Examining c-di-GMP and possible quorum sensing regulation in Pseudomonas fluorescens SBW25:links between intra and inter-cellular regulation benefits community cooperative activities such as biofilm formation

Bacterial success in colonizing complex environments requires individual response to micro-scale conditions as well as community-level cooperation to produce large-scale structures such as biofilms. Connecting individual and community responses could be achieved by linking the intracellular sensory and regulatory systems mediated by bis-(3′-5′)-cyclic dimeric guanosine monophosphate (c-di-GMP) and other compounds of individuals with intercellular quorum sensing (QS) regulation controlling populations. There is growing evidence to suggest that biofilm formation by many pseudomonads is regulated by both intra and intercellular systems, though in the case of the model Pseudomonas fluorescens SBW25 Wrinkly Spreader in which mutations increasing c-di-GMP levels result in the production of a robust cellulose-based air-liquid interface biofilm, no evidence for the involvement of QS regulation has been reported. However, our recent review of the P. fluorescens SBW25 genome has identified a potential QS regulatory pathway and other QS–associated genes linked to c-di-GMP homeostasis, and QS signal molecules have also been identified in culture supernatants. These findings suggest a possible link between c-di-GMP and QS regulation in P. fluorescens SBW25 which might allow a more sophisticated and responsive control of cellulose production and biofilm formation when colonising the soil and plant-associated environments P. fluorescens SBW25 normally inhabits.Анализ ц-ди-ГМФ и возможного чувства кворума у Pseudomonas fluorescens SBW 25: связь между внутри и межклеточной регуляцией способствует кооперативному поведению в сообществе и формированию биоплёнкиУспешность бактериальной колонизации сложных экониш требует индивидуального ответа на изменения условий на микроуровне равно как и кооперации на уровне сообщества для продукции таких крупно масштабных структур как биоплёнки. Координация индивидуальных ответ ов и ответов сообщества может быть достигнута путем связывания внутриклеточных сенсорных и регуляторных систем, опосредуемых бис-(3',5')-циклическим димерным гуанозинмонофосфатом (ц-ди-ГМФ) и другими соединениями индивидуумов с межклеточной регуляцией - чувством кворума (ЧК), контролирующем популяци ю. Накапливается всё больше доказательств того, что формирование биопленки многими псевдомонадами регулируется как внутри клеточными, так и меж клеточными регуляторными системами, хотя в случае модельной Pseudomonas fluorescens SBW25 Wrinkly Spreader, у которой мутации, повышающ ие уровни ц-ди-ГМФ, приводят к созданию прочной целлюлозной биоплёнки на границе раздела фаз воздух-жидкость, не было обнаружено ни ка кого свидетельства вовлечения кворум-зависимой регуляции. Однако наш недавний обзор генома P. fluorescens SBW25 выявил потенциальный ЧК-зависимый регуляторный пу ть и другие ЧК-зависимые гены, связанные с гомеостазом ц-ди-ГМФ, а молекулы ЧК-сигналинга были идентифицированы в культуре. Эти данные свидетельствуют о возможной связи между ц-ди-ГМФ-регуляцией и ЧК у P. fluorescens SBW25, что позволяет более сложный и гибкий контроль над продукцией целлюлозы и образовани ем биопленки при колонизации почв и экониш, aссоциированных с растениям и, - естественными средами обитания P. fluorescens SBW25

The MGDO software library for data analysis in Ge neutrinoless double-beta decay experiments

The GERDA and Majorana experiments will search for neutrinoless double-beta decay of germanium-76 using isotopically enriched high-purity germanium detectors. Although the experiments differ in conceptual design, they share many aspects in common, and in particular will employ similar data analysis techniques. The collaborations are jointly developing a C++ software library, MGDO, which contains a set of data objects and interfaces to encapsulate, store and manage physical quantities of interest, such as waveforms and high-purity germanium detector geometries. These data objects define a common format for persistent data, whether it is generated by Monte Carlo simulations or an experimental apparatus, to reduce code duplication and to ease the exchange of information between detector systems. MGDO also includes general-purpose analysis tools that can be used for the processing of measured or simulated digital signals. The MGDO design is based on the Object-Oriented programming paradigm and is very flexible, allowing for easy extension and customization of the components. The tools provided by the MGDO libraries are used by both GERDA and Majorana.Comment: 4 pages, 1 figure, proceedings for TAUP201

Лабораторные маркёры полиорганной патологии при тяжёлом течении и неблагоприятных исходах инфекции SARS-CoV-2 (систематический обзор литературы)

