Parametric Inference for Biological Sequence Analysis

One of the major successes in computational biology has been the unification, using the graphical model formalism, of a multitude of algorithms for annotating and comparing biological sequences. Graphical models that have been applied towards these problems include hidden Markov models for annotation, tree models for phylogenetics, and pair hidden Markov models for alignment. A single algorithm, the sum-product algorithm, solves many of the inference problems associated with different statistical models. This paper introduces the \emph{polytope propagation algorithm} for computing the Newton polytope of an observation from a graphical model. This algorithm is a geometric version of the sum-product algorithm and is used to analyze the parametric behavior of maximum a posteriori inference calculations for graphical models.Comment: 15 pages, 4 figures. See also companion paper "Tropical Geometry of Statistical Models" (q-bio.QM/0311009

Restriction Fragment Length Polymorphism Linkage Map for Arabidopsis thaliana

We have constructed a restriction fragment length polymorphism linkage map for the nuclear genome of the flowering plant Arabidopsis thaliana. The map, containing 90 randomly distributed molecular markers, is physically very dense; >50% of the genome is within 1.9 centimorgans, or approx 270 kilobase pairs, of the mapped DNA fragments. The map was based on the meiotic segregation of markers in two different crosses. The restriction fragment length polymorphism linkage groups were integrated with the five classically mapped linkage groups by virtue of mapped mutations included in these crosses. Markers consist of both cloned Arabidopsis genes and random low-copy-number genomic DNA clones that are able to detect polymorphisms with the restriction enzymes EcoRI, Bgl II, and/or Xba I. These cloned markers can serve as starting points for chromosome walking, allowing for the isolation of Arabidopsis genes of known map location. The restriction fragment length polymorphism map also can associate clones of unknown gene function with mutant phenotypes, and vice versa

Subtype-specific genomic alterations define new targets for soft tissue sarcoma therapy

2011 February 1Soft-tissue sarcomas, which result in approximately 10,700 diagnoses and 3,800 deaths per year in the United States1, show remarkable histologic diversity, with more than 50 recognized subtypes2. However, knowledge of their genomic alterations is limited. We describe an integrative analysis of DNA sequence, copy number and mRNA expression in 207 samples encompassing seven major subtypes. Frequently mutated genes included TP53 (17% of pleomorphic liposarcomas), NF1 (10.5% of myxofibrosarcomas and 8% of pleomorphic liposarcomas) and PIK3CA (18% of myxoid/round-cell liposarcomas, or MRCs). PIK3CA mutations in MRCs were associated with Akt activation and poor clinical outcomes. In myxofibrosarcomas and pleomorphic liposarcomas, we found both point mutations and genomic deletions affecting the tumor suppressor NF1. Finally, we found that short hairpin RNA (shRNA)-based knockdown of several genes amplified in dedifferentiated liposarcoma, including CDK4 and YEATS4, decreased cell proliferation. Our study yields a detailed map of molecular alterations across diverse sarcoma subtypes and suggests potential subtype-specific targets for therapy.Memorial Sloan-Kettering Cancer Center (Soft Tissue Sarcoma Program Project P01 CA047179

Unexpected phase locking of magnetic fluctuations in the multi-k magnet USb

The spin waves in the multi-k antiferromagnet USb soften and become quasielastic well below the antiferromagnetic ordering temperature TN. This occurs without a magnetic or structural transition. It has been suggested that this change is in fact due to dephasing of the different multi-k components: a switch from 3-k to 1-k behavior. In this work, we use inelastic neutron scattering with tridirectional polarization analysis to probe the quasielastic magnetic excitations and reveal that the 3-k structure does not dephase. More surprisingly, the paramagnetic correlations also maintain the same clear phase correlations well above TN (up to at least 1.4TN)

