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Article: Transcriptomic Context of

Dybska, Emilia / Nowak, Jan Krzysztof / Walkowiak, Jarosław

2023 Volume 11, Issue 6

Abstract: The runt-related transcription factor 3 (RUNX3) regulates the differentiation of monocytes and their response to inflammation. However, the transcriptomic context ... ...

Abstract	The runt-related transcription factor 3 (RUNX3) regulates the differentiation of monocytes and their response to inflammation. However, the transcriptomic context of
Language	English
Publishing date	2023-06-13
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	2720867-9
ISSN	2227-9059
ISSN	2227-9059
DOI	10.3390/biomedicines11061698
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Article ; Online: Reply.

Nowak, Jan Krzysztof / Kalla, Rahul / Satsangi, Jack

Gastroenterology

2021 Volume 160, Issue 7, Page(s) 2622–2623

Language	English
Publishing date	2021-02-04
Publishing country	United States
Document type	Letter ; Research Support, Non-U.S. Gov't ; Comment
ZDB-ID	80112-4
ISSN	1528-0012 ; 0016-5085
ISSN (online)	1528-0012
ISSN	0016-5085
DOI	10.1053/j.gastro.2021.02.011
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Article ; Online: Transcriptomic Context of RUNX3 Expression in Monocytes

Emilia Dybska / Jan Krzysztof Nowak / Jarosław Walkowiak

Biomedicines, Vol 11, Iss 1698, p

A Cross-Sectional Analysis

2023 Volume 1698

Abstract: The runt-related transcription factor 3 (RUNX3) regulates the differentiation of monocytes and their response to inflammation. However, the transcriptomic context of RUNX3 expression in blood monocytes remains poorly understood. We aim to learn about ... ...

Abstract	The runt-related transcription factor 3 (RUNX3) regulates the differentiation of monocytes and their response to inflammation. However, the transcriptomic context of RUNX3 expression in blood monocytes remains poorly understood. We aim to learn about RUNX3 from its relationships within transcriptomes of bulk CD14+ cells in adults. This study used immunomagnetically sorted CD14+ cell gene expression microarray data from the Multi-Ethnic Study of Atherosclerosis (MESA, n = 1202, GSE56047) and the Correlated Expression and Disease Association Research (CEDAR, n = 281, E-MTAB-6667) cohorts. The data were preprocessed, subjected to RUNX3 -focused correlation analyses and random forest modeling, followed by the gene ontology analysis. Immunity-focused differential ratio analysis with intermediary inference (DRAIMI) was used to integrate the data with protein–protein interaction network. Correlation analysis of RUNX3 expression revealed the strongest positive association for EVL (r mean = 0.75, p FDR-MESA = 5.37 × 10 −140 , p FDR-CEDAR = 5.52 × 10 −80 ), ARHGAP17 (r mean = 0.74, p FDR-MESA = 1.13 × 10 −169 , p FDR-CEDAR = 9.20 × 10 −59 ), DNMT1 (r mean = 0.74, p FDR-MESA = 1.10 × 10 −169 , p FDR-CEDAR = 1.67 × 10 −58 ), and CLEC16A (r mean = 0.72, p FDR-MESA = 3.51 × 10 −154 , p FDR-CEDAR = 2.27 × 10 −55 ), while the top negative correlates were C2ORF76 (r mean = −0.57, p FDR-MESA = 8.70 × 10 −94 , p FDR-CEDAR = 1.31 × 10 −25 ) and TBC1D7 (r mean = −0.55, p FDR-MESA = 1.36 × 10 −69 , p FDR-CEDAR = 7.81 × 10 −30 ). The RUNX3 -associated transcriptome signature was involved in mRNA metabolism, signal transduction, and the organization of cytoskeleton, chromosomes, and chromatin, which may all accompany mitosis. Transcriptomic context of RUNX3 expression in monocytes hints at its relationship with cell growth, shape maintenance, and aspects of the immune response, including tyrosine kinases.
Keywords	monocyte ; RUNX3 expression ; transcriptome ; immunity ; inflammation ; Biology (General) ; QH301-705.5
Subject code	333 ; 290
Language	English
Publishing date	2023-06-01T00:00:00Z
Publisher	MDPI AG
Document type	Article ; Online
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Article: Immune cell-specific smoking-related expression characteristics are revealed by re-analysis of transcriptomes from the CEDAR cohort.