The aim of the review: to present up-to-date scientifically based information about the laboratory parameters of patients associated with severe SARS-CoV-2 infection and internal organ damage. Materials and methods: full-text publications of clinical, randomized and cohort studies, systematic reviews and meta-analyses from scientific databases PubMed, Elsevier, Scopus, Google Scholar, E-library for the period from 2019 to 2022 were analyzed. Results. Specific biomarkers were identified, including inflammatory and immunological parameters (C-reactive protein, procalcitonin, IL6), hematological (number of lymphocytes and neutrophils, NLR, D-dimer, ferritin, RDW), myocardial (troponin, creatinekinase-MB, myoglobin), hepatic (AST, ALT, total bilirubin, albumin) and characterizing lung injury (KL-6), which can be used for risk stratification, as prognostic biomarkers of adverse clinical consequences, including death in patients with COVID-19. The studies demonstrated new biomarkers of inflammatory and systemic manifestations of COVID19: procalcitonin, calprotectin and presepsin.Представлены современные научно обоснованные сведения о лабораторных параметрах пациентов с тяжёлым течением и неблагоприятными исходами инфекции SARS-CoV-2. Проанализированы полнотекстовые публикации клинических, рандомизированных и когортных исследований, систематические обзоры и мета-анализы из научных баз PubMed, Elsevier, Scopus, Google Scholar, E-library за период с 2019 по 2022 г. Определены конкретные биомаркеры, включая воспалительные и иммунологические параметры (C-реактивный белок, прокальцитонин, интерлейкин-6, D-димер, ферритин), гематологические (количество нейтрофилов, лимфоцитов, их соотношение, RDW), миокардиальные (тропонин, креатинкиназа, миоглобин), печеночные (АСТ, АЛТ, общий билирубин, альбумин) и характеризующие повреждение легких (гликопротеин Кребса фон ден Лунгена-6), которые могут быть использованы для стратификации риска, в качестве прогностических критериев неблагоприятного течения заболевания, в том числе полиорганной недостаточности, тяжёлого  течения и летального исхода пациентов с COVID-19. В исследованиях продемонстрирована роль новых биомаркеров воспалительных и системных проявлений COVID-19: прокальцитонина, кальпротектина и пресепсина

The background in the neutrinoless double beta decay experiment GERDA

The GERmanium Detector Array (GERDA) experiment at the Gran Sasso underground laboratory (LNGS) of INFN is searching for neutrinoless double beta decay of 76Ge. The signature of the signal is a monoenergetic peak at 2039 keV, the Q-value of the decay, Q_bb. To avoid bias in the signal search, the present analysis does not consider all those events, that fall in a 40 keV wide region centered around Q_bb. The main parameters needed for the neutrinoless double beta decay analysis are described. A background model was developed to describe the observed energy spectrum. The model contains several contributions, that are expected on the basis of material screening or that are established by the observation of characteristic structures in the energy spectrum. The model predicts a flat energy spectrum for the blinding window around Q_bb with a background index ranging from 17.6 to 23.8*10^{-3} counts/(keV kg yr). A part of the data not considered before has been used to test if the predictions of the background model are consistent. The observed number of events in this energy region is consistent with the background model. The background at Q-bb is dominated by close sources, mainly due to 42K, 214Bi, 228Th, 60Co and alpha emitting isotopes from the 226Ra decay chain. The individual fractions depend on the assumed locations of the contaminants. It is shown, that after removal of the known gamma peaks, the energy spectrum can be fitted in an energy range of 200 kev around Q_bb with a constant background. This gives a background index consistent with the full model and uncertainties of the same size

Advanced liver disease in Russian children and adolescents with chronic hepatitis C

