A High-Order Method for Stiff Boundary Value Problems with Turning Points

This paper describes some high-order collocation-like methods for the numerical solution of stiff boundary-value problems with turning points. The presentation concentrates on the implementation of these methods in conjunction with the implementation of the a priori mesh construction algorithm introduced by Kreiss, Nichols and Brown [SIAM J. Numer. Anal., 23 (1986), pp. 325–368] for such problems. Numerical examples are given showing the high accuracy which can be obtained in solving the boundary value problem for singularly perturbed ordinary differential equations with turning points

Infrared fundus photography

Color infrared fundus photographs were made of normal and pathological eyes. These were compared to conventional fundus photographs of the same eyes. Skilled judges rated the visibility of selected fundus features. Infrared photography produces pictures with false color, altered contrast and increased tissue penetration. These characteristics of infrared film were found to be useful in visualizing the choroidal vessel pattern, showing areas of extensive exudates and retinal atropgy, and showing fundus changes deep to the retina. A convenient method of focusing for infrared pictures was found and an explanation of the reported variations in the color renditions of infrared photographs is suggested

Redox Regulation, Rather than Stress-Induced Phosphorylation, of a Hog1 Mitogen-Activated Protein Kinase Modulates Its Nitrosative-Stress-Specific Outputs

Data availability. The RNA sequencing dataset is available at EBI (www.ebi.ac.uk/arrayexpress/) under accession number E-MTAB-5990. Other data that support the findings of this study are available from the corresponding author upon reasonable request. ACKNOWLEDGMENTS We thank Debbie Smith for constructing the strains JC41 and JC310, Arnab Pradhan for help with DHE control experiments, and our colleagues in the Aberdeen Fungal Group and Newcastle Yeast Group for insightful discussions. We are also grateful to Mike Gustin for his advice. We are grateful to the Centre for Genome Enabled Biology and Medicine, Aberdeen Proteomics, the Iain Fraser Cytometry Centre, the Microscopy and Histology Facility, and the qPCR facility at the University of Aberdeen for their help, advice, and support. This work was funded by the UK Biotechnology and Biological Research Council (http://www.bbsrc.ac.uk) (grants BB/K017365/1 and BB/F00513X/1 to A.J.P.B. and grant BB/K016393/1 to J.Q.). This work was also supported by the European Research Council (http://erc.europa.eu/) (STRIFE advanced grant C-2009-AdG-249793 to A.J.P.B.), the UK Medical Research Council (http://www.mrc.ac.uk) (grant MR/M026663/1 to A.J.P.B. and grant MR/M000923/1 to P.S.S.), the Wellcome Trust (https://wellcome.ac.uk) (grant 097377 to A.J.P.B. and J.Q.), the MRC Centre for Medical Mycology and the University of Aberdeen (grant MR/M026663/1 to A.J.P.B.). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.Peer reviewedPublisher PD

Genome-wide Association Mapping of Qualitatively Inherited Traits in a Germplasm Collection

Genome-wide association (GWA) has been used as a tool for dissecting the genetic architecture of quantitatively inherited traits. We demonstrate here that GWA can also be highly useful for detecting many major genes governing categorically defined phenotype variants that exist for qualitatively inherited traits in a germplasm collection. Genome-wide association mapping was applied to categorical phenotypic data available for 10 descriptive traits in a collection of ~13,000 soybean [Glycine max (L.) Merr.] accessions that had been genotyped with a 50,000 single nucleotide polymorphism (SNP) chip. A GWA on a panel of accessions of this magnitude can offer substantial statistical power and mapping resolution, and we found that GWA mapping resulted in the identification of strong SNP signals for 24 classical genes as well as several heretofore unknown genes controlling the phenotypic variants in those traits. Because some of these genes had been cloned, we were able to show that the narrow GWA mapping SNP signal regions that we detected for the phenotypic variants had chromosomal bp spans that, with just one exception, overlapped the bp region of the cloned genes, despite local variation in SNP number and nonuniform SNP distribution in the chip set

Structure and Migration Mechanisms of Small Vacancy Clusters in Cu: A Combined EAM and DFT Study

Voids in face-centered cubic (fcc) metals are commonly assumed to form via the aggregation of vacancies; however, the mechanisms of vacancy clustering and diffusion are not fully understood. In this study, we use computational modeling to provide a detailed insight into the structures and formation energies of primary vacancy clusters, mechanisms and barriers for their migration in bulk copper, and how these properties are affected at simple grain boundaries. The calculations were carried out using embedded atom method (EAM) potentials and density functional theory (DFT) and employed the site-occupation disorder code (SOD), the activation relaxation technique nouveau (ARTn) and the knowledge led master code (KLMC). We investigate stable structures and migration paths and barriers for clusters of up to six vacancies. The migration of vacancy clusters occurs via hops of individual constituent vacancies with di-vacancies having a significantly smaller migration barrier than mono-vacancies and other clusters. This barrier is further reduced when di-vacancies interact with grain boundaries. This interaction leads to the formation of self-interstitial atoms and introduces significant changes into the boundary structure. Tetra-, penta-, and hexa-vacancy clusters exhibit increasingly complex migration paths and higher barriers than smaller clusters. Finally, a direct comparison with the DFT results shows that EAM can accurately describe the vacancy-induced relaxation effects in the Cu bulk and in grain boundaries. Significant discrepancies between the two methods were found in structures with a higher number of low-coordinated atoms, such as penta-vacancies and di-vacancy absortion by grain boundary. These results will be useful for modeling the mechanisms of diffusion of complex defect structures and provide further insights into the structural evolution of metal films under thermal and mechanical stress

