Publications by authors named "Jiří Novák"

88 Publications

Current possibilities of diagnostics and treatment of immunological causes of female infertility.

Cas Lek Cesk 2021 ;160(1):5-13

The immune system plays an important role in many processes of human reproduction. During pregnancy, mother's body has to accept the semialogenic fetus, therefore the role of immune processes has a high importance. Tolerance of the fetus by the mother's immune system is ensured by a complex of immune mechanisms, the knowledge of which brings us to the new insights into human reproduction processes and in seeking of new ways to modulate immunity in repeated embryo implantation failures, miscarriages, premature births, preeclampsia, and other fertility disorders and pregnancy complications. The review article is a summary of current possibilities of immunological laboratory diagnostics in reproductive immunology, presents indications for these tests and their interpretation, and mentions possible methods of therapeutic immune intervention.
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April 2021

Bringing SEM and MSI Closer Than Ever Before: Visualizing and Infection in the Rat Lungs.

J Fungi (Basel) 2020 Oct 30;6(4). Epub 2020 Oct 30.

Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, 142 20 Prague, Czech Republic.

A procedure for processing frozen rat lung tissue sections for scanning electron microscopy (SEM) from deeply frozen samples initially collected and stored for matrix-assisted laser desorption/ionization mass spectrometry imaging (MALDI-MSI) was developed. The procedure employed slow thawing of the frozen sections while floating on the surface and melting in a fixative solution. After the float-washing step, the sections were dehydrated in a graded ethanol series and dried in a critical point dryer. The SEM generated images with well-preserved structures, allowing for monitoring of bacterial cells and fungal hyphae in the infected tissue. Importantly, the consecutive nonfixed frozen sections were fully compatible with MALDI-MSI, providing molecular biomarker maps of . The protocol enables bimodal image fusion in the in-house software CycloBranch, as demonstrated by SEM and MALDI-MSI.
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http://dx.doi.org/10.3390/jof6040257DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7711807PMC
October 2020

Airborne PAHs inhibit gap junctional intercellular communication and activate MAPKs in human bronchial epithelial cell line.

Environ Toxicol Pharmacol 2020 Oct 31;79:103422. Epub 2020 May 31.

RECETOX, Faculty of Science, Masaryk University, Brno 62500, Czech Republic. Electronic address:

Inhalation exposures to polycyclic aromatic hydrocarbons (PAHs) have been associated with various adverse health effects, including chronic lung diseases and cancer. Using human bronchial epithelial cell line HBE1, we investigated the effects of structurally different PAHs on tissue homeostatic processes, namely gap junctional intercellular communication (GJIC) and MAPKs activity. Rapid (<1 h) and sustained (up to 24 h) inhibition of GJIC was induced by low/middle molecular weight (MW) PAHs, particularly by those with a bay- or bay-like region (1- and 9-methylanthracene, fluoranthene), but also by fluorene and pyrene. In contrast, linear low MW (anthracene, 2-methylanthracene) or higher MW (chrysene) PAHs did not affect GJIC. Fluoranthene, 1- and 9-methylanthracene induced strong and sustained activation of MAPK ERK1/2, whereas MAPK p38 was activated rather nonspecifically by all tested PAHs. Low/middle MW PAHs can disrupt tissue homeostasis in human airway epithelium via structure-dependent nongenotoxic mechanisms, which can contribute to their human health hazards.
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http://dx.doi.org/10.1016/j.etap.2020.103422DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7486243PMC
October 2020

Toxic potentials of particulate and gaseous air pollutant mixtures and the role of PAHs and their derivatives.

Environ Int 2020 06 20;139:105634. Epub 2020 May 20.

RECETOX, Faculty of Science, Masaryk University, Kamenice 753/5, 625 00 Brno, Czech Republic. Electronic address:

Background: Air pollution, which represents a major environmental risk to human health, comprises a complex mixture of compounds where only little is known about its specific toxicities.

Objectives: This study examined the specific toxicities associated with ambient air pollutant mixtures with respect to gas/particle partitioning, particulate matter (PM) size, pollutant polarity and bioaccessibility from PM, and evaluated the contribution of PAHs and their oxygenated and nitrated derivatives (OPAHs, NPAHs).

Methods: Air samples (gas phase, PM and size-segregated PM), were collected at urban (in winter and summer) and background (winter) sites in the Czech Republic. The total and bioaccessible concentrations were addressed using organic solvent extraction and simulated lung fluid extraction, respectively. Organic extracts were also further fractionated according to polarity. Aryl hydrocarbon receptor (AhR)-mediated activity, anti-/estrogenicity, anti-/androgenicity, thyroid receptor (TR)-mediated activity and cytotoxicity for bronchial cells were determined by human cell-based in vitro bioassays. The contribution of studied compounds to observed effects was assessed by both modelling and reconstructing the mixtures.

Results: Significant effects were detected in the sub-micrometre size fraction of PM (estrogenicity, androgenicity, TR- and AhR-mediated activities) and in the gas phase (TR-mediated activity, antiandrogenicity). Compounds interacting with TR showed high bioaccessibility to simulated lung fluid. Relatively lower bioaccessibility was observed for estrogenicity and AhR-mediated activity. However, the toxicity testing of reconstructed mixtures revealed that the targeted pollutants are not the main contributors, except for urban PM air pollution in winter, where they accounted for 5-88% of several effects detected in the original complex environmental samples.

