GemTools: A fast and efficient approach to estimating genetic ancestry

To uncover the genetic basis of complex disease, individuals are often measured at a large number of genetic variants (usually SNPs) across the genome. GemTools provides computationally efficient tools for modeling genetic ancestry based on SNP genotypes. The main algorithm creates an eigenmap based on genetic similarities, and then clusters subjects based on their map position. This process is continued iteratively until each cluster is relatively homogeneous. For genetic association studies, GemTools matches cases and controls based on genetic similarity.Comment: 5 pages, 1 figur

Transcriptional Response to Acute Thermal Exposure in Juvenile Chinook Salmon Determined by RNAseq.

Thermal exposure is a serious and growing challenge facing fish species worldwide. Chinook salmon (Oncorhynchus tshawytscha) living in the southern portion of their native range are particularly likely to encounter warmer water due to a confluence of factors. River alterations have increased the likelihood that juveniles will be exposed to warm water temperatures during their freshwater life stage, which can negatively impact survival, growth, and development and pose a threat to dwindling salmon populations. To better understand how acute thermal exposure affects the biology of salmon, we performed a transcriptional analysis of gill tissue from Chinook salmon juveniles reared at 12° and exposed acutely to water temperatures ranging from ideal to potentially lethal (12° to 25°). Reverse-transcribed RNA libraries were sequenced on the Illumina HiSeq2000 platform and a de novo reference transcriptome was created. Differentially expressed transcripts were annotated using Blast2GO and relevant gene clusters were identified. In addition to a high degree of downregulation of a wide range of genes, we found upregulation of genes involved in protein folding/rescue, protein degradation, cell death, oxidative stress, metabolism, inflammation/immunity, transcription/translation, ion transport, cell cycle/growth, cell signaling, cellular trafficking, and structure/cytoskeleton. These results demonstrate the complex multi-modal cellular response to thermal stress in juvenile salmon

Spitzer View of Massive Star Formation in the Tidally Stripped Magellanic Bridge

The Magellanic Bridge is the nearest low-metallicity, tidally stripped environment, offering a unique high-resolution view of physical conditions in merging and forming galaxies. In this paper we present analysis of candidate massive young stellar objects (YSOs), i.e., {\it in situ, current} massive star formation (MSF) in the Bridge using {\it Spitzer} mid-IR and complementary optical and near-IR photometry. While we definitely find YSOs in the Bridge, the most massive are $\sim10 M_\odot$, $\ll45 M_\odot$ found in the Large Magellanic Cloud (LMC). The intensity of MSF in the Bridge also appears decreasing, as the most massive YSOs are less massive than those formed in the past. To investigate environmental effects on MSF, we have compared properties of massive YSOs in the Bridge to those in the LMC. First, YSOs in the Bridge are apparently less embedded than in the LMC: 81% of Bridge YSOs show optical counterparts, compared to only 56% of LMC sources with the same range of mass, circumstellar dust mass, and line-of-sight extinction. Circumstellar envelopes are evidently more porous or clumpy in the Bridge's low-metallicity environment. Second, we have used whole samples of YSOs in the LMC and the Bridge to estimate the probability of finding YSOs at a given \hi\ column density, N(HI). We found that the LMC has $\sim3\times$ higher probability than the Bridge for N(HI) $>10\times10^{20}$ cm$^{-2}$, but the trend reverses at lower N(HI). Investigating whether this lower efficiency relative to HI is due to less efficient molecular cloud formation, or less efficient cloud collapse, or both, will require sensitive molecular gas observations.Comment: 41 pages, 20 figures, 6 tables; accepted for publication in ApJ; several figures are in low resolution due to the size limit here and a high resolution version can be downloaded via http://www.astro.virginia.edu/~cc5ye/ms_bridge20140215.pd

The contribution of non-CO2 greenhouse gas mitigation to achieving long-term temperature goals

