Autoimmunity in common variable immunodeficiency

immunodeficiency (CVID), the most common symptomatic primary immunodeficiency in adulthood. Different authors report high prevalences of autoimmune diseases in CVID, and several mechanisms have been proposed to explain this apparent paradox. Genetic predisposition, under current surveillance, innate and adaptive immunity deficiencies leading to persistent/recurrent infections, variable degrees of immune dysregulation, and possible failure in central and peripheral mechanisms of tolerance induction or maintenance may all contribute to increased autoimmunity. Conclusions Data on the clinical/immunological profile of affected patients and treatment are available mostly concerning autoimmune cytopenias, the most common autoimmune diseases in CVID. Treatment is based on conventional alternatives, in association with short experience with new agents, including rituximab and infliximab. Benefits of early immunoglobulin substitutive treatment and hypothetical premature predictors of autoimmunity are discussed as potential improvements to CVID patients` follow-up.

Reduced frequency of CD4(+)CD25(HIGH)FOXP3(+) cells and diminished FOXP3 expression in patients with Common Variable Immunodeficiency: A link to autoimmunity?

Common Variable Immunodeficiency (CVID) is a primary immunodeficiency disease characterized by defective immunoglobulin production and often associated with autoimmunity. We used flow cytometry to analyze CD4(+)CD25(HIGH)FOXP3(+) T regulatory (Treg) cells and ask whether perturbations in their frequency in peripheral blood could underlie the high incidence of autoimmune disorders in CVID patients. In this study, we report for the first time that CVID patients with autoimmune disease have a significantly reduced frequency of CD4(+)CD25(HIGH)FOXP3(+) cells in their peripheral blood accompanied by a decreased intensity of FOXP3 expression. Notably, although CVID patients in whom autoimmunity was not diagnosed had a reduced frequency of CD4(+)CD25(HIGH)FOXP3(+) cells, FOXP3 expression levels did not differ from those in healthy controls. In conclusion, these data suggest compromised homeostasis of CD4(+)CD25(HIGH)FOXP3(+) cells in a subset of CVID patients with autoimmunity, and may implicate Treg cells in pathological mechanisms of CVID. (C) 2009 Elsevier Inc. All rights reserved.

Upgrading a TCABR data analysis and acquisition system for remote participation using Java, XML, RCP and modern client/server communication/authentication

The TCABR data analysis and acquisition system has been upgraded to support a joint research programme using remote participation technologies. The architecture of the new system uses Java language as programming environment. Since application parameters and hardware in a joint experiment are complex with a large variability of components, requirements and specification solutions need to be flexible and modular, independent from operating system and computer architecture. To describe and organize the information on all the components and the connections among them, systems are developed using the extensible Markup Language (XML) technology. The communication between clients and servers uses remote procedure call (RPC) based on the XML (RPC-XML technology). The integration among Java language, XML and RPC-XML technologies allows to develop easily a standard data and communication access layer between users and laboratories using common software libraries and Web application. The libraries allow data retrieval using the same methods for all user laboratories in the joint collaboration, and the Web application allows a simple graphical user interface (GUI) access. The TCABR tokamak team in collaboration with the IPFN (Instituto de Plasmas e Fusao Nuclear, Instituto Superior Tecnico, Universidade Tecnica de Lisboa) is implementing this remote participation technologies. The first version was tested at the Joint Experiment on TCABR (TCABRJE), a Host Laboratory Experiment, organized in cooperation with the IAEA (International Atomic Energy Agency) in the framework of the IAEA Coordinated Research Project (CRP) on ""Joint Research Using Small Tokamaks"". (C) 2010 Elsevier B.V. All rights reserved.

Effect on the heavy-ion fusion and elastic scattering cross sections of common approximations assumed in coupled-channel calculations

We study the effects of several approximations commonly used in coupled-channel analyses of fusion and elastic scattering cross sections. Our calculations are performed considering couplings to inelastic states in the context of the frozen approximation, which is equivalent to the coupled-channel formalism when dealing with small excitation energies. Our findings indicate that, in some cases, the effect of the approximations on the theoretical cross sections can be larger than the precision of the experimental data.

