Clinical Utility of Microarray-Based Gene Expression Profiling in the Diagnosis and Subclassification of Leukemia: Report From the International Microarray Innovations in Leukemia Study Group

The Microarray Innovations in Leukemia study assessed the clinical utility of gene expression profiling as a single test to subtype leukemias into conventional categories of myeloid and lymphoid malignancies. METHODS: The investigation was performed in 11 laboratories across three continents and included 3,334 patients. An exploratory retrospective stage I study was designed for biomarker discovery and generated whole-genome expression profiles from 2,143 patients with leukemias and myelodysplastic syndromes. The gene expression profiling-based diagnostic accuracy was further validated in a prospective second study stage of an independent cohort of 1,191 patients. RESULTS: On the basis of 2,096 samples, the stage I study achieved 92.2% classification accuracy for all 18 distinct classes investigated (median specificity of 99.7%). In a second cohort of 1,152 prospectively collected patients, a classification scheme reached 95.6% median sensitivity and 99.8% median specificity for 14 standard subtypes of acute leukemia (eight acute lymphoblastic leukemia and six acute myeloid leukemia classes, n = 693). In 29 (57%) of 51 discrepant cases, the microarray results had outperformed routine diagnostic methods. CONCLUSION: Gene expression profiling is a robust technology for the diagnosis of hematologic malignancies with high accuracy. It may complement current diagnostic algorithms and could offer a reliable platform for patients who lack access to today's state-of-the-art diagnostic work-up. Our comprehensive gene expression data set will be submitted to the public domain to foster research focusing on the molecular understanding of leukemias

Translating policy into practice: A case study in the secondary prevention of coronary heart disease

Background: This paper focuses on the relationships between health ‘policy’ as it is embodied in official documentation, and health ‘practice’ as reported and reflected on in the talk of policy makers, health professionals and patients. The specific context for the study involves a comparison of policies relating to the secondary prevention of coronary heart disease (CHD) in the two jurisdictions of Ireland – involving as they do a predominantly state funded (National Health Service) system in the north and a mixed healthcare economy in the south. The key question is to determine how the rhetoric of health policy as contained in policy documents connects to, and gets translated into practice and action.

Methods: The data sources for the study include relevant healthcare policy documents (N=5) and progress reports (N=6) in the two Irish jurisdictions, and semi-structured interviews with a range of policy-makers (N=28), practice nurses (14), general practitioners (12) and patients (13) to explore their awareness of the documents’ contents and how they saw the impact of ‘policy’ on primary care practice.

Results: The findings suggest that although strategic policy documents can be useful for highlighting and channelling attention to health issues that require concerted action, they have little impact on what either professionals or lay people do.

Conclusion: To influence the latter and to encourage a systematic approach to the delivery of health care it seems likely that contractual arrangements – specifying tasks to be undertaken and methods for monitoring and reporting on activity - are required.

Direct Quantification of Inorganic Polyphosphate in Microbial Cells Using 4 '-6-Diamidino-2-Phenylindole (DAPI)

Inorganic polyphosphate (polyP) is increasingly being recognized as an important phosphorus sink within the environment, playing a central role in phosphorus exchange and phosphogenesis. Yet despite the significant advances made in polyP research there is a lack of rapid and efficient analytical approaches for the quantification of polyP accumulation in microbial cultures and environmental samples. A major drawback is the need to extract polyP from cells prior to analysis. Due to extraction inefficiencies this can lead to an underestimation of both intracellular polyP levels and its environmental pool size: we observed 23-58% loss of polyP using standard solutions and current protocols. Here we report a direct fluorescence based DAPI assay system which removes the requirement for prior polyP extraction before quantification. This increased the efficiency of polyP detection by 28-55% in microbial cultures suggesting quantitative measurement of the intracellular polyP pool. It provides a direct polyP assay which combines quantification capability with technical simplicity. This is an important step forward in our ability to explore the role of polyP in cellular biology and biogeochemical nutrient cycling.

