Prioritization of candidate cancer genes-an aid to oncogenomic studies

The development of techniques for oncogenomic analyses such as array comparative genomic hybridization, messenger RNA expression arrays and mutational screens have come to the fore in modern cancer research. Studies utilizing these techniques are able to highlight panels of genes that are altered in cancer. However, these candidate cancer genes must then be scrutinized to reveal whether they contribute to oncogenesis or are coincidental and non-causative. We present a computational method for the prioritization of candidate (i) proto-oncogenes and (ii) tumour suppressor genes from oncogenomic experiments. We constructed computational classifiers using different combinations of sequence and functional data including sequence conservation, protein domains and interactions, and regulatory data. We found that these classifiers are able to distinguish between known cancer genes and other human genes. Furthermore, the classifiers also discriminate candidate cancer genes from a recent mutational screen from other human genes. We provide a web-based facility through which cancer biologists may access our results and we propose computational cancer gene classification as a useful method of prioritizing candidate cancer genes identified in oncogenomic studies.

Osteometric analysis of the scapula and humerus of Rangifer tarandus and Cervus elaphus : A contribution to the discrimination of Late Pleistocene cervids

Fossil remains of reindeer (Rangifer tarandus) occurring outside their present range are an important indicator of formerly cold climatic conditions, but are easily confused with those of the red deer (Cervus elaphus). The locality of Kiputz IX has yielded one of the best-preserved Late Pleistocene reindeer populations of the southern Pyrenees, occurring in association with Bison priscus and the much more abundant Cervus elaphus. Fossil remains from this site are mostly complete and not affected by human intervention, thus creating the perfect conditions for reliable osteometric analyses. Here, we quantify diagnostic morphological features of the scapula and the humerus of Cervus elaphus and Rangifer tarandus to establish the potential of these bones to aid in interspecific discrimination. In the case of the scapula, the best species discriminator is the ratio of the minimum anteroposterior diameter of the scapular neck and the development of the articular process, while the breadth of the trochlea is the best discriminator in the case of the humerus.

Contributions to the efficient use of general purpose coprocessors: kernel density estimation as case study

142 p.

A Demographic Profile of Participants in Two Gulf of Mexico Inshore Shrimp Fisheries and Their Response to the Texas Closure

A social study of the shrimp fisheries of Galveston Bay, Tex., and Calcasieu Lake, La., was made during the summer of 1987 to examine the impacts of the seasonal closure of the Federal waters off Texas and to understand the infrastructure and demographic processes of these two diverse fisheries. Survey instruments were administered to 159 shrimp boat captains: 89 from Galveston Bay and 70 from Calcasieu Lake. Shrimp-house owners were interviewed in each region as well. The results suggest that the inshore fisheries (i.e., shrimpers and shrimp houses) are distinct from the offshore fisheries. The infrastructure of the two inshore fisheries examined differ in that the market distribution of shrimp from Galveston Bay was more diffuse than from Calcasieu Lake. Much more of the shrimp harvested from Galveston Bay was channelled into the surrounding community than from Calcasieu Lake. The distribution of age,years as a commercial fisherman, and family involvement in fishing suggest that participation in Calcasieu Lake's and Galveston Bay's inshore fisheries have expanded concurrent with declining economies. While overall the Texas closure had little impact on either of the inshore fisheries, the Galveston Bay shrimpers experienced more of a direct impact on their livelihood than Calcasieu Lake shrimpers.

Strategies for surgically assisted rapid maxillary expansion according to the region of transverse maxillary deficiency

This study evaluated different techniques for surgically assisted rapid maxillary expansion (SARME) according to the type of transverse maxillary deficiency using computed tomography (CT). Six adult patients with bilateral transverse maxillary deficiencies underwent SARME. the patients were equally divided into three groups: Group I, maxillary atresia in both the anterior and posterior regions; Group II, greater maxillary atresia in the anterior region; and Group ill, increased maxillary atresia in the posterior region. in Group I, a subtotal Le Fort I osteotomy was used. in Group II, a subtotal Le Fort I osteotomy was used without pterygomaxillary suture disjunction. in Group III, a subtotal Le Fort I osteotomy was used with pterygomaxillary suture disjunction and fixation of the anterior nasal spine with steel wire. the midpalatal suture opening was evaluated preoperatively and immediately after the activation period using CT. for Group I, the opening occurred parallel to midpalatal suture; for Group II, the opening comprised a V-shape with a vertex on the posterior nasal spine; and for Group III, the opening comprised a V-shape with a vertex at the anterior nasal spine. the conclusion was that the SARME technique should be individualized according to the type of transverse maxillary deficiency.