Discussion: Studied toxicities were mostly driven by polar compounds largely attributed to the easily inhalable PM, which is of high relevance for human health risk assessment. Except of parent PAHs in some cases, the targeted compounds contributed to the detected effects mostly to a relatively low extent implying huge data gaps in terms of endocrine disruptive potencies of targeted substances and the significance of other polar compounds present in ambient air.
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http://dx.doi.org/10.1016/j.envint.2020.105634DOI Listing
June 2020

Seasonal variation of endocrine disrupting potentials of pollutant mixtures associated with various size-fractions of inhalable air particulate matter.

Environ Pollut 2020 Sep 25;264:114654. Epub 2020 Apr 25.

RECETOX, Masaryk University, Kamenice 753/5, 625 00, Brno, Czech Republic. Electronic address:

Ambient air pollution, namely exposure to air particulate matter (PM), has been shown to be connected with a number of adverse health effects. At least part of the effects can be caused by organic pollutant mixtures associated with PM, which can elicit a wide range of specific toxic potentials. These potentials could be affected by seasonal variation of pollutant mixtures and PM size fraction. To examine this, six size subfractions of PM were collected at rural and urban site in the Czech Republic in a year-long sampling campaign. The samples were assessed for aryl hydrocarbon (AhR)-mediated activity, estrogenicity and anti-androgenicity using mammalian cell models. The concentrations of detected toxic potentials differed among seasons. The greatest levels were observed in samples collected during winter when AhR-mediated effects and estrogenicity were at least 10-times greater than in summer. While the observed potentials were mostly less pronounced in samples from rural area, during winter, their AhR-mediated activity was twice as great as at the urban site. This was probably caused by the low-quality of fuel used for heating at the rural site. Assessed toxic potentials were associated mainly with PM size fractions with lesser aerodynamic diameters (<1 μm). Toxic potentials were compared with data from chemical analyses covering 102 chemicals from different pollutant groups to model their contribution to the observed effects. For AhR-mediated activity, chemical analyses explained on average 44% of the effect and the main identified effect-drivers were polycyclic aromatic hydrocarbons. For estrogenicity and anti-androgenicity, detected chemicals were able to explain on average less than 1.6% and 11% of the potentials, with their highest explicability reaching 13% and 57%, respectively. This was affected by the lack of data on specific toxic potency of some detected air pollutants, but also indicates a possible role of further not analyzed chemicals in these effects.
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http://dx.doi.org/10.1016/j.envpol.2020.114654DOI Listing
September 2020

CycloBranch 2: Molecular Formula Annotations Applied to imzML Data Sets in Bimodal Fusion and LC-MS Data Files.

Anal Chem 2020 05 8;92(10):6844-6849. Epub 2020 May 8.

Institute of Microbiology of the Czech Academy of Sciences, Videnska 1083, 142 20 Prague 4, Czech Republic.

Natural product chemistry, microbiology, and food, human, and plant metabolomics represent a few sources of complex metabolomics data generated by mass spectrometry. Among the medley of software tools used to handle these data sets, no universal tool can qualitatively, quantitatively, or statistically address major biological questions or tasks. CycloBranch 2, an open and platform-free software, at least now provides the generation of molecular formulas of unknown compounds in both liquid chromatography/mass spectrometry and mass spectrometry imaging datafiles. For imaging files, this database-free approach was documented in the bimodal image fusion and characterization of three small molecules, including metallophores. The fine isotope ratio data filtering step distinguished S/C and K/C features. The standalone software package is implemented in C++ and can be downloaded from https://ms.biomed.cas.cz/cyclobranch/ and used under GNU General Public License.
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http://dx.doi.org/10.1021/acs.analchem.0c00170DOI Listing
May 2020

Effect of the anti-inflammatory drug diclofenac on lipid composition of bacterial strain Raoultella sp. KDF8.

Folia Microbiol (Praha) 2020 Aug 21;65(4):763-773. Epub 2020 Apr 21.

Institute of Microbiology, Czech Academy of Sciences, Vídeňská 1083, 142 20, Prague 4, Czech Republic.

The strain Raoultella sp. KDF8 was cultivated on three sources of carbon and energy, glycerol, ethanol and diclofenac, for periods of time ranging from 24 to 72 h. Using thin-layer chromatography, nine classes of phospholipids were detected and the amount of phosphatidylethanolamine (PtdEtn) decreased with increasing cultivation time. Conversely, the ratio of phospholipids having three or four acyls (acyl-phosphatidylglycerol (APtdGro), N-acyl-PtdEtn (NAPtdEtn) and cardiolipin (PtdGro) increased during cultivation. GC-MS analysis showed that the percentage of fatty acids containing a cyclopropane ring increased almost tenfold whereas the amount of fatty acids bearing even-numbered chains dropped to less than one-third after 24 h and 72 h in cultures on glycerol and diclofenac, respectively. Shotgun analysis showed significant changes in the representation of molecular species of phospholipids. For instance, there was a 36-fold change in the ratio of 16:1/16:1/16:1-APtdGro to c17:0/c17:0/c17:0-APtdGro and a 12-fold ratio change for 16:1/16:1/16:1-NAPtdEtn to c17:0/c17:0/c17:0-NAPtdEtn; the PtdGro ratio of 16:1 to c17:0 acids equalled 1750. Our results show that the bacteria overcome destabilization of the inner cytoplasmic cell membrane and a bacterial outer membrane by altering the geometric arrangement of acyl chains, i.e. switching from monounsaturated to cyclopropane fatty acids (16:1 versus c17:0).
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http://dx.doi.org/10.1007/s12223-020-00790-9DOI Listing
August 2020

Tuning Spin Current Injection at Ferromagnet-Nonmagnet Interfaces by Molecular Design.

