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Article ; Online: Scdrake: a reproducible and scalable pipeline for scRNA-seq data analysis.

Kubovčiak, Jan / Kolář, Michal / Novotný, Jiří

Bioinformatics advances

2023 Volume 3, Issue 1, Page(s) vbad089

Abstract: ... scripts. There is no fully automated pipeline in the R statistical environment, which would follow ... in the R language and built within the drake framework. The pipeline includes quality control, cell and ...

Abstract	Motivation: While the workflow for primary analysis of single-cell RNA-seq (scRNA-seq) data is well established, the secondary analysis of the feature-barcode matrix is usually done by custom scripts. There is no fully automated pipeline in the R statistical environment, which would follow the current best programming practices and requirements for reproducibility. Results: We have developed scdrake, a fully automated workflow for secondary analysis of scRNA-seq data, which is fully implemented in the R language and built within the drake framework. The pipeline includes quality control, cell and gene filtering, normalization, detection of highly variable genes, dimensionality reduction, clustering, cell type annotation, detection of marker genes, differential expression analysis and integration of multiple samples. The pipeline is reproducible and scalable, has an efficient execution, provides easy extendability and access to intermediate results and outputs rich HTML reports. Scdrake is distributed as a Docker image, which provides a straightforward setup and enhances reproducibility. Availability and implementation: The source code and documentation are available under the MIT license at https://github.com/bioinfocz/scdrake and https://bioinfocz.github.io/scdrake, respectively. Supplementary information: Supplementary data are available at
Language	English
Publishing date	2023-07-06
Publishing country	England
Document type	Journal Article
ISSN	2635-0041
ISSN (online)	2635-0041
DOI	10.1093/bioadv/vbad089
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Article ; Online: Accelerated reactive dissolution model of drug release from long-acting injectable formulations.

Sonntag, Erik / Kolář, Jiří / Djukaj, Suada / Lehocký, Róbert / Štěpánek, František

European journal of pharmaceutics and biopharmaceutics : official journal of Arbeitsgemeinschaft fur Pharmazeutische Verfahrenstechnik e.V

2023 Volume 189, Page(s) 122–132

Abstract: Long-acting injectable formulations represent a rapidly emerging category of drug delivery systems that offer several advantages compared to orally administered medicines. Rather than having to frequently swallow tablets, the medication is administered ... ...

Abstract	Long-acting injectable formulations represent a rapidly emerging category of drug delivery systems that offer several advantages compared to orally administered medicines. Rather than having to frequently swallow tablets, the medication is administered to the patient by intramuscular or subcutaneous injection of a nanoparticle suspension that forms a local depot from which the drug is steadily released over a period of several weeks or months. The benefits of this approach include improved medication compliance, reduced fluctuations of drug plasma level, or the suppression of gastrointestinal tract irritation. The mechanism of drug release from injectable depot systems is complex, and there is a lack of models that would enable quantitative parametrisation of the process. In this work, an experimental and computational study of drug release from a long-acting injectable depot system is reported. A population balance model of prodrug dissolution from asuspension with specific particle size distribution has been coupled with the kinetics of prodrug hydrolysis to its parent drug and validated using in vitro experimental data obtained from an accelerated reactive dissolution test. Using the developed model, it is possible to predict the sensitivity of drug release profiles to the initial concentration and particle size distribution of the prodrug suspension, and subsequently simulate various drug dosing scenarios. Parametric analysis of the system has identified the boundaries of reaction- and dissolution-limited drug release regimes, and the conditions for the existence of a quasi-steady state. This knowledge is crucial for the rational design of drug formulations in terms of particle size distribution, concentration and intended duration of drug release.
MeSH term(s)	Humans ; Antipsychotic Agents ; Prodrugs ; Drug Liberation ; Solubility ; Injections, Intramuscular ; Suspensions ; Delayed-Action Preparations
Chemical Substances	Antipsychotic Agents ; Prodrugs ; Suspensions ; Delayed-Action Preparations
Language	English
Publishing date	2023-06-14
Publishing country	Netherlands
Document type	Journal Article
ZDB-ID	1065368-5
ISSN	1873-3441 ; 0939-6411
ISSN (online)	1873-3441
ISSN	0939-6411
DOI	10.1016/j.ejpb.2023.06.003
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Article: How to Tackle Phylogenetic Discordance in Recent and Rapidly Radiating Groups? Developing a Workflow Using

