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The new effect of photostimulated dissolution of as-evaporated and annealed Ge-based chalcogenide glass (ChG) films was investigated in detail. The etching rate increases with the illumination intensity, and its spectral dependence is correlated with absorption in the film at the absorption edge. A possible mechanism for the photoinduced etching of ChG films has been discussed. The high-frequency diffraction gratings on germanium ChG - more environmentally acceptable compounds than traditionally used arsenic chalcogenides - were recorded using the method of interference immersion photolithography with photoinduced etching. [ABSTRACT FROM AUTHOR]

The spectrum of the photoconductivity induced by the polarization field of charges at surface states and traps in the film bulk has been analyzed to determine the energy band diagram at the c-Si-SiO interface and the changes in the electronic states after the film annealing. It is found that the energy bands are bent at the Si-SiO interface and the Si surface is enriched in electrons. In equilibrium the photocurrent peak at 1.1 eV is due to the band-to-band transitions in the silicon part of the interface. Annealing shifts the peak to higher energies; this shift increases with an increase in the annealing temperature from 650 to 1000°C. This effect is accompanied by a decrease in the photocurrent at ≤1.1 eV and weakening of the band-edge photoluminescence near the Si surface. The changes revealed are explained by the formation of an oxide layer with Si nanoclusters at the Si-SiO interface upon annealing. This process is caused by oxygen diffusion from the SiO film, which occurs mainly via defects on the Si wafer surface. The photoconductivity spectrum of the samples charged by short-term application of a negative potential to silicon exhibits electronic transitions in the SiO film, both from the matrix electronic states and from the states of the defects and Si nanoclusters in the film. [ABSTRACT FROM AUTHOR]

Morphological and optical studies (ellipsometry and reflectance spectroscopy in the ranges 400–750 nm and 1.4–25 μm) of thin GaSe films fabricated by thermal evaporation on the n-Si (111) single-crystal substrates are reported. The film thickness was 15–60 nm. It is established that, in the initial stage of growth, the growth of GaSe on the n-Si (111) substrates occurs via formation of islands (three-dimensional growth). It is shown that, as the thickness increases, the physical parameters of the film change and the films approach single crystals in crystalline and energy band structure. For films with a thickness of 60 nm, the reflectance band peak is attributed to indirect optical transitions enhanced by reflection from the film-substrate interface. From the results of optical studies, quantum effects in the surface region of the thin films are conjectured. [ABSTRACT FROM AUTHOR]

Morphological and optical studies of the Si-doped GaN films (doping level NSi = 1.5 × 1019 cm−3) grown by vapor-phase epitaxy from metalorganic compounds on a sapphire substrate oriented along the c axis are conducted. For the grown GaN films, the following characteristics are obtained: energy of electron transition E0, absorption coefficient α, refractive index n, and frequencies of transverse and longitudinal optical lattice vibrations characteristic of the crystalline GaN films. [ABSTRACT FROM AUTHOR]

Morphological and optical (with reflection spectra in the range of 200–750 nm, transmission spectra in the range of 2–25 μm, and ellipsometry) studies were performed for AlN films that had a thickness of 2–3 μm and were obtained by the method of high-frequency magnetron sputtering of an aluminum target in a gas mixture of Ar and N2 (1: 3) with deposition onto single-crystal n-Si (100) substrates with a resistivity of 20–60 Ω cm. It is shown that the films are dense and transparent; they are amorphous with crystalline grains and can be used efficiently in thin-film technology for fabrication of modern microelectronic and optoelectronic devices. [ABSTRACT FROM AUTHOR]

Application of inorganic photoresist based on chalcogenide films for fabrication of submicrometer periodic relief on silicon wafers was investigated. For this purpose, technological process of resistive two-layer chalcogenide-Cr mask formation on a silicon surface was developed, and silicon anisotropic etching was optimized, too. This technology has been used for the fabrication of high-quality diffraction gratings on Si (100) surface with symmetric triangular and trapezium grooves and two-dimentional periodic structures. Relief parameters and diffraction properties of the obtained structures and their dependences on etching time were determined. [ABSTRACT FROM AUTHOR]

