana Stetkarova, Ibrahim Ibrahim, Kamila Řasová, Jaroslav Tintera, Jan Havlik, Jindra Reissigová, Barbora Miznerova, Libor Vasa, Jakub Frank, Michael Hudec, Lubomir Rodina, Anna Herynkova, Jan Rydlo, Valerie B O’Leary, Iva Jurickova, Marketa Pokorna, Tom Philipp, and Jana Hlinovska

Subjects
Medicine
Abstract

Introduction Upper limb (UL) impairment is common in people with multiple sclerosis (pwMS), and functional recovery of the UL is a key rehabilitation goal. Technology-based approaches, like virtual reality (VR), are increasingly promising. While most VR environments are task-oriented, our clinical approach integrates neuroproprioceptive ‘facilitation and inhibition’ (NFI) principles. To advance this, we developed immersive VR software based on NFI principles targeting UL function and sit-to-stand ability. This study aims to evaluate the effectiveness of this VR therapy compared with conventional NFI-based physical therapy in pwMS. Our study uniquely applies advanced imaging techniques, along with biological molecular assessments, to explore adaptive processes induced by VR rehabilitation.Methods and analysis This double-arm, randomised, assessor-blinded, controlled trial runs over 2 months (1 hour, 2 times per week). PwMS with mild to severe disability will receive either VR therapy or real-world physical therapy. Primary outcomes include the nine-hole peg test, box and block test, handgrip strength, tremor and five times sit-to-stand test. Secondary measures include the Multiple Sclerosis Impact Scale, the 5-level EQ-5D questionnaire and kinematic analysis. Adaptive processes will be monitored using imaging techniques (functional MRI and tractography), molecular genetic methods (long non-coding RNAs) and immune system markers (leukocytes, dendritic cells). The International Classification of Functioning, Disability and Health brief set for MS will map the bio-psycho-social context of participants.Ethics and dissemination This project and its amendments were approved by the Ethics Committee of the Institute for Clinical and Experimental Medicine and Thomayer Hospital (1983/21+4772/21 (G-21–02) and the Ethics Committee of Kralovske Vinohrady University Hospital (EK-VP/38/0/2021) in Prague, Czechia (with single enrolment). The findings of this project will be disseminated through scientific publications, conferences, professional networks, public engagement, educational materials and stakeholder briefings to ensure a broad impact across clinical, academic and public domains.Trial registration number clinicaltrials.gov (NCT04807738).

Published
2025
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14. Wound Care Curriculum

Author

Holloway, Samantha, Pokorná, Andrea, Probst, Sebastian, Kielo-Viljamaa, Emilia, editor, Stolt, Minna, editor, and Suhonen, Riitta, editor

Published
2024
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16. Real-World Performance of Integrative Clinical Genomics in Pediatric Precision Oncology

Author

Pokorna, Petra, Palova, Hana, Adamcova, Sona, Jugas, Robin, Al Tukmachi, Dagmar, Kyr, Michal, Knoflickova, Dana, Kozelkova, Katerina, Bystry, Vojtech, Mejstrikova, Sona, Merta, Tomas, Trachtova, Karolina, Podlipna, Eliska, Mudry, Peter, Pavelka, Zdenek, Bajciova, Viera, Tinka, Pavel, Jarosova, Marie, Catela Ivkovic, Tina, Madlener, Sibylle, Pal, Karol, Stepien, Natalia, Mayr, Lisa, Tichy, Boris, Drabova, Klara, Jezova, Marta, Kozakova, Sarka, Vanackova, Jitka, Radova, Lenka, Steininger, Karin, Haberler, Christine, Gojo, Johannes, Sterba, Jaroslav, and Slaby, Ondrej

Published
2024
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19. European Aerosol Phenomenology -- 8: Harmonised Source Apportionment of Organic Aerosol using 22 Year-long ACSM/AMS Datasets

