Matching of a multimodule plasma opening switch to a liner load

One of the key problems of the Baikal project, intended to create a superpower pulsed generator for ICF experiments, is that of matching a multimodule plasma opening switch (POS) to a liner load. An intermediate inductance or a separating discharger is proposed to be used as a matching element between the POS and the load. An analysis is made of the effect of both versions of the matching system on the synchronization of the POS modules and the energy transfer from the inductive storage to the load. Methods for optimizing the matching element are examined. It is shown that the POS modules can be synchronized and the inductive storage energy can be efficiently transferred to a low-impedance load. A multigap vacuum discharger with a point anode and plane cathode is to be used as a separating discharger. Such an electrode system make it possible to concentrate the electric field at the point anode and to substantially enhance the electric strength of the inter-electrode gap. Results are presented from experimental studies of vacuum breakdown in such an electrode system with a gap length of about 1 mm.     

Plasma opening switch for the MOL generator

Problems related to creating a superpower pulsed current generator (Baikal project, ≈10 MV, ≈50 MA, ≈150 ns) for inertial confinement fusion are considered. In order to test the circuit design of the generator, the MOL unit (3.7 MA, 5 MV, 150 ns), in which a plasma opening switch (POS) is proposed for use as an output power sharpener, is now under construction. Results are presented from experimental testing of a number of proposals enabling the POS operation under the MOL conditions: (i) plasma guns were employed to connect the POS to the inductive storage circuit, (ii) a separating discharger was used to avoid a POS reclosure and to switch the current to a load whose impedance was initially low and increased with time, and (iii) a programmable filling of the POS gap with plasma was implemented in order for the POS to pass a long current prepulse with parameters close to those in actual systems.     

Dynamics of the plasma injected into the gap of a plasma opening switch across a strong magnetic field

A method is proposed to increase the linear charge density transferred through a plasma opening switch (POS) and, accordingly, reduce the POS diameter by enhancing the external magnetic field in the POS gap. Results are presented from experimental studies of the dynamics of the plasma injected into the POS gap across a strong magnetic field. The possibility of closing the POS gap by the plasma injected across an external magnetic field of up to 60 kG is demonstrated.     

Distribution of leakage currents in the cylindrical and conical sections of the magnetically insulated transmission line of the Angara-5-1 facility in experiments with wire arrays

Current leakages in the magnetically insulated transmission lines (MITL) impose restrictions on the transmission of electromagnetic pulses to the load in high-power electrophysical facilities. The multimodule Angara-5-1 facility with an output electric power of up to 6 TW is considered. In this work, the experimental and calculated profiles of leakage currents in two sections of the line are compared when the eight-module facility is loaded by a wire array. The azimuthal distribution of the current in the cylindrical section of the MITL is also considered.     

Limiting Parameters of the Plasma Opening Switch

Implementing programs for nuclear fusion research and X-ray generation requires the creation of superpower generators based on plasma opening switches (POSs) capable of commutating currents as high as several tens of megaamperes at output voltages of up to 5 MV and higher. The physical mechanisms limiting the POS voltage are investigated. It is shown that, as the generator voltage U _g increases, the voltage multiplication factor k = U_POS/U_g (where U_POS is the POS voltage) decreases. An explanation for such a dependence is proposed, and the maximum value of the POS voltage is estimated. A POS design that enables operating in the above current and voltage ranges is considered. The design is based on applying an external magnetic field to the POS interelectrode gap, increasing the initial generator voltage, and decreasing the linear (along the perimeter of the outer electrode) density of the charge passing through the POS during the conduction phase.     

Influence of the electrode system on the emission characteristics of a vacuum spark

The influence of the electrode system on the emission characteristics of a high-current low-inductance vacuum spark is investigated. It is shown that the structure and composition of the spark plasma radiating in the X-ray spectral range depend substantially on the geometry and relative position of the electrodes. A mechanism related to the effect of the initial distribution of the electric field in the electrode gap is proposed to explain such a dependence. The conditions in which the radiating plasma forms from the erosion products of one or both electrodes are determined.     

Suprathermal electrons in a vacuum spark discharge

Results of experiments on the detection of suprathermal electron beams in the plasma of a highcurrent low-inductance vacuum spark by means of space-resolved spectral X-ray polarimetry are presented. It is shown that the observed polarization of bremsstrahlung may be caused by an ~100-keV electron beam propagating along the discharge axis from the pinching region toward the anode. The influence of the discharge initiation conditions on the parameters of the generated electron beams is analyzed.     

