Odyssey: a semi-automated pipeline for phasing, imputation, and analysis of genome-wide genetic data

BACKGROUND: Genome imputation, admixture resolution and genome-wide association analyses are timely and computationally intensive processes with many composite and requisite steps. Analysis time increases further when building and installing the run programs required for these analyses. For scientists that may not be as versed in programing language, but want to perform these operations hands on, there is a lengthy learning curve to utilize the vast number of programs available for these analyses. RESULTS: In an effort to streamline the entire process with easy-to-use steps for scientists working with big data, the Odyssey pipeline was developed. Odyssey is a simplified, efficient, semi-automated genome-wide imputation and analysis pipeline, which prepares raw genetic data, performs pre-imputation quality control, phasing, imputation, post-imputation quality control, population stratification analysis, and genome-wide association with statistical data analysis, including result visualization. Odyssey is a pipeline that integrates programs such as PLINK, SHAPEIT, Eagle, IMPUTE, Minimac, and several R packages, to create a seamless, easy-to-use, and modular workflow controlled via a single user-friendly configuration file. Odyssey was built with compatibility in mind, and thus utilizes the Singularity container solution, which can be run on Linux, MacOS, and Windows platforms. It is also easily scalable from a simple desktop to a High-Performance System (HPS). CONCLUSION: Odyssey facilitates efficient and fast genome-wide association analysis automation and can go from raw genetic data to genome: phenome association visualization and analyses results in 3-8 h on average, depending on the input data, choice of programs within the pipeline and available computer resources. Odyssey was built to be flexible, portable, compatible, scalable, and easy to setup. Biologists less familiar with programing can now work hands on with their own big data using this easy-to-use pipeline

QED(1+1) at Finite Temperature -- a Study with Light-Cone Quantisation

We explore quantum electrodynamics in (1+1) dimensions at finite temperature using the method of Discretized Light-Cone Quantisation. The partition function, energy and specific heat are computed in the canonical ensemble using the spectrum of invariant masses computed with a standard DLCQ numerical routine. In particular, the specific heat exhibits a peak which grows as the continuum limit is numerically approached. A critical exponent is tentatively extracted. The surprising result is that the density of states contains significant finite size artifacts even for a relatively high harmonic resolution. These and the other outstanding problems in the present calculation are discussed.Comment: 10 pages, 11 Postscript figures, uses epsf.st

Invasive pulmonary aspergillosis complicating COVID-19 in the ICU - A case report.

It is not yet known, if critically ill COVID-19 patients are prone to fungal infections. We report a 69-year-old patient without typical risk factors for invasive pulmonary aspergillosis (IPA), who developed IPA two weeks after onset of symptoms. Our report shows that IPA may occur in critically ill COVID-19 patients

Ineffective off-label use of recombinant activated factor VII in a case of bone-marrow transplantation-related gastrointestinal bleeding

BACKGROUND: For patients with a normal coagulation system, who experience serious bleeding, sound evidence for recombinant activated factor VII (rFVIIa) as an effective haemostatic agent is only scarcely available so far from controlled clinical trials. In systematic reviews on the clinical use of rFVIIa, treatment failures were only rarely reported. CASE PRESENTATION: We present a 45-year old, Caucasian male with persistent intestinal bleeding due to enterocolitis associated with cytomegalovirus infection and acute graft-versus-host-disease. He had received allogeneic peripheral blood stem cell transplantation from an unrelated HLA-identical donor because of chronic myelogenous leukaemia diagnosed two years earlier. Bleeding started at day 18 after transplantation with bloody diarrhea, which was treated with multiple transfusions of fresh frozen plasma, platelet, and red blood cell concentrates, and continued relentlessly, despite all efforts, including continued transfusions, high-dose prednisolone, broad antibiotic and antiviral coverage, and tranexamic acid. Recombinant FVIIa was started at boluses of 90–120 μg/kg every 4–8 hours. Despite more than 10 doses, recurrent severe bleeding progressed to refractory shock, multiorgan failure and death. CONCLUSIONS: Little can be concluded from single case reports of clinical improvement, because publication bias in favour of positive effects is likely. Our case suggests that rFVIIa is not a panacea, in particular for severe bleeding after bone-marrow transplantation. As long as rigorous, controlled studies or comprehensive registries are lacking, conventional interventions remain the standard of care in non-haemophilic patients with severe bleeding