Author

Chen, Gang, Canonaco, Francesco, Tobler, Anna, Aas, Wenche, Alastuey, Andres, Allan, James, Atabakhsh, Samira, Aurela, Minna, Baltensperger, Urs, Bougiatioti, Aikaterini, De Brito, Joel F., Ceburnis, Darius, Chazeau, Benjamin, Chebaicheb, Hasna, Daellenbach, Kaspar R., Ehn, Mikael, Haddad, Imad El, Eleftheriadis, Konstantinos, Favez, Olivier, Flentje, Harald, Font, Anna, Fossum, Kirsten, Freney, Evelyn, Gini, Maria, Green, David C, Heikkinen, Liine, Herrmann, Hartmut, Kalogridis, Athina-Cerise, Keernik, Hannes, Lhotka, Radek, Lin, Chunshui, Lunder, Chris, Maasikmets, Marek, Manousakas, Manousos I., Marchand, Nicolas, Marin, Cristina, Marmureanu, Luminita, Mihalopoulos, Nikolaos, Močnik, Griša, Nęcki, Jaroslaw, O'Dowd, Colin, Ovadnevaite, Jurgita, Peter, Thomas, Petit, Jean-Eudes, Pikridas, Michael, Platt, Stephen Matthew, Pokorná, Petra, Poulain, Laurent, Priestman, Max, Riffault, Véronique, Rinaldi, Matteo, Różański, Kazimierz, Schwarz, Jaroslav, Sciare, Jean, Simon, Leïla, Skiba, Alicja, Slowik, Jay G., Sosedova, Yulia, Stavroulas, Iasonas, Styszko, Katarzyna, Teinemaa, Erik, Timonen, Hilkka, Tremper, Anja, Vasilescu, Jeni, Via, Marta, Vodička, Petr, Wiedensohler, Alfred, Zografou, Olga, Minguillón, María Cruz, and Prévôt, André S. H.

Subjects
Physics - Atmospheric and Oceanic Physics
Abstract

Organic aerosol (OA) is a key component to total submicron particulate matter (PM1), and comprehensive knowledge of OA sources across Europe is crucial to mitigate PM1 levels. Europe has a well-established air quality research infrastructure from which yearlong datasets using 21 aerosol chemical speciation monitors (ACSMs) and 1 aerosol mass spectrometer (AMS) were gathered during 2013-2019. It includes 9 non-urban and 13 urban sites. This study developed a state-of-the-art source apportionment protocol to analyse long-term OA mass spectrum data by applying the most advanced source apportionment strategies (i.e., rolling PMF, ME-2, and bootstrap). This harmonised protocol enables the quantifications of the most common OA components such as hydrocarbon-like OA (HOA), biomass burning OA (BBOA), cooking-like OA (COA), more oxidised-oxygenated OA (MO-OOA), and less oxidised-oxygenated OA (LO-OOA). Other components such as coal combustion OA (CCOA), solid fuel OA (SFOA: mainly mixture of coal and peat combustion), cigarette smoke OA (CSOA), sea salt (mostly inorganic but part of the OA mass spectrum), coffee OA, and ship industry OA could also be separated at a few specific sites. Oxygenated OA (OOA) components make up most of the submicron OA mass (average = 71.1%, a range of 43.7-100%). Solid fuel combustion-related OA components (i.e., BBOA, CCOA, and SFOA) are still considerable with in total 16.0% yearly contribution to the OA, yet mainly during winter months (21.4%). Overall, this comprehensive protocol works effectively across all sites governed by different sources and generates robust and consistent source apportionment results. Our work presents a comprehensive overview of OA sources in Europe with a unique combination of high time resolution and long-term data coverage (9-36 months), providing essential information to improve/validate air quality, health impact, and climate models.