Kandziora, Martha / Sklenář, Petr / Kolář, Filip / Schmickl, Roswitha

Frontiers in plant science

2022 Volume 12, Page(s) 765719

Abstract: A major challenge in phylogenetics and -genomics is to resolve young rapidly radiating groups. The fast succession of species increases the probability of incomplete lineage sorting (ILS), and different topologies of the gene trees are expected, leading ... ...

Abstract	A major challenge in phylogenetics and -genomics is to resolve young rapidly radiating groups. The fast succession of species increases the probability of incomplete lineage sorting (ILS), and different topologies of the gene trees are expected, leading to gene tree discordance, i.e., not all gene trees represent the species tree. Phylogenetic discordance is common in phylogenomic datasets, and apart from ILS, additional sources include hybridization, whole-genome duplication, and methodological artifacts. Despite a high degree of gene tree discordance, species trees are often well supported and the sources of discordance are not further addressed in phylogenomic studies, which can eventually lead to incorrect phylogenetic hypotheses, especially in rapidly radiating groups. We chose the high-Andean Asteraceae genus
Language	English
Publishing date	2022-01-07
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	2613694-6
ISSN	1664-462X
ISSN	1664-462X
DOI	10.3389/fpls.2021.765719
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Article ; Online: An update on the epidemiology of eating disorders in Latin America: current findings and future challenges.

Kolar, David R / Mebarak, Moises

Current opinion in psychiatry

2022 Volume 35, Issue 6, Page(s) 385–389

Abstract: Purpose of review: We systematically reviewed the recent literature on the epidemiology of eating disorders in Latin America.: Recent findings: Most screened articles only investigated risk for eating disorders or disordered eating behaviors. Four ... ...

Abstract	Purpose of review: We systematically reviewed the recent literature on the epidemiology of eating disorders in Latin America. Recent findings: Most screened articles only investigated risk for eating disorders or disordered eating behaviors. Four studies reported prevalence for eating disorders. One study reported age-standardized prevalence ranging from 0.04% [95% confidence interval, CI (0.03, 0.06)] to 0.09% [95% CI (0.07, 0.13)] for anorexia nervosa and from 0.13% [95% CI (0.08, 0.17)] to 0.27% [95% CI (0.18, 0.37)] for bulimia nervosa. Three additional studies conducted in Brazil identified a general eating disorder point-prevalence of 0.40% in children aged 6--14 years and a point-prevalence of 0.7 % [95% CI (0.34, 1.55)] for bulimia nervosa, 1.4% [95% CI (0.81, 2.43)] for binge-eating disorder and 6.2% [95% CI (3.10, 5.27)] for recurrent binge eating. Summary: Since 2020, only few studies were published on the epidemiology of full-threshold eating disorders in Latin America. Prevalence was in a comparable range to previous findings. No studies regarding new DSM-5 eating disorder diagnoses were identified, and studies investigating the impact of the COVID-19 pandemic on prevalence or incidence of eating disorders in these countries are needed.
MeSH term(s)	Anorexia Nervosa ; Binge-Eating Disorder/epidemiology ; Bulimia Nervosa/diagnosis ; Bulimia Nervosa/epidemiology ; COVID-19 ; Child ; Feeding and Eating Disorders/epidemiology ; Humans ; Latin America/epidemiology ; Pandemics
Language	English
Publishing date	2022-07-18
Publishing country	United States
Document type	Journal Article ; Systematic Review
ZDB-ID	645162-7
ISSN	1473-6578 ; 0951-7367
ISSN (online)	1473-6578
ISSN	0951-7367
DOI	10.1097/YCO.0000000000000813
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Article: [Bacterial complications in surgical management of esophageal cancer].

