A Monte Carlo model of DNA double-strand break clustering and rejoining kinetics for the analysis of pulsed-field gel electrophoresis data

In studies of radiation-induced DNA fragmentation and repair, analytical models may provide rapid and easy-to-use methods to test simple hypotheses regarding the breakage and rejoining mechanisms involved. The random breakage model, according to which lesions are distributed uniformly and independently of each other along the DNA, has been the model most used to describe spatial distribution of radiation-induced DNA damage. Recently several mechanistic approaches have been proposed that model clustered damage to DNA. In general, such approaches focus on the study of initial radiation-induced DNA damage and repair, without considering the effects of additional (unwanted and unavoidable) fragmentation that may take place during the experimental procedures. While most approaches, including measurement of total DNA mass below a specified value, allow for the occurrence of background experimental damage by means of simple subtractive procedures, a more detailed analysis of DNA fragmentation necessitates a more accurate treatment. We have developed a new, relatively simple model of DNA breakage and the resulting rejoining kinetics of broken fragments. Initial radiation-induced DNA damage is simulated using a clustered breakage approach, with three free parameters: the number of independently located clusters, each containing several DNA double-strand breaks (DSBs), the average number of DSBs within a cluster (multiplicity of the cluster), and the maximum allowed radius within which DSBs belonging to the same cluster are distributed. Random breakage is simulated as a special case of the DSB clustering procedure. When the model is applied to the analysis of DNA fragmentation as measured with pulsed-field gel electrophoresis (PFGE), the hypothesis that DSBs in proximity rejoin at a different rate from that of sparse isolated breaks can be tested, since the kinetics of rejoining of fragments of varying size may be followed by means of computer simulations. The problem of how to account for background damage from experimental handling is also carefully considered. We have shown that the conventional procedure of subtracting the background damage from the experimental data may lead to erroneous conclusions during the analysis of both initial fragmentation and DSB rejoining. Despite its relative simplicity, the method presented allows both the quantitative and qualitative description of radiation-induced DNA fragmentation and subsequent rejoining of double-stranded DNA fragments. (C) 2004 by Radiation Research Society.

Evidence for complexity at the nanometer scale of radiation-induced DNA DSBs as a determinant of rejoining kinetics

The rejoining kinetics of double-stranded DNA fragments, along with measurements of residual damage after postirradiation incubation, are often used as indicators of the biological relevance of the damage induced by ionizing radiation of different qualities. Although it is widely accepted that high-LET radiation-induced double-strand breaks (DSBs) tend to rejoin with kinetics slower than low-LET radiation-induced DSBs, possibly due to the complexity of the DSB itself, the nature of a slowly rejoining DSB-containing DNA lesion remains unknown. Using an approach that combines pulsed-field gel electrophoresis (PFGE) of fragmented DNA from human skin fibroblasts and a recently developed Monte Carlo simulation of radiation-induced DNA breakage and rejoining kinetics, we have tested the role of DSB-containing DNA lesions in the 8-kbp-5.7-Mbp fragment size range in determining the DSB rejoining kinetics. It is found that with low-LET X rays or high LET alpha particles, DSB rejoining kinetics data obtained with PFGE can be computer-simulated assuming that DSB rejoining kinetics does not depend on spacing of breaks along the chromosomes. After analysis of DNA fragmentation profiles, the rejoining kinetics of X-ray-induced DSBs could be fitted by two components: a fast component with a half-life of 0.9 +/- 0.5 h and a slow component with a half-life of 16 +/- 9 h. For a particles, a fast component with a half-life of 0.7 +/- 0.4 h and a slow component with a half-life of 12 5 h along with a residual fraction of unrepaired breaks accounting for 8% of the initial damage were observed. In summary, it is shown that genomic proximity of breaks along a chromosome does not determine the rejoining kinetics, so the slowly rejoining breaks induced with higher frequencies after exposure to high-LET radiation (0.37 +/- 0.12) relative to low-LET radiation (0.22 +/- 0.07) can be explained on the basis of lesion complexity at the nanometer scale, known as locally multiply damaged sites. (c) 2005 by Radiation Research Society.

