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Bean common mosaic virus from the genus Potyvirus has a wide range of hosts and a very negative impact on cultivated crops from the genus Phaseolus. The risk of viral infection of economically important crops increases even if the carriers of the virus are related plant species growing on agroecological interfaces. Such plant species have emerged as new hosts for BCMV, usually harboring novel genetic variants of the virus. A novel genetic variant of BCMV was isolated from a symptomatic crownvetch plant, where the presence of this virus was confirmed via Western blot analysis and via amino acid identities in peptide fragments of CI, HC-pro, and CP proteins using the nanoLC-ESI-Q-TOF. The novel BCMV SVK isolate differed from the most genetically similar one in 0.91% of nucleotides and 1.55% of amino acids. The highest number of amino acid substitutions (8.8% of amino acids) was in the P1 protein, followed by CP (2.44% of amino acids). Minor substitutions were in Hc-pro, CI, and Nib proteins. The symptomatic crownvetch plant was confirmed as a new host and carrier of the novel BCMV isolate.

Bean common mosaic virus from the genus Potyvirus has a wide range of hosts and a very negative impact on cultivated crops from the genus Phaseolus. The risk of viral infection of economically important crops increases even if the carriers of the virus are related plant species growing on agroecological interfaces. Such plant species have emerged as new hosts for BCMV, usually harboring novel genetic variants of the virus. A novel genetic variant of BCMV was isolated from a symptomatic crownvetch plant, where the presence of this virus was confirmed by Western-blotting analysis and by amino acid identities in peptide fragments of CI, HC-pro, and CP proteins using the nanoLC-ESI-Q-TOF. The novel BCMV SVK isolate differed from the most genetically similar one in 0.91% of nucleotides and 1.55% of amino acids. The highest number of amino acid substitutions (8.8% of amino acids) was in the P1 protein, followed by CP (2.44% of amino acids). Minor substitutions were in Hc-pro, CI, and Nib proteins. The symptomatic crownvetch plant was confirmed as a new host and carrier of the novel BCMV isolate.

We propose a protocol for transitionless driving of a bound quantum system in its parameter space using repeated measurement-like interactions with an external spectator system. As a consequence of the quantum Zeno effect, the fidelity of the final state preparation is equal to unity in the limit of infinite-rate interactions. For finite-rate interactions, the maximal fidelity is achieved for the driving trajectory having a minimal geometric length and keeping a constant speed with respect to the Provost-Vallee metric in the parameter space. We numerically test the protocol in an interacting multiqubit system, demonstrating its dominance over the method of coherent driving., 6 pages, 5 figures, submitted to Physical Review A

Dynamical phase transitions are defined through non-analyticities of the survival probability of an out-of-equilibrium time-evolving state at certain critical times. They ensue from zeros of the corresponding survival amplitude. By extending the time variable onto the complex domain, we formulate the complex-time survival amplitude. The complex zeros of this quantity near the time axis correspond, in the infinite-size limit, to non-analytical points where the survival probability abruptly vanishes. Our results are numerically exemplified in the fully-connected transverse-field Ising model, which displays a symmetry-broken phase delimited by an excited-state quantum phase transition. A detailed study of the behavior of the complex-time survival amplitude when the characteristics of the out-of-equilibrium protocol changes is presented. The influence of the excited-state quantum phase transition is also put into context., Comment: 12+ pages, 9 figures, added comments

Using the adiabatic perturbation theory of driven dynamics [Phys. Rev. A 78, 052508 (2008)] we design a hierarchy of quantum state preparation protocols that systematically increase the fidelity at very long driving times. We test these and other protocols, including those based on the geometric analysis of the parameter space, in a single-qubit system and in a fully connected multi-qubit system showing in its infinite-size limit several quantum phase transitions. The new protocols excel in the asymptotic driving regime, above a crossover time from the Landau-Zener regime which increases with a decreasing minimal energy gap along the driving path (with the size of the system). In the medium-time domain, the performance of all tested protocols is indecisive., 16 pages, 14 figures

