Estimation of prediction error variances via Monte Carlo sampling methods using different formulations of the prediction error variance

Calculation of the exact prediction error variance covariance matrix is often computationally too demanding, which limits its application in REML algorithms, the calculation of accuracies of estimated breeding values and the control of variance of response to selection. Alternatively Monte Carlo sampling can be used to calculate approximations of the prediction error variance, which converge to the true values if enough samples are used. However, in practical situations the number of samples, which are computationally feasible, is limited. The objective of this study was to compare the convergence rate of different formulations of the prediction error variance calculated using Monte Carlo sampling. Four of these formulations were published, four were corresponding alternative versions, and two were derived as part of this study. The different formulations had different convergence rates and these were shown to depend on the number of samples and on the level of prediction error variance. Four formulations were competitive and these made use of information on either the variance of the estimated breeding value and on the variance of the true breeding value minus the estimated breeding value or on the covariance between the true and estimated breeding values

Parallel multicentre randomised trial of a clinical trial question prompt list in patients considering participation in phase 3 cancer treatment trials

Accepted 9 February 2017Objective: To evaluate the effect of a clinical trial question prompt list in patients considering enrolment in cancer treatment trials. Setting: Tertiary cancer referral hospitals in three state capital cities in Australia. Participants: 88 patients with cancer attending three cancer centres in Australia, who were considering enrolment in phase 3 treatment trials, were invited to enrol in an unblinded randomised trial of provision of a clinical trial question prompt list (QPL) before consenting to enrol in the treatment trial. Interventions: We developed and pilot tested a targeted QPL for patients with cancer considering clinical trial participation (the clinical trial QPL). Consenting patients were randomised to receive the clinical trial QPL or not before further discussion with their oncologist and/or trial nurse about the treatment trial. Primary and secondary outcomes: Questionnaires were completed at baseline and within 3â €..weeks of deciding on treatment trial participation. Main outcome measure: scores on the Quality of Informed Consent questionnaire (QuIC). Results: 88 patients of 130 sought for the study were enrolled (43 males), and 45 received the clinical trial QPL. 49% of trials were chemotherapy interventions for patients with advanced disease, 35% and 16% were surgical adjuvant and radiation adjuvant trials respectively. 70 patients completed all relevant questionnaires. 28 of 43 patients in the control arm compared with 39 of 45 patients receiving the clinical trial QPL completed the QuIC (p=0.0124). There were no significant differences in the QuIC scores between the randomised groups (QuIC part A p=0.08 and QuIC part B p=0.92). There were no differences in patient satisfaction with decisions or in anxiety levels between the randomised groups. Conclusions: Use of a question prompt list did not significantly change the QuIC scores in this randomised trial. ANZCTR 12606000214538 prospectively registered 31/5/2006. Trial registration number: Results, ACTRN12606000214538.Martin H N Tattersall, Michael Jefford, Andrew Martin, Ian Olver, John F Thompson, Richard F Brown, Phyllis N Buto

Multiple sequence alignment based on set covers

We introduce a new heuristic for the multiple alignment of a set of sequences. The heuristic is based on a set cover of the residue alphabet of the sequences, and also on the determination of a significant set of blocks comprising subsequences of the sequences to be aligned. These blocks are obtained with the aid of a new data structure, called a suffix-set tree, which is constructed from the input sequences with the guidance of the residue-alphabet set cover and generalizes the well-known suffix tree of the sequence set. We provide performance results on selected BAliBASE amino-acid sequences and compare them with those yielded by some prominent approaches

Prevalence of true vein graft aneurysms: Implications for aneurysm pathogenesis

AbstractBackground: Circumstantial evidence suggests that arterial aneurysms have a different cause than atherosclerosis and may form part of a generalized dilating diathesis. The aim of this study was to compare the rates of spontaneous aneurysm formation in vein grafts performed either for popliteal aneurysms or for occlusive disease. The hypothesis was that if arterial aneurysms form a part of a systemic process, then the rates of vein graft aneurysms should be higher for patients with popliteal aneurysms than for patients with lower limb ischemia caused by atherosclerosis. Methods: Infrainguinal vein grafting procedures performed from 1990 to 1995 were entered into a prospective audit and graft surveillance program. Aneurysmal change was defined as a focal increase in the graft diameter of 1.5 cm or greater, excluding false aneurysms and dilatations after graft angioplasty. Results: During the study period, 221 grafting procedures were performed in 200 patients with occlusive disease and 24 grafting procedures were performed in 21 patients with popliteal aneurysms. Graft surveillance revealed spontaneous aneurysm formation in 10 of the 24 bypass grafts (42%) for popliteal aneurysms but in only 4 of the 221 grafting procedures (2%) that were performed for chronic lower limb ischemia. Conclusion:This study provides further evidence that aneurysmal disease is a systemic process, and this finding has clinical implications for the treatment of popliteal aneurysms. (J Vasc Surg 1999;29:403-8.

