IL28B SNP screening and distribution in the French Canadian population using a rapid PCR-based test

Single nucleotide polymorphisms (SNPs) in the proximity of the interleukin-28B (IL28B) gene can predict spontaneous resolution of hepatitis C virus (HCV) infection and response to interferon therapy. Screening for this polymorphism has become part of the standard criteria for the management of HCV-infected patients, hence the need for a rapid, cost-effective screening method. Here, we describe a rapid PCR-based test to screen for two IL28B SNPs (rs12979860 and rs8099917). We used this test to investigate IL28B polymorphism and prevalence in a cohort of French Canadian injection drug users who are part of a unique population known to have a strong genetic founder effect. This population had lower linkage disequilibrium between the two tested SNPs as compared to other cohorts (|d′| = 0.68, r = 0.59). The special genetic makeup should be considered in the management of HCV-infected patients within that population

Chondrosarcoma presenting as dyspnea in a 19-year-old man: a case report

<p>Abstract</p> <p>Introduction</p> <p>Acute pulmonary embolism has varied presentations ranging from asymptomatic, incidentally discovered emboli to massive embolism, causing immediate death. Tumor embolism is a rare but unique complication of malignancies. This uncommon catastrophe of a malignant tumor in a young patient, culminating as a pulmonary embolism, is being reported for the first time.</p> <p>Case presentation</p> <p>A 19-year-old Asian man presented to the emergency service at our hospital with acute onset dyspnea. His clinical examination led to the suspicion of an acute pulmonary embolism with a lower lumbosacral radiculopathy. A magnetic resonance imaging scan of the pelvis demonstrated a chondrosarcoma arising from the right iliac wing, eroding into the common iliac vein and creeping up the inferior vena cava to lodge in the pulmonary artery, thus producing a saddle embolus.</p> <p>Conclusion</p> <p>The importance of exploring for malignancies in the event of an idiopathic pulmonary embolism is highlighted. Early detection of such malignancies can substantially affect the outcome in young patients.</p

Effect of changes in climate and emissions on future sulfate-nitrate-ammonium aerosol levels in the United States

Global simulations of sulfate, nitrate, and ammonium aerosols are performed for the present day and 2050 using the chemical transport model GEOS-Chem. Changes in climate and emissions projected by the IPCC A1B scenario are imposed separately and together, with the primary focus of the work on future inorganic aerosol levels over the United States. Climate change alone is predicted to lead to decreases in levels of sulfate and ammonium in the southeast U.S. but increases in the Midwest and northeast U.S. Nitrate concentrations are projected to decrease across the U.S. as a result of climate change alone. In the U.S., climate change alone can cause changes in annually averaged sulfate-nitrate-ammonium of up to 0.61 μg/m^3, with seasonal changes often being much larger in magnitude. When changes in anthropogenic emissions are considered (with or without changes in climate), domestic sulfate concentrations are projected to decrease because of sulfur dioxide emission reductions, and nitrate concentrations are predicted to generally increase because of higher ammonia emissions combined with decreases in sulfate despite reductions in emissions of nitrogen oxides. The ammonium burden is projected to increase from 0.24 to 0.36 Tg, and the sulfate burden to increase from 0.28 to 0.40 Tg S as a result of globally higher ammonia and sulfate emissions in the future. The global nitrate burden is predicted to remain essentially constant at 0.35 Tg, with changes in both emissions and climate as a result of the competing effects of higher precursor emissions and increased temperature

High-Energy Vector-Boson Scattering with Non-Standard Interactions and the Role of a Scalar Sector

The high-energy behavior of vector-boson scattering amplitudes is examined within an effective theory for non-standard self-interactions of electroweak vector-bosons. Irrespectively of whether this theory is brought into a gauge invariant form by including non-standard interactions of a Higgs particle I find that terms that grow particularly strongly with increasing scattering energy are absent. Different theories are compared concerning their high-energy behavior and the appearance of divergences at the one-loop level.Comment: 21 pages LaTeX, condensed version of BI-TP 93/5

Modelling charge self-trapping in wide-gap dielectrics: Localization problem in local density functionals

We discuss the adiabatic self-trapping of small polarons within the density functional theory (DFT). In particular, we carried out plane-wave pseudo-potential calculations of the triplet exciton in NaCl and found no energy minimum corresponding to the self-trapped exciton (STE) contrary to the experimental evidence and previous calculations. To explore the origin of this problem we modelled the self-trapped hole in NaCl using hybrid density functionals and an embedded cluster method. Calculations show that the stability of the self-trapped state of the hole drastically depends on the amount of the exact exchange in the density functional: at less than 30% of the Hartree-Fock exchange, only delocalized hole is stable, at 50% - both delocalized and self-trapped states are stable, while further increase of exact exchange results in only the self-trapped state being stable. We argue that the main contributions to the self-trapping energy such as the kinetic energy of the localizing charge, the chemical bond formation of the di-halogen quasi molecule, and the lattice polarization, are represented incorrectly within the Kohn-Sham (KS) based approaches.Comment: 6 figures, 1 tabl

