Structural analysis of DNA binding by C.Csp231I, a member of a novel class of R-M controller proteins regulating gene expression

In a wide variety of bacterial restriction–modification systems, a regulatory `controller' protein (or C-protein) is required for effective transcription of its own gene and for transcription of the endonuclease gene found on the same operon. We have recently turned our attention to a new class of controller proteins (exemplified by C.Csp231I) that have quite novel features, including a much larger DNA-binding site with an 18 bp (∼60 Å) spacer between the two palindromic DNA-binding sequences and a very different recognition sequence from the canonical GACT/AGTC. Using X-ray crystallography, the structure of the protein in complex with its 21 bp DNA-recognition sequence was solved to 1.8 Å resolution, and the molecular basis of sequence recognition in this class of proteins was elucidated. An unusual aspect of the promoter sequence is the extended spacer between the dimer binding sites, suggesting a novel interaction between the two C-protein dimers when bound to both recognition sites correctly spaced on the DNA. A U-bend model is proposed for this tetrameric complex, based on the results of gel-mobility assays, hydrodynamic analysis and the observation of key contacts at the interface between dimers in the crystal.</jats:p

Numerical Simulation of Multicomponent Ion Beam from Ion Sources

A program library for numerical simulation of a multicomponent charged particle beam from ion sources is presented. The library is aimed for simulation of high current, low energy multicomponent ion beam from ion source through beamline and realized under the Windows user interface for the IBM PC. It is used for simulation and optimization of beam dynamics and based on successive and consistent application of two methods: the momentum method of distribution function (RMS technique) and particle in cell method. The library has been used to simulate and optimize the transportation of tantalum ion beam from the laser ion source (CERN) and calcium ion beam from the ECR ion source (JINR, Dubna)

SRSF1 modulates the organization of splicing factors in nuclear speckles and regulates transcription

The mammalian cell nucleus is compartmentalized into non-membranous subnuclear domains that regulate key nuclear functions. Nuclear speckles are subnuclear domains that contain pre-mRNA processing factors and non-coding RNAs. Many of the nuclear speckle constituents work in concert to coordinate multiple steps of gene expression, including transcription, pre-mRNA processing and mRNA transport. The mechanism that regulates the formation and maintenance of nuclear speckles in the interphase nucleus is poorly understood. In the present study, we provide evidence for the involvement of nuclear speckle resident proteins and RNA components in the organization of nuclear speckles. SR-family splicing factors and their binding partner, long non-coding MALAT1 RNA, can nucleate the assembly of nuclear speckles in the interphase nucleus. Depletion of SRSF1 in human cells compromises the association of splicing factors to nuclear speckles and influences the levels and activity of other SR proteins. Furthermore, on a stably integrated reporter gene locus, we demonstrate the role for SRSF1 in RNA polymerase II-mediated transcription. Our results suggest that SR proteins mediate the assembly of nuclear speckles and regulate gene expression by influencing both transcriptional and posttranscriptional activities within the cell nucleus

A Tailward Moving Current Sheet Normal Magnetic Field Front Followed by an Earthward Moving Dipolarization Front

A case study is presented using measurements from the Cluster spacecraft and ground-based magnetometers that show a substorm onset propagating from the inner to outer plasma sheet. On 3 October 2005, Cluster, traversing an ion-scale current sheet at the near-Earth plasma sheet, detected a sudden enhancement of Bz, which was immediately followed by a series of flux rope structures. Both the local Bz enhancement and flux ropes propagated tailward. Approximately 5 min later, another Bz enhancement, followed by a large density decrease, was observed to rapidly propagate earthward. Between the two Bz enhancements, a significant removal of magnetic flux occurred, possibly resulting from the tailward moving Bz enhancement and flux ropes. In our scenario, this flux removal caused the magnetotail to be globally stretched so that the thinnest sheet formed tailward of Cluster. The thinned current sheet facilitated magnetic reconnection that quickly evolved from plasma sheet to lobe and generated the later earthward moving dipolarization front (DF) followed by a reduction in density and entropy. Ground magnetograms located near the meridian of Cluster's magnetic foot points show two-step bay enhancements. The positive bay associated with the first Bz enhancement indicates that the substorm onset signatures propagated from the inner to the outer plasma sheet, consistent with the Cluster observation. The more intense bay features associated with the later DF are consistent with the earthward motion of the front. The event suggests that current disruption signatures that originated in the near-Earth current sheet propagated tailward, triggering or facilitating midtail reconnection, thereby preconditioning the magnetosphere for a later strong substorm enhancement

The effect of dry extract of Geranium Palustre herb on coagulation system = Вплив сухого екстракту трави герані болотної на систему зсідання крові

