Development and validation of 'AutoRIF': Software for the automated analysis of radiation-induced foci

Copyright @ 2012 McVean et al; licensee BioMed Central Ltd. 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.This article has been made available through the Brunel Open Access Publishing Fund.Background: The quantification of radiation-induced foci (RIF) to investigate the induction and subsequent repair of DNA double strands breaks is now commonplace. Over the last decade systems specific for the automatic quantification of RIF have been developed for this purpose, however to ask more mechanistic questions on the spatio-temporal aspects of RIF, an automated RIF analysis platform that also quantifies RIF size/volume and relative three-dimensional (3D) distribution of RIF within individual nuclei, is required. Results: A java-based image analysis system has been developed (AutoRIF) that quantifies the number, size/volume and relative nuclear locations of RIF within 3D nuclear volumes. Our approach identifies nuclei using the dynamic Otsu threshold and RIF by enhanced Laplacian filtering and maximum entropy thresholding steps and, has an application ‘batch optimisation’ process to ensure reproducible quantification of RIF. AutoRIF was validated by comparing output against manual quantification of the same 2D and 3D image stacks with results showing excellent concordance over a whole range of sample time points (and therefore range of total RIF/nucleus) after low-LET radiation exposure. Conclusions: This high-throughput automated RIF analysis system generates data with greater depth of information and reproducibility than that which can be achieved manually and may contribute toward the standardisation of RIF analysis. In particular, AutoRIF is a powerful tool for studying spatio-temporal relationships of RIF using a range of DNA damage response markers and can be run independently of other software, enabling most personal computers to perform image analysis. Future considerations for AutoRIF will likely include more complex algorithms that enable multiplex analysis for increasing combinations of cellular markers.This article is made available through the Brunel Open Access Publishing Fund

Apparent correlation of palaeomagnetic intensity and climatic records in deep-sea sediments

Most reports of a correlation between Pleistocene climate and geomagnetic field intensity rely strongly on the assumption that sediment natural remanent magnetic (NRM) intensity provides a record of geomagnetic field strength and is not sensitive to local changes in properties of the sediment. Critical assessment of relevant data presented here and elsewhere from deep-sea sediment cores shows that a pronounced dependence of NRM intensity on sediment composition can occur which implies that this assumption is unlikely to be generally valid. As sediment composition often reflects varying depositional conditions induced by climatic change, the significance of correlations proposed between Pleistocene palaeomagnetism and climatic indicators in deep-sea sediments may be less dramatic than sometimes supposed

‘Devolution and Cultural Catch-Up: Decoupling England and its Literature from English Literature’

Robert McLiam Wilson’s 1989 novel Ripley Bogle uses an unreliable narrator to expose the differences – regional, linguistic and national – between communities Bogle, the protagonist, experiences in Cambridge and Northern Ireland. Bogle is an English Literature student and then drop-out whose rejection of canonical study is the rejection of Arnoldianism and a traditionally organist and imperialist discipline that reanimates the debate about civic values and literary culture. A similar device is used in Sebastian Faulks’s 2007 novel Engleby in which Mike Engleby abandons English Literature at University only to later become a journalist probing the political landscape and personalities of the 1980s and after. Embroiled in disappearance and death, Engleby’s psychological unpredictability enables a reading of Britain’s socio-political death. These interconnected novels stand either side of Britain’s devolutionary divide and, as a pair, are suggestive of England’s need to readdress its own literary culture in the face of devolution. They are also symptomatic of a wider cultural catch-up required within England after 1999. Where the other devolved nations have sought to advance new and challenging national literary concerns and forms distinct from the pan-British literary canon of the past (and its restrictive exclusion based on class, gender and race), England has only recently come to view its literary culture as national. However, this has provided a potential filled moment of redefinition that will help free England and its authors from the pan-British sensibility of imperial dominance. This chapter argues that such redefinition, and resistance to the canon, developed immediately before and dramatically after devolution is evident in Graham Swift’s Last Orders (1996) with its resistive yet civic working class community and in the representations of marginalised, disempowered sections of England’s population offered in Alan Kent’s Proper Job, Charlie Kurnow (2005), Stella Duffy’s The Room of Lost Things (2009) and Jim Crace’s All That Follows (2010). These authors seize the opportunity provided by devolution to re-examine England’s national identity and to probe its relation to political enfranchisement, civic responsibility and literary vitality as England culturally catches up with its own socio-political reality

Relative judgement is relatively difficult: evidence against the role of relative judgement in absolute identification