Phys Rev Lett 2020 Jan;124(2):027204

Optoelectronics Group, Cavendish Laboratory, University of Cambridge, J. J. Thompson Avenue, Cambridge CB3 0HE, United Kingdom.

There is a growing interest in utilizing the distinctive material properties of organic semiconductors for spintronic applications. Here, we explore the injection of pure spin current from Permalloy into a small molecule system based on dinaphtho[2,3-b:2,3-f]thieno[3,2-b]thiophene (DNTT) at ferromagnetic resonance. The unique tunability of organic materials by molecular design allows us to study the impact of interfacial properties on the spin injection efficiency systematically. We show that both the spin injection efficiency at the interface and the spin diffusion length can be tuned sensitively by the interfacial molecular structure and side chain substitution of the molecule.
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http://dx.doi.org/10.1103/PhysRevLett.124.027204DOI Listing
January 2020

Oxygenated and Nitrated Polycyclic Aromatic Hydrocarbons in Ambient Air-Levels, Phase Partitioning, Mass Size Distributions, and Inhalation Bioaccessibility.

Environ Sci Technol 2020 03 11;54(5):2615-2625. Epub 2020 Feb 11.

Multiphase Chemistry Department, Max Planck Institute for Chemistry, Mainz 55128, Germany.

Among the nitrated and oxygenated polycyclic aromatic hydrocarbons (NPAHs and OPAHs) are some of the most hazardous substances to public health, mainly because of their carcinogenicity and oxidative potential. Despite these concerns, the concentrations and fate of NPAHs and OPAHs in the atmospheric environment are largely unknown. Ambient air concentrations of 18 NPAHs, 5 quinones, and 5 other OPAHs were determined at two urban and one regional background sites in central Europe. At one of the urban sites, the total (gas and particulate) concentrations of ΣOPAHs were 10.0 ± 9.2 ng/m in winter and 3.5 ± 1.6 ng/m in summer. The gradient to the regional background site exceeded 1 order of magnitude. ΣNPAH concentrations were typically 1 order of magnitude lower than OPAHs. Among OPAHs, 9-fluorenone and (9,10)-anthraquinone were the most abundant species, accompanied by benzanthrone in winter. (9,10)-Anthraquinone represented two-thirds of quinones. We found that a large fraction of the target substance particulate mass was carried by submicrometer particles. The derived inhalation bioaccessibility in the PM size fraction is found to be ≈5% of the total ambient concentration of OPAHs and up to ≈2% for NPAHs. For 9-fluorenone and (9,10)-anthraquinone, up to 86 and 18%, respectively, were found at the rural site. Our results indicate that water solubility could function as a limiting factor for bioaccessibility of inhaled particulate NPAHs and OPAHs, without considerable effect of surfactant lipids and proteins in the lung lining fluid.
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http://dx.doi.org/10.1021/acs.est.9b06820DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7307896PMC
March 2020

Point spread function of an optical system with defocus and spherical aberration-analytical formulas.

Appl Opt 2019 Jul;58(21):5823-5829

This work describes a procedure for an analytical calculation of the point spread function (PSF) of an optical system affected by defocus and spherical aberration. Explicit formulas are derived for the approximate calculation of the PSF of an optical system with spherical aberration up to the ninth order. Application of the derived formulas is performed on an example of optical systems with spherical aberration up to the third order.
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http://dx.doi.org/10.1364/AO.58.005823DOI Listing
July 2019

Method of paraxial design of rifle scope with four-element image-erecting zoom system and high zoom factor.

Appl Opt 2019 Jun;58(17):4787-4796

An analysis and a description of methods for a paraxial design of rifle scopes with a four-element image-erecting zoom system is performed. It is described a method of the calculation of basic design parameters of the rifle scope with the four-element image-erecting zoom system, where two inner elements are movable for ensuring zooming of the rifle scope. The method is demonstrated on two examples of the rifle scope design with the zoom factor 10×. Moreover, the possibility to design the rifle scope with the fixed position of the exit pupil using the four-element image-erecting zoom system with three movable elements is analyzed. The method of the initial paraxial design is demonstrated on two examples of the calculation of the basic rifle scope design parameters. The calculated parameters from proposed methods can be used in the aberration analysis and the optimization of the rifle scope parameters in optical design software.
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http://dx.doi.org/10.1364/AO.58.004787DOI Listing
June 2019

Paraxial focal length calculation using Strehl definition measurement.

Appl Opt 2019 Jun;58(17):4665-4670

This work describes a method for determination of a paraxial focal length of optical systems using measurements of the Strehl definition. The influence of spherical aberration on the value of the measured effective focal length of an optical system is analyzed, and a method is proposed for an elimination of this influence and determination of the paraxial focus position and the paraxial focal length of a lens from the measurement of the effective focal length and the Strehl definition.
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http://dx.doi.org/10.1364/AO.58.004665DOI Listing
June 2019

Influence of astigmatism and field curvature on the correction zones of an optical imaging system.

