Hydrological variability of middle European peatland during the Holocene, inferred from subfossil bog pine and bog oak dendrochronology and high-resolution peat multiproxy analysis of the Budwity peatland (northern Poland).

Subfossil pine and oak tree trunks were excavated during exploitation of the Budwity peatland in Northern Poland. Based on dendrochronological analysis, the woodland successions in peatland were reconstructed and correlated with moisture dynamics of the peatland ecosystem inferred from the high-resolution multi-proxy analysis of the peatland deposits. From the results of dendrochronological analysis and the 14C wiggle matching methods, four floating pine chronologies (5882-5595; 5250-5089; 3702-3546; and 2222-1979 mod. cal BP) and two oak chronologies (4932-4599 and 4042-3726 mod. cal BP) were developed. The organic sediments of the peatland (6 m thick) were deposited over approximately nine thousand years. The lower complex (525-315 cm) comprises minerogenic peat, while the upper complex (315.0-0.0 cm) is composed of ombrogenic peat. Subfossil tree trunks are distributed across various peat horizons, which suggests multiple stages of tree colonisation followed by subsequent dying-off phases. Multiproxy sediment analyses (lithological, geochemical and δ13C stable isotope, pollen, plant macrofossils, Cladocera, diatom, and Diptera analyses) indicate that the two earliest phases of pine colonisation (5882-5595 and 5250-5089 mod. cal BP) and the two stages of oak colonisation (4932-4599 and 4042-3726 mod. cal BP) were associated with periodic drying of the peatland. Conversely, tree dying-off phases occurred during periods of increased water levels in the peatland, coinciding with stages of increasing climate humidity during the Holocene. The two most recent phases of pine colonisation occurred during the ombrogenic stage of mire development. Remnants of the dead forest from these phases, marked by subfossil trunks still rooted in the ground, were preserved and exposed presently during peat exploitation, approximately 2.5 m below ground level. The identified phases of tree colonisation and subsequent dying-off phases show correlation with analogical phenomena observed in the other investigated European peatlands.

Boundary of ecosystem services: A response to.

Chen et al. (2023) have proposed a scheme to define which services should be included as ecosystem services and which should be excluded so as to avoid "an all-encompassing metaphor that captures any benefit". We discuss the proposals, drawing attention in particular to definitions of 'natural capital' and 'ecosystems', the complexities of separating biotic from abiotic flows, and the importance of geodiversity and geosystem services in delivering societal benefits. We conclude that rather than trying to separate out bits of nature in order to draw the boundary of ecosystem services, it is perhaps time to avoid using 'nature' and 'biodiversity' as synonyms and think instead of a more holistic and integrated approach involving 'environmental', 'natural' or 'nature's services', in which the role of abiotic nature is fully recognised in both ecosystem services and non-ecosystem domains.

Environmental Attitudes in 28 European Countries Derived From Atheoretically Compiled Opinions and Self-Reports of Behavior.

People differ in their personal commitment to fighting climate change and protecting the environment. The question is, can we validly measure people's commitment by what they say and what they claim they do in opinion polls? In our research, we demonstrate that opinions and reports of past behavior can be aggregated into comparable depictions of people's personal commitment to fighting climate change and protecting the environment (i.e., their environmental attitudes). In contrast to the commonly used operational scaling approaches, we ground our measure of people's environmental attitudes in a mathematically formalized psychological theory of the response process-the Campbell paradigm. This theory of the response process has already been extensively validated, and its relevance for manifest behavior has repeatedly been shown as well. In our secondary analysis of Eurobarometer data (N = 27,998) from 28 European countries, we apply the Campbell paradigm to a set of indicators that was not originally collected to be aggregated into a single scale. With our research, we propose a distinct way to measure behavior-relevant environmental attitudes that can be used even with a set of indicators that was originally atheoretically compiled. Overall, our study suggests that the Campbell paradigm provides a sound psychological measurement theory that can be applied to cross-cultural comparisons in the environmental protection domain.

The COVID-19 crisis does not diminish environmental motivation: Evidence from two panel studies of decision making and self-reported pro-environmental behavior.

