Showing papers by "University of California, Santa Cruz published in 2002"

The Human Genome Browser at UCSC

Abstract: As vertebrate genome sequences near completion and research refocuses to their analysis, the issue of effective genome annotation display becomes critical. A mature web tool for rapid and reliable display of any requested portion of the genome at any scale, together with several dozen aligned annotation tracks, is provided at http://genome.ucsc.edu. This browser displays assembly contigs and gaps, mRNA and expressed sequence tag alignments, multiple gene predictions, cross-species homologies, single nucleotide polymorphisms, sequence-tagged sites, radiation hybrid data, transposon repeats, and more as a stack of coregistered tracks. Text and sequence-based searches provide quick and precise access to any region of specific interest. Secondary links from individual features lead to sequence details and supplementary off-site databases. One-half of the annotation tracks are computed at the University of California, Santa Cruz from publicly available sequence data; collaborators worldwide provide the rest. Users can stably add their own custom tracks to the browser for educational or research purposes. The conceptual and technical framework of the browser, its underlying MYSQL database, and overall use are described. The web site currently serves over 50,000 pages per day to over 3000 different users.

BLAT—The BLAST-Like Alignment Tool

Abstract: Analyzing vertebrate genomes requires rapid mRNA/DNA and cross-species protein alignments A new tool, BLAT, is more accurate and 500 times faster than popular existing tools for mRNA/DNA alignments and 50 times faster for protein alignments at sensitivity settings typically used when comparing vertebrate sequences BLAT's speed stems from an index of all nonoverlapping K-mers in the genome This index fits inside the RAM of inexpensive computers, and need only be computed once for each genome assembly BLAT has several major stages It uses the index to find regions in the genome likely to be homologous to the query sequence It performs an alignment between homologous regions It stitches together these aligned regions (often exons) into larger alignments (typically genes) Finally, BLAT revisits small internal exons possibly missed at the first stage and adjusts large gap boundaries that have canonical splice sites where feasible This paper describes how BLAT was optimized Effects on speed and sensitivity are explored for various K-mer sizes, mismatch schemes, and number of required index matches BLAT is compared with other alignment programs on various test sets and then used in several genome-wide applications http://genomeucscedu hosts a web-based BLAT server for the human genome

Initial sequencing and comparative analysis of the mouse genome.

Abstract: The sequence of the mouse genome is a key informational tool for understanding the contents of the human genome and a key experimental tool for biomedical research. Here, we report the results of an international collaboration to produce a high-quality draft sequence of the mouse genome. We also present an initial comparative analysis of the mouse and human genomes, describing some of the insights that can be gleaned from the two sequences. We discuss topics including the analysis of the evolutionary forces shaping the size, structure and sequence of the genomes; the conservation of large-scale synteny across most of the genomes; the much lower extent of sequence orthology covering less than half of the genomes; the proportions of the genomes under selection; the number of protein-coding genes; the expansion of gene families related to reproduction and immunity; the evolution of proteins; and the identification of intraspecies polymorphism.

Six views of embodied cognition.

Abstract: The emerging viewpoint of embodied cognition holds that cognitive processes are deeply rooted in the body’s interactions with the world. This position actually houses a number of distinct claims, some of which are more controversial than others. This paper distinguishes and evaluates the following six claims: (1) cognition is situated; (2) cognition is time-pressured; (3) we off-load cognitive work onto the environment; (4) the environment is part of the cognitive system; (5) cognition is for action; (6) offline cognition is body based. Of these, the first three and the fifth appear to be at least partially true, and their usefulness is best evaluated in terms of the range of their applicability. The fourth claim, I argue, is deeply problematic. The sixth claim has received the least attention in the literature on embodied cognition, but it may in fact be the best documented and most powerful of the six claims.

