Fluorescent labeling is an established method for visualizing cellular structures and dynamics. The fundamental diffraction limit in image resolution was recently bypassed with the development of ...super-resolution microscopy. Notably, both localization microscopy and stimulated emission depletion (STED) microscopy impose tight restrictions on the physico-chemical properties of labels. One of them-the requirement for high photostability-can be satisfied by transiently interacting labels: a constant supply of transient labels from a medium replenishes the loss in the signal caused by photobleaching. Moreover, exchangeable tags are less likely to hinder the intrinsic dynamics and cellular functions of labeled molecules. Low-affinity labels may be used both for fixed and living cells in a range of nanoscopy modalities. Nevertheless, the design of optimal labeling and imaging protocols with these novel tags remains tricky. In this review, we highlight the pros and cons of a wide variety of transiently interacting labels. We further discuss the state of the art and future perspectives of low-affinity labeling methods.
In this work, we have shown that the introduction of a trifluoromethyl group into the me-ta-position of arylidene imidazolones (GFP chromophore core) leads to a dramatic increase in their ...fluorescence in nonpolar and aprotic media. The presence of a pronounced solvent-dependent gradation of fluorescence intensity makes it possible to use these substances as fluorescent polarity sensors. In particular, we showed that one of the created compounds could be used for selective labeling of the endoplasmic reticulum of living cells.
Methods for the application of neural networks in searches for new physics in collider experiments are described. Mechanisms of selecting observables, optimizing hyperparameters, and constructing ...cascades of deep neural networks are considered. Methods for a statistical analysis of neural-network discriminants in theta and CombinedLimit packages with allowance for various uncertainties are presented.
The Effective Field Theory (EFT) approach is widely used in the search for possible deviations from the predictions of the Standard Model. Such an approximation of possible BSM physics is valid up to ...a certain levels of energy scale and accuracy. In this article, we investigate potential limitation of the EFT approach related to unitarity to describe possible contributions of flavor-changing neutral currents (FCNC) involving the top quark. The numerical and analytical calculations of the FCNC processes used in the EFT approach demonstrate the constant asymptotic behavior of the total cross section with increasing energy. It is shown that the EFT approach for studying the possible contribution of FCNC does not violate the restrictions following from perturbative unitarity, the asymptotic behavior of the cross section does not exceed the Froissart bound, and the approach itself can be used to set the corresponding experimental limits for FCNC couplings or Wilson coefficients at present and future colliders.
The recessive form of dystrophic epidermolysis bullosa (RDEB) is a crippling disease caused by impairments in the junctions of the dermis and the basement membrane of the epidermis. Using ectopic ...expression of hTERT/hTERT + BMI-1 in primary cells, we developed expansible cultures of RDEB fibroblasts and keratinocytes. We showed that they display the properties of their founders, including morphology, contraction ability and expression of the respective specific markers including reduced secretion of type VII collagen (C7). The immortalized keratinocytes retained normal stratification in 3D skin equivalents. The comparison of secreted protein patterns from immortalized RDEB and healthy keratinocytes revealed the differences in the contents of the extracellular matrix that were earlier observed specifically for RDEB. We demonstrated the possibility to reverse the genotype of immortalized cells to the state closer to the progenitors by the Cre-dependent hTERT switch off. Increased β-galactosidase activity and reduced proliferation of fibroblasts were shown after splitting out of transgenes. We anticipate our cell lines to be tractable models for studying RDEB from the level of single-cell changes to the evaluation of 3D skin equivalents. Our approach permits the creation of standardized and expandable models of RDEB that can be compared with the models based on primary cell cultures.
Recent advancements in model-independent approaches in high energy physics have encountered challenges due to the limited effectiveness of unsupervised algorithms when compared to their supervised ...counterparts. In this paper, we present a novel approach utilizing a one-class deep neural network (DNN) to achieve accuracy levels comparable to supervised learning methods. Our proposed novelty detection algorithm uses a multilayer perceptron to learn and distinguish a specific class from simulated noise signals. By training on a single class, our algorithm constructs a hyperplane similar to one-class support vector machines (SVMs) but with enhanced accuracy and significantly reduced training and inference times. This research contributes to the advancement of model-independent techniques for uncovering New Physics phenomena, showcasing the potential of one-class DNNs as a viable alternative to traditional supervised learning approaches. For the demonstration of the method, the distinguishing of flavour changing neutral currents in top quark interactions from the Standard Model processes has been considered. The obtained results demonstrate the effectiveness of our proposed algorithm, paving the way for improved anomaly detection and exploration of uncharted territories in high energy physics.
Modeling of the pair and single top quark production are discussed in the context of searches for the anomalous
couplings. For the simulation of the anomalous
couplings in the top quark production ...and/or decay, the Subsidiary Fields method allows to generate a minimal number of event samples to cover all possible values of the couplings. In the paper the Subsidiary Fields method is applied to simulate the full
process with
final state including the subsequent top quark and
boson decays. Correctness of the differential cross sections for arbitrary values of the
couplings is demonstrated for the case of the simultaneous presence of the left- and right-handed vector operators in the Wtb vertex.
The paper presents a method for separating contributions of pair and single top quark production to tWb associated final state using a neural network. The proposed method makes it possible to ...calculate such processes in a gauge-invariant way, taking into account interference contributions and dividing the phase space into single-resonant and double-resonant regions. The optimized set of observables is used to separate single-resonant and double-resonant contributions to the overall process for neural network training. A usage of the method allows for avoiding the disadvantages that are inherent in the schemes used in collider physics for calculation of the tWb associated top quark production with the removal of Feynman diagrams, which leads to violation of gauge invariance, or the addition of a subtraction scheme, which leads to the appearance of negative weights for the part of simulated events. The proposed method can be used to increase the efficiency of the search for deviations from the predictions of the Standard Model in the interaction of the top quark with the W boson and b-quark.
The high brightness and photostability of the green fluorescent protein StayGold make it a particularly attractive probe for long-term live-cell imaging; however, its dimeric nature precludes its ...application as a fluorescent tag for some proteins. Here, we report the development and crystal structures of a monomeric variant of StayGold, named mBaoJin, which preserves the beneficial properties of its precursor, while serving as a tag for structural proteins and membranes. Systematic benchmarking of mBaoJin against popular green fluorescent proteins and other recently introduced monomeric and pseudomonomeric derivatives of StayGold established mBaoJin as a bright and photostable fluorescent protein, exhibiting rapid maturation and high pH/chemical stability. mBaoJin was also demonstrated for super-resolution, long-term live-cell imaging and expansion microscopy. We further showed the applicability of mBaoJin for neuronal labeling in model organisms, including Caenorhabditis elegans and mice.
The discovery of the bioluminescence pathway in the fungus Neonothopanus nambi enabled engineering of eukaryotes with self-sustained luminescence. However, the brightness of luminescence in ...heterologous hosts was limited by performance of the native fungal enzymes. Here we report optimized versions of the pathway that enhance bioluminescence by one to two orders of magnitude in plant, fungal and mammalian hosts, and enable longitudinal video-rate imaging.
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