Development of a commissioning plan for the APT linac

The Accelerator Production of Tritium (APT) facility is based on a linac which incorporates both normal-conducting and superconducting RF technology and accelerates a 100-mA cw proton beam to an energy of 1,030 MeV or higher, depending on the desired production rate. Commissioning plans to achieve full power operation with minimum beam-induced activation of components have been evolving. This paper presents the main issues and the basic approaches that are now being discussed

Nanopore native RNA sequencing of a human poly(A) transcriptome

High-throughput complementary DNA sequencing technologies have advanced our understanding of transcriptome complexity and regulation. However, these methods lose information contained in biological RNA because the copied reads are often short and modifications are not retained. We address these limitations using a native poly(A) RNA sequencing strategy developed by Oxford Nanopore Technologies. Our study generated 9.9 million aligned sequence reads for the human cell line GM12878, using thirty MinION flow cells at six institutions. These native RNA reads had a median length of 771 bases, and a maximum aligned length of over 21,000 bases. Mitochondrial poly(A) reads provided an internal measure of read-length quality. We combined these long nanopore reads with higher accuracy short-reads and annotated GM12878 promoter regions to identify 33,984 plausible RNA isoforms. We describe strategies for assessing 3′ poly(A) tail length, base modifications and transcript haplotypes

Anthropogenic disturbance in a changing environment : modelling lifetime reproductive success to predict the consequences of multiple stressors on a migratory population

This study was supported by Office of Naval Research grant N00014‐16‐1‐2858: ‘PCoD+: Developing widely‐applicable models of the population consequences of disturbance’. DPC, MM, EAM and LKS were supported by the E&P Sound and Marine Life Joint Industry Project of the International Association of Oil and Gas Producers. JAG was supported by funding from the Young Investigator Program at the Office of Naval Research (award no. N00014‐16‐1‐2477). VH was funded by European Research Council Grant No. 322814 awarded to A.M. de Roos.Animals make behavioural and reproductive decisions that maximise their lifetime reproductive success, and thus their fitness, in light of periodic and stochastic variability of the environment. Modelling the variation of an individual's energy levels formalises this tradeoff and helps to quantify the population‐level consequences of stressors (e.g. disturbance from human activities and environmental change) that can affect behaviour or physiology. In this study, we develop a dynamic state variable model for the spatially explicit behaviour, physiology and reproduction of a female, long‐lived, migratory marine vertebrate. The model can be used to investigate the spatio‐temporal patterns of behaviour and reproduction that allow an individual to maximise its overall reproductive output. We parametrised the model for eastern North Pacific blue whales Balaenoptera musculus, and used it to predict the effects of changing environmental conditions and increasing human disturbance on the population's vital rates. In baseline conditions, the model output had high fidelity to observed energy dynamics, movement patterns and reproductive strategies. Simulated scenarios suggested that environmental changes could have severe consequences on the population's vital rates, but that individuals could tolerate high levels of anthropogenic disturbance. However, this ability depended on where, when and how often disturbance occurred. In scenarios with both environmental change and anthropogenic disturbance, synergistic interactions caused stronger effects than in isolation. In general, larger body size offered a buffer against stochasticity and disturbance, and, consequently, we predicted juveniles to be more susceptible to disturbance. We also predicted that females prioritise their own survival at the expense of the current reproductive attempt, presumably the result of their long lifespan. Our approach provides a general framework to make predictions of the cumulative and synergistic effects of human disturbance and climate change on migratory populations, which can inform effective management and conservation efforts.Publisher PDFPeer reviewe

Macroparticle simulation studies of a proton beam haloexperiment

We report macroparticle simulations for comparison withmeasured results from a proton beam-halo experiment in a 52-quadrupoleperiodic-focusing channel. An important issue is that the inputphase-space distribution is not experimentally known. Three differentinitial distributions with different shapes predict different beamprofiles in the transport system. Simulations have been fairly successfulin reproducing the core of the measured matched-beam profiles and thetrend of emittance growth as a function of mismatch factor, butunderestimate the growth rate of halo and emittance for mismatched beams.In this study, we find that knowledge of the Courant-Snyder parametersand emittances of the input beam is not sufficient for reliableprediction of the halo. Input distributions iwth greater population inthe tails produce larger rates of emittance growth, a result that isqualitatively consistent with the particle-core model of halo formationin mismatched beams

ANALOG FRONT-END ELECTRONICS FOR BEAM POSITION MEASUREMENT ON THE BEAM HALO MEASUREMENT

Enhancements have been made to the log-ratio analog front-end electronics based on the Analog Devices 8307 logarithmic amplifier as used on the LEDA accelerator. The dynamic range of greater than 85 dB, has been extended to nearly the full capability of the AD8307 from the previous design of approximately 65 dB through the addition of a 350 MHz band-pass filter, careful use of ground and power plane placement, signal routing, and power supply bypassing. Additionally, selection of high-isolation RF switches (55dB) has been an integral part of a new calibration technique, which is fully described in another paper submitted to this conference. Provision has also been made for insertion of a first-stage low-noise amplifier for using the circuit under low-signal conditions