Women's contribution to the development of the English novel: 1621-1818

Women's contribution to literature is no arbitrary or artificial distinction. However much the reformer may welcome, or the conservative lament, the growth of a harmonious sharing of ideals between men and women, that growth has been a hard-fought struggle. It has been an escape from a prison, which, when it did not entirely shut out the greater world, at least enclosed a little world of education meant for women, literature adapted to the supposed limitations of their intellect, and a course of action prescribed by the other sex. To show how the literary efforts of women developed and justified their claims to free activity is the purpose of this thesis.

From respect for nature to agency as realisation in response to the ecological emergency

'The ecological emergency’ describes both our emergence into, and the way we relate within, a set of globally urgent circumstances, brought about through anthropogenic impact. I identify two phases to this emergency. Firstly, there is the anthropogenic impact itself, interpreted through various conceptual models. Secondly, however, is the increasingly entrenched commitment to divergent conceptual positions, that leads to a growing disparateness in attitudes, and a concurrent difficulty with finding any grounds for convergence in response. I begin by reviewing the environmental ethics literature in order to clarify which components of the implicit narratives and beliefs of different positions create the foundations for such disparateness of views. I identify the conceptual frameworks through which moral agency and human responsibility are viewed, and that justify an ethical response to the ecological emergency. In particular, I focus on Paul Taylor's thesis of 'respect for nature' as a framework for revising both the idea that we are ‘moral’ and the idea that we are ‘agents’ in this unique way, and I open to question the idea that any response to the ecological emergency need be couched in ethical terms. This revision leads me to formulate an alternative conceptual model that makes use of Timothy Morton’s idea of enmeshment. I propose that we dramatically revise our idea of moral agency using the idea of enmeshment as a starting point. I develop an alternative framework that locates our capacity for responsibility within our capacity for realisation, both in the sense of understanding, and of making real, sets of conditions within our enmeshment. I draw parallels between this idea of ‘realisation as agency’ and the work of Dōgen and other non-dualists. I then propose a revised understanding of ‘the good’ of systems from a biophysical perspective, and compare this with certain features of Asian traditions of thought. I consider the practical implications of these revisions, and I conclude that the act of paying close attention, or realising, contains our agency, as does the attitude, or manner, with which we focus. This gives us the basis for a convergent response to the ecological emergency: the way of our engagement that is the key to responding to the ecological emergency

Development of a decision aid to inform patients' and families' renal replacement therapy selection decisions.

BACKGROUND: Few educational resources have been developed to inform patients' renal replacement therapy (RRT) selection decisions. Patients progressing toward end stage renal disease (ESRD) must decide among multiple treatment options with varying characteristics. Complex information about treatments must be adequately conveyed to patients with different educational backgrounds and informational needs. Decisions about treatment options also require family input, as families often participate in patients' treatment and support patients' decisions. We describe the development, design, and preliminary evaluation of an informational, evidence-based, and patient-and family-centered decision aid for patients with ESRD and varying levels of health literacy, health numeracy, and cognitive function. METHODS: We designed a decision aid comprising a complementary video and informational handbook. We based our development process on data previously obtained from qualitative focus groups and systematic literature reviews. We simultaneously developed the video and handbook in "stages." For the video, stages included (1) directed interviews with culturally appropriate patients and families and preliminary script development, (2) video production, and (3) screening the video with patients and their families. For the handbook, stages comprised (1) preliminary content design, (2) a mixed-methods pilot study among diverse patients to assess comprehension of handbook material, and (3) screening the handbook with patients and their families. RESULTS: The video and handbook both addressed potential benefits and trade-offs of treatment selections. The 50-minute video consisted of demographically diverse patients and their families describing their positive and negative experiences with selecting a treatment option. The video also incorporated health professionals' testimonials regarding various considerations that might influence patients' and families' treatment selections. The handbook was comprised of written words, pictures of patients and health care providers, and diagrams describing the findings and quality of scientific studies comparing treatments. The handbook text was written at a 4th to 6th grade reading level. Pilot study results demonstrated that a majority of patients could understand information presented in the handbook. Patient and families screening the nearly completed video and handbook reviewed the materials favorably. CONCLUSIONS: This rigorously designed decision aid may help patients and families make informed decisions about their treatment options for RRT that are well aligned with their values.

Can density functional theory (DFT) be used as an aid to a deeper understanding of tandem mass spectrometric fragmentation pathways?