Russia has one of the highest prevalences of paediatric chronic hepatitis C infection (CHC). Our aim was to provide a detailed characterization of children and adolescents with CHC including treatment outcomes.Thus, an observational study of children with CHC aged <18 years was conducted in three hepatology centres from November 2014 to May 2017. Of 301 children(52% male), 196(65%) acquired HCV vertically, 70(23%) had a history of blood transfusion or invasive procedures, 1 injecting drug use and 34(11%) had no known risk factors. Median age at HCV diagnosis was 3.1[IQR 1.1,8.2] and 10.8[7.4,14.7] at last follow-up. The most common genotype was 1b(51%), followed by 3(31%). Over a quarter of patients (84,28%) had raised liver transaminases. Of 92 with liver biopsy, 38(41%) had bridging fibrosis (median age 10.4[7.1,14.1]). Of 223 evaluated by transient elastography (TE), 67(30%) had liver stiffness ≥5.0kPa. For each year increase in age mean stiffness increased by 0.09kPa(95%CI 0.05,0.13, p<0.001). There was significant correlation between liver stiffness and biopsy results (Tau-b=0.29, p=0.042). Of 205 treated with IFN-based regimens, 100(49%) had SVR24. Most children (191,93%) experienced adverse reactions, leading to treatment discontinuation in 6(3%). In conclusion, a third of children acquired HCV via non-vertical routes and a substantial proportion of those with liver biopsy had advanced liver disease. Only half of children achieved SVR24 with IFN-based regimens highlighting the need for more effective and better tolerated treatments with direct-acting antivirals. Further studies are warranted in Russia on causes and prevention of non-vertical transmission of HCV in children. This article is protected by copyright. All rights reserved

\textsc{MaGe} - a {\sc Geant4}-based Monte Carlo Application Framework for Low-background Germanium Experiments

We describe a physics simulation software framework, MAGE, that is based on the GEANT4 simulation toolkit. MAGE is used to simulate the response of ultra-low radioactive background radiation detectors to ionizing radiation, specifically the MAJORANA and GERDA neutrinoless double-beta decay experiments. MAJORANA and GERDA use high-purity germanium detectors to search for the neutrinoless double-beta decay of 76Ge, and MAGE is jointly developed between these two collaborations. The MAGE framework contains the geometry models of common objects, prototypes, test stands, and the actual experiments. It also implements customized event generators, GEANT4 physics lists, and output formats. All of these features are available as class libraries that are typically compiled into a single executable. The user selects the particular experimental setup implementation at run-time via macros. The combination of all these common classes into one framework reduces duplication of efforts, eases comparison between simulated data and experiment, and simplifies the addition of new detectors to be simulated. This paper focuses on the software framework, custom event generators, and physics lists.Comment: 12 pages, 6 figure

Insights to scaling remote plasma sources sustained in NF3 mixtures

Remote plasma sources (RPSs) are being developed for low damage materials processing during semiconductor fabrication. Plasmas sustained in NF3 are often used as a source of F atoms. NF3 containing gas mixtures such as NF3/O2 and NF3/H2 provide additional opportunities to produce and control desirable reactive species such as F and NO. In this paper, results from computational investigations of RPS sustained in capacitively coupled plasmas are discussed using zero-dimensional global and two-dimensional reactor scale models. A comprehensive reaction mechanism for plasmas sustained in Ar/NF3/O2 was developed using electron impact cross sections for NF2 and NF calculated by ab initio molecular R-matrix methods. For validation of the reaction mechanism, results from the simulations were compared with optical emission spectroscopy measurements of radical densities. Dissociative attachment and dissociative excitation of NFx are the major sources of F radicals. The exothermicity from these Franck–Condon dissociative processes is the dominant gas heating mechanism, producing gas temperatures in excess of 1500 K. The large fractional dissociation of the feedstock gases enables a larger variety of end-products. Reactions between NFx and O atom containing species lead to the formation of NO and N2O through endothermic reactions facilitated by the gas heating, followed by the formation of NO2 and FNO from exothermic reactions. The downstream composition in the flowing afterglow is an ion–ion plasma maintained by, in oxygen containing mixtures, [F−] ≈ [NO+] since NO has the lowest ionization potential and F has the highest electron affinity among the major neutral species

Status of the GERDA experiment

The study of neutrinoless double beta (0nbb) decay is the only one presently known approach to the fundamental question if the neutrino is a Majorana particle, i.e. its own anti-particle. The observation of 0nbb decay would prove that lepton number is not conserved, establish that neutrino has a Majorana component and, assuming that light neutrino is the dominating process, provide a method for the determination of its effective mass. GERDA is a new 0nbb decay experiment which is currently taking data at the Laboratori Nazionali del Gran Sasso (LNGS) of INFN in Italy. It implements a new shielding concept by operating bare diodes made from Ge with enriched 76Ge in high purity liquid argon supplemented by a water shield. The aim of GERDA is to verify or refute the recent claim of discovery, and, in a second phase, to achieve a two orders of magnitude lower background index than past experiments, to increase the sensitive mass and to collect an exposure of 100 kg yr. The paper will discuss design, physics reach, and status of data taking of GERDA.JRC.D.4-Standards for Nuclear Safety, Security and Safeguard