Millisecond X-ray reflectometry and neural network analysis: unveiling fast processes in spin coating.

X-ray reflectometry (XRR) is a powerful tool for probing the structural characteristics of nanoscale films and layered structures, which is an important field of nanotechnology and is often used in semiconductor and optics manufacturing. This study introduces a novel approach for conducting quantitative high-resolution millisecond monochromatic XRR measurements. This is an order of magnitude faster than in previously published work. Quick XRR (qXRR) enables real time and in situ monitoring of nanoscale processes such as thin film formation during spin coating. A record qXRR acquisition time of 1.4 ms is demonstrated for a static gold thin film on a silicon sample. As a second example of this novel approach, dynamic in situ measurements are performed during PMMA spin coating onto silicon wafers and fast fitting of XRR curves using machine learning is demonstrated. This investigation primarily focuses on the evolution of film structure and surface morphology, resolving for the first time with qXRR the initial film thinning via mass transport and also shedding light on later thinning via solvent evaporation. This innovative millisecond qXRR technique is of significance for in situ studies of thin film deposition. It addresses the challenge of following intrinsically fast processes, such as thin film growth of high deposition rate or spin coating. Beyond thin film growth processes, millisecond XRR has implications for resolving fast structural changes such as photostriction or diffusion processes.

Theoretical analysis of a compensator of the secondary longitudinal chromatic aberration.

A theoretical analysis of an afocal compensator of the secondary longitudinal chromatic aberration is provided. Such a compensator is able to compensate for chromatic aberration of an achromatic optical system and make an apochromatic correction of the system. The parameters of the proposed chromatic aberration compensator are described and the principle is presented in examples.

Endocrine disrupting potential of total and bioaccessible extracts of dust from seven different types of indoor environment.

Information on the indoor environment as a source of exposure with potential adverse health effects is mostly limited to a few pollutant groups and indoor types. This study provides a comprehensive toxicological profile of chemical mixtures associated with dust from various types of indoor environments, namely cars, houses, prefabricated apartments, kindergartens, offices, public spaces, and schools. Organic extracts of two different polarities and bioaccessible extracts mimicking the gastrointestinal conditions were prepared from two different particle size fractions of dust. These extracts were tested on a battery of human cell-based bioassays to assess endocrine disrupting potentials. Furthermore, 155 chemicals from different pollutant groups were measured and their relevance for the bioactivity was determined using concentration addition modelling. The exhaustive and bioaccessible extracts of dust from the different microenvironments interfered with aryl hydrocarbon receptor, estrogen, androgen, glucocorticoid, and thyroid hormone (TH) receptor signalling, and with TH transport. Noteably, bioaccessible extracts from offices and public spaces showed higher estrogenic effects than the organic solvent extracts. 114 of the 155 targeted chemicals were detectable, but the observed bioactivity could be only marginally explained by the detected chemicals. Diverse toxicity patterns across different microenvironments that people inhabit throughout their lifetime indicate potential health and developmental risks, especially for children. Limited data on the endocrine disrupting potency of relevant chemical classes, especially those deployed as replacements for legacy contaminants, requires further study.

Calculation of the wave aberration of an axial bundle of rays.

A differential equation is derived for the calculation of the wave aberration of an axial bundle of rays affected by spherical aberration. The solution of the derived equation is analyzed, and the influence of the radius of the reference sphere on the value of the wave aberration is presented. The approximate formula for wave aberration is obtained, which allows the splitting of the wave aberration into a part relative to an infinitely distant reference sphere and a part showing the dependence of the wave aberration on the radius of the reference sphere. Furthermore, the case of third-order and fifth-order spherical aberration is investigated, and the formulas for the calculation of the Strehl definition for the case of small aberrations are derived. The accuracy of the approximated formulas for the wave aberration is analyzed in an example.

Optical Absorption Properties in Pentacene/Tetracene Solid Solutions.

Modifying the optical and electronic properties of crystalline organic thin films is of great interest for improving the performance of modern organic semiconductor devices. Therein, the statistical mixing of molecules to form a solid solution provides an opportunity to fine-tune optical and electronic properties. Unfortunately, the diversity of intermolecular interactions renders mixed organic crystals highly complex, and a holistic picture is still lacking. Here, we report a study of the optical absorption properties in solid solutions of pentacene and tetracene, two prototypical organic semiconductors. In the mixtures, the optical properties can be continuously modified by statistical mixing at the molecular level. Comparison with time-dependent density functional theory calculations on occupationally disordered clusters unravels the electronic origin of the low energy optical transitions. The disorder partially relaxes the selection rules, leading to additional optical transitions that manifest as optical broadening. Furthermore, the contribution of diabatic charge-transfer states is modified in the mixtures, reducing the observed splitting in the 0-0 vibronic transition. Additional comparisons with other blended systems generalize our results and indicate that changes in the polarizability of the molecular environment in organic thin-film blends induce shifts in the absorption spectrum.

