Radio-frequency discharges in Oxygen. Part 1: Modeling

In this series of three papers we present results from a combined experimental and theoretical effort to quantitatively describe capacitively coupled radio-frequency discharges in oxygen. The particle-in-cell Monte-Carlo model on which the theoretical description is based will be described in the present paper. It treats space charge fields and transport processes on an equal footing with the most important plasma-chemical reactions. For given external voltage and pressure, the model determines the electric potential within the discharge and the distribution functions for electrons, negatively charged atomic oxygen, and positively charged molecular oxygen. Previously used scattering and reaction cross section data are critically assessed and in some cases modified. To validate our model, we compare the densities in the bulk of the discharge with experimental data and find good agreement, indicating that essential aspects of an oxygen discharge are captured.Comment: 11 pages, 10 figure

Детектирование индуцированных тепловым потоком напряжений в твердом теле с помощью фотоупругого микроскопа

Мета цієї статті полягає в представленні переваг практичного та ефективного методу модуляційної поляриметрії (МПМ), застосованого до зразка кварцового скла у вигляді пластини для виявлення його найменших внутрішніх термонапружень, викликаних поширення теплової хвилі. Описаний МПМ дозволив провести точні вимірювання двопроменезаломлення, яке супроводжує динаміку термопружності, що зробило можливим обчислення значення розподілу напружень вздовж і поперек напрямку теплового потоку в певні моменти часу, а також їх залежність від часу в певних координатах теплового потоку. Основна мета даної роботи є не тільки вирішення обернених задач нестаціонарної термопружності, що дозволяє отримати просторово-часові температурні функції графічним інтегруванням експериментальних характеристик, але й дослідження динаміки точки максимуму кривизни температурної функції T(t), що є характеристикою теплового фронту в процесі встановлення теплового потоку. Окрім того, було показано, що завдяки високій виявній здатності МПМ застосованої у фотопружному мікроскопі, стало можливим спостерігати радіаційну складову теплопереносу.The aim of this paper is to present adventures of practical and effective modulation polarimetry method (MPM) applied to the plate sample of quartz glass for detection of its minute internal thermoelastic stresses induced by heat wave propagation. Described MPM allowed to make accurate measuring of birefringence that accompany the dynamics of thermoelasticity and made possible to calculate the value of stress distribution along and crosswise to the direction of heat flow at certain moments of time, as well as its dependence on time in defined heat flux coordinates. The main goal of this paper is not only the solution of inverse problems of nonstationary thermoelasticity that allowed obtaining spatio-temporal temperature functions by graphical integration of the experimental characteristics but researching the dynamics of the maximum curvature point of the temperature function T(t) that is a characteristic of the thermal front in the process of heat flow establishment. In addition, it is shown that due to the high detectability of MPM applied in photoelastic microscope became possible to observe the radiation component of the heat transfer process.Цель этой статьи заключается в представлении преимуществ практического и эффективного метода модуляционной поляриметрии (МПМ), примененного к образцу кварцевого стекла в виде пластины для выявления его самых малых внутренних термонапряжений, вызванных распространением тепловой волны. Описанный МПМ позволил провести точные измерения двулучепреломления, которое сопровождает динамику термоупругости, что сделало возможным вычисление значения распределения напряжений вдоль и поперек направления теплового потока в определенные моменты времени, а также их зависимость от времени в определенных координатах теплового потока. Основная цель данной работы является не только решение обратной задачи нестационарной термоупругости, что позволяет получить пространственно-временные температурные функции графическим интегрированием экспериментальных характеристик, но и исследование динамики точки максимума кривизны температурной функции T(t), что является характеристикой теплового фронта в процессе установления теплового потока. Кроме того, было показано, что благодаря применению высокой обнаружительной способности МПМ в фотоупругом микроскопе сделало возможным наблюдать радиационную составляющую теплопереноса

Long-term disease control in advanced renal cell cancer with brain metastases with pazopanib (case report and literature review)

We report the case of advanced clear cell renal cell carcinoma with brain, pulmonary, hepatic and bone metastases treated with pazopanib.We observed the complete response in brain metastases and stable extracranial disease after 4 years of the treatment. According to the literature review this is the first reported case of complete response to pazopanib in brain metastases in renal cell carcinoma

