The Butterflies of Malawi

Volume: XX

What if the Doha Round Fails? Implications for Canadian Agriculture

Many commentators assume that the WTO Doha Round negotiations have already failed and that this failure will not matter for Canadian agriculture. Neither view is correct. Most countries appear willing to make the effort needed to bring the negotiations to a make or break point in early 2008. If the Doha Round does eventually fail, an important opportunity to make the agricultural trading system significantly less distorted, more open and fair will have been lost. For Canadian agriculture, the failure to move the Doha Development Agenda (DDA) forward has more serious consequences than just missing the chance to improve the rules governing agricultural trade; it could signal a return to increased protectionism, more managed trade, a return to competitive subsidization, and an escalation in the number of trade disputes.International Relations/Trade,

What if the Doha Round Fails? Implications for Canadian Agriculture

Many commentators assume that the WTO Doha Round negotiations have already failed and that this failure will not matter for Canadian agriculture. Neither view is correct. Most countries appear willing to make the effort needed to bring the negotiations to a make or break point in early 2008. If the Doha Round does eventually fail, an important opportunity to make the agricultural trading system significantly less distorted, more open and fair will have been lost. For Canadian agriculture, the failure to move the Doha Development Agenda (DDA) forward has more serious consequences than just missing the chance to improve the rules governing agricultural trade; it could signal a return to increased protectionism, more managed trade, a return to competitive subsidization, and an escalation in the number of trade disputes.International Relations/Trade,

Tracking system study

A digital computer program was generated which mathematically describes an optimal estimator-controller technique as applied to the control of antenna tracking systems used by NASA. Simulation studies utilizing this program were conducted using the IBM 360/91 computer. The basic ideas of applying optimal estimator-controller techniques to antenna tracking systems are discussed. A survey of existing tracking methods is given along with shortcomings and inherent errors. It is explained how these errors can be considerably reduced if optimal estimation and control are used. The modified programs generated in this project are described and the simulation results are summarized. The new algorithms for direct synthesis and stabilization of the systems including nonlinearities, are presented

Co-option of an endogenous retrovirus envelope for host defense in hominid ancestors

Endogenous retroviral sequences provide a molecular fossil record of ancient infections whose analysis might illuminate mechanisms of viral extinction. A close relative of gammaretroviruses, HERV-T, circulated in primates for ~25 million years (MY) before apparent extinction within the past ~8 MY. Construction of a near-complete catalog of HERV-T fossils in primate genomes allowed us to estimate a ~32 MY old ancestral sequence and reconstruct a functional envelope protein (ancHTenv) that could support infection of a pseudotyped modern gammaretrovirus. Using ancHTenv, we identify monocarboxylate transporter-1 (MCT-1) as a receptor used by HERV-T for attachment and infection. A single HERV-T provirus in hominid genomes includes an env gene (hsaHTenv) that has been uniquely preserved. This apparently exapted HERV-T env could not support virion infection but could block ancHTenv mediated infection, by causing MCT-1 depletion from cell surfaces. Thus, hsaHTenv may have contributed to HERV-T extinction, and could also potentially regulate cellular metabolism

Evaluation of the Sustainability of an Intervention to Increase HIV Testing

BACKGROUND Sustainability—the routinization and institutionalization of processes that improve the quality of healthcare—is difficult to achieve and not often studied. OBJECTIVE To evaluate the sustainability of increased rates of HIV testing after implementation of a multi-component intervention in two Veterans Health Administration healthcare systems. DESIGN Quasi-experimental implementation study in which the effect of transferring responsibility to conduct the provider education component of the intervention from research to operational staff was assessed. PATIENTS Persons receiving healthcare between 2005 and 2006 (intervention year) and 2006 and 2007 (sustainability year). MEASUREMENTS Monthly HIV testing rate, stratified by frequency of clinic visits RESULTS The monthly adjusted testing rate increased from 2% at baseline to 6% at the end intervention year and then declined reaching 4% at the end of the sustainability year. However, the stratified, visit-specific testing rate for persons newly exposed to the intervention (i.e., having their first through third visits during the study period) increased throughout the intervention and sustainability years. Increases in the proportion of visits by patients who remained untested despite multiple, prior exposures to the intervention accounted for the aggregate attenuation of testing during the sustainability year. Overall, the percentage of patients who received an HIV test in the sustainability year was 11.6%, in the intervention year 11.1%, and in the pre-intervention year 5.0% CONCLUSIONS Provider education combined with informatics and organizational support had a sustainable effect on HIV testing rates. The effect was most pronounced during patients' early contacts with the healthcare system.Health Services Research & Development Service (SDP 06–001