The slope of the black hole mass versus velocity dispersion correlation

Abstract: Observations of nearby galaxies reveal a strong correlation between the mass of the central dark object MBH and the velocity dispersionof the host galaxy, of the form logðMBH=M� Þ¼ � þ � logð�=� 0Þ; how- ever, published estimates of the slopespan a wide range (3.75-5.3). Merritt & Ferrarese have argued that low slopes (d4) arise because of neglect of random measurement errors in the dispersions and an incorrect choice for the dispersion of the Milky Way Galaxy. We show that these explanations and several others account for at most a small part of the slope range. Instead, the range of slopes arises mostly because of sys- tematic differences in the velocity dispersions used by different groups for the same galaxies. The origin of these differences remains unclear, but we suggest that one significant component of the difference results from Ferrarese & Merritt's extrapolation of central velocity dispersions to re= 8( re is the effective radius) using an empirical formula. Another component may arise from dispersion-dependent systematic errors in the mea- surements. A new determination of the slope using 31 galaxies yields � ¼ 4:02 � 0:32, � ¼ 8:13 � 0:06 for � 0 ¼ 200 km s � 1 . The MBH-� relation has an intrinsic dispersion in log MBH that is no larger than 0.25-0.3 dex and may be smaller if observational errors have been underestimated. In an appendix, we present a simple kinematic model for the velocity-dispersion profile of the Galactic bulge. Subject headings: black hole physics — galaxies: bulges — galaxies: fundamental parameters — galaxies: nuclei — Galaxy: bulge — Galaxy: kinematics and dynamics

The evolution and explosion of massive stars

Abstract: amount of energy, a tiny fraction of which is sufficient to explode the star as a supernova. The authors examine our current understanding of the lives and deaths of massive stars, with special attention to the relevant nuclear and stellar physics. Emphasis is placed upon their post-helium-burning evolution. Current views regarding the supernova explosion mechanism are reviewed, and the hydrodynamics of supernova shock propagation and ‘‘fallback’’ is discussed. The calculated neutron star masses, supernova light curves, and spectra from these model stars are shown to be consistent with observations. During all phases, particular attention is paid to the nucleosynthesis of heavy elements. Such stars are capable of producing, with few exceptions, the isotopes between mass 16 and 88 as well as a large fraction of still heavier elements made by the r and p processes.

The Bioperl Toolkit: Perl Modules for the Life Sciences

Abstract: The Bioperl project is an international open-source collaboration of biologists, bioinformaticians, and computer scientists that has evolved over the past 7 yr into the most comprehensive library of Perl modules available for managing and manipulating life-science information. Bioperl provides an easy-to-use, stable, and consistent programming interface for bioinformatics application programmers. The Bioperl modules have been successfully and repeatedly used to reduce otherwise complex tasks to only a few lines of code. The Bioperl object model has been proven to be flexible enough to support enterprise-level applications such as EnsEMBL, while maintaining an easy learning curve for novice Perl programmers. Bioperl is capable of executing analyses and processing results from programs such as BLAST, ClustalW, or the EMBOSS suite. Interoperation with modules written in Python and Java is supported through the evolving BioCORBA bridge. Bioperl provides access to data stores such as GenBank and SwissProt via a flexible series of sequence input/output modules, and to the emerging common sequence data storage format of the Open Bioinformatics Database Access project. This study describes the overall architecture of the toolkit, the problem domains that it addresses, and gives specific examples of how the toolkit can be used to solve common life-sciences problems. We conclude with a discussion of how the open-source nature of the project has contributed to the development effort.