Appl Opt 2019 May;58(14):3921-3925

By a detailed analysis of the dependence of aberrations on the numerical aperture and the field of view of the optical system, it is possible to find such values of the numerical aperture and the field of view, where the residual wave aberration is zero. These values can be called correction zones. Our work presents a theoretical analysis of the described problem, and general formulas are derived for the expression of wave aberration coefficients using correction zones for astigmatism and field curvature of the third and fifth order. Finally, an analysis of optimum values of correction zones and the optimum position of the image plane has been performed using derived equations with respect to maximization of the Strehl definition. The analysis of the correction zone and the position of the image plane is presented on two examples of the same optical system, where the image plane is located either in the paraxial image plane or in the optimum image plane.
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http://dx.doi.org/10.1364/AO.58.003921DOI Listing
May 2019

Three-component zoom lens with fixed position of optical center.

Appl Opt 2019 May;58(14):3844-3847

A method is proposed for calculation of initial parameters of a three-element zoom lens with an identical position of object and image principal planes of the optical system and approximately zero Petzval sum. Such an optical system has a fixed position of its optical center, which does not depend on object distance. The proposed method makes it possible to determine focal length values of individual elements and trajectories of their movements during zooming. The analysis is presented on examples of the calculation of parameters of such optical systems. These systems could be useful in optical measuring methods, photogrammetry, and machine vision techniques.
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http://dx.doi.org/10.1364/AO.58.003844DOI Listing
May 2019

Analysis of Microbial Siderophores by Mass Spectrometry.

Methods Mol Biol 2019 ;1996:131-153

Institute of Microbiology of the Czech Academy of Sciences, Prague, Czech Republic.

Siderophores represent important microbial virulence factors and infection biomarkers. Their monitoring in fermentation broths, bodily fluids, and tissues should be reproducible. Similar isolation, characterization, and quantitation studies can often have conflicting results, and without proper documentation of sample collection, data processing, and analysis methods, it is difficult to reexamine the data and reconcile these differences. In this Springer Nature Protocol, we present the procedure optimized for ferricrocin/triacetylfusarinine C extraction from biological material as well as for tissue fixation and cryosectioning for optical microscopy and for both elemental and molecular mass spectrometry imaging. Special attention is paid to siderophore data mining from conventional and product ion mass spectra, liquid chromatography, and mass spectrometry imaging datasets, performed here by our free software called CycloBranch.
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http://dx.doi.org/10.1007/978-1-4939-9488-5_12DOI Listing
April 2020

Repeatability and Reproducibility of the RTgill-W1 Cell Line Assay for Predicting Fish Acute Toxicity.

Toxicol Sci 2019 06;169(2):353-364

Eawag, Swiss Federal Institute of Aquatic Science and Technology, Department of Environmental Toxicology, 8600 Dübendorf, Switzerland.

Predicting fish acute toxicity of chemicals in vitro is an attractive alternative method to the conventional approach using juvenile and adult fish. The rainbow trout (Oncorhynchus mykiss) cell line assay with RTgill-W1 cells has been designed for this purpose. It quantifies cell viability using fluorescent measurements for metabolic activity, cell- and lysosomal-membrane integrity on the same set of cells. Results from over 70 organic chemicals attest to the high predictive capacity of this test. We here report on the repeatability (intralaboratory variability) and reproducibility (interlaboratory variability) of the RTgill-W1 cell line assay in a round-robin study focusing on 6 test chemicals involving 6 laboratories from the industrial and academic sector. All participating laboratories were able to establish the assay according to preset quality criteria even though, apart from the lead laboratory, none had previously worked with the RTgill-W1 cell line. Concentration-response modeling, based on either nominal or geometric mean-derived measured concentrations, yielded effect concentrations (EC50) that spanned approximately 4 orders of magnitude over the chemical range, covering all fish acute toxicity categories. Coefficients of variation for intralaboratory and interlaboratory variability for the average of the 3 fluorescent cell viability measurements were 15.5% and 30.8%, respectively, which is comparable to other fish-derived, small-scale bioassays. This study therefore underlines the robustness of the RTgill-W1 cell line assay and its accurate performance when carried out by operators in different laboratory settings.
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http://dx.doi.org/10.1093/toxsci/kfz057DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6542334PMC
June 2019

Metabolic profiling of Fusarium oxysporum f. sp. conglutinans race 2 in dual cultures with biocontrol agents Bacillus amyloliquefaciens, Pseudomonas aeruginosa, and Trichoderma harzianum.

Folia Microbiol (Praha) 2019 Nov 12;64(6):779-787. Epub 2019 Feb 12.

Institute of Microbiology of the CAS, v.v.i., Vídeňská 1083, 14220, Prague 4, Czech Republic.