Vrba, Radek / Kučová, Pavla / Ľubušká, Lucie / Fišerová, Kateřina / Kolář, Milan

Klinicka mikrobiologie a infekcni lekarstvi

2022 Volume 27, Issue 3, Page(s) 93–97

Abstract: One of the most common cancers is esophageal carcinoma. The basic therapeutic approach is esophagectomy, one of the most extensive procedures in general surgery, potentially leading to serious postoperative complications, in particular respiratory ... ...

Abstract	One of the most common cancers is esophageal carcinoma. The basic therapeutic approach is esophagectomy, one of the most extensive procedures in general surgery, potentially leading to serious postoperative complications, in particular respiratory complications. The objective was clinical and microbiological characterization of patients after the surgical removal of the esophagus for carcinoma. In 2020, a total of 14 patients underwent the surgery. Respiratory complications occurred in 57 % of them, with pneumonia leading to respiratory failure and acute respiratory distress syndrome being noted in 21 %. The identified bacterial pathogens were strains of Acinetobacter johnsonii, Enterobacter cloacae, Serratia marcescens, Pseudomonas aeruginosa, Stenotrophomonas maltophilia and Enterococcus faecium. In one case, the patient's condition was complicated by fungal infection caused by Candida krusei. The study results warrant the need for close collaboration between the physician caring for a particular patient and a microbiologist that must be continuous and based on daily assessment of both microbiology test results and the patient's clinical condition.
MeSH term(s)	Enterococcus faecium ; Esophageal Neoplasms/surgery ; Humans ; Microbial Sensitivity Tests ; Pseudomonas aeruginosa ; Stenotrophomonas maltophilia
Language	Czech
Publishing date	2022-02-14
Publishing country	Czech Republic
Document type	Journal Article
ZDB-ID	2214815-2
ISSN	1211-264X
ISSN	1211-264X
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Article: Photoplethysmographic analysis of retinal videodata based on the Fourier domain approach.

Kolář, Radim / Odstrčilík, Jan / Tornow, Ralf-Peter

Biomedical optics express

2021 Volume 12, Issue 12, Page(s) 7405–7421

Abstract: Assessment of retinal blood flow inside the optic nerve head (ONH) and the peripapillary area is an important task in retinal imaging. For this purpose, an experimental binocular video ophthalmoscope that acquires precisely synchronized video sequences ... ...

Abstract	Assessment of retinal blood flow inside the optic nerve head (ONH) and the peripapillary area is an important task in retinal imaging. For this purpose, an experimental binocular video ophthalmoscope that acquires precisely synchronized video sequences of the optic nerve head and peripapillary area from both eyes has been previously developed. It enables to compare specific characteristics of both eyes and efficiently detect the eye asymmetry. In this paper, we describe a novel methodology for the analysis of acquired video data using a photoplethysmographic approach. We describe and calculate the pulsatile attenuation amplitude (PAA) spatial map, which quantifies the maximum relative change of blood volume during a cardiac cycle using a frequency domain approach. We also describe in detail the origin of PAA maps from the fundamental (the first) and the second harmonic component of the pulsatile signal, and we compare the results obtained by time-based and frequency-based approaches. In several cases, we show the advantages and possibilities of this device and the appropriate image analysis approach - fast measurement and comparison of blood flow characteristics of both eyes at a glance, the robustness of this approach, and the possibility of easy detection of asymmetry.
Language	English
Publishing date	2021-11-09
Publishing country	United States
Document type	Journal Article
ZDB-ID	2572216-5
ISSN	2156-7085
ISSN	2156-7085
DOI	10.1364/BOE.441451
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Article ; Online: Erratum: Steady-State Coherences by Composite System-Bath Interactions [Phys. Rev. Lett. 121, 070401 (2018)].

Guarnieri, Giacomo / Kolář, Michal / Filip, Radim

Physical review letters

2021 Volume 127, Issue 12, Page(s) 129901

Abstract: This corrects the article DOI: 10.1103/PhysRevLett.121.070401. ...

