Selective extracellular vesicle-mediated export of an overlapping set of microRNAs from multiple cell types

Background: MicroRNAs (miRNAs) are a class of small RNA molecules that regulate expression of specific mRNA targets. They can be released from cells, often encapsulated within extracellular vesicles (EVs), and therefore have the potential to mediate intercellular communication. It has been suggested that certain miRNAs may be selectively exported, although the mechanism has yet to be identified. Manipulation of the miRNA content of EVs will be important for future therapeutic applications. We therefore wished to assess which endogenous miRNAs are enriched in EVs and how effectively an overexpressed miRNA would be exported.<br/><br/>Results: Small RNA libraries from HEK293T cells and vesicles before or after transfection with a vector for miR-146a overexpression were analysed by deep sequencing. A subset of miRNAs was found to be enriched in EVs; pathway analysis of their predicted target genes suggests a potential role in regulation of endocytosis. RT-qPCR in additional cell types and analysis of publicly available data revealed that many of these miRNAs tend to be widely preferentially exported. Whilst overexpressed miR-146a was highly enriched both in transfected cells and their EVs, the cellular:EV ratios of endogenous miRNAs were not grossly altered. MiR-451 was consistently the most highly exported miRNA in many different cell types. Intriguingly, Argonaute2 (Ago2) is required for miR-451 maturation and knock out of Ago2 has been shown to decrease expression of other preferentially exported miRNAs (eg miR-150 and miR-142-3p).<br/><br/>Conclusion: The global expression data provided by deep sequencing confirms that specific miRNAs are enriched in EVs released by HEK293T cells. Observation of similar patterns in a range of cell types suggests that a common mechanism for selective miRNA export may exist.

Partial and total multiphoton detachment rates for H- in a perturbative B-spline-based approach

An ab initio approach has been applied to study multiphoton detachment rates for the negative hydrogen ion in the lowest nonvanishing order of perturbation theory. The approach is based on the use of B splines allowing an accurate treatment of the electronic repulsion. Total detachment rates have been determined for two- to six-photon processes as well as partial rates for detachment into the different final symmetries. It is shown that B-spline expansions can yield accurate continuum and bound-state wave functions in a very simple manner. The calculated total rates for two- and three-photon detachment are in good agreement with other perturbative calculations. For more than three-photon detachment little information has been available before now. While the total cross sections show little structure, a fair amount of structure is predicted in the partial cross sections. In the two-photon process, it is shown that the detached electrons mainly have s character. For four- and six-photon processes, the contribution from the d channel is the most important. For three- and five-photon processes p electrons dominate the electron emission spectrum. Detachment rates for s and p electrons show minima as a function of photon energy. © 1994 The American Physical Society.

Organizational structure and the periphery of the gene regulatory network in B-cell lymphoma

Background: <br/>The physical periphery of a biological cell is mainly described by signaling pathways which are triggered by transmembrane proteins and receptors that are sentinels to control the whole gene regulatory network of a cell. However, our current knowledge about the gene regulatory mechanisms that are governed by extracellular signals is severely limited.Results: The purpose of this paper is three fold. First, we infer a gene regulatory network from a large-scale B-cell lymphoma expression data set using the C3NET algorithm. Second, we provide a functional and structural analysis of the largest connected component of this network, revealing that this network component corresponds to the peripheral region of a cell. Third, we analyze the hierarchical organization of network components of the whole inferred B-cell gene regulatory network by introducing a new approach which exploits the variability within the data as well as the inferential characteristics of C3NET. As a result, we find a functional bisection of the network corresponding to different cellular components.<br/><br/>Conclusions: <br/>Overall, our study allows to highlight the peripheral gene regulatory network of B-cells and shows that it is centered around hub transmembrane proteins located at the physical periphery of the cell. In addition, we identify a variety of novel pathological transmembrane proteins such as ion channel complexes and signaling receptors in B-cell lymphoma. © 2012 Simoes et al.; licensee BioMed Central Ltd.

