95 research outputs found

    Developing site-specific guidelines for orchard soils based on bioaccessibility – Can it be done?

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    Horticultural land within the periurban fringe of NZ towns and cities increasingly is being developed for residential subdivision. Recent surveys have shown that concentrations of As, Cd, Cu, Pb, and ΣDDT (sum of DDT and its degradation products DDE and DDD) in such soils can exceed criteria protective of human health.¹ Soil ingestion is a key exposure pathway for non-volatile contaminants in soil. Currently in NZ, site-specific risk assessments and the derivation of soil guidelines protective of human health assume that all of the contaminant present in the soil is available for uptake and absorption by the human gastrointestinal tract. This assumption can overestimate health risks and has implications for the remediation of contaminated sites.² In comparison, the bioavailability of contaminants is considered when estimating exposure via dermal absorption and by ingestion of home-grown produce.³ Dermal absorption factors and plant uptake factors are included in the calculations for estimating exposures via these routes

    Student Housing Overview: Assessing Issues and Potential Options

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    report: 59 pp.; ill., digital file.This report sets out for the administration of the University of Winnipeg some of the contexts, considerations and principles necessary when undertaking any future housing-oriented development. The report provides general support for the proposition that – given demonstrated need for affordable and accessible housing in the neighbourhoods surrounding the University of Winnipeg – some kind of mixed-use development – incorporating affordable, accessible housing for a range of household types, as well as other services that would cater to both the student body and residents and organizations of the surrounding communities – would be beneficial to the university and be consistent with both the surrounding community as well as its overall strategic plan.University of Winnipeg. The report concludes with very general recommendation

    British signals intelligence and the 1916 Easter Rising in Ireland

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    Historians for decades have placed Room 40, the First World War British naval signals intelligence organization, at the centre of narratives about the British anticipation of and response to the Easter Rising in Ireland in 1916. A series of crucial decrypts of telegrams between the German embassy in Washington and Berlin, it has been believed, provided significant advance intelligence about the Rising before it took place. This article upends previous accounts by demonstrating that Room 40 possessed far less advance knowledge about the Rising than has been believed, with most of the supposedly key decrypts not being generated until months after the Rising had taken place

    Chromatin loop anchors are associated with genome instability in cancer and recombination hotspots in the germline

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    Abstract Background Chromatin loops form a basic unit of interphase nuclear organization, with chromatin loop anchor points providing contacts between regulatory regions and promoters. However, the mutational landscape at these anchor points remains under-studied. Here, we describe the unusual patterns of somatic mutations and germline variation associated with loop anchor points and explore the underlying features influencing these patterns. Results Analyses of whole genome sequencing datasets reveal that anchor points are strongly depleted for single nucleotide variants (SNVs) in tumours. Despite low SNV rates in their genomic neighbourhood, anchor points emerge as sites of evolutionary innovation, showing enrichment for structural variant (SV) breakpoints and a peak of SNVs at focal CTCF sites within the anchor points. Both CTCF-bound and non-CTCF anchor points harbour an excess of SV breakpoints in multiple tumour types and are prone to double-strand breaks in cell lines. Common fragile sites, which are hotspots for genome instability, also show elevated numbers of intersecting loop anchor points. Recurrently disrupted anchor points are enriched for genes with functions in cell cycle transitions and regions associated with predisposition to cancer. We also discover a novel class of CTCF-bound anchor points which overlap meiotic recombination hotspots and are enriched for the core PRDM9 binding motif, suggesting that the anchor points have been foci for diversity generated during recent human evolution. Conclusions We suggest that the unusual chromatin environment at loop anchor points underlies the elevated rates of variation observed, marking them as sites of regulatory importance but also genomic fragility

    Genome Sequencing of SHH Medulloblastoma Predicts Genotype-Related Response to Smoothened Inhibition

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    SummarySmoothened (SMO) inhibitors recently entered clinical trials for sonic-hedgehog-driven medulloblastoma (SHH-MB). Clinical response is highly variable. To understand the mechanism(s) of primary resistance and identify pathways cooperating with aberrant SHH signaling, we sequenced and profiled a large cohort of SHH-MBs (n = 133). SHH pathway mutations involved PTCH1 (across all age groups), SUFU (infants, including germline), and SMO (adults). Children >3 years old harbored an excess of downstream MYCN and GLI2 amplifications and frequent TP53 mutations, often in the germline, all of which were rare in infants and adults. Functional assays in different SHH-MB xenograft models demonstrated that SHH-MBs harboring a PTCH1 mutation were responsive to SMO inhibition, whereas tumors harboring an SUFU mutation or MYCN amplification were primarily resistant