Notes from Some Small Countries: A Study of the 'New Punitiveness' in Ireland, Scotland and New Zealand

In recent years there has been a remarkable surge of interest in the concept of punitiveness in theoretical criminology. Accounts serve to emphasise rupture over continuity, drawing attention to the increased focus on managerialism, risk and expressive penal policies in countries such as England and the US. Criticisms of these accounts have drawn attention to the weak empirical base for such assertions and the continued relevance of local cultural, historical and political conditions in mediating the effect of more punitive trends. In light of the relative neglect of smaller jurisdictions in this literature it was decided to locate these debates in three small common law jurisdictions, namely, Ireland, Scotland and New Zealand over the period 1976-2006 with a view to assessing the empirical evidence for penal change. This was done using a broader definition of punitiveness than normally employed incorporating indices relating to the ‘front end’ (eg police powers) as well as the ‘back end’ (eg prison and probation) of the criminal justice system. Data were collected on the three case studies using a multi-method approach involving examination of extensive quantitative data, interviews with key criminal justice stakeholders and documentary analysis. The data provide some support for the ‘new punitiveness’ thesis in these countries through a pattern of increased legislative activity aimed at controlling violent and sexual offenders and significant increases in the lengths of sentences imposed. However, analysis of qualitative data and a larger number of variables reveals distinctly different patterns of punitiveness over the thirty year period in the three countries. It is argued that the study holds important lessons for comparative criminology into the ‘new punitiveness’. There is a need for qualitative as well as quantitative data; for multiple rather than singular indices across a wide range of areas (juvenile justice, prison conditions, etc); and for ‘front end’ as well as ‘back end’ indices.

Prospective control of manual interceptive actions:comparative simulations of extant and new model constructs

Two prospective controllers of hand movements in catching-both based on required velocity control-were simulated. Under certain conditions, this required velocity control led to overshoots of the future interception point. These overshoots were absent in pertinent experiments. To remedy this shortcoming, the required velocity model was reformulated in terms of a neural network, the Vector Integration To Endpoint model, to create a Required Velocity Integration To Endpoint model. Addition of a parallel relative velocity channel, resulting in the Relative and Required Velocity Integration To Endpoint model, provided a better account for the experimentally observed kinematics than the existing, purely behavioral models. Simulations of reaching to intercept decelerating and accelerating objects in the presence of background motion were performed to make distinct predictions for future experiments.

Choice of contracts in the British National Health Service: An empirical study

Following major reforms of the British National Health Service (NHS) in 1990, the roles of purchasing and providing health services were separated, with the relationship between purchasers and providers governed by contracts. Using a mixed multinomial logit analysis, we show how this policy shift led to a selection of contracts that is consistent with the predictions of a simple model, based on contract theory, in which the characteristics of the health services being purchased and of the contracting parties influence the choice of contract form. The paper thus provides evidence in support of the practical relevance of theory in understanding health care market reform. © 2008 Elsevier B.V. All rights reserved.

Welfare regime and social class variation in poverty and economic vulnerability in Europe: an analysis of EU-SILC

In this paper we address a set of interrelated issues. These comprise increasing concerns about reliance on nationally based income poverty measures in the context of EU enlargement, the relative merits of one-dimensional versus multidimensional approaches to poverty and social exclusion and the continuing relevance of class-based explanations of life chances. When identifying economically vulnerable groups we find that, contrary to the situation with national income poverty measures, levels of vulnerability vary systematically across welfare regimes. The multidimensional profile of the economically vulnerable sharply differentiates them from the remainder of the population. While they are also characterised by distinctively higher levels of multiple deprivation, a substantial majority of the economically vulnerable are not exposed to such deprivation. Unlike the national relative income approach, the focus on economic vulnerability reveals a pattern of class differentiation that is not dominated by the contrast between the self-employed and all others. In contrast to a European-wide relative income approach, it also simultaneously captures the fact that absolute levels of vulnerability are distinctively higher among the lower social classes in the less comprehensive and generous welfare regimes while class relativities are significantly sharper at the other end of the spectrum.

Marginalization, deprivation, and fatalism in the Republic of Ireland. Class and underclass perspectives

The emergence of large-scale long-term unemployment in the Republic of Ireland suggests that it might provide an interesting case to which to apply the concept of an 'underclass'. In this paper we explore the relationship between labour-market marginality, deprivation, and fatalism. The available evidence in relation to both social isolation and milieu effects suggests that the term 'underclass' can have only a very limited applicability in the Irish case. Instead, what we ate confronted with is different types of working-class marginalization arising from the rapid and uneven nature of class transformation in Ireland and changing patterns of emigration. In relation to what we have termed 'pervasive marginalization' the costs of economic change have been borne disproportionately by those members of the younger cohorts originating in the lower working class rather than by those in particular locations. The evidence relating to the social and psychological consequences of labour-market detachment, rather than providing support for the value of an 'underclass' perspective, confirms the continued relevance of class analysis.

