Understanding human genome regulation through entropic graph-based regularization and submodular optimization

Thesis (Ph.D.)--University of Washington, 2016-06

Graph-based Semi-Supervised Learning in Acoustic Modeling for Automatic Speech Recognition

Thesis (Ph.D.)--University of Washington, 2016-06

Testing Independence in High Dimensions & Identifiability of Graphical Models

Thesis (Ph.D.)--University of Washington, 2016-06

Successive nonparametric estimation of conditional distributions

Spatial characterization of non-Gaussian attributes in earth sciences and engineering commonly requires the estimation of their conditional distribution. The indicator and probability kriging approaches of current nonparametric geostatistics provide approximations for estimating conditional distributions. They do not, however, provide results similar to those in the cumbersome implementation of simultaneous cokriging of indicators. This paper presents a new formulation termed successive cokriging of indicators that avoids the classic simultaneous solution and related computational problems, while obtaining equivalent results to the impractical simultaneous solution of cokriging of indicators. A successive minimization of the estimation variance of probability estimates is performed, as additional data are successively included into the estimation process. In addition, the approach leads to an efficient nonparametric simulation algorithm for non-Gaussian random functions based on residual probabilities.

Patched 1 conditional null allele in mice

The patched gene (Ptc) is a member of the hedgehog signaling pathway which plays a central role in the development of many invertebrate and vertebrate tissues. In addition, Ptc and a number of other pathway members are mutated in some common human cancers. Patched is the receptor for the hedgehog ligand and in the mouse ablation of the Ptc gene leads to developmental defects and an embryonic lethal phenotype. Here we describe a conditional Ptc allele in mice which will have utility for the temporospatial ablation of Ptc function. genesis 36:158-161, 2003. (C) 2003 Wiley-Liss, Inc.

Conditional inactivation of the Men1 gene leads to pancreatic and pituitary tumorigenesis but does not affect normal development of these tissues

Mutations of the MEN1 gene, encoding the tumor suppressor menin, predispose individuals to the cancer syndrome multiple endocrine neoplasia type 1, characterized by the development of tumors of the endocrine pancreas and anterior pituitary and parathyroid glands. We have targeted the murine Men1 gene by using Cre recombinase-loxP technology to develop both total and tissue-specific knockouts of the gene. Conditional homozygous inactivation of the Men1 gene in the pituitary gland and endocrine pancreas bypasses the embryonic lethality associated with a constitutional Men1(-/-) genotype and leads to beta-cell hyperplasia in less than 4 months and insulinomas and prolactinomas starting at 9 months. The pituitary gland and pancreas develop normally in the conditional absence of menin, but loss of this transcriptional cofactor is sufficient to cause beta-cell hyperplasia in some islets; however, such loss is not sufficient to initiate pituitary gland tumorigenesis, suggesting that additional genetic events are necessary for the latter.

Teleonomic entropy: measuring the phase-space of end-directed systems

We introduce a novel way of measuring the entropy of a set of values undergoing changes. Such a measure becomes useful when analyzing the temporal development of an algorithm designed to numerically update a collection of values such as artificial neural network weights undergoing adjustments during learning. We measure the entropy as a function of the phase-space of the values, i.e. their magnitude and velocity of change, using a method based on the abstract measure of entropy introduced by the philosopher Rudolf Carnap. By constructing a time-dynamic two-dimensional Voronoi diagram using Voronoi cell generators with coordinates of value- and value-velocity (change of magnitude), the entropy becomes a function of the cell areas. We term this measure teleonomic entropy since it can be used to describe changes in any end-directed (teleonomic) system. The usefulness of the method is illustrated when comparing the different approaches of two search algorithms, a learning artificial neural network and a population of discovering agents. (C) 2004 Elsevier Inc. All rights reserved.