Kelp forest ecosystems: biodiversity, stability, resilience and future

Abstract: Kelp forests are phyletically diverse, structurally complex and highly productive components of coldwater rocky marine coastlines. This paper reviews the conditions in which kelp forests develop globally and where, why and at what rate they become deforested. The ecology and long archaeological history of kelp forests are examined through case studies from southern California, the Aleutian Islands and the western North Atlantic, well-studied locations that represent the widest possible range in kelp forest biodiversity. Global distribution of kelp forests is physiologically constrained by light at high latitudes and by nutrients, warm temperatures and other macrophytes at low latitudes. Within mid-latitude belts (roughly 40–60° latitude in both hemispheres) well-developed kelp forests are most threatened by herbivory, usually from sea urchins. Overfishing and extirpation of highly valued vertebrate apex predators often triggered herbivore population increases, leading to widespread kelp deforestation. Such deforestations have the most profound and lasting impacts on species-depauperate systems, such as those in Alaska and the western North Atlantic. Globally urchin-induced deforestation has been increasing over the past 2–3 decades. Continued fishing down of coastal food webs has resulted in shifting harvesting targets from apex predators to their invertebrate prey, including kelp-grazing herbivores. The recent global expansion of sea urchin harvesting has led to the widespread extirpation of this herbivore, and kelp forests have returned in some locations but, for the first time, these forests are devoid of vertebrate apex predators. In the western North Atlantic, large predatory crabs have recently filled this void and they have become the new apex predator in this system. Similar shifts from fish- to crab-dominance may have occurred in coastal zones of the United Kingdom and Japan, where large predatory finfish were extirpated long ago. Three North American case studies of kelp forests were examined to determine their long history with humans and project the status of future kelp forests to the year 2025. Fishing impacts on kelp forest systems have been both profound and much longer in duration than previously thought. Archaeological data suggest that coastal peoples exploited kelp forest organisms for thousands of years, occasionally resulting in localized losses of apex predators, outbreaks of sea urchin populations and probably small-scale deforestation. Over the past two centuries, commercial exploitation for export led to the extirpation of sea urchin predators, such as the sea otter in the North Pacific and predatory fishes like the cod in the North Atlantic. The large-scale removal of predators for export markets increased sea urchin abundances and promoted the decline of kelp forests over vast areas. Despite southern California having one of the longest known associations with coastal kelp forests, widespread deforestation is rare. It is possible that functional redundancies among predators and herbivores make this most diverse system most stable. Such biodiverse kelp forests may also resist invasion from non-native species. In the species-depauperate western North Atlantic, introduced algal competitors carpet the benthos and threaten future kelp dominance. There, other non-native herbivores and predators have become established and dominant components of this system. Climate changes have had measurable impacts on kelp forest ecosystems and efforts to control the emission of greenhouse gasses should be a global priority. However, overfishing appears to be the greatest manageable threat to kelp forest ecosystems over the 2025 time horizon. Management should focus on minimizing fishing impacts and restoring populations of functionally important species in these systems.

The Nucleosynthetic Signature of Population III

Abstract: Growing evidence suggests that the first generation of stars may have been quite massive (~100-300 M?). Could these stars have left a distinct nucleosynthetic signature? We explore the nucleosynthesis of helium cores in the mass range MHe = 64-133 M?, corresponding to main-sequence star masses of approximately 140-260 M?. Above MHe = 133 M?, without rotation and using current reaction rates, a black hole is formed, and no nucleosynthesis is ejected. For lighter helium core masses, ~40-63 M?, violent pulsations occur, induced by the pair instability and accompanied by supernova-like mass ejection, but the star eventually produces a large iron core in hydrostatic equilibrium. It is likely that this core, too, collapses to a black hole, thus cleanly separating the heavy-element nucleosynthesis of pair instability supernovae from those of other masses, both above and below. Indeed, black hole formation is a likely outcome for all Population III stars with main-sequence masses between about 25 and 140 M? (MHe = 9-63 M?) as well as those above 260 M?. Nucleosynthesis in pair instability supernovae varies greatly with the mass of the helium core. This core determines the maximum temperature reached during the bounce. At the upper range of exploding core masses, a maximum of 57 M? of 56Ni is produced, making these the most energetic and the brightest thermonuclear explosions in the universe. Integrating over a distribution of masses, we find that pair instability supernovae produce a roughly solar distribution of nuclei having even nuclear charge (Si, S, Ar, etc.) but are remarkably deficient in producing elements with odd nuclear charge?Na, Al, P, V, Mn, etc. This is because there is no stage of stable post-helium burning to set the neutron excess. Also, essentially no elements heavier than zinc are produced owing to a lack of s- and r-processes. The Fe/Si ratio is quite sensitive to whether the upper bound on the initial mass function is over 260 M? or somewhere between 140 and 260 M?. When the yields of pair instability supernovae are combined with reasonable estimates of the nucleosynthesis of Population III stars from 12 to 40 M?, this distinctive pattern of deficient production of odd-Z elements persists. Some possible strategies for testing our predictions are discussed.