The literature shows that threats unrelated to environmental problems can shift attention away from these problems and affect pro-environmental behavior. It is not clear whether the COVID-19 crisis that started in 2019 had any uniform effect on pro-environmental behavior and decision making. In two preregistered panel studies conducted before and during the first COVID wave (n1 = 206, n2 = 164) and before and during the second COVID wave (n3 = n4 = 260), we found that the crisis had had no uniform effect on pro-environmental behaviors, environmental attitude, nor on the behavioral costs of general pro-environmental behavior. Analysis of one specific pro-environmental behavior, the choice of environmentally friendly delivery of products, revealed that the general preference for green delivery services and heightened preference for green delivery services among people with higher attitude levels remained unchanged by the COVID-19 crisis. Thus, if the COVID-19 crisis has had any effects on pro-environmental behaviors, these effects are probably fragmented, specific to certain population segments, and not visible in the short-term perspective.

Hand disinfectants and their activity against clinical isolates of Bordetella pertussis.

OBJECTIVES: The aim of the study was to investigate possible emergence of resistance to disinfectants in Bordetella pertussis strains isolated from patients with whooping cough in the Czech Republic in 2014 and 2015. METHODS: In an EN1500-based study, clean and dry fingertips of volunteers were always contaminated with one of the two clinical isolates of B. pertussis. Clinical isolates of B. pertussis were obtained from the National Reference Laboratory for Pertussis and Diphtheria, National Institute of Public Health (NIPH), Prague, Czech Republic. Dry and contaminated fingertips were immersed in 10 ml medium and then rubbed with the fingers for 1 minute. After that, the hands were treated with isopropanol 60% v/v or tested products, and then the fingertips were rubbed again into 10 ml of pure medium for 1 minute. The suspensions obtained were immediately diluted and plated on charcoal medium. RESULTS: Ethanol-based product A and propanol-based product B showed bactericidal activity after 30 s of contact. The confidence interval limit for product A and B was 0.12 and 0.19, respectively. Quaternary ammonium compound-based product C was found to be ineffective after 30 s of contact. The confidence interval limit for product C was 0.62. CONCLUSION: Products A and B were assessed as effective against clinical isolates of B. pertussis in accordance with EN 1500. Quaternary ammonium compound-based product C did not comply with the requirements of EN 1500.

The Role of CX3CL1 and ADAM17 in Pathogenesis of Diffuse Parenchymal Lung Diseases.

Fractalkine (CX3CL1) is a unique chemokine that functions as a chemoattractant for effector cytotoxic lymphocytes and macrophages expressing fractalkine receptor CX3CR1. CX3CL1 exists in two forms-a soluble and a membrane-bound form. The soluble CX3CL1 is released from cell membranes by proteolysis by the TNF-α-converting enzyme/disintegrin-like metalloproteinase 17 (TACE/ADAM17) and ADAM10. In this study, we evaluated the diagnostic relevance and potential roles of CX3CL1 and ADAM17 in the pathogenesis of diffuse parenchymal lung diseases (DPLDs) in the human population. The concentration of CX3CL1 and ADAM17 was measured by the enzyme-linked immunosorbent assay (ELISA) test in bronchoalveolar lavage fluids of patients suffering from different DPLDs. The concentration of CX3CL1 was significantly higher in patients suffering from idiopathic pulmonary fibrosis (IPF) and hypersensitivity pneumonitis patients compared to the control group. A significantly higher concentration of CX3CL1 was measured in fibrotic DPLDs compared to non-fibrotic DLPD patients. We found a positive correlation of CX3CL1 levels with the number of CD8+ T cells, and a negative correlation with CD4+ T cells in BALF and diffusion capacity for carbon monoxide. The concentration of ADAM17 was significantly lower in the IPF group compared to the other DPLD groups. We noticed a significantly higher CX3CL1/ADAM17 ratio in the IPF group compared to the other DPLD groups. We suggest that CX3CL1 has a distinctive role in the pathogenesis of DPLDs. The level of CX3CL1 strongly correlates with the severity of lung parenchyma impairment. The results suggest that high values of CX3CL1/ADAM17 could be diagnostic markers for IPF.

