Multicanonical Study of Coarse-Grained Off-Lattice Models for Folding Heteropolymers

We have performed multicanonical simulations of hydrophobic-hydrophilic heteropolymers with two simple effective, coarse-grained off-lattice models to study the influence of specific interactions in the models on conformational transitions of selected sequences with 20 monomers. Another aspect of the investigation was the comparison with the purely hydrophobic homopolymer and the study of general conformational properties induced by the "disorder" in the sequence of a heteropolymer. Furthermore, we applied an optimization algorithm to sequences with up to 55 monomers and compared the global-energy minimum found with lowest-energy states identified within the multicanonical simulation. This was used to find out how reliable the multicanonical method samples the free-energy landscape, in particular for low temperatures.Comment: 11 pages, RevTeX, 10 Postscript figures, Author Information under http://www.physik.uni-leipzig.de/index.php?id=2

Collagen Deposition During Wound Repair

Collagen fiber diameters, amount of birefringent collagen (brightness) and birefringence retardation were measured in implanted collagen-based sponges containing hyaluronic acid (HA) and fibronectin (FN). In the presence of HA and FN, increased number of fibroblasts and brightness were observed 6 days after wounding. Increased brightness in the presence of HA and FN reflected increased deposition of oriented collagen fibers. From days 9 to 12, increased fiber diameters were similar in implanted collagen-based sponges with or without HA and FN. Increased birefringence retardation in sponges containing HA and FN was consistent with increased packing density of collagen fibers observed by scanning electron microscopy. Our results suggest that HA and FN are effective in promoting fibroblast movement into a collagen sponge and deposition of collagen fibers during the early phases of wound healing. Use of a collagen-based sponge containing HA and FN may enhance collagen deposition in situations where healing is compromised as in the case of dermal ulcers

Assay of phospholipases A2 and their inhibitors by kinetic analysis in the scooting mode

Several cellular processes are regulated by interfacial catalysis on biomembrane surfaces. Phospholipases A2 (PLA2) are interesting not only as prototypes for interfacial catalysis, but also because they mobilize precursors for the biosynthesis of eicosanoids and platelet activating factor, and these agents ultimately control a wide range of secretory and inflammatory processes. Since PLA2 carry out their catalytic function at membrane surfaces, the kinetics of these enzymes depends on what the enzyme ‘sees’ at the interface, and thus the observed rate is profoundly influenced by the organization and dynamics of the lipidwater interface (‘quality of the interface’). In this review we elaborate the advantages of monitoring interfacial catalysis in the scooting mode, that is, under the conditions where the enzyme remains bound to vesicles for several thousand catalytic turnover cycles. Such a highly processive catalytic turnover in the scooting mode is useful for a rigorous and quantitative characterization of the kinetics of interfacial catalysis. This analysis is now extended to provide insights into designing strategy for PLA2 assays and screens for their inhibitors

Glueball masses in the large N limit

The lowest-lying glueball masses are computed in SU($N$) gauge theory on a spacetime lattice for constant value of the lattice spacing $a$ and for $N$ ranging from 3 to 8. The lattice spacing is fixed using the deconfinement temperature at temporal extension of the lattice $N_T = 6$. The calculation is conducted employing in each channel a variational ansatz performed on a large basis of operators that includes also torelon and (for the lightest states) scattering trial functions. This basis is constructed using an automatic algorithm that allows us to build operators of any size and shape in any irreducible representation of the cubic group. A good signal is extracted for the ground state and the first excitation in several symmetry channels. It is shown that all the observed states are well described by their large $N$ values, with modest ${\cal O}(1/N^2)$ corrections. In addition spurious states are identified that couple to torelon and scattering operators. As a byproduct of our calculation, the critical couplings for the deconfinement phase transition for N=5 and N=7 and temporal extension of the lattice $N_T=6$ are determined.Comment: 1+36 pages, 22 tables, 21 figures. Typos corrected, conclusions unchanged, matches the published versio

The glueball spectrum from an anisotropic lattice study

The spectrum of glueballs below 4 GeV in the SU(3) pure-gauge theory is investigated using Monte Carlo simulations of gluons on several anisotropic lattices with spatial grid separations ranging from 0.1 to 0.4 fm. Systematic errors from discretization and finite volume are studied, and the continuum spin quantum numbers are identified. Care is taken to distinguish single glueball states from two-glueball and torelon-pair states. Our determination of the spectrum significantly improves upon previous Wilson action calculations.Comment: 14 pages, 8 figures, uses REVTeX and epsf.sty (final version published in Physical Review D

Effect of vitamin K2 on postural sway in older people who fall:a randomized controlled trial

OBJECTIVES: Vitamin K is thought to be involved in both bone health and maintenance of neuromuscular function. We tested the effect of vitamin K2 supplementation on postural sway, falls, healthcare costs, and indices of physical function in older people at risk of falls.DESIGN: Parallel-group double-blind randomized placebo-controlled trial.SETTING: Fourteen primary care practices in Scotland, UK.PARTICIPANTS: A total of 95 community-dwelling participants aged 65 and older with at least two falls, or one injurious fall, in the previous year.INTERVENTION: Once/day placebo, 200 μg or 400 μg of oral vitamin K2 for 1 year.MEASUREMENTS: The primary outcome was anteroposterior sway measured using sway plates at 12 months, adjusted for baseline. Secondary outcomes included the Short Physical Performance Battery, Berg Balance Scale, Timed Up &amp; Go Test, quality of life, health and social care costs, falls, and adverse events.RESULTS: Mean participant age was 75 (standard deviation [SD] = 7) years. Overall, 58 of 95 (61%) were female; 77 of 95 (81%) attended the 12-month visit. No significant effect of either vitamin K2 dose was seen on the primary outcome of anteroposterior sway (200 μg vs placebo: -.19 cm [95% confidence interval [CI] -.68 to .30; P = .44]; 400 μg vs placebo: .17 cm [95% CI -.33 to .66; P = .50]; or 400 μg vs 200 μg: .36 cm [95% CI -.11 to .83; P = .14]). Adjusted falls rates were similar in each group. No significant treatment effects were seen for other measures of sway or secondary outcomes. Costs were higher in both vitamin K2 arms than in the placebo arm.CONCLUSION: Oral vitamin K2 supplementation did not improve postural sway or physical function in older people at risk of falls.</p

