Jumble Java Byte Code to Measure the Effectiveness of Unit Tests

Jumble is a byte code level mutation testing tool for Java which inter-operates with JUnit. It has been designed to operate in an industrial setting with large projects. Heuristics have been included to speed the checking of mutations, for example, noting which test fails for each mutation and running this first in subsequent mutation checks. Significant effort has been put into ensuring that it can test code which uses custom class loading and reflection. This requires careful attention to class path handling and coexistence with foreign class-loaders. Jumble is currently used on a continuous basis within an agile programming environment with approximately 370,000 lines of Java code under source control. This checks out project code every fifteen minutes and runs an incremental set of unit tests and mutation tests for modified classes. Jumble is being made available as open source

A national scale inventory of resource provision for biodiversity within domestic gardens

The human population is increasingly disconnected from nature due to urbanisation. To counteract this phenomenon, the UK government has been actively promoting wildlife gardening. However, the extent to which such activities are conducted and the level of resource provision for biodiversity (e.g., food and nesting sites) within domestic gardens remains poorly documented. Here we generate estimates for a selection of key resources provided within gardens at a national scale, using 12 survey datasets gathered across the UK. We estimate that 22.7 million households (87% of homes) have access to a garden. Average garden SiZe is 190 m(2), extrapolating to a total area of 432,924 ha. Although substantial, this coverage is still an order of magnitude less than that of statutory protected areas. Approximately 12.6 million (48%) households provide supplementary food for birds, 7.4 million of which specifically use bird feeders. Similarly, there are a minimum of 4.7 million nest boxes within gardens. These figures equate to one bird feeder for every nine potentially feeder-using birds in the UK, and at least one nest box for every six breeding pairs of cavity nesting birds. Gardens also contain 2.5-3.5 million ponds and 28.7 million trees, which is just under a quarter of all trees occurring outside woodlands. Ongoing urbanisation, characterised by increased housing densities, is inevitable throughout the UK and elsewhere. The important contribution domestic gardens make to the green space infrastructure in residential areas must be acknowledged, as their reduction will impact biodiversity conservation, ecosystem services, and the well-being of the human population

Separable approximation to two-body matrix elements

Two-body matrix elements of arbitrary local interactions are written as the sum of separable terms in a way that is well suited for the exchange and pairing channels present in mean-field calculations. The expansion relies on the transformation to center of mass and relative coordinate (in the spirit of Talmi's method) and therefore it is only useful (finite number of expansion terms) for harmonic oscillator single particle states. The converge of the expansion with the number of terms retained is studied for a Gaussian two body interaction. The limit of a contact (delta) force is also considered. Ways to handle the general case are also discussed.Comment: 10 pages, 5 figures (for high resolution versions of some of the figures contact the author

The role of aerodynamic forces in a mathematical model for suspension bridges

In a fish-bone model for suspension bridges studied by us in a previous paper we introduce linear aerodynamic forces. We numerically analyze the role of these forces and we theoretically show that they do not influence the onset of torsional oscillations. This suggests a new explanation for the origin of instability in suspension bridges: it is a combined interaction between structural nonlinearity and aerodynamics and it follows a precise pattern. This gives an answer to a long-standing question about the origin of torsional instability in suspension bridges

Mass Dependence of M3Y-Type Interactions and the Effects of Tensor Correlations

The mass dependence of the M3Y-type effective interactions and the effects of tensor correlations are examined. Two-body nuclear matrix elements are obtained by the lowest order constrained variational (LOCV) technique with and without tensor correlations. We have found that the tensor correlations are important especially in the triplet-even (TE) and tensor-even (TNE) channels in order to reproduce the G-matrix elements obtained previously. Then M3Y-type potentials for inelastic scattering are obtained by fitting our two-body matrix elements to those of a sum of Yukawa functions for the mass numbers A=24, A=40 and A=90.Comment: 13 pages, 6 table

The Simple Chordate \u3cem\u3eCiona intestinalis\u3c/em\u3e Has a Reduced Complement of Genes Associated with Fanconi Anemia

Fanconi anemia (FA) is a human genetic disease characterized by congenital defects, bone marrow failure, and increased cancer risk. FA is associated with mutation in one of 24 genes. The protein products of these genes function cooperatively in the FA pathway to orchestrate the repair of DNA interstrand cross-links. Few model organisms exist for the study of FA. Seeking a model organism with a simpler version of the FA pathway, we searched the genome of the simple chordate Ciona intestinalis for homologs of the human FA-associated proteins. BLAST searches, sequence alignments, hydropathy comparisons, maximum likelihood phylogenetic analysis, and structural modeling were used to infer the likelihood of homology between C. intestinalis and human FA proteins. Our analysis indicates that C. intestinalis indeed has a simpler and potentially functional FA pathway. The C. intestinalis genome was searched for candidates for homology to 24 human FA and FA-associated proteins. Support was found for the existence of homologs for 13 of these 24 human genes in C. intestinalis. Members of each of the three commonly recognized FA gene functional groups were found. In group I, we identified homologs of FANCE, FANCL, FANCM, and UBE2T/FANCT. Both members of group II, FANCD2 and FANCI, have homologs in C. intestinalis. In group III, we found evidence for homologs of FANCJ, FANCO, FANCQ/ERCC4, FANCR/RAD51, and FANCS/BRCA1, as well as the FA-associated proteins ERCC1 and FAN1. Evidence was very weak for the existence of homologs in C. intestinalis for any other recognized FA genes. This work supports the notion that C. intestinalis, as a close relative of vertebrates, but having a much reduced complement of FA genes, offers a means of studying the function of certain FA proteins in a simpler pathway than that of vertebrate cells