There are increasing efforts to identify biocontrol-active microbial metabolites in order to improve strategies for biocontrol of phytopathogens. In this work, Fusarium oxysporum f. sp. conglutinans was confronted with three different biocontrol agents: Trichoderma harzianum, Bacillus amyloliquefaciens, and Pseudomonas aeruginosa in dual culture bioassays. Metabolites produced during the microbial interactions were screened by a matrix-assisted laser desorption/ionization mass spectrometry (MALDI-MS). T. harzianum exhibited the strongest inhibition of growth of F. oxysporum resulting in overlay of the pathogen colony with its mycelium. Recorded metabolite profiles suggested a direct attack of F. oxysporum mycelium by T. harzianum and B. amyloliquefaciens by means of membrane-attacking peptaibols and a set of antimicrobial lipopeptides and siderophores, respectively. The direct mode of the biocontrol activity of T. harzianum and B. amyloliquefaciens corresponded to their ability to suppress F. oxysporum production of mycotoxin beauvericin suggesting that this ability is not specific only for Trichoderma species. In the case of P. aeruginosa, siderophores pyoverdine E/D and two rhamnolipids were produced as major bacterial metabolites; the rhamnolipid production was blocked by F. oxysporum. The results showed that this type of biocontrol activity was the least effective against F. oxysporum. The effective application of MALDI-MS profiling to the screening of nonvolatile microbial metabolites produced during the interaction of the phytopathogen and the biocontrol microorganisms was demonstrated.
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http://dx.doi.org/10.1007/s12223-019-00690-7DOI Listing
November 2019

Analytical and bioanalytical assessments of organic micropollutants in the Bosna River using a combination of passive sampling, bioassays and multi-residue analysis.

Sci Total Environ 2019 Feb 27;650(Pt 1):1599-1612. Epub 2018 Aug 27.

Masaryk University, Faculty of Science, RECETOX, Kamenice 753/5, 625 00 Brno, Czech Republic. Electronic address:

Complex mixtures of contaminants from multiple sources, including agriculture, industry or wastewater enter aquatic environments and might pose hazards or risks to humans or wildlife. Targeted analyses of a few priority substances provide limited information about water quality. In this study, a combined chemical and effect screening of water quality in the River Bosna, in Bosnia and Herzegovina was carried out, with focus on occurrence and effects of contaminants of emerging concern. Chemicals in water were sampled at 10 sites along the Bosna River by use of passive sampling. The combination of semipermeable membrane devices (SPMDs) and polar organic chemical integrative samplers (POCIS) enabled sampling of a broad range of contaminants from hydrophobic (PAHs, PCBs, OCPs) to hydrophilic compounds (pesticides, pharmaceuticals and hormones), which were determined by use of GC-MS and LC-MS (MS). In vitro, cell-based bioassays were applied to assess (anti)androgenic, estrogenic and dioxin-like potencies of extracts of the samplers. Of a total of 168 targeted compounds, 107 were detected at least once. Cumulative pollutant concentrations decreased downstream from the city of Sarajevo, which was identified as the major source of organic pollutants in the area. Responses in all bioassays were observed for samples from all sites. In general, estrogenicity could be well explained by analysis of target estrogens, while the drivers of the other observed effects remained largely unknown. Profiling of hazard quotients identified two sites downstream of Sarajevo as hotspots of biological potency. Risk assessment of detected compounds revealed, that 7 compounds (diazinon, diclofenac, 17β-estradiol, estrone, benzo[k]fluoranthene, fluoranthene and benzo[k]fluoranthene) might pose risks to aquatic biota in the Bosna River. The study brings unique results of a complex water quality assessment in a region with an insufficient water treatment infrastructure.
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http://dx.doi.org/10.1016/j.scitotenv.2018.08.336DOI Listing
February 2019

CycloBranch: An open tool for fine isotope structures in conventional and product ion mass spectra.

J Mass Spectrom 2018 Nov;53(11):1097-1103

Institute of Microbiology of the CAS, v.v.i., Videnska 1083, 142 20, Prague 4, Czech Republic.

Within the growing community of Fourier transform mass spectrometry users, the identification of fine isotope structure has become an indispensable method for molecular formula determination. In this work, the fine isotope envelopes for accessing the mutual ratio of 2 closely related pyoverdines in a mixture were used. Bacterial siderophores pyoverdines D and E cannot be easily separated via liquid chromatography-mass spectrometry because their structures differ in (de)amidation at the respective chromophore parts only. Their mutual ratio was determined in a mixture via nuclear magnetic resonance spectroscopy and semiquantitative mass spectrometry using our open-source software CycloBranch, which represents a genuine free tool supporting the determination of fine isotope structures in both conventional and product ion mass spectra. Native Bruker, Thermo, and Waters data formats are supported in addition to XML and plain text formats.
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http://dx.doi.org/10.1002/jms.4285DOI Listing
November 2018

Second cancers in Hodgkin's lymphoma long-term survivals: A 60-year single institutional experience with real-life cohort of 871 patients.

Int J Clin Pract 2018 Jul 16:e13235. Epub 2018 Jul 16.

Department of Comprehensive Cancer Care, Masaryk Memorial Cancer Institute, Brno, Czech Republic.

Background And Purpose: Appropriate surveillance guidelines for patients after successful treatment of Hodgkin's lymphoma (HL) are needed to reduce mortality of iatrogenic secondary cancers (SC). This large single institutional retrospective study analyses the risk of SC in HL patients treated outside of clinical trials over past decades.

Material And Methods: Consecutive series of HL patients were analysed with median follow-up 12 years. Standardised incidence ratio (SIR) and absolute excess risk (AER) were calculated for site-specific risk of SC.

