Parameter estimation in pair hidden Markov models

This paper deals with parameter estimation in pair hidden Markov models (pair-HMMs). We first provide a rigorous formalism for these models and discuss possible definitions of likelihoods. The model being biologically motivated, some restrictions with respect to the full parameter space naturally occur. Existence of two different Information divergence rates is established and divergence property (namely positivity at values different from the true one) is shown under additional assumptions. This yields consistency for the parameter in parametrization schemes for which the divergence property holds. Simulations illustrate different cases which are not covered by our results.Comment: corrected typo

Depression, Relationship Quality, and Couples’ Demand/Withdraw and Demand/Submit Sequential Interactions

This study investigated the associations among depression, relationship quality, and demand/withdraw and demand/submit behavior in couples’ conflict interactions. Two 10-min conflict interactions were coded for each couple (N = 97) using Structural Analysis of Social Behavior (SASB; Benjamin, 1979a, 1987, 2000a). Depression was assessed categorically (via the presence of depressive disorders) and dimensionally (via symptom reports). Results revealed that relationship quality was negatively associated with demanding behavior, as well as receiving submissive or withdrawing behavior from one’s partner. Relationship quality was positively associated with withdrawal. Demanding behavior was positively associated with women’s depression symptoms but negatively associated with men’s depression symptoms. Sequential analysis revealed couples’ behavior was highly stable across time. Initiation of demand/withdraw and demand/submit sequences were negatively associated with partners’ relationship adjustment. Female demand/male withdraw was positively associated with men’s depression diagnosis. Results underscore the importance of sequential analysis when investigating associations among depression, relationship quality, and couples’ interpersonal behavior

X-Ray Synchrotron White Beam Excitation of Auger Electrons

Auger electron spectra have been measured at the Cornell High Energy Synchrotron Source (CHESS), using the full white beam x-ray spectrum as the excitation source. Ordinary Auger spectra obtained in the laboratory with an electron beam source must employ derivative techniques to distinguish the Auger structures from the large background due to the excitation beam. The synchrotron white beam eliminates this source of background and produces signal rates as high as 107 cps. Superior signal-to-background ratios are found for Auger peaks above a few hundred eV, and count rates are large enough to suggest microprobe applications. X-ray induced Auger satellite peaks were observed with intensities much greater than the electron-induced counterpart; this anomaly is not completely understood

Polarization rotation via a monoclinic phase in the piezoelectric 92%PbZn1/3Nb2/3O3-8%PbTiO3

The origin of ultrahigh piezoelectricity in the relaxor ferroelectric PbZn1/3Nb2/3O3-PbTiO3 was studied with an electric field applied along the [001] direction. The zero-field rhombohedral R phase starts to follow the direct polarization path to tetragonal symmetry via an intermediate monoclinic M phase, but then jumps irreversibly to an alternate path involving a different type of monoclinic distortion. Details of the structure and domain configuration of this novel phase are described. This result suggests that there is a nearby R-M phase boundary as found in the Pb(Ti,Zr)O3 system.Comment: REVTeX file. 4 pages. New version after referees' comment

An analytical treatment of the Clock Paradox in the framework of the Special and General Theories of Relativity

In this paper we treat the so called clock paradox in an analytical way by assuming that a constant and uniform force F of finite magnitude acts continuously on the moving clock along the direction of its motion assumed to be rectilinear. No inertial motion steps are considered. The rest clock is denoted as (1), the to-and-fro moving clock is (2), the inertial frame in which (1) is at rest in its origin and (2) is seen moving is I and, finally, the accelerated frame in which (2) is at rest in its origin and (1) moves forward and backward is A. We deal with the following questions: I) What is the effect of the finite force acting on (2) on the proper time intervals measured by the two clocks when they reunite? Does a differential aging between the two clocks occur, as it happens when inertial motion and infinite values of the accelerating force is considered? The Special Theory of Relativity is used in order to describe the hyperbolic motion of (2) in the frame I II) Is this effect an absolute one, i.e. does the accelerated observer A comoving with (2) obtain the same results as that in I, both qualitatively and quantitatively, as it is expected? We use the General Theory of Relativity in order to answer this question.Comment: LaTex2e, 19 pages, no tables, no figures. Rewritten version, it amends the previous one whose results about the treatment with General Relativity were wrong. References added. Eq. (55) corrected. More refined version. Comments and suggestions are warmly welcom