In the latest (fifth) assessment from the Intergovernmental Panel on Climate Change (IPCC) non-CO2 emssions accounted for 28% of total GHG emissions in 2010, when measured on the basis of their global warming potential (relative to CO2) over a 100-year and nitrous oxide (N2O) accounting for about half of all non-CO2 GHGs. With population and incomes increasing, especially in emerging economies, these emissions could grow significantly in the future. Other major sources of non-CO2 GHGs are fugitive CH4 from the extraction and distribution of fossil fuels, N2O from industrial production of nitric and adipic acid, as well as fluorinated gases (F-gases) from a range of industrial manufacturing and product uses. This paper analyses the emissions and cost impacts of mitigation of non-CO2 greenhouse gases (GHGs) at a global level, in scenarios which are focused on meeting a range of long-term temperature goals (LTTGs). The paper demonstrates how an integrated assessment model (TIAM-Grantham) representing CO2 emissions (and their mitigation) from the fossil fuel combustion and industrial sectors is coupled with a model covering non-CO2 emissions (GAINS) in order to provide a complete picture of GHG emissions in a reference scenario in which there is no mitigation of either CO2 or non-CO2 gases, as well as in scenarios in which both CO2 and non-CO2 gases are mitigated in order to achieve different LTTGs

Assessing the challenges of global long-term mitigation scenarios

The implications of global mitigation to achieve different long-term temperature goals (LTTGs) can be investigated in integrated assessment models (IAMs), which provide a large number of outputs including technology deployment levels, economic costs, carbon prices, annual rates of decarbonisation, degree of global net negative emissions required, as well as utilisation levels for fossil fuel plants. All of these factors can be considered in detail when judging the real-world feasibility of the mitigation scenarios produced by these models. This study presents a model inter-comparison of three widely used IAMs (TIAM, MESSAGE and WITCH) to analyse multiple mitigation scenarios exploring a range of LTTGs and a range of constraints, including delayed mitigation action, limited end-use electrification and delayed deployment of carbon capture technologies. The scenario outputs across the three models are examined and discussed and a matrix of the different factors concerning scenario feasibility is presented

Scenario and modelling uncertainty in global mean temperature change derived from emission-driven global climate models

We compare future changes in global mean temperature in response to different future scenarios which, for the first time, arise from emission-driven rather than concentration-driven perturbed parameter ensemble of a global climate model (GCM). These new GCM simulations sample uncertainties in atmospheric feedbacks, land carbon cycle, ocean physics and aerosol sulphur cycle processes. We find broader ranges of projected temperature responses arising when considering emission rather than concentration-driven simulations (with 10–90th percentile ranges of 1.7 K for the aggressive mitigation scenario, up to 3.9 K for the high-end, business as usual scenario). A small minority of simulations resulting from combinations of strong atmospheric feedbacks and carbon cycle responses show temperature increases in excess of 9 K (RCP8.5) and even under aggressive mitigation (RCP2.6) temperatures in excess of 4 K. While the simulations point to much larger temperature ranges for emission-driven experiments, they do not change existing expectations (based on previous concentration-driven experiments) on the timescales over which different sources of uncertainty are important. The new simulations sample a range of future atmospheric concentrations for each emission scenario. Both in the case of SRES A1B and the Representative Concentration Pathways (RCPs), the concentration scenarios used to drive GCM ensembles, lies towards the lower end of our simulated distribution. This design decision (a legacy of previous assessments) is likely to lead concentration-driven experiments to under-sample strong feedback responses in future projections. Our ensemble of emission-driven simulations span the global temperature response of the CMIP5 emission-driven simulations, except at the low end. Combinations of low climate sensitivity and low carbon cycle feedbacks lead to a number of CMIP5 responses to lie below our ensemble range. The ensemble simulates a number of high-end responses which lie above the CMIP5 carbon cycle range. These high-end simulations can be linked to sampling a number of stronger carbon cycle feedbacks and to sampling climate sensitivities above 4.5 K. This latter aspect highlights the priority in identifying real-world climate-sensitivity constraints which, if achieved, would lead to reductions on the upper bound of projected global mean temperature change. The ensembles of simulations presented here provides a framework to explore relationships between present-day observables and future changes, while the large spread of future-projected changes highlights the ongoing need for such work