Two new bright Ae stars

Two newly identified Ae stars, nu Cyg and kappa UMa, were discovered in the course of the Magnetic Survey of Bright MS stars (Monin et al. 2002). We pre sent their Halpha profiles along with measurements of their equivalent width and parameters of emission features. Emission in the Halpha line of nu Cyg is variable on a time scale of 3 years. kappa UMa exhibits weak emission which is rather stable. The emission is thought to arise from a circumstellar disk, and we have estimated the size of that disk.Both new emission stars are IRAS sources. Their IR color excesses are consistent with those of classical Ae stars. Thus, nu Cyg and kappa UMa appear not to belong to the class of Herbig Ae/Be stars. We argue that the frequency of Ae stars may be underestimated due to the difficulty of detection of weak emission in some A stars.Comment: 6 pages,3 figures, submitted to A&

Identification of valid reference genes for the normalization of RT qPCR gene expression data in human brain tissue

<p>Abstract</p> <p>Background</p> <p>Studies of gene expression in post mortem human brain can contribute to understanding of the pathophysiology of neurodegenerative diseases, including Alzheimer's disease (AD), Parkinson's disease (PD) and dementia with Lewy bodies (DLB). Quantitative real-time PCR (RT qPCR) is often used to analyse gene expression. The validity of results obtained using RT qPCR is reliant on accurate data normalization. Reference genes are generally used to normalize RT qPCR data. Given that expression of some commonly used reference genes is altered in certain conditions, this study aimed to establish which reference genes were stably expressed in post mortem brain tissue from individuals with AD, PD or DLB.</p> <p>Results</p> <p>The present study investigated the expression stability of 8 candidate reference genes, (ubiquitin C [UBC], tyrosine-3-monooxygenase [YWHAZ], RNA polymerase II polypeptide [RP II], hydroxymethylbilane synthase [HMBS], TATA box binding protein [TBP], β-2-microglobulin [B2M], glyceraldehyde-3-phosphate dehydrogenase [GAPDH], and succinate dehydrogenase complex-subunit A, [SDHA]) in cerebellum and medial temporal gyrus of 6 AD, 6 PD, 6 DLB subjects, along with 5 matched controls using RT qPCR (TaqMan^®Gene Expression Assays). Gene expression stability was analysed using geNorm to rank the candidate genes in order of decreasing stability in each disease group. The optimal number of genes recommended for accurate data normalization in each disease state was determined by pairwise variation analysis.</p> <p>Conclusion</p> <p>This study identified validated sets of mRNAs which would be appropriate for the normalization of RT qPCR data when studying gene expression in brain tissue of AD, PD, DLB and control subjects.</p

Albedo and Reflection Spectra of Extrasolar Giant Planets

We generate theoretical albedo and reflection spectra for a full range of extrasolar giant planet (EGP) models, from Jovian to 51-Pegasi class objects. Our albedo modeling utilizes the latest atomic and molecular cross sections, a Mie theory treatment of extinction by condensates, a variety of particle size distributions, and an extension of the Feautrier radiative transfer method which allows for a general treatment of the scattering phase function. We find that due to qualitative similarities in the compositions and spectra of objects within each of five broad effective temperature ranges, it is natural to establish five representative EGP albedo classes: a ``Jovian'' class (T$_{\rm eff} \lesssim 150$ K; Class I) with tropospheric ammonia clouds, a ``water cloud'' class (T$_{\rm eff} \sim 250$ K; Class II) primarily affected by condensed H$_2$O, a ``clear'' class (T$_{\rm eff} \gtrsim 350$ K; Class III) which lacks clouds, and two high-temperature classes: Class IV (900 K $\lesssim$ T$_{\rm{eff}}$ $\lesssim$ 1500 K) for which alkali metal absorption predominates, and Class V (T$_{\rm{eff}}$ $\gtrsim$ 1500 K and/or low surface gravity ($\lesssim$ 10$^3$ cm s$^{-2}$)) for which a high silicate layer shields a significant fraction of the incident radiation from alkali metal and molecular absorption. The resonance lines of sodium and potassium are expected to be salient features in the reflection spectra of Class III, IV, and V objects. We derive Bond albedos and effective temperatures for the full set of known EGPs and explore the possible effects of non-equilibrium condensed products of photolysis above or within principal cloud decks. As in Jupiter, such species can lower the UV/blue albedo substantially, even if present in relatively small mixing ratios.Comment: revised LaTeX manuscript accepted to Ap.J.; also available at http://jupiter.as.arizona.edu/~burrows/paper

Spin Hall effect transistor

Spin transistors and spin Hall effects have been two separate leading directions of research in semiconductor spintronics which seeks new paradigms for information processing technologies. We have brought the two directions together to realize an all-semiconductor spin Hall effect transistor. Our scheme circumvents semiconductor-ferromagnet interface problems of the original Datta-Das spin transistor concept and demonstrates the utility of the spin Hall effects in microelectronics. The devices use diffusive transport and operate without electrical current, i.e., without Joule heating in the active part of the transistor. We demonstrate a spin AND logic function in a semiconductor channel with two gates. Our experimental study is complemented by numerical Monte Carlo simulations of spin-diffusion through the transistor channel.Comment: 11 pages, 3 figure