pncA and bptA Are Not Sufficient To Complement Ixodes scapularis Colonization and Persistence by Borrelia burgdorferi in a Linear Plasmid lp25-Deficient Background

The complex segmented genome of Borrelia burgdorferi is comprised of a linear chromosome along with numerous linear and circular plasmids essential for tick and/or mammalian infectivity. The pathogenic necessity for specific borrelial plasmids has been identified; most notably, infections of the tick vector and mammalian host both require linear plasmid 25 (lp25). Genes carried on lp25, specifically bptA and pncA, are postulated to play a role for B. burgdorferi to infect and persist in Ixodes ticks. In this study, we complemented an lp25-deficient borrelial strain with pncA alone or pncA accompanied by bptA to evaluate the ability of the complemented strains to restore larval colonization and persistence through transstadial transmission relative to that of wild-type B. burgdorferi. The acquisition of the complemented strains by tick larvae from infected mice and/or the survival of these strains was significantly decreased when assayed by cultivation and quantitative PCR (qPCR). Only 10% of the pncA-complemented strain organisms were found by culture to survive 17 days following larval feeding, while 45% of the pncA- and bptA-complemented strain organisms survived, with similar results by PCR. However, neither of the complemented B. burgdorferi strains was capable of persisting through the molt to the nymphal stage as analyzed by culture. qPCR analyses of unfed nymphs detected B. burgdorferi genomes in several nymphs at low copy numbers, likely indicating the presence of DNA from dead or dying cells. Overall, the data indicate that pncA and bptA cannot independently support infection, suggesting that lp25 carries additional gene(s) or regulatory elements critical for B. burgdorferi survival and pathogenesis in the Ixodes vector

Towards Improved Quantum Simulations and Sensing with Trapped 2D Ion Crystals via Parametric Amplification

Improving coherence is a fundamental challenge in quantum simulation and sensing experiments with trapped ions. Here we discuss, experimentally demonstrate, and estimate the potential impacts of two different protocols that enhance, through motional parametric excitation, the coherent spin-motion coupling of ions obtained with a spin-dependent force. The experiments are performed on 2D crystal arrays of approximately one hundred $^9$Be$^+$ ions confined in a Penning trap. By modulating the trapping potential at close to twice the center-of-mass mode frequency, we squeeze the motional mode and enhance the spin-motion coupling while maintaining spin coherence. With a stroboscopic protocol, we measure $5.4 \pm 0.9$ dB of motional squeezing below the ground-state motion, from which theory predicts a $10$ dB enhancement in the sensitivity for measuring small displacements using a recently demonstrated protocol [Science $\textbf{373}$, 673 (2021)]. With a continuous squeezing protocol, we measure and accurately calibrate the parametric coupling strength. Theory suggests this protocol can be used to improve quantum spin squeezing, limited in our system by off-resonant light scatter. We illustrate numerically the trade-offs between strong parametric amplification and motional dephasing in the form of center-of-mass frequency fluctuations for improving quantum spin squeezing in our set-up.Comment: 11 pages, 6 figure

Evaluation of work-based screening for early signs of alcohol-related liver disease in hazardous and harmful drinkers: the PrevAIL study

Background The direct cost of excessive alcohol consumption to health services is substantial but dwarfed by the cost borne by the workplace as a result of lost productivity. The workplace is also a promising setting for health interventions. The Preventing Alcohol Harm in Liverpool and Knowsley (PrevAIL) project aimed to evaluate a mechanism for detecting the prevalence of alcohol related liver disease using fibrosis biomarkers. Secondary aims were to identify the additive effect of obesity as a risk factor for early liver disease; to assess other impacts of alcohol on work, using a cross-sectional survey. Methods Participants (aged 36-55y) from 13 workplaces participated (March 2011–April 2012). BMI, waist circumference, blood pressure and self-reported alcohol consumption in the previous week was recorded. Those consuming more than the accepted UK threshold (men: >21 units; female: >14 units alcohol) provided a 20 ml venous blood sample for a biomarker test (Southampton Traffic Light Test) and completed an alcohol questionnaire (incorporating the Severity of Alcohol Dependence Questionnaire). Results The screening mechanism enrolled 363 individuals (52 % women), 39 % of whom drank above the threshold and participated in the liver screen (n = 141, complete data = 124 persons). Workplaces with successful participation were those where employers actively promoted, encouraged and facilitated attendance. Biomarkers detected that 30 % had liver disease (25 %, intermediate; 5 % probable). Liver disease was associated with the frequency of visits to the family physician (P = 0.036) and obesity (P = 0.052). Conclusions The workplace is an important setting for addressing alcohol harm, but there are barriers to voluntary screening that need to be addressed. Early detection and support of cases in the community could avert deaths and save health and social costs. Alcohol and obesity should be addressed simultaneously, because of their known multiplicative effect on liver disease risk, and because employers preferred a general health intervention to one that focused solely on alcohol consumption

