Models and algorithms for detection and tracking of coordinated groups

In this paper, we describe models and algorithms for detection and tracking of group and individual targets. We develop two novel group dynamical models, within a continuous time setting, that aim to mimic behavioural properties of groups. We also describe two possible ways of modeling interactions between closely using Markov Random Field (MRF) and repulsive forces. These can be combined together with a group structure transition model to create realistic evolving group models. We use a Markov Chain Monte Carlo (MCMC)-Particles Algorithm to perform sequential inference. Computer simulations demonstrate the ability of the algorithm to detect and track targets within groups, as well as infer the correct group structure over time. ©2008 IEEE.

Models and algorithms for tracking of maneuvering objects using variable rate particle filters

Standard algorithms in tracking and other state-space models assume identical and synchronous sampling rates for the state and measurement processes. However, real trajectories of objects are typically characterized by prolonged smooth sections, with sharp, but infrequent, changes. Thus, a more parsimonious representation of a target trajectory may be obtained by direct modeling of maneuver times in the state process, independently from the observation times. This is achieved by assuming the state arrival times to follow a random process, typically specified as Markovian, so that state points may be allocated along the trajectory according to the degree of variation observed. The resulting variable dimension state inference problem is solved by developing an efficient variable rate particle filtering algorithm to recursively update the posterior distribution of the state sequence as new data becomes available. The methodology is quite general and can be applied across many models where dynamic model uncertainty occurs on-line. Specific models are proposed for the dynamics of a moving object under internal forcing, expressed in terms of the intrinsic dynamics of the object. The performance of the algorithms with these dynamical models is demonstrated on several challenging maneuvering target tracking problems in clutter. © 2006 IEEE.

Term Structure and the Estimated Monetary Policy Rule in the Eurozone

Published as an article in: Spanish Economic Review, 2008, vol. 10, issue 4, pages 251-277.

Population age structure and private consumption in Spain

In this paper we study the effect of population age distribution upon private consumption expenditure in Spain from 1964 to 1997 using aggregate data. We obtain four main results. First, changes in the population pyramid have substantial effects upon the behaviour of private consumption. Second, the pattern of the coefficients of the demographic variables is not consistent with the simplest version of the life cycle hypothesis. Third, we estimate the impact of the demographic transition upon consumption and find positive values associated with episodes in which the shares of groups of individuals with expenditure levels higher (lower) than the mean increased (decreased). Fourth, the results are robust to alternative specifications for the population age distribution.

Structure and Historical Changes in the Groundfish Complex of the Eastern Bering Sea

The eastern Bering Sea is a major marine ecosystem containing some of the largest populations of groundfish, crabs, birds, and marine mammals in the world. Commercial catches of groundfish in this region have averaged about 1.6 million tons (t) annually in 1970-86. This report describes the species and relative importance of species in the eastern Bering Sea groundfish complex, the environment in which they live, and the history of the fisheries and management during the years 1954 - 1985. Historical changes in abundance and the condition of the principal species at the end of this first 30 years of exploitation are also examined. Results suggest that the biomass of the groundfish complex is characterized by variability rather than stability. The most reliable data (1979 to 1985) suggests that the biomass of the complex fluctuated between 11.8 and 15.7 million t. Even greater variability is suggested by the less reliable data from earlier years. Because of its dominance in the complex and wide fluctuations in abundance, walleye pollock (Theragra chalcogramma) is primarily responsible for the major variations in abundance of the complex. After 30 years of exploitation, the complex was generally in excellent condition. (PDF file contains 100 pages.)

NOAA/MLML Radiometric Data Acquisition and Processing

This report is a detailed description of data processing of NOAA/MLML spectroradiometry data. It introduces the MLML_DBASE programs, describes the assembly of diverse data fues, and describes general algorithms and how individual routines are used. Definitions of data structures are presented in Appendices. [PDF contains 48 pages]

Electronic structure and phonon thermodynamics of iron alloys

Inelastic neutron scattering (INS) and nuclear-resonant inelastic x-ray scattering (NRIXS) were used to measure phonon spectra of FeV as a B2- ordered compound and as a bcc solid solution. Contrary to the behavior of ordering alloys studied to date, the phonons in the B2-ordered phase are softer than in the solid solution. Ordering increases the vibrational entropy, which stabilizes the ordered phase to higher temperatures. Ab initio calculations show that the number of electronic states at the Fermi level increases upon ordering, enhancing the screening between ions, and reducing the interatomic force constants. The effect of screening is larger at the V atomic sites than at the Fe atomic sites.