Charge-Tagged DNA Radicals in the Gas Phase Characterized by UV/Vis Photodissociation Action Spectroscopy.

Adenosine radicals tagged with a fixed-charge group were generated in the gas phase and structurally characterized by tandem mass spectrometry, deuterium labeling, and UV/Vis action spectroscopy. Experimental results in combination with Born-Oppenheimer molecular dynamics, ab initio, and excited-state calculations led to unambiguous assignment of adenosine radicals as N-7 hydrogen atom adducts. The charge-tagged radicals were found to be electronically equivalent to natural DNA nucleoside radicals.

Formation and fragmentation of the tungsten clusters in gas phase.

We present a theoretical study of accumulation of clusters consisting of up to 100 tungsten atoms based on information extracted from molecular dynamics trajectory simulations. The description is based on the rates corresponding to the single W atom attachment to Wn clusters and their dissociation processes. The results display a strong Arrhenius dependence of the dissociation rate constant on temperature. The preferred products of dissociation of the clusters composed of more than ten atoms are single W atoms and fragments with six to nine atoms. On the other hand, the association rate constants depend weakly on temperature. The obtained rate constants are used to calculate the chemical equilibrium of the W clusters that results in significant traces of small clusters only at high initial W atoms concentrations.

Total and partial electron impact ionization cross sections of fusion-relevant diatomic molecules.

We report calculations of total (and absolute) electron-impact ionization cross sections (EICSs) for the fusion-relevant diatomic molecular species BeH, BeN, BeO, WH, WBe, WN, WO, O2, and N2 by means of the Deutsch-Märk and the binary-encounter-Bethe methods in the energy range from threshold to 10 keV. In addition, we discuss an empirical scheme to estimate partial cross sections from the total ones based on reaction energetics and empirical threshold laws and explore its accuracy by assessing available experimental data on total and partial EICSs. Finally, we also report parameters obtained by fitting the calculated cross sections to an expression commonly used in fusion edge plasma modeling.

UV-Vis Action Spectroscopy Reveals a Conformational Collapse in Hydrogen-Rich Dinucleotide Cation Radicals.

We report the generation of deoxyriboadenosine dinucleotide cation radicals by gas-phase electron transfer to dinucleotide dications and their noncovalent complexes with crown ether ligands. Stable dinucleotide cation radicals of a novel hydrogen-rich type were generated and characterized by tandem mass spectrometry and UV-vis photodissociation (UVPD) action spectroscopy. Electron structure theory analysis indicated that upon electron attachment the dinucleotide dications underwent a conformational collapse followed by intramolecular proton migrations between the nucleobases to give species whose calculated UV-vis absorption spectra matched the UVPD action spectra. Hydrogen-rich cation radicals generated from chimeric riboadenosine 5'-diesters gave UVPD action spectra that pointed to novel zwitterionic structures consisting of aromatic π-electron anion radicals intercalated between stacked positively charged adenine rings. Analogies with DNA ionization are discussed.

Energetics and reactivity of small beryllium deuterides.

Enthalpies and free energies of reaction for small neutral and charged beryllium deuterides BeD, BeD2, and BeD3 that have been calculated are reported for a temperature range of 0 K to 1000 K. We discuss probable dissociation channels and possible ways of producing BeD by localizing the relevant transition states and by calculating corresponding rate constants. BeD and BeD+ are found to be the most stable ones among the considered compounds. BeD2 and [Formula: see text] are more likely to decompose into Be0,+ + D2 than into BeD0,+ + D. The metastable BeD3 and [Formula: see text] predominantly decompose into BeD0,+ + D2. In light of our results on the reaction energetics, we can interpret the pathways for production of BeD via BeD2 and BeD3 intermediates observed in molecular dynamics simulations.

Super-resolved 3-D imaging of live cells' organelles from bright-field photon transmission micrographs.