Precision near-infrared radial velocity instrumentation II: Non-Circular Core Fiber Scrambler

We have built and commissioned a prototype agitated non-circular core fiber scrambler for precision spectroscopic radial velocity measurements in the near-infrared H band. We have collected the first on-sky performance and modal noise tests of these novel fibers in the near-infrared at H and K bands using the CSHELL spectrograph at the NASA InfraRed Telescope Facility (IRTF). We discuss the design behind our novel reverse injection of a red laser for co-alignment of star-light with the fiber tip via a corner cube and visible camera. We summarize the practical details involved in the construction of the fiber scrambler, and the mechanical agitation of the fiber at the telescope. We present radial velocity measurements of a bright standard star taken with and without the fiber scrambler to quantify the relative improvement in the obtainable blaze function stability, the line spread function stability, and the resulting radial velocity precision. We assess the feasibility of applying this illumination stabilization technique to the next generation of near-infrared spectrographs such as iSHELL on IRTF and an upgraded NIRSPEC at Keck. Our results may also be applied in the visible for smaller core diameter fibers where fiber modal noise is a significant factor, such as behind an adaptive optics system or on a small < 1 meter class telescope such as is being pursued by the MINERVA and LCOGT collaborations.Comment: Proceedings of the SPIE Optics and Photonics Conference "Techniques and Instrumentation for Detection of Exoplanets VI" held in San Diego, CA, August 25-29, 201

The influence of remote aerosol forcing from industrialised economies on the future evolution of East and West African rainfall

Past changes in global industrial aerosol emissions have played a significant role in historical shifts in African rainfall and yet assessment of the impact on African rainfall of near term (10-40 year) potential aerosol emission pathways remains largely unexplored. Whilst existing literature links future aerosol declines to a northward shift of Sahel rainfall, existing climate projections rely on RCP scenarios that do not explore the range of air quality drivers. Here we present projections from two emission scenarios that better envelope the range of potential aerosol emissions. More aggressive emission cuts results in northward shifts of the tropical rain-bands whose signal can emerge from expected internal variability on short, 10-20 year, time horizons. We also show for the first time that this northward shift also impacts East Africa, with evidence of delays to both onset and withdrawal of the Short Rains. However, comparisons of rainfall impacts across models suggest that only certain aspects of both the West and East African model responses may be robust, given model uncertainties. This work motivates the need for wider exploration of air quality scenarios in the climate science community to assess the robustness of these projected changes and to provide evidence to underpin climate adaptation in Africa. In particular, revised estimates of emission impacts of legislated measures every 5-10 years would have a value in providing near term climate adaptation information for African stakeholders

Motivational Interviewing Post-Stroke: An Analysis of Stroke Survivors' Concerns and Adjustment

Our earlier research demonstrated that participation in four sessions of motivational interviewing (MI) early post-stroke has a positive impact on stroke survivors' mood. However, the theoretical underpinnings of MI in supporting adjustment (rather than its traditional use in supporting behavior change) require clarification. This article describes a content analysis of MI transcripts for 10 participants in our previous study, to identify the focus of discussions (patient "concerns") and potential effective components of our MI approach. Patients' post-stroke concerns were shown in 16 categories, including frustration, family impact, and getting well. There was a pattern of change discourse across sessions: "Sustain talk" (reasons for not changing) reduced from Session 1 onward, "change talk" (intent to change) increased then reduced, and "change expressed" (changes achieved) increased from Sessions 1 to 4. MI facilitates healthy adjustment post-stroke in some patients, in turn affecting mood, but clarification of how this effect is achieved requires further exploration

A pleiotropic missense variant in SLC39A8 is associated with Crohn's disease and human gut microbiome composition

Genome-wide association studies have identified 200 inflammatory bowel disease (IBD) loci, but the genetic architecture of Crohn's disease (CD) and ulcerative colitis remain incompletely defined. Here, we aimed to identify novel associations between IBD and functional genetic variants using the Illumina ExomeChip (San Diego, CA)