Concentrations of Dark Halos from Their Assembly Histories

Abstract: We study the relation between the density profiles of dark matter halos and their mass assembly histories using a statistical sample of halos in a high-resolution N-body simulation of the ΛCDM cosmology. For each halo at z = 0, we identify its merger history tree and determine concentration parameters cvir for all progenitors, thus providing a structural merger tree for each halo. We fit the mass accretion histories by a universal function with one parameter, the formation epoch ac, defined when the log mass accretion rate d log M/d log a falls below a critical value S. We find that late-forming galaxies tend to be less concentrated, such that cvir "observed" at any epoch ao is strongly correlated with ac via cvir = c1ao/ac. Scatter about this relation is mostly due to measurement errors in cvir and ac, implying that the actual spread in cvir for halos of a given mass can be mostly attributed to scatter in ac. We demonstrate that this relation can also be used to predict the mass and redshift dependence of cvir and the scatter about the median cvir(M, z) using accretion histories derived from the extended Press-Schechter (EPS) formalism, after adjusting for a constant offset between the formation times as predicted by EPS and as measured in the simulations; this new ingredient can thus be easily incorporated into semianalytic models of galaxy formation. The correlation found between halo concentration and mass accretion rate suggests a physical interpretation: for high mass infall rates, the central density is related to the background density; when the mass infall rate slows, the central density stays approximately constant, and the halo concentration just grows as Rvir. Because of the direct connection between halo concentration and velocity rotation curves and because of probable connections between halo mass assembly history and star formation history, the tight correlation between these properties provides an essential new ingredient for galaxy formation modeling.

Three-Dimensional Interaction between a Planet and an Isothermal Gaseous Disk. I. Corotation and Lindblad Torques and Planet Migration

Abstract: Gravitational interaction between a planet and a three-dimensional isothermal gaseous disk is studied. In the present paper we mainly examine the torque on a planet and the resultant radial migration of the planet. A planet excites density waves at Lindblad and corotation resonances and experiences a negative torque by the density waves, which causes a rapid inward migration of the planet during its formation in a protoplanetary disk. We formulate the linear wave excitation in three-dimensional isothermal disks and calculate the torques of Lindblad resonances and corotation resonances. For corotation resonances, a general torque formula is newly derived, which is also applicable to two-dimensional disks. The new formula succeeds in reproducing numerical results on the corotation torques, which do not agree with the previously well-known formula. The net torque of the inner and the outer Lindblad resonances (i.e., the differential Lindblad torque) is caused by asymmetry such as the radial pressure gradient and the scale height variation. In three-dimensional disks, the differential Lindblad torques are generally smaller than those in two-dimensional disks. Especially, the effect of a pressure gradient becomes weak. The scale height variation, which is a purely three-dimensional effect, makes the differential Lindblad torque decrease. As a result, the migration time of a planet is obtained as of the order of 106 yr for an Earth-size planet at 5 AU for a typical disk model, which is longer than the result of two-dimensional calculation by the factor of 2 or 3. The reflected waves from disk edges, which are neglected in the torque calculation, can further weaken the disk-planet interaction.

Nucleosynthesis in massive stars with improved nuclear and stellar physics

Abstract: We present the first calculations to follow the evolution of all stable nuclei and their radioactive progeni- tors in stellar models computed from the onset of central hydrogen burning through explosion as Type II supernovae. Calculations are performed for Population I stars of 15, 19, 20, 21, and 25 Musing the most recently available experimental and theoretical nuclear data, revised opacity tables, neutrino losses, and weak interaction rates and taking into account mass loss due to stellar winds. A novel '' adaptive '' reaction net- work is employed with a variable number of nuclei (adjusted each time step) ranging from � 700 on the main sequence to e2200 during the explosion. The network includes, at any given time, all relevant isotopes from hydrogen through polonium (Z ¼ 84). Even the limited grid of stellar masses studied suggests that overall good agreement can be achieved with the solar abundances of nuclei between 16 O and 90 Zr. Interesting dis- crepancies are seen in the 20 Mmodel and (so far, only in that model) are a consequence of the merging of the oxygen, neon, and carbon shells about a day prior to core collapse. We find that, in some stars, most of the '' p-process '' nuclei can be produced in the convective oxygen-burning shell moments prior to collapse; in others, they are made only in the explosion. Serious deficiencies still exist in all cases for the p-process isotopes of Ru and Mo. Subject headings: nuclear reactions, nucleosynthesis, abundances — stars: evolution — supernovae: general On-line material: machine-readable tables