Ostapets M. O., Shevtsov I. I., Karabut L. V., Bereznyakova M. E. The effect of dry extract of Geranium Palustre herb on coagulation system = Вплив сухого екстракту трави герані болотної на систему зсідання крові. Journal of Education, Health and Sport. 2015;5(8):119-125. ISSN 2391-8306. DOI 10.5281/zenodo.27484http://dx.doi.org/10.5281/zenodo.27484http://ojs.ukw.edu.pl/index.php/johs/article/view/2015%3B5%288%29%3A119-125https://pbn.nauka.gov.pl/works/605723Formerly Journal of Health Sciences. ISSN 1429-9623 / 2300-665X. Archives 2011–2014 http://journal.rsw.edu.pl/index.php/JHS/issue/archive Deklaracja.Specyfika i zawartość merytoryczna czasopisma nie ulega zmianie.Zgodnie z informacją MNiSW z dnia 2 czerwca 2014 r., że w roku 2014 nie będzie przeprowadzana ocena czasopism naukowych; czasopismo o zmienionym tytule otrzymuje tyle samo punktów co na wykazie czasopism naukowych z dnia 31 grudnia 2014 r.The journal has had 5 points in Ministry of Science and Higher Education of Poland parametric evaluation. Part B item 1089. (31.12.2014).© The Author (s) 2015;This article is published with open access at Licensee Open Journal Systems of Kazimierz Wielki University in Bydgoszcz, Poland and Radom University in Radom, PolandOpen Access. This article is distributed under the terms of the Creative Commons Attribution Noncommercial License which permits any noncommercial use, distribution, and reproduction in any medium, provided the original author(s) and source are credited. This is an open access article licensed under the terms of the Creative Commons Attribution Non Commercial License (http://creativecommons.org/licenses/by-nc/3.0/) which permits unrestricted, non commercial use, distribution and reproduction in any medium, provided the work is properly cited.This is an open access article licensed under the terms of the Creative Commons Attribution Non Commercial License (http://creativecommons.org/licenses/by-nc/3.0/) which permits unrestricted, non commercialuse, distribution and reproduction in any medium, provided the work is properly cited.The authors declare that there is no conflict of interests regarding the publication of this paper.Received: 05.06.2015. Revised 15.07.2015. Accepted: 25.07.2015. UDC 615.322:582.751:615.273 THE EFFECT OF DRY EXTRACT OF GERANIUM PALUSTRE HERB ON COAGULATION SYSTEMВПЛИВ СУХОГО ЕКСТРАКТУ ТРАВИ ГЕРАНІ БОЛОТНОЇ НА СИСТЕМУ ЗСІДАННЯ КРОВІ M. O. Ostapets, I. I. Shevtsov, L. V. Karabut, M. E. BereznyakovaМ. О. Остапець, І. І. Шевцов, Л. В. Карабут, М. Є. Березнякова National University of Pharmacy, Kharkiv, UkraineНаціональний фармацевтичний університет, Харків, Україна[email protected] AbstractThe article is devoted to the studying of mechanism action on coagulation system the dry extract of Geranium Palustre herb. Established, those during 20-ty days of introduction the investigation extract increasing the activity of platelet’s mechanism of hemostasis (increasing platelet’s amount, their aggregation activity and retraction of blood clotting). On the background of introduction the investigation extract decreasing indicators of I and III phase of coagulation cascade (activated partial thromboplastin time, thrombin time), increasing prothrombin time and level of fibrinogen. Obtaining result suggest about active action the dry extract of Geranium Palustre herb on «external» way activation of hemocoagulation by possibility effect of accelerate the formation of thromboplastin, causing the hypercoagulation.The mechanism of antihemmorhagic action of dry extract of Geranium Palustre herb due to the presence in the composition biological active substances (such as tannins, flavonoids, elagic, galic and ascorbinic organic acids) that acting complex on vascular-platelet and coagulation hemostasis at the expense of increasing the strength and sealing vascular-tissue barriers, P-vitamin activity – it is ability to reduce capillary fragility and permeability and increasing their resistance.Key words: dry extract of Geranium Palustre herb, platelets, coagulation, phenolic compounds.  РефератСтаття присвячена дослідженню механізму дії сухого екстракту трави герані болотної на систему зсідання крові. Встановлено, що протягом 20-ти денного введення досліджуваного екстракту підвищувалася активність тромбоцитарної ланки гемостазу (підвищувалася кількість тромбоцитів, їх агрегаційна здатність та ретракція кров’яного згустку). На фоні введення сухого екстракту трави герані болотної знижувалися показники I та III фази коагуляційного гемостазу (активований частковий тромбопластиновий час, тромбіновий час), підвищувався протромбіновий час та рівень фібриногену. Отримані дані свідчать про вплив сухого екстракту трави герані болотної на «внутрішній» шлях активації зсідання крові за рахунок прискорення формування тромбопластину, що призводить до гіперкоагуляції.Механізм антигеморагічної дії сухого екстракту трави герані болотної обумовлений наявністю у складі біологічно активних речовин (дубильних речовин, флавоноїдів, елагової, галової та аскорбінової органічних кислот), які діють комплексно як на судинно-тромбоцитарний, так і на коагуляційний гемостаз за рахунок ущільнення та збільшення міцності судинно-тканинних бар’єрів, Р-вітамінної активності – здатності зменшувати проникність та ламкість капілярів, підвищувати їх резистентність.Ключові слова: сухий екстракт трави герані болотної, тромбоцити, зсідання крові, фенольні сполуки. РефератВЛИЯНИЕ СУХОГО ЭКСТРАКТА ТРАВЫ ГЕРАНИ БОЛОТНОЙ НА СИСТЕМУ СВЕРТЫВАНИЯ КРОВИ. Статья посвящена исследованию механизма действия сухого экстракта травы герани болотной на систему свертывания крови. Установлено, что на протяжении 20-ти дневного введения исследуемого экстракта повышалась активность тромбоцитарного звена гемостаза (увеличивалось количество тромбоцитов, их агрегационная способность и ретракция кровяного сгустка). На фоне введения сухого экстракта травы герани болотной снижались показатели I и III фазы коагуляционного гемостаза (активированное частичное тромбопластиновое время, тромбиновое время), повышалось  протромбиновое время и уровень фибриногена. Полученные данные свидетельствуют о влиянии сухого экстракта травы герани болотной на «внутренний» путь активации свертывания крови за счет ускорения формирования тромбопластина, что приводит к гиперкоагуляции.Механизм антигеморрагического действия сухого экстракта травы герани болотной обусловлен наличием в составе биологически активных соединений (дубильных веществ, флавоноидов, эллаговой, галловой и аскорбиновой органических кислот), которые действуют комплексно как на сосудисто-тромбоцитарный, так и на коагуляционный гемостаз за счет уплотнения и увеличения прочности сосудисто-тканевых барьеров, Р-витаминной активности – способности уменьшать проницаемость и ломкость капилляров, повышать их резистентность.Ключевые слова: сухой экстракт травы герани болотной, тромбоциты, свертывание крови, фенольные соединения