Nowak, Jan Krzysztof / Dybska, Emilia / Adams, Alex T / Walkowiak, Jaroslaw

Central-European journal of immunology

2022 Volume 47, Issue 3, Page(s) 246–259

Abstract: Introduction: Smoking is known to affect whole-blood expression and methylation profiles. Although whole-genome methylation studies indicated that effects observed in blood may be driven by changes within leukocyte subtypes, these phenomena have not ... ...

Abstract	Introduction: Smoking is known to affect whole-blood expression and methylation profiles. Although whole-genome methylation studies indicated that effects observed in blood may be driven by changes within leukocyte subtypes, these phenomena have not been explored using expression profiling. Material and methods: This study reanalyzed data from the Correlated Expression and Disease Association Research (CEDAR) patient cohort recruited by Momozawa et al. (E-MTAB-6667). Data from gene expression profiling of immunomagnetically sorted CD4 Results: Ninety-four differentially expressed genes were found (CD8 Conclusions: Smoking specifically alters vital immune regulation genes in lymphocyte subtypes, especially CD4
Language	English
Publishing date	2022-11-16
Publishing country	Poland
Document type	Journal Article
ZDB-ID	1336421-2
ISSN	1644-4124 ; 1426-3912
ISSN (online)	1644-4124
ISSN	1426-3912
DOI	10.5114/ceji.2022.120618
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Article: Autoantibodies and Clinical Correlations in Polish Systemic Sclerosis Patients: A Cross-Sectional Study.

Żebryk, Paweł / Przymuszała, Piotr / Nowak, Jan Krzysztof / Piorunek, Tomasz / Mularek-Kubzdela, Tatiana / Puszczewicz, Mariusz

Journal of clinical medicine

2023 Volume 12, Issue 2

Abstract: We evaluated the prevalence of systemic sclerosis (SSc)-related autoantibodies and their clinical significance and compared the sensitivity of two line immunoblot assays on a prospective study group of 96 Polish SSc patients (ACR-EULAR 2013 criteria) ... ...

Abstract	We evaluated the prevalence of systemic sclerosis (SSc)-related autoantibodies and their clinical significance and compared the sensitivity of two line immunoblot assays on a prospective study group of 96 Polish SSc patients (ACR-EULAR 2013 criteria) whose sera were assessed by indirect immunofluorescence (HEp-2 and monkey liver) and line immunoblot assays: ANA Profile 3 and Systemic Sclerosis Profile by EUROIMMUN (Lübeck, Germany). Organ involvement was evaluated according to the EUSTAR Minimal Essential Data Set. The following autoantibodies’ prevalence was found: Scl-70 (36%), Ro-52 (28%), CENP-B (22%), CENP-A (20%), PM-Scl-75 (20%), PM-Scl-100 (14%), fibrillarin (7%), Th/To (7%), RNA polymerase III 11 kDa (5%), RNA polymerase III 155 kDa (3%), PDGFR (3%), NOR-90 (2%), and Ku (1%). Significant associations between the autoantibodies’ presence and organ involvement were found: ATA (dcSSc > lcSSc, less prevalent muscle weakness), Ro-52 (gangrene, DLCO < 60), CENP-B and A (lcSSc > dcSSc, normal CK), CENP-B (rarer digital ulcers and joint contractures), PM-Scl-100 and 75 (PM/SSc overlap, CK increase, muscle weakness, muscle atrophy), PM-Scl-100 (dcSSc unlikely), PM-Scl-75 (lung fibrosis), fibrillarin (muscle atrophy, proteinuria, conduction blocks, palpitations), Th/To (proteinuria, arthritis, muscle weakness, and rarer esophageal symptoms), RNA Polymerase III 11 kDa (arterial hypertension, renal crisis), RNA polymerase III 155 kDa (renal crisis), and PDGFR (dcSSc, tendon friction rubs). Additionally, the Systemic Sclerosis Profile was significantly more sensitive in detecting SSc-related autoantibodies than ANA Profile 3 (p = 0.002). In conclusion, individual autoantibodies associated with specific characteristics of SSc.
Language	English
Publishing date	2023-01-13
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	2662592-1
ISSN	2077-0383
ISSN	2077-0383
DOI	10.3390/jcm12020657
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Article ; Online: Autoantibodies and Clinical Correlations in Polish Systemic Sclerosis Patients

