Perspectives on Traceability and BSE Testing in the U.S. Beef Industry

Food Consumption/Nutrition/Food Safety, Livestock Production/Industries,

Hospital Ward Alarm Fatigue Reduction Through Integrated Medical Device and Hospital System Policy Instruction

The objective of this project is to reduce alarm fatigue in American hospital systems and improve patient care. This objective will be addressed by providing a secure online knowledge base of proper settings for medical devices in conjunction with hospital­specific policy about alarm protocol, at the point of care, to instruct clinical staff with accuracy and consistency

Inferring Species Trees Directly from Biallelic Genetic Markers: Bypassing Gene Trees in a Full Coalescent Analysis

The multi-species coalescent provides an elegant theoretical framework for estimating species trees and species demographics from genetic markers. Practical applications of the multi-species coalescent model are, however, limited by the need to integrate or sample over all gene trees possible for each genetic marker. Here we describe a polynomial-time algorithm that computes the likelihood of a species tree directly from the markers under a finite-sites model of mutation, effectively integrating over all possible gene trees. The method applies to independent (unlinked) biallelic markers such as well-spaced single nucleotide polymorphisms (SNPs), and we have implemented it in SNAPP, a Markov chain Monte-Carlo sampler for inferring species trees, divergence dates, and population sizes. We report results from simulation experiments and from an analysis of 1997 amplified fragment length polymorphism (AFLP) loci in 69 individuals sampled from six species of {\em Ourisia} (New Zealand native foxglove)

Deducing topology of protein-protein interaction networks from experimentally measured sub-networks.

BackgroundProtein-protein interaction networks are commonly sampled using yeast two hybrid approaches. However, whether topological information reaped from these experimentally-measured sub-networks can be extrapolated to complete protein-protein interaction networks is unclear.ResultsBy analyzing various experimental protein-protein interaction datasets, we found that they are not random samples of the parent networks. Based on the experimental bait-prey behaviors, our computer simulations show that these non-random sampling features may affect the topological information. We tested the hypothesis that a core sub-network exists within the experimentally sampled network that better maintains the topological characteristics of the parent protein-protein interaction network. We developed a method to filter the experimentally sampled network to result in a core sub-network that more accurately reflects the topology of the parent network. These findings have fundamental implications for large-scale protein interaction studies and for our understanding of the behavior of cellular networks.ConclusionThe topological information from experimental measured networks network as is may not be the correct source for topological information about the parent protein-protein interaction network. We define a core sub-network that more accurately reflects the topology of the parent network

Bright Variable Stars in NGC 6819 - An Open Cluster in the Kepler Field

We describe a variability study of the moderately old open cluster NGC 6819. We have detected 4 new detached eclipsing binaries near the cluster turnoff (one of which may be in a triple system). Several of these systems should be able to provide mass and radius information, and can therefore constrain the age of the cluster. We have also newly detected one possible detached binary member about 3.5 magnitudes below the turnoff. One EW-type binary (probably not a cluster member) shows unusually strong night-to-night light curve variations in sets of observations separated by 8 years. According to the best current information, the three brightest variables we detected (2 of them new) are cluster members, making them blue stragglers. One is a delta Scu pulsating variable, one is a close but detached binary, and the third contains a detached short period binary that shows total eclipses. In each case, however, there is evidence hinting that the system may have been produced through the interaction of more than two stars.Comment: 33 pages, 15 figures, accepted to A

Remote Sensing of Chiral Signatures on Mars

We describe circular polarization as a remote sensing diagnostic of chiral signatures which may be applied to Mars. The remarkable phenomenon of homochirality provides a unique biosignature which can be amenable to remote sensing through circular polarization spectroscopy. The natural tendency of microbes to congregate in close knit communities would be beneficial for such a survey. Observations of selected areas of the Mars surface could reveal chiral signatures and hence explore the possibility of extant or preserved biological material. We describe a new instrumental technique that may enable observations of this form.Comment: 14 pages, 3 figures; to be published in Planetary and Space Scienc