Multidimensional modelling of X-ray spectra for AGN accretion disc outflows

We use a multidimensional Monte Carlo code to compute X-ray spectra for a variety of active galactic nucleus (AGN) disc-wind outflow geometries. We focus on the formation of blueshifted absorption features in the Fe K band and show that line features similar to those which have been reported in observations are often produced for lines of sight through disc-wind geometries. We also discuss the formation of other spectral features in highly ionized outflows. In particular, we show that, for sufficiently high wind densities, moderately strong Fe K emission lines can form and that electron scattering in the flow may cause these lines to develop extended red wings. We illustrate the potential relevance of such models to the interpretation of real X-ray data by comparison with observations of a well-known AGN, Mrk 766. Journal compilation © 2008 RAS.

Demographic and psychosocial characteristics of asthmatic children in a Canadian rehabilitation setting

This study investigated the demographic and psychosocial characteristics of patients attending a residential treatment program for children with asthma. Measures of background information and standardized psychosocial variables were administered to 54 inpatients over an 18-month period. Typically, our patients presented with moderate to severe chronic asthma, mostly diagnosed before 3 years of age and often associated with atopic dermatitis. The families exhibited normal levels of emotional bonding and flexibility in response to stress. Psychosocially, most children were experiencing behavioral and school-related problems, with 6-11-year-old boys exhibiting global social competency problems as well. Girls exhibited lower self-esteem. Locus of control was within the normal range for all age groups. Half the children had not previously attended an asthma education program and two-thirds of the family members either smoked and/or had a pet. The treatment implications of these characteristics of our asthma population were considered.

The Interlaboratory Robustness Of Next-Generation Sequencing (IRON) Study Phase II: Deep-Sequencing Analyses Of Hematological Malignancies Performed In 8,867 Cases By An International Network Involving 27 Laboratories

Introduction: Amplicon deep-sequencing using second-generation sequencing technology is an innovative molecular diagnostic technique and enables a highly-sensitive detection of mutations. As an international consortium we had investigated previously the robustness, precision, and reproducibility of 454 amplicon next-generation sequencing (NGS) across 10 laboratories from 8 countries (Leukemia, 2011;25:1840-8).

Aims: In Phase II of the study, we established distinct working groups for various hematological malignancies, i.e. acute myeloid leukemia (AML), acute lymphoblastic leukemia (ALL), chronic lymphocytic leukemia (CLL), chronic myelogenous leukemia (CML), myelodysplastic syndromes (MDS), myeloproliferative neoplasms (MPN), and multiple myeloma. Currently, 27 laboratories from 13 countries are part of this research consortium. In total, 74 gene targets were selected by the working groups and amplicons were developed for a NGS deep-sequencing assay (454 Life Sciences, Branford, CT). A data analysis pipeline was developed to standardize mutation interpretation both for accessing raw data (Roche Amplicon Variant Analyzer, 454 Life Sciences) and variant interpretation (Sequence Pilot, JSI Medical Systems, Kippenheim, Germany).

Results: We will report on the design, standardization, quality control aspects, landscape of mutations, as well as the prognostic and predictive utility of this assay in a cohort of 8,867 cases. Overall, 1,146 primer sequences were designed and tested. In detail, for example in AML, 924 cases had been screened for CEBPA mutations. RUNX1 mutations were analyzed in 1,888 cases applying the deep-sequencing read counts to study the stability of such mutations at relapse and their utility as a biomarker to detect residual disease. Analyses of DNMT3A (n=1,041) were focused to perform landscape investigations and to address the prognostic relevance. Additionally, this working group is focusing on TET2, ASXL1, and TP53 analyses. A novel prognostic model is being developed allowing stratification of AML into prognostic subgroups based on molecular markers only. In ALL, 1,124 pediatric and adult cases have been screened, including 763 assays for TP53 mutations both at diagnosis and relapse of ALL. Pediatric and adult leukemia expert labs developed additional content to study the mutation incidence of other B and T lineage markers such as IKZF1, JAK2, IL7R, PAX5, EP300, LEF1, CRLF2, PHF6, WT1, JAK1, PTEN, AKT1, IL7R, NOTCH1, CREBBP, or FBXW7. Further, the molecular landscape of CLL is changing rapidly. As such, a separate working group focused on analyses including NOTCH1, SF3B1, MYD88, XPO1, FBXW7 and BIRC3. Currently, 922 cases were screened to investigate the range of mutational burden of NOTCH1 mutations for their prognostic relevance. In MDS, RUNX1 mutation analyses were performed in 977 cases. The prognostic relevance of TP53 mutations in MDS was assessed in additional 327 cases, including isolated deletions of chromosome 5q. Next, content was developed targeting genes of the cellular splicing component, e.g. SF3B1, SRSF2, U2AF1, and ZRSR2. In BCR-ABL1-negative MPN, nine genes of interest (JAK2, MPL, TET2, CBL, KRAS, EZH2, IDH1, IDH2, ASXL1) have been analyzed in a cohort of 155 primary myelofibrosis cases searching for novel somatic mutations and addressing their relevance for disease progression and leukemia transformation. Moreover, an assay was developed and applied to CMML cases allowing the simultaneous analysis of 25 leukemia-associated target genes in a single sequencing run using just 20 ng of starting DNA. Finally, nine laboratories are studying CML, applying ultra-deep sequencing of the BCR-ABL1 tyrosine kinase domain. Analyses were performed on 615 cases investigating the dynamics of expansion of mutated clones under various tyrosine kinase inhibitor therapies.