Six-body Light-Front Tamm-Dancoff approximation and wave functions for the massive Schwinger model

The spectrum of the massive Schwinger model in the strong coupling region is obtained by using the light-front Tamm-Dancoff (LFTD) approximation up to including six-body states. We numerically confirm that the two-meson bound state has a negligibly small six-body component. Emphasis is on the usefulness of the information about states (wave functions). It is used for identifying the three-meson bound state among the states below the three-meson threshold. We also show that the two-meson bound state is well described by the wave function of the relative motion.Comment: 19 pages, RevTeX, 7 figures are available upon request; Minor errors have been corrected; Final version to appear in Phys.Rev.

The impact of biofuel poplar cultivation on ground-level ozone and premature human mortality depends on cultivar selection and planting location

Isoprene and other volatile organic compounds emitted from vegetation play a key role in governing the formation of ground-level ozone. Emission rates of such compounds depend critically on the plant species. Future land use change, driven by the cultivation of biofuel feedstocks, will change the distribution of plant species and hence the magnitude and distribution of emissions. Here we use relationships between biomass yield and isoprene emissions derived from experimental data for 29 commercially available poplar hybrids to assess the impact that the large-scale cultivation of poplar for use as a biofuel feedstock will have on air quality in Europe. We show that the increases in ground-level ozone across Europe will increase the number of premature deaths attributable to ozone pollution each year by up to 6%. Substantial crop losses (up to ~9 Mt y-1 of wheat and maize) are also projected. We further demonstrate that these impacts are strongly dependent on the location of the poplar plantations, due to the prevailing meteorology, the population density and the dominant crop type of the region. Our findings indicate the need for a concerted and centralized decision-making process that considers all aspects of future land use change in Europe, and not just the effect on greenhouse gas emissions

Effects of intergroup contact and relative gratification vs. deprivation on prejudice on both sides of the U.S./Mexico status divide

A study in the U.S.–Mexican intergroup context examined how collective relative gratification (RG) versus deprivation affects the relationship between intergroup contact and interpersonal closeness and subtle prejudice towards an out‐group. Participants were Mexican university students in Mexico (N = 239) and non‐Mexican students in California (N = 90). As predicted, Mexicans experienced less gratification/higher relative deprivation (RD), and low quality intergroup contact and expressed lower interpersonal closeness and higher subtle prejudice than U.S. Americans. Differences between countries were larger amongst participants reporting higher RD. Second‐stage moderated mediation analysis showed that the mediating effects of contact between country and interpersonal closeness and subtle prejudice, respectively, were larger amongst participants who felt relatively gratified than those who felt relatively deprived. These findings underline the importance of recognizing the moderating effect of differences in the RG versus RD levels of minority and majority groups when anticipating the potential benefits of intergroup contact for prejudice reduction

Zero Modes in a c=2c = 2 Matrix Model

Recently \REF\dk{Simon Dalley and Igor Klebanov,'Light Cone Quantization of the $c=2$ Matrix Model', PUPT-1333, hepth@xxx/920705} \refend Dalley and Klebanov proposed a light-cone quantized study of the $c=2$ matrix model, but which ignores $k^{+}=0$ contributions. Since the non-critical string limit of the matrix model involves taking the parameters $\lambda$ and $\mu$ of the matrix model to a critical point, zero modes of the field might be important in this study. The constrained light-cone quantization (CLCQ) approach of Heinzl, Krusche and Werner is applied . It is found that there is coupling between the zero mode sector and the rest of the theory, hence CLCQ should be implemented.Comment: phyzxx, 14 pages, SLAC-PUB-59x

Renormal-order improvement of the Schwinger mass

The massive Schwinger model may be analysed by a perturbation expansion in the fermion mass. However, the results of this mass perturbation theory are sensible only for sufficiently small fermion mass. By performing a renormal-ordering, we arrive at a chiral perturbation expansion where the expansion parameter remains small even for large fermion mass. We use this renormal-ordered chiral perturbation theory for a computation of the Schwinger mass and compare our results with lattice computations.Comment: Latex file, 13 pages, 3 figures, needed macro: psbox.te