rbrothers: R Package for Bayesian Multiple Change-Point Recombination Detection.

Phylogenetic recombination detection is a fundamental task in bioinformatics and evolutionary biology. Most of the computational tools developed to attack this important problem are not integrated into the growing suite of R packages for statistical analysis of molecular sequences. Here, we present an R package, rbrothers, that makes a Bayesian multiple change-point model, one of the most sophisticated model-based phylogenetic recombination tools, available to R users. Moreover, we equip the Bayesian change-point model with a set of pre- and post- processing routines that will broaden the application domain of this recombination detection framework. Specifically, we implement an algorithm that forms the set of input trees required by multiple change-point models. We also provide functionality for checking Markov chain Monte Carlo convergence and creating estimation result summaries and graphics. Using rbrothers, we perform a comparative analysis of two Salmonella enterica genes, fimA and fimH, that encode major and adhesive subunits of the type 1 fimbriae, respectively. We believe that rbrothers, available at R-Forge: http://evolmod.r-forge.r-project.org/, will allow researchers to incorporate recombination detection into phylogenetic workflows already implemented in R

Land surface Verification Toolkit (LVT)

LVT is a framework developed to provide an automated, consolidated environment for systematic land surface model evaluation Includes support for a range of in-situ, remote-sensing and other model and reanalysis products. Supports the analysis of outputs from various LIS subsystems, including LIS-DA, LIS-OPT, LIS-UE. Note: The Land Information System Verification Toolkit (LVT) is a NASA software tool designed to enable the evaluation, analysis and comparison of outputs generated by the Land Information System (LIS). The LVT software is released under the terms and conditions of the NASA Open Source Agreement (NOSA) Version 1.1 or later. Land Information System Verification Toolkit (LVT) NOSA

Counting Wobbling Dual-Giants

We derive the BPS equations for D3-branes embedded in AdS_5 X S^5 that preserve at least two supercharges. These are given in terms of conditions on the pullbacks of some space-time differential four-forms. Solutions to our equations are shown to describe all the known giant and dual-giant gravitons in AdS_5 X S^5. We then argue that the configuration spaces of dual-giants can be mapped to non-compact hyperbolic versions of complex projective spaces, in contrast with the giants, whose configuration spaces have been mapped to complex projective spaces. We quantize the configuration space of the 1/8-BPS dual-giants with two angular momenta in AdS_5 and one angular momentum in S^5 and find agreement with the partition function in the literature obtained both from counting appropriate 1/8-BPS configurations of giants and the boundary gauge theory considerations.Comment: 36 page

Development of Global Operational Snow Analysis at the US Air Force 557th Weather Wing

The outdated SNODEP snow depth retrieval algorithm is replaced by the Foster et al. (1997; 2005) approach, which considers the effects of variations in forest cover. The simple blending algorithm (IDW) is replaced by the Bratseth scheme, a successive correction algorithm that converges to the solution provided by Optimal Interpolation (OI). Outdated quality control datasets are updated and quality control algorithms are reorganized to ensure the performance of the snow analysis. The spatial resolution of snow and ice estimates are increased from 25-km to 10-km.USAF-SI are fully integrated into the global operational land analysis configuration at the USAF 557th WW

Validation and Verification of Operational Land Analysis Activities at the Air Force Weather Agency

The NASA developed Land Information System (LIS) is the Air Force Weather Agency's (AFWA) operational Land Data Assimilation System (LDAS) combining real time precipitation observations and analyses, global forecast model data, vegetation, terrain, and soil parameters with the community Noah land surface model, along with other hydrology module options, to generate profile analyses of global soil moisture, soil temperature, and other important land surface characteristics. (1) A range of satellite data products and surface observations used to generate the land analysis products (2) Global, 1/4 deg spatial resolution (3) Model analysis generated at 3 hours. AFWA recognizes the importance of operational benchmarking and uncertainty characterization for land surface modeling and is developing standard methods, software, and metrics to verify and/or validate LIS output products. To facilitate this and other needs for land analysis activities at AFWA, the Model Evaluation Toolkit (MET) -- a joint product of the National Center for Atmospheric Research Developmental Testbed Center (NCAR DTC), AFWA, and the user community -- and the Land surface Verification Toolkit (LVT), developed at the Goddard Space Flight Center (GSFC), have been adapted to operational benchmarking needs of AFWA's land characterization activities

A Modeling and Verification Study of Summer Precipitation Systems Using NASA Surface Initialization Datasets