Prediction of tandem mass spectrometric (MS/MS) fragmentation for non-peptidic molecules based on structure is of immense interest to the mass spectrometrist. If a reliable approach to MS/MS prediction could be achieved its impact within the pharmaceutical industry could be immense. Many publications have stressed that the fragmentation of a molecular ion or protonated molecule is a complex process that depends on many parameters, making prediction difficult. Commercial prediction software relies on a collection of general heuristic rules of fragmentation, which involve cleaving every bond in the structure to produce a list of 'expected' masses which can be compared with the experimental data. These approaches do not take into account the thermodynamic or molecular orbital effects that impact on the molecule at the point of protonation which could influence the potential sites of bond cleavage based on the structural motif. A series of compounds have been studied by examining the experimentally derived high-resolution MS/MS data and comparing it with the in silico modelling of the neutral and protonated structures. The effect that protonation at specific sites can have on the bond lengths has also been determined. We have calculated the thermodynamically most stable protonated species and have observed how that information can help predict the cleavage site for that ion. The data have shown that this use of in silico techniques could be a possible way to predict MS/MS spectra. Copyright (C) 2009 John Wiley & Sons, Ltd.

Guide to the coastal and surface zooplankton of the south-western Indian Ocean. Occasional Publication of the Marine Biological Association 15

A guide compiled as an aid to researchers in the identification of the coastal and shallow water, south-western Indian Ocean pelagic zooplankton, as much of the identification literature covering this area of amazing biodiversity is currently spread through the scientific literature and not accessible without extensive library resources. Most zooplankton groups, except fish larvae and eggs, have been covered, but some specialist groups have not yet been dealt with in great detail. However, a selection of representative members of most groups have been given, so that organisms can at least be assigned to perhaps a particular genus within the main group. The species list is based on zooplankton sampling carried out round the coastal areas of the islands of Mahé and Aldabra (Seychelles), Rodrigues (Mauritius), Madagascar and from a sampling transect between Seychelles and Rodrigues. The guide therefore includes a high proportion of the island-coastal and surface water zooplankton of the whole Indian Ocean. The location where a particular species has been sampled has been noted and some species that have not been sampled, but are known to occur in the region, have been included. Comprehensive taxonomic information has not been presented, but sufficient information should be given to identify each species. Keys have not yet been included for genera, as further species will be added. A bibliography of relevant plankton references has also been included.

'An aid to mental health': natural history, alienists and therapeutics in Victorian Scotland

In the nineteenth century natural history was widely regarded as a rational and ‘distracting’ pursuit that countered the ill-effects, physical and mental, of urban life. This familiar argument was not only made by members of naturalists’ societies but was also borrowed and adapted by alienists concerned with the moral treatment of the insane. This paper examines the work of five long-serving superintendents in Victorian Scotland and uncovers the connections made between an interest in natural history and the management of mental disease. In addition to recovering a significant influence on the conduct of several alienists the paper explores arguments made outside the asylum walls in favour of natural history as an aid to mental health. Investigating the promotion of natural history as a therapeutic recreation in Scotland and elsewhere reveals more fully the moral and cultural significance attached to natural history pursuits in the nineteenth century.

Light-color and body-mass. The subjectivity of the Argentinean nation, according to the painting of Pío Collivadino

Pío Collivadino was a highly recognized painter in life, occupying the most important charges in the artistic field and receiving awards in his country and abroad, which turned him into an inescapable reference of young Argentinean artists who earned recognition throughout the twentieth century. Why, then, with the time, his work began to fall to the wayside? In response to this question, the present article, based on the analysis of the work of that artist, proposes to problematize the notion of subjectivity, both in its individual dimension and its national character, underlining the role that the figure of the artist meets for its formation. Developing the concepts of light-color and body-mass, from Collivadino painting, this article will attempt to explain the relation between the emergence of an Argentinean subjectivity, at the beginning of 20th century, and the art, not only at the level of the issues addressed, but, especially, taking into consideration its formal characteristics.

Tracing Inspiration in Proverbial Material: From 'The Royal Dictionary' (1699 & 1729) of Abel Boyer to 'The English-Irish Dictionary' (1732) of Begley-McCurtin.

This metalexicographic study examines the relationship between the proverbial material in The English-Irish Dictionary (1732) of Begley and McCurtin, Abel Boyer’s The Royal Dictionary (First edition 1699, second edition 1729), and Nathaniel Bailey’s An Universal Etymological English Dictionary (1721). It will show, for the first time, that both the English macrostructure and microstructure of the proverbial entries in Begley and McCurtin (1732) were reproduced directly from Boyer’s dictionary and, in spite of claims to the contrary, the impact of Bailey’s (1721) dictionary was negligible. Furthermore, empirical data gleaned from a comparative linguistic analysis of the various editions of The Royal Dictionary prior to 1732, will prove that it was the second official edition (1729) that was used as the framework for The English-Irish Dictionary. A quantitative and qualitative analysis of the nature of the proverbial entries will also outline the various translation strategies that were used to compose the Irish material— particularly literal translation—and show that there are extremely high-levels of borrowings from Boyer (1729), both in terms of the English entries under the lemma, and the French entries in the comment.