The formation of nanodimensional structures on the surface of p-CdTe crystals has been studied as a function of the radiation-power density of a laser under a single irradiation dose. The best conditions for laser irradiation of the crystals are found. Under these conditions, a homogeneous structure with a period of 100 nm is formed. The lateral size of the structure is ∼(19–20) nm, and the average height is ∼(3.40–9.38) nm. It is found that periodicity manifests itself clearly in one crystallography direction. © 2005 Pleiades Publishing, Inc. [ABSTRACT FROM AUTHOR]

The investigation results of holographic diffraction gratings recording processes by radiation of helium-neon laser have been represented. Inorganic As40S20Se40 photoresist treated by the newly developed selective etching solution was chosen as a registering media. Angular and spectral dependencies of grating diffractive efficiency absolute values were measured. A comparison of fabricated gratings characteristics with corresponding parameters of gratings recorded on As40Se60 photoresist was carried out. Numericall simulation of groove profiles inherent to holographic gratings made in various experimental conditions was performed. Shown is that photoresists based on As40S20Se40 are suitable for production of high quality holographic optical elements. [ABSTRACT FROM AUTHOR]

One of the essential issues of the benches’ development procedure is the choice of the method of seam development in the complex structure: joint development of rock and coal seams in one complex face or their separate excavation in blocks of 50-100 m in length. The decision of this question is connected with the mode of mining works, represented by the schedule of stripping and winning works. The choice of one or another method is connected with operative-dispatching control of haul trucks delivery. When rock and coal are mined together in a complex face, overburden haul trucks should be supplied for loading rock and coal haul trucks for coal in turns. It is organizationally difficult to supply haul trucks of different purposes during the shift. It is necessary to proceed from the shift (daily) planning of haul trucks supply for specific faces. In addition, it is necessary to take into account that rock and coal faces are often located on opposite sides of the quarry pit. This article studies the issue of organizing the operation of excavation and loading equipment during the mining of the coal-bearing zone of the open pit in order to reduce the loss of output of haul trucks.

Hydraulic excavators currently used at open pit mines, in particular backhoes, are more maneuverable, mobile and have more digging capabilities than rope shovels. This makes them suitable for a variety of conditions: top and bottom digging, loading lower, higher and at the standing level. The variants of mutual arrangement of the excavator and the dump truck, respectively, affect the duration of the excavator cycle, which, in turn, directly affects the productivity of the excavator. This article evaluates changes in the productivity of an excavator, depending on its angle of rotation and options for digging and loading. It is determined that the smaller the swing angle of an excavator, the greater its impact on productivity. Based on the executed calculations relative decrease in productivity (in percent from the most optimum variant) is established. Results of work can be used at planning of open pit mining for the purpose of definition, for example, speed of mining front movement at change of parameters of an excavator face and a type of a digging and loading.

As is known from the classic works on open pit mining, the bench is a separately developed part of the rock layer, having the form of a step. It should also be noted that it is necessary to clearly differentiate the concepts of “bench height” and “height of the layer to be removed.” The benches are often divided into subbenches, developed by different excavation equipment or by the same equipment both sequentially and simultaneously, but having transport routes that are uniform for the bench. As an example, an excavator stripping of the upper and lower subbenches with loading, respectively, at the level of the excavator and above this level, is usually given, that is, the transport route (road) passes through an intermediate platform bench located in the middle of its height. Therefore, the excavation layer of any height, which is, in fact, a part of the working bench, can be considered as an independent bench with all its attributes, but in order to avoid duplication of definitions, this paper suggests the name “extraction layer”. When developing this element various digging modes can be applied. In this paper, we studied the main modes and selected the one that provides the highest performance.