Large-Scale Purification of Porcine or Bovine Photoreceptor Outer Segments for Phagocytosis Assays on Retinal Pigment Epithelial Cells

Analysis of one of the vital functions of retinal pigment epithelial (RPE) cells, the phagocytosis of spent aged distal fragments of photoreceptor outer segments (POS) can be performed in vitro. Photoreceptor outer segments with stacks of membranous discs containing the phototransduction machinery are continuously renewed in the retina. Spent POS are eliminated daily by RPE cells. Rodent, porcine/bovine and human RPE cells recognize POS from various species in a similar manner. To facilitate performing large series of experiments with little variability, a large stock of POS can be isolated from porcine eyes and stored frozen in aliquots. This protocol takes advantage of the characteristic of photopigments that display an orange color when kept in the dark. Under dim red light, retinae are collected in a buffer from opened eyecups cut in halves. The retinal cell suspension is homogenized, filtered and loaded onto a continuous sucrose gradient. After centrifugation, POS are located in a discrete band in the upper part of the gradient that has a characteristic orange color. POS are then collected, spun, resuspended sequentially in wash buffers, counted and aliquoted. POS obtained this way can be used for phagocytosis assays and analysis of protein activation, localization or interaction at various times after POS challenge. Alternatively, POS can be labeled with fluorophores, e.g., FITC, before aliquoting for subsequent fluorescence quantification of POS binding or engulfment. Other possible applications include the use of modified POS or POS challenge combined with stress conditions to study the effect of oxidative stress or aging on RPE cells.     

Dynamic structure of plasma fibronectin

Fibronectin is a large vertebrate glycoprotein that is found in soluble and insoluble forms and involved in diverse processes. Protomeric fibronectin is a dimer of subunits, each of which comprises 29–31 modules – 12 type I, two type II and 15–17 type III. Plasma fibronectin is secreted by hepatocytes and circulates in a compact conformation before it binds to cell surfaces, converts to an extended conformation and is assembled into fibronectin fibrils. Here we review biophysical and structural studies that have shed light on how plasma fibronectin transitions from the compact to the extended conformation. The three types of modules each have a well-organized secondary and tertiary structure as defined by NMR and crystallography and have been likened to “beads on a string”. There are flexible sequences in the N-terminal tail, between the fifth and sixth type I modules, between the first two and last two of the type III modules, and at the C-terminus. Several specific module–module interactions have been identified that likely maintain the compact quaternary structure of circulating fibronectin. The quaternary structure is perturbed in response to binding events, including binding of fibronectin to the surface of vertebrate cells for fibril assembly and to bacterial adhesins.     

Inositol phospho-oligosaccharide stimulates cell proliferation in the early developing inner ear

The ability of an inositol phospho-oligosaccharide (POS) to mimic the mitogenic effects of nerve growth factor (NGF) and insulin on the early development of the inner ear was investigated. POS (10 microM) stimulated the incorporation of [3H]thymidine into the cochleovestibular ganglion by 3.9-fold. NGF (50 ng/ml) stimulation was 4.7-fold. POS and NGF showed no additivity. Cells induced to proliferate by POS overlapped with those expressing NGF receptors. POS, like insulin, potentiated the mitogenic effect of bombesin on the otic vesicle epithelium. DNA synthesis in the presence of bombesin (100 nM) plus POS (10 microM) was increased by 6.4-fold. POS stimulation was not additive with insulin. The results suggest that POS may play a role in growth factor regulation of cell proliferation during embryonic development.     

Assessing the structural complexity of manufacturing systems configurations

Modern manufacturing systems are increasingly required to be flexible and adaptable to changing market demands, which adds to their structural and operational complexity. One of the major challenges at the early design stages is to select a manufacturing system configuration that both satisfies the production functional requirements and is easy to operate and manage. A new metric for assessing the structural complexity of manufacturing system configurations is presented in this paper. The proposed complexity metric incorporates the quantity of information using an entropy approach. It accounts for the complexity inherent in the various modules in the manufacturing system through the use of an index derived from a newly developed manufacturing systems classification code. The code captures the effect of various component types and technologies used in a manufacturing system on the system’s structural complexity. The presented metric would be helpful in selecting the least complex manufacturing system configuration that meets the requirements. An engine cylinder head production system is used to illustrate the application of the proposed methodology in comparing feasible but different manufacturing system configurations capable of producing the cylinder head based on their structurally inherent complexity.     

Interferometric studies of the electron density dynamics at the periphery of a micropinch discharge

Results are presented from experimental studies of the electron density dynamics at the periphery of a low-inductance vacuum spark. The measurements were performed using a newly developed homodyne quadrature interferometer possessing fairly high dynamic range and performance. The experiments demonstrated the presence of a plasma with an electron density of n _e ≥ 10¹⁸ cm^?3 at the periphery of the discharge gap. The radial electron density distribution was shown to have a pronounced tubular structure. The relatively high values of the peripheral electron density indicate that the process of pinching can be substantially affected by shunt currents flowing at the discharge periphery.     

