Physiology of Ethyl Alcohol

The physiological effects of ethyl alcohol depend almost entirely on its concentration in the blood stream. This concentration, expressed in per cent, is referred to as the blood alcohol level and has become of increasing medico-legal importance in determining the degree of alcoholic intoxication

Dietary Analysis of Batfishes (Lophiiformes: Ogcocephalidae) in the Gulf of Mexico

Stomach content analyses, performed on three species of batfishes, Halieutichthys aculeatus, Ogcocephalus declivirostris, and Ogcocephalus pantosticus collected in the Gulf of Mexico in summer (June-July) and fall (Oct.-Nov.) 2002 and 2003, revealed a variety of benthic invertebrates, particularly gastropods, polychaete worms, and xanthid crabs. Schoener\u27s dietary overlap indices (Sl) were calculated between the three species within the same seasons, and within each species between seasons. SI values indicated that each species consumed a different assemblage of prey and that two of the species exhibited temporal variation in diet

Hierarchically-coupled hidden Markov models for learning kinetic rates from single-molecule data

We address the problem of analyzing sets of noisy time-varying signals that all report on the same process but confound straightforward analyses due to complex inter-signal heterogeneities and measurement artifacts. In particular we consider single-molecule experiments which indirectly measure the distinct steps in a biomolecular process via observations of noisy time-dependent signals such as a fluorescence intensity or bead position. Straightforward hidden Markov model (HMM) analyses attempt to characterize such processes in terms of a set of conformational states, the transitions that can occur between these states, and the associated rates at which those transitions occur; but require ad-hoc post-processing steps to combine multiple signals. Here we develop a hierarchically coupled HMM that allows experimentalists to deal with inter-signal variability in a principled and automatic way. Our approach is a generalized expectation maximization hyperparameter point estimation procedure with variational Bayes at the level of individual time series that learns an single interpretable representation of the overall data generating process.Comment: 9 pages, 5 figure

Allosteric collaboration between elongation factor G and the ribosomal L1 stalk directs tRNA movements during translation

Determining the mechanism by which transfer RNAs (tRNAs) rapidly and precisely transit through the ribosomal A, P and E sites during translation remains a major goal in the study of protein synthesis. Here, we report the real-time dynamics of the L1 stalk, a structural element of the large ribosomal subunit that is implicated in directing tRNA movements during translation. Within pre-translocation ribosomal complexes, the L1 stalk exists in a dynamic equilibrium between open and closed conformations. Binding of elongation factor G (EF-G) shifts this equilibrium towards the closed conformation through one of at least two distinct kinetic mechanisms, where the identity of the P-site tRNA dictates the kinetic route that is taken. Within post-translocation complexes, L1 stalk dynamics are dependent on the presence and identity of the E-site tRNA. Collectively, our data demonstrate that EF-G and the L1 stalk allosterically collaborate to direct tRNA translocation from the P to the E sites, and suggest a model for the release of E-site tRNA

HAPMAP: a computer program for the linkage analysis of haploids.

The development of technology for the detection of variations in DNA sequence is permitting the rapid mapping of the genomes of many organisms

Historic emissions from deforestation and forest degradation in Mato Grosso, Brazil: 1) source data uncertainties

<p>Abstract</p> <p>Background</p> <p>Historic carbon emissions are an important foundation for proposed efforts to Reduce Emissions from Deforestation and forest Degradation and enhance forest carbon stocks through conservation and sustainable forest management (REDD+). The level of uncertainty in historic carbon emissions estimates is also critical for REDD+, since high uncertainties could limit climate benefits from credited mitigation actions. Here, we analyzed source data uncertainties based on the range of available deforestation, forest degradation, and forest carbon stock estimates for the Brazilian state of Mato Grosso during 1990-2008.</p> <p>Results</p> <p>Deforestation estimates showed good agreement for multi-year periods of increasing and decreasing deforestation during the study period. However, annual deforestation rates differed by > 20% in more than half of the years between 1997-2008, even for products based on similar input data. Tier 2 estimates of average forest carbon stocks varied between 99-192 Mg C ha^-1, with greatest differences in northwest Mato Grosso. Carbon stocks in deforested areas increased over the study period, yet this increasing trend in deforested biomass was smaller than the difference among carbon stock datasets for these areas.</p> <p>Conclusions</p> <p>Estimates of source data uncertainties are essential for REDD+. Patterns of spatial and temporal disagreement among available data products provide a roadmap for future efforts to reduce source data uncertainties for estimates of historic forest carbon emissions. Specifically, regions with large discrepancies in available estimates of both deforestation and forest carbon stocks are priority areas for evaluating and improving existing estimates. Full carbon accounting for REDD+ will also require filling data gaps, including forest degradation and secondary forest, with annual data on all forest transitions.</p

Graphical models for inferring single molecule dynamics

The recent explosion of experimental techniques in single molecule biophysics has generated a variety of novel time series data requiring equally novel computational tools for analysis and inference. This article describes in general terms how graphical modeling may be used to learn from biophysical time series data using the variational Bayesian expectation maximization algorithm (VBEM). The discussion is illustrated by the example of single-molecule fluorescence resonance energy transfer (smFRET) versus time data, where the smFRET time series is modeled as a hidden Markov model (HMM) with Gaussian observables. A detailed description of smFRET is provided as well. The VBEM algorithm returns the model’s evidence and an approximating posterior parameter distribution given the data. The former provides a metric for model selection via maximum evidence (ME), and the latter a description of the model’s parameters learned from the data. ME/VBEM provide several advantages over the more commonly used approach of maximum likelihood (ML) optimized by the expectation maximization (EM) algorithm, the most important being a natural form of model selection and a well-posed (non-divergent) optimization problem. The results demonstrate the utility of graphical modeling for inference of dynamic processes in single molecule biophysics