Conclusion: Molecular characterization of hematological malignancies today requires high diagnostic sensitivity and specificity. As part of the IRON-II study, a network of laboratories analyzed a variety of disease entities applying amplicon-based NGS assays. Importantly, the consortium not only standardized assay design for disease-specific panels, but also achieved consensus on a common data analysis pipeline for mutation interpretation. Distinct working groups have been forged to address scientific tasks and in total 8,867 cases had been analyzed thus far.

PIC simulation of a thermal anisotropy-driven Weibel instability in a circular rarefaction wave

The expansion of an initially unmagnetized planar rarefaction wave has recently been shown to trigger a thermal anisotropy-driven Weibel instability (TAWI), which can generate magnetic fields from noise levels. It is examined here whether the TAWI can also grow in a curved rarefaction wave. The expansion of an initially unmagnetized circular plasma cloud, which consists of protons and hot electrons, into a vacuum is modelled for this purpose with a two-dimensional particle-in-cell (PIC) simulation. It is shown that the momentum transfer from the electrons to the radially accelerating protons can indeed trigger a TAWI. Radial current channels form and the aperiodic growth of a magnetowave is observed, which has a magnetic field that is oriented orthogonal to the simulation plane. The induced electric field implies that the electron density gradient is no longer parallel to the electric field. Evidence is presented here that this electric field modification triggers a environments, which are needed to explain the electromagnetic emissions by astrophysical jets. It is outlined how this instability could be examined experimentally.second magnetic instability, which results in a rotational low-frequency magnetowave. The relevance of the TAWI is discussed for the growth of small-scale magnetic fields in astrophysical

Fundus autofluorescence in the diagnosis of cystoid macular oedema

Aim: To determine the sensitivity and specificity of the non-invasive imaging technique, fundus autofluorescence (AF), in the diagnosis of cystoid macular oedema (CMO), using fluorescein angiography as the reference standard. Design: Retrospective, consecutive, observational case series. Methods: Ninety-six consecutive patients with CMO suspected clinically were selected from the AF database of the Retina Unit, Ophthalmology Department, Grampian University Hospitals-NHS Trust, between August 2004 and June 2006. Only patients in whom CMO was secondary to (1) cataract extraction, (2) inherited retinopathies, (3) inflammatory eye disease or (4) idiopathic cases were included in this study. Only patients in whom AF images had been performed within 2 weeks of FFA and, when obtained following FFA, there was a minimum gap of 4 days ("washing out" period), were considered eligible for this study. A total of 34 eyes from 34 patients were eligible and were included in this study. FFA was used as the reference test to confirm the presence of CMO, and, based on fluorescein angiography (FFA), CMO was graded as either mild or florid. AF images were examined in a masked fashion for the presence or absence of CMO. The sensitivity and specificity of AF in detecting CMO were then calculated. Results: CMO was seen on AF imaging as round or oval areas at the fovea with an AF signal similar to that of background levels. At this site (fovea), the AF signal is usually reduced compared with background, due to the blockage caused by luteal pigment. The diagnosis of CMO based on AF imaging had 81% sensitivity and 69% specificity when compared with the reference standard FFA. Based on the FFA, there were 12 cases of florid CMO and eight of mild CMO. Of the former, CMO was detected with AF imaging in 100% (12/12 eyes), and of the latter, in 50% (4/8 eyes). Conclusions: AF imaging can be used as a rapid, non-invasive technique in the diagnosis of CMO.