Addition of adult-to-adult living donation to liver transplant programs improves survival but at an increased cost

Using outcomes data from the Adult-to-Adult Living Donor Liver Transplantation Cohort Study, we performed a cost-effectiveness analysis exploring the costs and benefits of living donor liver transplantation (LDLT). A multistage Markov decision analysis model was developed with treatment, including medical management only (strategy 1), waiting list with possible deceased donor liver transplantation (DDLT; strategy 2), and waiting list with possible LDLT or DDLT (strategy 3) over 10 years. Decompensated cirrhosis with medical management offered survival of 2.0 quality-adjusted life years (QALYs) while costing an average of $65,068, waiting list with possible DDLT offered 4.4-QALY survival and a mean cost of$151,613, and waiting list with possible DDLT or LDLT offered 4.9-QALY survival and a mean cost of $208,149. Strategy 2 had an incremental cost-effectiveness ratio (ICER) of$35,976 over strategy 1, whereas strategy 3 produced an ICER of $106,788 over strategy 2. On average, strategy 3 cost$47,693 more per QALY than strategy 1. Both DDLT and LDLT were cost-effective compared to medical management of cirrhosis over our 10-year study period. The addition of LDLT to a standard waiting list DDLT program is effective at improving recipient survival and preventing waiting list deaths but at a greater cost. Liver Transpl 15:148–162, 2009. © 2009 AASLD.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/61905/1/21671_ftp.pd

Effects of plant pathogens on population dynamics and community composition in grassland ecosystems: two case studies

Grassland ecosystems comprise a major portion of the earth’s terrestrial surface, ranging from high-input cultivated monocultures or simple species mixtures to relatively unmanaged but dynamic systems. Plant pathogens are a component of these systems with their impact dependent on many interacting factors, including grassland species population dynamics and community composition, the topics covered in this paper. Plant pathogens are affected by these interactions and also act reciprocally by modifying their nature. We review these features of disease in grasslands and then introduce the 150-year long-term Park Grass Experiment (PGE) at Rothamsted Research in the UK. We then consider in detail two plant-pathogen systems present in the PGE, Tragopogon pratensis-Puccinia hysterium and Holcus lanata-Puccinia coronata. These two systems have very different life history characteristics: the first, a biennial member of the Asteraceae infected by its host-specific, systemic rust; the second, a perennial grass infected by a host-non-specific rust. We illustrate how observational, experimental and modelling studies can contribute to a better understanding of population dynamics, competitive interactions and evolutionary outcomes. With Tragopogon pratensis-Puccinia hysterium, characterised as an “outbreak” species in the PGE, we show that pathogen-induced mortality is unlikely to be involved in host population regulation; and that the presence of even a short-lived seed-bank can affect the qualitative outcomes of the host-pathogen dynamics. With Holcus lanata-Puccinia coronata, we show how nutrient conditions can affect adaptation in terms of host defence mechanisms, and that co-existence of competing species affected by a common generalist pathogen is unlikely

TRIP/NOPO E3 Ubiquitin Ligase Promotes Ubiquitylation of DNA Polymerase η

We previously identified a Drosophila maternal effect-lethal mutant named ‘no poles’ (nopo). Embryos from nopo females undergo mitotic arrest with barrel-shaped, acentrosomal spindles during the rapid cycles of syncytial embryogenesis because of activation of a Chk2-mediated DNA checkpoint. NOPO is the Drosophila homolog of human TNF receptor associated factor (TRAF)-interacting protein (TRIP), which has been implicated in TNF signaling. NOPO and TRIP contain RING domains closely resembling those of known E3 ubiquitin ligases. We herein sought to elucidate the mechanism by which TRIP/NOPO promotes genomic stability by performing a yeast two-hybrid screen to identify potential substrates/interactors. We identified members of the Y-family of DNA polymerases that facilitate replicative bypass of damaged DNA (translesion synthesis) as TRIP interactors. We show that TRIP and NOPO co-immunoprecipitate with human and Drosophila Polη, respectively, from cultured cells. We generated a null mutation in Drosophila Polη (dPolη) and found that dPolη-derived embryos have increased sensitivity to ultraviolet irradiation and exhibit nopo-like mitotic spindle defects. dPolη and nopo interact genetically in that overexpression of dPolηn hypomorphic nopo-derived embryos suppresses nopo phenotypes. We observed enhanced ubiquitylation of Polη by TRIP and NOPO E3 ligases in human cells and Drosophila embryos, respectively, and show that TRIP promotes hPolη localization to nuclear foci in human cells. We present a model in which TRIP/NOPO ubiquitylates Polη to positively regulate its activity in translesion synthesis

Efficient glueball simulations on anisotropic lattices

Monte Carlo results for the low-lying glueball spectrum using an improved, anisotropic action are presented. Ten simulations at lattice spacings ranging from 0.2 to 0.4 fm and two different anisotropies have been performed in order demonstrate the advantages of using coarse, anisotropic lattices to calculate glueball masses. Our determinations of the tensor (2++) and pseudovector (1+-) glueball masses are more accurate than previous Wilson action calculations.Comment: 43 pages, LaTeX (with revtex). 13 postscript figures. Submitted to Phys. Rev.