Lycopodiopsis derbyi Renault from the Corumbatai Formation in the state of Sao Paulo (Guadalupian of Parana Basin, Southern Brazil): New data from compressed silicified stems

Lycopodiopsis derbyi Renault was analyzed on the basis of compressed silicified stems from four Guadalupian outcrops of the Parana Basin (Corumbatai Formation) in the State of Sao Paulo, Southern Brazil. Dichotomous stems have been recorded, and three different branch regions related to apoxogenesis are described. The most proximal region has larger, clearly rhomboidal leaf cushions, with protruding upper edges; the intermediate transitional region also has rhombic leaf cushions, but they are smaller and less elongated than the lower in the same axis; finally, the most distal region reveals only incipient cushions, with inconspicuous infrafoliar bladders; interspersed microphylls were still attached. A well preserved branch representative of this most distal region was sectioned; it has a siphonostelic cylinder similar to that previously described for L derbyi. The cortex, however, shows new traits, such as a short portion of elongated cells between the periderm and the external cortex (or leaf cushion tissue). The stems were apparently silicified prior to their final burial but were probably not transported for long distances. Their final burial may have taken place during storm events, which were common during the deposition of the Corumbatai Formation. These stems are commonly deformed due to compression, mainly because the internal cortical portions rapidly decayed prior to silicification due to their thin-walled tissue, and are therefore not preserved. The common alkalinity of a shallow marine environment such as that in which the Corumbatai Formation was deposited, should mobilize the silica and favors petrifaction. Based on the new data, an emended diagnosis is proposed and a modification of the identification key published by Thomas and Meyen in 1984 for Upper Paleozoic Lycopsida is suggested. (C) 2009 Elsevier B.V. All rights reserved.

An all-substrings common subsequence algorithm

Given two strings A and B of lengths n(a) and n(b), n(a) <= n(b), respectively, the all-substrings longest common subsequence (ALCS) problem obtains, for every substring B` of B, the length of the longest string that is a subsequence of both A and B. The ALCS problem has many applications, such as finding approximate tandem repeats in strings, solving the circular alignment of two strings and finding the alignment of one string with several others that have a common substring. We present an algorithm to prepare the basic data structure for ALCS queries that takes O(n(a)n(b)) time and O(n(a) + n(b)) space. After this preparation, it is possible to build that allows any LCS length to be retrieved in constant time. Some trade-offs between the space required and a matrix of size O(n(b)(2)) the querying time are discussed. To our knowledge, this is the first algorithm in the literature for the ALCS problem. (C) 2007 Elsevier B.V. All rights reserved.

Comparing diagnostic tests with missing data

When missing data occur in studies designed to compare the accuracy of diagnostic tests, a common, though naive, practice is to base the comparison of sensitivity, specificity, as well as of positive and negative predictive values on some subset of the data that fits into methods implemented in standard statistical packages. Such methods are usually valid only under the strong missing completely at random (MCAR) assumption and may generate biased and less precise estimates. We review some models that use the dependence structure of the completely observed cases to incorporate the information of the partially categorized observations into the analysis and show how they may be fitted via a two-stage hybrid process involving maximum likelihood in the first stage and weighted least squares in the second. We indicate how computational subroutines written in R may be used to fit the proposed models and illustrate the different analysis strategies with observational data collected to compare the accuracy of three distinct non-invasive diagnostic methods for endometriosis. The results indicate that even when the MCAR assumption is plausible, the naive partial analyses should be avoided.

Testing common nonlinear features in vector nonlinear autoregressive models

This paper studies a special class of vector smooth-transition autoregressive (VSTAR) models that contains common nonlinear features (CNFs), for which we proposed a triangular representation and developed a procedure of testing CNFs in a VSTAR model. We first test a unit root against a stable STAR process for each individual time series and then examine whether CNFs exist in the system by Lagrange Multiplier (LM) test if unit root is rejected in the first step. The LM test has standard Chi-squared asymptotic distribution. The critical values of our unit root tests and small-sample properties of the F form of our LM test are studied by Monte Carlo simulations. We illustrate how to test and model CNFs using the monthly growth of consumption and income data of United States (1985:1 to 2011:11).

Solar Energy assessment based on weather station data for direct site monitoring in Indonesia

This thesis evaluates different sites for a weather measurement system and a suitable PV- simulation for University of Surabaya (UBAYA) in Indonesia/Java. The weather station is able to monitor all common weather phenomena including solar insolation. It is planned to use the data for scientific and educational purposes in the renewable energy studies. During evaluation and installation it falls into place that official specifications from global meteorological organizations could not be meet for some sensors caused by the conditions of UBAYA campus. After arranging the hardware the weather at the site was monitored for period of time. A comparison with different official sources from ground based and satellite bases measurements showed differences in wind and solar radiation. In some cases the monthly average solar insolation was deviating 42 % for satellite-based measurements. For the ground based it was less than 10 %. The average wind speed has a difference of 33 % compared to a source, which evaluated the wind power in Surabaya. The wind direction shows instabilities towards east compared with data from local weather station at the airport. PSET has the chance to get some investments to investigate photovoltaic on there own roof. With several simulations a suitable roof direction and the yearly and monthly outputs are shown. With a 7.7 kWpeak PV installation with the latest crystalline technology on the market 8.82 MWh/year could be achieved with weather data from 2012. Thin film technology could increase the value up to 9.13 MWh/year. However, the roofs have enough area to install PV. Finally the low price of electricity in Indonesia makes it not worth to feed in the energy into the public grid.

