A combined statistical model for multiple motifs search

Transcription factor binding sites (TFBS) play key roles in genebior 6.8 wavelet expression and regulation. They are short sequence segments with de¯nite structure and can be recognized by the corresponding transcription factors correctly. From the viewpoint of statistics, the candidates of TFBS should be quite di®erent from the segments that are randomly combined together by nucleotide. This paper proposes a combined statistical model for ¯nding over- represented short sequence segments in di®erent kinds of data set. While the over-represented short sequence segment is described by position weight matrix, the nucleotide distribution at most sites of the segment should be far from the background nucleotide distribution. The central idea of this approach is to search for such kind of signals. This algorithm is tested on 3 data sets, including binding sites data set of cyclic AMP receptor protein in E.coli, PlantProm DB which is a non-redundant collection of proximal promoter sequences from di®erent species, collection of the intergenic sequences of the whole genome of E.Coli. Even though the complexity of these three data sets is quite di®erent, the results show that this model is rather general and sensible.

In search of slow-moving ionizing massive particles

Many particles proposed by theories, such as GUT monopoles, nuclearites and 1/5 charge superstring particles, can be categorized as Slow-moving, Ionizing, Massive Particles (SIMPs).

Detailed calculations of the signal-to-noise ratios in vanous acoustic and mechanical methods for detecting such SIMPs are presented. It is shown that the previous belief that such methods are intrinsically prohibited by the thermal noise is incorrect, and that ways to solve the thermal noise problem are already within the reach of today's technology. In fact, many running and finished gravitational wave detection ( GWD) experiments are already sensitive to certain SIMPs. As an example, a published GWD result is used to obtain a flux limit for nuclearites.

The result of a search using a scintillator array on Earth's surface is reported. A flux limit of 4.7 x 10^(-12) cm^(-2)sr^(-1)s^(-1) (90% c.l.) is set for any SIMP with 2.7 x 10^(-4) less than β less than 5 x 10^(-3) and ionization greater than 1/3 of minimum ionizing muons. Although this limit is above the limits from underground experiments for typical supermassive particles (10^(16)GeV), it is a new limit in certain β and ionization regions for less massive ones (~10^9 GeV) not able to penetrate deep underground, and implies a stringent limit on the fraction of the dark matter that can be composed of massive electrically and/ or magnetically charged particles.

The prospect of the future SIMP search in the MACRO detector is discussed. The special problem of SIMP trigger is examined and a circuit proposed, which may solve most of the problems of the previous ones proposed or used by others and may even enable MACRO to detect certain SIMP species with β as low as the orbital velocity around the earth.

The biological sense of smell: olfactory search behavior and a metabolic view for olfactory perception

Part I of the thesis describes the olfactory searching and scanning behaviors of rats in a wind tunnel, and a detailed movement analysis of terrestrial arthropod olfactory scanning behavior. Olfactory scanning behaviors in rats may be a behavioral correlate to hippocampal place cell activity.

Part II focuses on the organization of olfactory perception, what it suggests about a natural order for chemicals in the environment, and what this in tum suggests about the organization of the olfactory system. A model of odor quality space (analogous to the "color wheel") is presented. This model defines relationships between odor qualities perceived by human subjects based on a quantitative similarity measure. Compounds containing Carbon, Nitrogen, or Sulfur elicit odors that are contiguous in this odor representation, which thus allows one to predict the broad class of odor qualities a compound is likely to elicit. Based on these findings, a natural organization for olfactory stimuli is hypothesized: the order provided by the metabolic process. This hypothesis is tested by comparing compounds that are structurally similar, perceptually similar, and metabolically similar in a psychophysical cross-adaptation paradigm. Metabolically similar compounds consistently evoked shifts in odor quality and intensity under cross-adaptation, while compounds that were structurally similar or perceptually similar did not. This suggests that the olfactory system may process metabolically similar compounds using the same neural pathways, and that metabolic similarity may be the fundamental metric about which olfactory processing is organized. In other words, the olfactory system may be organized around a biological basis.

The idea of a biological basis for olfactory perception represents a shift in how olfaction is understood. The biological view has predictive power while the current chemical view does not, and the biological view provides explanations for some of the most basic questions in olfaction, that are unanswered in the chemical view. Existing data do not disprove a biological view, and are consistent with basic hypotheses that arise from this viewpoint.

Search for color transparency in A(e,e'p) at high momentum transfer

Rates for A(e, e'p) on the nuclei ^2H, C, Fe, and Au have been measured at momentum transfers Q^2 = 1, 3, 5, and 6.8 (GeV fc)^2 . We extract the nuclear transparency T, a measure of the importance of final state interactions (FSI) between the outgoing proton and the recoil nucleus. Some calculations based on perturbative QCD predict an increase in T with momentum transfer, a phenomenon known as Color Transparency. No statistically significant rise is seen in the present experiment.