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Article ; Online: Glucose exchange parameters in a subset of physiological conditions.

Mareš, J / Karjalainen, J / Håkansson, P / Michaeli, S / Liimatainen, T

Physical chemistry chemical physics : PCCP

2023 Volume 25, Issue 34, Page(s) 22965–22978

Abstract: The chemical exchange of labile protons of the hydroxyl groups can be exploited in a variety of magnetic resonance experiments to gain information about the groups and their physicochemical environment. The exchangeable -OH protons provide important ... ...

Abstract	The chemical exchange of labile protons of the hydroxyl groups can be exploited in a variety of magnetic resonance experiments to gain information about the groups and their physicochemical environment. The exchangeable -OH protons provide important contributions to the
MeSH term(s)	Protons ; Glucose ; Temperature ; Water
Chemical Substances	Protons ; Glucose (IY9XDZ35W2) ; Water (059QF0KO0R)
Language	English
Publishing date	2023-08-30
Publishing country	England
Document type	Journal Article
ZDB-ID	1476244-4
ISSN	1463-9084 ; 1463-9076
ISSN (online)	1463-9084
ISSN	1463-9076
DOI	10.1039/d3cp01973j
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Article ; Online: Gait disorder classification based on effective feature selection and unsupervised methodology.

Shayestegan, Mohsen / Kohout, Jan / Trnková, Kateřina / Chovanec, Martin / Mareš, Jan

Computers in biology and medicine

2024 Volume 170, Page(s) 108077

Abstract: In gait stability analysis, patients suffering from dysfunction problems are impacted by shifts in their dynamic balance. Monitoring the patients' progress is important for allowing physicians and patients to observe the rehabilitation process accurately. ...

Abstract	In gait stability analysis, patients suffering from dysfunction problems are impacted by shifts in their dynamic balance. Monitoring the patients' progress is important for allowing physicians and patients to observe the rehabilitation process accurately. In this study, we designed a new methodology for classifying gait disorders to quantify patients' progress. The dataset in this study includes 84 measurements of 37 patients based on a physician's opinion. In this study, the system, which includes a Kinect camera to observe and store the frames of patients walking down a hallway, a key-point detector to detect the skeletal key points, and an encoder transformer classifier network integrated with generator-discriminator networks (ET-GD), is designed to evaluate the classification of gait dysfunction. The detector extracts the skeletal key points of patients. After feature engineering, the selected high-level features are fed into the proposed neural network to analyse patient movement and perform the final evaluation of gait dysfunction. The proposed network is inspired by the 1D encoder transformer, which is integrated with two main networks: a network for classification and a network to generate fake output data similar to the input data. Furthermore, we used a discriminator structure to distinguish between the actual data (input) and fake data (generated data). Due to the multi-structural networks in the proposed method, multi-loss functions need to be optimised; this increases the accuracy of the encoder transformer classifier.
MeSH term(s)	Humans ; Gait ; Walking ; Movement Disorders ; Neural Networks, Computer ; Gait Analysis
Language	English
Publishing date	2024-01-30
Publishing country	United States
Document type	Journal Article
ZDB-ID	127557-4
ISSN	1879-0534 ; 0010-4825
ISSN (online)	1879-0534
ISSN	0010-4825
DOI	10.1016/j.compbiomed.2024.108077
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Article ; Online: Prognostic value of cerebrospinal fluid biomarkers in multiple sclerosis: The key role of kappa free light chains and a multivariate predictor for disease progression.

Miklušová, Martina / Fürst, Tomáš / Zimek, Dalibor / Mareš, Jan

Multiple sclerosis and related disorders

2023 Volume 82, Page(s) 105402

Abstract: Objective: Multiple sclerosis (MS) is a chronic, inflammatory, demyelinating disease of the central nervous system with varying progression rates among individuals. The ability to predict disease progression is crucial for treatment decisions with ... ...