Status of RF system for VEPP-5 damping ring

The paper presents the RF system of VEPP-5 damping ring created at BINP Novosibirsk. The RF system operates at 700 MHz and consists of the generator based on KU-393 klystron, transmitting waveguide with wave-to-coax adapters, accelerating cavity, and control system. HOM cavities are damped with resistive loads to eliminate the beam instability. Parameters and results of cold measurement tests and high power level tests are presented.Представлена ВЧ-система накопителя-охладителя для ВЭПП-5, созданная в БИЯФ, Новосибирск. ВЧ-система работает на частоте 700 МГц и состоит из генератора на клистроне КУ-393,передающего волновода с коаксиально-волноводными переходами, ускоряющего резонатора и системы управления и контроля. Для устранения пучковой неустойчивости высшие моды резонатора подавлены с помощью резистивных нагрузок. Приведены параметры и результаты холодных измерений и горячих испытаний ВЧ-системы.Представлено ВЧ-система нагромаджувача-охолоджувача для ВЕПП-5, що створена в БІЯФ, Новосибірськ. ВЧ-система працює на частоті 700 МГц і складається з генератора на клістроні КУ-393, передаючого хвилеводу з коаксіально-хвилеводними переходами, прискорюючого резонатора і системи керування і контролю. Для усунення пучкової нестійкості вищі моди резонатора подавлені за допомогою резистивних навантажень. Наведено параметри і результати холодних вимірів і гарячих випробувань ВЧ- системи

The role of thermal energy accommodation and atomic recombination probabilities in low pressure oxygen plasmas

International audienceSurface interaction probabilities are critical parameters that determine the behaviour of low pressure plasmas and so are crucial input parameters for plasma simulations that play a key role in determining their accuracy. However, these parameters are difficult to estimate without in situ measurements. In this work, the role of two prominent surface interaction probabilities, the atomic oxygen recombination coefficient ? O and the thermal energy accommodation coefficient ? E in determining the plasma properties of low pressure inductively coupled oxygen plasmas are investigated using two-dimensional fluid-kinetic simulations. These plasmas are the type used for semiconductor processing. It was found that ? E plays a crucial role in determining the neutral gas temperature and neutral gas density. Through this dependency, the value of ? E also determines a range of other plasma properties such as the atomic oxygen density, the plasma potential, the electron temperature, and ion bombardment energy and neutral-to-ion flux ratio at the wafer holder. The main role of ? O is in determining the atomic oxygen density and flux to the wafer holder along with the neutral-to-ion flux ratio. It was found that the plasma properties are most sensitive to each coefficient when the value of the coefficient is small causing the losses of atomic oxygen and thermal energy to be surface interaction limited rather than transport limited

The role of dimensionality in neuronal network dynamics

The research leading to these results has received funding from the European Union’s Seventh Framework Programme under grant agreement FP7 ICT 2011 – 284553 (Acronym: Si-CODE), the NEUROSCAFFOLDS Project n. 604263, the National Natural Science Foundation of China (Grant number: 51361130033) and the Ministry of Science and Technology of China (973 Grant number: 2014CB965003)

Computational Characterization of 3′ Splice Variants in the GFAP Isoform Family

Glial fibrillary acidic protein (GFAP) is an intermediate filament (IF) protein specific to central nervous system (CNS) astrocytes. It has been the subject of intense interest due to its association with neurodegenerative diseases, and because of growing evidence that IF proteins not only modulate cellular structure, but also cellular function. Moreover, GFAP has a family of splicing isoforms apparently more complex than that of other CNS IF proteins, consistent with it possessing a range of functional and structural roles. The gene consists of 9 exons, and to date all isoforms associated with 3′ end splicing have been identified from modifications within intron 7, resulting in the generation of exon 7a (GFAPδ/ε) and 7b (GFAPκ). To better understand the nature and functional significance of variation in this region, we used a Bayesian multiple change-point approach to identify conserved regions. This is the first successful application of this method to a single gene – it has previously only been used in whole-genome analyses. We identified several highly or moderately conserved regions throughout the intron 7/7a/7b regions, including untranslated regions and regulatory features, consistent with the biology of GFAP. Several putative unconfirmed features were also identified, including a possible new isoform. We then integrated multiple computational analyses on both the DNA and protein sequences from the mouse, rat and human, showing that the major isoform, GFAPα, has highly conserved structure and features across the three species, whereas the minor isoforms GFAPδ/ε and GFAPκ have low conservation of structure and features at the distal 3′ end, both relative to each other and relative to GFAPα. The overall picture suggests distinct and tightly regulated functions for the 3′ end isoforms, consistent with complex astrocyte biology. The results illustrate a computational approach for characterising splicing isoform families, using both DNA and protein sequences

Mitochondrial Oxidative Stress Alters a Pathway in Caenorhabditis elegans Strongly Resembling That of Bile Acid Biosynthesis and Secretion in Vertebrates

