Showing papers by "University of California, Santa Cruz published in 2005"

A haplotype map of the human genome

Abstract: Inherited genetic variation has a critical but as yet largely uncharacterized role in human disease. Here we report a public database of common variation in the human genome: more than one million single nucleotide polymorphisms (SNPs) for which accurate and complete genotypes have been obtained in 269 DNA samples from four populations, including ten 500-kilobase regions in which essentially all information about common DNA variation has been extracted. These data document the generality of recombination hotspots, a block-like structure of linkage disequilibrium and low haplotype diversity, leading to substantial correlations of SNPs with many of their neighbours. We show how the HapMap resource can guide the design and analysis of genetic association studies, shed light on structural variation and recombination, and identify loci that may have been subject to natural selection during human evolution.

Evolutionarily conserved elements in vertebrate, insect, worm, and yeast genomes

Abstract: We have conducted a comprehensive search for conserved elements in vertebrate genomes, using genome-wide multiple alignments of five vertebrate species (human, mouse, rat, chicken, and Fugu rubripes). Parallel searches have been performed with multiple alignments of four insect species (three species of Drosophila and Anopheles gambiae), two species of Caenorhabditis, and seven species of Saccharomyces. Conserved elements were identified with a computer program called phastCons, which is based on a two-state phylogenetic hidden Markov model (phylo-HMM). PhastCons works by fitting a phylo-HMM to the data by maximum likelihood, subject to constraints designed to calibrate the model across species groups, and then predicting conserved elements based on this model. The predicted elements cover roughly 3%-8% of the human genome (depending on the details of the calibration procedure) and substantially higher fractions of the more compact Drosophila melanogaster (37%-53%), Caenorhabditis elegans (18%-37%), and Saccharaomyces cerevisiae (47%-68%) genomes. From yeasts to vertebrates, in order of increasing genome size and general biological complexity, increasing fractions of conserved bases are found to lie outside of the exons of known protein-coding genes. In all groups, the most highly conserved elements (HCEs), by log-odds score, are hundreds or thousands of bases long. These elements share certain properties with ultraconserved elements, but they tend to be longer and less perfectly conserved, and they overlap genes of somewhat different functional categories. In vertebrates, HCEs are associated with the 3' UTRs of regulatory genes, stable gene deserts, and megabase-sized regions rich in moderately conserved noncoding sequences. Noncoding HCEs also show strong statistical evidence of an enrichment for RNA secondary structure.

Galaxy: A platform for interactive large-scale genome analysis

Abstract: Accessing and analyzing the exponentially expanding genomic sequence and functional data pose a challenge for biomedical researchers. Here we describe an interactive system, Galaxy, that combines the power of existing genome annotation databases with a simple Web portal to enable users to search remote resources, combine data from independent queries, and visualize the results. The heart of Galaxy is a flexible history system that stores the queries from each user; performs operations such as intersections, unions, and subtractions; and links to other computational tools. Galaxy can be accessed at http://g2.bx.psu.edu.

The tRNAscan-SE, snoscan and snoGPS web servers for the detection of tRNAs and snoRNAs

Abstract: Transfer RNAs (tRNAs) and small nucleolar RNAs (snoRNAs) are two of the largest classes of non-protein-coding RNAs. Conventional gene finders that detect protein-coding genes do not find tRNA and snoRNA genes because they lack the codon structure and statistical signatures of protein-coding genes. Previously, we developed tRNAscan-SE, snoscan and snoGPS for the detection of tRNAs, methylation-guide snoRNAs and pseudouridylation-guide snoRNAs, respectively. tRNAscan-SE is routinely applied to completed genomes, resulting in the identification of thousands of tRNA genes. Snoscan has successfully detected methylation-guide snoRNAs in a variety of eukaryotes and archaea, and snoGPS has identified novel pseudouridylation-guide snoRNAs in yeast and mammals. Although these programs have been quite successful at RNA gene detection, their use has been limited by the need to install and configure the software packages on UNIX workstations. Here, we describe online implementations of these RNA detection tools that make these programs accessible to a wider range of research biologists. The tRNAscan-SE, snoscan and snoGPS servers are available at http://lowelab.ucsc.edu/tRNAscan-SE/, http://lowelab.ucsc.edu/snoscan/ and http://lowelab.ucsc.edu/snoGPS/, respectively.

SCAPE: shape completion and animation of people

Abstract: We introduce the SCAPE method (Shape Completion and Animation for PEople)---a data-driven method for building a human shape model that spans variation in both subject shape and pose. The method is based on a representation that incorporates both articulated and non-rigid deformations. We learn a pose deformation model that derives the non-rigid surface deformation as a function of the pose of the articulated skeleton. We also learn a separate model of variation based on body shape. Our two models can be combined to produce 3D surface models with realistic muscle deformation for different people in different poses, when neither appear in the training set. We show how the model can be used for shape completion --- generating a complete surface mesh given a limited set of markers specifying the target shape. We present applications of shape completion to partial view completion and motion capture animation. In particular, our method is capable of constructing a high-quality animated surface model of a moving person, with realistic muscle deformation, using just a single static scan and a marker motion capture sequence of the person.