A variety of processes have been put forward to explain absolute identification performance. One difference between current models of absolute identification is the extent to which the task involves accessing stored representations in long-term memory (e.g. exemplars in memory, Kent & Lamberts, Journal of Experimental Psychology: Learning Memory and Cognition, 31, 289–305, 2005) or relative judgement (comparison of the current stimulus to the stimulus on the previous trial, Stewart, Brown & Chater, Psychological Review, 112, 881–911, 2005). In two experiments we explored this by tapping into these processes. In Experiment 1 participants completed an absolute identification task using eight line lengths whereby a single stimulus was presented on each trial for identification. They also completed a matching task aimed at mirroring exemplar comparison in which eight line lengths were presented in a circular array and the task was to report which of these matched a target presented centrally. Experiment 2 was a relative judgement task and was similar to Experiment 1 except that the task was to report the difference (jump-size) between the current stimulus and that on the previous trial. The absolute identification and matching data showed clear similarities (faster and more accurate responding for stimuli near the edges of the range and similar stimulus-response confusions). In contrast, relative judgment performance was poor suggesting relative judgement is not straightforward. Moreover, performance as a function of jump-size differed considerably between the relative judgement and absolute identification tasks. Similarly, in the relative judgement task, predicting correct stimulus identification based on successful relative judgement yielded the reverse pattern of performance observed in the absolute identification task. Overall, the data suggest that relative judgement does not underlie absolute identification and that the task is more likely reliant on an exemplar comparison process

Logopenic and nonfluent variants of primary progressive aphasia are differentiated by acoustic measures of speech production

Differentiation of logopenic (lvPPA) and nonfluent/agrammatic (nfvPPA) variants of Primary Progressive Aphasia is important yet remains challenging since it hinges on expert based evaluation of speech and language production. In this study acoustic measures of speech in conjunction with voxel-based morphometry were used to determine the success of the measures as an adjunct to diagnosis and to explore the neural basis of apraxia of speech in nfvPPA. Forty-one patients (21 lvPPA, 20 nfvPPA) were recruited from a consecutive sample with suspected frontotemporal dementia. Patients were diagnosed using the current gold-standard of expert perceptual judgment, based on presence/absence of particular speech features during speaking tasks. Seventeen healthy age-matched adults served as controls. MRI scans were available for 11 control and 37 PPA cases; 23 of the PPA cases underwent amyloid ligand PET imaging. Measures, corresponding to perceptual features of apraxia of speech, were periods of silence during reading and relative vowel duration and intensity in polysyllable word repetition. Discriminant function analyses revealed that a measure of relative vowel duration differentiated nfvPPA cases from both control and lvPPA cases (r2 = 0.47) with 88% agreement with expert judgment of presence of apraxia of speech in nfvPPA cases. VBM analysis showed that relative vowel duration covaried with grey matter intensity in areas critical for speech motor planning and programming: precentral gyrus, supplementary motor area and inferior frontal gyrus bilaterally, only affected in the nfvPPA group. This bilateral involvement of frontal speech networks in nfvPPA potentially affects access to compensatory mechanisms involving right hemisphere homologues. Measures of silences during reading also discriminated the PPA and control groups, but did not increase predictive accuracy. Findings suggest that a measure of relative vowel duration from of a polysyllable word repetition task may be sufficient for detecting most cases of apraxia of speech and distinguishing between nfvPPA and lvPPA

Assessing and reporting heterogeneity in treatment effects in clinical trials: a proposal

Mounting evidence suggests that there is frequently considerable variation in the risk of the outcome of interest in clinical trial populations. These differences in risk will often cause clinically important heterogeneity in treatment effects (HTE) across the trial population, such that the balance between treatment risks and benefits may differ substantially between large identifiable patient subgroups; the "average" benefit observed in the summary result may even be non-representative of the treatment effect for a typical patient in the trial. Conventional subgroup analyses, which examine whether specific patient characteristics modify the effects of treatment, are usually unable to detect even large variations in treatment benefit (and harm) across risk groups because they do not account for the fact that patients have multiple characteristics simultaneously that affect the likelihood of treatment benefit. Based upon recent evidence on optimal statistical approaches to assessing HTE, we propose a framework that prioritizes the analysis and reporting of multivariate risk-based HTE and suggests that other subgroup analyses should be explicitly labeled either as primary subgroup analyses (well-motivated by prior evidence and intended to produce clinically actionable results) or secondary (exploratory) subgroup analyses (performed to inform future research). A standardized and transparent approach to HTE assessment and reporting could substantially improve clinical trial utility and interpretability