Pricing Python Parallelism: A Dynamic Language Cost Model for Heterogeneous Platforms

Execution times may be reduced by offloading parallel loop nests to a GPU. Auto-parallelizing compilers are common for static languages, often using a cost model to determine when the GPU execution speed will outweigh the offload overheads. Nowadays scientific software is increasingly written in dynamic languages and would benefit from compute accelerators. The ALPyNA framework analyses moderately complex Python loop nests and automatically JIT compiles code for heterogeneous CPU and GPU architectures. We present the first analytical cost model for auto-parallelizing loop nests in a dynamic language on heterogeneous architectures. Predicting execution time in a language like Python is extremely challenging, since aspects like the element types, size of the iteration space, and amenability to parallelization can only be determined at runtime. Hence the cost model must be both staged, to combine compile and run-time information, and lightweight to minimize runtime overhead. GPU execution time prediction must account for factors like data transfer, block-structured execution, and starvation. We show that a comparatively simple, staged analytical model can accurately determine during execution when it is profitable to offload a loop nest. We evaluate our model on three heterogeneous platforms across 360 experiments with 12 loop-intensive Python benchmark programs. The results show small misprediction intervals and a mean slowdown of just 13.6%, relative to the optimal (oracular) offload strategy

An Overview of the Atmospheric Component of the Energy Exascale Earth System Model

The Energy Exascale Earth System Model Atmosphere Model version 1, the atmospheric component of the Department of Energy’s Energy Exascale Earth System Model is described. The model began as a fork of the wellâ known Community Atmosphere Model, but it has evolved in new ways, and coding, performance, resolution, physical processes (primarily cloud and aerosols formulations), testing and development procedures now differ significantly. Vertical resolution was increased (from 30 to 72 layers), and the model top extended to 60 km (~0.1 hPa). A simple ozone photochemistry predicts stratospheric ozone, and the model now supports increased and more realistic variability in the upper troposphere and stratosphere. An optional improved treatment of lightâ absorbing particle deposition to snowpack and ice is available, and stronger connections with Earth system biogeochemistry can be used for some science problems. Satellite and groundâ based cloud and aerosol simulators were implemented to facilitate evaluation of clouds, aerosols, and aerosolâ cloud interactions. Higher horizontal and vertical resolution, increased complexity, and more predicted and transported variables have increased the model computational cost and changed the simulations considerably. These changes required development of alternate strategies for tuning and evaluation as it was not feasible to â brute forceâ tune the highâ resolution configurations, so shortâ term hindcasts, perturbed parameter ensemble simulations, and regionally refined simulations provided guidance on tuning and parameterization sensitivity to higher resolution. A brief overview of the model and model climate is provided. Model fidelity has generally improved compared to its predecessors and the CMIP5 generation of climate models.Plain Language SummaryThis study provides an overview of a new computer model of the Earth’s atmosphere that is used as one component of the Department of Energy’s latest Earth system model. The model can be used to help understand past, present, and future changes in Earth’s behavior as the system responds to changes in atmospheric composition (like pollution and greenhouse gases), land, and water use and to explore how the atmosphere interacts with other components of the Earth system (ocean, land, biology, etc.). Physical, chemical, and biogeochemical processes treated within the atmospheric model are described, and pointers to previous and recent work are listed to provide additional information. The model is compared to presentâ day observations and evaluated for some important tests that provide information about what could happen to clouds and the environment as changes occur. Strengths and weaknesses of the model are listed, as well as opportunities for future work.Key PointsA brief description and evaluation is provided for the atmospheric component of the Department of Energy’s Energy Exascale Earth System ModelModel fidelity has generally improved compared to predecessors and models participating in past international model evaluationsStrengths and weaknesses of the model, as well as opportunities for future work, are describedPeer Reviewedhttps://deepblue.lib.umich.edu/bitstream/2027.42/151811/1/jame20932_am.pdfhttps://deepblue.lib.umich.edu/bitstream/2027.42/151811/2/jame20932.pd

Acute mountain sickness.

Acute mountain sickness (AMS) is a clinical syndrome occurring in otherwise healthy normal individuals who ascend rapidly to high altitude. Symptoms develop over a period ofa few hours or days. The usual symptoms include headache, anorexia, nausea, vomiting, lethargy, unsteadiness of gait, undue dyspnoea on moderate exertion and interrupted sleep. AMS is unrelated to physical fitness, sex or age except that young children over two years of age are unduly susceptible. One of the striking features ofAMS is the wide variation in individual susceptibility which is to some extent consistent. Some subjects never experience symptoms at any altitude while others have repeated attacks on ascending to quite modest altitudes. Rapid ascent to altitudes of 2500 to 3000m will produce symptoms in some subjects while after ascent over 23 days to 5000m most subjects will be affected, some to a marked degree. In general, the more rapid the ascent, the higher the altitude reached and the greater the physical exertion involved, the more severe AMS will be. Ifthe subjects stay at the altitude reached there is a tendency for acclimatization to occur and symptoms to remit over 1-7 days