Relative Sensitivities of Mammalian Carnivores to Habitat Fragmentation

Abstract: I examined the effects of habitat fragmentation on the distribution and abundance of mamma- lian carnivores in coastal southern California and tested the prediction that responses to fragmentation var- ied with the body size of carnivore species. I conducted track surveys for nine native and two exotic carnivore species in 29 urban habitat fragments and 10 control sites. Fragment area and isolation were the two stron- gest landscape descriptors of predator distribution and abundance. Six species were sensitive to fragmenta- tion, generally disappearing as habitat patches became smaller and more isolated; three species were en- hanced by fragmentation, with increased abundance in highly fragmented sites; and two species were tolerant of fragmentation, with little to no effect of landscape variables on their distribution and abundance. Within urban habitat fragments, the carnivore visitation rate increased at sites with more exotic cover and closer to the urban edge, a pattern driven largely by the increased abundance of fragmentation-enhanced carnivores at edge sites. Finally, body size, in conjunction with other ecological characteristics, partially ac- counted for the heterogeneity in responses to fragmentation among carnivore species. These differential sensi- tivities are useful criteria for choosing appropriate focal species for ecological research and conservation planning, a choice that depends on the scale of fragmentation in a region and the commensurate responses of carnivore populations at that scale.

Array seismology: Methods and applications

Abstract: [1] Since their development in the 1960s, seismic arrays have given a new impulse to seismology. Recordings from many uniform seismometers in a well-defined, closely spaced configuration produce high-quality and homogeneous data sets, which can be used to study the Earth's structure in great detail. Apart from an improvement of the signal-to-noise ratio due to the simple summation of the individual array recordings, seismological arrays can be used in many different ways to study the fine-scale structure of the Earth's interior. They have helped to study such different structures as the interior of volcanos, continental crust and lithosphere, global variations of seismic velocities in the mantle, the core-mantle boundary and the structure of the inner core. For this purpose many different, specialized array techniques have been developed and applied to an increasing number of high-quality array data sets. Most array methods use the ability of seismic arrays to measure the vector velocity of an incident wave front, i.e., slowness and back azimuth. This information can be used to distinguish between different seismic phases, separate waves from different seismic events and improve the signal-to-noise ratio by stacking with respect to the varying slowness of different phases. The vector velocity information of scattered or reflected phases can be used to determine the region of the Earth from whence the seismic energy comes and with what structures it interacted. Therefore seismic arrays are perfectly suited to study the small-scale structure and variations of the material properties of the Earth. In this review we will give an introduction to various array techniques which have been developed since the 1960s. For each of these array techniques we give the basic mathematical equations and show examples of applications. The advantages and disadvantages and the appropriate applications and restrictions of the techniques will also be discussed. The main methods discussed are the beam-forming method, which forms the basis for several other methods, different slant stacking techniques, and frequency–wave number analysis. Finally, some methods used in exploration geophysics that have been adopted for global seismology are introduced. This is followed by a description of temporary and permanent arrays installed in the past, as well as existing arrays and seismic networks. We highlight their purposes and discuss briefly the advantages and disadvantages of different array configurations.