Algebraic solution for aplanatic cemented doublets with aspherical surfaces of second degree.

An algebraic method of an initial design of the aplanatic cemented doublet with a unit focal length is described. Based on the third-order aberration theory, algebraic equations are derived for calculating the design parameters of an aplanatic thin cemented doublet with spherical surfaces and aspherical surfaces of the second degree. These equations make it easy to determine whether there exists a real solution of the doublet design for required parameters. The results of the calculations of selected cemented doublet solutions are presented in the examples. The obtained parameters can be used as the starting solution for the final optimization of doublet designs.

Method for algebraic calculation of initial design parameters of a two-element telecentric f-theta lens.

A method for the algebraic calculation of paraxial design parameters of a telecentric f-theta lens is described. Moreover, a third-order aberration analysis is performed for a telecentric f-theta lens composed of two optical elements. The method can be used to calculate the starting optical design of telecentric f-theta lenses, which can be used, for example, in laser material processing, optical imaging systems, and optical metrology. The initial design parameters then can be used for further optimization in optical design software.

Bioanalytical and chemical characterization of organic micropollutant mixtures in long-term exposed passive samplers from the Joint Danube Survey 4: Setting a baseline for water quality monitoring.

Monitoring methodologies reflecting the long-term quality and contamination of surface waters are needed to obtain a representative picture of pollution and identify risk drivers. This study sets a baseline for characterizing chemical pollution in the Danube River using an innovative approach, combining continuous three-months use of passive sampling technology with comprehensive chemical (747 chemicals) and bioanalytical (seven in vitro bioassays) assessment during the Joint Danube Survey (JDS4). This is one of the world's largest investigative surface-water monitoring efforts in the longest river in the European Union, which water after riverbank filtration is broadly used for drinking water production. Two types of passive samplers, silicone rubber (SR) sheets for hydrophobic compounds and AttractSPETM HLB disks for hydrophilic compounds, were deployed at nine sites for approximately 100 days. The Danube River pollution was dominated by industrial compounds in SR samplers and by industrial compounds together with pharmaceuticals and personal care products in HLB samplers. Comparison of the Estimated Environmental Concentrations with Predicted No-Effect Concentrations revealed that at the studied sites, at least one (SR) and 4-7 (HLB) compound(s) exceeded the risk quotient of 1. We also detected AhR-mediated activity, oxidative stress response, peroxisome proliferator-activated receptor gamma-mediated activity, estrogenic, androgenic, and anti-androgenic activities using in vitro bioassays. A significant portion of the AhR-mediated and estrogenic activities could be explained by detected analytes at several sites, while for the other bioassays and other sites, much of the activity remained unexplained. The effect-based trigger values for estrogenic and anti-androgenic activities were exceeded at some sites. The identified drivers of mixture in vitro effects deserve further attention in ecotoxicological and environmental pollution research. This novel approach using long-term passive sampling provides a representative benchmark of pollution and effect potentials of chemical mixtures for future water quality monitoring of the Danube River and other large water bodies.

Quantitation of small molecules from liquid chromatography-mass spectrometric accurate mass datasets using CycloBranch.

Gaussian and exponentially modified Gaussian functions were incorporated into integrating algorithms used by an open-source, cross-platform tool called CycloBranch. The quantitation is demonstrated on bacterial pyoverdines separated by fine isotope features. Using our algorithm, we can separate the m/z values 694.25802 and 694.26731 (a 0.009 Da difference), where the former belongs to the most intense peak of pyoverdine D (PvdD), and the latter to the second most intense peak of pyoverdine E (PvdE) in the respective isotopic clusters of [M + Fe-H]2+ ions. The areas under chromatographic curves of standards were analyzed for the limit of detection (LOD), limit of quantitation (LOQ), and regression coefficient calculations. The quantitative module returned a LOD and LOQ of 1.4 and 4.3 ng/mL, respectively, for both PvdD and PvdE in human urine. If present and detected in mass spectra, the intensities of user-defined [M + H]+, [M + Na]+, [M + K]+, [M + Fe-H]2+, or other ion types, can be accumulated and used for quantitation. The quantitation result is returned by CycloBranch in seconds or minutes, contrary to an hours-long manual approach, prone to user-born errors originating from necessary copying among various software environments. Native Bruker, Waters, Thermo, txt, mgf, mzML, and mzXML data formats are supported in CycloBranch, which is freely available at https://ms.biomed.cas.cz/cyclobranch.

Method of initial design of a two-element double-sided telecentric optical system.