Wise, a context-dependent activator and inhibitor of Wnt signalling

We have isolated a novel secreted molecule, Wise, by a functional screen for activities that alter the anteroposterior character of neuralised Xenopus animal caps. Wise encodes a secreted protein capable of inducing posterior neural markers at a distance. Phenotypes arising from ectopic expression or depletion of Wise resemble those obtained when Wnt signalling is altered. In animal cap assays, posterior neural markers can be induced by Wnt family members, and induction of these markers by Wise requires components of the canonical Wnt pathway. This indicates that in this context Wise activates the Wnt signalling cascade by mimicking some of the effects of Wnt ligands. Activation of the pathway was further confirmed by nuclear accumulation of beta-catenin driven by Wise. By contrast, in an assay for secondary axis induction, extracellularly Wise antagonises the axis-inducing ability of Wnt8. Thus, Wise can activate or inhibit Wnt signalling in a context-dependent manner. The Wise protein physically interacts with the Wnt co-receptor, lipoprotein receptor-related protein 6 (LRP6), and is able to compete with Wnt8 for binding to LRP6. These activities of Wise provide a new mechanism for integrating inputs through the Wnt coreceptor complex to modulate the balance of Wnt signalling.</p

Life in Hot Carbon Monoxide: The Complete Genome Sequence of Carboxydothermus hydrogenoformans Z-2901

We report here the sequencing and analysis of the genome of the thermophilic bacterium Carboxydothermus hydrogenoformans Z-2901. This species is a model for studies of hydrogenogens, which are diverse bacteria and archaea that grow anaerobically utilizing carbon monoxide (CO) as their sole carbon source and water as an electron acceptor, producing carbon dioxide and hydrogen as waste products. Organisms that make use of CO do so through carbon monoxide dehydrogenase complexes. Remarkably, analysis of the genome of C. hydrogenoformans reveals the presence of at least five highly differentiated anaerobic carbon monoxide dehydrogenase complexes, which may in part explain how this species is able to grow so much more rapidly on CO than many other species. Analysis of the genome also has provided many general insights into the metabolism of this organism which should make it easier to use it as a source of biologically produced hydrogen gas. One surprising finding is the presence of many genes previously found only in sporulating species in the Firmicutes Phylum. Although this species is also a Firmicutes, it was not known to sporulate previously. Here we show that it does sporulate and because it is missing many of the genes involved in sporulation in other species, this organism may serve as a “minimal” model for sporulation studies. In addition, using phylogenetic profile analysis, we have identified many uncharacterized gene families found in all known sporulating Firmicutes, but not in any non-sporulating bacteria, including a sigma factor not known to be involved in sporulation previously

Using digital elevation models to measure the surface and volumetric change of Athabasca Glacier, Alberta, Canada, 1919-1979

The Athabasca Glacier (52˚12\u27N, 117˚14\u27W) located at the Alberta-British Columbia border was studied to quantify its volumetric, area and elevation changes below 2400 m between 1919 and 1979. The data sources consist of maps produced using aerial and terrestrial photogrammetry in the years between 1919 and 1979. The maps were digitized and converted into raster digital elevation models (DEMs), the manipulation of which allowed values of surface and volumetric change to be calculated. These DEMs showed that between 1919 and 1979 the glacier lost 2.344 x 108m3 of volume and receded more than 1 km. Each of the source maps has a precision of vertical estimation associated with the photogrammetric process used to generate it. This imprecision was quantified and used to calculate, display and compare the uncertainty of volume and elevation change measures with the calculated volume and elevation change. The magnitude of uncertainty between maps was often larger than the change measured between the maps. many of the maps used to generate DEMs were used in a previous study to calculate volumetric and elevation change using planimetric methods. The software package which produced the DEMs and calculated output was used to recalculate volumetric change measures using the same methodology for the period 1969-1979. The recalculated results were similar to the planimetric results for that time period. Several other stories of Canadian glacier maps exist. It is recommended that a similar study be carried out using these data