Good prospects: high-resolution telemetry data suggests novel brood site selection behaviour in waterfowl

Breeding success should increase with prior knowledge of the surrounding environment, which is dependent upon an animal\u27s ability to evaluate habitat. Prospecting for nesting locations and migratory stopover sites are well-established behaviours among bird species. We assessed whether three species of California dabbling ducks – mallards, Anas platyrhynchos, gadwall, Mareca strepera, and cinnamon teal, Spatula cyanoptera – in Suisun Marsh, California, U.S.A., a brackish marsh, prospect for suitable wetlands in the week prior to brooding. K-means cluster analyses grouped 29 mallard and gadwall hens into three groups. One group (N = 13) demonstrated evidence of brood site prospecting, with the fewest and latest prebrooding wetland visits. Of these hens, seven visited their future brood pond an average of 1.14 times and only shortly before brooding (1.29 days), obtaining current information on habitat suitability. For the remaining six hens, we did not detect a brooding wetland visit, possibly due to data limitations or because these hens acquired sufficient familiarity with the wetland habitat during nest breaks in adjacent wetlands, obviating the need to prospect the specific brood pond. The second identified group of hens (N = 11) visited the brooding wetland most frequently (on 4.55 days), further in advance (5.27 days), with the fewest unique wetland visits and the earliest brooding date (26 May). The final group of hens (N = 5) were the latest to brood (21 June) and visited the most wetlands, possibly due to less water or more broods present across the landscape. Brood ponds were always farther from the nest than the nearest ponds, indicating that habitat suitability or presence of conspecifics is more important to brood site selection. Prospecting provides hens with knowledge about current habitat conditions and allows them to ‘crowdsource’ public information regarding use of that habitat by other brooding hens. Prospecting may, therefore, benefit ducks inhabiting ephemeral habitats like those within Suisun Marsh, where brood habitat is limited and water cover changes rapidly during the breeding season

Evolution of the Bianchi I, the Bianchi III and the Kantowski-Sachs Universe: Isotropization and Inflation

We study the Einstein-Klein-Gordon equations for a convex positive potential in a Bianchi I, a Bianchi III and a Kantowski-Sachs universe. After analysing the inherent properties of the system of differential equations, the study of the asymptotic behaviors of the solutions and their stability is done for an exponential potential. The results are compared with those of Burd and Barrow. In contrast with their results, we show that for the BI case isotropy can be reached without inflation and we find new critical points which lead to new exact solutions. On the other hand we recover the result of Burd and Barrow that if inflation occurs then isotropy is always reached. The numerical integration is also done and all the asymptotical behaviors are confirmed.Comment: 22 pages, 12 figures, Self-consistent Latex2e File. To be published in Phys. Rev.

Identification of Very Red Counterparts of SiO Maser and OH/IR Objects in the GLIMPSE Survey

Using the 3.6/4.5/5.8/8.0 micron images with 1.2 arcsec pixel resolution from the Spitzer/GLIMPSE survey, we investigated 23 masing and 18 very red objects that were not identified in the 2MASS survey. Counterparts for all selected objects were found in the GLIMPSE images. Color indices in these IR bands suggest the presence of a high-extinction layer of more than a few tenths of a solar mass in front of the central star. Furthermore, radio observations in the SiO and H2O maser lines found characteristic maser-line spectra of the embedded objects, e.g., the SiO J=1-0 line intensity in the v=2 state stronger than that of the v=1 state, or very widespread H2O maser emission spectra. This indicates that these objects are actually enshrouded by very thick circumstellar matter, some of which cannot be ascribed to the AGB wind of the central star. Individually interesting objects are discussed, including two newly found water fountains and an SiO source with nebulosity.Comment: High resolution figures available at ftp://ftp.nro.nao.ac.jp/nroreport/no653.pdf.gz. ApJ No. 655 no.1 issue in pres

Phase-plane analysis of Friedmann-Robertson-Walker cosmologies in Brans-Dicke gravity

We present an autonomous phase-plane describing the evolution of Friedmann-Robertson-Walker models containing a perfect fluid (with barotropic index gamma) in Brans-Dicke gravity (with Brans-Dicke parameter omega). We find self-similar fixed points corresponding to Nariai's power-law solutions for spatially flat models and curvature-scaling solutions for curved models. At infinite values of the phase-plane variables we recover O'Hanlon and Tupper's vacuum solutions for spatially flat models and the Milne universe for negative spatial curvature. We find conditions for the existence and stability of these critical points and describe the qualitative evolution in all regions of the (omega,gamma) parameter space for 0-3/2. We show that the condition for inflation in Brans-Dicke gravity is always stronger than the general relativistic condition, gamma<2/3.Comment: 24 pages, including 9 figures, LaTe