Reproducibility of fundus autofluorescence measurements obtained using a confocal scanning laser ophthalmoscope

Aim - To evaluate the reproducibility of the background fundus autofluorescence measurements obtained using a confocal scanning laser ophthalmoscope. Methods - 10 normal volunteers and 10 patients with retinal disease were included in the study. One eye per subject was chosen randomly. Five images of the same eye of each individual were obtained, after pupillary dilatation, by two investigators using a confocal scanning laser ophthalmoscope. Background fundus autofluorescence was measured at 7 degrees temporal to the fovea in normal volunteers and between 7 and 15 degrees temporal to the fovea in patients. Within session reproducibility of the measurements obtained by each investigator and interobserver reproducibility were evaluated. Results - For investigator 1 the median values of fundus autofluorescence obtained were 31.9 units for normal volunteers and 27.3 units for patients. The median largest difference in readings in normal volunteers was 5.7 units (range 1.4-13.5 units) and in patients 4.2 units (1.5-15.1 units). For investigator 2 the median values of fundus autofluorescence obtained were 28.9 units for normal volunteers and 27.4 units for patients. The median largest difference in readings in normal volunteers was 3.6 units (2.7-11.7 units), and in patients 4.1 units (1.5-9.3 units). The median interobserver difference in readings in normal volunteers was 3.3 units and for patients 6.6 units. The median greatest interobserver difference in measurements obtained for normal volunteers was 8.8 units (8.4-23.0 units) and for patients 11.1 units (7.1-40.8 units). Conclusion - Within session reproducibility of the measurements of background fundus autofluorescence was satisfactory. Although interobserver reproducibility was moderate, the variability of the measurements of fundus autofluorescence between observers appears to be small when compared with variation in fundus autofluorescence with age and disease.

Charity accountability in the UK: through the eyes of the donor

Purpose – The purpose of this paper is to explore accountability from the perspective of charity donors.

Design/methodology/approach – The research utilises semi-structured interviews with a range of donors. In addition, it summarises the main findings from key related research (that uses document content analysis and questionnaire surveys) as a basis for better appreciating donor engagement.

Findings – This research offers evidence that while donors are viewed as the key stakeholder to whom a charity should be accountable, the relevance of the information commonly disclosed in formal charity communications is questionable. This is viewed as significant in terms of small dependent donors, although less critical in the case of non-dependent large donors who have power to demand individualised information. However, although all donors do not particularly engage with these formal communications, they are viewed by them as having significance and their production and publication serves as an important legitimising tool in the sector (enhancing trust and reputation).

Research limitations/implications – This research is based on semi-structured interviews with individual small donors and large institutional donors to large UK charities and therefore any generalising of the conclusions beyond large charities, and beyond the UK, should be undertaken with care. In addition, it focuses solely on the perceptions of donors, and other stakeholder groups are also important in this process.

Originality/value – Despite the widespread acceptance that charities have a duty to discharge accountability to their stakeholders, there is limited knowledge of their information needs and whether the performance information currently being disclosed fulfils them. This study provides a unique insight into the perspective of a key stakeholder group (donors) with respect to accountability.

NF-κB is a critical mediator of BRCA1-induced chemoresistance

BRCA1 mediates resistance to apoptosis in response to DNA-damaging agents, causing BRCA1 wild-type tumours to be significantly more resistant to DNA damage than their mutant counterparts. In this study, we demonstrate that following treatment with the DNA-damaging agents, etoposide or camptothecin, BRCA1 is required for the activation of nuclear factor-?B (NF-?B), and that BRCA1 and NF-?B cooperate to regulate the expression of the NF-?B antiapoptotic targets BCL2 and XIAP. We show that BRCA1 and the NF-?B subunit p65/RelA associate constitutively, whereas the p50 NF-?B subunit associates with BRCA1 only upon DNA damage treatment. Consistent with this BRCA1 and p65 are present constitutively on the promoters of BCL2 and XIAP, whereas p50 is recruited to these promoters only in damage treated cells. Importantly, we demonstrate that the recruitment of p50 onto the promoters of BCL2 and XIAP is dependent upon BRCA1, but independent of its NF-?B partner subunit p65. The functional relevance of NF-?B activation by BRCA1 in response to etoposide and camptothecin is demonstrated by the significantly reduced survival of BRCA1 wild-type cells upon NF-?B inhibition. This study identifies a novel BRCA1-p50 complex, and demonstrates for the first time that NF-?B is required for BRCA1-mediated resistance to DNA damage. It reveals a functional interdependence between BRCA1 and NF-?B, further elucidating the role played by NF-?B in mediating cellular resistance of BRCA1 wild-type tumours to DNA-damaging agents.