Reply to discussion on 'A high-precision U-Pb age constraint on the Rhynie Chert Konservat-Lagerstatte: time scale and other implications': Journal, 168, 863-872

We welcome the opportunity to address the points raised by Mark et al. in their discussion of the chemical abrasion isotope dilution thermal ionization mass spectrometry (CA–ID–TIMS) U–Pb age constraint on the Rhynie Chert Konservat-Lagerstätte presented by Parry et al. (2011) and also to make some further observations of our own. We begin by briefly providing some context for the benefit of the wider readership. Two radio-isotopic age constraints on the Rhynie Chert Konservat-Lagerstätte and, by corollary, its parental hydrothermal (hot-spring) system have recently been published. The first of these is a weighted mean 40Ar/39Ar plateau age of 403.9 ± 2.1 Ma (2σ) derived from the analysis of two samples of vein-hosted hydrothermal K-feldspar and a single sample of hydrothermally altered andesite (Mark et al. 2011). In order to account for systematic uncertainties associated with the 40Ar/39Ar geochronometer, Mark et al. (2011) recalculated their individual sample ages with reference to the Fish Canyon Tuff sanidine (FCs) age of 28.201 Ma (Kuiper et al. 2008), thereby producing a ‘U–Pb comparable’ mean age of 407.1 ± 2.2 Ma (2σ). An alternative ‘preferred age’ for the Rhynie hot-spring activity (407.6 ± 2.2 Ma (2σ)) has now been produced from the ‘raw’ data using the optimization model of Renne et al. (2010, 2011) (this discussion). The 40Ar/39Ar system calibrations on which these various ages are based are summarized in Table 1. The second radio-isotopic age constraint in question is a weighted mean 206Pb/238U zircon age of 411.5 ± 1.3 Ma (2σ, including decay constant- and tracer calibration-related uncertainties; MSWD = 0.12, n = 4) yielded by the Milton of Noth Andesite, a moderately altered basaltic andesite lava flow (cum near-surface sill?) that lies along the northwestern margin of the Rhynie Outlier (Parry et al. 2011). U–Pb titanite data corroborate the zircon data, and c. 411.5 Ma is interpreted as the crystallization-eruption age of the Milton of Noth Andesite. Lavas and tuffs of andesitic composition occur elsewhere within the northern half of the Rhynie Outlier (Rice & Ashcroft 2004) and a holistic view of the available evidence would suggest that these volcanic rocks represent the surficial expression of the thermal drive for the Rhynie hot-spring system. Parry et al. (2011) therefore concluded that that the U–Pb zircon age yielded by the Milton of Noth Andesite dates the Rhynie hydrothermal activity within error [our italics]

Reconstruction of MIS 5 climate in the central Levant using a stalagmite from Kanaan Cave, Lebanon

Lying at the transition between the temperate Mediterranean domain and subtropical deserts, the Levant is a key area to study the palaeoclimatic response over glacial–interglacial cycles. This paper presents a precisely dated last interglacial (MIS 5) stalagmite (129–84 ka) from the Kanaan Cave, Lebanon. Variations in growth rate and isotopic records indicate a warm humid phase at the onset of the last interglacial at ~ 129 ka that lasted until ~ 125 ka. A gradual shift in speleothem isotopic composition (125–122 ka) is driven mainly by the δ18O source effect of the eastern Mediterranean surface waters during sapropel 5 (S5). The onset of glacial inception began after ~ 122 ka, interrupted by a short wet pulse during the sapropel 4 (S4) event. Low growth rates and enriched oxygen and carbon values until ~ 84 ka indicate a transition to drier conditions during Northern Hemisphere glaciation

Nonintegrable Interaction of Ion-Acoustic and Electromagnetic Waves in a Plasma

In this paper we re-examine the one-dimensional interaction of electromagnetic and ion acoustic waves in a plasma. Our model is similar to one solved by Rao et al. (Phys. Fluids, vol. 26, 2488 (1983)) under a number of analytical approximations. Here we perform a numerical investigation to examine the stability of the model. We find that for slightly over dense plasmas, the propagation of stable solitary modes can occur in an adiabatic regime where the ion acoustic electric field potential is enslaved to the electromagnetic field of a laser. But if the laser intensity or plasma density increases or the laser frequency decreases, the adiabatic regime loses stability via a transition to chaos. New asymptotic states are attained when the adiabatic regime no longer exists. In these new states, the plasma becomes rarefied, and the laser field tends to behave like a vacuum field.Comment: 19 pages, REVTeX, 6 ps figures, accepted for publication in Phys. Rev.

An Integrated TCGA Pan-Cancer Clinical Data Resource to Drive High-Quality Survival Outcome Analytics

For a decade, The Cancer Genome Atlas (TCGA) program collected clinicopathologic annotation data along with multi-platform molecular profiles of more than 11,000 human tumors across 33 different cancer types. TCGA clinical data contain key features representing the democratized nature of the data collection process. To ensure proper use of this large clinical dataset associated with genomic features, we developed a standardized dataset named the TCGA Pan-Cancer Clinical Data Resource (TCGA-CDR), which includes four major clinical outcome endpoints. In addition to detailing major challenges and statistical limitations encountered during the effort of integrating the acquired clinical data, we present a summary that includes endpoint usage recommendations for each cancer type. These TCGA-CDR findings appear to be consistent with cancer genomics studies independent of the TCGA effort and provide opportunities for investigating cancer biology using clinical correlates at an unprecedented scale. Analysis of clinicopathologic annotations for over 11,000 cancer patients in the TCGA program leads to the generation of TCGA Clinical Data Resource, which provides recommendations of clinical outcome endpoint usage for 33 cancer types