Assessing computational tools for the discovery of transcription factor binding sites.

Abstract: The prediction of regulatory elements is a problem where computational methods offer great hope. Over the past few years, numerous tools have become available for this task. The purpose of the current assessment is twofold: to provide some guidance to users regarding the accuracy of currently available tools in various settings, and to provide a benchmark of data sets for assessing future tools.

The photometric performance and calibration of the Hubble Space Telescope advanced camera for surveys

Abstract: We present the photometric calibration of the Advanced Camera for Surveys (ACS). The ACS was installed in the Hubble Space Telescope (HST) in 2002 March. It comprises three cameras: the Wide Field Channel (WFC), optimized for deep near‐IR survey imaging programs; the High Resolution Channel (HRC), a high‐resolution imager that fully samples the HST point‐spread function (PSF) in the visible; and the Solar Blind Channel (SBC), a far‐UV imager. A significant amount of data has been collected to characterize the on‐orbit performance of the three channels. We give here an overview of the performance and calibration of the two CCD cameras (WFC and HRC) and a description of the best techniques for reducing ACS CCD data. The overall performance is as expected from prelaunch testing of the camera. Surprises were a better‐than‐predicted sensitivity in the visible and near‐IR for both the WFC and HRC and an unpredicted dip in the HRC UV response at ∼3200 A. On‐orbit observations of spectrophotometric stand...

The great Sumatra-Andaman earthquake of 26 December 2004

Abstract: The two largest earthquakes of the past 40 years ruptured a 1600-kilometer-long portion of the fault boundary between the Indo-Australian and southeastern Eurasian plates on 26 December 2004 [seismic moment magnitude (Mw) = 9.1 to 9.3] and 28 March 2005 (Mw = 8.6). The first event generated a tsunami that caused more than 283,000 deaths. Fault slip of up to 15 meters occurred near Banda Aceh, Sumatra, but to the north, along the Nicobar and Andaman Islands, rapid slip was much smaller. Tsunami and geodetic observations indicate that additional slow slip occurred in the north over a time scale of 50 minutes or longer.

Rapid acidification of the ocean during the Paleocene-Eocene thermal maximum.

Abstract: The Paleocene-Eocene thermal maximum (PETM) has been attributed to the rapid release of ∼2000 × 10 9 metric tons of carbon in the form of methane. In theory, oxidation and ocean absorption of this carbon should have lowered deep-sea pH, thereby triggering a rapid ( 100,000 years). These findings indicate that a large mass of carbon (»2000 × 10 9 metric tons of carbon) dissolved in the ocean at the Paleocene-Eocene boundary and that permanent sequestration of this carbon occurred through silicate weathering feedback.

Control-flow integrity

Abstract: Current software attacks often build on exploits that subvert machine-code execution. The enforcement of a basic safety property, Control-Flow Integrity (CFI), can prevent such attacks from arbitrarily controlling program behavior. CFI enforcement is simple, and its guarantees can be established formally even with respect to powerful adversaries. Moreover, CFI enforcement is practical: it is compatible with existing software and can be done efficiently using software rewriting in commodity systems. Finally, CFI provides a useful foundation for enforcing further security policies, as we demonstrate with efficient software implementations of a protected shadow call stack and of access control for memory regions.

Marked Decline in Atmospheric Carbon Dioxide Concentrations During the Paleogene

Abstract: The relation between the partial pressure of atmospheric carbon dioxide (pCO2) and Paleogene climate is poorly resolved. We used stable carbon isotopic values of di-unsaturated alkenones extracted from deep sea cores to reconstruct pCO2 from the middle Eocene to the late Oligocene (approximately 45 to 25 million years ago). Our results demonstrate that pCO2 ranged between 1000 to 1500 parts per million by volume in the middle to late Eocene, then decreased in several steps during the Oligocene, and reached modern levels by the latest Oligocene. The fall in pCO2 likely allowed for a critical expansion of ice sheets on Antarctica and promoted conditions that forced the onset of terrestrial C4 photosynthesis.

Energy analysis of public-key cryptography for wireless sensor networks

Abstract: In this paper, we quantify the energy cost of authentication and key exchange based on public-key cryptography on an 8-bit microcontroller platform. We present a comparison of two public-key algorithms, RSA and elliptic curve cryptography (ECC), and consider mutual authentication and key exchange between two untrusted parties such as two nodes in a wireless sensor network. Our measurements on an Atmel ATmega128L low-power microcontroller indicate that public-key cryptography is very viable on 8-bit energy-constrained platforms even if implemented in software. We found ECC to have a significant advantage over RSA as it reduces computation time and also the amount of data transmitted and stored.