Exploring the Local Milky Way: M Dwarfs as Tracers of Galactic Populations

We have assembled a spectroscopic sample of low-mass dwarfs observed as part of the Sloan Digital Sky Survey along one Galactic sightline, designed to investigate the observable properties of the thin and thick disks. This sample of ~7400 K and M stars also has measured ugriz photometry, proper motions, and radial velocities. We have computed UVW space motion distributions, and investigate their structure with respect to vertical distance from the Galactic Plane. We place constraints on the velocity dispersions of the thin and thick disks, using two-component Gaussian fits. We also compare these kinematic distributions to a leading Galactic model. Finally, we investigate other possible observable differences between the thin and thick disks, such as color, active fraction and metallicity.Comment: 11 pages, 12 figures, Accepted by A

Early-branching gut fungi possess a large, comprehensive array of biomass-degrading enzymes

available in PMC 2016 November 07The fungal kingdom is the source of almost all industrial enzymes in use for lignocellulose bioprocessing. We developed a systems-level approach that integrates transcriptomic sequencing, proteomics, phenotype, and biochemical studies of relatively unexplored basal fungi. Anaerobic gut fungi isolated from herbivores produce a large array of biomass-degrading enzymes that synergistically degrade crude, untreated plant biomass and are competitive with optimized commercial preparations from Aspergillus and Trichoderma. Compared to these model platforms, gut fungal enzymes are unbiased in substrate preference due to a wealth of xylan-degrading enzymes. These enzymes are universally catabolite-repressed and are further regulated by a rich landscape of noncoding regulatory RNAs. Additionally, we identified several promising sequence-divergent enzyme candidates for lignocellulosic bioprocessing.United States. Dept. of Energy. Office of Science (Biological and Environmental Research (BER) program)United States. Department of Energy (DOE Grant DE-SC0010352)United States. Department of Agriculture (Award 2011-67017-20459)Institute for Collaborative Biotechnologies (grant W911NF-09-0001

THE COMMUNITY LEVERAGED UNIFIED ENSEMBLE (CLUE) IN THE 2016 NOAA/HAZARDOUS WEATHER TESTBED SPRING FORECASTING EXPERIMENT

One primary goal of annual Spring Forecasting Experiments (SFEs), which are coorganized by NOAA’s National Severe Storms Laboratory and Storm Prediction Center and conducted in the National Oceanic and Atmospheric Administration’s (NOAA) Hazardous Weather Testbed, is documenting performance characteristics of experimental, convection-allowing modeling systems (CAMs). Since 2007, the number of CAMs (including CAM ensembles) examined in the SFEs has increased dramatically, peaking at six different CAM ensembles in 2015. Meanwhile, major advances have been made in creating, importing, processing, verifying, and developing tools for analyzing and visualizing these large and complex datasets. However, progress toward identifying optimal CAM ensemble configurations has been inhibited because the different CAM systems have been independently designed, making it difficult to attribute differences in performance characteristics. Thus, for the 2016 SFE, a much more coordinated effort among many collaborators was made by agreeing on a set of model specifications (e.g., model version, grid spacing, domain size, and physics) so that the simulations contributed by each collaborator could be combined to form one large, carefully designed ensemble known as the Community Leveraged Unified Ensemble (CLUE). The 2016 CLUE was composed of 65 members contributed by five research institutions and represents an unprecedented effort to enable an evidence-driven decision process to help guide NOAA’s operational modeling efforts. Eight unique experiments were designed within the CLUE framework to examine issues directly relevant to the design of NOAA’s future operational CAM-based ensembles. This article will highlight the CLUE design and present results from one of the experiments examining the impact of single versus multicore CAM ensemble configurations