An algebraic method for finding fundamental parameters of a starting design of a two-element double-sided telecentric lens is introduced in this work. The telecentric lens is formed by two objectives composed of an afocal meniscus lens followed by a cemented doublet. It is used the third-order aberration theory to find the fundamental parameters of the starting configuration of a given optical system. The method gives results which make possible to obtain a good initial design of such a telecentric lens for further optimization using optical design software. The proposed method is presented on an example of finding initial design parameters of the double-sided telecentric lens.

Algebraic method for finding the initial design parameters of a two-element optical system with an afocal meniscus lens.

This work introduces an algebraic method of the calculation of an initial design of a two-element optical system composed of a thick afocal meniscus lens and a thin lens element, which can be formed, for example, by a cemented doublet. The third-order aberration theory is used to find the fundamental parameters of the starting configuration of a given optical system. The method gives results that make it possible to obtain a good starting design for further optimization of such imaging systems using optical design software. The proposed method is presented on two examples of finding the initial design parameters of the objective with an afocal meniscus lens and a cemented doublet.

Lorentz-Boost-Driven Magneto-Optics in a Dirac Nodal-Line Semimetal.

Optical response of crystalline solids is to a large extent driven by excitations that promote electrons among individual bands. This allows one to apply optical and magneto-optical methods to determine experimentally the energy band gap -a fundamental property crucial to our understanding of any solid-with a great precision. Here it is shown that such conventional methods, applied with great success to many materials in the past, do not work in topological Dirac semimetals with a dispersive nodal line. There, the optically deduced band gap depends on how the magnetic field is oriented with respect to the crystal axes. Such highly unusual behavior is explained in terms of band-gap renormalization driven by Lorentz boosts which results from the Lorentz-covariant form of the Dirac Hamiltonian relevant for the nodal line at low energies.

Method of calculation of initial design parameters of microscope objective lenses with a long working distance.

We describe an analytic method of the initial design of microscope objectives with a long working distance. The optical system of a microscope objective is composed of two thin optical elements and a frontal optical element from several thick lenses. The paper describes formulas that make it possible to calculate fundamental parameters of the objective, namely Seidel aberration coefficients, radii of curvature, refractive indices of individual lenses of the microscope objective, etc. The proposed method of calculation of the initial design parameters of the microscope objective, which is based on the theory of aberrations of the third order and chromatic aberrations of the first order, enables us to obtain a good starting design for further optimization using optical design software. The method of the design is presented in an example of the microscope objective with a long working distance.

Teratogenicity of retinoids detected in surface waters in zebrafish embryos and its predictability by in vitro assays.

Retinoids are newly detected compounds in aquatic ecosystems associated with cyanobacterial water blooms. Their potential health risks are only scarcely described despite numerous detections of all-trans retinoic acid (ATRA) and its derivatives in the environment. Besides the known teratogen ATRA there is only little or no information about their potency and namely their effects in vivo. We characterize ATRA and 8 other retinoids reported to occur in the environment for their bioactivity and teratogenicity using four in vitro reporter gene assays and zebrafish (Danio rerio) embryotoxicity assay. Our results document the ability of these compounds to interfere with retinoid signalling and cause teratogenicity at environmentally relevant levels with EC50 values at nM (hundreds of ng/L) levels and teratogenic indexes ranging from 2.8 (9cis retinoic acid) to 15.8 (retinal). The relative potency of individual compounds for teratogenicity ranged from 0.059 (retinal) to 0.96 (5,6-epoxy ATRA) when compared to ATRA. An environmentally relevant mixture of retinoids was tested showing good predictability of teratogenicity from the in vitro activities and additive toxicity of the mixture. The high teratogenicity of the newly described compounds associated with cyanobacteria presents a concern for developmental stages due to high conservation of the retinoid signalling across vertebrates.

Risk Factors for Severe COVID-19 and Hospital Admission in Patients With Inborn Errors of Immunity - Results From a Multicenter Nationwide Study.

Despite the progress in the understanding how COVID-19 infection may impact immunocompromised patients, the data on inborn errors of immunity (IEI) remain limited and ambiguous. Therefore, we examined the risk of severe infection course and hospital admission in a large cohort of patients with IEI. In this multicenter nationwide retrospective survey-based trial, the demographic, clinical, and laboratory data were collected by investigating physicians from 8 national referral centers for the diagnosis and treatment of IEI using a COVID-19-IEI clinical questionnaire. In total, 81 patients with IEI (including 16 with hereditary angioedema, HAE) and confirmed SARS-CoV-2 infection were enrolled, and were found to have a 2.3-times increased (95%CI: 1.44-3.53) risk ratio for hospital admission and a higher mortality ratio (2.4% vs. 1.7% in the general population). COVID-19 severity was associated with the presence of clinically relevant comorbidities, lymphopenia, and hypogammaglobulinemia, but not with age or BMI. No individuals with HAE developed severe disease, despite a hypothesized increased risk due to perturbed bradykinin metabolism. We also demonstrated a high seroconversion rate in antibody-deficient patients and the safety of anti-spike SARS CoV-2 monoclonal antibodies and convalescent plasma. Thus, IEI except for HAE, represent significant risk factors for a severe COVID-19. Therefore, apart from general risk factors, immune system dysregulation may also be involved in the poor outcomes of COVID-19. Despite the study limitations, our results support the findings from previously published trials.