Results: In total of 871 patients (491 men; median age 34 years), chemotherapy alone, radiotherapy alone, and combined treatment underwent 36%, 40%, and 24% patients. 154 SC were found with significantly increased SIR = 2.9 and AER = 80.8 for all cancers except of nonmelanoma-skin cancer. SC-related death occurred in 71 patients (15% of those who died, 8% of whole cohort). The most common SC were lung (17.5% of all malignancies, SIR = 3.2), breast carcinoma (15.6%, SIR = 4.4), and haematological malignancy (non-Hodgkin's lymphoma SIR = 13.1; leukaemia SIR = 5.8). For SC within radiation field, the highest AER was in breast (AER = 46.9), colorectal (AER = 22.8), and lung cancer (AER = 17).

Conclusions: Patients with HL are generally at great risk of developing SC, which is significantly increased especially by the use of radiotherapy. We suggested special follow-up schema for patients after initial HL treatment suitable for daily real-world clinical practice. The system depends on gender, form of HL treatment and especially the form of radiation therapy in terms of location of radiation fields.
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http://dx.doi.org/10.1111/ijcp.13235DOI Listing
July 2018

Analysis of the optical center position of an optical system of a camera lens.

Appl Opt 2018 Jun;57(16):4409-4414

A theory of an optical center of a camera lens is described. The concept of an optical center (a camera center) is used widely in various methods dedicated to the calibration of optical imaging and measuring systems in photogrammetry, computer vision, triangulation sensors, fringe projection techniques, surveying, and machine vision, where the so-called pinhole camera model is used as the camera's basic model. It is shown that the optical center of the optical system with a fixed position does not exist generally, even for an ideal optical system. The optical center can be defined unambiguously for an ideal lens only for one specific object distance in general. Moreover, equations are derived for the calculation of initial design parameters of the three-element optical system composed of thin lens elements having the identical position of object and image principal planes. Such optical systems will have a fixed-position optical center, which does not depend on the object distance. The analysis was presented on several examples of the calculation of parameters of these optical systems.
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http://dx.doi.org/10.1364/AO.57.004409DOI Listing
June 2018

Third-order aberration coefficients of a thick lens with a given value of its focal length.

Appl Opt 2018 May;57(15):4263-4266

The formulas are derived for calculation of the third-order aberration (Seidel) coefficients for a thick spherical lens in air with a given value of its focal length and for an object at infinity in this paper. The explicit analytic dependence of individual aberration coefficients on a lens thickness is derived. Equations were described for the re-calculation of aberration coefficients for a different value of focal length and different values of entrance pupil and object positions. Such formulas make it possible to analyze analytically an influence of the lens thickness on lens aberration properties and the replacement of a thin lens optical system by a thick lens model.
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http://dx.doi.org/10.1364/AO.57.004263DOI Listing
May 2018

Mobile dynamic passive sampling of trace organic compounds: Evaluation of sampler performance in the Danube River.

Sci Total Environ 2018 Sep 30;636:1597-1607. Epub 2018 Mar 30.

Environmental Institute, Okružná 784/42, 972 41 Koš, Slovakia.

A "dynamic" passive sampling (DPS) device, consisting of an electrically driven large volume water pumping device coupled to a passive sampler exposure cell, was designed to enhance the sampling rate of trace organic compounds. The purpose of enhancing the sampling rate was to achieve sufficient method sensitivity, when the period available for sampling is limited to a few days. Because the uptake principle in the DPS remains the same as for conventionally-deployed passive samplers, free dissolved concentrations can be derived from the compound uptake using available passive sampler calibration parameters. This was confirmed by good agreement between aqueous concentrations of polycyclic aromatic hydrocarbons (PAHs), polychlorinated biphenyls (PCBs) and hexachlorobenzene (HCB) derived from DPS and conventional caged passive sampler. The DPS device enhanced sampling rates of compounds that are accumulated in samplers under water boundary layer control (WBL) more than five times compared with the conventionally deployed samplers. The DPS device was deployed from a ship cruising downstream the Danube River to provide temporally and spatially integrated concentrations. A DPS-deployed sampler with surface area of 400cm can reach sampling rates up to 83Ld. The comparison of three passive samplers made of different sorbents and co-deployed in the DPS device, namely silicone rubber (SR), low density polyethylene (LDPE) and SDB-RPS Empore™ disks showed a good correlation of surface specific uptake for compounds that were sampled integratively during the entire exposure period. This provided a good basis for a cross-calibration between the samplers. The good correlation of free dissolved PAHs, PCBs and HCB concentration estimates obtained using SR and LDPE confirmed that both samplers are suitable for the identification of concentration gradients and trends in the water column. We showed that the differences in calculated aqueous concentrations between sampler types are mainly associated with different applied uptake models.
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http://dx.doi.org/10.1016/j.scitotenv.2018.03.242DOI Listing
September 2018

Effect-based monitoring of the Danube River using mobile passive sampling.

Sci Total Environ 2018 Sep 10;636:1608-1619. Epub 2018 Mar 10.