Neutron Diffraction Study of Field Cooling Effects on Relaxor Ferroelectrics Pb[(Zn_{1/3} Nb_{2/3})_{0.92} Ti_{0.08}] O_{3}

High-temperature (T) and high-electric-field (E) effects on Pb[(Zn_{1/3} Nb_{2/3})_{0.92} Ti_{0.08}]O_3 (PZN-8%PT) were studied comprehensively by neutron diffraction in the ranges 300 <= T <= 550 K and 0 <= E <= 15 kV/cm. We have focused on how phase transitions depend on preceding thermal and electrical sequences. In the field cooling process (FC, E parallel [001] >= 0.5 kV/cm), a successive cubic (C) --> tetragonal (T) --> monoclinic (M_C) transition was observed. In the zero field cooling process (ZFC), however, we have found that the system does not transform to the rhombohedral (R) phase as widely believed, but to a new, unidentified phase, which we call X. X gives a Bragg peak profile similar to that expected for R, but the c-axis is always slightly shorter than the a-axis. As for field effects on the X phase, we found an irreversible X --> M_C transition via another monoclinic phase (M_A) as expected from a previous report [Noheda et al. Phys. Rev. Lett. 86, 3891 (2001)]. At a higher electric field, we confirmed a c-axis jump associated with the field-induced M_C --> T transition, which was observed by strain and x-ray diffraction measurements.Comment: 8 pages, 9 figures, revise

Addition-Deletion Networks

We study structural properties of growing networks where both addition and deletion of nodes are possible. Our model network evolves via two independent processes. With rate r, a node is added to the system and this node links to a randomly selected existing node. With rate 1, a randomly selected node is deleted, and its parent node inherits the links of its immediate descendants. We show that the in-component size distribution decays algebraically, c_k ~ k^{-beta}, as k-->infty. The exponent beta=2+1/(r-1) varies continuously with the addition rate r. Structural properties of the network including the height distribution, the diameter of the network, the average distance between two nodes, and the fraction of dangling nodes are also obtained analytically. Interestingly, the deletion process leads to a giant hub, a single node with a macroscopic degree whereas all other nodes have a microscopic degree.Comment: 8 pages, 5 figure

Empirical 2MASS-WFC3/IR filter transformations from synthetic photometry

Near-infrared bandpasses on spaceborne observatories diverge from their ground-based counterparts as they are free of atmospheric telluric absorption. Available transformations between respective filter systems in the literature rely on theoretical stellar atmospheres, which are known to have difficulties reproducing observed spectral energy distributions of cool giants. We present new transformations between the 2MASS $JHK_S$ and HST WFC3/IR F110W, F125W, & F160W photometric systems based on synthetic photometry of empirical stellar spectra from four spectral libraries. This sample comprises over 1000 individual stars, which together span nearly the full HR diagram and sample stellar populations from the solar neighborhood out to the Magellanic Clouds, covering a broad range of ages, metallicities, and other relevant stellar properties. In addition to global color-dependent transformations, we examine band-to-band differences for cool, luminous giant stars in particular, including multiple types of primary distance indicators.Comment: 24 pages, 15 figures, accepted to A

The Sequence Ontology: a tool for the unification of genome annotations

The Sequence Ontology ( SO) is a structured controlled vocabulary for the parts of a genomic annotation. SO provides a common set of terms and definitions that will facilitate the exchange, analysis and management of genomic data. Because SO treats part-whole relationships rigorously, data described with it can become substrates for automated reasoning, and instances of sequence features described by the SO can be subjected to a group of logical operations termed extensional mereology operators