Abstract	Objective: Multiple sclerosis (MS) is a chronic, inflammatory, demyelinating disease of the central nervous system with varying progression rates among individuals. The ability to predict disease progression is crucial for treatment decisions with disease-modifying therapies (DMTs). A few cerebrospinal fluid (CSF) biomarkers have been investigated in relation to disease progression, but few have been effectively translated into clinical practice. The aim of this study was to evaluate the diagnostic and prognostic value of known CSF markers, to compare their sensitivity and specificity, and to develop a prognostic model using a combination of markers to predict disease progression. Methods: This retrospective cohort study included 82 patients with a first episode of inflammatory demyelinating symptoms suggestive of MS between January 2018 and January 2021. Patients underwent diagnostic lumbar puncture and other investigations according to the multiple sclerosis (MS) protocol. They were divided into three groups according to MRI findings, relapse rate and EDSS score. CSF marker concentrations were determined by laser nephelometry and electrochemiluminescence immunoassay. Results: The results showed that the number of oligoclonal bands could discriminate the progression-free group from the other groups, but had a lower discriminatory power compared to CSF marker concentrations. Among CSF markers, FLC kappa showed the best discriminatory performance. By combining FLC kappa with gender and lesion localization information, a simple predictor of progression-free group membership was proposed. This predictor showed good sensitivity (91 %) and specificity (65 %). Conclusion: In conclusion, CSF FLC kappa concentration, together with gender and lesion localization, may be a valuable predictor of disease progression in MS patients. This study highlights the potential of using CSF biomarkers for prognostic purposes and offers a simple approach to predicting disease progression.
MeSH term(s)	Humans ; Multiple Sclerosis/diagnostic imaging ; Multiple Sclerosis/cerebrospinal fluid ; Prognosis ; Retrospective Studies ; Immunoglobulin kappa-Chains/cerebrospinal fluid ; Biomarkers/cerebrospinal fluid ; Disease Progression
Chemical Substances	Immunoglobulin kappa-Chains ; Biomarkers
Language	English
Publishing date	2023-12-22
Publishing country	Netherlands
Document type	Journal Article
ZDB-ID	2645330-7
ISSN	2211-0356 ; 2211-0348
ISSN (online)	2211-0356
ISSN	2211-0348
DOI	10.1016/j.msard.2023.105402
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Article: Overview of the Current Pathophysiology of Fatigue in Multiple Sclerosis, Its Diagnosis and Treatment Options - Review Article.

Zimek, Dalibor / Miklusova, Martina / Mares, Jan

Neuropsychiatric disease and treatment

2023 Volume 19, Page(s) 2485–2497

Abstract: Fatigue is a common, debilitating and often underestimated symptom in patients with multiple sclerosis (MS). The exact pathophysiological mechanism of fatigue in MS is still unknown. However, there are many theories involving different immunological, ... ...

Abstract	Fatigue is a common, debilitating and often underestimated symptom in patients with multiple sclerosis (MS). The exact pathophysiological mechanism of fatigue in MS is still unknown. However, there are many theories involving different immunological, metabolic and inflammatory mechanisms of fatigue. Owing to the subjective nature of this symptom, its diagnosis is still very limited and is still based only on diagnostic questionnaires. Although several therapeutic agents have been used in the past to try to influence fatigue in MS patients, no single effective approach for the treatment of fatigue has yet been found. This review article aims to provide the reader with information on the current theories on the origin and mechanism of fatigue in MS, as well as diagnostic procedures and, finally, current therapeutic strategies for the management of fatigue in MS patients.
Language	English
Publishing date	2023-11-20
Publishing country	New Zealand
Document type	Journal Article ; Review
ZDB-ID	2186503-6
ISSN	1178-2021 ; 1176-6328
ISSN (online)	1178-2021
ISSN	1176-6328
DOI	10.2147/NDT.S429862
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Article ; Online: An updated classification of cyanobacterial orders and families based on phylogenomic and polyphasic analysis.