The phonon spectra of Au-rich alloys of fcc Au-Fe were also measured. The main effect on the vibrational entropy of alloying comes from a stiffening of the Au partial phonon density of states (DOS) with Fe concentration that increases the miscibility gap temperature. The magnitude of the effect is non- linear and it is reduced at higher Fe concentrations. Force constants were calculated for several compositions and show a local stiffening of Au–Au bonds close to Fe atoms, but Au–Au bonds that are farther away do not show this effect. Phonon DOS curves calculated from the force constants reproduced the experimental trends. The Au–Fe bond is soft and favors ordering, but a charge transfer from the Fe to the Au atoms stiffens the Au–Au bonds enough to favor unmixing. The stiffening is attributed to two main effects comparable in magnitude: an increase in electron density in the free-electron-like states, and stronger sd-hybridization.

INS and NRIXS measurements were performed at elevated temperatures on B2-ordered FeTi and NRIXS measurements were performed at high pressures. The high-pressure behavior is quasi- harmonic. The softening of the phonon DOS curves with temperature is strongly nonharmonic. Calculations of the force constants and Born-von Karman fits to the experimental data show that the bonds between second nearest neighbors (2nn) are much stiffer than those between 1nn, but fits to the high temperature data show that the former softens at a faster rate with temperature. The Fe–Fe bond softens more than the Ti–Ti bond. The unusual stiffness of the 2nn bond is explained by the calculated charge distribution, which is highly aspherical and localized preferentially in the t2g orbitals. Ab initio molecular dynamics (AIMD) simulations show a charge transfer from the t2g orbitals to the eg orbitals at elevated temperatures. The asphericity decreases linearly with temperature and is more severe at the Fe sites.

Influence of composition on the structure and properties of Fe-Pd-P and Ni-Pd-P amorphous alloys

Ternary alloys of nickel-palladium-phosphorus and iron-palladium- phosphorus containing 20 atomic % phosphorus were rapidly quenched from the liquid state. The structure of the quenched alloys was investigated by X-ray diffraction. Broad maxima in the diffraction patterns, indicative of a glass-like structure, were obtained for 13 to 73 atomic % nickel and 13 to 44 atomic % iron, with palladium adding up to 80%.

Radial distribution functions were computed from the diffraction data and yielded average interatomic distances and coordination numbers. The structure of the amorphous alloys could be explained in terms of structural units analogous to those existing in the crystalline Pd₃P, Ni₃P and Fe₃P phases, with iron or nickel substituting for palladium. A linear relationship between interatomic distances and composition, similar to Vegard's law, was shown for these metallic glasses.

Electrical resistivity measurements showed that the quenched alloys were metallic. Measurements were performed from liquid helium temperatures (4.2°K) up to the vicinity of the melting points (900°K- 1000°K). The temperature coefficient in the glassy state was very low, of the order of 10^-4/°K. A resistivity minimum was found at low temperature, varying between 9°K and 14°K for Ni_x-Pd_80-x -P₂₀ and between 17°K and 96°K for Fe_x-Pd_80-x -P₂₀, indicating the presence of a Kondo effect. Resistivity measurements, with a constant heating rate of about 1.5°C/min,showed progressive crystallization above approximately 600°K.

The magnetic moments of the amorphous Fe-Pd-P alloys were measured as a function of magnetic field and temperature. True ferromagnetism was found for the alloys Fe₃₂-Pd₄₈-P₂₀ and Fe₄₄-Pd₃₆-P₂₀ with Curie points at 165° K and 380° K respectively. Extrapolated values of the saturation magnetic moments to 0° K were 1.70 µ_B and 2.10 µ_B respectively. The amorphous alloy Fe₂₃-Pd₅₇-P₂₀ was assumed to be superparamagnetic. The experimental data indicate that phosphorus contributes to the decrease of moments by electron transfer, whereas palladium atoms probably have a small magnetic moment. A preliminary investigation of the Ni-Pd-P amorphous alloys showed that these alloys are weakly paramagnetic.

Functional genomic studies of the structure and regulation of eukaryotic transcriptomes

The main focus of this thesis is the use of high-throughput sequencing technologies in functional genomics (in particular in the form of ChIP-seq, chromatin immunoprecipitation coupled with sequencing, and RNA-seq) and the study of the structure and regulation of transcriptomes. Some parts of it are of a more methodological nature while others describe the application of these functional genomic tools to address various biological problems. A significant part of the research presented here was conducted as part of the ENCODE (ENCyclopedia Of DNA Elements) Project.