Paweł Żebryk / Piotr Przymuszała / Jan Krzysztof Nowak / Tomasz Piorunek / Tatiana Mularek-Kubzdela / Mariusz Puszczewicz

Journal of Clinical Medicine, Vol 12, Iss 657, p

A Cross-Sectional Study

2023 Volume 657

Abstract	We evaluated the prevalence of systemic sclerosis (SSc)-related autoantibodies and their clinical significance and compared the sensitivity of two line immunoblot assays on a prospective study group of 96 Polish SSc patients (ACR-EULAR 2013 criteria) whose sera were assessed by indirect immunofluorescence (HEp-2 and monkey liver) and line immunoblot assays: ANA Profile 3 and Systemic Sclerosis Profile by EUROIMMUN (Lübeck, Germany). Organ involvement was evaluated according to the EUSTAR Minimal Essential Data Set. The following autoantibodies’ prevalence was found: Scl-70 (36%), Ro-52 (28%), CENP-B (22%), CENP-A (20%), PM-Scl-75 (20%), PM-Scl-100 (14%), fibrillarin (7%), Th/To (7%), RNA polymerase III 11 kDa (5%), RNA polymerase III 155 kDa (3%), PDGFR (3%), NOR-90 (2%), and Ku (1%). Significant associations between the autoantibodies’ presence and organ involvement were found: ATA (dcSSc > lcSSc, less prevalent muscle weakness), Ro-52 (gangrene, DLCO < 60), CENP-B and A (lcSSc > dcSSc, normal CK), CENP-B (rarer digital ulcers and joint contractures), PM-Scl-100 and 75 (PM/SSc overlap, CK increase, muscle weakness, muscle atrophy), PM-Scl-100 (dcSSc unlikely), PM-Scl-75 (lung fibrosis), fibrillarin (muscle atrophy, proteinuria, conduction blocks, palpitations), Th/To (proteinuria, arthritis, muscle weakness, and rarer esophageal symptoms), RNA Polymerase III 11 kDa (arterial hypertension, renal crisis), RNA polymerase III 155 kDa (renal crisis), and PDGFR (dcSSc, tendon friction rubs). Additionally, the Systemic Sclerosis Profile was significantly more sensitive in detecting SSc-related autoantibodies than ANA Profile 3 ( p = 0.002). In conclusion, individual autoantibodies associated with specific characteristics of SSc.
Keywords	systemic sclerosis ; autoantibodies ; antibodies ; antinuclear ; scleroderma ; systemic ; Medicine ; R
Subject code	610 ; 616
Language	English
Publishing date	2023-01-01T00:00:00Z
Publisher	MDPI AG
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Whose Tweets on COVID-19 Gain the Most Attention: Celebrities, Political, or Scientific Authorities?

Kamiński, Mikołaj / Szymańska, Cyntia / Nowak, Jan Krzysztof

Cyberpsychology, behavior and social networking

2020 Volume 24, Issue 2, Page(s) 123–128

Abstract: Twitter has considerable capacity for health education and proves to be an efficient and accessible communication tool in the coronavirus disease-19 (COVID-19) pandemic. Although many stakeholders saturate Twitter with COVID-19-related information, it ... ...