Doxycycline inhibits elastin degradation and reduces metalloproteinase activity in a model of aneurysmal disease

AbstractPurpose: Abdominal aortic aneurysms are characterized by degradation of the extracellular matrix, with a reduction in the elastin concentration of the arterial media. These changes are mediated by increased levels of endogenous metalloproteinases (MMPs) within the aorta, which provide a potential therapeutic target for pharmacologic agents aimed at reducing the growth rate of small aneurysms. In this study, the ability of doxycycline—an MMP inhibitor—to reduce matrix degradation was assessed in a previously described model of aneurysmal disease that used a brief pulse of elastase to induce MMP production and elastin degradation in arterial organ cultures. Methods: Porcine aortic segments (n = 8) were preincubated in exogenous pancreatic elastase for 24 hours before culture in standard conditions for 13 days with both 1 and 10 mg/L doxycycline. Control segments were cultured both without doxycycline and without elastase. At the termination of culture, MMPs were extracted from the tissue and quantified by a combination of substrate gel enzymography and immunoblotting. The volume fractions of elastin and collagen were determined by stereologic analysis of sections stained with Miller's elastin and van Gieson's stain. Results: Stereologic analysis demonstrated a significant preservation of elastin in aorta treated with doxycycline 10 mg/L (p < 0.001) and demonstrated that this preservation was accompanied by a significant reduction in MMP-9 activity (p < 0.02). Immunoblotting for tissue inhibitors of metalloproteinases (TIMP-1 and TIMP-2) showed no decreased production in the doxycycline-treated groups. Conclusions: Therapeutic ranges of doxycycline significantly inhibited elastin degradation and MMP-9 production within aortic organ cultures. These data suggest that doxycycline may have a potential application in reducing the growth rates of small abdominal aortic aneurysms. (J Vasc Surg 1998;27:354-61.

Elastic scattering and breakup of 17^F at 10 MeV/nucleon

Angular distributions of fluorine and oxygen produced from 170 MeV 17^F incident on 208^Pb were measured. The elastic scattering data are in good agreement with optical model calculations using a double-folding potential and parameters similar to those obtained from 16^O+208^Pb. A large yield of oxygen was observed near \theta_lab=36 deg. It is reproduced fairly well by a calculation of the (17^F,16^O) breakup, which is dominated by one-proton stripping reactions. The discrepancy between our previous coincidence measurement and theoretical predictions was resolved by including core absorption in the present calculation.Comment: 9 pages, 5 figure

Evolution of active and polar photospheric magnetic fields during the rise of Cycle 24 compared to previous cycles

The evolution of the photospheric magnetic field during the declining phase and minimum of Cycle 23 and the recent rise of Cycle 24 are compared with the behavior during previous cycles. We used longitudinal full-disk magnetograms from the NSO's three magnetographs at Kitt Peak, the Synoptic Optical Long-term Investigations of the Sun (SOLIS) Vector Spectro-Magnetograph (VSM), the Spectromagnetograph and the 512-Channel Magnetograph instruments, and longitudinal full-disk magnetograms from the Mt. Wilson 150-foot tower. We analyzed 37 years of observations from these two observatories that have been observing daily, weather permitting, since 1974, offering an opportunity to study the evolving relationship between the active region and polar fields in some detail over several solar cycles. It is found that the annual averages of a proxy for the active region poloidal magnetic field strength, the magnetic field strength of the high-latitude poleward streams, and the time derivative of the polar field strength are all well correlated in each hemisphere. These results are based on statistically significant cyclical patterns in the active region fields and are consistent with the Babcock-Leighton phenomenological model for the solar activity cycle. There was more hemispheric asymmetry in the activity level, as measured by total and maximum active region flux, during late Cycle 23 (after around 2004), when the southern hemisphere was more active, and Cycle 24 up to the present, when the northern hemisphere has been more active, than at any other time since 1974. The active region net proxy poloidal fields effectively disappeared in both hemispheres around 2004, and the polar fields did not become significantly stronger after this time. We see evidence that the process of Cycle 24 field reversal has begun at both poles.Comment: Accepted for publication in Solar Physic

Breakup of 17^{17}F on 208^{208}Pb near the Coulomb barrier

Angular distributions of oxygen produced in the breakup of $^{17}$F incident on a $^{208}$Pb target have been measured around the grazing angle at beam energies of 98 and 120 MeV. The data are dominated by the proton stripping mechanism and are well reproduced by dynamical calculations. The measured breakup cross section is approximately a factor of 3 less than that of fusion at 98 MeV. The influence of breakup on fusion is discussed.Comment: 7 pages, 8 figure

New Structural Insights into the Genome and Minor Capsid Proteins of BK Polyomavirus using Cryo-Electron Microscopy

BK polyomavirus is the causative agent of several diseases in transplant patients and the immunosuppressed. In order to better understand the structure and life cycle of BK, we produced infectious virions and VP1-only virus-like particles in cell culture, and determined their three-dimensional structures using cryo-electron microscopy (EM) and single-particle image processing. The resulting 7.6-Å resolution structure of BK and 9.1-Å resolution of the virus-like particles are the highest-resolution cryo-EM structures of any polyomavirus. These structures confirm that the architecture of the major structural protein components of these human polyomaviruses are similar to previous structures from other hosts, but give new insight into the location and role of the enigmatic minor structural proteins, VP2 and VP3. We also observe two shells of electron density, which we attribute to a structurally ordered part of the viral genome, and discrete contacts between this density and both VP1 and the minor capsid proteins