Next-Generation cDNA Screening for Oncogene and Resistance Phenotypes

There is a pressing need for methods to define the functional relevance of genetic alterations identified by next-generation sequencing of cancer specimens. We developed new approaches to efficiently construct full-length cDNA libraries from small amounts of total RNA, screen for transforming and resistance phenotypes, and deconvolute by next-generation sequencing. Using this platform, we screened a panel of cDNA libraries from primary specimens and cell lines in cytokine-dependent murine Ba/F3 cells. We demonstrate that cDNA library-based screening can efficiently identify DNA and RNA alterations that confer either cytokine-independent proliferation or resistance to targeted inhibitors, including RNA alterations and intergenic fusions. Using barcoded next-generation sequencing, we simultaneously deconvoluted cytokine-independent clones recovered after transduction of 21 cDNA libraries. This approach identified multiple gain-of-function alleles, including KRAS G12D, NRAS Q61K and an activating splice variant of ERBB2. This approach has broad applicability for identifying transcripts that confer proliferation, resistance and other phenotypes in vitro and potentially in vivo

Caledonian hot zone magmatism in the “Newer Granites”: insight from the Cluanie and Clunes plutons, Northern Scottish Highlands

Scottish “Newer” Granites record the evolution of the Caledonides resulting from Iapetus subduction and slab breakoff during the Silurian-Devonian Scandian Orogeny, but relationships between geodynamics, petrogenesis and emplacement are incomplete. Laser ablation U-Pb results from magmatic zircons at the Cluanie Pluton (Northern Highlands) identify clusters of concordant Silurian data points. A cluster with a weighted mean 206Pb/238U age of 431.6 ± 1.3 Ma (2 confidence interval, n = 6) records emplacement whilst older points (clustered at 441.8 ± 2.3 Ma, n = 9) record deep crustal hot zone magmatism prior to ascent. The Cluanie Pluton, and its neighbour the ∼428 Ma Clunes tonalite, have adakite-like high Na, Sr/Y, La/Yb and low Mg, Ni and Cr characteristics, and lack mafic facies common in other “Newer Granites”. These geochemical signatures indicate the tapping of batches of homogenised, evolved magma from the deeper crust. The emplacement age of the Cluanie Pluton confirms volumetrically modest subduction-related magmatism occurred beneath the Northern Highlands before slab breakoff, probably as a result of crustal thickening during the ∼450 Ma Grampian 2 event. Extensive new in-situ geochemical-geochronological studies for this terrane may further substantiate the deep crustal hot zone model and the association between Caledonian magmatism and potentially metallogenesis. The term “Newer Granites” is outdated as it ignores the demonstrated relationships between magmatism, Scandian orogenesis and slab breakoff. Hence, “Caledonian intrusions” would be a more appropriate generic term to cover those bodies related to either Iapetus subduction or to slab breakoff

Are ultrahigh energy cosmic rays signals of supersymmetry?

We investigate the possibility that cosmic rays of energy larger than the Greisen-Zatsepin-Kuzmin cutoff are not nucleons, but a new stable, massive, hadron that appears in many extensions of the standard model. We focus primarily on the S^0, a uds-gluino bound state. The range of the S^0 through the cosmic background radiation is significantly longer than the range of nucleons, and therefore can originate from sources at cosmoglogical distances.Comment: 20 page LaTeX file with 5 PostScript figures included with epsf. Discussion of acceleration mechanisms has been elaborated and some new references have been added. No change in conclusions or figure

Lorentz invariance violation in top-down scenarios of ultrahigh energy cosmic ray creation

The violation of Lorentz invariance (LI) has been invoked in a number of ways to explain issues dealing with ultrahigh energy cosmic ray (UHECR) production and propagation. These treatments, however, have mostly been limited to examples in the proton-neutron system and photon-electron system. In this paper we show how a broader violation of Lorentz invariance would allow for a series of previously forbidden decays to occur, and how that could lead to UHECR primaries being heavy baryonic states or Higgs bosons.Comment: Replaced with heavily revised (see new Abstract) version accepted by Phys. Rev. D. 6 page

Comparing verbal autopsy cause of death findings as determined by physician coding and probabilistic modelling: a public health analysis of 54 000 deaths in Africa and Asia.