The first part of the thesis focuses on the structure and diversity of the human transcriptome. Chapter 1 contains an analysis of the diversity of the human polyadenylated transcriptome based on RNA-seq data generated for the ENCODE Project. Chapter 2 presents a simulation-based examination of the performance of some of the most popular computational tools used to assemble and quantify transcriptomes. Chapter 3 includes a study of variation in gene expression, alternative splicing and allelic expression bias on the single-cell level and on a genome-wide scale in human lymphoblastoid cells; it also brings forward a number of critical to the practice of single-cell RNA-seq measurements methodological considerations.

The second part presents several studies applying functional genomic tools to the study of the regulatory biology of organellar genomes, primarily in mammals but also in plants. Chapter 5 contains an analysis of the occupancy of the human mitochondrial genome by TFAM, an important structural and regulatory protein in mitochondria, using ChIP-seq. In Chapter 6, the mitochondrial DNA occupancy of the TFB2M transcriptional regulator, the MTERF termination factor, and the mitochondrial RNA and DNA polymerases is characterized. Chapter 7 consists of an investigation into the curious phenomenon of the physical association of nuclear transcription factors with mitochondrial DNA, based on the diverse collections of transcription factor ChIP-seq datasets generated by the ENCODE, mouseENCODE and modENCODE consortia. In Chapter 8 this line of research is further extended to existing publicly available ChIP-seq datasets in plants and their mitochondrial and plastid genomes.

The third part is dedicated to the analytical and experimental practice of ChIP-seq. As part of the ENCODE Project, a set of metrics for assessing the quality of ChIP-seq experiments was developed, and the results of this activity are presented in Chapter 9. These metrics were later used to carry out a global analysis of ChIP-seq quality in the published literature (Chapter 10). In Chapter 11, the development and initial application of an automated robotic ChIP-seq (in which these metrics also played a major role) is presented.

The fourth part presents the results of some additional projects the author has been involved in, including the study of the role of the Piwi protein in the transcriptional regulation of transposon expression in Drosophila (Chapter 12), and the use of single-cell RNA-seq to characterize the heterogeneity of gene expression during cellular reprogramming (Chapter 13).

The last part of the thesis provides a review of the results of the ENCODE Project and the interpretation of the complexity of the biochemical activity exhibited by mammalian genomes that they have revealed (Chapters 15 and 16), an overview of the expected in the near future technical developments and their impact on the field of functional genomics (Chapter 14), and a discussion of some so far insufficiently explored research areas, the future study of which will, in the opinion of the author, provide deep insights into many fundamental but not yet completely answered questions about the transcriptional biology of eukaryotes and its regulation.

Protein structure refinement algorithms

Protein structure prediction has remained a major challenge in structural biology for more than half a century. Accelerated and cost efficient sequencing technologies have allowed researchers to sequence new organisms and discover new protein sequences. Novel protein structure prediction technologies will allow researchers to study the structure of proteins and to determine their roles in the underlying biology processes and develop novel therapeutics.

Difficulty of the problem stems from two folds: (a) describing the energy landscape that corresponds to the protein structure, commonly referred to as force field problem; and (b) sampling of the energy landscape, trying to find the lowest energy configuration that is hypothesized to be the native state of the structure in solution. The two problems are interweaved and they have to be solved simultaneously. This thesis is composed of three major contributions. In the first chapter we describe a novel high-resolution protein structure refinement algorithm called GRID. In the second chapter we present REMCGRID, an algorithm for generation of low energy decoy sets. In the third chapter, we present a machine learning approach to ranking decoys by incorporating coarse-grain features of protein structures.

Structure and properties of an amorphous ferromagnetic alloy

The structure and the electrical and magnetic properties of an amorphous alloy containing approximately 80 at .% iron, 13 at.% phos phorus and 7 at.% carbon (Fe_(80)Fe_(13)C_7) obtained by rapid quenching from the liquid state have been studied. Transmission electron diffraction data confirm the amorphous nature of this alloy. An analysis of the radial distribution function obtained from X-ray diffraction data indicates that the number of nearest neighbors is approximately seven, at a distance of 2.6A. The structure of the alloy can be related to that of silicate glasses and is based on a random arrangement of trigonal prisms of Fe_2P and Fe_3C types in which the iron atoms have an average ligancy of seven. Electrical resistance measurements show that the alloys are metallic. A minimum in the electrical resistivity vs. temperature curve is observed between 10° K to 50° K depending on the specimen, and the temperature at which the minimum occurs is related to the degree of local ordering. The Fe-P-C amorphous alloys are ferromagnetic. The Curie temperature measured by the induction method and by Mossbauer spectroscopy is 315° C. The field dependence of the magneto-resistance at temperatures from liquid helium to room temperature is similar to that found in crystalline iron. The ordinary Hall coefficient is approximately 10^(-11) volt-cm/amp-G. The spontaneous Hall coefficient is about 0.6 x 10^(-9) volt-cm/amp-G and is practically independent of temperature from liquid helium temperature up to 300° c.