Abundant Human DNA Contamination Identified in Non-Primate Genome Databases

During routine screens of the NCBI databases using human repetitive elements we discovered an unlikely level of nucleotide identity across a broad range of phyla. To ascertain whether databases containing DNA sequences, genome assemblies and trace archive reads were contaminated with human sequences, we performed an in depth search for sequences of human origin in non-human species. Using a primate specific SINE, AluY, we screened 2,749 non-primate public databases from NCBI, Ensembl, JGI, and UCSC and have found 492 to be contaminated with human sequence. These represent species ranging from bacteria (B. cereus) to plants (Z. mays) to fish (D. rerio) with examples found from most phyla. The identification of such extensive contamination of human sequence across databases and sequence types warrants caution among the sequencing community in future sequencing efforts, such as human re-sequencing. We discuss issues this may raise as well as present data that gives insight as to how this may be occurring

Features of mammalian microRNA promoters emerge from polymerase II chromatin immunoprecipitation data

Background: MicroRNAs (miRNAs) are short, non-coding RNA regulators of protein coding genes. miRNAs play a very important role in diverse biological processes and various diseases. Many algorithms are able to predict miRNA genes and their targets, but their transcription regulation is still under investigation. It is generally believed that intragenic miRNAs (located in introns or exons of protein coding genes) are co-transcribed with their host genes and most intergenic miRNAs transcribed from their own RNA polymerase II (Pol II) promoter. However, the length of the primary transcripts and promoter organization is currently unknown. Methodology: We performed Pol II chromatin immunoprecipitation (ChIP)-chip using a custom array surrounding regions of known miRNA genes. To identify the true core transcription start sites of the miRNA genes we developed a new tool (CPPP). We showed that miRNA genes can be transcribed from promoters located several kilobases away and that their promoters share the same general features as those of protein coding genes. Finally, we found evidence that as many as 26% of the intragenic miRNAs may be transcribed from their own unique promoters. Conclusion: miRNA promoters have similar features to those of protein coding genes, but miRNA transcript organization is more complex. © 2009 Corcoran et al

Ecological Modeling of Aedes aegypti (L.) Pupal Production in Rural Kamphaeng Phet, Thailand

Background - Aedes aegypti (L.) is the primary vector of dengue, the most important arboviral infection globally. Until an effective vaccine is licensed and rigorously administered, Ae. aegypti control remains the principal tool in preventing and curtailing dengue transmission. Accurate predictions of vector populations are required to assess control methods and develop effective population reduction strategies. Ae. aegypti develops primarily in artificial water holding containers. Release recapture studies indicate that most adult Ae. aegypti do not disperse over long distances. We expect, therefore, that containers in an area of high development site density are more likely to be oviposition sites and to be more frequently used as oviposition sites than containers that are relatively isolated from other development sites. After accounting for individual container characteristics, containers more frequently used as oviposition sites are likely to produce adult mosquitoes consistently and at a higher rate. To this point, most studies of Ae. aegypti populations ignore the spatial density of larval development sites. Methodology - Pupal surveys were carried out from 2004 to 2007 in rural Kamphaeng Phet, Thailand. In total, 84,840 samples of water holding containers were used to estimate model parameters. Regression modeling was used to assess the effect of larval development site density, access to piped water, and seasonal variation on container productivity. A varying-coefficients model was employed to account for the large differences in productivity between container types. A two-part modeling structure, called a hurdle model, accounts for the large number of zeroes and overdispersion present in pupal population counts. Findings - The number of suitable larval development sites and their density in the environment were the primary determinants of the distribution and abundance of Ae. aegypti pupae. The productivity of most container types increased significantly as habitat density increased. An ecological approach, accounting for development site density, is appropriate for predicting Ae. aegypti population levels and developing efficient vector control program

Stochastic Gravity: Theory and Applications

Whereas semiclassical gravity is based on the semiclassical Einstein equation with sources given by the expectation value of the stress-energy tensor of quantum fields, stochastic semiclassical gravity is based on the Einstein-Langevin equation, which has in addition sources due to the noise kernel.In the first part, we describe the fundamentals of this new theory via two approaches: the axiomatic and the functional. In the second part, we describe three applications of stochastic gravity theory. First, we consider metric perturbations in a Minkowski spacetime: we compute the two-point correlation functions for the linearized Einstein tensor and for the metric perturbations. Second, we discuss structure formation from the stochastic gravity viewpoint. Third, we discuss the backreaction of Hawking radiation in the gravitational background of a quasi-static black hole.Comment: 75 pages, no figures, submitted to Living Reviews in Relativit