Motif Discovery through Predictive Modeling of Gene Regulation

We present MEDUSA, an integrative method for learning motif models of transcription factor binding sites by incorporating promoter sequence and gene expression data. We use a modern large-margin machine learning approach, based on boosting, to enable feature selection from the high-dimensional search space of candidate binding sequences while avoiding overfitting. At each iteration of the algorithm, MEDUSA builds a motif model whose presence in the promoter region of a gene, coupled with activity of a regulator in an experiment, is predictive of differential expression. In this way, we learn motifs that are functional and predictive of regulatory response rather than motifs that are simply overrepresented in promoter sequences. Moreover, MEDUSA produces a model of the transcriptional control logic that can predict the expression of any gene in the organism, given the sequence of the promoter region of the target gene and the expression state of a set of known or putative transcription factors and signaling molecules. Each motif model is either a $k$-length sequence, a dimer, or a PSSM that is built by agglomerative probabilistic clustering of sequences with similar boosting loss. By applying MEDUSA to a set of environmental stress response expression data in yeast, we learn motifs whose ability to predict differential expression of target genes outperforms motifs from the TRANSFAC dataset and from a previously published candidate set of PSSMs. We also show that MEDUSA retrieves many experimentally confirmed binding sites associated with environmental stress response from the literature.Comment: RECOMB 200

Winter Mass Mortality of Animals in Texas Bays

The Texas coast experienced three unusually cold weather periods in the 1980\u27s, one in 1983 and two in 1989, that caused massive fish kills. Identification of organisms killed and estimation of the number of estuarine fishes and invertebrates killed was accomplished through a systematic standardized approach utilizing airplanes, ground qualitative observations and quantitative counts, and trawling. Of 159 species identified, 103 were fishes, 45 were invertebrates, and 11 were vertebrates other than fishes. About 14 million fishes were killed in December 1983, 11 million in February 1989 and 6 million in December 1989; number of invertebrates killed ranged from 13,000 in February 1989 to 1,000,000 in 1983. These assessments are the largest in area and most comprehensive to be documented in the literature with known levels of precision. Methodology used provides reasonably precise estimates which managers can use to assess extensive widespread kills and subsequent impacts on affected populations. It is recommended that managers consider reducing fishing mortality on the remaining economically important populations after extensive kills to speed recovery of those populations

Observed Effect of Magnetic Fields on the Propagation of Magnetoacoustic Waves in the Lower Solar Atmosphere

We study Hinode/SOT-FG observations of intensity fluctuations in Ca II H-line and G-band image sequences and their relation to simultaneous and co-spatial magnetic field measurements. We explore the G-band and H-line intensity oscillation spectra both separately and comparatively via their relative phase differences, time delays and cross-coherences. In the non-magnetic situations, both sets of fluctuations show strong oscillatory power in the 3 - 7 mHz band centered at 4.5 mHz, but this is suppressed as magnetic field increases. A relative phase analysis gives a time delay of H-line after G-band of 20\pm1 s in non-magnetic situations implying a mean effective height difference of 140 km. The maximum coherence is at 4 - 7 mHz. Under strong magnetic influence the measured delay time shrinks to 11 s with the peak coherence near 4 mHz. A second coherence maximum appears between 7.5 - 10 mHz. Investigation of the locations of this doubled-frequency coherence locates it in diffuse rings outside photospheric magnetic structures. Some possible interpretations of these results are offered.Comment: 19 pages, 6 figure

Entanglement can increase asymptotic rates of zero-error classical communication over classical channels

It is known that the number of different classical messages which can be communicated with a single use of a classical channel with zero probability of decoding error can sometimes be increased by using entanglement shared between sender and receiver. It has been an open question to determine whether entanglement can ever increase the zero-error communication rates achievable in the limit of many channel uses. In this paper we show, by explicit examples, that entanglement can indeed increase asymptotic zero-error capacity, even to the extent that it is equal to the normal capacity of the channel. Interestingly, our examples are based on the exceptional simple root systems E7 and E8.Comment: 14 pages, 2 figur

Dibaryon Spectroscopy

The AdS/CFT correspondence relates dibaryons in superconformal gauge theories to holomorphic curves in Kaehler-Einstein surfaces. The degree of the holomorphic curves is proportional to the gauge theory conformal dimension of the dibaryons. Moreover, the number of holomorphic curves should match, in an appropriately defined sense, the number of dibaryons. Using AdS/CFT backgrounds built from the generalized conifolds of Gubser, Shatashvili, and Nekrasov (1999), we show that the gauge theory prediction for the dimension of dibaryonic operators does indeed match the degree of the corresponding holomorphic curves. For AdS/CFT backgrounds built from cones over del Pezzo surfaces, we are able to match the degree of the curves to the conformal dimension of dibaryons for the n'th del Pezzo surface, n=1,2,...,6. Also, for the del Pezzos and the A_k type generalized conifolds, for the dibaryons of smallest conformal dimension, we are able to match the number of holomorphic curves with the number of possible dibaryon operators from gauge theory.Comment: 30 pages, 6 figures, corrected refs; v3 typos correcte