Strunecký, Otakar / Ivanova, Anna Pavlovna / Mareš, Jan

Journal of phycology

2023 Volume 59, Issue 1, Page(s) 12–51

Abstract: Cyanobacterial taxonomy is facing a period of rapid changes thanks to the ease of 16S rRNA gene sequencing and established workflows for description of new taxa. Since the last comprehensive review of the cyanobacterial system in 2014 until 2021, at ... ...

Abstract	Cyanobacterial taxonomy is facing a period of rapid changes thanks to the ease of 16S rRNA gene sequencing and established workflows for description of new taxa. Since the last comprehensive review of the cyanobacterial system in 2014 until 2021, at least 273 species in 140 genera were newly described. These taxa were mainly placed into previously defined orders and families although several new families were proposed. However, the classification of most taxa still relied on hierarchical relationships inherited from the classical morphological taxonomy. Similarly, the obviously polyphyletic orders such as Synechococcales and Oscillatoriales were left unchanged. In this study, the rising number of genomic sequences of cyanobacteria and well-described reference strains allowed us to reconstruct a robust phylogenomic tree for taxonomic purposes. A less robust but better sampled 16S rRNA gene phylogeny was mapped to the phylogenomic backbone. Based on both these phylogenies, a polyphasic classification throughout the whole phylum of Cyanobacteria was created, with ten new orders and fifteen new families. The proposed system of cyanobacterial orders and families relied on a phylogenomic tree but still employed phenotypic apomorphies where possible to make it useful for professionals in the field. It was, however, confirmed that morphological convergence of phylogenetically distant taxa was a frequent phenomenon in cyanobacteria. Moreover, the limited phylogenetic informativeness of the 16S rRNA gene, resulting in ambiguous phylogenies above the genus level, emphasized the integration of genomic data as a prerequisite for the conclusive taxonomic placement of a vast number of cyanobacterial genera in the future.
MeSH term(s)	Phylogeny ; RNA, Ribosomal, 16S/genetics ; Cyanobacteria/genetics ; Genome ; Sequence Analysis, DNA
Chemical Substances	RNA, Ribosomal, 16S
Language	English
Publishing date	2023-01-13
Publishing country	United States
Document type	Journal Article ; Review ; Research Support, Non-U.S. Gov't
ZDB-ID	281226-5
ISSN	1529-8817 ; 0022-3646
ISSN (online)	1529-8817
ISSN	0022-3646
DOI	10.1111/jpy.13304
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Article ; Online: Lutein and Zeaxanthin Isomers in Eye Health and Disease.

Mares, Julie

Annual review of nutrition

2016 Volume 36, Page(s) 571–602

Abstract: Current evidence suggests lutein and its isomers play important roles in ocular development in utero and throughout the life span, in vision performance in young and later adulthood, and in lowering risk for the development of common age-related eye ... ...