Ordering effects and choice set awareness in repeat-response stated preference studies

We present an experiment designed to investigate the presence and nature of ordering effects within repeat-response stated preference (SP) studies. Our experiment takes the form of a large sample, full-factorial, discrete choice SP exercise investigating preferences for tap water quality improvements. Our study simultaneously investigates a variety of different forms of position-dependent and precedent-dependent ordering effect in preferences for attributes and options and in response randomness. We also examine whether advanced disclosure of the choice tasks impacts on the probability of exhibiting ordering effects of those different types. We analyze our data both non-parametrically and parametrically and find robust evidence for ordering effects. We also find that the patterns of order effect in respondents' preferences are significantly changed but not eradicated by the advanced disclosure of choice tasks a finding that offers insights into the choice behaviors underpinning order effects. © 2011 Elsevier Inc.

The geriatric minimum data set for clinical trials (GMDS)

To overcome the weak evidence base coming from often poor and insufficient clinical research in older people, a minimum data set to achieve harmonisation is highly advisable. This will lead to uniform nomenclature and to the standardisation of the assessment tools. Our primary objective was to develop a Geriatric Minimum Data Set (GMDS) for clinical research.

Urban housing and the role of 'underclass' processes: the case of Ireland

Rising levels of urban deprivation and a perception that poverty has become more concentrated in such areas and has taken on a qualitatively different character have provoked a variety of popular and academic responses. The potentially most fruitful set of hypotheses focuses on the unintended of weak labour force attachment and social isolation is perceived to lead to behaviour and orientations that contribute to a vicious circle of deprivation. In examining the value of this conceptual framework in the Irish case we proceed by measuring directly the social-psychological factors which ave hypothesized to mediate the 'underclass' process.

A significantly higher level of poverty is found in urban public-sector tenant households. This finding cannot be accounted for entirely by socio-demographic differences. It is the assessment of this net or residual effect that is crucial to an evaluation of vicious circle explanations. Controlling for the critical social-psychological factors we found that net effect was reduced by less than a quarter and concluded that the remaining effect is more plausibly attributed to the role of selection than to underclass processes. Analysis of the changing relationship between urban public-sector tenancy and poverty provides support for this interpretation.

For the main part the distinctiveness of social housing tenants is a consequence of the disadvantages they stiffer in relation to employment opportunities and living standards. Ultimately it is these problems that policy interventions, whatever the level at which they take place, must address.

Homologous size-extension of hybrid vanadate capsules – solid state structures, solution stability and surface deposition

The dimensions and cavity sizes of the molecular capsules with the general formula [Vb>10b>Ob>18b>Lb>4b>]¹⁰⁻ can be controlled modularly through the nature of the bifunctional, rigid organophosphonate ligands L¹ and L² (L¹ = bis(4-phosphonatophenyl)ethyne and L² = bis(4-phosphonatophenyl)butadiyne); the solution stability of the molecular entities as demonstrated by ESI-MS studies permits their assembly on the Au(111) surface on a sub-monolayer scale giving rise to a 2D supramolecular structure that is comparable to the packing arrangements of the capsules in the crystal structures.

Core Outcomes in Ventilation Trials (COVenT): protocol for a core outcome set using a Delphi survey with a nested randomised trial and observational cohort study

Background<br/>Among clinical trials of interventions that aim to modify time spent on mechanical ventilation for critically ill patients there is considerable inconsistency in chosen outcomes and how they are measured. The Core Outcomes in Ventilation Trials (COVenT) study aims to develop a set of core outcomes for use in future ventilation trials in mechanically ventilated adults and children.<br/><br/>Methods/design<br/>We will use a mixed methods approach that incorporates a randomised trial nested within a Delphi study and a consensus meeting. Additionally, we will conduct an observational cohort study to evaluate uptake of the core outcome set in published studies at 5 and 10 years following core outcome set publication. The three-round online Delphi study will use a list of outcomes that have been reported previously in a review of ventilation trials. The Delphi panel will include a range of stakeholder groups including patient support groups. The panel will be randomised to one of three feedback methods to assess the impact of the feedback mechanism on subsequent ranking of outcomes. A final consensus meeting will be held with stakeholder representatives to review outcomes.<br/><br/>Discussion<br/>The COVenT study aims to develop a core outcome set for ventilation trials in critical care, explore the best Delphi feedback mechanism for achieving consensus and determine if participation increases use of the core outcome set in the long term.