The BABAR detector

Abstract: BABAR, the detector for the SLAC PEP-II asymmetric e+e- B Factory operating at the upsilon 4S resonance, was designed to allow comprehensive studies of CP-violation in B-meson decays. Charged particle tracks are measured in a multi-layer silicon vertex tracker surrounded by a cylindrical wire drift chamber. Electromagentic showers from electrons and photons are detected in an array of CsI crystals located just inside the solenoidal coil of a superconducting magnet. Muons and neutral hadrons are identified by arrays of resistive plate chambers inserted into gaps in the steel flux return of the magnet. Charged hadrons are identified by dE/dx measurements in the tracking detectors and in a ring-imaging Cherenkov detector surrounding the drift chamber. The trigger, data acquisition and data-monitoring systems, VME- and network-based, are controlled by custom-designed online software. Details of the layout and performance of the detector components and their associated electronics and software are presented.

Spatial distribution of δ18O in meteoric precipitation

Abstract: Proxy data reflecting the oxygen isotope composition of meteoric precipitation (δ18Oppt) are widely used in reconstructions of continental paleoclimate and paleohydrology. However, actual geographic variation in modern water compositions is difficult to estimate from often sparse data. A first step toward understanding the geologic pattern of change in δ18Oppt is to describe the modern distribution in terms of principal geographic parameters. To this end, we empirically model relationships between 18O in modern precipitation and latitude and altitude. We then identify geographic areas where large-scale vapor transport patterns give rise to significant deviations from model δ18Oppt compositions based on latitude and altitude. Model value and residual grids are combined to derive a high-resolution global map of δ18Oppt that can serve as a spatial reference against which proxy data for paleoprecipitation can be compared. Reiteration of the procedure outlined here, for paleo-δ18Oppt data, may illuminate past changes in the climatic and physiographic parameters controlling the distribution of δ18O regimes.

The snowmass Points and slopes: benchmarks for SUSY searches

Abstract: The ”Snowmass Points and Slopes” (SPS) are a set of benchmark points and parameter lines in the MSSM parameter space corresponding to different scenarios in the search for Supersymmetry at present and future experiments. This set of benchmarks was agreed upon at the 2001 ”Snowmass Workshop on the Future of Particle Physics” as a consensus based on different existing proposals.

General considerations for skin test procedures in the diagnosis of drug hypersensitivity

Abstract: K. Brockow, A. Romano, M. Blanca, J. Ring, W. Pichler, P. Demoly Klinik und Poliklinik fur Dermatologie und Allergologie, Muenchen, Germany; Department of Internal Medicine and Geriatrics, UCSC, Allergy Unit, CI Columbus, Rome and IRCS Oasi Maria SS, Troina, Italy; Research Unit for Allergic Diseases, Carlos Haya Hospital, Malaga, Spain; Clinic for Rheumatology and Clinical Immunology/Allergology, Inselspital, Bern, Switzerland; Maladies Respiratoires, Hopital Arnaud de Villeneuve, Montpellier, France

Incorporating concentration dependence in stable isotope mixing models

Abstract: Stable isotopes are often used as natural labels to quantify the contributions of multiple sources to a mixture. For example, C and N isotopic signatures can be used to determine the fraction of three food sources in a consumer's diet. The standard dual isotope, three source linear mixing model assumes that the proportional contribution of a source to a mixture is the same for both elements (e.g., C, N). This may be a reasonable assumption if the concentrations are similar among all sources. However, one source is often particularly rich or poor in one element (e.g., N), which logically leads to a proportionate increase or decrease in the contribution of that source to the mixture for that element relative to the other element (e.g., C). We have developed a concentration-weighted linear mixing model, which assumes that for each element, a source's contribution is proportional to the contributed mass times the elemental concentration in that source. The model is outlined for two elements and three sources, but can be generalized to n elements and n+1 sources. Sensitivity analyses for C and N in three sources indicated that varying the N concentration of just one source had large and differing effects on the estimated source contributions of mass, C, and N. The same was true for a case study of bears feeding on salmon, moose, and N-poor plants. In this example, the estimated biomass contribution of salmon from the concentration-weighted model was markedly less than the standard model estimate. Application of the model to a captive feeding study of captive mink fed on salmon, lean beef, and C-rich, N-poor beef fat reproduced very closely the known dietary proportions, whereas the standard model failed to yield a set of positive source proportions. Use of this concentration-weighted model is recommended whenever the elemental concentrations vary substantially among the sources, which may occur in a variety of ecological and geochemical applications of stable isotope analysis. Possible examples besides dietary and food web studies include stable isotope analysis of water sources in soils, plants, or water bodies; geological sources for soils or marine systems; decomposition and soil organic matter dynamics, and tracing animal migration patterns. A spreadsheet for performing the calculations for this model is available at http://www.epa.gov/wed/pages/models.htm.