The case for motor involvement in perceiving conspecifics.

Abstract: Perceiving other people's behaviors activates imitative motor plans in the perceiver, but there is disagreement as to the function of this activation. In contrast to other recent proposals (e.g., that it subserves overt imitation, identification and understanding of actions, or working memory), here it is argued that imitative motor activation feeds back into the perceptual processing of conspecifics' behaviors, generating top-down expectations and predictions of the unfolding action. Furthermore, this account incorporates recent ideas about emulators in the brain-mental simulations that run in parallel to the external events they simulate-to provide a mechanism by which motoric involvement could contribute to perception. Evidence from a variety of literatures is brought to bear to support this account of perceiving human body movement.

Combining sources in stable isotope mixing models: alternative methods.

Abstract: Stable isotope mixing models are often used to quantify source contributions to a mixture. Examples include pollution source identification; trophic web studies; analysis of water sources for soils, plants; or water bodies, and many others. A common problem is having too many sources to allow a unique solution. We discuss two alternative procedures for addressing this problem. One option is a priori to combine sources with similar signatures so the number of sources is small enough to provide a unique solution. Aggregation should be considered only when isotopic signatures of clustered sources are not significantly different, and sources are related so the combined source group has some functional significance. For example, in a food web analysis, lumping several species within a trophic guild allows more interpretable results than lumping disparate food sources, even if they have similar isotopic signatures. One result of combining mixing model sources is increased uncertainty of the combined end-member isotopic signatures and consequently the source contribution estimates; this effect can be quantified using the IsoError model ( http://www.epa.gov/wed/pages/models/isotopes/isoerror1_04.htm ). As an alternative to lumping sources before a mixing analysis, the IsoSource mixing model ( http://www.epa.gov/wed/pages/models/isosource/isosource.htm ) can be used to find all feasible solutions of source contributions consistent with isotopic mass balance. While ranges of feasible contributions for each individual source can often be quite broad, contributions from functionally related groups of sources can be summed a posteriori, producing a range of solutions for the aggregate source that may be considerably narrower. A paleohuman dietary analysis example illustrates this method, which involves a terrestrial meat food source, a combination of three terrestrial plant foods, and a combination of three marine foods. In this case, a posteriori aggregation of sources allowed strong conclusions about temporal shifts in marine versus terrestrial diets that would not have otherwise been discerned.

Presupernova evolution of differentially rotating massive stars including magnetic fields

Abstract: As a massive star evolves through multiple stages of nuclear burning on its way to becoming a supernova, a complex, differentially rotating structure is set up. Angular momentum is transported by a variety of classic instabilities and also by magnetic torques from fields generated by the differential rotation. We present the first stellar evolution calculations to follow the evolution of rotating massive stars including, at least approximately, all these effects, magnetic and nonmagnetic, from the zero-age main sequence until the onset of iron-core collapse. The evolution and action of the magnetic fields is as described by Spruit in 2002, and a range of uncertain parameters is explored. In general, we find that magnetic torques decrease the final rotation rate of the collapsing iron core by about a factor of 30-50 when compared with the nonmagnetic counterparts. Angular momentum in that part of the presupernova star destined to become a neutron star is an increasing function of main-sequence mass. That is, pulsars derived from more massive stars rotate faster and rotation plays a more important role in the star's explosion. The final angular momentum of the core has been determined—to within a factor of 2—by the time the star ignites carbon burning. For the lighter stars studied, around 15 M☉, we predict pulsar periods at birth near 15 ms, though a factor of 2 range is easily tolerated by the uncertainties. Several mechanisms for additional braking in a young neutron star, especially by fallback, are explored.

An Extension of the Blinder-Oaxaca Decomposition Technique to Logit and Probit Models

Abstract: The Blinder-Oaxaca decomposition technique is widely used to identify and quantify the separate contributions of group differences in measurable characteristics, such as education, experience, marital status, and geographical differences to racial and gender gaps in outcomes. The technique cannot be used directly, however, if the outcome is binary and the coefficients are from a logit or probit model. I describe a relatively simple method of performing a decomposition that uses estimates from a logit or probit model. Expanding on the original application of the technique in Fairlie [3], I provide a more thorough discussion of how to apply the technique, an analysis of the sensitivity of the decomposition estimates to different parameters, and the calculation of standard errors. I also compare the estimates to Blinder-Oaxaca decomposition estimates and discuss an example of when the Blinder-Oaxaca technique may be problematic.