Current biological and medical research is aimed at obtaining a detailed spatiotemporal map of a live cell's interior to describe and predict cell's physiological state. We present here an algorithm for complete 3-D modelling of cellular structures from a z-stack of images obtained using label-free wide-field bright-field light-transmitted microscopy. The method visualizes 3-D objects with a volume equivalent to the area of a camera pixel multiplied by the z-height. The computation is based on finding pixels of unchanged intensities between two consecutive images of an object spread function. These pixels represent strongly light-diffracting, light-absorbing, or light-emitting objects. To accomplish this, variables derived from Rényi entropy are used to suppress camera noise. Using this algorithm, the detection limit of objects is only limited by the technical specifications of the microscope setup-we achieve the detection of objects of the size of one camera pixel. This method allows us to obtain 3-D reconstructions of cells from bright-field microscopy images that are comparable in quality to those from electron microscopy images.

Modifications of the chromophore of Spinach aptamer based on QM:MM calculations.

Spinach aptamer was developed as an RNA analog of the green fluorescent protein. The aptamer interacts with its ligand and modifies its electronic spectrum so that it fluoresces brightly at the wavelength of 501 nm. Song et al. investigated modifications of the ligand in their experimental study and found a molecule emitting at 523 nm upon creating a complex with the Spinach aptamer. The crystal structure of the aptamer in complex with its original ligand has been published, which enabled us to study the system computationally. In this article, we suggest several new modifications of the ligand that shift the emission maximum of the complex to even longer wavelengths. Our results are based on combined quantum mechanical/molecular mechanical calculations with DFT method used for geometry optimization and TD-DFT for calculations of absorption and emission energies.

BioWes-from design of experiment, through protocol to repository, control, standardization and back-tracking.

BACKGROUND: One of the main challenges in modern science is the amount of data produced by the experimental work; it is difficult to store, organize and share the scientific data and to extract the wealth of knowledge. Experimental method descriptions in scientific publications are often incomplete, which complicates experimental reproducibility. The proposed system was created in order to address these issues. It provides a solution for management of the experimental data and metadata to support the reproducibility. IMPLEMENTATION: The system is implemented as a repository for experiment descriptions and experimental data. It has three main entry points: desktop application for protocol design and data processing, web interface dedicated for protocol and data management, and web-based interface for mobile devices suitable for the field experiments. The functionality of desktop client can be extended using the custom plug-ins for data extraction and data processing. The system provides several methods to support experimental reproducibility: standardized terminology support, data and metadata at a single location, standardized protocol design or protocol evolution. RESULTS AND DISCUSSION: The system was tested in the framework of international infrastructure project AQUAEXCEL with five pilot installations at different institutes. The general testing in Tissue culture certified laboratory, Institute of complex systems and IFREMER verified the usability under different research infrastructures. The specific testing focused on the data processing modules and plug-ins demonstrated the modularity of the system for the specific conditions. The BioWes system represents experimental data as black box and therefore can handle any data type so as to provide broad usability for a variety of experiments and provide the data management infrastructure to improve the reproducibility and data sharing. CONCLUSIONS: The proposed system provides the tools for standard data management operations and extends the support by the standardization possibilities, protocol evolution with visualization features and modularity based on the data processing modules and device communication plug-ins. The software can be used at different organization levels: from a single researcher (to improve data organization) to research consortium through the central protocols management repository. Support from the protocol design until being shared with the standardization features helps to improve the reproducibility of research work. The platform provides support from experimental protocol design to cooperation using simple sharing.

False precision of mass domain in HPLC-HRMS data representation.

The term precision of a value describes the total number of significant digits that are used to express that value. False precision is presented in data, where the sampling and chosen data file format coding return values with extra non-valid digits. The proper precision in value thus depends on so-called magnitude in digital data coding. The presence of the false precision is file format dependent. The amount of dataset points could be decreased by removing false precision (where it is present) to almost 10% of the raw measurement without loss of information.

A computational study of the interaction between dopamine and DNA/RNA nucleosides.

The interaction between protonated dopamine and neutral RNA and DNA nucleosides was studied by means of density functional theory calculations in vacuum and in implicit water. On the most stable complexes formed with each of the nucleosides, the vertical absorption excitation energies were evaluated and compared with the values of separated dopamine and corresponding nucleoside. The most stable complex was formed with guanosine and the spectral changes in this complex resulted in a significant reduction of the oscillator strength of the first dopamine's transition. In the first guanosine's transition, a redshift of 0.2 eV was found combined with a reduction of the oscillator strength.