Currently, two types of handling machines are mainly used on coal open pit mines in Kuzbass, characterized by complex structural deposits: mechanical (rope) and hydraulic (backhoe) shovels. Moreover, both types of equipment are supplied to the quarries: mechanical shovels are purchased, as a rule, powerful with a bucket capacity up to 56 m3, backhoes – small and medium-size models with a bucket capacity of 2.8-14 m3. On the other hand, it is common to divide the areas of equipment use in the open pit on complex-structured deposits into a coalless (outside the strata of coalbeds) and coal-bearing (actually a series of beds, including coal strata and rock interbeds). The use of these equipment types in both design and industrial practice is observed in both zones. At the same time, it is known that each of these zones has different conditions for the efficient operation of excavation machines. The seams, therefore, do not complicate the coalless zone when working in it, favorable conditions are provided for the excavator: the constant height of the bench, which is necessary for the full filling of the bucket for one scoop, the constant width of the panel and the length of the front of the work. In these conditions, the maximum productivity of the excavator is ensured.

Numerical simulation of bulk technogenic rock arrays, unlike the full-scale, has a number of advantages. They are: the large amount of low cost measurements; operative selection of parameters necessary for the environment with the given properties; calculation of stress-strain state and assessment of the array sustainability; calculation of rock arrays filtration properties that are used as filters for mining enterprises sewage, etc. The article describes the method of numerical simulation of structure of bulk disjointed rock arrays, describes the basic initial and boundary conditions of the model; represents the numerical model visualization of the array, created with the use of peripheral dumping (as an array with more textured and visual segregation of granulometric composition adjustment). The basic applications of numerical modeling of technogenic rock arrays in the mining processes are described. Comparative analysis of the real and simulated array structure shows the adequacy of the numerical model and the developed for its creation algorithm, which in turn allows judging the quality of the study. Also, the adequacy of building models is supported by a high convergence of the experimental and calculated figures depending on the filtration rate values of the particle size distribution of technogenic rock arrays.

Features of geological structure of the Kuznetsk coal basin stipulate the application of a low-cost open technique of coal mining, which is more advantageous both from the economic standpoint, and by safety criteria of mining. However, open mining affects significantly the water resources of region. Intensive pollution of reservoirs and water courses, exhaustion of the underground water-bearing layers, violation of a hydrographic network, etc. be-long to the main disadvantages of an open technique of coal mining. Besides, the volume of the water coming into the mining producers exceeds signi-ficantly the needed quantity. According to the data of annual reports of ecology and natural resources department, 348.277 million m3 of water were ta-ken away during production of soft coal, brown coal and lignum fossil from waters of Kemerovo region in 2013 (mostly from underground water objects (96,5%) when draining of mine openings). At the same time, only 87.018 million m3 of water (25%) has been used within a year.

The examples of mining rock panels by different types of equipment are given in this paper. In such conditions, it is most expedient to use wide stopes to improve the productivity of equipment by reducing the time for auxiliary works. Also technological schemes of equipment operation in different conditions for several quarries of the Kuzbass are proposed. The coal-bearing zone is worked “layer by layer” with one or two benches or subbenches. The bottom of the quarry in this case is flat, without leaving “peak” of overburden rocks in the pillars. Cutting of the benches is carried out by trench with a wide bottom on the side of the roof of the coal bed and simultaneously working it with the same excavator or with setting up a additional excavator for coal mining operations. Interbeds are mined out with the use of wide stopes, often to the theirs entire horizontal width. Complex rock-and-coal blocks, including one-three coal beds, are also worked out by wide stopes.

Recent screening of drug sensitivity in large panels of cancer cell lines provides a valuable resource towards developing algorithms that predict drug response. Since more samples provide increased statistical power, most approaches to prediction of drug sensitivity pool multiple cancer types together without distinction. However, pan-cancer results can be misleading due to the confounding effects of tissues or cancer subtypes. On the other hand, independent analysis for each cancer-type is hampered by small sample size. To balance this trade-off, we present CHER (Contextual Heterogeneity Enabled Regression), an algorithm that builds predictive models for drug sensitivity by selecting predictive genomic features and deciding which ones should-and should not-be shared across different cancers, tissues and drugs. CHER provides significantly more accurate models of drug sensitivity than comparable elastic-net-based models. Moreover, CHER provides better insight into the underlying biological processes by finding a sparse set of shared and type-specific genomic features.