SuperConga: an open-source framework for mesoscopic superconductivity

We present SuperConga, an open-source framework for simulating equilibrium properties of unconventional and ballistic singlet superconductors, confined to two-dimensional (2D) mesoscopic grains in a perpendicular external magnetic field, at arbitrary low temperature. It aims at being both fast and easy to use, enabling research without access to a computer cluster, and visualization in real-time with OpenGL. The core is written in C++ and CUDA, exploiting the embarrassingly parallel nature of the quasiclassical theory of superconductivity by utilizing the parallel computational power of modern GPUs. The framework self-consistently computes both the superconducting order-parameter and the induced vector potential, and finds the current density, free energy, induced flux density, local density of states, as well as the magnetic moment. A user-friendly Python frontend is provided, enabling simulation parameters to be defined via intuitive configuration files, or via the command-line interface, without requiring a deep understanding of implementation details. For example, complicated geometries can be created with relative ease. The framework ships with simple tools for analyzing and visualizing the results, including an interactive plotter for spectroscopy. An overview of the theory is presented, as well as examples showcasing the framework's capabilities and ease of use. The framework is free to download from https://gitlab.com/superconga/superconga, which also links to the extensive user manual, containing even more examples, tutorials and guides.Comment: Accepted version. Review-style article, 31 pages and link to software at https://gitlab.com/superconga/supercong

Contribution of Alexey Suvorin and His Newspaper Novoye Vremya into Russian Culture of the Second Half of 19th – Early 20th Century’