For the understanding of pathological states of bone tissues in oral surgery, it would be desirable to have the possibility to simulate these processes on bone cell models in vitro. These cultures, similarly to bone tissues, contain numerous proteins entrapped in the insoluble matrix. The major goal of this study was to verify whether a method based on direct in-matrix protein digestion could be suitable for the discrimination between different induced pathological states of bone cell models cultivated in vitro. Using in-sample specific protein digestion with trypsin followed by liquid chromatography-tandem mass spectrometry analysis of released peptides, 446 proteins (in average per sample) were identified in a bone cell in vitro model with induced cancer, 440 proteins were found in a model with induced inflammation, 451 proteins were detected in control in vitro culture, and 491 proteins were distinguished in samples of vestibular laminas of maxillary bone tissues originating from six different patients. Subsequent partial least squares - discrimination analysis of obtained liquid chromatography-tandem mass spectrometry data was able to discriminate among in vitro cultures with induced cancer, with induced inflammation, and control cultivation. Thus, the direct in-sample protein digestion by trypsin followed by liquid chromatography-tandem mass spectrometry analysis of released specific peptide fragments from the insoluble matrix and mathematical analysis of the mass spectrometry data seems to be a promising tool for the routine proteomic characterization of in vitro human bone models with induced different pathological states.

Proteomic characterization of alveolar bones in oral surgery represents an analytical challenge due to their insoluble character. The implementation of a straightforward technique could lead to the routine use of proteomics in this field. This work thus developed a simple technique for the characterization of bone tissue for human maxillary and mandibular bones. It is based on the direct in-bone tryptic digestion of proteins in both healthy and pathological human maxillary and mandibular bone samples. The released peptides were then identified by the LC-MS/MS. Using this approach, a total of 1120 proteins were identified in the maxillary bone and 1151 proteins in the mandibular bone. The subsequent partial least squares-discrimination analysis (PLS-DA) of protein data made it possible to reach 100% discrimination between the samples of healthy alveolar bones and those of the bone tissue surrounding the inflammatory focus. These results indicate that the in-bone protein digestion followed by the LC-MS/MS and subsequent statistical analysis can provide a deeper insight into the field of oral surgery at the molecular level. Furthermore, it could also have a diagnostic potential in the differentiation between the proteomic patterns of healthy and pathological alveolar bone tissue. Data are available via ProteomeXchange with the identifier PXD026775.

Three analytic solutions to the Schr\"{o}dinger equation for the time-dependent Landau-Zener Hamiltonian are presented. They correspond to specific finite-time driving paths in a bounded parameter space of a two-level system. Two of these paths go through the avoided crossing of levels, either with a constant speed or with variable speed that decreases in the region of reduced energy gap, the third path bypasses the crossing such that the energy gap remains constant. The solutions yield exact time dependencies of the excitation probability for the system evolving from the ground state of the initial Hamiltonian. The Landau-Zener formula emerges as an approximation valid within a certain interval of driving times for the constant-speed driving through the avoided crossing. For long driving times, all solutions converge to the prediction of the adiabatic perturbation theory. The excitation probability vanishes at some discrete time instants., Comment: 21 pages, 8 figures

The commonly used histological assessment of pathological states of alveolar bone tissues in oral surgery needs laborious and time-consuming processing by an experienced histologist. Therefore, a simpler and faster methodology is required in this field. Following this demand, this paper reports a straightforward approach using the tryptic cleavage of proteins directly in bone without its demineralization, followed by the capillary electrophoresis-ultraviolet detection profiling of the yielded protein digest. Cleavage-derived peptides were separated by capillary electrophoresis in acidic background electrolytes, pH 2.01-2.54. The best resolution of peptide fragments with the highest peak capacity was achieved in the background electrolyte composed of 55 mM H3 PO4 , 14 mM tris(hydroxymethyl)aminomethan, pH 2.01. The differences in the obtained capillary electrophoresis-ultraviolet detection profiles with characteristic patterns for particular bone samples were subsequently discriminated by linear discriminant analysis over principal components. This approach was first verified on porcine bone tissues as model samples; jawbone and calf bone tissues could be discriminated with an accuracy of 100%. Subsequently, the method was capable of differentiating unequivocally between human healthy and inflammatory alveolar bone tissues obtained from oral surgery. This procedure seems to be promising as complement or even an alternative to the traditional histological discrimination between healthy and inflammatory bone tissues in oral surgery.