Ethnic and immigrant politics vs. mainstream politics: the role of ethnic organizations in shaping the political participation of immigrant-origin individuals in Europe

Previous scholarship has reported contradictory results regarding the impact of involvement by immigrant-origin individuals (IOIs) in ethnic organizations on political participation. In this article, we assess the effect of involvement in different types of organizations (ethnic, pan-immigrant and native) on participation in various types of political activities. We use cross-national micro-data from a population survey undertaken in 2004–2008 to IOIs in nine European cities. Our findings indicate that ethnic organizations perform an integrative function for IOIs in the political sphere, but they mainly affect participation linked to immigration-related issues concerning specific ethnic groups and IOIs. Moreover, most effects of involvement in ethnic organizations on the different types of political participation examined are similar in closed and in open political opportunity structures (POS). We only find evidence that involvement in ethnic organizations depresses conventional political action in open POS settings while it increases political action in closed POS settings.     

Cleavage of Mer Tyrosine Kinase (MerTK) from the Cell Surface Contributes to the Regulation of Retinal Phagocytosis

Phagocytosis of apoptotic cells by macrophages and spent photoreceptor outer segments (POS) by retinal pigment epithelial (RPE) cells requires several proteins, including MerTK receptors and associated Gas6 and protein S ligands. In the retina, POS phagocytosis is rhythmic, and MerTK is activated promptly after light onset via the αvβ5 integrin receptor and its ligand MFG-E8, thus generating a phagocytic peak. The phagocytic burst is limited in time, suggesting a down-regulation mechanism that limits its duration. Our previous data showed that MerTK helps control POS binding of integrin receptors at the RPE cell surface as a negative feedback loop. Our present results show that a soluble form of MerTK (sMerTK) is released in the conditioned media of RPE-J cells during phagocytosis and in the interphotoreceptor matrix of the mouse retina during the morning phagocytic peak. In contrast to macrophages, the two cognate MerTK ligands have an opposite effect on phagocytosis and sMerTK release, whereas the integrin ligand MFG-E8 markedly increases both phagocytosis and sMerTK levels. sMerTK acts as a decoy receptor blocking the effect of both MerTK ligands. Interestingly, stimulation of sMerTK release decreases POS binding. Conversely, blocking MerTK cleavage increased mostly POS binding by RPE cells. Therefore, our data suggest that MerTK cleavage contributes to the acute regulation of RPE phagocytosis by limiting POS binding to the cell surface.     

DNA complexes with synthetic oligopeptides: a model for studying the regularity of DNA compactization in vivo

The electron microscopic data on compactization of DNA at interaction with the synthetic oligopeptides having the trend of beta-structures formation in solutions are summarized. The new types of intramolecular and intermolecular compact structures are described in brief. Sequence of compactization process steps is discussed, the models of DNA packaging in the structures are presented. On the basis of the data presented the general principles of arrangement of the described compact structures are formulated, the mechanisms are proposed for formation of different types of compact particles on the final stage of the process of DNA condensation. Some processes of the genetic material compactization in vivo are discussed in which the proposed mechanisms for compact structures formation may have realization.     

Interdomain compactization in human tyrosyl-tRNA synthetase studied by the hierarchical rotations technique

Aminoacyl-tRNA synthetases are key enzymes of protein biosynthesis which usually possess multidomain structures. Mammalian tyrosyl-tRNA synthetase is composed of two structural modules: N-terminal catalytic core and an EMAPII-like C-terminal domain separated by long flexible linker. The structure of full-length human cytoplasmic tyrosyl-tRNA synthetase is still unknown. The structures of isolated N-terminal and C-terminal domains of the protein are resolved, but their compact packing in a functional enzyme is a subject of debates. In this work we studied putative compactization of the N- and C-terminal modules of human tyrosyl-tRNA synthetase by the coarse-grained hierarchical rotations technique (HIEROT). The large number of distinct types of binding interfaces between N- and C-terminal modules is revealed in the absence of enzyme substrates. The binding propensities of different residues are computed and several binding "hot spots" are observed on the surfaces of N and C modules. These results could be used to govern atomistic molecular dynamics simulations, which will sample preferable binding interfaces effectively.     