Acute myeloid leukemia (AML) manifests as phenotypically and functionally diverse cells, often within the same patient. Intratumor phenotypic and functional heterogeneity have been linked primarily by physical sorting experiments, which assume that functionally distinct subpopulations can be prospectively isolated by surface phenotypes. This assumption has proven problematic, and we therefore developed a data-driven approach. Using mass cytometry, we profiled surface and intracellular signaling proteins simultaneously in millions of healthy and leukemic cells. We developed PhenoGraph, which algorithmically defines phenotypes in high-dimensional single-cell data. PhenoGraph revealed that the surface phenotypes of leukemic blasts do not necessarily reflect their intracellular state. Using hematopoietic progenitors, we defined a signaling-based measure of cellular phenotype, which led to isolation of a gene expression signature that was predictive of survival in independent cohorts. This study presents new methods for large-scale analysis of single-cell heterogeneity and demonstrates their utility, yielding insights into AML pathophysiology., (Copyright © 2015 Elsevier Inc. All rights reserved.)

Drugs that inhibit the MAPK pathway have therapeutic benefit in melanoma, but responses vary between patients, for reasons that are still largely unknown. Here we aim at explaining this variability using pre- and post-MEK inhibition transcriptional profiles in a panel of melanoma cell lines. We found that most targets are context specific, under the influence of the pathway in only a subset of cell lines. We developed a computational method to identify context-specific targets, and found differences in the activity levels of the interferon pathway, driven by a deletion of the interferon locus. We also discovered that IFNα/β treatment strongly enhances the cytotoxic effect of MEK inhibition, but only in cell lines with low activity of interferon pathway. Taken together, our results suggest that the interferon pathway plays an important role in, and predicts, the response to MAPK inhibition in melanoma. Our analysis demonstrates the value of system-wide perturbation data in predicting drug response., (Copyright © 2015 Elsevier Inc. All rights reserved.)

Cellular circuits sense the environment, process signals, and compute decisions using networks of interacting proteins. To model such a system, the abundance of each activated protein species can be described as a stochastic function of the abundance of other proteins. High-dimensional single-cell technologies, such as mass cytometry, offer an opportunity to characterize signaling circuit-wide. However, the challenge of developing and applying computational approaches to interpret such complex data remains. Here, we developed computational methods, based on established statistical concepts, to characterize signaling network relationships by quantifying the strengths of network edges and deriving signaling response functions. In comparing signaling between naïve and antigen-exposed CD4(+) T lymphocytes, we find that although these two cell subtypes had similarly wired networks, naïve cells transmitted more information along a key signaling cascade than did antigen-exposed cells. We validated our characterization on mice lacking the extracellular-regulated mitogen-activated protein kinase (MAPK) ERK2, which showed stronger influence of pERK on pS6 (phosphorylated-ribosomal protein S6), in naïve cells as compared with antigen-exposed cells, as predicted. We demonstrate that by using cell-to-cell variation inherent in single-cell data, we can derive response functions underlying molecular circuits and drive the understanding of how cells process signals., (Copyright © 2014, American Association for the Advancement of Science.)

Cataloging the association of transcripts to genetic variants in recent years holds the promise for functional dissection of regulatory structure of human transcription. Here, we present a novel approach, which aims at elucidating the joint relationships between transcripts and single-nucleotide polymorphisms (SNPs). This entails detection and analysis of modules of transcripts, each weakly associated to a single genetic variant, together exposing a high-confidence association signal between the module and this 'main' SNP. To explore how transcripts in a module are related to causative loci for that module, we represent such dependencies by a graphical model. We applied our method to the existing data on genetics of gene expression in the liver. The modules are significantly more, larger and denser than found in permuted data. Quantification of the confidence in a module as a likelihood score, allows us to detect transcripts that do not reach genome-wide significance level. Topological analysis of each module identifies novel insights regarding the flow of causality between the main SNP and transcripts. We observe similar annotations of modules from two sources of information: the enrichment of a module in gene subsets and locus annotation of the genetic variants. This and further phenotypic analysis provide a validation for our methodology.