DFT and MD study of the divalent-cation-mediated interaction of ochratoxin A with DNA nucleosides.

Aptamers are ligand-binding nucleic acids with affinities and selectivities that make them useful for the detection of a variety of compounds, including ochratoxin A. Theoretical methods can be applied to study the recognition interaction between aptamers and the ochratoxin A molecule. In this work, molecular dynamics simulations and quantum chemical calculations performed at the DFT level of theory were used to study the structures and energies of aptamers and aptamer-ochratoxin A complexes. The optimal structures as well as the interaction energies of these structures were elucidated. Divalent cations in the water solvent were shown to be an important influence on the structures and stabilities of the complexes.

Linking traffic noise, noise annoyance and life satisfaction: a case study.

The primary purpose of this study was to explore the link between rail and road traffic noise and overall life satisfaction. While the negative relationship between residential satisfaction and traffic noise is relatively well-established, much less is known about the effect of traffic noise on overall life satisfaction. Based on results of previous studies, we propose a model that links objective noise levels, noise sensitivity, noise annoyance, residential satisfaction and life satisfaction. Since it is not clear whether a bottom-up or top-down relationship between residential satisfaction and life satisfaction holds, we specify models that incorporate both of these theoretical propositions. Empirical models are tested using structural equation modeling and data from a survey among residents of areas with high levels of road traffic noise (n1 = 354) and rail traffic noise (n2 = 228). We find that traffic noise has a negative effect on residential satisfaction, but no significant direct or indirect effects on overall life satisfaction. Noise annoyance due to road and rail traffic noise has strong negative effect on residential satisfaction rather than on overall life satisfaction. These results are very similar for the road and railway traffic contexts and regardless of whether the model assumes the top-down or bottom-up direction of the causation between life satisfaction and residential satisfaction.

Estimation of ion competition via correlated responsivity offset in linear ion trap mass spectrometry analysis: theory and practical use in the analysis of cyanobacterial hepatotoxin microcystin-LR in extracts of food additives.

Responsivity is a conversion qualification of a measurement device given by the functional dependence between the input and output quantities. A concentration-response-dependent calibration curve represents the most simple experiment for the measurement of responsivity in mass spectrometry. The cyanobacterial hepatotoxin microcystin-LR content in complex biological matrices of food additives was chosen as a model example of a typical problem. The calibration curves for pure microcystin and its mixtures with extracts of green alga and fish meat were reconstructed from the series of measurement. A novel approach for the quantitative estimation of ion competition in ESI is proposed in this paper. We define the correlated responsivity offset in the intensity values using the approximation of minimal correlation given by the matrix to the target mass values of the analyte. The estimation of the matrix influence enables the approximation of the position of a priori unknown responsivity and was easily evaluated using a simple algorithm. The method itself is directly derived from the basic attributes of the theory of measurements. There is sufficient agreement between the theoretical and experimental values. However, some theoretical issues are discussed to avoid misinterpretations and excessive expectations.

Effect of the aminoacid composition of model α-helical peptides on the physical properties of lipid bilayers and peptide conformation: a molecular dynamics simulation.

The interaction of a model Lys flanked α-helical peptides K2-X24-K2, (X = A,I,L,L+A,V) with lipid bilayers composed of dimyristoylphosphatidylcholine (DMPC) and dipalmitoylphosphatidylcholine (DPPC) both, in a gel and in a liquid-crystalline state, has been studied by molecular dynamics simulations. It has been shown that these peptides cause disordering of the lipid bilayer in the gel state but only small changes have been monitored in a liquid-crystalline state. The peptides affect ordering of the surrounding lipids depending on the helix stability which is determined by amino acid side chains - their volume, shape, etc. We have shown that the helix does not keep the linear shape in all simulations but often bends or breaks. During some simulations with a very small difference between hydrophobic length of peptide and membrane thickness the peptide exhibits negligible tilt. At the same time changes in peptide conformations during simulations resulted in appearance of superhelix.