The Third Data Release of the Sloan Digital Sky Survey

Abstract: This paper describes the Third Data Release of the Sloan Digital Sky Survey (SDSS). This release, containing data taken up through 2003 June, includes imaging data in five bands over 5282 deg2, photometric and astrometric catalogs of the 141 million objects detected in these imaging data, and spectra of 528,640 objects selected over 4188 deg2. The pipelines analyzing both images and spectroscopy are unchanged from those used in our Second Data Release.

DAMPED LYα SYSTEMS

Abstract: ▪ Abstract Observations of damped Lyα systems offer a unique window on the neutral-gas reservoirs that gave rise to galaxies at high redshifts. This review focuses on critical properties such as the H I and metal content of the gas and on independent evidence for star formation. Together, these provide an emerging picture of gravitationally bound objects in which accretion of gas from the IGM replenishes gas consumed by star formation. Other properties such as dust content, molecular content, ionized-gas content, gas kinematics, and galaxy identifications are also reviewed. These properties point to a multiphase ISM in which radiative and hydrodynamic feedback processes are present. Numerical simulations and other types of models used to describe damped Lyα systems within the context of galaxy formation are also discussed.

The Genome of the Basidiomycetous Yeast and Human Pathogen Cryptococcus Neoformans

Abstract: Cryptococcus neoformans is a basidionnycetous yeast ubiquitous in the environment, a model for fungal pathogenesis, and an opportunistic human pathogen of global importance. We have sequenced its similar to20-megabase genome, which contains similar to6500 intron-rich gene structures and encodes a transcriptome abundant in alternatively spliced and antisense messages. The genome is rich in transposons, many of which cluster at candidate centromeric regions. The presence of these transposons may drive karyotype instability and phenotypic variation. C. neoformans encodes unique genes that may contribute to its unusual virulence properties, and comparison of two phenotypically distinct strains reveals variation in gene content in addition to sequence polymorphisms between the genomes.

Empirical Exchange Rate Models of the Nineties: Are Any Fit to Survive?

Abstract: Previous assessments of nominal exchange rate determination have focused upon a narrow set of models typically of the 1970's vintage. The canonical papers in this literature are by Meese and Rogoff (1983, 1988), who examined monetary and portfolio balance models. Succeeding works by Mark (1995) and Chinn and Meese (1995) focused on similar models. In this paper we re-assess exchange rate prediction using a wider set of models that have been proposed in the last decade: interest rate parity, productivity based models, and behavioral equilibrium exchange rate' models. The performance of these models is compared against a benchmark model the Dornbusch-Frankel sticky price monetary model. The models are estimated in error correction and first-difference specifications. Rather than estimating the cointegrating vector over the entire sample and treating it as part of the ex ante information set as is commonly done in the literature, we recursively update the cointegrating vector, thereby generating true ex ante forecasts. We examine model performance at various forecast horizons (1 quarter, 4 quarters, 20 quarters) using differing metrics (mean squared error, direction of change), as well as the consistency' test of Cheung and Chinn (1998). No model consistently outperforms a random walk, by a mean squared error measure; however, along a direction-of-change dimension, certain structural models do outperform a random walk with statistical significance. Moreover, one finds that these forecasts are cointegrated with the actual values of exchange rates, although in a large number of cases, the elasticity of the forecasts with respect to the actual values is different from unity. Overall, model/specification/currency combinations that work well in one period will not necessarily work well in another period.

Damped Lyman alpha Systems

Abstract: Observations of damped Lyman alpha systems offer a unique window on the neutral-gas reservoirs that gave rise to galaxies at high redshifts. This review focuses on critical properties such as the H I and metal content of the gas and on independent evidence for star formation. Together, these provide an emerging picture of gravitationally bound objects in which accretion of gas from the IGM replenishes gas consumed by star formation. Other properties such as dust content, molecular content, ionized-gas content, gas kinematics, and galaxy identifications are also reviewed. These properties point to a multiphase ISM in which radiative and hydrodynamic feedback processes are present. Numerical simulations and other types of models used to describe damped Lyman alpha systems within the context of galaxy formation are also discussed.

Relationships Between Intergroup Contact and Prejudice Among Minority and Majority Status Groups

Abstract: Considerable research has shown that greater intergroup contact corresponds with lower intergroup prejudice, yet little is known regarding how the relationships between contact and prejudice may vary for members of minority and majority status groups. The present research examined differences in contact-prejudice relationships among members of minority and majority status groups, using data from a larger meta-analytic study of the effects of intergroup contact. Results indicate that the relationships between contact and prejudice tend to be weaker among members of minority status groups than among members of majority status groups. Moreover, establishing Allport's (1954) proposed conditions for optimal intergroup contact significantly predicts stronger contact-prejudice relationships among members of majority status groups, but not among members of minority status groups. Implications of these findings for future research on contact between minority and majority status groups are discussed.