Velocity-space sensitivity of the time-of-flight neutron spectrometer at JET

The velocity-space sensitivities of fast-ion diagnostics are often described by so-called weight functions. Recently, we formulated weight functions showing the velocity-space sensitivity of the often dominant beam-target part of neutron energy spectra. These weight functions for neutron emission spectrometry (NES) are independent of the particular NES diagnostic. Here we apply these NES weight functions to the time-of-flight spectrometer TOFOR at JET. By taking the instrumental response function of TOFOR into account, we calculate time-of-flight NES weight functions that enable us to directly determine the velocity-space sensitivity of a given part of a measured time-of-flight spectrum from TOFOR

On the mechanisms governing gas penetration into a tokamak plasma during a massive gas injection

A new 1D radial fluid code, IMAGINE, is used to simulate the penetration of gas into a tokamak plasma during a massive gas injection (MGI). The main result is that the gas is in general strongly braked as it reaches the plasma, due to mechanisms related to charge exchange and (to a smaller extent) recombination. As a result, only a fraction of the gas penetrates into the plasma. Also, a shock wave is created in the gas which propagates away from the plasma, braking and compressing the incoming gas. Simulation results are quantitatively consistent, at least in terms of orders of magnitude, with experimental data for a D 2 MGI into a JET Ohmic plasma. Simulations of MGI into the background plasma surrounding a runaway electron beam show that if the background electron density is too high, the gas may not penetrate, suggesting a possible explanation for the recent results of Reux et al in JET (2015 Nucl. Fusion 55 093013)

Relationship of edge localized mode burst times with divertor flux loop signal phase in JET

A phase relationship is identified between sequential edge localized modes (ELMs) occurrence times in a set of H-mode tokamak plasmas to the voltage measured in full flux azimuthal loops in the divertor region. We focus on plasmas in the Joint European Torus where a steady H-mode is sustained over several seconds, during which ELMs are observed in the Be II emission at the divertor. The ELMs analysed arise from intrinsic ELMing, in that there is no deliberate intent to control the ELMing process by external means. We use ELM timings derived from the Be II signal to perform direct time domain analysis of the full flux loop VLD2 and VLD3 signals, which provide a high cadence global measurement proportional to the voltage induced by changes in poloidal magnetic flux. Specifically, we examine how the time interval between pairs of successive ELMs is linked to the time-evolving phase of the full flux loop signals. Each ELM produces a clear early pulse in the full flux loop signals, whose peak time is used to condition our analysis. The arrival time of the following ELM, relative to this pulse, is found to fall into one of two categories: (i) prompt ELMs, which are directly paced by the initial response seen in the flux loop signals; and (ii) all other ELMs, which occur after the initial response of the full flux loop signals has decayed in amplitude. The times at which ELMs in category (ii) occur, relative to the first ELM of the pair, are clustered at times when the instantaneous phase of the full flux loop signal is close to its value at the time of the first ELM

Driver Fusions and Their Implications in the Development and Treatment of Human Cancers.

Gene fusions represent an important class of somatic alterations in cancer. We systematically investigated fusions in 9,624 tumors across 33 cancer types using multiple fusion calling tools. We identified a total of 25,664 fusions, with a 63% validation rate. Integration of gene expression, copy number, and fusion annotation data revealed that fusions involving oncogenes tend to exhibit increased expression, whereas fusions involving tumor suppressors have the opposite effect. For fusions involving kinases, we found 1,275 with an intact kinase domain, the proportion of which varied significantly across cancer types. Our study suggests that fusions drive the development of 16.5% of cancer cases and function as the sole driver in more than 1% of them. Finally, we identified druggable fusions involving genes such as TMPRSS2, RET, FGFR3, ALK, and ESR1 in 6.0% of cases, and we predicted immunogenic peptides, suggesting that fusions may provide leads for targeted drug and immune therapy

Grand challenges in entomology: priorities for action in the coming decades

Entomology is key to understanding terrestrial and freshwater ecosystems at a time of unprecedented anthropogenic environmental change and offers substantial untapped potential to benefit humanity in a variety of ways, from improving agricultural practices to managing vector-borne diseases and inspiring technological advances. We identified high priority challenges for entomology using an inclusive, open, and democratic four-stage prioritisation approach, conducted among the membership and affiliates (hereafter ‘members’) of the UK-based Royal Entomological Society (RES). A list of 710 challenges was gathered from 189 RES members. Thematic analysis was used to group suggestions, followed by an online vote to determine initial priorities, which were subsequently ranked during an online workshop involving 37 participants. The outcome was a set of 61 priority challenges within four groupings of related themes: (i) ‘Fundamental Research’ (themes: Taxonomy, ‘Blue Skies’ [defined as research ideas without immediate practical application], Methods and Techniques); (ii) ‘Anthropogenic Impacts and Conservation’ (themes: Anthropogenic Impacts, Conservation Options); (iii) ‘Uses, Ecosystem Services and Disservices’ (themes: Ecosystem Benefits, Technology and Resources [use of insects as a resource, or as inspiration], Pests); (iv) ‘Collaboration, Engagement and Training’ (themes: Knowledge Access, Training and Collaboration, Societal Engagement). Priority challenges encompass research questions, funding objectives, new technologies, and priorities for outreach and engagement. Examples include training taxonomists, establishing a global network of insect monitoring sites, understanding the extent of insect declines, exploring roles of cultivated insects in food supply chains, and connecting professional with amateur entomologists. Responses to different challenges could be led by amateur and professional entomologists, at all career stages. Overall, the challenges provide a diverse array of options to inspire and initiate entomological activities and reveal the potential of entomology to contribute to addressing global challenges related to human health and well-being, and environmental change