AUDIT OF ANTIBIOTIC USAGE IN A MEDIUM-SIZED GENERAL-HOSPITAL OVER AN 11-YEAR PERIOD - THE IMPACT OF ANTIBIOTIC POLICIES

The objective of the present study was to evaluate trends in antibiotic expenditure over an 11-year period (1982-1992) in a 370-bed district general hospital in Northern Ireland and to examine the impact of two separate antibiotic policies on antibiotic usage. A further objective was to examine the attitudes of prescribers to the second policy. Drug utilization review was used to collect information on antibiotic expenditure and usage before and after introduction of separate antibiotic policies in 1985 (not intensively monitored) and 1989 (intensively monitored). A mail questionnaire was used to determine the attitudes of prescribers. The first policy (1985) showed no benefits with regard to the number of antibiotic entities stocked (45 before, 45 after), number of dosage units issued (9.35 increase) or expenditure (33.35 increase). The 1989 policy led to significant reductions in the number of antibiotic entities stocked (28.9%), number of antibiotics issued (11.9%) and expenditure (6.1%). Expenditure began to spiral upwards when active monitoring of the second policy was suspended. The majority of prescribers (87.2%) who responded to the questionnaire (56.5% response rate) felt that the 1989 policy made a positive contribution to antibiotic usage in the hospital.

Physiological effects of platyhelminth RFamide peptides on muscle-strip preparations of Fasciola hepatica (Trematoda: Digenea)

The effects of each of the known platyhelminth neuropeptides were determined on muscle-strip preparations from the liver fluke, Fasciola hepatica. The activity of synthetic replicates of the C-terminal nonapeptide of neuropeptide F (NPF9, Moniezia expansa), and the FMRFamide-related peptides (FaRPs), GNFFRFamide, RYIRFamide, GYIRFamide and YIRFamide, were examined. Muscle-strip activity was recorded from 1 mm segments of muscle prepared from 28 to 32-day-old worms, using a photo-optic transducer system. None of the peptides (less than or equal to 10 mu M) altered baseline tension significantly; however, each of the peptides increased the amplitude and frequency of muscle contraction. The threshold for activity of each of the peptides examined was, respectively, 1 nM (RYIRFamide), 0.3 mu M (GYIRFamide and YIRFamide), and 10 mu M (GNFFRFamide and NPF9). All of the effects were reversible and repeatable, following wash-out. Muscle-strip integrity was tested following experimentation, using arecoline (10 mu M) and high-K+ bathing medium (90 mM K+).

Analysis of Betaine and Choline Contents of Aleurone, Bran, and Flour Fractions of Wheat (Triticum aestivum L.) Using 1H Nuclear Magnetic Resonance (NMR) Spectroscopy

In conventional milling, the aleurone layer is combined with the bran fraction. Studies indicate that the bran fraction of wheat contains the majority of the phytonutrients betaine and choline, with relatively minor concentrations in the refined flour. This present study suggests that the wheat aleurone layer (Triticum aestivum L. cv. Tiger) contains the greatest concentration of both betaine and choline (1553.44 and 209.80 mg/100 g of sample, respectively). The bran fraction contained 866.94 and 101.95 mg/100 g of sample of betaine and choline, respectively, while the flour fraction contained 23.30 mg/100 g of sample (betaine) and 28.0 mg/100 g of sample (choline). The betaine content for
the bran was lower, and the choline content was higher compared to previous studies, although it is known that there is large variation in betaine and choline contents between wheat cultivars. The ratio of betaine/choline in the aleurone fraction was approximately 7:1; in the bran, the ratio was approximately 8:1; and in the flour fraction, the ratio was approximately 1:1. The study further
emphasizes the superior phytonutrient composition of the aleurone layer.
INTRODUCTION
Wheat is a valuable source of betaine, choline (1, 2), B
vitamins, vitamin E, and a number of minerals, including iron,
zinc, magnesium, and phosphorus (3). Epidemiological studies
indicate that whole-grain consumption is protective against
several chronic diseases (4-12). It has not been fully elucidated
how whole-grain cereals or specific fractions (13) exert their
protective effect, but it is thought to be due to their content of
several nutrients associated with the reduced risk of disease.
Conventionally, whole grain is separated during milling into
bran, germ, and flour (14). The nutrient composition of these
fractions differ markedly; refined wheat flour contains approximately
50% less vitamins and minerals than whole-grain
flour (

“It’s like a problem that doesn’t exist”: The emotional well-being of mothers caring for a child with brain injury.

Background: Although research has shown that significant burden and adverse psychological impact are associated with caring for a child with brain injury, limited knowledge exists concerning the qualitative experience and impact of this burden.
Objective: To provide an account of the experiences of mothers who care for a childhood survivor of brain injury.
Research design: Postal survey.
Methods and procedures: A self-report questionnaire was sent to a consecutive sample of mothers (n=86) of children (aged 8-28) with acquired brain injury, registered with a UK children’s brain injury charity. Five essay style questions enabled mothers to reflect on and describe at length their caring experiences, with particular emphasis placed on the perceived impact on emotional well-being.
Main outcomes and results: Thematic analysis identified five key themes: Perpetually Anxious, The Guilty Carer, The Labour of Caring, A Self-Conscious Apologist and Perpetually Grieving. Collectively, these themes highlight two core processes shaping mothers’ caring experiences and concomitant mental well-being. Firstly, the collective and enduring nature of caregiver burden over time. Second, the crucial role played by socio-cultural values in perpetuating caregiver burden.
Conclusions: Societal norms, particularly those relating to the nature and outcome of brain injury and motherhood, serve to marginalise mothers and increase feelings of isolation. Findings suggest the value of peer support programs as an effective means of providing appropriate social support.

