On the use of qualitative reasoning to simulate and identify metabolic pathways

King, R.D., Garrett, S.M., Coghill, G.M. (2005). On the use of qualitative reasoning to simulate and identify metabolic pathways. Bioinformatics 21(9):2017-2026 RAE2008

Fuzzy interpolative reasoning via scale and move transformation

Z. Huang and Q. Shen. Fuzzy interpolative reasoning via scale and move transformation. IEEE Transactions on Fuzzy Systems, 14(2):340-359.

Common genetic variation and the control of HIV-1 in humans.

To extend the understanding of host genetic determinants of HIV-1 control, we performed a genome-wide association study in a cohort of 2,554 infected Caucasian subjects. The study was powered to detect common genetic variants explaining down to 1.3% of the variability in viral load at set point. We provide overwhelming confirmation of three associations previously reported in a genome-wide study and show further independent effects of both common and rare variants in the Major Histocompatibility Complex region (MHC). We also examined the polymorphisms reported in previous candidate gene studies and fail to support a role for any variant outside of the MHC or the chemokine receptor cluster on chromosome 3. In addition, we evaluated functional variants, copy-number polymorphisms, epistatic interactions, and biological pathways. This study thus represents a comprehensive assessment of common human genetic variation in HIV-1 control in Caucasians.

USE OF VARIATION AND FUGUE IN PIANO MUSIC FOLLOWING THE CLASSICAL PERIOD

The variation and fugue originated from the 15th and 16th centuries and blossomed during the Baroque and Classical Periods. In a variation, a theme with a particular structure precedes a series of pieces that usually have the same or very similar structure. A fugue is a work written in imitative counterpoint in which the theme is stated successively in all voices of polyphonic texture. Beethoven’s use of variation and fugue in large scale works greatly influenced his contemporaries. After the Classical Period, variations continued to be popular, and numerous composers employed the technique in various musical genres. Fugues had pedagogical associations, and by the middle of 19th century became a requirement in conservatory instruction, modeled after Bach’s Well-Tempered Clavier. In the 20th century, the fugue was revived in the spirit of neoclassicism; it was incorporated in sonatas, and sets of preludes and fugues were composed. Schubert's Wanderer Fantasy presents his song Der Wanderer through thematic transformations, including a fugue and a set of variations. Liszt was highly influenced by this, as shown in his thematic transformations and the fugue as one of the transformations in his Sonata in b. In Schumann’s Symphonic Études, Rachmaninoff's Rhapsody on a Theme of Paganini and Copland’s Piano Variations, the variation serves as the basis for the entire work. Prokofiev and Schubert take a different approach in Piano Concerto No. 3 and Wanderer Fantasy, employing the variation in a single movement. Unlike Schubert and Liszt's use of the fugue as a part of the piece or movement, Franck’s Prelude Chorale et Fugue and Shchedrin’s Polyphonic Notebook use it in its independent form. Since the Classical Period, the variation and fugue have evolved from stylistic and technical influences of earlier composers. It is interesting and remarkable to observe the unique effects each had on a particular work. As true and dependable classic forms, they remain popular by offering the composer an organizational framework for musical imagination.

Evaluating the effectiveness of Z: The claims made about CICS and where we go from here

There have been few genuine success stories about industrial use of formal methods. Perhaps the best known and most celebrated is the use of Z by IBM (in collaboration with Oxford University's Programming Research Group) during the development of CICS/ESA (version 3.1). This work was rewarded with the prestigious Queen's Award for Technological Achievement in 1992 and is especially notable for two reasons: 1) because it is a commercial, rather than safety- or security-critical, system and 2) because the claims made about the effectiveness of Z are quantitative as well as qualitative. The most widely publicized claims are: less than half the normal number of customer-reported errors and a 9% savings in the total development costs of the release. This paper provides an independent assessment of the effectiveness of using Z on CICS based on the set of public domain documents. Using this evidence, we believe that the case study was important and valuable, but that the quantitative claims have not been substantiated. The intellectual arguments and rationale for formal methods are attractive, but their widespread commercial use is ultimately dependent upon more convincing quantitative demonstrations of effectiveness. Despite the pioneering efforts of IBM and PRG, there is still a need for rigorous, measurement-based case studies to assess when and how the methods are most effective. We describe how future similar case studies could be improved so that the results are more rigorous and conclusive.