The recognition of motion patterns belongs to very important research areas related to neurology, rehabilitation, and robotics. It is based on modern sensor technologies and general mathematical methods, multidimensional signal processing, and machine learning. The present paper is devoted to the detection of features associated with accelerometric data acquired by 31 time-synchronized sensors located at different parts of the body. Experimental data sets were acquired from 25 individuals diagnosed as healthy controls and ataxic patients. The proposed method includes the application of the discrete Fourier transform for the estimation of the mean power in selected frequency bands and the use of these features for data segments classification. The study includes a comparison of results obtained from signals recorded at different positions. Evaluations are based on classification accuracy and cross-validation errors estimated by support vector machine, Bayesian, nearest neighbours (k-NN], and neural network (NN) methods. Results show that highest accuracies of 77.1%, 78.9%, 89.9%, 98.0%, and 98.5% were achieved by NN method for signals acquired from the sensors on the feet, legs, uplegs, shoulders, and head/spine, respectively, recorded in 201 signal segments. The entire study is based on observations in the clinical environment and suggests the importance of augmented reality to decisions and diagnosis in neurology.

Due to known information processing capabilities of the brain, neurons are modeled at many different levels. Circuit theory is also often used to describe the function of neurons, especially in complex multi-compartment models, but when used for simple models, there is no subsequent biological justification of used parts. We propose a new single-compartment model of excitatory and inhibitory neuron, the capacitor-switch model of excitatory and inhibitory neuron, as an extension of the existing integrate-and-fire model, preserving the signal properties of more complex multi-compartment models. The correspondence to existing structures in the neuronal cell is then discussed for each part of the model. We demonstrate that a few such inter-connected model units are capable of acting as a chaotic oscillator dependent on fire patterns of the input signal providing a complex deterministic and specific response through the output signal. The well-known necessary conditions for constructing a chaotic oscillator are met for our presented model. The capacitor-switch model provides a biologically-plausible concept of chaotic oscillator based on neuronal cells.

We study exceptional points (EPs) of a nonhermitian Hamiltonian $\hat{H}(\lambda,\delta)$ whose parameters $\lambda \in {\mathbb C}$ and $\delta \in {\mathbb R}$. As the real control parameter $\delta$ is varied, the $k$-th EP (or $k$-th cluster of simultaneously existing EPs) of $\hat{H}(\lambda,\delta)$ moves in the complex plane of $\lambda$ along a continuous trajectory, $\lambda_k(\delta)$. We derive a self contained set of equations of motion (EOM) for the trajectory $\lambda_k(\delta)$, while interpreting $\delta$ as the propagation time. Such EOM become of interest whenever one wishes to study the response of EPs to external perturbations or continuous parametric changes of the pertinent Hamiltonian. This is e.g.~the case of EPs emanating from hermitian curve crossings/degeneracies (which turn into avoided crossings/near-degeneracies when the Hamiltonian parameters are continuously varied). The presented EOM for EPs have not only their theoretical merits, they possess also a substantial practical relevance. Namely, the just presented approach can be regarded even as an efficient numerical method, useful for generating EPs for a broad class of complex quantum systems encountered in atomic, nuclear and condensed matter physics. Performance of such a method is tested here numerically on a simple yet nontrivial toy model., Comment: 28 pages, 9 figures

At present, Alzheimer´s disease is detected mainly using psychological tests, which, can only confirm the disease in its more advanced phases. Therefore, bioanalytical possibilities for detecting this disease earlier are being investigated. To date, the results of analyses, which focus mainly on the study of lipids and proteins either in cerebrospinal fluid or much less often in blood plasma, do not provide satisfactory results. In addition, cerebrospinal fluid sampling is uncomfortable for the patients and involves many health risks. In this work, we deal with proteomic analysis using Matrix-Assisted Laser Desorption/Ionisation - Time Of Flight and Liquid Chromatography coupled to tandem Mass Spectrometry of blood plasma with a focus on various ways of pre-analytical sample treatments. This should lead to results improvement and facilitate the subsequent evaluation using principal component analysis and partial least squares discriminant analysis. The obtained results indicate the direction of further research, namely the study of interactions between proteins and lipids contained in blood plasma. These substances may be regarded as potential biomarkers allowing for the diagnosis of Alzheimer´s disease even in its early stages. This article is protected by copyright. All rights reserved.