CONFINED ANIMAL PRODUCTION AND MANURE NUTRIENTS

Using data from the Census of Agriculture on animal inventory and sales, we estimate manure nutrient production on farms with confined livestock. Using reported on-farm production of crops on these same farms, we estimate the nutrient uptake for major field crops and pastureland. This enables us to examine the balance between manure nutrient production and nutrient need measured by crop uptake at a farm level. Examination at alternative spatial scales, shows that 75 percent of counties in the U.S. have farms that produce more manure nutrients than can be assimilated on the farm of production (excess nitrogen).The vast majority of the counties that produce excess nitrogen have adequate land in the county to spread the manure at agronomic rates. Thus, proposed policies that focus on land application have the potential to limit manure nutrient movement to waterways in most areas, if properly managed. However, moving manure to crop farms that formerly had not used manure will increase costs. There were about 5 percent of counties where the manure nitrogen production levels from confined animal production exceeded half the nitrogen assimilative capacity of all the cropland and pastureland in the county. These areas have the greatest need for mechanisms to encourage off-farm solutions to utilize manure as a feedstock for commercial enterprises or central processing.Livestock Production/Industries,

CONFINED ANIMAL PRODUCTION AND MANURE NUTRIENTS

Census of agriculture data were used to estimate manure nutrient production and the capacity of cropland and pastureland to assimilate nutrients. Most farms (78 percent for nitrogen and 69 percent for phosphorus) have adequate land on which it is physically feasible to apply the manure produced onfarm at agronomic rates. (The costs of applying manure at these rates have not been assessed). Even so, manure that is produced on operations that cannot fully apply it to their own land at agronomic rates accounts for 60 percent of the Nation's manure nitrogen and 70 percent of the manure phosphorus. In these cases, most counties with farms that produce "excess" nutrients have adequate crop acres not associated with animal operations, but within the county, on which it is feasible to spread the manure at agronomic rates. However, barriers to moving manure to other farms need to be studied. About 20 percent of the Nation's onfarm excess manure nitrogen is produced in counties that have insufficient cropland for its application at agronomic rates (23 percent for phosphorus). For areas without adequate land, alternatives to local land application-such as energy production-will need to be developed.Manure, nutrients, manure nutrients, animal waste, confined livestock, confined animal feeding operation, CAFO, feedlot beef, dairy cows, swine, poultry, animal unit, manure nitrogen, manure phosphorus, water quality, Livestock Production/Industries,

5d-5f Electric-multipole Transitions in Uranium Dioxide Probed by Non-resonant Inelastic X-ray Scattering

Non-resonant inelastic x ray scattering (NIXS) experiments have been performed to probe the 5d-5f electronic transitions at the uranium O(4,5) absorption edges in uranium dioxide. For small values of the scattering vector q, the spectra are dominated by dipole-allowed transitions encapsulated within the giant resonance, whereas for higher values of q the multipolar transitions of rank 3 and 5 give rise to strong and well-defined multiplet structure in the pre-edge region. The origin of the observed non-dipole multiplet structures is explained on the basis of many-electron atomic spectral calculations. The results obtained demonstrate the high potential of NIXS as a bulk-sensitive technique for the characterization of the electronic properties of actinide materials.Comment: Submitted to Physical Review Letters on 31 December 200

Tagged particle in a sheared suspension: effective temperature determines density distribution in a slowly varying external potential beyond linear response

We consider a sheared colloidal suspension under the influence of an external potential that varies slowly in space in the plane perpendicular to the flow and acts on one selected (tagged) particle of the suspension. Using a Chapman-Enskog type expansion we derive a steady state equation for the tagged particle density distribution. We show that for potentials varying along one direction only, the tagged particle distribution is the same as the equilibrium distribution with the temperature equal to the effective temperature obtained from the violation of the Einstein relation between the self-diffusion and tagged particle mobility coefficients. We thus prove the usefulness of this effective temperature for the description of the tagged particle behavior beyond the realm of linear response. We illustrate our theoretical predictions with Brownian dynamics computer simulations.Comment: Accepted for publication in Europhys. Let