Abstract	Current evidence suggests lutein and its isomers play important roles in ocular development in utero and throughout the life span, in vision performance in young and later adulthood, and in lowering risk for the development of common age-related eye diseases in older age. These xanthophyll (oxygen-containing) carotenoids are found in a wide variety of vegetables and fruits, and they are present in especially high concentrations in leafy green vegetables. Additionally, egg yolks and human milk appear to be bioavailable sources. The prevalence of lutein, zeaxanthin, and meso-zeaxanthin in supplements is increasing. Setting optimal and safe ranges of intake requires additional research, particularly in pregnant and lactating women. Accumulating evidence about variable interindividual response to dietary intake of these carotenoids, based on genetic or metabolic influences, suggests that there may be subgroups that benefit from higher levels of intake and/or alternate strategies to improve lutein and zeaxanthin status.
MeSH term(s)	Age Factors ; Animals ; Anti-Inflammatory Agents, Non-Steroidal/adverse effects ; Anti-Inflammatory Agents, Non-Steroidal/chemistry ; Anti-Inflammatory Agents, Non-Steroidal/metabolism ; Anti-Inflammatory Agents, Non-Steroidal/therapeutic use ; Antioxidants/adverse effects ; Antioxidants/chemistry ; Antioxidants/metabolism ; Antioxidants/therapeutic use ; Dietary Supplements ; Eye Diseases/immunology ; Eye Diseases/metabolism ; Eye Diseases/pathology ; Eye Diseases/prevention & control ; Healthy Diet ; Humans ; Lutein/adverse effects ; Lutein/analogs & derivatives ; Lutein/metabolism ; Lutein/therapeutic use ; Models, Biological ; Organ Specificity ; Oxidative Stress ; Retina/growth & development ; Retina/immunology ; Retina/metabolism ; Retina/pathology ; Stereoisomerism ; Vision Disorders/immunology ; Vision Disorders/metabolism ; Vision Disorders/pathology ; Vision Disorders/prevention & control ; Zeaxanthins/adverse effects ; Zeaxanthins/chemistry ; Zeaxanthins/metabolism ; Zeaxanthins/therapeutic use
Chemical Substances	Anti-Inflammatory Agents, Non-Steroidal ; Antioxidants ; Zeaxanthins ; Lutein (X72A60C9MT)
Language	English
Publishing date	2016-07-17
Publishing country	United States
Document type	Journal Article ; Review
ZDB-ID	406980-8
ISSN	1545-4312 ; 0199-9885
ISSN (online)	1545-4312
ISSN	0199-9885
DOI	10.1146/annurev-nutr-071715-051110
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Article ; Online: Endoscopic clips versus overstitch suturing system device for mucosotomy closure after peroral endoscopic pyloromyotomy (G-POEM): a prospective single-center study.

Hustak, R / Vackova, Z / Krajciova, J / Spicak, J / Kieslichova, E / Mares, J / Martinek, Jan

Surgical endoscopy

2022 Volume 36, Issue 12, Page(s) 9254–9261

Abstract: Background and aims: G-POEM is an emerging method for treatment of severe gastroparesis. Safe mucosal closure is necessary to avoid adverse events. The aim of this study was to compare the efficacy of two closure methods: clips and endoscopic suturing ( ... ...

Abstract	Background and aims: G-POEM is an emerging method for treatment of severe gastroparesis. Safe mucosal closure is necessary to avoid adverse events. The aim of this study was to compare the efficacy of two closure methods: clips and endoscopic suturing (ES) after G-POEM. Methods: We performed a single center, prospective study. The closure method was assigned at the discretion of an endoscopist prior to the procedure. The main outcome was the proportion of subjects with successful closure. Unsuccessful closure was defined as a need for a rescue method, or a need for an additional intervention or incomplete closure-related adverse events. Secondary outcomes were the easiness of closure (VAS score 1 = very difficult, 10 = easy), closure time, and cost. Results: A total of 40 patients [21 female; mean age, range 47.5; (20-74)] were included; 20 received ES and 20 clips [mean number of clips 6; range (4-19)]. All 20 patients with ES (100%, 95% CI 84-100%) and 18 patients with clips (89%, 95% CI 70-97%) had successful closure (p = 0.49). One patient needed a rescue method (KING closure) and the other patient an additional clipping on POD1. Closure with clips was quicker [mean time 9.8 (range 4-20) min vs. 14.1 (5-21) min; p = 0.007] and cheaper [mean cost 807 USD (± 402) vs. 2353 USD (± 145); p < 0.001]. Endoscopist assessed the easiness of ES and clips as comparable [mean VAS, range 7.5 (3-10) (ES) vs. 6.9 (3-10) (clips); p = 0.3]. Conclusions: Both ES and clips are effective methods for mucosal closure in patients undergoing G-POEM. However, centres using clips should have a rescue closure method available as clips may fail in some patients. Closure with ES is more costly than with clips.
MeSH term(s)	Humans ; Female ; Pyloromyotomy/methods ; Prospective Studies ; Gastroparesis/surgery ; Endoscopy ; Surgical Instruments ; Treatment Outcome ; Esophageal Achalasia/surgery
Language	English
Publishing date	2022-07-18
Publishing country	Germany
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	639039-0
ISSN	1432-2218 ; 0930-2794
ISSN (online)	1432-2218
ISSN	0930-2794
DOI	10.1007/s00464-022-09417-1
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Article ; Online: Crocosphaera watsonii - A widespread nitrogen-fixing unicellular marine cyanobacterium.