Gait disorders accompany a number of neurological and musculoskeletal disorders that significantly reduce the quality of life. Motion sensors enable high-quality modelling of gait stereotypes. However, they produce large volumes of data, the evaluation of which is a challenge. In this publication, we compare different data reduction methods and classification of reduced data for use in clinical practice. The best accuracy achieved between a group of healthy individuals and patients with ataxic gait extracted from the records of 43 participants (23 ataxic, 20 healthy), forming 418 segments of straight gait pattern, is 98% by random forest classifier preprocessed by t-distributed stochastic neighbour embedding.

The dynamics of a quantum system following a sudden, highly non-adiabatic change of its control parameter (quantum quench) is studied with quasiclassical techniques. Recent works have shown, using exact quantum mechanical approach, that equilibration after quantum quench exhibits specific features in the presence of excited-state quantum phase transitions. In this paper, we demonstrate that these features can be understood from the classical evolution of the Wigner function in phase space.

Following our work [Phys. Rev. Lett. 125, 020401 (2020)], we discuss a semiclassical description of one-dimensional quantum tunneling through multibarrier potentials in terms of complex time. We start by defining a complex-extended continuum level density of unbound systems and show its relation to a complex time shift of the transmitted wave. While the real part of the level density and time shift describes the passage of the particle through classically allowed coordinate regions, the imaginary part is connected with an instanton-like picture of the tunneling through forbidden regions. We describe singularities in the real and imaginary parts of the level density and time shift caused by stationary points of the tunneling potential, and show that they represent a dual extension of excited-state quantum phase transitions from bound to continuum systems. Using the complex scaling method, we numerically verify the predicted effects in several tunneling potentials., Comment: 16 pages, 7 figures

We study a system of a single qubit (or a few qubits) interacting with a soft-mode bosonic field. Considering an extended version of the Rabi model with both parity-conserving and parity-violating interactions, we disclose a complex arrangement of quantum phase transitions in the ground- and excited-state domains. An experimentally testable signature of some of these transitions is a dynamical stabilization of a fully factorized qubit-field state involving the field vacuum. It happens in the ultrastrong coupling regime where the superradiant field equilibrium is far from the vacuum state. The degree of stabilization varies abruptly with interaction parameters and increases with the softness of the field mode. We analyze semiclassical origins of these effects and show their connection to various forms of excited-state quantum phase transitions., Comment: 16 pages, 9 figures

Texture analysis and classification of image components belong to common problems of the interdisciplinary area of digital signal and image processing. The paper is devoted to the pattern matrix construction using features evaluated by the discrete Fourier transform (DFT) or the discrete wavelet transform (DWT) using the relative power in selected frequency bands or scale levels, respectively. Image features are then used to recognize groups of similar pattern vectors by self-organizing neural networks forming a mathematical tool for cluster analysis. Further classification methods including the decision tree, support vector machine, nearest neighbour method and neural networks are then applied for construction of specific models and evaluation of their accuracy and cross validation errors. The proposed algorithm is applied for analysis of given microscopic images representing wax structures covering breathing openings on leaves affected by environmental pollution in different locations. The classification accuracy depends upon the method used and it is higher than 92% for all experiments.

We introduce a complex-extended continuum level density and apply it to one-dimensional scattering problems involving tunneling through finite-range potentials. We show that the real part of the density is proportional to a real "time shift" of the transmitted particle, while the imaginary part reflects the imaginary time of an instanton-like tunneling trajectory. We confirm these assumptions for several potentials using the complex scaling method. In particular, we show that stationary points of the potentials give rise to specific singularities of both real and imaginary densities which represent close analogues of excited-state quantum phase transitions in bound systems., 6 pages, 3 figures

We review the effects of excited-state quantum phase transitions (ESQPTs) in interacting many-body systems with finite numbers of collective degrees of freedom. We classify typical ESQPT signatures in the spectra of energy eigenstates with respect to the underlying classical dynamics and outline a variety of quantum systems in which they occur. We describe thermodynamic and dynamic consequences of ESQPTs, like those in microcanonical thermodynamics, quantum quench dynamics, and in the response to nearly adiabatic or periodic driving. We hint at some generalizations of the ESQPT concept in periodic lattices and in resonant tunneling systems., Comment: 78 pages, 21 figures, review article