Novoye Vremya (The New Time) newspaper was considered as the leading daily periodical of the pre-revolutionary Russia. In 1876, Aleksey Suvorin, an outstanding Russian publisher and literary figure, became its owner and chief editor. He turned the newspaper into a source of information, which seriously influenced the public opinion in Russia. Novoye Vremya provoked constant interest among readers of all social levels. It was popular both among high-ranking government officials and people without any ranks, conservatives and liberals, people with higher education and those who did not even graduate a gymnasium. Newspaper stories were apprehensible not only for educated people but for any common person. Young and old, men and women liked Novoye Vremya. It had never forced its opinion and suggested the readers to make personal judgement through its reports. Suvorin managed to form the audience that valued the newspaper and believed in it. Not only Novoye Vremya stood out for its excellent materials on politics, economy, and non-fiction. In its reviews the newspaper gave a fair evaluation of the Russian authors’ works. Moreover, it became famous with the literary works of the top writers, the classics of Russian literature. Therefore, it is not by accident that the author of this article pays special attention to the cooperation between Novoye Vremya and the most known Russian writers of the second half of the 19th century and early 20th century. Thanks to Suvorin, the talent of Anton Chekhov, who started publishing his works in the newspaper under a different name, opened up. Novoye Vremya published the stories which were later included into his collection In the Twilight. Here he also published his famous novella The Duel. Despite the fact that Novoye Vremya was considered to be a newspaper rather than a literary magazine, it worked together with such writers as Leo Tolstoy, Nikolay Nekrasov, Nikolay Leskov, Mikhail Saltykov-Shchedrin, for whom the newspaper was not only a serious periodical but also a source of education and knowledge. In Soviet times the directive was to forget about Suvorin. And when they did remember, they certainly wrote about him as a reactionary, chauvinist, notorious monarchist. And if another major pre-revolutionary publisher I.D. Sytin was recognized by the Soviet government, although he lost his printing house and real estate, then Suvorin was in disgrace

Towards improving adaptability of capability driven development methodology in complex environment

We are triggered to incorporate adaptability in information system designs and methodologies corresponding to complex and unpredictable environment of today and tomorrow and to complex adaptive systems they are aimed for. Adaptability as non-functional requirement is being portrayed and investigated from broad multidisciplinary perspective that influences how dynamic business-IT alignment can be accomplished. Capability Driven Development methodology has supported delivering dynamic capabilities by providing context-aware self-adaptive platform in the CaaS project implementations, as our case study. Along with the already incorporated mechanisms, components that enable adaptability, there is open space for further evolutionary and deliberate change towards becoming truly appropriate methodology for dynamic reconfigurations of capabilities in organizations and business ecosystems that operate in complexity and uncertainty. The analysis and evaluation of adaptability of the CDD methodology through three dimensions (complexity of the external and internal environment, managerial profiling and artifact-integrated components) in this paper conclude with instigation of starting points towards achieving higher adaptability for complexity of the CDD methodology

Response of the ATLAS tile calorimeter prototype to muons

A study of high energy muons traversing the ATLAS hadron Tile calorimeter in the barrel region in the energy range between 10 and 300~GeV is presented. Both test beam experimental data and Monte Carlo simulations are given and show good agreement. The Tile calorimeter capability of detecting isolated muons over the above energy range is demonstrated. A signal to background ratio of about 10 is expected for the nominal LHC luminosity ($10^{34} cm^{-2} sec^{-1}$). The photoelectron statistics effect in the muon shape response is shown. The e/mip ratio is found to be $0.81 \pm 0.03$; the e/$\mu$ ratio is in the range 0.91 - 0.97. The energy loss of a muon in the calorimeter, dominated by the energy lost in the absorber, can be correlated to the energy loss in the active material. This correlation allows one to correct on an event by event basis the muon energy loss in the calorimeter and therefore reduce the low energy tails in the muon momentum distribution

The Optical Instrumentation of the ATLAS Tile Calorimeter

The purpose of this Note is to describe the optical assembly procedure called here Optical Instrumentation and the quality tests conducted on the assembled units. Altogether, 65 Barrel (or LB) modules were constructed - including one spare - together with 129 Extended Barrel (EB) modules (including one spare). The LB modules were mechanically assembled at JINR (Dubna, Russia) and transported to CERN, where the optical instrumentation was performed with personnel contributed by several Institutes. The modules composing one of the two Extended Barrels (known as EBA) were mechanically assembled in the USA, and instrumented in two US locations (ANL, U. of Michigan), while the modules of the other Extended barrel (EBC) were assembled in Spain and instrumented at IFAE (Barcelona). Each of the EB modules includes a subassembly known as ITC that contributes to the hermeticity of the calorimeter; all ITCs were assembled at UTA (Texas), and mounted onto the module mechanical structures at the EB mechanical assembly locations.The Tile Calorimeter, covering the central region of the ATLAS experiment up to pseudorapidities of ±1.7, is a sampling device built with scintillating tiles that alternate with iron plates. The light is collected in wave-length shifting (WLS) fibers and is read out with photomultipliers. In the characteristic geometry of this calorimeter the tiles lie in planes perpendicular to the beams, resulting in a very simple and modular mechanical and optical layout. This paper focuses on the procedures applied in the optical instrumentation of the calorimeter, which involved the assembly of about 460,000 scintillator tiles and 550,000 WLS fibers. The outcome is a hadronic calorimeter that meets the ATLAS performance requirements, as shown in this paper