Abstract	This corrects the article DOI: 10.1103/PhysRevLett.121.070401.
Language	English
Publishing date	2021-10-01
Publishing country	United States
Document type	Published Erratum
ZDB-ID	208853-8
ISSN	1079-7114 ; 0031-9007
ISSN (online)	1079-7114
ISSN	0031-9007
DOI	10.1103/PhysRevLett.127.129901
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Article: [Direct identification of bacteria in blood cultures by MALDI-TOF MS].

Homolová, Radka / Bogdanová, Kateřina / Bardoň, Jan / Kolář, Milan

Klinicka mikrobiologie a infekcni lekarstvi

2021 Volume 26, Issue 2, Page(s) 45–50

Abstract: Background: Early and causal administration of antibiotics in patients with a positive blood culture is an essential prerequisite for successful treatment of infection. However, isolation and subsequent identification of bacteria in a blood culture by ... ...

Abstract	Background: Early and causal administration of antibiotics in patients with a positive blood culture is an essential prerequisite for successful treatment of infection. However, isolation and subsequent identification of bacteria in a blood culture by classical (culture) methods may last several days. MALDI-TOF MS is a method allowing rapid identification of bacteria, not only cultures from culture media, but also directly in clinical specimens. Methods: The study included samples of positive blood cultures taken from patients in the University Hospital Olomouc between 2016 and 2018 and examined at the Department of Microbiology of the Faculty of Medicine, Palacký University Olomouc. Positive blood culture samples were processed using an in-house method involving the removal of blood cells by low-speed centrifugation. Subsequently, a pellet obtained by high-speed centrifugation and sample washing was tested by MALDI-TOF MS. Results: A total of 110 positive blood cultures were examined using the method of direct identification. At a species level, more Gram-negative bacteria (88 %) than Gram-positive bacteria (79 %) were correctly identified, with higher identification score values being obtained for the former. Identification score values of 2.0 or higher were found in 62 % of blood cultures containing Gram-negative bacteria and 17 % of blood cultures containing Gram-positive bacteria. Identification score values ranging from 1.7 to 2.0 were found in 21 % of Gram-negative blood cultures and 33 % of blood cultures containing Gram-positive bacteria. Conclusion: Direct identification of microorganisms from positive blood cultures using MALDI-TOF MS enables more rapid diagnosis. By reducing the time required to obtain the result of pathogen identification, it may positively affect the antibiotic treatment of patients.
MeSH term(s)	Bacteremia/diagnosis ; Bacteremia/microbiology ; Bacteria/classification ; Bacteria/isolation & purification ; Blood Culture ; Czech Republic ; Humans ; Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization
Language	Czech
Publishing date	2021-01-03
Publishing country	Czech Republic
Document type	Journal Article
ZDB-ID	2214815-2
ISSN	1211-264X
ISSN	1211-264X
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Article: Bacterial Community- and Hospital-Acquired Pneumonia in Patients with Critical COVID-19-A Prospective Monocentric Cohort Study.

Doubravská, Lenka / Htoutou Sedláková, Miroslava / Fišerová, Kateřina / Klementová, Olga / Turek, Radovan / Langová, Kateřina / Kolář, Milan

Antibiotics (Basel, Switzerland)

2024 Volume 13, Issue 2

Abstract: The impact of bacterial pneumonia on patients with COVID-19 infection remains unclear. This prospective observational monocentric cohort study aims to determine the incidence of bacterial community- and hospital-acquired pneumonia (CAP and HAP) and its ... ...