Mammalian bile acids (BAs) are oxidized metabolites of cholesterol whose amphiphilic properties serve in lipid and cholesterol uptake. BAs also act as hormone-like substances that regulate metabolism. The Caenorhabditis elegans clk-1 mutants sustain elevated mitochondrial oxidative stress and display a slow defecation phenotype that is sensitive to the level of dietary cholesterol. We found that: 1) The defecation phenotype of clk-1 mutants is suppressed by mutations in tat-2 identified in a previous unbiased screen for suppressors of clk-1. TAT-2 is homologous to ATP8B1, a flippase required for normal BA secretion in mammals. 2) The phenotype is suppressed by cholestyramine, a resin that binds BAs. 3) The phenotype is suppressed by the knock-down of C. elegans homologues of BA–biosynthetic enzymes. 4) The phenotype is enhanced by treatment with BAs. 5) Lipid extracts from C. elegans contain an activity that mimics the effect of BAs on clk-1, and the activity is more abundant in clk-1 extracts. 6) clk-1 and clk-1;tat-2 double mutants show altered cholesterol content. 7) The clk-1 phenotype is enhanced by high dietary cholesterol and this requires TAT-2. 8) Suppression of clk-1 by tat-2 is rescued by BAs, and this requires dietary cholesterol. 9) The clk-1 phenotype, including the level of activity in lipid extracts, is suppressed by antioxidants and enhanced by depletion of mitochondrial superoxide dismutases. These observations suggest that C. elegans synthesizes and secretes molecules with properties and functions resembling those of BAs. These molecules act in cholesterol uptake, and their level of synthesis is up-regulated by mitochondrial oxidative stress. Future investigations should reveal whether these molecules are in fact BAs, which would suggest the unexplored possibility that the elevated oxidative stress that characterizes the metabolic syndrome might participate in disease processes by affecting the regulation of metabolism by BAs

Attenuation of the Sensing Capabilities of PhoQ in Transition to Obligate Insect–Bacterial Association

Sodalis glossinidius, a maternally inherited endosymbiont of the tsetse fly, maintains genes encoding homologues of the PhoP-PhoQ two-component regulatory system. This two-component system has been extensively studied in facultative bacterial pathogens and is known to serve as an environmental magnesium sensor and a regulator of key virulence determinants. In the current study, we show that the inactivation of the response regulator, phoP, renders S. glossinidius sensitive to insect derived cationic antimicrobial peptides (AMPs). The resulting mutant strain displays reduced expression of genes involved in the structural modification of lipid A that facilitates resistance to AMPs. In addition, the inactivation of phoP alters the expression of type-III secretion system (TTSS) genes encoded within three distinct chromosomal regions, indicating that PhoP-PhoQ also serves as a master regulator of TTSS gene expression. In the absence of phoP, S. glossinidius is unable to superinfect either its natural tsetse fly host or a closely related hippoboscid louse fly. Furthermore, we show that the S. glossinidius PhoQ sensor kinase has undergone functional adaptations that result in a substantially diminished ability to sense ancestral signals. The loss of PhoQ's sensory capability is predicted to represent a novel adaptation to the static symbiotic lifestyle, allowing S. glossinidius to constitutively express genes that facilitate resistance to host derived AMPs

Biophysical Studies of the Membrane-Embedded and Cytoplasmic Forms of the Glucose-Specific Enzyme II of the E. coli Phosphotransferase System (PTS)

The glucose Enzyme II transporter complex of the Escherichia coli phosphotransferase system (PTS) exists in at least two physically distinct forms: a membrane-integrated dimeric form, and a cytoplasmic monomeric form, but little is known about the physical states of these enzyme forms. Six approaches were used to evaluate protein-protein and protein-lipid interactions in this system. Fluorescence energy transfer (FRET) using MBP-IIGlc-YFP and MBP-IIGlc-CFP revealed that the homodimeric Enzyme II complex in cell membranes is stable (FRET-) but can be dissociated and reassociated to the heterodimer only in the presence of Triton X100 (FRET+). The monomeric species could form a heterodimeric species (FRET+) by incubation and purification without detergent exposure. Formaldehyde cross linking studies, conducted both in vivo and in vitro, revealed that the dimeric MBP-IIGlc activity decreased dramatically with increasing formaldehyde concentrations due to both aggregation and activity loss, but that the monomeric MBP-IIGlc retained activity more effectively in response to the same formaldehyde treatments, and little or no aggregation was observed. Electron microscopy of MBP-IIGlc indicated that the dimeric form is larger than the monomeric form. Dynamic light scattering confirmed this conclusion and provided quantitation. NMR analyses provided strong evidence that the dimeric form is present primarily in a lipid bilayer while the monomeric form is present as micelles. Finally, lipid analyses of the different fractions revealed that the three lipid species (PE, PG and CL) are present in all fractions, but the monomeric micellar structure contains a higher percentage of anionic lipids (PG & CL) while the dimeric bilayer form has a higher percentage of zwitterion lipids (PE). Additionally, evidence for a minor dimeric micellar species, possibly an intermediate between the monomeric micellar and the dimeric bilayer forms, is presented. These results provide convincing evidence for interconvertible physical forms of Enzyme-IIGlc