Randomized control trial of a smoking cessation intervention directed at men whose partners are pregnant

Background. Although smoking cessation programs significantly reduce smoking rates in the general population, some sectors are poorly motivated by them, especially healthy men from lower socioeconomic classes. Methods. By using a significant life event (approaching birth of a child) we exploited a time of increased receptiveness to smoking cessation influences. A multicomponent intervention was conducted and evaluated using a stratified, randomised control trial, with an intention to treat analysis. Results. Five hundred and sixty-one men were enrolled and 505 (90%) followed to the end of their partners' pregnancy. At 6-month follow-up 16.5% of 291 smokers of the intervention group and 9.3% of 270 in the control group reported they had stopped smoking (P = 0.011, OR = 0.52, 95% CI 0.31 - 0.86). The strongest predictors of smoking cessation were being in a skilled occupation, having a higher number of quit attempts in the previous year and having the first cigarette of the day relatively later. Conclusions. The number of smoking men who had to be treated to achieve one stopping smoking (NNT) during their partner's pregnancy was 13 to 14. Innovative antismoking population health measures for the partners of antenatal patients are effective and perhaps should be more widely adopted. (C) 2003 American Health Foundation and Elsevier Inc. All rights reserved.

Conditional production of superpositions of coherent states with inefficient photon detection

It is shown that a linear superposition of two macroscopically distinguishable optical coherent states can be generated using a single photon source and simple all-optical operations. Weak squeezing on a single photon, beam mixing with an auxiliary coherent state, and photon detecting with imperfect threshold detectors are enough to generate a coherent state superposition in a free propagating optical field with a large coherent amplitude (alpha>2) and high fidelity (F>0.99). In contrast to all previous schemes to generate such a state, our scheme does not need photon number resolving measurements nor Kerr-type nonlinear interactions. Furthermore, it is robust to detection inefficiency and exhibits some resilience to photon production inefficiency.

Future long-horizon performance measurement conditional on past survival

This paper examines the measurement of long-horizon abnormal performance when stock selection is conditional on an extended period of past survival. Filtering on survival results in a sample driven towards more-established, frequently traded stocks and this has implications for the choice of benchmark used in performance measurement (especially in the presence of the well-documented size effect). A simulation study is conducted to document the properties of commonly employed performance measures conditional on past survival. The results suggest that the popular index benchmarks used in long-horizon event studies are severely biased and yield test statistics that are badly misspecified. In contrast, a matched-stock benchmark based on size and industry performs consistently well. Also, an eligible-stock index designed to mitigate the influence of the size effect proves effective.

Conditional performance evaluation and the relevance of money flows for Australian international equity funds

This paper assesses the importance of fund flows in the performance evaluation of Australian international equity funds. Two concepts of fund flows are considered in the context of a conditional asset pricing model. The first measure is net fund flow relative to fund size and the second is net fund flow relative to sector flows. We find that incorporating a fund flow measure relative to the sector flow results in a reduction of measured perverse market timing. The results indicate that, at the individual fund level, cash flows are relevant in assessing management outcomes.

Site-directed mutagenesis and kinetic studies of the West Nile virus NS3 protease identify key enzyme-substrate interactions

The flavivirus West Nile virus (WNV) has spread rapidly throughout the world in recent years causing fever, meningitis, encephalitis, and fatalities. Because the viral protease NS2B/NS3 is essential for replication, it is attracting attention as a potential therapeutic target, although there are currently no antiviral inhibitors for any flavivirus. This paper focuses on elucidating interactions between a hexapeptide substrate (Ae-KPGLKR-p-nitroanilide) and residues at S1 and S2 in the active site of WNV protease by comparing the catalytic activities of selected mutant recombinant proteases in vitro. Homology modeling enabled the predictions of key mutations in VWNV NS3 protease at S1 (V115A/F, D129A/ E/N, S135A, Y150A/F, S160A, and S163A) and S2 (N152A) that might influence substrate recognition and catalytic efficiency. Key conclusions are that the substrate P1 Arg strongly interacts with S1 residues Asp-129, Tyr-150, and Ser-163 and, to a lesser extent, Ser-160, and P2 Lys makes an essential interaction with Asn-152 at S2. The inferred substrate-enzyme interactions provide a basis for rational protease inhibitor design and optimization. High sequence conservation within flavivirus proteases means that this study may also be relevant to design of protease inhibitors for other flavivirus proteases.