Reductions in the dietary niche of southern sea otters (Enhydra lutris nereis) from the Holocene to the Anthropocene.

The sea otter (Enhydra lutris) is a marine mammal hunted to near extinction during the 1800s. Despite their well-known modern importance as a keystone species, we know little about historical sea otter ecology. Here, we characterize the ecological niche of ancient southern sea otters (E. lutris nereis) using δ13C analysis and δ15N analysis of bones recovered from archaeological sites spanning ~7,000 to 350 years before present (N = 112 individuals) at five regions along the coast of California. These data are compared with previously published data on modern animals (N = 165) and potential modern prey items. In addition, we analyze the δ15N of individual amino acids for 23 individuals to test for differences in sea otter trophic ecology through time. After correcting for tissue-specific and temporal isotopic effects, we employ nonparametric statistics and Bayesian niche models to quantify differences among ancient and modern animals. We find ancient otters occupied a larger isotopic niche than nearly all modern localities; likely reflecting broader habitat and prey use in prefur trade populations. In addition, ancient sea otters at the most southerly sites occupied an isotopic niche that was more than twice as large as ancient otters from northerly regions. This likely reflects greater invertebrate prey diversity in southern California relative to northern California. Thus, we suggest the potential dietary niche of sea otters in southern California could be larger than in central and northern California. At two sites, Año Nuevo and Monterey Bay, ancient otters had significantly higher δ15N values than modern populations. Amino acid δ15N data indicated this resulted from shifting baseline isotope values, rather than a change in sea otter trophic ecology. Our results help in better understanding the contemporary ecological role of sea otters and exemplify the strength of combing zooarchaeological and biological information to provide baseline data for conservation efforts

Hierarchical Dirichlet Process-Based Models For Discovery of Cross-species Mammalian Gene Expression

An important research problem in computational biology is theidentification of expression programs, sets of co-activatedgenes orchestrating physiological processes, and thecharacterization of the functional breadth of these programs. Theuse of mammalian expression data compendia for discovery of suchprograms presents several challenges, including: 1) cellularinhomogeneity within samples, 2) genetic and environmental variationacross samples, and 3) uncertainty in the numbers of programs andsample populations. We developed GeneProgram, a new unsupervisedcomputational framework that uses expression data to simultaneouslyorganize genes into overlapping programs and tissues into groups toproduce maps of inter-species expression programs, which are sortedby generality scores that exploit the automatically learnedgroupings. Our method addresses each of the above challenges byusing a probabilistic model that: 1) allocates mRNA to differentexpression programs that may be shared across tissues, 2) ishierarchical, treating each tissue as a sample from a population ofrelated tissues, and 3) uses Dirichlet Processes, a non-parametricBayesian method that provides prior distributions over numbers ofsets while penalizing model complexity. Using real gene expressiondata, we show that GeneProgram outperforms several popularexpression analysis methods in recovering biologically interpretablegene sets. From a large compendium of mouse and human expressiondata, GeneProgram discovers 19 tissue groups and 100 expressionprograms active in mammalian tissues. Our method automaticallyconstructs a comprehensive, body-wide map of expression programs andcharacterizes their functional generality. This map can be used forguiding future biological experiments, such as discovery of genesfor new drug targets that exhibit minimal "cross-talk" withunintended organs, or genes that maintain general physiologicalresponses that go awry in disease states. Further, our method isgeneral, and can be applied readily to novel compendia of biologicaldata