BACKGROUND: Coverage of civil registration and vital statistics varies globally, with most deaths in Africa and Asia remaining either unregistered or registered without cause of death. One important constraint has been a lack of fit-for-purpose tools for registering deaths and assigning causes in situations where no doctor is involved. Verbal autopsy (interviewing care-givers and witnesses to deaths and interpreting their information into causes of death) is the only available solution. Automated interpretation of verbal autopsy data into cause of death information is essential for rapid, consistent and affordable processing. METHODS: Verbal autopsy archives covering 54 182 deaths from five African and Asian countries were sourced on the basis of their geographical, epidemiological and methodological diversity, with existing physician-coded causes of death attributed. These data were unified into the WHO 2012 verbal autopsy standard format, and processed using the InterVA-4 model. Cause-specific mortality fractions from InterVA-4 and physician codes were calculated for each of 60 WHO 2012 cause categories, by age group, sex and source. Results from the two approaches were assessed for concordance and ratios of fractions by cause category. As an alternative metric, the Wilcoxon matched-pairs signed ranks test with two one-sided tests for stochastic equivalence was used. FINDINGS: The overall concordance correlation coefficient between InterVA-4 and physician codes was 0.83 (95% CI 0.75 to 0.91) and this increased to 0.97 (95% CI 0.96 to 0.99) when HIV/AIDS and pulmonary TB deaths were combined into a single category. Over half (53%) of the cause category ratios between InterVA-4 and physician codes by source were not significantly different from unity at the 99% level, increasing to 62% by age group. Wilcoxon tests for stochastic equivalence also demonstrated equivalence. CONCLUSIONS: These findings show strong concordance between InterVA-4 and physician-coded findings over this large and diverse data set. Although these analyses cannot prove that either approach constitutes absolute truth, there was high public health equivalence between the findings. Given the urgent need for adequate cause of death data from settings where deaths currently pass unregistered, and since the WHO 2012 verbal autopsy standard and InterVA-4 tools represent relatively simple, cheap and available methods for determining cause of death on a large scale, they should be used as current tools of choice to fill gaps in cause of death data

Treatment and Intervention for Opiate Dependence in the United Kingdom:Lessons from Triumph and Failure

The history of opiate treatment in the United Kingdom (UK) since the early 1980s is a rich source of learning about the benefits and pitfalls of drug treatment policy. We present five possible lessons to be learnt about how factors outside the clinic, including government, charities and researchers can influence treatment and outcomes. First, do not let a crisis go to waste. The philosophical shift from abstinence to harm reduction in the 1980s, in response to an HIV outbreak in injecting users, facilitated expansion in addiction services and made a harm reduction approach more acceptable. Second, studies of drug-related deaths can lead to advances in care. By elucidating the pattern of mortality, and designing interventions to address the causes, researchers have improved patient safety in certain contexts, though significant investment in Scotland has not arrested rising mortality. Third, collection of longitudinal data and its use to inform clinical guidelines, as pursued from the mid-1990s, can form an enduring evidence base and shape policy, sometimes in unintended ways. Fourth, beware of the presentation of harm reduction and recovery as in conflict. At the least, this reduces patient choice, and at worst, it has caused some services to be redesigned in a manner that jeopardises patient safety. Fifth, the relationship between the third and state sectors must be carefully nurtured. In the UK, early collaboration has been replaced by competition, driven by changes in funding, to the detriment of service provision

Using UAV-Based Photogrammetry Coupled with In Situ Fieldwork and U-Pb Geochronology to Decipher Multi-Phase Deformation Processes: A Case Study from Sarclet, Inner Moray Firth Basin, UK

Constraining the age of formation and repeated movements along fault arrays in superimposed rift basins helps us to better unravel the kinematic history as well as the role of inherited structures in basin evolution. The Inner Moray Firth Basin (IMFB, western North Sea) overlies rocks of the Caledonian basement, the pre-existing Devonian–Carboniferous Orcadian Basin, and a regionally developed Permo–Triassic North Sea basin system. IMFB rifting occurred mainly in the Upper Jurassic–Lower Cretaceous. The rift basin then experienced further regional tilting, uplift and fault reactivation during the Cenozoic. The Devonian successions exposed onshore along the northwestern coast of IMFB and the southeastern onshore exposures of the Orcadian Basin at Sarclet preserve a variety of fault orientations and structures. Their timing and relationship to the structural development of the wider Orcadian and IMFB are poorly understood. In this study, drone airborne optical images are used to create high-resolution 3D digital outcrops. Analyses of these images are then coupled with detailed field observations and U-Pb geochronology of syn-faulting mineralised veins in order to constrain the orientations and absolute timing of fault populations and decipher the kinematic history of the area. In addition, the findings help to better identify deformation structures associated with earlier basin-forming events. This holistic approach helped identify and characterise multiple deformation events, including the Late Carboniferous inversion of Devonian rifting structures, Permian minor fracturing, Late Jurassic–Early Cretaceous rifting and Cenozoic reactivation and local inversion. We were also able to isolate characteristic structures, fault kinematics, fault rock developments and associated mineralisation types related to these event