Identification of drug resistance mutations in HIV from constraints on natural evolution

Human immunodeficiency virus (HIV) evolves with extraordinary rapidity. However, its evolution is constrained by interactions between mutations in its fitness landscape. Here we show that an Ising model describing these interactions, inferred from sequence data obtained prior to the use of antiretroviral drugs, can be used to identify clinically significant sites of resistance mutations. Successful predictions of the resistance sites indicate progress in the development of successful models of real viral evolution at the single residue level, and suggest that our approach may be applied to help design new therapies that are less prone to failure even where resistance data is not yet available.Comment: 5 pages, 3 figure

Economic Potential of Substituting Legumes for Synthetic Nitrogen in Warm Season Perennial Grasses used for Stocker Cattle Grazing

Stocker cattle grazing warm season perennial grasses is an important economic activity in the southern Great Plains. Substantial increases in the price of nitrogen fertilizer is negatively affecting forage producers’ profitability. Two alternative nitrogen management systems that use annual and perennial legumes have been developed for bermudagrass pastures. The goal of the study is to determine if the legumes systems are more profitable than the conventional practice of applying synthetic sources of nitrogen. Results of the two-year grazing study show that the legume systems could not compete economically with the common practice.economics, grazing, legumes, bermudagrass, nitrogen fertilizer, stocker cattle, Crop Production/Industries, Farm Management, Production Economics,

Molecular and Ultrastructural Confirmation of Classification of ATCC 35122 as a Strain of Pirellula staleyi

A freshwater isolate from Campus Lake, Baton Rouge, LA, USA, strain ATCC 35122 (= ICPB 4362 = Schmidt CLPM White = Tekniepe BT2 white), which had been proposed as a putative reference strain for 'Planctomyces staleyi' (later reclassified as Pirellula staleyi), has been re-examined to establish its relationship to the type strain of Pirellula staleyi, ATCC 27377T. 16S rRNA sequencing confirms its very close relationship to ATCC 27377T and its membership of the order Planctomycetales. Ultrastructural characteristics are also consistent with its membership of the planctomycetes and of the genus Pirellula. These characteristics include polar crateriform structures and the occurrence of the unique internal, single- membrane-bounded compartment enclosing the nucleoid and ribosome-like particles, the pirellulosome, and a polar cap region. Cells of strain ATCC 35122 often displayed pointed, hump-like protrusions opposite each other on the cell, constituting prosthecae, and these were also found to be present on cells of strain ATCC 27377T. The original identification of ATCC 35122 as a strain of Pirellula staleyi is confirmed on both molecular and phenotypic grounds

Development of an orthogonal-stripe CdZnTe gamma radiation imaging spectrometer

We report performance measurements of a sub-millimeter resolution CdZnTe strip detector developed as a prototype for astronomical instruments operating with good efficiency in the 30-300 keV photon energy range. The prototype is a 1.4 mm thick, 64×64 contact stripe CdZnTe array of 0.375 mm pitch in both dimensions. Pulse height spectra were recorded in orthogonal-stripe coincidence mode which demonstrate room-temperature energy resolution \u3c10 keV (FWHM) for 122 keV photons with a peak-to-valley ratio \u3e5:1. Good response is also demonstrated at higher energies using a coplanar grid readout configuration. Spatial resolution capabilities finer than the stripe pitch are demonstrated. We present the image of a 133Ba source viewed through a collimator slit produced by a 4×4 stripe detector segment. Charge signals from electron and hole collecting contacts are also discussed

Large-area submillimeter resolution CdZnTe strip detector for astronomy

We report the first performance measurements of a sub-millimeter CdZnTe strip detector developed as a prototype for space-borne astronomical instruments. Strip detector arrays can be used to provide two-dimensional position resolution with fewer electronic channels than pixellated arrays. Arrays of this type and other candidate technologies are under investigation for the position-sensitive backplane detector for a coded-aperture telescope operating in the range of 30 - 300 keV. The prototype is a 1.4 mm thick, 64 multiplied by 64 stripe CdZnTe array of 0.375 mm pitch in both dimensions, approximately one square inch of sensitive area. Pulse height spectra in both single and orthogonal stripe coincidence mode were recorded at several energies. The results are compared to slab- and pixel-geometry detector spectra. The room-temperature energy resolution is less than 10 keV (FWHM) for 122 keV photons with a peak-to-valley ratio greater than 5:1. The response to photons with energies up to 662 keV appears to be considerably improved relative to that of previously reported slab and pixel detectors. We also show that strip detectors can yield spatial and energy resolutions similar to those of pixellated arrays with the same dimensions. Electrostatic effects on the pulse heights, read-out circuit complexity, and issues related to design of space borne instruments are also discussed

Development and Testing of The Gait Assessment and Intervention Tool (G.A.I.T.): A Measure of Coordinated Gait Components