Systematic characterization of cancer genomes has revealed a staggering number of diverse aberrations that differ among individuals, such that the functional importance and physiological impact of most tumor genetic alterations remain poorly defined. We developed a computational framework that integrates chromosomal copy number and gene expression data for detecting aberrations that promote cancer progression. We demonstrate the utility of this framework using a melanoma data set. Our analysis correctly identified known drivers of melanoma and predicted multiple tumor dependencies. Two dependencies, TBC1D16 and RAB27A, confirmed empirically, suggest that abnormal regulation of protein trafficking contributes to proliferation in melanoma. Together, these results demonstrate the ability of integrative Bayesian approaches to identify candidate drivers with biological, and possibly therapeutic, importance in cancer., (Copyright © 2010 Elsevier Inc. All rights reserved.)

We present a method that harnesses massively parallel DNA synthesis and sequencing for the high-throughput functional analysis of regulatory sequences at single-nucleotide resolution. As a proof of concept, we quantitatively assayed the effects of all possible single-nucleotide mutations for three bacteriophage promoters and three mammalian core promoters in a single experiment per promoter. The method may also serve as a rapid screening tool for regulatory element engineering in synthetic biology.

The experience of pancreaticoduodenal resection performance in 110 patients in 1996-2008 yrs was presented. The comparative analysis of the operations results was conducted between 49 patients, in whom standard methods were applied (I group), and 61 patients, who were operated on, using transplantation technologies (II group). Transplantation technologies application have permitted to reduce essentially the postoperative pancreatitis occurrence--from 30.6 to 9.8% and pancreatic fistula formation--from 18.3 to 4.9%. After the operation all the patients are alive.

Understanding the effect of genetic sequence variation on phenotype is a major challenge that lies at the heart of genetics. We developed GOLPH (GenOmic Linkage to PHenotype), a statistical method to identify genetic interactions, and used it to characterize the landscape of genetic interactions between gene expression quantitative trait loci. Our results reveal that allele-specific interactions, in which a gene only exerts an influence on the phenotype in the presence of a particular allele at the primary locus, are widespread and that genetic interactions are predominantly nonadditive. The data portray a complex picture in which interacting loci influence the expression of modules of coexpressed genes involved in coherent biological processes and pathways. We show that genetic variation at a single gene can have a major impact on the global transcriptional response, altering interactions between genes through shutdown or activation of pathways. Thus, different cellular states occur not only in response to the external environment but also result from intrinsic genetic variation.

Connexins had been considered to be the only class of the vertebrate proteins capable of gap junction formation; however, new candidates for this function with no homology to connexins, termed pannexins were discovered. So far three pannexins were described in rodent and human genomes: Panx1, Panx2 and Panx3. Expressions of pannexins can be detected in numerous brain structures, and now found both in neuronal and glial cells. Hypothetical roles of pannexins in the nervous system include participating in sensory processing, hippocampal plasticity, synchronization between hippocampus and cortex, and propagation of the calcium waves supported by glial cells, which help maintain and modulate neuronal metabolism. Pannexin also may participate in pathological reactions of the neural cells, including their damage after ischemia and subsequent cell death. Recent study revealed non-gap junction function of Panx1 hemichannels in erythrocytes, where they serve as the conduits for the ATP release in response to the osmotic stress. High-throughput studies produced some evidences of the pannexin involvement in the process of tumorigenesis. According to brain cancer gene expression database REMBRANDT, PANX2 expression levels can predict post diagnosis survival for patients with glial tumors. Further investigations are needed to verify or reject hypotheses listed.

Mice housed in standard cages show impaired brain development, abnormal repetitive behaviours (stereotypies) and an anxious behavioural profile, all of which can be lessened by making the cage environment more stimulating. But concerns have been raised that enriched housing might disrupt standardization and so affect the precision and reproducibility of behavioural-test results (for example, see ref. 4). Here we show that environmental enrichment increases neither individual variability in behavioural tests nor the risk of obtaining conflicting data in replicate studies. Our findings indicate that the housing conditions of laboratory mice can be markedly improved without affecting the standardization of results.