Expression of the NF-kappaB targets BCL2 and BIRC5/Survivin characterizes small B-cell and aggressive B-cell lymphomas, respectively

Nuclear factor kappa B (NF-kappaB) activation has been proposed as a cardinal feature of tumourigenesis, although the precise mechanism, frequency, relevance, and extent of NF-kappaB activation in lymphomas remain to be fully elucidated. In this study, expression profiling and tissue microarray studies of 209 and 323 non-Hodgkin's lymphomas (NHLs) respectively, including the most frequent sub-types of NHL, were employed to generate a hypothesis concerning the most common NF-kappaB targets in NHL. These analyses showed that NF-kappaB activation is a common phenomenon in NHL, resulting in the expression of distinct sets of NF-kappaB target genes, depending on the cell context. BCL2 and BIRC5/Survivin were identified as key NF-kappaB targets and their expression distinguished small and aggressive B-cell lymphomas, respectively. Interestingly, in the vast majority of B-cell lymphomas, the expression of these markers was mutually exclusive. A set of genes was identified whose expression correlates either with BIRC5/Survivin or with BCL2. BIRC5/Survivin expression, in contrast to BCL2, was associated with a signature of cell proliferation (overexpression of cell cycle control, DNA repair, and polymerase genes), which may contribute to the aggressive phenotype and poor prognosis of these lymphomas. Strikingly, mantle cell lymphoma and chronic lymphocytic leukaemia expressed highly elevated levels of BCL2 protein and mRNA, higher than that observed in reactive mantle zone cells or even in follicular lymphomas, where BCL2 expression is deregulated through the t(14;18) translocation. In parallel with this observation, BIRC5/Survivin expression was higher in Burkitt's lymphoma and diffuse large B-cell lymphoma than in non-tumoural germinal centre cells. In vitro studies confirmed that NF-kappaB activation contributes to the expression of both markers. In cell lines representing aggressive lymphomas, NF-kappaB inhibition resulted in a decrease in BIRC5/Survivin expression. Meanwhile, in chronic lymphocytic leukaemia (CLL)-derived lymphocytes, NF-kappaB inhibition resulted in a marked decrease in BCL2 expression.

Semantics for possibilistic answer set programs: uncertain rules versus rules with uncertain conclusions

Although Answer Set Programming (ASP) is a powerful framework for declarative problem solving, it cannot in an intuitive way handle situations in which some rules are uncertain, or in which it is more important to satisfy some constraints than others. Possibilistic ASP (PASP) is a natural extension of ASP in which certainty weights are associated with each rule. In this paper we contrast two different views on interpreting the weights attached to rules. Under the first view, weights reflect the certainty with which we can conclude the head of a rule when its body is satisfied. Under the second view, weights reflect the certainty that a given rule restricts the considered epistemic states of an agent in a valid way, i.e. it is the certainty that the rule itself is correct. The first view gives rise to a set of weighted answer sets, whereas the second view gives rise to a weighted set of classical answer sets.

Characterizing and Extending Answer Set Semantics using Possibility Theory

Answer Set Programming (ASP) is a popular framework for modelling combinatorial problems. However, ASP cannot be used easily for reasoning about uncertain information. Possibilistic ASP (PASP) is an extension of ASP that combines possibilistic logic and ASP. In PASP a weight is associated with each rule, whereas this weight is interpreted as the certainty with which the conclusion can be established when the body is known to hold. As such, it allows us to model and reason about uncertain information in an intuitive way. In this paper we present new semantics for PASP in which rules are interpreted as constraints on possibility distributions. Special models of these constraints are then identified as possibilistic answer sets. In addition, since ASP is a special case of PASP in which all the rules are entirely certain, we obtain a new characterization of ASP in terms of constraints on possibility distributions. This allows us to uncover a new form of disjunction, called weak disjunction, that has not been previously considered in the literature. In addition to introducing and motivating the semantics of weak disjunction, we also pinpoint its computational complexity. In particular, while the complexity of most reasoning tasks coincides with standard disjunctive ASP, we find that brave reasoning for programs with weak disjunctions is easier.

