All-fiber high-power erbium-doped laser system generating optical pulses with a duration of 200 µs to 5 ms for fractional photo-rejuvenation.

An all-fiber high-power erbium-doped fiber laser (EDFL) source generating optical pulses from 200 µs to 5 ms with a stable rectangular envelope for fractional photo-rejuvenation is proposed and experimentally demonstrated. A master oscillator power amplifier (MOPA) configuration composed of a master oscillator, an acousto-optic modulator (AOM), and a one-stage amplifier is designed and employed in the EDFL to serve as an efficient laser system with excellent output performance. To avoid multistage amplifiers, the master oscillator generates 1.5 W, and a Yb-free Er-doped large-mode-area (LMA) active fiber is used for a one-stage power amplifier. There are two benefits to this approach: first, modulation of both pump and seed pulses is used to achieve clear rectangular shaped pulses without amplified spontaneous emission (ASE) growth; and second, there are no power limitations in the amplifier and undesirable 1 µm ASE compared to Er/Yb systems. We have reached 28.6 W of peak power with 26% slope efficiency limited only by available pump power, so the system can be easily scaled for achieving a higher peak power.

Rheology and microrheology of deformable droplet suspensions.

Dense suspensions of soft colloidal particles display a broad range of physical and rheological properties which are still far from being fully understood. To elucidate the role of deformability on colloidal flow, we employ computer simulations to measure the apparent viscosity of a system of droplets of variable surface tension subjected to a pressure-driven flow. We confirm that our suspension generically undergoes discontinuous shear thinning, and determine the dependence of the onset of the discontinuity on surface tension. We find that the effective viscosity of the suspension is mainly determined by a capillary number. We present active microrheology simulations, where a single droplet is dragged through the suspension. These also show a dynamical phase transition, analogous to the one associated with discontinuous shear thinning in our interpretation. Such a transition is signalled by a discontinuity in the droplet velocity versus applied force.

Extrusion without a motor: a new take on the loop extrusion model of genome organization.

Chromatin loop extrusion is a popular model for the formation of CTCF loops and topological domains. Recent HiC data have revealed a strong bias in favour of a particular arrangement of the CTCF binding motifs that stabilize loops, and extrusion is the only model to date which can explain this. However, the model requires a motor to generate the loops, and although cohesin is a strong candidate for the extruding factor, a suitable motor protein (or a motor activity in cohesin itself) has yet to be found. Here we explore a new hypothesis: that there is no motor, and thermal motion within the nucleus drives extrusion. Using theoretical modelling and computer simulations we ask whether such diffusive extrusion could feasibly generate loops. Our simulations uncover an interesting ratchet effect (where an osmotic pressure promotes loop growth), and suggest, by comparison to recent in vitro and in vivo measurements, that diffusive extrusion can in principle generate loops of the size observed in the data. Extra View on : C. A. Brackley, J. Johnson, D. Michieletto, A. N. Morozov, M. Nicodemi, P. R. Cook, and D. Marenduzzo "Non-equilibrium chromosome looping via molecular slip-links", Physical Review Letters 119 138101 (2017).

Flow of Deformable Droplets: Discontinuous Shear Thinning and Velocity Oscillations.

We study the rheology of a suspension of soft deformable droplets subjected to a pressure-driven flow. Through computer simulations, we measure the apparent viscosity as a function of droplet concentration and pressure gradient, and provide evidence of a discontinuous shear thinning behavior, which occurs at a concentration-dependent value of the forcing. We further show that this response is associated with a nonequilibrium transition between a "hard" (or less deformable) phase, which is nearly jammed and flows very slowly, and a "soft" (or more deformable) phase, which flows much more easily. The soft phase is characterized by flow-induced time dependent shape deformations and internal currents, which are virtually absent in the hard phase. Close to the transition, we find sustained oscillations in both the droplet and fluid velocities. Polydisperse systems show similar phenomenology but with a smoother transition, and less regular oscillations.

Nonequilibrium Chromosome Looping via Molecular Slip Links.

We propose a model for the formation of chromatin loops based on the diffusive sliding of molecular slip links. These mimic the behavior of molecules like cohesin, which, along with the CTCF protein, stabilize loops which contribute to organizing the genome. By combining 3D Brownian dynamics simulations and 1D exactly solvable nonequilibrium models, we show that diffusive sliding is sufficient to account for the strong bias in favor of convergent CTCF-mediated chromosome loops observed experimentally. We also find that the diffusive motion of multiple slip links along chromatin is rectified by an intriguing ratchet effect that arises if slip links bind to the chromatin at a preferred "loading site." This emergent collective behavior favors the extrusion of loops which are much larger than the ones formed by single slip links.

A one-dimensional statistical mechanics model for nucleosome positioning on genomic DNA.

