Two distinct conformational states define the interaction of human RAD51-ATP with single-stranded DNA.

An essential mechanism for repairing DNA double-strand breaks is homologous recombination (HR). One of its core catalysts is human RAD51 (hRAD51), which assembles as a helical nucleoprotein filament on single-stranded DNA, promoting DNA-strand exchange. Here, we study the interaction of hRAD51 with single-stranded DNA using a single-molecule approach. We show that ATP-bound hRAD51 filaments can exist in two different states with different contour lengths and with a free-energy difference of ~4 kBT per hRAD51 monomer. Upon ATP hydrolysis, the filaments convert into a disassembly-competent ADP-bound configuration. In agreement with the single-molecule analysis, we demonstrate the presence of two distinct protomer interfaces in the crystal structure of a hRAD51-ATP filament, providing a structural basis for the two conformational states of the filament. Together, our findings provide evidence that hRAD51-ATP filaments can exist in two interconvertible conformational states, which might be functionally relevant for DNA homology recognition and strand exchange

Multi-membership gene regulation in pathway based microarray analysis

This article is available through the Brunel Open Access Publishing Fund. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.Background: Gene expression analysis has been intensively researched for more than a decade. Recently, there has been elevated interest in the integration of microarray data analysis with other types of biological knowledge in a holistic analytical approach. We propose a methodology that can be facilitated for pathway based microarray data analysis, based on the observation that a substantial proportion of genes present in biochemical pathway databases are members of a number of distinct pathways. Our methodology aims towards establishing the state of individual pathways, by identifying those truly affected by the experimental conditions based on the behaviour of such genes. For that purpose it considers all the pathways in which a gene participates and the general census of gene expression per pathway. Results: We utilise hill climbing, simulated annealing and a genetic algorithm to analyse the consistency of the produced results, through the application of fuzzy adjusted rand indexes and hamming distance. All algorithms produce highly consistent genes to pathways allocations, revealing the contribution of genes to pathway functionality, in agreement with current pathway state visualisation techniques, with the simulated annealing search proving slightly superior in terms of efficiency. Conclusions: We show that the expression values of genes, which are members of a number of biochemical pathways or modules, are the net effect of the contribution of each gene to these biochemical processes. We show that by manipulating the pathway and module contribution of such genes to follow underlying trends we can interpret microarray results centred on the behaviour of these genes.The work was sponsored by the studentship scheme of the School of Information Systems, Computing and Mathematics, Brunel Universit

A framework for Distributional Formal Semantics

Formal semantics and distributional semantics offer complementary strengths in capturing the meaning of natural language. As such, a considerable amount of research has sought to unify them, either by augmenting formal semantic systems with a distributional component, or by defining a formal system on top of distributed representations. Arriving at such a unified framework has, however, proven extremely challenging. One reason for this is that formal and distributional semantics operate on a fundamentally different `representational currency': formal semantics defines meaning in terms of models of the world, whereas distributional semantics defines meaning in terms of linguistic co-occurrence. Here, we pursue an alternative approach by deriving a vector space model that defines meaning in a distributed manner relative to formal models of the world. We will show that the resulting Distributional Formal Semantics offers probabilistic distributed representations that are also inherently compositional, and that naturally capture quantification and entailment. We moreover show that, when used as part of a neural network model, these representations allow for capturing incremental meaning construction and probabilistic inferencing. This framework thus lays the groundwork for an integrated distributional and formal approach to meaning

The Human Fungal Pathogen Cryptococcus neoformans Escapes Macrophages by a Phagosome Emptying Mechanism That Is Inhibited by Arp2/3 Complex-Mediated Actin Polymerisation

The lysis of infected cells by disease-causing microorganisms is an efficient but risky strategy for disseminated infection, as it exposes the pathogen to the full repertoire of the host's immune system. Cryptococcus neoformans is a widespread fungal pathogen that causes a fatal meningitis in HIV and other immunocompromised patients. Following intracellular growth, cryptococci are able to escape their host cells by a non-lytic expulsive mechanism that may contribute to the invasion of the central nervous system. Non-lytic escape is also exhibited by some bacterial pathogens and is likely to facilitate long-term avoidance of the host immune system during latency. Here we show that phagosomes containing intracellular cryptococci undergo repeated cycles of actin polymerisation. These actin ‘flashes’ occur in both murine and human macrophages and are dependent on classical WASP-Arp2/3 complex mediated actin filament nucleation. Three dimensional confocal imaging time lapse revealed that such flashes are highly dynamic actin cages that form around the phagosome. Using fluorescent dextran as a phagosome membrane integrity probe, we find that the non-lytic expulsion of Cryptococcus occurs through fusion of the phagosome and plasma membranes and that, prior to expulsion, 95% of phagosomes become permeabilised, an event that is immediately followed by an actin flash. By using pharmacological agents to modulate both actin dynamics and upstream signalling events, we show that flash occurrence is inversely related to cryptococcal expulsion, suggesting that flashes may act to temporarily inhibit expulsion from infected phagocytes. In conclusion, our data reveal the existence of a novel actin-dependent process on phagosomes containing cryptococci that acts as a potential block to expulsion of Cryptococcus and may have significant implications for the dissemination of, and CNS invasion by, this organism.\ud \u

Diagnostic performance of the basic and advanced life support termination of resuscitation rules: A systematic review and diagnostic meta-analysis

