Modeling Symmetric Macromolecular Structures in Rosetta3

Symmetric protein assemblies play important roles in many biochemical processes. However, the large size of such systems is challenging for traditional structure modeling methods. This paper describes the implementation of a general framework for modeling arbitrary symmetric systems in Rosetta3. We describe the various types of symmetries relevant to the study of protein structure that may be modeled using Rosetta's symmetric framework. We then describe how this symmetric framework is efficiently implemented within Rosetta, which restricts the conformational search space by sampling only symmetric degrees of freedom, and explicitly simulates only a subset of the interacting monomers. Finally, we describe structure prediction and design applications that utilize the Rosetta3 symmetric modeling capabilities, and provide a guide to running simulations on symmetric systems

Phenomenology of the superconducting state in Sr2RuO4

The symmetry of the superconducting phase of Sr2RuO4 is identified as the odd-parity pairing state d(k)=\hat{z}(k_x \pm i k_y) based on recent experiments. The experimental evidence for the so-called orbital dependent superconductivity leads to a single-band description of superconductivity based on spin fluctuation mechanism. It is shown that the state \hat{z}(k_x \pm i k_y) can be stabilized by the spin fluctuation feedback mechanism analogous to the A-phase in 3He and by spin-orbit coupling effects.Comment: 7 pages, 1 figure, to be published in Proc. of the conference "Anomalous Complex Superconductors" (Crete, 1998

Cases of advanced visual field loss at referral to glaucoma clinics - more men than women?

Purpose In many medical conditions ‘late presentation’ of disease is more of a problem for men than women. Risk of sight loss from glaucoma is certainly greater in those detected with advanced disease. We performed a retrospective study to test the hypothesis that men are more likely than women to have advanced visual field loss at referral to glaucoma clinics. Methods We used 152 918 Humphrey visual fields from 32 147 patients from three regionally different hospitals in England; no other clinical data were made available apart from patient's age, sex and examination dates. The study population was defined as patients with measureable visual field loss in at least one eye at referral to glaucoma clinics. Cases of advanced visual field loss as defined by the Enhanced Glaucoma Severity Staging method at the first visit to secondary care were used as a proxy measure for late presentation of glaucoma. Age-adjusted relative risk (RR) was calculated as the ratio of the proportion of men to women with this proxy measure. Results Median (interquartile range) age and MD (worse eye) for 3733 men and 4264 women was 72 (63, 79) and 74 (64, 81) years and −6.4 (−11.7, −3.8) and −6.3 (−11.0, −3.8) dB respectively. Overall proportion of patients with advanced visual field loss at referral to glaucoma clinics was slightly higher in men (25.0%) than in women (22.3%); this difference was statistically significant (p < 0.01). Overall age-standardised RR was statistically significant (1.16; p < 0.001); a person with late presentation of glaucoma is 16% (95% confidence interval: 7–25%) more likely to be a man than a woman. Conclusions A large number of patients with glaucomatous visual field defects are estimated to have advanced loss in at least one eye on referral to secondary care in England; risk for men more likely presenting with late disease is slightly greater than for women

Real-Time On-Board Airborne Demonstration of High-Speed On-Board Data Processing for Science Instruments (HOPS)

The project called High-Speed On-Board Data Processing for Science Instruments (HOPS) has been funded by NASA Earth Science Technology Office (ESTO) Advanced Information Systems Technology (AIST) program since April, 2012. The HOPS team recently completed two flight campaigns during the summer of 2014 on two different aircrafts with two different science instruments. The first flight campaign was in July, 2014 based at NASA Langley Research Center (LaRC) in Hampton, VA on the NASA's HU-25 aircraft. The science instrument that flew with HOPS was Active Sensing of CO2 Emissions over Nights, Days, and Seasons (ASCENDS) CarbonHawk Experiment Simulator (ACES) funded by NASA's Instrument Incubator Program (IIP). The second campaign was in August, 2014 based at NASA Armstrong Flight Research Center (AFRC) in Palmdale, CA on the NASA's DC-8 aircraft. HOPS flew with the Multifunctional Fiber Laser Lidar (MFLL) instrument developed by Excelis Inc. The goal of the campaigns was to perform an end-to-end demonstration of the capabilities of the HOPS prototype system (HOPS COTS) while running the most computationally intensive part of the ASCENDS algorithm real-time on-board. The comparison of the two flight campaigns and the results of the functionality tests of the HOPS COTS are presented in this paper

Split transition in ferromagnetic superconductors

The split superconducting transition of up-spin and down-spin electrons on the background of ferromagnetism is studied within the framework of a recent model that describes the coexistence of ferromagnetism and superconductivity induced by magnetic fluctuations. It is shown that one generically expects the two transitions to be close to one another. This conclusion is discussed in relation to experimental results on URhGe. It is also shown that the magnetic Goldstone modes acquire an interesting structure in the superconducting phase, which can be used as an experimental tool to probe the origin of the superconductivity.Comment: REVTeX4, 15 pp, 7 eps fig

Evaluation of stability of directly standardized rates for sparse data using simulation methods.