Masaryk University, Faculty of Science, Research Centre for Toxic Compounds in the Environment (RECETOX), Kamenice 753/5, 625 00 Brno, Czech Republic. Electronic address:

Many aquatic pollutants can be present at low concentrations, but their mixtures can still affect health or behavior of exposed organisms. In this study, toxicological and chemical analyses were combined for spatial contamination profiling using an innovative passive sampling approach. A novel Dynamic Passive Sampler (DPS) was employed as a mobile sampler from a ship cruising along 2130km of the Danube river during the Joint Danube Survey 3 (JDS3). The sampling was performed in eight subsequent river stretches with two types of complementary passive samplers: silicone rubber sheets (SR) used for non-polar chemicals and SDB-RPS Empore™ disks (ED) for more hydrophilic compounds. Besides extensive chemical analyses, the bioactivity of samples was characterized by a battery of reporter gene bioassays. Cross-calibration of the employed passive samplers enabled robust estimation of water concentrations applicable for compounds with a wide range of physicochemical properties. DPS was suitable for sampling of water contaminants even at pgL levels, with 209 of 267 analyzed compounds detected in the samples. Biological effects were detected in both ED and SR extracts across all river stretches by bioassays focused on xenobiotic metabolism mediated by the aryl hydrocarbon and pregnane X receptors, endocrine disruptive potential mediated by estrogen and androgen receptors and the oxidative stress response. The bioassay responses expressed as bioanalytical equivalent concentrations (BEQ) were comparable with data obtained from large volume active sampling. The extracts of the ED samplers were more biologically active than extracts of SR samplers. Except of estrogenicity, where the analyzed chemicals explained on average 62% of the effects in ED samples, the detected chemicals explained <8% of BEQ values. The study shows the utility of the combination of the innovative passive sampling approach with effect-based tools for efficient and fast monitoring even in water bodies with relatively low levels of contamination.
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http://dx.doi.org/10.1016/j.scitotenv.2018.02.201DOI Listing
September 2018

Mixture effects in samples of multiple contaminants - An inter-laboratory study with manifold bioassays.

Environ Int 2018 05 28;114:95-106. Epub 2018 Feb 28.

Institute for the Environment, Brunel University, Uxbridge, Middlesex UB8 3PH, United Kingdom.

Chemicals in the environment occur in mixtures rather than as individual entities. Environmental quality monitoring thus faces the challenge to comprehensively assess a multitude of contaminants and potential adverse effects. Effect-based methods have been suggested as complements to chemical analytical characterisation of complex pollution patterns. The regularly observed discrepancy between chemical and biological assessments of adverse effects due to contaminants in the field may be either due to unidentified contaminants or result from interactions of compounds in mixtures. Here, we present an interlaboratory study where individual compounds and their mixtures were investigated by extensive concentration-effect analysis using 19 different bioassays. The assay panel consisted of 5 whole organism assays measuring apical effects and 14 cell- and organism-based bioassays with more specific effect observations. Twelve organic water pollutants of diverse structure and unique known modes of action were studied individually and as mixtures mirroring exposure scenarios in freshwaters. We compared the observed mixture effects against component-based mixture effect predictions derived from additivity expectations (assumption of non-interaction). Most of the assays detected the mixture response of the active components as predicted even against a background of other inactive contaminants. When none of the mixture components showed any activity by themselves then the mixture also was without effects. The mixture effects observed using apical endpoints fell in the middle of a prediction window defined by the additivity predictions for concentration addition and independent action, reflecting well the diversity of the anticipated modes of action. In one case, an unexpectedly reduced solubility of one of the mixture components led to mixture responses that fell short of the predictions of both additivity mixture models. The majority of the specific cell- and organism-based endpoints produced mixture responses in agreement with the additivity expectation of concentration addition. Exceptionally, expected (additive) mixture response did not occur due to masking effects such as general toxicity from other compounds. Generally, deviations from an additivity expectation could be explained due to experimental factors, specific limitations of the effect endpoint or masking side effects such as cytotoxicity in in vitro assays. The majority of bioassays were able to quantitatively detect the predicted non-interactive, additive combined effect of the specifically bioactive compounds against a background of complex mixture of other chemicals in the sample. This supports the use of a combination of chemical and bioanalytical monitoring tools for the identification of chemicals that drive a specific mixture effect. Furthermore, we demonstrated that a panel of bioassays can provide a diverse profile of effect responses to a complex contaminated sample. This could be extended towards representing mixture adverse outcome pathways. Our findings support the ongoing development of bioanalytical tools for (i) compiling comprehensive effect-based batteries for water quality assessment, (ii) designing tailored surveillance methods to safeguard specific water uses, and (iii) devising strategies for effect-based diagnosis of complex contamination.
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http://dx.doi.org/10.1016/j.envint.2018.02.013DOI Listing
May 2018

Deformation of a prestressed liquid lens membrane.

Appl Opt 2017 Dec;56(34):9368-9376

This paper presents a complete model for analysis of the deformed shape of a prestressed circular axisymmetric membrane of a liquid lens. The governing equations are derived using the exact relation between displacements and the Green-Lagrange strains combined with the Saint Venant-Kirchhoff material law, which postulates a linear relation between the Green-Lagrange strains and the second Piola-Kirchoff stresses. A numerical solution based on minimization of potential energy is illustrated by an example, and the dependence of the maximum membrane deflection on material properties and initial prestress is analyzed. The theoretical model is then experimentally validated. It is shown that the model is suitable for large-strain analysis of liquid lens membranes and provides sufficiently accurate results that can be used in further analyses and simulations of imaging properties of active optical elements based on liquid lenses.
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http://dx.doi.org/10.1364/AO.56.009368DOI Listing
December 2017

Non-invasive and invasive diagnoses of aspergillosis in a rat model by mass spectrometry.