The first level of folding of DNA in eukaryotes is provided by the so-called '10 nm chromatin fibre', where DNA wraps around histone proteins (∼10 nm in size) to form nucleosomes, which go on to create a zig-zagging bead-on-a-string structure. In this work we present a one-dimensional statistical mechanics model to study nucleosome positioning within one such 10 nm fibre. We focus on the case of genomic sheep DNA, and we start from effective potentials valid at infinite dilution and determined from high-resolution in vitro salt dialysis experiments. We study positioning within a polynucleosome chain, and compare the results for genomic DNA to that obtained in the simplest case of homogeneous DNA, where the problem can be mapped to a Tonks gas. First, we consider the simple, analytically solvable, case where nucleosomes are assumed to be point-like. Then, we perform numerical simulations to gauge the effect of their finite size on the nucleosomal distribution probabilities. Finally we compare nucleosome distributions and simulated nuclease digestion patterns for the two cases (homogeneous and sheep DNA), thereby providing testable predictions of the effect of sequence on experimentally observable quantities in experiments on polynucleosome chromatin fibres reconstituted in vitro.

[PREDICTION OF RISK FACTORS OF LATERAL LYMPH NODE METASTASIS IN RECTAL CANCER].

Standard methods of diagnostics haven't got a proper sensitivity and specificity concerning assessment of regional nodal involvement in case of rectal cancer. Therefore it is necessary to look for new method of diagnostics, detect risk factors and unfavorable prognosis in relation to lateral lymph node metastasis. At the same time, there should be a differentiated approach to the choice of therapeutic management in rectal cancer. Investigation of variability of blood supply of the rectum could be an additional method of diagnostics in rectal cancer.

[ABOUT PROFESSIONAL TRAINING OF ROENTGENOLOGISTS FOR WORKING ON MAGNETIC RESONANCE TOMOGRAPHIC SCANNER].

The article considers main problems conditioned demand of development of model of professional training of roentgenologists for working on magnetic resonance tomographic scanner in conditions of non-public medical diagnostic center in accordance with the concept of continuous medical education. The developed model is presented in graphic form i.e. folded in the form of generic structure and unfolded in the form of algorithmic and structural models of separate blocks. The detailed description of components of model and their functional designation are presented.

Models for twistable elastic polymers in Brownian dynamics, and their implementation for LAMMPS.

An elastic rod model for semi-flexible polymers is presented. Theory for a continuum rod is reviewed, and it is shown that a popular discretised model used in numerical simulations gives the correct continuum limit. Correlation functions relating to both bending and twisting of the rod are derived for both continuous and discrete cases, and results are compared with numerical simulations. Finally, two possible implementations of the discretised model in the multi-purpose molecular dynamics software package LAMMPS are described.

Switching of Swimming Modes in Magnetospirillium gryphiswaldense.

The microaerophilic magnetotactic bacterium Magnetospirillum gryphiswaldense swims along magnetic field lines using a single flagellum at each cell pole. It is believed that this magnetotactic behavior enables cells to seek optimal oxygen concentration with maximal efficiency. We analyze the trajectories of swimming M. gryphiswaldense cells in external magnetic fields larger than the earth's field, and show that each cell can switch very rapidly (in <0.2 s) between a fast and a slow swimming mode. Close to a glass surface, a variety of trajectories were observed, from straight swimming that systematically deviates from field lines to various helices. A model in which fast (slow) swimming is solely due to the rotation of the trailing (leading) flagellum can account for these observations. We determined the magnetic moment of this bacterium using a to our knowledge new method, and obtained a value of (2.0±0.6) × 10(-16) A · m(2). This value is found to be consistent with parameters emerging from quantitative fitting of trajectories to our model.

Filling an emulsion drop with motile bacteria.

We have measured the spatial distribution of motile Escherichia coli inside spherical water droplets emulsified in oil. At low cell concentrations, the cell density peaks at the water-oil interface; at increasing concentration, the bulk of each droplet fills up uniformly while the surface peak remains. Simulations and theory show that the bulk density results from a "traffic" of cells leaving the surface layer, increasingly due to cell-cell scattering as the surface coverage rises above ∼10%. Our findings show similarities with the physics of a rarefied gas in a spherical cavity with attractive walls.

[Endoscopic and laboratory data in diagnostics of traumatic TMJ lesions].

Twenty-seven patients with various types of internal TMJ disorders were examined at Voronezh Dental School Oral and Maxillofacial Surgery Department. All the patients underwent comprehensive examination and double-circuit TMJ arthroscopy, as well as joint fluid sampling for subsequent biochemical studies. A correlation between the degree of pathological changes of the TMJ intraarticular structures and biochemical parameters in traumatic TMJ lesions was discovered. The patterns observed may serve as a useful tool for more accurate diagnostics and treatment planning.

Bulk rheology and microrheology of active fluids.

We simulate macroscopic shear experiments in active nematics and compare them with microrheology simulations where a spherical probe particle is dragged through an active fluid. In both cases we define an effective viscosity: in the case of bulk shear simulations this is the ratio between shear stress and shear rate, whereas in the microrheology case it involves the ratio between the friction coefficient and the particle size. We show that this effective viscosity, rather than being solely a property of the active fluid, is affected by the way chosen to measure it, and strongly depends on details such as the anchoring conditions at the probe surface and on both the system size and the size of the probe particle.