Recent neuroscience methods have provided the basis upon which to develop effective gait training methods for recovery of the coordinated components of gait after neural injury. We determined that there was not an existing observational measure that was, at once, adequately comprehensive, scored in an objectively-based manner, and capable of assessing incremental improvements in the coordinated components of gait. Therefore, the purpose of this work was to use content valid procedures in order to develop a relatively inexpensive, more comprehensive measure, scored with an objectively-based system, capable of incrementally scoring improvements in given items, and that was both reliable and capable of discriminating treatment response for those who had a stroke. Eight neurorehabilitation specialists developed criteria for the gait measure, item content, and scoring method. In subjects following stroke (\u3e12 months), the new measure was tested for intra- and inter-rater reliability using the Intraclass Correlation Coefficient; capability to detect treatment response using Wilcoxon Signed Ranks Test; and discrimination between treatment groups, using the Plum Ordinal Regression. The Gait Assessment and Intervention Tool (G.A.I.T.) is a 31-item measure of the coordinated movement components of gait and associated gait deficits. It exhibited the following advantages: comprehensive, objective-based scoring method, incremental measurement of improvement within given items. The G.A.I.T. had good intra- and inter-rater reliability (ICC = .98, p = .0001, 95% CI = .95, .99; ICC = .83, p = .007, 95% CI = .32, .96, respectively. The inexperienced clinician who had training, had an inter-rater reliability with an experienced rater of ICC = .99 (p = .0001, CI = .97, .999). The G.A.I.T. detected improvement in response to gait training for two types of interventions: comprehensive gait training (z = −2.93, p = .003); and comprehensive gait training plus functional electrical stimulation (FES; z = −3.3, p = .001). The G.A.I.T. was capable of discriminating between two gait training interventions, showing an additive advantage of FES to otherwise comparable comprehensive gait training (parameter estimate = 1.72, p = .021; CI, .25, 3.1)

Development and Testing of The Gait Assessment and Intervention Tool (G.A.I.T.): A Measure of Coordinated Gait Components

Recent neuroscience methods have provided the basis upon which to develop effective gait training methods for recovery of the coordinated components of gait after neural injury. We determined that there was not an existing observational measure that was, at once, adequately comprehensive, scored in an objectively-based manner, and capable of assessing incremental improvements in the coordinated components of gait. Therefore, the purpose of this work was to use content valid procedures in order to develop a relatively inexpensive, more comprehensive measure, scored with an objectively-based system, capable of incrementally scoring improvements in given items, and that was both reliable and capable of discriminating treatment response for those who had a stroke. Eight neurorehabilitation specialists developed criteria for the gait measure, item content, and scoring method. In subjects following stroke (\u3e12 months), the new measure was tested for intra- and inter-rater reliability using the Intraclass Correlation Coefficient; capability to detect treatment response using Wilcoxon Signed Ranks Test; and discrimination between treatment groups, using the Plum Ordinal Regression. The Gait Assessment and Intervention Tool (G.A.I.T.) is a 31-item measure of the coordinated movement components of gait and associated gait deficits. It exhibited the following advantages: comprehensive, objective-based scoring method, incremental measurement of improvement within given items. The G.A.I.T. had good intra- and inter-rater reliability (ICC = .98, p = .0001, 95% CI = .95, .99; ICC = .83, p = .007, 95% CI = .32, .96, respectively. The inexperienced clinician who had training, had an inter-rater reliability with an experienced rater of ICC = .99 (p = .0001, CI = .97, .999). The G.A.I.T. detected improvement in response to gait training for two types of interventions: comprehensive gait training (z = −2.93, p = .003); and comprehensive gait training plus functional electrical stimulation (FES; z = −3.3, p = .001). The G.A.I.T. was capable of discriminating between two gait training interventions, showing an additive advantage of FES to otherwise comparable comprehensive gait training (parameter estimate = 1.72, p = .021; CI, .25, 3.1)

Five Intermediate-Period Planets from the N2K Sample

We report the detection of five Jovian mass planets orbiting high metallicity stars. Four of these stars were first observed as part of the N2K program and exhibited low RMS velocity scatter after three consecutive observations. However, follow-up observations over the last three years now reveal the presence of longer period planets with orbital periods ranging from 21 days to a few years. HD 11506 is a G0V star with a planet of \msini = 4.74 \mjup in a 3.85 year orbit. HD 17156 is a G0V star with a 3.12 \mjup planet in a 21.2 day orbit. The eccentricity of this orbit is 0.67, one of the highest known for a planet with a relatively short period. The orbital period for this planet places it in a region of parameter space where relatively few planets have been detected. HD 125612 is a G3V star with a planet of \msini = 3.5 \mjup in a 1.4 year orbit. HD 170469 is a G5IV star with a planet of \msini = 0.67 \mjup in a 3.13 year orbit. HD 231701 is an F8V star with planet of 1.08 \mjup in a 142 day orbit. All of these stars have supersolar metallicity. Three of the five stars were observed photometrically but showed no evidence of brightness variability. A transit search conducted for HD 17156 was negative but covered only 25% of the search space and so is not conclusive.Comment: 13 pages, 9 figures, accepted ApJ Resubmitted here with some additional data, modified Keplerian orbit