Sci Rep 2017 11 28;7(1):16523. Epub 2017 Nov 28.

Institute of Microbiology of the Czech Academy of Sciences, Prague 4, 142 20, Czech Republic.

Invasive pulmonary aspergillosis results in 450,000 deaths per year and complicates cancer chemotherapy, transplantations and the treatment of other immunosuppressed patients. Using a rat model of experimental aspergillosis, the fungal siderophores ferricrocin and triacetylfusarinine C were identified as markers of aspergillosis and quantified in urine, serum and lung tissues. Biomarkers were analyzed by matrix-assisted laser desorption ionization (MALDI) and electrospray ionization mass spectrometry using a 12T SolariX Fourier transform ion cyclotron resonance (FTICR) mass spectrometer. The limits of detection of the ferri-forms of triacetylfusarinine C and ferricrocin in the rat serum were 0.28 and 0.36 ng/mL, respectively. In the rat urine the respective limits of detection achieved 0.02 and 0.03 ng/mL. In the sera of infected animals, triacetylfusarinine C was not detected but ferricrocin concentration fluctuated in the 3-32 ng/mL range. Notably, the mean concentrations of triacetylfusarinine C and ferricrocin in the rat urine were 0.37 and 0.63 μg/mL, respectively. The MALDI FTICR mass spectrometry imaging illustrated the actual microbial ferricrocin distribution in the lung tissues and resolved the false-positive results obtained by the light microscopy and histological staining. Ferricrocin and triacetylfusarinine C detection in urine represents an innovative non-invasive indication of Aspergillus infection in a host.
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http://dx.doi.org/10.1038/s41598-017-16648-zDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5705710PMC
November 2017

Calculation of nonlinearly deformed membrane shape of liquid lens caused by uniform pressure.

Appl Opt 2017 Jul;56(21):5939-5947

The paper discusses a numerical calculation of deformation of a circular axisymmetric membrane of a liquid lens caused by the pressure of an optical liquid. Since such deflections of the membrane are many times larger than the membrane thickness, a nonlinear model is applied and generalized relationships are derived that characterize the resulting shape with a high precision and permit an accurate analysis of imaging properties of the lens and of optical aberrations. By comparison with experimental data, it is shown that the presented model is suitable to describe the deformation of the membrane of the lens.
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http://dx.doi.org/10.1364/AO.56.005939DOI Listing
July 2017

Method of first-order analysis of a three-element two-conjugate zoom lens.

Appl Opt 2017 Jun;56(18):5301-5306

A method is described for the first-order analysis of a two-conjugate zoom lens composed of three movable elements. Such an optical system satisfies the requirement that the object, image, and pupil planes are fixed within the change of its magnification. General formulas are derived for the calculation of parameters of a three-component two-conjugate zoom lens system, which enable us to calculate the optical power of individual optical elements and their distances for a different range of magnification and imposed conditions. The application of derived formulas is presented on three examples of optical systems with different parameters.
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http://dx.doi.org/10.1364/AO.56.005301DOI Listing
June 2017

Development of a bioanalytical test battery for water quality monitoring: Fingerprinting identified micropollutants and their contribution to effects in surface water.

Water Res 2017 10 9;123:734-750. Epub 2017 Jul 9.

The University of Queensland, National Research Centre for Environmental Toxicology (Entox), Brisbane, QLD, 4108, Australia; UFZ - Helmholtz Centre for Environmental Research, 04318 Leipzig, Germany; Eberhard Karls University Tübingen, Environmental Toxicology, Center for Applied Geosciences, 72074 Tübingen, Germany. Electronic address:

Surface waters can contain a diverse range of organic pollutants, including pesticides, pharmaceuticals and industrial compounds. While bioassays have been used for water quality monitoring, there is limited knowledge regarding the effects of individual micropollutants and their relationship to the overall mixture effect in water samples. In this study, a battery of in vitro bioassays based on human and fish cell lines and whole organism assays using bacteria, algae, daphnids and fish embryos was assembled for use in water quality monitoring. The selection of bioassays was guided by the principles of adverse outcome pathways in order to cover relevant steps in toxicity pathways known to be triggered by environmental water samples. The effects of 34 water pollutants, which were selected based on hazard quotients, available environmental quality standards and mode of action information, were fingerprinted in the bioassay test battery. There was a relatively good agreement between the experimental results and available literature effect data. The majority of the chemicals were active in the assays indicative of apical effects, while fewer chemicals had a response in the specific reporter gene assays, but these effects were typically triggered at lower concentrations. The single chemical effect data were used to improve published mixture toxicity modeling of water samples from the Danube River. While there was a slight increase in the fraction of the bioanalytical equivalents explained for the Danube River samples, for some endpoints less than 1% of the observed effect could be explained by the studied chemicals. The new mixture models essentially confirmed previous findings from many studies monitoring water quality using both chemical analysis and bioanalytical tools. In short, our results indicate that many more chemicals contribute to the biological effect than those that are typically quantified by chemical monitoring programs or those regulated by environmental quality standards. This study not only demonstrates the utility of fingerprinting single chemicals for an improved understanding of the biological effect of pollutants, but also highlights the need to apply bioassays for water quality monitoring in order to prevent underestimation of the overall biological effect.
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http://dx.doi.org/10.1016/j.watres.2017.07.016DOI Listing
October 2017