Abstract	Twitter has considerable capacity for health education and proves to be an efficient and accessible communication tool in the coronavirus disease-19 (COVID-19) pandemic. Although many stakeholders saturate Twitter with COVID-19-related information, it remains unknown who disseminates information most efficaciously. COVID-19-related tweets were obtained from Twitter accounts of health agencies, governmental authorities, universities, scientific journals, medical associations, and celebrities. Posts' impact was measured with the nominal and relative (%followers) number of likes and retweets. A sentiment analysis was conducted.We have identified 17,331 COVID-19-related tweets posted by 338 accounts in >4 months since the virus began to spread. The largest number of likes was received by tweets of celebrities (median nominal, relative likes; 14,918, 0.036 percent), politicians (259, 0.174 percent), and health agencies (231, 0.007 percent). Most retweeted messages were also posted by celebrities (2,366, 0.005 percent), health agencies (130, 0.004 percent), and politicians (55, 0.041 percent). Retweets and likes peaked in March 2020, and the overall sentiment of the tweets was growing steadily. Whereas celebrities and politicians posted positive messages, the scientific and health authorities often employed a negative vocabulary. The posts with positive sentiment gained more likes and relative likes than nonpositive. During the pandemic, the tweets of celebrities and politicians related to COVID-19 outperform those coming from health and scientific institutions. Active engagement of Twitter influencers may help key messages go viral.
MeSH term(s)	Attention ; COVID-19 ; Communication ; Famous Persons ; Government Agencies ; Humans ; Pandemics ; Politics ; SARS-CoV-2 ; Social Media ; Vocabulary
Keywords	covid19
Language	English
Publishing date	2020-09-23
Publishing country	United States
Document type	Journal Article
ZDB-ID	2545735-4
ISSN	2152-2723 ; 2152-2715
ISSN (online)	2152-2723
ISSN	2152-2715
DOI	10.1089/cyber.2020.0336
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Article ; Online: Methodology of generation of CFD meshes and 4D shape reconstruction of coronary arteries from patient-specific dynamic CT.

Psiuk-Maksymowicz, Krzysztof / Borys, Damian / Melka, Bartlomiej / Gracka, Maria / Adamczyk, Wojciech P / Rojczyk, Marek / Wasilewski, Jaroslaw / Głowacki, Jan / Kruk, Mariusz / Nowak, Marcin / Ostrowski, Ziemowit / Bialecki, Ryszard A

Scientific reports

2024 Volume 14, Issue 1, Page(s) 2201

Abstract: Due to the difficulties in retrieving both the time-dependent shapes of the vessels and the generation of numerical meshes for such cases, most of the simulations of blood flow in the cardiac arteries use static geometry. The article describes a ... ...

Abstract	Due to the difficulties in retrieving both the time-dependent shapes of the vessels and the generation of numerical meshes for such cases, most of the simulations of blood flow in the cardiac arteries use static geometry. The article describes a methodology for generating a sequence of time-dependent 3D shapes based on images of different resolutions and qualities acquired from ECG-gated coronary artery CT angiography. The precision of the shape restoration method has been validated using an independent technique. The original proposed approach also generates for each of the retrieved vessel shapes a numerical mesh of the same topology (connectivity matrix), greatly simplifying the CFD blood flow simulations. This feature is of significant importance in practical CFD simulations, as it gives the possibility of using the mesh-morphing utility, minimizing the computation time and the need of interpolation between boundary meshes at subsequent time instants. The developed technique can be applied to generate numerical meshes in arteries and other organs whose shapes change over time. It is applicable to medical images produced by other than angio-CT modalities.
MeSH term(s)	Humans ; Coronary Vessels/diagnostic imaging ; Coronary Vessels/surgery ; Hemodynamics ; Coronary Angiography/methods ; Prostheses and Implants ; Tomography, X-Ray Computed
Language	English
Publishing date	2024-01-25
Publishing country	England
Document type	Journal Article
ZDB-ID	2615211-3
ISSN	2045-2322 ; 2045-2322
ISSN (online)	2045-2322
ISSN	2045-2322
DOI	10.1038/s41598-024-52398-5
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Article ; Online: Automated Bowel Sound Analysis: An Overview.