Masuda, Takako / Mareš, Jan / Shiozaki, Takuhei / Inomura, Keisuke / Fujiwara, Amane / Prášil, Ondřej

Journal of phycology

2024

Abstract: Crocosphaera watsonii is a unicellular ... ...

Abstract	Crocosphaera watsonii is a unicellular N
Language	English
Publishing date	2024-03-29
Publishing country	United States
Document type	Journal Article ; Review
ZDB-ID	281226-5
ISSN	1529-8817 ; 0022-3646
ISSN (online)	1529-8817
ISSN	0022-3646
DOI	10.1111/jpy.13450
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Article: Multilocus and SSU rRNA gene phylogenetic analyses of available cyanobacterial genomes, and their relation to the current taxonomic system

Mareš, Jan

Hydrobiologia. 2018 Apr., v. 811, no. 1

2018

Abstract: Despite the global significance of cyanobacteria, their taxonomy is still heavily lagging behind the progress in genome sequencing. Besides nomenclatural issues and difficulties in species identification, this problem is largely a consequence of missing ... ...

Abstract	Despite the global significance of cyanobacteria, their taxonomy is still heavily lagging behind the progress in genome sequencing. Besides nomenclatural issues and difficulties in species identification, this problem is largely a consequence of missing reference strains and sequences for many cyanobacterial taxa. In this study, a robust multilocus phylogenetic tree based on 23 conserved proteins from the current set of available genomes is presented and compared to a respective 16S rRNA gene tree. To facilitate further progress in achieving a stable system of monophyletic taxa, the phylogenetic status of eight cyanobacterial orders recently proposed in the botanical system was evaluated. While several orders addressed by previous studies (Gloeobacterales, Spirulinales, Chroococcidiopsidales, Nostocales) retain their monophyly, the remaining big groups (Synechococcales, Pleurocapsales, Chroococcales, Oscillatoriales) are polyphyletic and require thorough revision. Comparison of the 16S rRNA tree to the multilocus tree supports the careful use of this gene in distinguishing cyanobacterial genera, whereas its application at other taxonomic levels is limited.
Keywords	Chroococcales ; Gloeobacterales ; Nostocales ; Oscillatoriales ; Pleurocapsales ; Synechococcales ; genes ; monophyly ; polyphyly ; proteins ; ribosomal RNA ; sequence analysis ; species identification ; trees
Language	English
Dates of publication	2018-04
Size	p. 19-34.
Publishing place	Springer International Publishing
Document type	Article
ZDB-ID	214428-1
ISSN	1573-5117 ; 0018-8158
ISSN (online)	1573-5117
ISSN	0018-8158
DOI	10.1007/s10750-017-3373-2
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Article: Úvodník.

Mareš, Jan

Ceskoslovenska fysiologie

2015 Volume 64, Issue 1, Page(s) 1

Title translation	Editorial.
MeSH term(s)	Humans ; Periodicals as Topic ; Physiology ; Students
Language	Slovak
Publishing date	2015
Publishing country	Czech Republic
Document type	Editorial
ZDB-ID	419220-5
ISSN	1210-6313 ; 0009-0557
ISSN	1210-6313 ; 0009-0557
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