SSW Library: An SIMD Smith-Waterman C/C++ Library for Use in Genomic Applications

Summary: The Smith Waterman (SW) algorithm, which produces the optimal pairwise alignment between two sequences, is frequently used as a key component of fast heuristic read mapping and variation detection tools, but current implementations are either designed as monolithic protein database searching tools or are embedded into other tools. To facilitate easy integration of the fast Single Instruction Multiple Data (SIMD) SW algorithm into third party software, we wrote a C/C++ library, which extends Farrars Striped SW (SSW) to return alignment information in addition to the optimal SW score. Availability: SSW is available both as a C/C++ software library, as well as a stand alone alignment tool wrapping the librarys functionality at https://github.com/mengyao/Complete- Striped-Smith-Waterman-Library Contact: [email protected]: 3 pages, 2 figure

A higher category approach to twisted actions on C*-algebras

C*-algebras form a 2-category with \Star{}homomorphisms or correspondences as morphisms and unitary intertwiners as 2-morphisms. We use this structure to define weak actions of 2-categories, weakly equivariant maps between weak actions, and modifications between weakly equivariant maps. In the group case, we identify the resulting notions with known ones, including Busby-Smith twisted actions and equivalence of such actions, covariant representations, and saturated Fell bundles. For 2-groups, weak actions combine twists in the sense of Green and Busby-Smith. The Packer-Raeburn Stabilisation Trick implies that all Busby-Smith twisted group actions of locally compact groups are Morita equivalent to classical group actions. We generalise this to actions of strict 2-groupoids

The Environmental Context and Function of Burnt-Mounds : New Studies of Irish Fulachtaí Fiadh

The authors acknowledge funding from The Leverhulme Trust (F/00144/AI) and assistance from a large number of individuals including; Margaret Gowen (access to sites and assistance throughout),A. Ames, H, Essex (pollen processing), S. Rouillard & R. Smith (illustrations), C. McDermott, S. Bergerbrandt, all the staff of Margaret Gowen & Co. Ltd, TVAS Ireland and CRDS. Excavation works and some post-excavation analysis was paid for my Bord Gáis and the National Roads Authority (now Transport Infrastructure Ireland). Thanks also to David Smith for access to the Maureen Girling collection and assistance with identifications.Peer reviewedPostprintPostprin

Quantitative genetic studies on livestock improvement and on familial disease in man