THE COMMUNITY LEVERAGED UNIFIED ENSEMBLE (CLUE) IN THE 2016 NOAA/HAZARDOUS WEATHER TESTBED SPRING FORECASTING EXPERIMENT

One primary goal of annual Spring Forecasting Experiments (SFEs), which are coorganized by NOAA’s National Severe Storms Laboratory and Storm Prediction Center and conducted in the National Oceanic and Atmospheric Administration’s (NOAA) Hazardous Weather Testbed, is documenting performance characteristics of experimental, convection-allowing modeling systems (CAMs). Since 2007, the number of CAMs (including CAM ensembles) examined in the SFEs has increased dramatically, peaking at six different CAM ensembles in 2015. Meanwhile, major advances have been made in creating, importing, processing, verifying, and developing tools for analyzing and visualizing these large and complex datasets. However, progress toward identifying optimal CAM ensemble configurations has been inhibited because the different CAM systems have been independently designed, making it difficult to attribute differences in performance characteristics. Thus, for the 2016 SFE, a much more coordinated effort among many collaborators was made by agreeing on a set of model specifications (e.g., model version, grid spacing, domain size, and physics) so that the simulations contributed by each collaborator could be combined to form one large, carefully designed ensemble known as the Community Leveraged Unified Ensemble (CLUE). The 2016 CLUE was composed of 65 members contributed by five research institutions and represents an unprecedented effort to enable an evidence-driven decision process to help guide NOAA’s operational modeling efforts. Eight unique experiments were designed within the CLUE framework to examine issues directly relevant to the design of NOAA’s future operational CAM-based ensembles. This article will highlight the CLUE design and present results from one of the experiments examining the impact of single versus multicore CAM ensemble configurations

LSST: from Science Drivers to Reference Design and Anticipated Data Products

(Abridged) We describe here the most ambitious survey currently planned in the optical, the Large Synoptic Survey Telescope (LSST). A vast array of science will be enabled by a single wide-deep-fast sky survey, and LSST will have unique survey capability in the faint time domain. The LSST design is driven by four main science themes: probing dark energy and dark matter, taking an inventory of the Solar System, exploring the transient optical sky, and mapping the Milky Way. LSST will be a wide-field ground-based system sited at Cerro Pach\'{o}n in northern Chile. The telescope will have an 8.4 m (6.5 m effective) primary mirror, a 9.6 deg$^2$ field of view, and a 3.2 Gigapixel camera. The standard observing sequence will consist of pairs of 15-second exposures in a given field, with two such visits in each pointing in a given night. With these repeats, the LSST system is capable of imaging about 10,000 square degrees of sky in a single filter in three nights. The typical 5$\sigma$ point-source depth in a single visit in $r$ will be $\sim 24.5$ (AB). The project is in the construction phase and will begin regular survey operations by 2022. The survey area will be contained within 30,000 deg$^2$ with $\delta<+34.5^\circ$, and will be imaged multiple times in six bands, $ugrizy$, covering the wavelength range 320--1050 nm. About 90\% of the observing time will be devoted to a deep-wide-fast survey mode which will uniformly observe a 18,000 deg$^2$ region about 800 times (summed over all six bands) during the anticipated 10 years of operations, and yield a coadded map to $r\sim27.5$. The remaining 10\% of the observing time will be allocated to projects such as a Very Deep and Fast time domain survey. The goal is to make LSST data products, including a relational database of about 32 trillion observations of 40 billion objects, available to the public and scientists around the world.Comment: 57 pages, 32 color figures, version with high-resolution figures available from https://www.lsst.org/overvie

LSST Science Book, Version 2.0

A survey that can cover the sky in optical bands over wide fields to faint magnitudes with a fast cadence will enable many of the exciting science opportunities of the next decade. The Large Synoptic Survey Telescope (LSST) will have an effective aperture of 6.7 meters and an imaging camera with field of view of 9.6 deg^2, and will be devoted to a ten-year imaging survey over 20,000 deg^2 south of +15 deg. Each pointing will be imaged 2000 times with fifteen second exposures in six broad bands from 0.35 to 1.1 microns, to a total point-source depth of r~27.5. The LSST Science Book describes the basic parameters of the LSST hardware, software, and observing plans. The book discusses educational and outreach opportunities, then goes on to describe a broad range of science that LSST will revolutionize: mapping the inner and outer Solar System, stellar populations in the Milky Way and nearby galaxies, the structure of the Milky Way disk and halo and other objects in the Local Volume, transient and variable objects both at low and high redshift, and the properties of normal and active galaxies at low and high redshift. It then turns to far-field cosmological topics, exploring properties of supernovae to z~1, strong and weak lensing, the large-scale distribution of galaxies and baryon oscillations, and how these different probes may be combined to constrain cosmological models and the physics of dark energy.Comment: 596 pages. Also available at full resolution at http://www.lsst.org/lsst/sciboo