    Prevalence of visits to five types of complementary and alternative medicine practitioners by the general population: A systematic review

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    Objective To systematically review surveys of 12-month prevalence of visits to complementary and alternative medicine (CAM) practitioners for five therapies: acupuncture, homeopathy, osteopathy, chiropractic, and medical herbalism. Methods Studies were identified via database searches to 2011. Study quality was assessed using a six-item tool. Results Forty-one surveys across 12 countries were included. Twenty-five (61%) met four of six quality criteria. Prevalence of visits by adults were (median, range): acupuncturists 1.4% (0.2–7.5%, N = 27 surveys), homeopaths 1.5% (0.2–2.9%, N = 20 surveys), osteopaths 1.9% (0.2–4.4%, N = 9 surveys), chiropractors 7.5% (0.3–16.7, N = 33 surveys), medical herbalists 0.9% (0.3–4.7%, N = 14 surveys). Estimates were slightly lower for children and higher for older adults. There was little change over the past 15–20 years. Conclusions This review summarises 12-month prevalence of visits to CAM practitioners in Europe, North America, Australia, East Asia, Saudi Arabia and Israel. A small but significant percentage of these general populations visit CAM practitioners each year

    Prevalence of complementary and alternative medicine (CAM) use by the general population: a systematic review and update

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    Objectives:  To update previous systematic reviews of 12-month prevalence of complementary and alternative medicine (CAM) use by general populations; to explore trends in CAM use by national populations; to develop and apply a brief tool for assessing methodological quality of published CAM-use prevalence surveys. Design:  Nine databases were searched for published studies from 1998 onwards. Studies prior to 1998 were identified from two previous systematic reviews. A six-item literature-based tool was devised to assess robustness and interpretability of CAM-use estimates. Results:  Fifty-one reports from 49 surveys conducted in 15 countries met the inclusion criteria. We extracted 32 estimates of 12-month prevalence of use of any CAM (range 9.8–76%) and 33 estimates of 12-month prevalence of visits to CAM practitioners (range 1.8–48.7%). Quality of methodological reporting was variable; 30/51 survey reports (59%) met four or more of six quality criteria. Estimates of 12-month prevalence of any CAM use (excluding prayer) from surveys using consistent measurement methods showed remarkable stability in Australia (49%, 52%, 52%; 1993, 2000, 2004) and USA (36%, 38%; 2002, 2007). Conclusions:  There was evidence of substantial CAM use in the 15 countries surveyed. Where national trends were discernable because of consistent measurement, there was no evidence to suggest a change in 12-month prevalence of CAM use since the previous systematic reviews were published in 2000. Periodic surveys are important to monitor population-level CAM use. Use of government-sponsored health surveys may enhance robustness of population-based prevalence estimates. Comparisons across countries could be improved by standardising approaches to data collection

    Signal transduction underlying the control of urinary bladder smooth muscle tone by muscarinic receptors and β-adrenoceptors

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    The normal physiological contraction of the urinary bladder, which is required for voiding, is predominantly mediated by muscarinic receptors, primarily the M3 subtype, with the M2 subtype providing a secondary backup role. Bladder relaxation, which is required for urine storage, is mediated by β-adrenoceptors, in most species involving a strong β3-component. An excessive stimulation of contraction or a reduced relaxation of the detrusor smooth muscle during the storage phase of the micturition cycle may contribute to bladder dysfunction known as the overactive bladder. Therefore, interference with the signal transduction of these receptors may be a viable approach to develop drugs for the treatment of overactive bladder. The prototypical signaling pathway of M3 receptors is activation of phospholipase C (PLC), and this pathway is also activated in the bladder. Nevertheless, PLC apparently contributes only in a very minor way to bladder contraction. Rather, muscarinic-receptor-mediated bladder contraction involves voltage-operated Ca2+ channels and Rho kinase. The prototypical signaling pathway of β-adrenoceptors is an activation of adenylyl cyclase with the subsequent formation of cAMP. Nevertheless, cAMP apparently contributes in a minor way only to β-adrenoceptor-mediated bladder relaxation. BKCa channels may play a greater role in β-adrenoceptor-mediated bladder relaxation. We conclude that apart from muscarinic receptor antagonists and β-adrenoceptor agonists, inhibitors of Rho kinase and activators of BKCa channels may have potential to treat an overactive bladder

    Functionality and feedback: a realist synthesis of the collation, interpretation and utilisation of patient-reported outcome measures data to improve patient care

