Benchmarking implementations of functional languages with ‘Pseudoknot', a float-intensive benchmark

Over 25 implementations of different functional languages are benchmarked using the same program, a floating-point intensive application taken from molecular biology. The principal aspects studied are compile time and execution time for the various implementations that were benchmarked. An important consideration is how the program can be modified and tuned to obtain maximal performance on each language implementation. With few exceptions, the compilers take a significant amount of time to compile this program, though most compilers were faster than the then current GNU C compiler (GCC version 2.5.8). Compilers that generate C or Lisp are often slower than those that generate native code directly: the cost of compiling the intermediate form is normally a large fraction of the total compilation time. There is no clear distinction between the runtime performance of eager and lazy implementations when appropriate annotations are used: lazy implementations have clearly come of age when it comes to implementing largely strict applications, such as the Pseudoknot program. The speed of C can be approached by some implementations, but to achieve this performance, special measures such as strictness annotations are required by non-strict implementations. The benchmark results have to be interpreted with care. Firstly, a benchmark based on a single program cannot cover a wide spectrum of ‘typical' applications. Secondly, the compilers vary in the kind and level of optimisations offered, so the effort required to obtain an optimal version of the program is similarly varie

Survival and regrowth of fecal enterococci in desiccated and rewetted sediments

Fecal enterococci are bacteria widely used as indicators of fecal contamination in marine and estuarine waters. One assumption is that these bacteria do not persist or regrow in the environment. Our continuing problems with high numbers of fecal enterococci in sediment suggested that these bacteria may persist and regrow. Therefore, we conducted experiments with fecal enterococci to determine their ability to survive desiccation and to regrow in marine and estuarine sediments from Georgia, New Hampshire, and Puerto Rico after 0, 2, 30, and 60 days. Although numbers of fecal enterococci generally decreased with increased length of drying, many fecal enterococci survived desiccation and regrew in rewetted sediment, violating the assumption that fecal bacteria not persist or regrow in the environment. Because there is not a better alternative to fecal enterococci as fecal indicator bacteria, these results suggest that care should be taken not to disturb the sediment when sampling water for fecal contamination, or if the sediment is already disturbed (e.g., on windy days or during runoff conditions), then the influence of sediment should be considered.Sponsored by: Georgia Environmental Protection Division U.S. Geological Survey, Georgia Water Science Center U.S. Department of Agriculture, Natural Resources Conservation Service Georgia Institute of Technology, Georgia Water Resources Institute The University of Georgia, Water Resources Facult

Biodiversity of the Deep-Sea Continental Margin Bordering the Gulf of Maine (NW Atlantic): Relationships among Sub-Regions and to Shelf Systems

Background: In contrast to the well-studied continental shelf region of the Gulf of Maine, fundamental questions regarding the diversity, distribution, and abundance of species living in deep-sea habitats along the adjacent continental margin remain unanswered. Lack of such knowledge precludes a greater understanding of the Gulf of Maine ecosystem and limits development of alternatives for conservation and management. Methodology/Principal Findings: We use data from the published literature, unpublished studies, museum records and online sources, to: (1) assess the current state of knowledge of species diversity in the deep-sea habitats adjacent to the Gulf of Maine (39–43uN, 63–71uW, 150–3000 m depth); (2) compare patterns of taxonomic diversity and distribution of megafaunal and macrofaunal species among six distinct sub-regions and to the continental shelf; and (3) estimate the amount of unknown diversity in the region. Known diversity for the deep-sea region is 1,671 species; most are narrowly distributed and known to occur within only one sub-region. The number of species varies by sub-region and is directly related to sampling effort occurring within each. Fishes, corals, decapod crustaceans, molluscs, and echinoderms are relatively well known, while most other taxonomic groups are poorly known. Taxonomic diversity decreases with increasing distance from the continental shelf and with changes in benthic topography. Low similarity in faunal composition suggests the deep-sea region harbours faunal communities distinct from those of the continental shelf. Non-parametric estimators of species richness suggest a minimum of 50% of the deep-sea species inventory remains to be discovered. Conclusions/Significance: The current state of knowledge of biodiversity in this deep-sea region is rudimentary. Our ability to answer questions is hampered by a lack of sufficient data for many taxonomic groups, which is constrained by sampling biases, life-history characteristics of target species, and the lack of trained taxonomists

