University of Udine

About: University of Udine is a education organization based out in Udine, Italy. It is known for research contribution in the topics: Population & Large Hadron Collider. The organization has 6745 authors who have published 20530 publications receiving 669088 citations. The organization is also known as: Università degli Studi di Udine & Universita degli Studi di Udine.

Assemblathon 2: evaluating de novo methods of genome assembly in three vertebrate species

Abstract: Background: The process of generating raw genome sequence data continues to become cheaper, faster, and more accurate. However, assembly of such data into high-quality, finished genome sequences remains challenging. Many genome assembly tools are available, but they differ greatly in terms of their performance (speed, scalability, hardware requirements, acceptance of newer read technologies) and in their final output (composition of assembled sequence). More importantly, it remains largely unclear how to best assess the quality of assembled genome sequences. The Assemblathon competitions are intended to assess current state-of-the-art methods in genome assembly. Results: In Assemblathon 2, we provided a variety of sequence data to be assembled for three vertebrate species (a bird, a fish, and snake). This resulted in a total of 43 submitted assemblies from 21 participating teams. We evaluated these assemblies using a combination of optical map data, Fosmid sequences, and several statistical methods. From over 100 different metrics, we chose ten key measures by which to assess the overall quality of the assemblies. (Continued on next page)

Structural basis of end-stage failure in ischemic cardiomyopathy in humans.

Abstract: BACKGROUNDIschemic cardiomyopathy is characterized by myocyte loss, reactive cellular hypertrophy, and ventricular scarring. However, the relative contribution of these tissue and cellular processes to late failure remains to be determined.METHODS AND RESULTSTen hearts were obtained from individuals undergoing cardiac transplantation as a result of chronic coronary artery disease in its terminal stage. An identical number of control hearts were collected at autopsy from patients who died from causes other than cardiovascular disease, and morphometric methodologies were applied to the analysis of the left and right ventricular myocardium. Left ventricular hypertrophy evaluated as a change in organ weight, aggregate myocyte mass, and myocyte cell volume per nucleus showed increases of 85%, 47%, and 103%, respectively. Corresponding increases in the right ventricle were 75%, 74%, and 112%. Myocyte loss, which accounted for 28% and 30% in the left and right ventricles, was responsible for the difference in th...

Modeling temporal and large‐scale spatial variability of soil respiration from soil water availability, temperature and vegetation productivity indices

Abstract: [1] Field-chamber measurements of soil respiration from 17 different forest and shrubland sites in Europe and North America were summarized and analyzed with the goal to develop a model describing seasonal, interannual and spatial variability of soil respiration as affected by water availability, temperature, and site properties. The analysis was performed at a daily and at a monthly time step. With the daily time step, the relative soil water content in the upper soil layer expressed as a fraction of field capacity was a good predictor of soil respiration at all sites. Among the site variables tested, those related to site productivity (e.g., leaf area index) correlated significantly with soil respiration, while carbon pool variables like standing biomass or the litter and soil carbon stocks did not show a clear relationship with soil respiration. Furthermore, it was evidenced that the effect of precipitation on soil respiration stretched beyond its direct effect via soil moisture. A general statistical nonlinear regression model was developed to describe soil respiration as dependent on soil temperature, soil water content, and site-specific maximum leaf area index. The model explained nearly two thirds of the temporal and intersite variability of soil respiration with a mean absolute error of 0.82 μmol m−2 s−1. The parameterized model exhibits the following principal properties: (1) At a relative amount of upper-layer soil water of 16% of field capacity, half-maximal soil respiration rates are reached. (2) The apparent temperature sensitivity of soil respiration measured as Q10 varies between 1 and 5 depending on soil temperature and water content. (3) Soil respiration under reference moisture and temperature conditions is linearly related to maximum site leaf area index. At a monthly timescale, we employed the approach by Raich et al. [2002] that used monthly precipitation and air temperature to globally predict soil respiration (T&P model). While this model was able to explain some of the month-to-month variability of soil respiration, it failed to capture the intersite variability, regardless of whether the original or a new optimized model parameterization was used. In both cases, the residuals were strongly related to maximum site leaf area index. Thus, for a monthly timescale, we developed a simple T&P&LAI model that includes leaf area index as an additional predictor of soil respiration. This extended but still simple model performed nearly as well as the more detailed time step model and explained 50% of the overall and 65% of the site-to-site variability. Consequently, better estimates of globally distributed soil respiration should be obtained with the new model driven by satellite estimates of leaf area index. Before application at the continental or global scale, this approach should be further tested in boreal, cold-temperate, and tropical biomes as well as for non-woody vegetation.