Published
2022
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21. GRADE guidance 39: using GRADE-ADOLOPMENT to adopt, adapt or create contextualized recommendations from source guidelines and evidence syntheses

Author

Klugar, Miloslav, Lotfi, Tamara, Darzi, Andrea J., Reinap, Marge, Klugarová, Jitka, Kantorová, Lucia, Xia, Jun, Brignardello-Petersen, Romina, Pokorná, Andrea, Hazlewood, Glen, Munn, Zachary, Morgan, Rebecca L., Toews, Ingrid, Neumann, Ignacio, Bhatarasakoon, Patraporn, Stein, Airton Tetelbom, McCaul, Michael, Mathioudakis, Alexander G., D'Anci, Kristen E., Leontiadis, Grigorios I., Naude, Celeste, Vasanthan, Lenny T., Khabsa, Joanne, Bala, Malgorzata M., Mustafa, Reem, DiValerio Gibbs, Karen, Nieuwlaat, Robby, Santesso, Nancy, Pieper, Dawid, Mokrane, Saphia, Soghier, Israa, Lertwatthanawilat, Wanchai, Wiercioch, Wojtek, Sultan, Shahnaz, Rozmarinová, Jana, Drapačová, Pavla, Song, Yang, Amer, Marwa, Amer, Yasser S., Sayfi, Shahab, Verstijnen, Ilse M., Shin, Ein-Soon, Saz-Parkinson, Zuleika, Pottie, Kevin, Ruspi, Alessandra, Marušić, Ana, Saif-Ur-Rahman, K.M., Rojas, Maria X., Akl, Elie A., and Schünemann, Holger J.

Published
2024
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22. On the Connectivity and the Diameter of Betweenness-Uniform Graphs

Author

Hartman, David, Pokorná, Aneta, and Valtr, Pavel

Subjects
Mathematics - Combinatorics, Computer Science - Discrete Mathematics
Abstract

Betweenness centrality is a centrality measure based on the overall amount of shortest paths passing through a given vertex. A graph is betweenness-uniform if all its vertices have the same betweenness centrality. We study the properties of betweenness-uniform graphs. In particular, we show that every connected betweenness-uniform graph is either a cycle or a $3$-connected graph. Also, we show that betweenness uniform graphs of high maximal degree have small diameter., Comment: minor changes; to bepublished in Discrete Applied Mathematics

Published
2021

24. Constructions of betweenness-uniform graphs from trees

Author

Hartman, David and Pokorná, Aneta

Subjects
Mathematics - Combinatorics, Computer Science - Discrete Mathematics
Abstract

Betweenness centrality is a measure of the importance of a vertex x inside a network based on the fraction of shortest paths passing through x. We study a blow-up construction that has been shown to produce graphs with uniform distribution of betweenness. We disprove the conjecture about this procedure's universality by showing that trees with a diameter at least three cannot be transformed into betweenness-uniform by the blow-up construction. It remains open to characterize graphs for which the blow-up construction can produce betweenness-uniform graphs.

Published
2021

30. On Aharoni's rainbow generalization of the Caccetta-H\'{a}ggkvist conjecture

Author

Hompe, Patrick, Pelikanova, Petra, Pokorna, Aneta, and Spirkl, Sophie

Subjects
Mathematics - Combinatorics
Abstract

For a digraph $G$ and $v \in V(G)$, let $\delta^+(v)$ be the number of out-neighbors of $v$ in $G$. The Caccetta-H\"{a}ggkvist conjecture states that for all $k \ge 1$, if $G$ is a digraph with $n = |V(G)|$ such that $\delta^+(v) \ge k$ for all $v \in V(G)$, then G contains a directed cycle of length at most $\lceil n/k \rceil$. In [2], Aharoni proposes a generalization of this conjecture, that a simple edge-colored graph on $n$ vertices with $n$ color classes, each of size $k$, has a rainbow cycle of length at most $\lceil n/k \rceil$. In this paper, we prove this conjecture if each color class has size ${\Omega}(k \log k)$., Comment: Accepted manuscript. See DOI for journal version. arXiv admin note: text overlap with arXiv:2105.03373

Published
2021
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32. On 3-Coloring of $(2P_4,C_5)$-Free Graphs

Author

Jelínek, Vít, Klimošová, Tereza, Masařík, Tomáš, Novotná, Jana, and Pokorná, Aneta