In this dataset we provide MALDI-TOF MS spectra of Escherichia coli. The data presented in this article are related to the article entitled “Stress response of Escherichia coli to essential oil components – insights on low-molecular-weight proteins from MALDI-TOF” (Božik et al., 2018) [1]. Essential oils and their components are known for their antibacterial effect. Many studies evaluated the effect of essential oil components (EOCs) on the cell wall, bacterial membranes, and energetic metabolism. But data about low molecular weight proteins (

Wheat dwarf virus (WDV), an important cereal pathogen, is closely related to Maize streak virus (MSV), a model virus of the Mastrevirus genus. Based on its similarity to known MSV resistance strategies, a truncated part of the WDV replication-associated (RepA) gene (WDVRepA215) and the WDV RepA gene with a mutated retinoblastoma-related protein (RBR) interaction domain (WDVRepA215RBRmut) were cloned into the pIPKb002 expression vector and transformed into immature embryos of spring barley cv. Golden Promise plants through Agrobacterium-mediated transformation. A detailed study of T1-generation plants infected by leafhoppers (Psammotettix alienus) fed on infection sources of variable strength was performed over a 5-week period encompassing the initial stages of virus infection. A DNA WDV TaqMan qPCR assay normalized using the DNA puroindoline-b SYBR Green qPCR assay for samples on a per week basis revealed an approximately 2-week delay in WDVRepA215RBRmut plants to WDVRepA215 plants before significant increases in the WDV viral levels occurred. Both WDVRepA215 and WDVRepA215RBRmut plants showed similar levels of transgenic transcripts over the screened period; however, the transgenic plants also showed increased numbers of infected plants compared to the control plants.

The antibacterial effects of essential oils and their components (EOCs) are usually attributed to effects on membranes and metabolism. Studies of the effects of EOCs on protein expression have primarily analysed proteins larger than 10 kDa using gel electrophoresis. In the present study, we used MALDI-TOF-MS to investigate the effects of EOCs on low-molecular-weight proteins. From 297 m/z features, we identified 94 proteins with important differences in expression among untreated samples, samples treated with EOCs, and samples treated with antibiotics, peroxide, or chlorine. The targets of these treatments obviously differ, even among EOCs. In addition to ribosomal proteins, stress-, membrane- and biofilm-related proteins were affected. These findings may provide a basis for identifying new targets of essential oils and synergies with other antibiotics.

Rationale Explorative statistical analysis of mass spectrometry data is still a time-consuming step. We analyzed critical factors for application of principal component analysis (PCA) in mass spectrometry and focused on two whole spectrum based normalization techniques and their application in the analysis of registered peak data and, in comparison, in full spectrum data analysis. We used this technique to identify different metabolic patterns in the bacterial culture of Cronobacter sakazakii, an important foodborne pathogen. Methods Two software utilities, the ms-alone, a python-based utility for mass spectrometry data preprocessing and peak extraction, and the multiMS-toolbox, an R software tool for advanced peak registration and detailed explorative statistical analysis, were implemented. The bacterial culture of Cronobacter sakazakii was cultivated on Enterobacter sakazakii Isolation Agar, Blood Agar Base and Tryptone Soya Agar for 24 h and 48 h and applied by the smear method on an Autoflex speed MALDI-TOF mass spectrometer. Results For three tested cultivation media only two different metabolic patterns of Cronobacter sakazakii were identified using PCA applied on data normalized by two different normalization techniques. Results from matched peak data and subsequent detailed full spectrum analysis identified only two different metabolic patterns - a cultivation on Enterobacter sakazakii Isolation Agar showed significant differences to the cultivation on the other two tested media. The metabolic patterns for all tested cultivation media also proved the dependence on cultivation time. Conclusions Both whole spectrum based normalization techniques together with the full spectrum PCA allow identification of important discriminative factors in experiments with several variable condition factors avoiding any problems with improper identification of peaks or emphasis on bellow threshold peak data. The amounts of processed data remain still manageable. Both implemented software utilities are available free of charge from http://uprt.vscht.cz/ms.