Toxicity to bronchial cells and endocrine disruptive potentials of indoor air and dust extracts and their association with multiple chemical classes.

Pollution of indoor environment, where people spend much of their time, comprises complex mixtures of compounds with vastly understudied hazard potential. This study examined several important specific toxic effects and pollutant levels (177 compounds) of indoor samples (air gas phase, PM10 and dust) from different microenvironments after two extractions with focus on their gas/particle/dust distribution and polarity. The endocrine disruptive (ED) potential was assessed by human cell-based in vitro bioassays addressing anti-/estrogenicity, anti-/androgenicity, aryl hydrocarbon, thyroid and peroxisome proliferator-activated receptor-mediated activities. Potential toxicity to respiratory tract tissue was assessed using human bronchial cell line. The toxicological analyses pointed out the relevance of both inhalation and ingestion exposure, with significant effects detected after exposure to extracts from all three studied matrices with distinct gas/particle distribution patterns. Chemical analyses document the high complexity of indoor pollutant mixtures with greatest levels of phthalates, their emerging alternatives, and PAHs in dust. Despite the detection of up to 108 chemicals, effects were explained only to low extent. This emphasizes data gaps regarding ED potencies of many detected abundant indoor contaminants, but also potential presence of other unidentified ED compounds. The omnipresent ED potentials in indoor environment rise concern regarding associated human health risk.

Noninvasive Combined Diagnosis and Monitoring of Aspergillus and Pseudomonas Infections: Proof of Concept.

In acutely ill patients, particularly in intensive care units or in mixed infections, time to a microbe-specific diagnosis is critical to a successful outcome of therapy. We report the application of evolving technologies involving mass spectrometry to diagnose and monitor a patient's course. As proof of this concept, we studied five patients and used two rat models of mono-infection and coinfection. We report the noninvasive combined monitoring of Aspergillus fumigatus and Pseudomonas aeruginosa infection. The invasive coinfection was detected by monitoring the fungal triacetylfusarinine C and ferricrocin siderophore levels and the bacterial metabolites pyoverdin E, pyochelin, and 2-heptyl-4-quinolone, studied in the urine, endotracheal aspirate, or breath condensate. The coinfection was monitored by mass spectrometry followed by isotopic data filtering. In the rat infection model, detection indicated 100-fold more siderophores in urine compared to sera, indicating the diagnostic potential of urine sampling. The tools utilized in our studies can now be examined in large clinical series, where we could expect the accuracy and speed of diagnosis to be competitive with conventional methods and provide advantages in unraveling the complexities of mixed infections.

MassSpecBlocks: a web-based tool to create building blocks and sequences of nonribosomal peptides and polyketides for tandem mass spectra analysis.

Nonribosomal peptides and polyketides are natural products commonly synthesized by microorganisms. They are widely used in medicine, agriculture, environmental protection, and other fields. The structures of natural products are often analyzed by high-resolution tandem mass spectrometry, which becomes more popular with its increasing availability. However, the characterization of nonribosomal peptides and polyketides from tandem mass spectra is a nontrivial task because they are composed of many uncommon building blocks in addition to proteinogenic amino acids. Moreover, many of them have cyclic and branch-cyclic structures. Here, we introduce MassSpecBlocks - an open-source and web-based tool that converts the input chemical structures in SMILES format into sequences of building blocks. The structures can be searched in public databases PubChem, ChemSpider, ChEBI, NP Atlas, COCONUT, and Norine and edited in a user-friendly graphical interface. Although MassSpecBlocks can serve as a stand-alone database, our primary goal was to enable easy construction of custom sequence and building block databases, which can be used to annotate mass spectra in CycloBranch software. CycloBranch is an open-source, cross-platform, and stand-alone tool that we recently released for annotating spectra of linear, cyclic, branched, and branch-cyclic nonribosomal peptides and polyketide siderophores. The sequences and building blocks created in MassSpecBlocks can be easily exported into a plain text format used by CycloBranch. MassSpecBlocks is available online or can be installed entirely offline. It offers a REST API to cooperate with other tools.

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

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.

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

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 Pseudomonas aeruginosa. The protocol enables bimodal image fusion in the in-house software CycloBranch, as demonstrated by SEM and MALDI-MSI.