Phase separation and rotor self-assembly in active particle suspensions.

Adding a nonadsorbing polymer to passive colloids induces an attraction between the particles via the "depletion" mechanism. High enough polymer concentrations lead to phase separation. We combine experiments, theory, and simulations to demonstrate that using active colloids (such as motile bacteria) dramatically changes the physics of such mixtures. First, significantly stronger interparticle attraction is needed to cause phase separation. Secondly, the finite size aggregates formed at lower interparticle attraction show unidirectional rotation. These micro-rotors demonstrate the self-assembly of functional structures using active particles. The angular speed of the rotating clusters scales approximately as the inverse of their size, which may be understood theoretically by assuming that the torques exerted by the outermost bacteria in a cluster add up randomly. Our simulations suggest that both the suppression of phase separation and the self-assembly of rotors are generic features of aggregating swimmers and should therefore occur in a variety of biological and synthetic active particle systems.

[The volume of the liver and its functional status in primary and metastatic malignant lesions].

84 patients with primary and metastatic malignant liver lesions predominantly at stage T4N0M0 were studied liver volumes and volumes of foci of lesions, also personal normal liver formula. Obtained data was compared with the functional state of the liver, as determined by the scale of hepatotoxicity NIH-NIAD with additional index points of higher levels of ALT, SCHF and total bilirubin in serum. We found that liver increase in most cases is not only a total foci destruction and predominantly blood disorders and lymphokinesis bodies. Even with 50% dissemination of the malignant growth of functional compensation body remains at a sufficient level, which enables extensive cytoreductional intervention and chemotherapy.

Thermodynamics of a conformational change using a random walk in energy-reaction coordinate space: Application to methane dimer hydrophobic interactions.

A random walk sampling algorithm allows the extraction of the density of states distribution in energy-reaction coordinate space. As a result, the temperature dependences of thermodynamic quantities such as relative energy, entropy, and heat capacity can be calculated using first-principles statistical mechanics. The strategies for optimal convergence of the algorithm and control of its accuracy are proposed. We show that the saturation of the error [Q. Yan and J. J. de Pablo, Phys. Rev. Lett. 90, 035701 (2003); E. Belardinelli and V. D. Pereyra, J. Chem. Phys. 127, 184105 (2007)] is due to the use of histogram flatness as a criterion of convergence. An application of the algorithm to methane dimer hydrophobic interactions is presented. We obtained a quantitatively accurate energy-entropy decomposition of the methane dimer cavity potential. The presented results confirm the previous results, and they provide new information regarding the thermodynamics of hydrophobic interactions. We show that the finite-difference approximation, which is widely used in molecular dynamic simulations for the energy-entropy decomposition of a free energy potential, can lead to a significant error.

[Sialoendoscopy possibilities in diagnostics and comprehensive treatment of chronic sialoadenitis].

Checkup and treatment of 187 patients with different forms of chronic sialoadenitis was done, 38 from them parotid gland sialoendoscopy was performed. Sialoendoscopic criteria of chronic sialoadenitis forms and clinical results of the fulfilled sialoendoscopic procedures in the immediate postoperation period were described. The direct visual assessment of parotid duct system let with high degree of exactness to determine the sialoadenitis form and simultaneously to make surgical intervention that made sialoendoscopy the choosing method in diagnostic and treatment of chronic inflammatory pathology of major salivary glands.

Nonadditive interactions in protein folding: the zipper model of cytochrome C.

Hydrogen exchange experiments (Krishna et al. in J. Mol. Biol. 359:1410, 2006) reveal that folding-unfolding of cytochrome c occurs along a defined pathway in a sequential, stepwise manner. The simplified zipper-like model involving nonadditive coupling is proposed to describe the classical "on pathway" folding-unfolding behavior of cytochrome c. Using free energy factors extracted from HX experiments, the model can predict and explain cytochrome c behavior in spectroscopy studies looking at folding equilibria and kinetics. The implications of the proposed model are discussed for such problems as classical pathway vs. energy landscape conceptions, structure and function of a native fold, and interplay of secondary and tertiary interactions.

[Prospects of use of gene therapy in head trauma]. / Perspektivy ispol'zovaniia gennoi terapii pri cherepno-mozgovoi travme.

Neuronal injury may have one of the following three sequelae: death of the neurone, persistent atrophy or recovery. The ability of mature neurones to recover is dependent to a not inconsiderable degree on neurotrophins, on the basis of which consideration the following objective of genotherapy in craniocerebral injury (CCI) is formulated: achievement of therapeutically useful levels of expression of neutrophins by employment of genetical methodological approaches. The next prerequisite for institution of genotherapy in CCI is a proved dependance of CCI sequelae on individual genetic features, on APO E-genotype in particular, which fact suggests to us that specific correction is within the bounds of possibility. Another precondition for use of genotherapy in CCI is considered to be higher permeability of the blood-brain barrier in trauma, which even can facilitate the delivery of transgenes into the brain with the aid of those vectors the access of which to the central nervous system is limited under other conditions.