The material presented in this submission comprises original research publications by the author in the fields of quantitative genetics in animals and in man. The research on animal genetics was carried out between 1959 and 1968 at the A.R.C. Animal Breeding Research Organisation, Edinburgh, and the work on human genetics from 1968 to 1974 in the Department of Human Genetics at the University of Edinburgh.Within each field of study rather more than half of the papers are theoretical or operational in nature, dealing with results of general interest or with new methodology. The rest of the papers are more practical, estimating genetic parameters and responses in animals, or dealing with specific diseases and their prevention in human populations. The object of this precis is to present and integrate the various papers, to describe the main findings of the research and to discuss their relevance in the respective fields.RESEARCH PAPERS SUBMITTED (IN CHRONOLOGICAL ORDER) 1. Smith, C. 1959. A comparison of testing schemes for pigs. Anim. Prod. 1 : 113. || 2. Smith, C„ 1960. Efficiency of animal testing schemes. Biometrics. 16 : 408. || 3. Smith, C., King, J.W.B. and Gilbert, N. 1962. Genetic parameters of British Large White bacon pigs. Anim. Prod, k : 128. || k . Smith, C. 1962. Estimation of genetic change in farm livestock using field records. Anim. Prod, k : 239. || 5. Smith, C. 1963. Genetic change of backfat thickness in the Danish Landrace breed of pigs from 1932 to i960. Anim. Prod. 5 : 259. || 6. Smith, C. 1964. The use of specialised sire and dam lines in selection for meat production. Anim. Prod. 6 : 337. || 7. Smith, C. and King, J.W.B. 196^. Crossbreeding and litter production in British pigs. Anim. Prod. 6 : 265. || 8. Smith, C. 1965. Results of pig progeny testing in Great Britain. Anim. Prod. 7 : 133. || 9. Pease, A.H.R. and Smith, C. 1965. A note on the heritability of muscle colour in pigs. Anim. Prod. 7 : 273. || 10o Smith, C. and Ross, G.J.S. 1965. Genetic parameters of British Landrace bacon pigs. Anim. Prod. 7 • 291. || 11. Smith, C. 1966. A note on the heritability of leg weakness scores in pigs. Anim. Prod. 8 : 345 || 12. Smith, C. 1967. A note on the improvement of a trait by selection on its components. Anim. Prod. 9 s 12.7. || 13. Smith, C. 1967. Improvement of metric traits through specific genetic loci. Anim. Prod. 9 : 349. || 14. Smith, C., Jensen, E.L., Baker, L.N. and Cox, D.F. 1968. Quantitative studies on blood group and serum protein systems in pigs. I. Segregation ratios and gene frequencies. J. anim. Sci. 27 i 848. || 15. Jensen, E.L., Smith, C., Baker, L.N. and Cox, D.F. 1968. Quantitative studies on blood group and serum protein systems in pigs. II. Effects on production and reproduction. J. anim. Sci. 27 : 856. || 16. Cox, D.F. and Smith, C. 1968. Herd differences and genetic trends in Iowa pigs. J. anim. Sci. 27 : 577- || 17. King, J.W.B. and Smith, C. 1968. Development of a pig sire line by selection, with immigration. (Abstract). Anim. Prod. 10 : 245. || 18. Smith, C. 1969. Optimum selection procedures in animal breeding. Anim. Prod. 11 : 433. || 19. Smith, C. 1970. Heritability of liability and concordance in monozygous twins. Ann. Hum. Genet. 34 : 85. || 20. Emery, A.E.H. and Smith, C. 1970. Ascertainment and prevention of genetic disease. British Medical Journal. 3 • 636. || 21. Smith, C. 1970. Ascertaining those at risk in the prevention and treatment of genetic disease. In 'Modern Trends in Human Genetics'. Vol. 1, p. 350. Edited by A.E.H. Emery, Butterworth, London. || 22. Falconer, D.S., Duncan, L.P.J. and Smith, C. 1971. A statistical and genetical study of diabetes. I. Prevalence and Mortality. Ann. Hum. Genet. 34 ' 347. || 23. Smith, C. 1971. Recurrence risks with multifactorial inheritance. Amer. J. Human Genet. 23 : 578. || 24. Smith, C., Holloway, S, and Emery, A.E.H. 1971- Individuals at risk in families with genetic disease. Jour. Medical Genetics. 8 : 453- || 25. Smith, C. 1971. Discriminating between different modes of inheritance in genetic disease. Clinical Genet. 2 : 303. || 26. Smith, C., Falconer, D.S. and Duncan, L.J.P. 1972. A statistical and genetical study of diabetes. II. Heritability of liability. Ann. Hum. Genet. 35 : 281. || 27. Smith, C. 1972. Correlation in liability among relatives and concordance in twins. Human Heredity. 22 : 97. || 28. Darlow, J.M., Smith, C. and Duncan, L.J.P. 1973- A statistical and genetical study of diabetes. III. Empiric risks to relatives. Ann. Hum. Genet. 37 : 157. || 29. Smith, C. 1972. Computer programme to estimate recurrence risks for multifactorial familial disease. British Medical Journal. 1 : 495- || 30. Holloway, S.M. and Smith, C. 1973. Equilibrium frequencies in X-linked genetic disease. Amer. Jour. Hum. Gen. 25 : 388. || 31. Smith, C. and Watt, M., Boyd, A.E.W. and Holmes, J.C. 1973. Anencephaly, spina bifida and potato blight in the Edinburgh area. Lancet. 1973 (i) 269. || 32. Smith, C. 197^. Concordance in twins. Methods and interpretation. Amer. Jour. Hum. Genet. 26 : 454 || 33. Emery, A.E.H., Elliott, D., Moores, M. and Smith, C. 197^. A genetic register system (RAPID). Jour. Med. Gen. 1 1 : 1 45 || 34. Smith, C. 197^. Some implications of HL-A and disease associations. Lancet. 197^, (i) : 450 || 35. Bonaiti-Pellie, C. and Smith, C. 1974. Risk tables for genetic counselling in some common congenital malformations. Jour. Med. Genet. 11 : 374 || 36. Skinner, R., Smith, C. and Emery, A.E.H. 197^. Linkage between the loci for benign (Becker-type) X-borne muscular dystrophy and deutan colour blindness. Jour, Med. Gen. 11 : 317 || 37. Smith, C. and Mendell, N.R. 197^. Recurrence risks from family history and metric traits. Ann. Hum. Genet. 37 s 275. || 38. Holloway, S.M. and Smith, C. 1975. Effect of various medical and social practices on the frequency of genetic disorders. Amer. Jour. Hum. Genet. 27 : 614. || 39- Moores, H.M., Smith, C. and Emery, A.E.H. 1975. A computerised register system for ascertainment and prevention of inherited disease. In "Advances in Systems and Cybernetics". Gordon and Breach, London. || 40. Curnow, R.N. and Smith, C. 1975. Multifactorial models for familial disease in man. Jour. Royal Stat. Soc. Series A. 138 : 131- || 41. Emery, A.E.H., Davie, A.M. and Smith, C. 1975- Spinal muscular atrophy - resolution of heterogeneity. In 'Recent Advances in Myology', Excerpta Medica Inter. Congress (Series No. 360). Amsterdam. || 42. Smith, C. 1976. Resolution of genetic heterogeneity in familial disease. Ann. Hum. Genet. 39 s 281. || 43- Morton, N.E., Smith, C., Hill, R., Frackiewicz, Law, P. and Yee, S. 1976. Population structure of Barra (Outer Hebrides). Ann. Hum. Gen. 39 : 339- || 44. Van Regermorter, N. and Smith, C. 1976. The importance of determining the mode of inheritance for the estimation of recurrence risks. J. Genet. Hum. 24 : 46

A nesting aggregation of the solitary bee Megachile atrata (Hymenoptera: Megachilidae) in the Philippines

A nesting aggregation of Megachile (Creightonella) atrata Smith in the Philippines comprised almost 300 active nests.  The bees in rapid flight resemble the hornet Vespa tropica Linnaeus. The nest structure is similar to that reported for M. (C.) frontalis (Fabricius) in New Guinea