Possibilistic Answer Set Programming Revisited

Possibilistic answer set programming (PASP) extends answer set programming (ASP) by attaching to each rule a degree of certainty. While such an extension is important from an application point of view, existing semantics are not well-motivated, and do not always yield intuitive results. To develop a more suitable semantics, we first introduce a characterization of answer sets of classical ASP programs in terms of possibilistic logic where an ASP program specifies a set of constraints on possibility distributions. This characterization is then naturally generalized to define answer sets of PASP programs. We furthermore provide a syntactic counterpart, leading to a possibilistic generalization of the well-known Gelfond-Lifschitz reduct, and we show how our framework can readily be implemented using standard ASP solvers.

Towards Possibilistic Fuzzy Answer Set Programming

Fuzzy answer set programming (FASP) is a generalization of answer set programming to continuous domains. As it can not readily take uncertainty into account, however, FASP is not suitable as a basis for approximate reasoning and cannot easily be used to derive conclusions from imprecise information. To cope with this, we propose an extension of FASP based on possibility theory. The resulting framework allows us to reason about uncertain information in continuous domains, and thus also about information that is imprecise or vague. We propose a syntactic procedure, based on an immediate consequence operator, and provide a characterization in terms of minimal models, which allows us to straightforwardly implement our framework using existing FASP solvers.

Glycosylation of Vitamin D Binding Protein Reduced in Juvenile Idiopathic Arthritis Patients At Risk of Disease Extension.

Background/Purpose:Juvenile idiopathic arthritis (JIA) comprises a poorly understood group of chronic, childhood onset, autoimmune diseases with variable clinical outcomes. We investigated whether profiling of the synovial fluid (SF) proteome by a fluorescent dye based, two-dimensional gel (DIGE) approach could distinguish the subset of patients in whom inflammation extends to affect a large number of joints, early in the disease process. The post-translational modifications to candidate protein markers were verified by a novel deglycosylation strategy.Methods:SF samples from 57 patients were obtained around time of initial diagnosis of JIA. At 1 year from inclusion patients were categorized according to ILAR criteria as oligoarticular arthritis (n=26), extended oligoarticular (n=8) and polyarticular disease (n=18). SF samples were labeled with Cy dyes and separated by two-dimensional electrophoresis. Multivariate analyses were used to isolate a panel of proteins which distinguish patient subgroups. Proteins were identified using MALDI-TOF mass spectrometry with vitamin D binding protein (VDBP) expression and siaylation further verified by immunohistochemistry, ELISA test and immunoprecipitation. Candidate biomarkers were compared to conventional inflammation measure C-reactive protein (CRP). Sialic acid residues were enzymatically cleaved from immunopurified SF VDBP, enriched by hydrophilic interaction liquid chromatography (HILIC) and analysed by mass spectrometry.Results:Hierarchical clustering based on the expression levels of a set of 23 proteins segregated the extended-to-be oligoarticular from the oligoarticular patients. A cleaved isoform of VDBP, spot 873, is present at significantly reduced levels in the SF of oligoarticular patients at risk of disease extension, relative to other subgroups (p<0.05). Conversely total levels of vitamin D binding protein are elevated in plasma and ROC curves indicate an improved diagnostic sensitivity to detect patients at risk of disease extension, over both spot 873 and CRP levels. Sialysed forms of intact immunopurified VDBP were more prevalent in persistent oligoarticular patient synovial fluids.Conclusion:The data indicate that a subset of the synovial fluid proteome may be used to stratify patients to determine risk of disease extension. Reduced conversion of VDBP to a macrophage activation factor may represent a novel pathway contributing to increased risk of disease extension in JIA patients.