Common Features in Vector Nonlinear Time Series Models

This thesis consists of four manuscripts in the area of nonlinear time series econometrics on topics of testing, modeling and forecasting nonlinear common features. The aim of this thesis is to develop new econometric contributions for hypothesis testing and forecasting in these area. Both stationary and nonstationary time series are concerned. A definition of common features is proposed in an appropriate way to each class. Based on the definition, a vector nonlinear time series model with common features is set up for testing for common features. The proposed models are available for forecasting as well after being well specified. The first paper addresses a testing procedure on nonstationary time series. A class of nonlinear cointegration, smooth-transition (ST) cointegration, is examined. The ST cointegration nests the previously developed linear and threshold cointegration. An Ftypetest for examining the ST cointegration is derived when stationary transition variables are imposed rather than nonstationary variables. Later ones drive the test standard, while the former ones make the test nonstandard. This has important implications for empirical work. It is crucial to distinguish between the cases with stationary and nonstationary transition variables so that the correct test can be used. The second and the fourth papers develop testing approaches for stationary time series. In particular, the vector ST autoregressive (VSTAR) model is extended to allow for common nonlinear features (CNFs). These two papers propose a modeling procedure and derive tests for the presence of CNFs. Including model specification using the testing contributions above, the third paper considers forecasting with vector nonlinear time series models and extends the procedures available for univariate nonlinear models. The VSTAR model with CNFs and the ST cointegration model in the previous papers are exemplified in detail,and thereafter illustrated within two corresponding macroeconomic data sets.

Health care providers' perceptions of and attitudes towards induced abortions in sub-Saharan Africa and Southeast Asia : a systematic literature review of qualitative and quantitative data.

BACKGROUND: Unsafe abortions are a serious public health problem and a major human rights issue. In low-income countries, where restrictive abortion laws are common, safe abortion care is not always available to women in need. Health care providers have an important role in the provision of abortion services. However, the shortage of health care providers in low-income countries is critical and exacerbated by the unwillingness of some health care providers to provide abortion services. The aim of this study was to identify, summarise and synthesise available research addressing health care providers' perceptions of and attitudes towards induced abortions in sub-Saharan Africa and Southeast Asia. METHODS: A systematic literature search of three databases was conducted in November 2014, as well as a manual search of reference lists. The selection criteria included quantitative and qualitative research studies written in English, regardless of the year of publication, exploring health care providers' perceptions of and attitudes towards induced abortions in sub-Saharan Africa and Southeast Asia. The quality of all articles that met the inclusion criteria was assessed. The studies were critically appraised, and thematic analysis was used to synthesise the data. RESULTS: Thirty-six studies, published during 1977 and 2014, including data from 15 different countries, met the inclusion criteria. Nine key themes were identified as influencing the health care providers' attitudes towards induced abortions: 1) human rights, 2) gender, 3) religion, 4) access, 5) unpreparedness, 6) quality of life, 7) ambivalence 8) quality of care and 9) stigma and victimisation. CONCLUSIONS: Health care providers in sub-Saharan Africa and Southeast Asia have moral-, social- and gender-based reservations about induced abortion. These reservations influence attitudes towards induced abortions and subsequently affect the relationship between the health care provider and the pregnant woman who wishes to have an abortion. A values clarification exercise among abortion care providers is needed.