Temporal variation in the water chemistry of northern Victoria Land lakes (Antarctica)

Concentrations of major ions, silicate and nutrients (total N and P) were measured in samples of surface water from 28 lakes in ice-free areas of northern Victoria Land (East Antarctica). Sixteen lakes were sampled during austral summers 2001/02, 2003/04, 2004/05 and 2005/06 to assess temporal variation in water chemistry. Although samples showed a wide range in ion concentrations, their composition mainly reflected that of seawater. In general, as the distance from the sea increased, the input of elements from the marine environment (through aerosols and seabirds) decreased and there was an increase in nitrate and sulfate concentrations. Antarctic lakes lack outflows and during the austral summer the melting and/or ablation of ice cover, water evaporation and leaching processes in dry soils determine a progressive increase in water ion concentrations. During the five-year monitoring survey, no statistically significant variation in the water chemistry were detected, except for a slight (hardly significant) increase in TN concentrations. However, Canonical Correspondence Analysis (CCA) indicated that other factors besides distance from the sea, the presence of nesting seabirds, the sampling time and percentage of ice cover affect the composition of water in Antarctic cold desert environments.

Establishing optimal quantitative-polymerase chain reaction assays for routine diagnosis and tracking of minimal residual disease in JAK2-V617F-associated myeloproliferative neoplasms:a joint European LeukemiaNet/MPN&MPNr-EuroNet (COST action BM0902) study

Reliable detection of JAK2-V617F is critical for accurate diagnosis of myeloproliferative neoplasms (MPNs); in addition, sensitive mutation-specific assays can be applied to monitor disease response. However, there has been no consistent approach to JAK2-V617F detection, with assays varying markedly in performance, affecting clinical utility. Therefore, we established a network of 12 laboratories from seven countries to systematically evaluate nine different DNA-based quantitative PCR (qPCR) assays, including those in widespread clinical use. Seven quality control rounds involving over 21,500 qPCR reactions were undertaken using centrally distributed cell line dilutions and plasmid controls. The two best-performing assays were tested on normal blood samples (n=100) to evaluate assay specificity, followed by analysis of serial samples from 28 patients transplanted for JAK2-V617F-positive disease. The most sensitive assay, which performed consistently across a range of qPCR platforms, predicted outcome following transplant, with the mutant allele detected a median of 22 weeks (range 6-85 weeks) before relapse. Four of seven patients achieved molecular remission following donor lymphocyte infusion, indicative of a graft vs MPN effect. This study has established a robust, reliable assay for sensitive JAK2-V617F detection, suitable for assessing response in clinical trials, predicting outcome and guiding management of patients undergoing allogeneic transplant.

A new radiocarbon chronology of Baumkirchen, stratotype for the onset of the Upper Wurmian in the Alps

ABSTRACT

The start of the Upper Wurmian in the Alps was marked by massive fluvioglacial aggradation prior to the arrival of the Central Alpine glaciers. In 1984, the Subcommission on European Quaternary Stratigraphy defined the clay pit of Baumkirchen (in the foreland of the Inn Valley, Austria) as the stratotype for the Middle to Upper Wurmian boundary in the Alps. Key for the selection of this site was its radiocarbon chronology, which still ranks among the most important datasets of this time interval in the Alps. In this study we re-sampled all available original plant specimens and established an accelerator mass spectrometry chronology which supersedes the published 40-year-old chronology. The new data show a much smaller scatter and yielded slightly older conventional radiocarbon dates clustering at ca. 31 C-14 ka BP. When calibrated using INTCAL13 the new data suggest that the sampled interval of 653-681 m in the clay pit was deposited 34-36 cal ka BP. Using two new radiocarbon dates of bone fragments found in the fluvioglacial gravel above the banded clays allows us to constrain the timing of the marked change from lacustrine to fluvioglacial sedimentation to ca. 32-33 cal ka BP, which suggests a possible link to the Heinrich 3 event in the North Atlantic. Copyright (c) 2013 John Wiley & Sons, Ltd.