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    Background: The feedback of patient-reported outcome measures (PROMs) data is intended to support the care of individual patients and to act as a quality improvement (QI) strategy. Objectives: To (1) identify the ideas and assumptions underlying how individual and aggregated PROMs data are intended to improve patient care, and (2) review the evidence to examine the circumstances in which and processes through which PROMs feedback improves patient care. Design: Two separate but related realist syntheses: (1) feedback of aggregate PROMs and performance data to improve patient care, and (2) feedback of individual PROMs data to improve patient care. Interventions: Aggregate – feedback and public reporting of PROMs, patient experience data and performance data to hospital providers and primary care organisations. Individual – feedback of PROMs in oncology, palliative care and the care of people with mental health problems in primary and secondary care settings. Main outcome measures: Aggregate – providers’ responses, attitudes and experiences of using PROMs and performance data to improve patient care. Individual – providers’ and patients’ experiences of using PROMs data to raise issues with clinicians, change clinicians’ communication practices, change patient management and improve patient well-being. Data sources: Searches of electronic databases and forwards and backwards citation tracking. Review methods: Realist synthesis to identify, test and refine programme theories about when, how and why PROMs feedback leads to improvements in patient care. Results: Providers were more likely to take steps to improve patient care in response to the feedback and public reporting of aggregate PROMs and performance data if they perceived that these data were credible, were aimed at improving patient care, and were timely and provided a clear indication of the source of the problem. However, implementing substantial and sustainable improvement to patient care required system-wide approaches. In the care of individual patients, PROMs function more as a tool to support patients in raising issues with clinicians than they do in substantially changing clinicians’ communication practices with patients. Patients valued both standardised and individualised PROMs as a tool to raise issues, but thought is required as to which patients may benefit and which may not. In settings such as palliative care and psychotherapy, clinicians viewed individualised PROMs as useful to build rapport and support the therapeutic process. PROMs feedback did not substantially shift clinicians’ communication practices or focus discussion on psychosocial issues; this required a shift in clinicians’ perceptions of their remit. Strengths and limitations: There was a paucity of research examining the feedback of aggregate PROMs data to providers, and we drew on evidence from interventions with similar programme theories (other forms of performance data) to test our theories. Conclusions: PROMs data act as ‘tin openers’ rather than ‘dials’. Providers need more support and guidance on how to collect their own internal data, how to rule out alternative explanations for their outlier status and how to explore the possible causes of their outlier status. There is also tension between PROMs as a QI strategy versus their use in the care of individual patients; PROMs that clinicians find useful in assessing patients, such as individualised measures, are not useful as indicators of service quality. Future work: Future research should (1) explore how differently performing providers have responded to aggregate PROMs feedback, and how organisations have collected PROMs data both for individual patient care and to improve service quality; and (2) explore whether or not and how incorporating PROMs into patients’ electronic records allows multiple different clinicians to receive PROMs feedback, discuss it with patients and act on the data to improve patient care

    Pan-cancer analysis of whole genomes

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    Cancer is driven by genetic change, and the advent of massively parallel sequencing has enabled systematic documentation of this variation at the whole-genome scale(1-3). Here we report the integrative analysis of 2,658 whole-cancer genomes and their matching normal tissues across 38 tumour types from the Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium of the International Cancer Genome Consortium (ICGC) and The Cancer Genome Atlas (TCGA). We describe the generation of the PCAWG resource, facilitated by international data sharing using compute clouds. On average, cancer genomes contained 4-5 driver mutations when combining coding and non-coding genomic elements; however, in around 5% of cases no drivers were identified, suggesting that cancer driver discovery is not yet complete. Chromothripsis, in which many clustered structural variants arise in a single catastrophic event, is frequently an early event in tumour evolution; in acral melanoma, for example, these events precede most somatic point mutations and affect several cancer-associated genes simultaneously. Cancers with abnormal telomere maintenance often originate from tissues with low replicative activity and show several mechanisms of preventing telomere attrition to critical levels. Common and rare germline variants affect patterns of somatic mutation, including point mutations, structural variants and somatic retrotransposition. A collection of papers from the PCAWG Consortium describes non-coding mutations that drive cancer beyond those in the TERT promoter(4); identifies new signatures of mutational processes that cause base substitutions, small insertions and deletions and structural variation(5,6); analyses timings and patterns of tumour evolution(7); describes the diverse transcriptional consequences of somatic mutation on splicing, expression levels, fusion genes and promoter activity(8,9); and evaluates a range of more-specialized features of cancer genomes(8,10-18).Peer reviewe
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