Defining the role of common variation in the genomic and biological architecture of adult human height

Using genome-wide data from 253,288 individuals, we identified 697 variants at genome-wide significance that together explained one-fifth of the heritability for adult height. By testing different numbers of variants in independent studies, we show that the most strongly associated ∼2,000, ∼3,700 and ∼9,500 SNPs explained ∼21%, ∼24% and ∼29% of phenotypic variance. Furthermore, all common variants together captured 60% of heritability. The 697 variants clustered in 423 loci were enriched for genes, pathways and tissue types known to be involved in growth and together implicated genes and pathways not highlighted in earlier efforts, such as signaling by fibroblast growth factors, WNT/β-catenin and chondroitin sulfate-related genes. We identified several genes and pathways not previously connected with human skeletal growth, including mTOR, osteoglycin and binding of hyaluronic acid. Our results indicate a genetic architecture for human height that is characterized by a very large but finite number (thousands) of causal variants.2014

Modelling the Provenance of Data in Autonomous Systems

Determining the provenance of data, i.e. the process that led to that data, is vital in many disciplines. For example, in science, the process that produced a given result must be demonstrably rigorous for the result to be deemed reliable. A provenance system supports applications in recording adequate documentation about process executions to answer queries regarding provenance, and provides functionality to perform those queries. Several provenance systems are being developed, but all focus on systems in which the components are textitreactive, for example Web Services that act on the basis of a request, job submission system, etc. This limitation means that questions regarding the motives of autonomous actors, or textitagents, in such systems remain unanswerable in the general case. Such questions include: who was ultimately responsible for a given effect, what was their reason for initiating the process and does the effect of a process match what was intended to occur by those initiating the process? In this paper, we address this limitation by integrating two solutions: a generic, re-usable framework for representing the provenance of data in service-oriented architectures and a model for describing the goal-oriented delegation and engagement of agents in multi-agent systems. Using these solutions, we present algorithms to answer common questions regarding responsibility and success of a process and evaluate the approach with a simulated healthcare example.

A Resource Centric Approach For Advancing Collaboration Through Hydrologic Data And Model Sharing

HydroShare is an online, collaborative system being developed for open sharing of hydrologic data and models. The goal of HydroShare is to enable scientists to easily discover and access hydrologic data and models, retrieve them to their desktop or perform analyses in a distributed computing environment that may include grid, cloud or high performance computing model instances as necessary. Scientists may also publish outcomes (data, results or models) into HydroShare, using the system as a collaboration platform for sharing data, models and analyses. HydroShare is expanding the data sharing capability of the CUAHSI Hydrologic Information System by broadening the classes of data accommodated, creating new capability to share models and model components, and taking advantage of emerging social media functionality to enhance information about and collaboration around hydrologic data and models. One of the fundamental concepts in HydroShare is that of a Resource. All content is represented using a Resource Data Model that separates system and science metadata and has elements common to all resources as well as elements specific to the types of resources HydroShare will support. These will include different data types used in the hydrology community and models and workflows that require metadata on execution functionality. The HydroShare web interface and social media functions are being developed using the Drupal content management system. A geospatial visualization and analysis component enables searching, visualizing, and analyzing geographic datasets. The integrated Rule-Oriented Data System (iRODS) is being used to manage federated data content and perform rule-based background actions on data and model resources, including parsing to generate metadata catalog information and the execution of models and workflows. This presentation will introduce the HydroShare functionality developed to date, describe key elements of the Resource Data Model and outline the roadmap for future development.

Harmonization Of Vocabularies For Water Data

Observational data encodes values of properties associated with a feature of interest, estimated by a specified procedure. For water the properties are physical parameters like level, volume, flow and pressure, and concentrations and counts of chemicals, substances and organisms. Water property vocabularies have been assembled at project, agency and jurisdictional level. Organizations such as EPA, USGS, CEH, GA and BoM maintain vocabularies for internal use, and may make them available externally as text files. BODC and MMI have harvested many water vocabularies alongside others of interest in their domain, formalized the content using SKOS, and published them through web interfaces. Scope is highly variable both within and between vocabularies. Individual items may conflate multiple concerns (e.g. property, instrument, statistical procedure, units). There is significant duplication between vocabularies. Semantic web technologies provide the opportunity both to publish vocabularies more effectively, and achieve harmonization to support greater interoperability between datasets. - Models for vocabulary items (property, substance/taxon, process, unit-of-measure, etc) may be formalized OWL ontologies, supporting semantic relations between items in related vocabularies; - By specializing the ontology elements from SKOS concepts and properties, diverse vocabularies may be published through a common interface; - Properties from standard vocabularies (e.g. OWL, SKOS, PROV-O and VAEM) support mappings between vocabularies having a similar scope - Existing items from various sources may be assembled into new virtual vocabularies However, there are a number of challenges: - use of standard properties such as sameAs/exactMatch/equivalentClass require reasoning support; - items have been conceptualised as both classes and individuals, complicating the mapping mechanics; - re-use of items across vocabularies may conflict with expectations concerning URI patterns; - versioning complicates cross-references and re-use. This presentation will discuss ways to harness semantic web technologies to publish harmonized vocabularies, and will summarise how many of the challenges may be addressed.