A limit on the variation of the speed of light arising from quantum gravity effects

Abstract: A cornerstone of Einstein's special relativity is Lorentz invariance-the postulate that all observers measure exactly the same speed of light in vacuum, independent of photon-energy. While special relativity assumes that there is no fundamental length-scale associated with such invariance, there is a fundamental scale (the Planck scale, l(Planck) approximate to 1.62 x 10(-33) cm or E(Planck) = M(Planck)c(2) approximate to 1.22 x 10(19) GeV), at which quantum effects are expected to strongly affect the nature of space-time. There is great interest in the (not yet validated) idea that Lorentz invariance might break near the Planck scale. A key test of such violation of Lorentz invariance is a possible variation of photon speed with energy(1-7). Even a tiny variation in photon speed, when accumulated over cosmological light-travel times, may be revealed by observing sharp features in gamma-ray burst (GRB) light-curves(2). Here we report the detection of emission up to similar to 31GeV from the distant and short GRB090510. We find no evidence for the violation of Lorentz invariance, and place a lower limit of 1.2E(Planck) on the scale of a linear energy dependence (or an inverse wavelength dependence), subject to reasonable assumptions about the emission (equivalently we have an upper limit of l(Planck)/1.2 on the length scale of the effect). Our results disfavour quantum-gravity theories(3,6,7) in which the quantum nature of space-time on a very small scale linearly alters the speed of light.

Adjuvant Exemestane with Ovarian Suppression in Premenopausal Breast Cancer

Abstract: BACKGROUND Adjuvant therapy with an aromatase inhibitor improves outcomes, as compared with tamoxifen, in postmenopausal women with hormone-receptor–positive breast cancer. METHODS In two phase 3 trials, we randomly assigned premenopausal women with hormonereceptor–positive early breast cancer to the aromatase inhibitor exemestane plus ovarian suppression or tamoxifen plus ovarian suppression for a period of 5 years. Suppression of ovarian estrogen production was achieved with the use of the gonadotropin-releasing-hormone agonist triptorelin, oophorectomy, or ovarian irradiation. The primary analysis combined data from 4690 patients in the two trials. RESULTS After a median follow-up of 68 months, disease-free survival at 5 years was 91.1% in the exemestane–ovarian suppression group and 87.3% in the tamoxifen–ovarian suppression group (hazard ratio for disease recurrence, second invasive cancer, or death, 0.72; 95% confidence interval [CI], 0.60 to 0.85; P<0.001). The rate of freedom from breast cancer at 5 years was 92.8% in the exemestane–ovarian suppression group, as compared with 88.8% in the tamoxifen–ovarian suppression group (hazard ratio for recurrence, 0.66; 95% CI, 0.55 to 0.80; P<0.001). With 194 deaths (4.1% of the patients), overall survival did not differ significantly between the two groups (hazard ratio for death in the exemestane–ovarian suppression group, 1.14; 95% CI, 0.86 to 1.51; P = 0.37). Selected adverse events of grade 3 or 4 were reported for 30.6% of the patients in the exemestane–ovarian suppression group and 29.4% of those in the tamoxifen–ovarian suppression group, with profiles similar to those for postmenopausal women. CONCLUSIONS In premenopausal women with hormone-receptor–positive early breast cancer, adjuvant treatment with exemestane plus ovarian suppression, as compared with tamoxifen plus ovarian suppression, significantly reduced recurrence. (Funded by Pfizer and others; TEXT and SOFT ClinicalTrials.gov numbers, NCT00066703 and NCT00066690, respectively.)