Conservation of pollinators in traditional agricultural landscapes – New challenges in Transylvania (Romania) posed by EU accession and recommendations for future research

Farmland biodiversity is strongly declining in most of Western Europe, but still survives in traditional low intensity agricultural landscapes in Central and Eastern Europe. Accession to the EU however intensifies agriculture, which leads to the vanishing of traditional farming. Our aim was to describe the pollinator assemblages of the last remnants of these landscapes, thus set the baseline of sustainable farming for pollination, and to highlight potential measures of conservation. In these traditional farmlands in the Transylvanian Basin, Romania (EU accession in 2007), we studied the major pollinator groups-wild bees, hoverflies and butterflies. Landscape scale effects of semi-natural habitats, land cover diversity, the effects of heterogeneity and woody vegetation cover and on-site flower resources were tested on pollinator communities in traditionally managed arable fields and grasslands. Our results showed: (i) semi-natural habitats at the landscape scale have a positive effect on most pollinators, especially in the case of low heterogeneity of the direct vicinity of the studied sites; (ii) both arable fields and grasslands hold abundant flower resources, thus both land use types are important in sustaining pollinator communities; (iii) thus, pollinator conservation can rely even on arable fields under traditional management regime. This has an indirect message that the tiny flower margins around large intensive fields in west Europe can be insufficient conservation measures to restore pollinator communities at the landscape scale, as this is still far the baseline of necessary flower resources. This hypothesis needs further study, which includes more traditional landscapes providing baseline, and exploration of other factors behind the lower than baseline level biodiversity values of fields under agri-environmental schemes (AES)

Heterozygous missense variants of LMX1A lead to nonsyndromic hearing impairment and vestibular dysfunction

Unraveling the causes and pathomechanisms of progressive disorders is essential for the development of therapeutic strategies. Here, we identified heterozygous pathogenic missense variants of LMX1A in two families of Dutch origin with progressive nonsyndromic hearing impairment (HI), using whole exome sequencing. One variant, c.721G > C (p.Val241Leu), occurred de novo and is predicted to affect the homeodomain of LMX1A, which is essential for DNA binding. The second variant, c.290G > C (p.Cys97Ser), predicted to affect a zinc-binding residue of the second LIM domain that is involved in protein–protein interactions. Bi-allelic deleterious variants of Lmx1a are associated with a complex phenotype in mice, including deafness and vestibular defects, due to arrest of inner ear development. Although Lmx1a mouse mutants demonstrate neurological, skeletal, pigmentation and reproductive system abnormalities, no syndromic features were present in the participating subjects of either family. LMX1A has previously been suggested as a candidate gene for intellectual disability, but our data do not support this, as affected subjects displayed normal cognition. Large variability was observed in the age of onset (a)symmetry, severity and progression rate of HI. About half of the affected individuals displayed vestibular dysfunction and experienced symptoms thereof. The late-onset progressive phenotype and the absence of cochleovestibular malformations on computed tomography scans indicate that heterozygous defects of LMX1A do not result in severe developmental abnormalities in humans. We propose that a single LMX1A wild-type copy is sufficient for normal development but insufficient for maintenance of cochleovestibular function. Alternatively, minor cochleovestibular developmental abnormalities could eventually lead to the progressive phenotype seen in the families

Field-Testing Enterococcus Faecalis for Bacterial Source Tracking

Proceedings of the 2003 Georgia Water Resources Conference, held April 23-24, 2003, at the University of Georgia.A waste stabilization pond was suspected of causing fecal contamination to Holt Branch, a tributary of Juniper Creek, near Byron, Georgia. We used ribotyping, a genotypic (DNA-based) bacterial source tracking (BST) method, to match Enterococcus faecalis isolates from Holt Branch and the waste stabilization pond. Fecal enterococci in the effluent from the waste stabilization pond averaged 13,863 colony-forming units (CFU) per 100 mL, and numbers of fecal enterococci from Holt Branch averaged 3,290 CFU per 100 mL. The 17 Ent. faecalis isolates from the Holt Branch yielded 4 ribotypes, and the 41 isolates obtained from the waste stabilization pond yielded 9 ribotypes. All four ribotypes from Holt Branch matched the ribotypes from the waste stabilization pond at a 100% similarity index, which suggested that the waste stabilization pond was the source of fecal contamination to Holt Branch. This is the first use of Ent. faecalis for BST