Subjects
Computer Science - Data Structures and Algorithms, Computer Science - Discrete Mathematics, Mathematics - Combinatorics, 05C15, 05C85
Abstract

The 3-coloring of hereditary graph classes has been a deeply-researched problem in the last decade. A hereditary graph class is characterized by a (possibly infinite) list of minimal forbidden induced subgraphs $H_1,H_2,\ldots$; the graphs in the class are called $(H_1,H_2,\ldots)$-free. The complexity of 3-coloring is far from being understood, even for classes defined by a few small forbidden induced subgraphs. For $H$-free graphs, the complexity is settled for any $H$ on up to seven vertices. There are only two unsolved cases on eight vertices, namely $2P_4$ and $P_8$. For $P_8$-free graphs, some partial results are known, but to the best of our knowledge, $2P_4$-free graphs have not been explored yet. In this paper, we show that the 3-coloring problem is polynomial-time solvable on $(2P_4,C_5)$-free graphs., Comment: 18 pages, 13 figures. Accepted to International Workshop on Graph-Theoretic Concepts in Computer Science (WG) 2021

Published
2020
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33. Detection of H3F3A K27M or BRAF V600E in liquid biopsies of brain tumor patients as diagnostic and monitoring biomarker: impact of tumor localization and sampling method

Author

Madlener, Sibylle, Stepien, Natalia, Senfter, Daniel, Mayr, Lisa, Laemmerer, Anna, Hedrich, Cora, Baumgartner, Alicia, Lötsch-Gojo, Daniela, Sterba, Jaroslav, Pokorna, Petra, Kiesel, Barbara, Widhalm, Georg, Eckert, Franziska, Preusser, Matthias, Rössler, Karl, Azizi, Amedeo, Peyrl, Andreas, Czech, Thomas, Haberler, Christine, Slavc, Irene, Kasprian, Gregor, Dorfer, Christian, Furtner, Julia, and Gojo, Johannes

Published
2025
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36. Business Process Models and Eye Tracking System for BPMN Evaluation-Usability Study

Author

Pavlicek, Josef, Pavlickova, Petra, Pokorná, Alžběta, Brnka, Matej, van der Aalst, Wil, Series Editor, Ram, Sudha, Series Editor, Rosemann, Michael, Series Editor, Szyperski, Clemens, Series Editor, Guizzardi, Giancarlo, Series Editor, Babkin, Eduard, editor, Barjis, Joseph, editor, Malyzhenkov, Pavel, editor, Merunka, Vojtěch, editor, and Molhanec, Martin, editor

Published
2023
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44. The landscape of tumor cell states and spatial organization in H3-K27M mutant diffuse midline glioma across age and location

Author

Liu, Ilon, Jiang, Li, Samuelsson, Erik R., Marco Salas, Sergio, Beck, Alexander, Hack, Olivia A., Jeong, Daeun, Shaw, McKenzie L., Englinger, Bernhard, LaBelle, Jenna, Mire, Hafsa M., Madlener, Sibylle, Mayr, Lisa, Quezada, Michael A., Trissal, Maria, Panditharatna, Eshini, Ernst, Kati J., Vogelzang, Jayne, Gatesman, Taylor A., Halbert, Matthew E., Palova, Hana, Pokorna, Petra, Sterba, Jaroslav, Slaby, Ondrej, Geyeregger, Rene, Diaz, Aaron, Findlay, Izac J., Dun, Matthew D., Resnick, Adam, Suvà, Mario L., Jones, David T. W., Agnihotri, Sameer, Svedlund, Jessica, Koschmann, Carl, Haberler, Christine, Czech, Thomas, Slavc, Irene, Cotter, Jennifer A., Ligon, Keith L., Alexandrescu, Sanda, Yung, W. K. Alfred, Arrillaga-Romany, Isabel, Gojo, Johannes, Monje, Michelle, Nilsson, Mats, and Filbin, Mariella G.

Published
2022
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