Characterization of nucleic acids by nanopore analysis.

Abstract: Single-stranded DNA and RNA molecules in solution can be driven through a nanoscopic pore by an applied electric field. As each molecule occupies the pore, a characteristic blockade of ionic current is produced. Information about length, composition, structure, and dynamic motion of the molecule can be deduced from modulations of the current blockade.

Radial Velocities for 889 Late-Type Stars*

Abstract: We report radial velocities for 844 FGKM-type main-sequence and subgiant stars and 45 K giants, most of which had either low-precision velocity measurements or none at all. These velocities differ from the stand- ard stars of Udry et al. by 0.035 km s � 1 (rms) for the 26 FGK standard stars in common. The zero point of our velocities differs from that of Udry et al.: hVPresentVUdry i¼þ 0:053 km s � 1 . Thus, these new velocities agree with the best known standard stars both in precision and zero point, to well within 0.1 km s � 1 . Nonetheless, both these velocities and the standards suffer from three sources of systematic error, namely, convective blueshift, gravitational redshift, and spectral type mismatch of the reference spectrum. These sys- tematic errors are here forced to be zero for G2 V stars by using the Sun as reference, with Vesta and day sky as proxies. But for spectral types departing from solar, the systematic errors reach 0.3 km s � 1 in the F and K stars and 0.4 km s � 1 in M dwarfs. Multiple spectra were obtained for all 889 stars during 4 years, and 782 of them exhibit velocity scatter less than 0.1 km s � 1 . These stars may serve as radial velocity standards if they remain constant in velocity. We found 11 new spectroscopic binaries and report orbital parameters for them. Subject headings: binaries: spectroscopic — catalogs — stars: fundamental parameters — stars: kinematics — stars: late-type — techniques: radial velocities — techniques: spectroscopic On-line material: machine-readable tables

Remote sensing of planetary properties and biosignatures on extrasolar terrestrial planets.

Abstract: The major goals of NASA's Terrestrial Planet Finder (TPF) and the European Space Agency's Darwin missions are to detect terrestrial-sized extrasolar planets directly and to seek spectroscopic evidence of habitable conditions and life. Here we recommend wavelength ranges and spectral features for these missions. We assess known spectroscopic molecular band features of Earth, Venus, and Mars in the context of putative extrasolar analogs. The preferred wavelength ranges are 7-25 μm in the mid-IR and 0.5 to ~1.1 μm in the visible to near-IR. Detection of O2 or its photolytic product O3 merits highest priority. Liquid H2O is not a bioindicator, but it is considered essential to life. Substantial CO2 indicates an atmosphere and oxidation state typical of a terrestrial planet. Abundant CH4 might require a biological source, yet abundant CH4 also can arise from a crust and upper mantle more reduced than that of Earth. The range of characteristics of extrasolar rocky planets might far exceed that of the Solar Syst...

Evolutionary ecology of plant diseases in natural ecosystems

Abstract: Plant pathogens cause mortality and reduce fecundity of individual plants, drive host population dynamics, and affect the structure and composition of natural plant communities. Pathogens are responsible for both numerical changes in host populations and evolutionary changes through selection for resistant genotypes. Linking such ecological and evolutionary dynamics has been the focus of a growing body of literature on the effects of plant diseases in natural ecosystems. A guiding principle is the importance of understanding the spatial and temporal scales at which plants and pathogens interact. This review summarizes the effects of diseases on populations of wild plants, focusing in particular on the mediation of plant competition and succession, the maintenance of plant species diversity, as well as the process of rapid evolutionary changes in host-pathogen symbioses.