Studies on the role of histones in the structure and function of chromatin

Studies on the dissociation of histones from chromatin by increasing concentrations of sodium deoxycholate (DOC) have shown that histrone II is removed at lowest concentrations of DOC, while slightly higher concentrations remove histones III and IV. Still higher concentrations remove histone I.

The complete separation of chromatin and ¹⁴C-DOC by sucrose sedimentation indicated that the binding of DOC to chromatin is readily and completely reversible.

The dissociation of histones from chromatin by increasing concentrations of related cholanic acids and some of their conjugated derivatives were studied. The results suggested that the driving force for the interaction between the cholanic acid anion and histones is the lowering of the activity coefficient of the cholanic acid anion which occurs when it is partially removed from solution by interaction with hydrophobic regions of the positively charged histones.

The role of histones in the structure of chromatin has been studied by comparing the effects of selective removal of histones from chromatin by increasing concentrations of DOC with those caused by NaCl (removes histone I at lowest concentrations, while higher concentrations remove histones II, III, and IV). Properties studied included thermal denaturation, sedimentation velocity, flow dichroism, relaxation times of molecules oriented in a flow field, and the irreversible disruption of a 130 S, cross-linked component of sheared chromatin. The data indicated that none of the structural or chemical parameters with which these properties are correlated show a dependence on the presence of one particular histone fraction.

The template activity (ability to prime a 0.2 M KC1 DNA-dependent RNA synthesis system catalyzed by E. coli RNA polymerase) increases from that of native chromatin (approximately 25 per cent of that pure DNA) to that of pure DNA in a fashion which shows a nearly linear relationship to the amount of histone coverage of the template. The precipitability of partially dehistonized chromatin samples in 0.15 M NaCl shows a large dependence on the presence of histone I.

I. The structure and properties of closed circular duplex DNA. II. Chemically interacting systems at equilibrium in a buoyant density gradient

I. The binding of the intercalating dye ethidium bromide to closed circular SV 40 DNA causes an unwinding of the duplex structure and a simultaneous and quantitatively equivalent unwinding of the superhelices. The buoyant densities and sedimentation velocities of both intact (I) and singly nicked (II) SV 40 DNAs were measured as a function of free dye concentration. The buoyant density data were used to determine the binding isotherms over a dye concentration range extending from 0 to 600 µg/m1 in 5.8 M CsCl. At high dye concentrations all of the binding sites in II, but not in I, are saturated. At free dye concentrations less than 5.4 µg/ml, I has a greater affinity for dye than II. At a critical amount of dye bound I and II have equal affinities, and at higher dye concentration I has a lower affinity than II. The number of superhelical turns, τ, present in I is calculated at each dye concentration using Fuller and Waring's (1964) estimate of the angle of duplex unwinding per intercalation. The results reveal that SV 40 DNA I contains about -13 superhelical turns in concentrated salt solutions.

The free energy of superhelix formation is calculated as a function of τ from a consideration of the effect of the superhelical turns upon the binding isotherm of ethidium bromide to SV 40 DNA I. The value of the free energy is about 100 kcal/mole DNA in the native molecule. The free energy estimates are used to calculate the pitch and radius of the superhelix as a function of the number of superhelical turns. The pitch and radius of the native I superhelix are 430 Å and 135 Å, respectively.

A buoyant density method for the isolation and detection of closed circular DNA is described. The method is based upon the reduced binding of the intercalating dye, ethidium bromide, by closed circular DNA. In an application of this method it is found that HeLa cells contain in addition to closed circular mitochondrial DNA of mean length 4.81 microns, a heterogeneous group of smaller DNA molecules which vary in size from 0.2 to 3.5 microns and a paucidisperse group of multiples of the mitochondrial length.

II. The general theory is presented for the sedimentation equilibrium of a macromolecule in a concentrated binary solvent in the presence of an additional reacting small molecule. Equations are derived for the calculation of the buoyant density of the complex and for the determination of the binding isotherm of the reagent to the macrospecies. The standard buoyant density, a thermodynamic function, is defined and the density gradients which characterize the four component system are derived. The theory is applied to the specific cases of the binding of ethidium bromide to SV 40 DNA and of the binding of mercury and silver to DNA.