In vitro phototoxicity of rhodopsin photobleaching products in the retinal pigment epithelium (RPE)

Although the primary biological function of retinal photoreceptors is to absorb light and provide visual information, extensive exposure to intense light could increase the risk of phototoxic reactions mediated by products of rhodopsin bleaching that might accumulate in photoreceptor outer segments (POS). The phototoxicity of POS, isolated from bovine retinas, was examined in cultured retinal pigment epithelium cells (ARPE-19) containing phagocytised POS and in selected model systems by determining POS ability to photogenerate singlet oxygen, and photoinduce oxidation of cholesterol and serum albumin. Bleaching of rhodopsin-rich POS with green light resulted in the formation of retinoid products exhibiting distinct absorption spectra in the near-UV. Irradiation of POS-fed ARPE-19 cells with blue light reduced their survival in a dose-dependent manner with the effect being stronger for cells containing prebleached POS. The specific and non-specific phagocytic activity of ARPE-19 cells was inhibited by sub-lethal photic stress mediated by phagocytised POS. The oxidising ability of POS photobleaching products was demonstrated both in a model system consisting of serum albumin and in ARPE-19 cells. Distinct photooxidation of proteins, mediated by POS, was observed using coumarin boronic acid as a sensitive probe of protein hydroperoxides. Irradiation of POS with blue light also induced oxidation of liposomal cholesterol as determined by HPLC-EC(Hg). Time-resolved singlet oxygen phosphorescence demonstrated the efficiency of retinoids, extracted from POS by chloroform-methanol treatment, to photogenerate singlet oxygen. The results indicate that photic stress mediated by POS photobleaching products could inhibit phagocytic efficiency of RPE cells and, ultimately, compromise their important biological functions.     

A structural module in RNase P expands the variety of RNA kinks

RNA structures are built from recurrent modules that can be identified by structural and comparative sequence analysis. In order to assemble sets of helices in compact architectures, modules that introduce bends and kinks are necessary. Among such modules, kink-turns form an important family that presents sequence and structural characteristics. Here, we describe an internal loop in the bacterial type A RNase P RNA that sets helices bound at the junctions exactly in the same relative positions as in kink-turns but without the structural signatures typical of kink-turns. Our work suggests that identifying a structural module in a subset of RNA sequences constitutes a strategy to identify distinct sequential motifs sharing common structural characteristics.     

A mini-protein designed by removing a module from barnase: molecular modeling and NMR measurements of the conformation.

A globular domain can be decomposed into compact modules consisting of contiguous 10-30 amino acid residues. The correlation between modules and exons observed in different proteins suggests that each module was encoded by an ancestral exon and that modules were combined into globular domains by exon fusion. Barnase is a single domain RNase consisting of 110 amino acid residues and was decomposed into six modules. We designed a mini-protein by removing the second module, M2, from barnase in order to gain an insight into the structural and functional roles of the module. In the molecular modeling of the mini-protein, we evaluated thermodynamic stability and aqueous solubility together with mechanical stability of the model. We chemically synthesized a mini-barnase with (15)N-labeling at 10 residues, whose corresponding residues in barnase are all found in the region around the hydrophobic core. Circular dichroism and NMR measurements revealed that mini-barnase takes a non-random specific conformation that has a similar hydrophobic core structure to that of barnase. This result, that a module could be deleted without altering the structure of core region of barnase, supports the view that modules act as the building blocks of protein design.     

Improved Part-of-Speech Prediction in Suffix Analysis

Motivation

Predicting the part of speech (POS) tag of an unknown word in a sentence is a significant challenge. This is particularly difficult in biomedicine, where POS tags serve as an input to training sophisticated literature summarization techniques, such as those based on Hidden Markov Models (HMM). Different approaches have been taken to deal with the POS tagger challenge, but with one exception – the TnT POS tagger - previous publications on POS tagging have omitted details of the suffix analysis used for handling unknown words. The suffix of an English word is a strong predictor of a POS tag for that word. As a pre-requisite for an accurate HMM POS tagger for biomedical publications, we present an efficient suffix prediction method for integration into a POS tagger.

Results

We have implemented a fully functional HMM POS tagger using experimentally optimised suffix based prediction. Our simple suffix analysis method, significantly outperformed the probability interpolation based TnT method. We have also shown how important suffix analysis can be for probability estimation of a known word (in the training corpus) with an unseen POS tag; a common scenario with a small training corpus. We then integrated this simple method in our POS tagger and determined an optimised parameter set for both methods, which can help developers to optimise their current algorithm, based on our results. We also introduce the concept of counting methods in maximum likelihood estimation for the first time and show how counting methods can affect the prediction result. Finally, we describe how machine-learning techniques were applied to identify words, for which prediction of POS tags were always incorrect and propose a method to handle words of this type.

Availability and Implementation

Java source code, binaries and setup instructions are freely available at http://genomes.sapac.edu.au/text_mining/pos_tagger.zip.