We study a simple model describing superradiance in a system of two-level atoms interacting with a single-mode bosonic field. The model permits a continuous crossover between integrable and partially chaotic regimes and shows a complex thermodynamic and quantum phase structure. Several types of excited-state quantum phase transitions separate quantum phases that are characterized by specific energy dependences of various observables and by different atom–field and atom–atom entanglement properties. We observe an approximate revival of some states from the weak atom–field coupling limit in the strong coupling regime.

We study the finite-time effects in a quantum Otto cycle where a collective spin system is used as the working fluid. Starting from a simple one-qubit system we analyze the transition to the limit cycle in the case of a finite-time thermalization. If the system consists of a large sample of independent qubits interacting coherently with the heat bath, the superradiant equilibration is observed. We show that this phenomenon can boost the power of the engine. Mutual interaction of qubits in the working fluid is modeled by the Lipkin-Meshkov-Glick Hamiltonian. We demonstrate that in this case the quantum phase transitions for the ground and excited states may have a strong negative effect on the performance of the machine. Reversely, by analyzing the work output we can distinguish between the operational regimes with and without a phase transition., 13 pages, 11 figures

We study the effect of superradiance in open quantum systems, i.e., the separation of short- and long-living eigenstates when a certain subspace of states in the Hilbert space acquires an increasing decay width. We use several Hamiltonian forms of the initial closed system and generate their coupling to continuum by means of the random matrix theory. We average the results over a large number of statistical realizations of an effective non-Hermitian Hamiltonian and relate robust features of the superradiance process to the distribution of its exceptional points. We show that the superradiance effect is enhanced if the initial system is at the point of quantum criticality., 12 pages, 11 figures

The series of articles [Ann. Phys. 345, 73 (2014) and 356, 57 (2015)] devoted to excited-state quantum phase transitions (ESQPTs) in systems with $f=2$ degrees of freedom is continued by studying the interacting boson model of nuclear collective dynamics as an example of a truly many-body system. The intrinsic Hamiltonian formalism with angular momentum fixed to $L=0$ is used to produce a generic first-order ground-state quantum phase transition with an adjustable energy barrier between the competing equilibrium configurations. The associated ESQPTs are shown to result from various classical stationary points of the model Hamiltonian, whose analysis is more complex than in previous cases because of (i) a non-trivial decomposition to kinetic and potential energy terms and (ii) the boundedness of the associated classical phase space. Finite-size effects resulting from a partial separability of both degrees of freedom are analyzed. The features studied here are inherent in a great majority of interacting boson systems., 14 pages, 6 figures

SummaryAlthough many genetic manipulations of crops providing biofortified or safer food have been prepared, the acceptance of biotechnology crops still remains limited. We report on a transgenic barley expressing the multi-functional protein osmotin that improves plant defense under stress conditions. An Agrobacterium–mediated technique was used to transform immature embryos of the spring barley cultivar Golden Promise. Transgenic barley plants of the T0 and T1 generations were evaluated by molecular methods.Transgenic barley tolerance to stress was determined by chlorophyll, total protein, malondialdehyde and ascorbate peroxidase content. Transgenic plants maintained the same level of chlorophyll and protein, which significantly declined in wild-type barley under the same stressful conditions. Salt stress evoked higher ascorbate peroxidase level and correspondingly less malondialdehyde. Methanol extracts of i) Fusarium oxysporum infected or ii) salt-stressed plants, were characterized by their acute toxicity effect on human dermal fibroblasts (HDF). Osmotin expressing barley extracts exhibited a lower cytotoxicity effect of statistical significance than that of wild-type plants under both types of stress tested on human dermal fibroblasts. Extract of Fusarium oxysporum infected transgenic barley was not able to damage DNA in Comet assay, which is in opposite to control plants. Moreover, this particular barley did not affect the local biodiversity interactions, which was tested through monitoring barley natural virus pathogen – host interactions – the BYDV and WDV viruses transmitted to the plants by aphids and leafhoppers. Our findings provide a new perspective which could help to evaluate the safety of products from genetically modified crops.