Aim: To minimize termination of resuscitation (TOR) in potential survivors, the desired positive predictive value (PPV) for mortality and specificity of universal TOR-rules are ≥99%. In lack of a quantitative summary of the collective evidence, we performed a diagnostic meta-analysis to provide an overall estimate of the performance of the basic and advanced life support (BLS and ALS) termination rules. Data sources: We searched PubMed/EMBASE/Web-of-Science/CINAHL and Cochrane (until September 2019) for studies on either or both TOR-rules in non-traumatic, adult cardiac arrest. PRISMA-DTA-guidelines were followed. Results: There were 19 studies: 16 reported on the BLS-rule (205.073 patients, TOR-advice in 57%), 11 on the ALS-rule (161.850 patients, TOR-advice in 24%). Pooled specificities were 0.95 (0.89–0.98) and 0.98 (0.95–1.00) respectively, with a PPV of 0.99 (0.99–1.00) and 1.00 (0.99–1.00). Specificities were significantly lower in non-Western than Western regions: 0.84 (0.73–0.92) vs. 0.99 (0.97–0.99), p < 0.001 for the BLS rule. For the ALS-rule, specificities were 0.94 (0.87–0.97) vs. 1.00 (0.99–1.00), p < 0.001. For non-Western regions, 16 (BLS) or 6 (ALS) out of 100 potential survivors met the TOR-criteria. Meta-regression demonstrated decreasing performance in settings with lower rates of in-field shocks. Conclusions: Despite an overall high PPV, this meta-analysis highlights a clinically important variation in diagnostic performance of the BLS and ALS TOR-rules. Lower specificity and PPV were seen in non-Western regions, and populations with lower rates of in-field defibrillation. Improved insight in the varying diagnostic performance is highly needed, and local validation of the rules is warranted to prevent in-field termination of potential survivors

Assessing health-related quality-of-life changes in informal caregivers: an evaluation in parents of children with major congenital anomalies

Purpose: Relatively few attempts to measure the effects on the health-related quality of life (HRQoL) of informal caregivers within the context of economic evaluations have been reported. This paper is an exploratory attempt to find suitable methods to assess caregi

Protocol for north of England and Scotland study of tonsillectomy and adeno-tonsillectomy in children (NESSTAC). A pragmatic randomised controlled trial comparing surgical intervention with conventional medical treatment in children with recurrent sore throats

BACKGROUND: Uncertainties surrounding the effectiveness and cost-effectiveness of childhood tonsillectomy for recurrent sore throat led the NHS Health Technology Assessment Programme to commission this research to evaluate the effectiveness and cost-effectiveness of tonsillectomy and adeno-tonsillectomy in comparison with standard non-surgical management in children aged under 16 with recurrent throat infections. The aim is to evaluate if tonsillectomy and adeno-tonsillectomy reduces the number of episodes of sore throats among children to a clinically significant extent. METHODS/DESIGN: A simple prospective pragmatic randomised controlled trial with economic analysis and prospective cohort study of non-trial participants comparing surgical intervention with conventional medical treatment. The treatment arm will receive tonsillectomy and adeno-tonsillectomy while in the control arm non-surgical conventional medical treatment only will be used. The primary outcome measure will be reported number of episodes of sore throat over two years with secondary outcomes measures of reported number of episodes of sore throat, otitis media and upper respiratory tract infection which invoke a GP consultation; reported number of symptom-free days; reported severity of sore throats and surgical and anaesthetic morbidity. The study will take place in five hospitals in the UK. The trial population will be 406 children aged 4–15 on their last birthday with recurrent sore throat referred by primary care to the 5 otolaryngology departments. The duration of the study is seven years (July 2001- July 2008). DISCUSSION: As with all pragmatic randomised controlled trials it is impossible to control the external environment in which the research is taking place. Since this trial began a number of factors have arisen which could affect the outcome including; a reduction in the incidence of respiratory tract infections, marked socio-economic differences in consultation rates, the results from the National Prospective Tonsillectomy Audit and the Government's waiting list initiatives

Patients' experiences with quality of hospital care: the Consumer Quality Index Cataract Questionnaire

Background. Patients' feedback is of great importance in health care policy decisions. The Consumer Quality Index Cataract Questionnaire (CQI Cataract) was used to measure patients' experiences with quality of care after a cataract operation. This study aims to evaluate the reliability and the dimensional structure of this questionnaire and assesses its ability to measure differences between hospitals in patients' experiences with quality of care. Methods. Survey data of 4,635 respondents were available. An exploratory factor analysis was performed to evaluate the construct validity of the questionnaire and item-correlations and inter-factor correlations were calculated. Secondly, Cronbach's alpha coefficients were calculated to assess the internal consistency of the scales. Thirdly, to evaluate the ability of the questionnaire to discriminate between hospitals, multilevel analyses were performed with patients hierarchically nested within hospitals. Results. Exploratory factor analysis resulted in 14 quality of care items subdivided over three factors (i.e. communication with ophthalmologist, communication with nurses, and communication about medication). Cronbach's alpha coefficients of 0.89, 0.76 and 0.79 indicated good internal consistency. Multilevel analyses showed that the questionnaire was able to measure differences in patients' experiences with hospital care regarding communication with ophthalmologist and communication about medication. In addition, there was variation between hospitals regarding ophthalmologist ratings, hospital ratings and one dichotomous information item. Conclusion. These findings suggest that the CQI Cataract is a reliable and valid instrument. This instrument can be used to measure patients' experiences with three domains of hospital care after a cataract operation and is able to assess differences in evaluated care between hospitals