Writing about war: Jung, Much Ado About Nothing, and the Troy novels of Lindsay Clarke

Arguably, in a time of war literature, and indeed all writing, is saturated with deep psychic responses to conflict. So that not only in literary genres such as epic and tragedy, but also in the novel and comedy, can writing about war be discerned. C.G. Jung, Shakespeare and Lindsay Clarke are fundamentally writers of war who share allied literary strategies. Moreover, they diagnose similar origins to the malaise of a culture tending to war in the neglect of aspects of the feminine that patriarchy prefers to ignore. In repressing or evading the dark feminine, cultures as dissimilar as ancient Greece, the 21st century, Shakespeare's England and Jung's Europe prevent the healing energies of the conjunctio of masculine and feminine from stabilising an increasingly fragile consciousness. In the Troy novels of Clarke, Answer to Job by Jung and Much Ado About Nothing by Shakespeare, some attempt at spiritual nourishment is made through the writing. [From the Publisher]

Sex talk? overcoming barriers about sex and contraception after childbirth

Anecdotal evidence tells professionals that childbirth is the best form of contraception. However, sexual health problems are the very common after childbirth with Barrett et al (2000) arguing that only 15% of women who have a postnatal sexual problem reported discussing it with a health professional. As health professionals with a predilection for the ‘clinical’ and the ‘prescriptive’ we organise antenatal classes to discuss bathing the baby and post partum reunions to recount birth stories, but often fail to address sexual health problems and contraception after birth.(Glazener 1997). Many women who have carefully used contraception for years prior to pregnancy are often not helped to re-engage with the issues following birth. This would seem to be a particular problem for the most vulnerable parents such as adolescent mothers and their partners (Social Exclusion Unit 1999, 2004) where some young women go on to have more than one baby in a short time period (Reeves 2003). The focus of this paper is to explore the apparent general failure of health professionals to discuss sex after childbirth and provide information regarding reliable contraception. Glazener (1997) tells us that health professionals are encouraged to educate and prepare patients antenatally, for example to be trained to identify problems and deal with them openly and sympathetically. What is brought into question is why this form of rigorous support is not extended to providing sexual health advice in the immediate and often vulnerable postnatal period and why this provision is not a priority for some groups. The paper will explore if this situation caused by a lack of training or is it a symptom of our culture and a British attitude towards sex and contraception.

Food sources, behaviour, and distribution of hydrothermal vent shrimps at the Mid-Atlantic Ridge

Five species of bresilioid shrimp were investigated at seven hydrothermal sites on the Mid-Atlantic Ridge: Menez Gwen, Lucky Strike, Rainbow, Broken Spur, TAG, Snake Pit and Logatchev. Samples were prepared for analysis of stable isotopes, elemental composition and lipids. Shrimp behaviour was observed from the submersible ‘Alvin’ and in the laboratory aboard RV ‘Atlantis’. The distribution and zonation of the shrimp species was recorded. Juvenile shrimp of all species arrive at the vents carrying reserves of photosynthetic origin, built-up in the pelagic larval stages. These reserves are used while the shrimp metamorphose to the adult form and, in Rimicaris exoculata and Chorocaris chacei, while they develop epibiotic bacteria supporting structures, the modified mouthparts and the inside of the carapace. The main food of adult R. exoculata is filamentous bacteria that grow on these structures. The intermediate sizes of C. chacei also feed on such bacteria, but the final stage gets some food by scavenging or predation. Mirocaris species scavenge diverse sources; they are not trophically dependent on either R. exoculata or mussels. Adults of Alvinocaris markensis are predators of other vent animals, including R. exoculata. The dense swarms of R. exoculata, with their exosymbionts, can be compared to endosymbiont-containing animals such as Bathymodiolus and the vestimentiferan tube-worms of the Pacific vents. Such associations, whether endo- or ectosymbiotic, may be necessary for the development of flourishing communities at hydrothermal vents.

Habitat and distribution of the warm-water barnacle Solidobalanus fallax (Crustacea: Cirripedia)

New records are given of the occurrence of the warm-water barnacle Solidobalanus fallax in Britain and Europe. This barnacle is not found on rocks or stones, but settles on biological substrata, including algae, cnidarians, bivalves, gastropods and crustaceans. It also settles on plastic bags and nets, plastic-coated objects such as crab and lobster pots and octopus pots made of ceramic or plastic. With one exception the species was unrecorded in Europe before 1980; it may have increased in abundance during recent years as a result of rising temperatures. The cyprid larvae, which can metamorphose on plastic Petri dishes, appear to be adapted to seek out ‘low energy’ surfaces. One of the habitats colonized by S. fallax is the sea-fan Eunicella verrucosa, where it seems to have increased in recent years, possibly to the detriment of the cnidarian host. Solidobalanus fallax has the potential to be a serious pest of fish-farming structures to the south of Britain