Nitrogen cycling in the ocean: New perspectives on processes and paradigms

Abstract: The nitrogen (N) cycle is composed of multiple transformations of nitrogenous compounds, catalyzed primarily by microbes. The N cycle controls the availability of nitrogenous nutrients and biological productivity in marine systems ([84][1]) and thus is linked to the fixation of atmospheric carbon

Directing research to reduce the impacts of nonindigenous species

Abstract: Management of nonindigenous species is a crucial aspect of maintaining native biodiversity and normal ecosystem functions. We attempt to guide researchers in developing projects that will be of use to con- servation practitioners, tangibly improving applied conservation measures. We advocate a directed approach for conservation research to aid in prioritizing nonindigenous species for intervention by resource managers. This approach includes outlining what needs to be known to make such relative judgments about the impacts of nonindigenous species and the most promising methods by which to obtain such information. We also ad- dress active measures that should be taken once priorities have been set, highlighting the roles of risk assess- ment and research in improving control efforts. Ultimately, a better match between research and practical conservation needs should result in more effective reduction of the effects of nonindigenous species on native species.

The DEEP Groth Strip Survey. II. Hubble Space Telescope Structural Parameters of Galaxies in the Groth Strip

Abstract: The quantitative morphological classification of distant galaxies is essential to the understanding of the evolution of galaxies over the history of the universe This paper presents Hubble Space Telescope WFPC2 F606W and F814W photometric structural parameters for 7450 galaxies in the Groth Strip These parameters are based on a two-dimensional bulge + disk surface brightness model and were obtained using an automated reduction and analysis pipeline described in detail here A first set of fits was performed separately in each bandpass, and a second set of fits was performed simultaneously on both bandpasses The information produced by these two types of fits can be used to explore different science goals Systematic and random fitting errors in all structural parameters as well as bulge and disk colors are carefully characterized through extensive sets of simulations The results of these simulations are given in catalogs similar to the real science catalogs so that both real and simulated measurements can be sampled according to the same selection criteria to show biases and errors in the science data subset of interest The effects of asymmetric structures on the recovered bulge+disk fitting parameters are also explored through simulations The full multidimensional photometric survey selection function of the Groth Strip is also computed This selection function, coupled to bias maps from simulations, provides a complete and objective reproduction of the observational limits, and these limits can be applied to theoretical predictions from galaxy evolution models for direct comparisons with the data

Core top calibration of Mg/Ca in tropical foraminifera: Refining paleotemperature estimation

Abstract: [1] Optimal use of Mg/Ca as a paleotemperature proxy requires establishing calibrations for different species of foraminifera and quantifying the influence of dissolution. To achieve this goal, we have measured Mg/Ca and δ18O in a series of tropical and subtropical core tops, including four depth transects: the Ceara Rise, the Sierra Leone Rise, and the Rio Grande Plateau in the Atlantic, and the Ontong Java Plateau in the Pacific, focusing on spinose mixed layer dwelling species Globigerinoides ruber and Globigerinoides sacculifer, and nonspinose thermocline dwelling Neogloboquadrina dutertrei. Shell Mg/Ca in G. sacculifer is 5–15% lower than in G. ruber, while N. dutertrei Mg/Ca is 49–55% lower than in G. ruber. This statistically significant offset has allowed us to establish different calibrations for each species. Multilinear regression analysis was used to develop calibration equations that include a correction term for the dissolution effect on Mg/Ca in foraminiferal calcite. Presented in this paper are two sets of calibrations; one set using core depth as a dissolution correction and another using ΔCO32− as a dissolution parameter. The calibrations suggest that G. ruber is the most accurate recorder of surface temperature, while G. sacculifer records temperatures below the surface at 20–30 m. The depth habitat of N. dutertrei is more uncertain, owing to the wide range in habitat depths depending on hydrographic conditions, but on average, Mg/Ca and δ18O data suggest it is at ∼50 m. Of the three species, N. dutertrei is the most sensitive to dissolution (up to 23% decrease in shell Mg/Ca per km), while G. sacculifer is the most resistant.