One of the most challenging weather forecast problems in the southeastern U.S. is daily summertime pulse-type convection. During the summer, atmospheric flow and forcing are generally weak in this region; thus, convection typically initiates in response to local forcing along sea/lake breezes, and other discontinuities often related to horizontal gradients in surface heating rates. Numerical simulations of pulse convection usually have low skill, even in local predictions at high resolution, due to the inherent chaotic nature of these precipitation systems. Forecast errors can arise from assumptions within parameterization schemes, model resolution limitations, and uncertainties in both the initial state of the atmosphere and land surface variables such as soil moisture and temperature. For this study, it is hypothesized that high-resolution, consistent representations of surface properties such as soil moisture, soil temperature, and sea surface temperature (SST) are necessary to better simulate the interactions between the surface and atmosphere, and ultimately improve predictions of summertime pulse convection. This paper describes a sensitivity experiment using the Weather Research and Forecasting (WRF) model. Interpolated land and ocean surface fields from a large-scale model are replaced with high-resolution datasets provided by unique NASA assets in an experimental simulation: the Land Information System (LIS) and Moderate Resolution Imaging Spectroradiometer (MODIS) SSTs. The LIS is run in an offline mode for several years at the same grid resolution as the WRF model to provide compatible land surface initial conditions in an equilibrium state. The MODIS SSTs provide detailed analyses of SSTs over the oceans and large lakes compared to current operational products. The WRF model runs initialized with the LIS+MODIS datasets result in a reduction in the overprediction of rainfall areas; however, the skill is almost equally as low in both experiments using traditional verification methodologies. Output from object-based verification within NCAR s Meteorological Evaluation Tools reveals that the WRF runs initialized with LIS+MODIS data consistently generated precipitation objects that better matched observed precipitation objects, especially at higher precipitation intensities. The LIS+MODIS runs produced on average a 4% increase in matched precipitation areas and a simultaneous 4% decrease in unmatched areas during three months of daily simulations

Comparison of Four Precipitation Forcing Datasets in Land Information System Simulations over the Continental U.S.

This paper and poster presented a description of the current real-time SPoRT-LIS run over the southeastern CONUS to provide high-resolution, land surface initialization grids for local numerical model forecasts at NWS forecast offices. The LIS hourly output also offers a supplemental dataset to aid in situational awareness for convective initiation forecasts, assessing flood potential, and monitoring drought at fine scales. It is a goal of SPoRT and several NWS forecast offices to expand the LIS to an entire CONUS domain, so that LIS output can be utilized by NWS Western Region offices, among others. To make this expansion cleanly so as to provide high-quality land surface output, SPoRT tested new precipitation datasets in LIS as an alternative forcing dataset to the current radar+gauge Stage IV product. Similar to the Stage IV product, the NMQ product showed comparable patterns of precipitation and soil moisture distribution, but suffered from radar gaps in the intermountain West, and incorrectly set values to zero instead of missing in the data-void regions of Mexico and Canada. The other dataset tested was the next-generation GOES-R QPE algorithm, which experienced a high bias in both coverage and intensity of accumulated precipitation relative to the control (NLDAS2), Stage IV, and NMQ simulations. The resulting root zone soil moisture was substantially higher in most areas

Evaluating the Impacts of NASA/SPoRT Daily Greenness Vegetation Fraction on Land Surface Model and Numerical Weather Forecasts

The NASA Short-term Prediction Research and Transition (SPoRT) Center has developed a Greenness Vegetation Fraction (GVF) dataset, which is updated daily using swaths of Normalized Difference Vegetation Index data from the Moderate Resolution Imaging Spectroradiometer (MODIS) data aboard the NASA EOS Aqua and Terra satellites. NASA SPoRT began generating daily real-time GVF composites at 1-km resolution over the Continental United States (CONUS) on 1 June 2010. The purpose of this study is to compare the National Centers for Environmental Prediction (NCEP) climatology GVF product (currently used in operational weather models) to the SPoRT-MODIS GVF during June to October 2010. The NASA Land Information System (LIS) was employed to study the impacts of the SPoRT-MODIS GVF dataset on a land surface model (LSM) apart from a full numerical weather prediction (NWP) model. For the 2010 warm season, the SPoRT GVF in the western portion of the CONUS was generally higher than the NCEP climatology. The eastern CONUS GVF had variations both above and below the climatology during the period of study. These variations in GVF led to direct impacts on the rates of heating and evaporation from the land surface. In the West, higher latent heat fluxes prevailed, which enhanced the rates of evapotranspiration and soil moisture depletion in the LSM. By late Summer and Autumn, both the average sensible and latent heat fluxes increased in the West as a result of the more rapid soil drying and higher coverage of GVF. The impacts of the SPoRT GVF dataset on NWP was also examined for a single severe weather case study using the Weather Research and Forecasting (WRF) model. Two separate coupled LIS/WRF model simulations were made for the 17 July 2010 severe weather event in the Upper Midwest using the NCEP and SPoRT GVFs, with all other model parameters remaining the same. Based on the sensitivity results, regions with higher GVF in the SPoRT model runs had higher evapotranspiration and lower direct surface heating, which typically resulted in lower (higher) predicted 2-m temperatures (2-m dewpoint temperatures). Portions of the Northern Plains states experienced substantial increases in convective available potential energy as a result of the higher SPoRT/MODIS GVFs. These differences produced subtle yet quantifiable differences in the simulated convective precipitation systems for this event