Classification of protein interaction sentences via gaussian processes

The increase in the availability of protein interaction studies in textual format coupled with the demand for easier access to the key results has lead to a need for text mining solutions. In the text processing pipeline, classification is a key step for extraction of small sections of relevant text. Consequently, for the task of locating protein-protein interaction sentences, we examine the use of a classifier which has rarely been applied to text, the Gaussian processes (GPs). GPs are a non-parametric probabilistic analogue to the more popular support vector machines (SVMs). We find that GPs outperform the SVM and na\"ive Bayes classifiers on binary sentence data, whilst showing equivalent performance on abstract and multiclass sentence corpora. In addition, the lack of the margin parameter, which requires costly tuning, along with the principled multiclass extensions enabled by the probabilistic framework make GPs an appealing alternative worth of further adoption

Dibaryons from Exceptional Collections

We discuss aspects of the dictionary between brane configurations in del Pezzo geometries and dibaryons in the dual superconformal quiver gauge theories. The basis of fractional branes defining the quiver theory at the singularity has a K-theoretic dual exceptional collection of bundles which can be used to read off the spectrum of dibaryons in the weakly curved dual geometry. Our prescription identifies the R-charge R and all baryonic U(1) charges Q_I with divisors in the del Pezzo surface without any Weyl group ambiguity. As one application of the correspondence, we identify the cubic anomaly tr R Q_I Q_J as an intersection product for dibaryon charges in large-N superconformal gauge theories. Examples can be given for all del Pezzo surfaces using three- and four-block exceptional collections. Markov-type equations enforce consistency among anomaly equations for three-block collections.Comment: 47 pages, 11 figures, corrected ref

The frequency of transforming growth factor-TGF-B gene polymorphisms in a normal southern Iranian population

Several single nucleotide polymorphisms (SNPs) of the transforming growth factor-β1 gene (TGFB1) have been reported. Determination of TGFB1 SNPs allele frequencies in different ethnic groups is useful for both population genetic analyses and association studies with immunological diseases. In this study, five SNPs of TGFB1 were determined in 325 individuals from a normal southern Iranian population using polymerase chain reaction-restriction fragment length polymorphism method. This population was in Hardy-Weinberg equilibrium for these SNPs. Of the 12 constructed haplotypes, GTCGC and GCTGC were the most frequent in the normal southern Iranian population. Comparison of genotype and allele frequencies of TGFB SNPs between Iranian and other populations (meta-analysis) showed significant differences, and in this case the southern Iranian population seems genetically similar to Caucasoid populations. However, neighbour-joining tree using Nei's genetic distances based on TGF-β1 allele frequencies showed that southern Iranians are genetically far from people from the USA, Germany, UK, Denmark and the Czech Republic. In conclusion, this is the first report of the distribution of TGFB1 SNPs in an Iranian population and the results of this investigation may provide useful information for both population genetic and disease studies. © 2008 The Authors

Quiver theories, soliton spectra and Picard-Lefschetz transformations

Quiver theories arising on D3-branes at orbifold and del Pezzo singularities are studied using mirror symmetry. We show that the quivers for the orbifold theories are given by the soliton spectrum of massive 2d N=2 theory with weighted projective spaces as target. For the theories obtained from the del Pezzo singularities we show that the geometry of the mirror manifold gives quiver theories related to each other by Picard-Lefschetz transformations, a subset of which are simple Seiberg duals. We also address how one indeed derives Seiberg duality on the matter content from such geometrical transitions and how one could go beyond and obtain certain ``fractional Seiberg duals.'' Moreover, from the mirror geometry for the del Pezzos arise certain Diophantine equations which classify all quivers related by Picard-Lefschetz. Some of these Diophantine equations can also be obtained from the classification results of Cecotti-Vafa for the 2d N=2 theories.Comment: 34 pages, 11 figure

Relic neutrino masses and the highest energy cosmic rays

We consider the possibility that a large fraction of the ultrahigh energy cosmic rays are decay products of Z bosons which were produced in the scattering of ultrahigh energy cosmic neutrinos on cosmological relic neutrinos. We compare the observed ultrahigh energy cosmic ray spectrum with the one predicted in the above Z-burst scenario and determine the required mass of the heaviest relic neutrino as well as the necessary ultrahigh energy cosmic neutrino flux via a maximum likelihood analysis. We show that the value of the neutrino mass obtained in this way is fairly robust against variations in presently unknown quantities, like the amount of neutrino clustering, the universal radio background, and the extragalactic magnetic field, within their anticipated uncertainties. Much stronger systematics arises from different possible assumptions about the diffuse background of ordinary cosmic rays from unresolved astrophysical sources. In the most plausible case that these ordinary cosmic rays are protons of extragalactic origin, one is lead to a required neutrino mass in the range 0.08 eV - 1.3 eV at the 68 % confidence level. This range narrows down considerably if a particular universal radio background is assumed, e.g. to 0.08 eV - 0.40 eV for a large one. The required flux of ultrahigh energy cosmic neutrinos near the resonant energy should be detected in the near future by AMANDA, RICE, and the Pierre Auger Observatory, otherwise the Z-burst scenario will be ruled out.Comment: 19 pages, 22 figures, REVTeX