Nowak, Jan Krzysztof / Nowak, Robert / Radzikowski, Kacper / Grulkowski, Ireneusz / Walkowiak, Jaroslaw

Sensors (Basel, Switzerland)

2021 Volume 21, Issue 16

Abstract: Despite technological progress, we lack a consensus on the method of conducting automated bowel sound (BS) analysis and, consequently, BS tools have not become available to doctors. We aimed to briefly review the literature on BS recording and analysis, ... ...

Abstract	Despite technological progress, we lack a consensus on the method of conducting automated bowel sound (BS) analysis and, consequently, BS tools have not become available to doctors. We aimed to briefly review the literature on BS recording and analysis, with an emphasis on the broad range of analytical approaches. Scientific journals and conference materials were researched with a specific set of terms (Scopus, MEDLINE, IEEE) to find reports on BS. The research articles identified were analyzed in the context of main research directions at a number of centers globally. Automated BS analysis methods were already well developed by the early 2000s. Accuracy of 90% and higher had been achieved with various analytical approaches, including wavelet transformations, multi-layer perceptrons, independent component analysis and autoregressive-moving-average models. Clinical research on BS has exposed their important potential in the non-invasive diagnosis of irritable bowel syndrome, in surgery, and for the investigation of gastrointestinal motility. The most recent advances are linked to the application of artificial intelligence and the development of dedicated BS devices. BS research is technologically mature, but lacks uniform methodology, an international forum for discussion and an open platform for data exchange. A common ground is needed as a starting point. The next key development will be the release of freely available benchmark datasets with labels confirmed by human experts.
MeSH term(s)	Artificial Intelligence ; Automation ; Gastrointestinal Diseases/diagnosis ; Humans ; Neural Networks, Computer ; Sound
Language	English
Publishing date	2021-08-05
Publishing country	Switzerland
Document type	Journal Article ; Review
ZDB-ID	2052857-7
ISSN	1424-8220 ; 1424-8220
ISSN (online)	1424-8220
ISSN	1424-8220
DOI	10.3390/s21165294
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Article ; Online: Analysis of Gastrointestinal Acoustic Activity Using Deep Neural Networks.

Ficek, Jakub / Radzikowski, Kacper / Nowak, Jan Krzysztof / Yoshie, Osamu / Walkowiak, Jaroslaw / Nowak, Robert

Sensors (Basel, Switzerland)

2021 Volume 21, Issue 22

Abstract: Automated bowel sound (BS) analysis methods were already well developed by the early 2000s. Accuracy of ~90% had been achieved by several teams using various analytical approaches. Clinical research on BS had revealed their high potential in the non- ... ...

Abstract	Automated bowel sound (BS) analysis methods were already well developed by the early 2000s. Accuracy of ~90% had been achieved by several teams using various analytical approaches. Clinical research on BS had revealed their high potential in the non-invasive investigation of irritable bowel syndrome to study gastrointestinal motility and in a surgical setting. This article proposes a novel methodology for the analysis of BS using hybrid convolutional and recursive neural networks. It is one of the first methods of using deep learning to be widely explored. We have developed an experimental pipeline and evaluated our results with a new dataset collected using a device with a dedicated contact microphone. Data have been collected at night-time, which is the most interesting period from a neurogastroenterological point of view. Previous works had ignored this period and instead kept brief records only during the day. Our algorithm can detect bowel sounds with an accuracy >93%. Moreover, we have achieved a very high specificity (>97%), crucial in diagnosis. The results have been checked with a medical professional, and they successfully support clinical diagnosis. We have developed a client-server system allowing medical practitioners to upload the recordings from their patients and have them analyzed online. This system is available online. Although BS research is technologically mature, it still lacks a uniform methodology, an international forum for discussion, and an open platform for data exchange, and therefore it is not commonly used. Our server could provide a starting point for establishing a common framework in BS research.
MeSH term(s)	Acoustics ; Algorithms ; Humans ; Neural Networks, Computer
Language	English
Publishing date	2021-11-16
Publishing country	Switzerland
Document type	Consensus Development Conference ; Journal Article
ZDB-ID	2052857-7
ISSN	1424-8220 ; 1424-8220
ISSN (online)	1424-8220
ISSN	1424-8220
DOI	10.3390/s21227602
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