Abstract	The impact of bacterial pneumonia on patients with COVID-19 infection remains unclear. This prospective observational monocentric cohort study aims to determine the incidence of bacterial community- and hospital-acquired pneumonia (CAP and HAP) and its effect on mortality in critically ill COVID-19 patients admitted to the intensive care unit (ICU) at University Hospital Olomouc between 1 November 2020 and 31 December 2022. The secondary objectives of this study include identifying the bacterial etiology of CAP and HAP and exploring the capabilities of diagnostic tools, with a focus on inflammatory biomarkers. Data were collected from the electronic information hospital system, encompassing biomarkers, microbiological findings, and daily visit records, and subsequently evaluated by ICU physicians and clinical microbiologists. Out of 171 patients suffering from critical COVID-19, 46 (27%) had CAP, while 78 (46%) developed HAP. Critically ill COVID-19 patients who experienced bacterial CAP and HAP exhibited higher mortality compared to COVID-19 patients without any bacterial infection, with rates of 38% and 56% versus 11%, respectively. In CAP, the most frequent causative agents were chlamydophila and mycoplasma; Enterobacterales, which were multidrug-resistant in 71% of cases; Gram-negative non-fermenting rods; and
Language	English
Publishing date	2024-02-16
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	2681345-2
ISSN	2079-6382
ISSN	2079-6382
DOI	10.3390/antibiotics13020192
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Article ; Online: Mirror visual feedback as therapeutic modality in unilateral upper extremity complex regional pain syndrome type I: randomized controlled trial.

Machač, Stanislav / Chasáková, Ludmila / Kakawand, Soroush / Kozák, Jiří / Štěpánek, Lubomír / Vejvalka, Jan / Kolář, Pavel / Černý, Rudolf

European journal of physical and rehabilitation medicine

2024 Volume 60, Issue 2, Page(s) 280–291

Abstract: Background: There is growing evidence for the effectiveness of mirror therapy (MT) on pain reduction in patients with type I complex regional pain syndrome (CRPS I).: Aim: To evaluate the efficacy of MT on pain reduction and hand function in subjects ...

Abstract	Background: There is growing evidence for the effectiveness of mirror therapy (MT) on pain reduction in patients with type I complex regional pain syndrome (CRPS I). Aim: To evaluate the efficacy of MT on pain reduction and hand function in subjects with unilateral upper extremity CRPS I. Design: Randomized controlled trial with control group cross-over (half cross-over design). Setting: Subjects with CRPS I were outpatients of a university hospital and cooperating centers. All patients carried out the daily exercise at home. Population: Subjects with unilateral upper extremity CRPS I meeting the Budapest diagnostic criteria. Methods: Subjects were randomly divided into two groups. Group A (N.=13) carried out a ten-minute MT exercise daily, for a total duration of six weeks. Group B (N.=14) acted as a control group for six weeks followed by six weeks of MT with the same characteristics as Group A. Upper extremity active range of motion, strength, dexterity, limb volume, affected-to-unaffected hand temperature difference, and health-related quality of life were evaluated before and after each period. Daily records on the visual analogue scale were used for pain evaluation. Effectiveness was calculated using mixed-effects modelling for between-group comparisons and within-group variability, and identification of significant predictors. Results: Twenty-three females and four males with an average age of 56.1±9.6 years completed the study. Except for the affected-to-unaffected hand temperature difference, both groups consistently demonstrated significant or near-significant improvements in measured parameters after MT period. The improvements were evident upon an intergroup comparison of Group A and the control period of Group B as well as longitudinally within Group B. No significant improvement was found during the control period. Conclusions: Principles focused on mirror visual feedback to the central nervous system can sustain promising therapeutic potential as part of the treatment for pain reduction and hand function in CRPS I patients. Clinical rehabilitation impact: MT can be considered as part of the therapeutic regimen employed for the treatment of CRPS I.
MeSH term(s)	Male ; Female ; Humans ; Middle Aged ; Aged ; Reflex Sympathetic Dystrophy/therapy ; Quality of Life ; Feedback, Sensory ; Treatment Outcome ; Upper Extremity ; Complex Regional Pain Syndromes/therapy ; Pain
Language	English
Publishing date	2024-01-10
Publishing country	Italy
Document type	Randomized Controlled Trial ; Journal Article
ZDB-ID	2426908-6
ISSN	1973-9095 ; 1973-9087
ISSN (online)	1973-9095
ISSN	1973-9087
DOI	10.23736/S1973-9087.23.07625-6
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