Background Directly standardized rates (DSRs) adjust for different age distributions in different populations and enable, say, the rates of disease between the populations to be directly compared. They are routinely published but there is concern that a DSR is not valid when it is based on a “small” number of events. The aim of this study was to determine the value at which a DSR should not be published when analyzing real data in England. Methods Standard Monte Carlo simulation techniques were used assuming the number of events in 19 age groups (i.e., 0–4, 5–9, ... 90+ years) follow independent Poisson distributions. The total number of events, age specific risks, and the population sizes in each age group were varied. For each of 10,000 simulations the DSR (using the 2013 European Standard Population weights), together with the coverage of three different methods (normal approximation, Dobson, and Tiwari modified gamma) of estimating the 95% confidence intervals (CIs), were calculated. Results The normal approximation was, as expected, not suitable for use when fewer than 100 events occurred. The Tiwari method and the Dobson method of calculating confidence intervals produced similar estimates and either was suitable when the expected or observed numbers of events were 10 or greater. The accuracy of the CIs was not influenced by the distribution of the events across categories (i.e., the degree of clustering, the age distributions of the sampling populations, and the number of categories with no events occurring in them). Conclusions DSRs should not be given when the total observed number of events is less than 10. The Dobson method might be considered the preferred method due to the formulae being simpler than that of the Tiwari method and the coverage being slightly more accurate

A Catalog of Neutral and Deleterious Polymorphism in Yeast

The abundance and identity of functional variation segregating in natural populations is paramount to dissecting the molecular basis of quantitative traits as well as human genetic diseases. Genome sequencing of multiple organisms of the same species provides an efficient means of cataloging rearrangements, insertion, or deletion polymorphisms (InDels) and single-nucleotide polymorphisms (SNPs). While inbreeding depression and heterosis imply that a substantial amount of polymorphism is deleterious, distinguishing deleterious from neutral polymorphism remains a significant challenge. To identify deleterious and neutral DNA sequence variation within Saccharomyces cerevisiae, we sequenced the genome of a vineyard and oak tree strain and compared them to a reference genome. Among these three strains, 6% of the genome is variable, mostly attributable to variation in genome content that results from large InDels. Out of the 88,000 polymorphisms identified, 93% are SNPs and a small but significant fraction can be attributed to recent interspecific introgression and ectopic gene conversion. In comparison to the reference genome, there is substantial evidence for functional variation in gene content and structure that results from large InDels, frame-shifts, and polymorphic start and stop codons. Comparison of polymorphism to divergence reveals scant evidence for positive selection but an abundance of evidence for deleterious SNPs. We estimate that 12% of coding and 7% of noncoding SNPs are deleterious. Based on divergence among 11 yeast species, we identified 1,666 nonsynonymous SNPs that disrupt conserved amino acids and 1,863 noncoding SNPs that disrupt conserved noncoding motifs. The deleterious coding SNPs include those known to affect quantitative traits, and a subset of the deleterious noncoding SNPs occurs in the promoters of genes that show allele-specific expression, implying that some cis-regulatory SNPs are deleterious. Our results show that the genome sequences of both closely and distantly related species provide a means of identifying deleterious polymorphisms that disrupt functionally conserved coding and noncoding sequences

Evidence for Pervasive Adaptive Protein Evolution in Wild Mice

The relative contributions of neutral and adaptive substitutions to molecular evolution has been one of the most controversial issues in evolutionary biology for more than 40 years. The analysis of within-species nucleotide polymorphism and between-species divergence data supports a widespread role for adaptive protein evolution in certain taxa. For example, estimates of the proportion of adaptive amino acid substitutions (alpha) are 50% or more in enteric bacteria and Drosophila. In contrast, recent estimates of alpha for hominids have been at most 13%. Here, we estimate alpha for protein sequences of murid rodents based on nucleotide polymorphism data from multiple genes in a population of the house mouse subspecies Mus musculus castaneus, which inhabits the ancestral range of the Mus species complex and nucleotide divergence between M. m. castaneus and M. famulus or the rat. We estimate that 57% of amino acid substitutions in murids have been driven by positive selection. Hominids, therefore, are exceptional in having low apparent levels of adaptive protein evolution. The high frequency of adaptive amino acid substitutions in wild mice is consistent with their large effective population size, leading to effective natural selection at the molecular level. Effective natural selection also manifests itself as a paucity of effectively neutral nonsynonymous mutations in M. m. castaneus compared to humans

Spin fluctuations in nearly magnetic metals from ab-initio dynamical spin susceptibility calculations:application to Pd and Cr95V5

We describe our theoretical formalism and computational scheme for making ab-initio calculations of the dynamic paramagnetic spin susceptibilities of metals and alloys at finite temperatures. Its basis is Time-Dependent Density Functional Theory within an electronic multiple scattering, imaginary time Green function formalism. Results receive a natural interpretation in terms of overdamped oscillator systems making them suitable for incorporation into spin fluctuation theories. For illustration we apply our method to the nearly ferromagnetic metal Pd and the nearly antiferromagnetic chromium alloy Cr95V5. We compare and contrast the spin dynamics of these two metals and in each case identify those fluctuations with relaxation times much longer than typical electronic `hopping times'Comment: 21 pages, 9 figures. To appear in Physical Review B (July 2000