Showing papers by "Texas A&M University published in 2009"

Introducing mothur: Open-Source, Platform-Independent, Community-Supported Software for Describing and Comparing Microbial Communities

Abstract: mothur aims to be a comprehensive software package that allows users to use a single piece of software to analyze community sequence data. It builds upon previous tools to provide a flexible and powerful software package for analyzing sequencing data. As a case study, we used mothur to trim, screen, and align sequences; calculate distances; assign sequences to operational taxonomic units; and describe the alpha and beta diversity of eight marine samples previously characterized by pyrosequencing of 16S rRNA gene fragments. This analysis of more than 222,000 sequences was completed in less than 2 h with a laptop computer.

Selective gas adsorption and separation in metal–organic frameworks

Abstract: Adsorptive separation is very important in industry. Generally, the process uses porous solid materials such as zeolites, activated carbons, or silica gels as adsorbents. With an ever increasing need for a more efficient, energy-saving, and environmentally benign procedure for gas separation, adsorbents with tailored structures and tunable surface properties must be found. Metal–organic frameworks (MOFs), constructed by metal-containing nodes connected by organic bridges, are such a new type of porous materials. They are promising candidates as adsorbents for gas separations due to their large surface areas, adjustable pore sizes and controllable properties, as well as acceptable thermal stability. This critical review starts with a brief introduction to gas separation and purification based on selective adsorption, followed by a review of gas selective adsorption in rigid and flexible MOFs. Based on possible mechanisms, selective adsorptions observed in MOFs are classified, and primary relationships between adsorption properties and framework features are analyzed. As a specific example of tailor-made MOFs, mesh-adjustable molecular sieves are emphasized and the underlying working mechanism elucidated. In addition to the experimental aspect, theoretical investigations from adsorption equilibrium to diffusion dynamics via molecular simulations are also briefly reviewed. Furthermore, gas separations in MOFs, including the molecular sieving effect, kinetic separation, the quantum sieving effect for H2/D2 separation, and MOF-based membranes are also summarized (227 references).

Evolution of Organic Aerosols in the Atmosphere

Abstract: Organic aerosol (OA) particles affect climate forcing and human health, but their sources and evolution remain poorly characterized. We present a unifying model framework describing the atmospheric evolution of OA that is constrained by high-time-resolution measurements of its composition, volatility, and oxidation state. OA and OA precursor gases evolve by becoming increasingly oxidized, less volatile, and more hygroscopic, leading to the formation of oxygenated organic aerosol (OOA), with concentrations comparable to those of sulfate aerosol throughout the Northern Hemisphere. Our model framework captures the dynamic aging behavior observed in both the atmosphere and laboratory: It can serve as a basis for improving parameterizations in regional and global models.

The Sorghum bicolor genome and the diversification of grasses

Abstract: Sorghum, an African grass related to sugar cane and maize, is grown for food, feed, fibre and fuel. We present an initial analysis of the approximately 730-megabase Sorghum bicolor (L.) Moench genome, placing approximately 98% of genes in their chromosomal context using whole-genome shotgun sequence validated by genetic, physical and syntenic information. Genetic recombination is largely confined to about one-third of the sorghum genome with gene order and density similar to those of rice. Retrotransposon accumulation in recombinationally recalcitrant heterochromatin explains the approximately 75% larger genome size of sorghum compared with rice. Although gene and repetitive DNA distributions have been preserved since palaeopolyploidization approximately 70 million years ago, most duplicated gene sets lost one member before the sorghum-rice divergence. Concerted evolution makes one duplicated chromosomal segment appear to be only a few million years old. About 24% of genes are grass-specific and 7% are sorghum-specific. Recent gene and microRNA duplications may contribute to sorghum's drought tolerance.

Nonviral Vectors for Gene Delivery

Abstract: The development of nonviral vectors for safe and efficient gene delivery has been gaining considerable attention recently. An ideal nonviral vector must protect the gene against degradation by nuclease in the extracellular matrix, internalize the plasma membrane, escape from the endosomal compartment, unpackage the gene at some point and have no detrimental effects. In comparison to viruses, nonviral vectors are relatively easy to synthesize, less immunogenic, low in cost, and have no limitation in the size of a gene that can be delivered. Significant progress has been made in the basic science and applications of various nonviral gene delivery vectors; however, the majority of nonviral approaches are still inefficient and often toxic. To this end, two nonviral gene delivery systems using either biodegradable poly(D,Llactide-co-glycolide) (PLG) nanoparticles or cell penetrating peptide (CPP) complexes have been designed and studied using A549 human lung epithelial cells. PLG nanoparticles were optimized for gene delivery by varying particle surface chemistry using different coating materials that adsorb to the particle surface during formation. A variety of cationic coating materials were studied and compared to more conventional surfactants used for PLG nanoparticle fabrication. Nanoparticles (~200 nm) efficiently encapsulated plasmids encoding for luciferase (80-90%) and slowly released the same for two weeks. After a delay, moderate levels of gene expression appeared at day 5 for certain positively charged PLG particles and gene expression was maintained for at least two weeks. In contrast, gene expression mediated by polyethyleneimine (PEI) ended at day 5. PLG particles were also significantly less

Amino acids: metabolism, functions, and nutrition

Abstract: Recent years have witnessed the discovery that amino acids (AA) are not only cell signaling molecules but are also regulators of gene expression and the protein phosphorylation cascade. Additionally, AA are key precursors for syntheses of hormones and low-molecular weight nitrogenous substances with each having enormous biological importance. Physiological concentrations of AA and their metabolites (e.g., nitric oxide, polyamines, glutathione, taurine, thyroid hormones, and serotonin) are required for the functions. However, elevated levels of AA and their products (e.g., ammonia, homocysteine, and asymmetric dimethylarginine) are pathogenic factors for neurological disorders, oxidative stress, and cardiovascular disease. Thus, an optimal balance among AA in the diet and circulation is crucial for whole body homeostasis. There is growing recognition that besides their role as building blocks of proteins and polypeptides, some AA regulate key metabolic pathways that are necessary for maintenance, growth, reproduction, and immunity. They are called functional AA, which include arginine, cysteine, glutamine, leucine, proline, and tryptophan. Dietary supplementation with one or a mixture of these AA may be beneficial for (1) ameliorating health problems at various stages of the life cycle (e.g., fetal growth restriction, neonatal morbidity and mortality, weaning-associated intestinal dysfunction and wasting syndrome, obesity, diabetes, cardiovascular disease, the metabolic syndrome, and infertility); (2) optimizing efficiency of metabolic transformations to enhance muscle growth, milk production, egg and meat quality and athletic performance, while preventing excess fat deposition and reducing adiposity. Thus, AA have important functions in both nutrition and health.

Ultralong spin coherence time in isotopically engineered diamond

Abstract: As quantum mechanics ventures into the world of applications and engineering, materials science faces the necessity to design matter to quantum grade purity. For such materials, quantum effects define their physical behaviour and open completely new (quantum) perspectives for applications. Carbon-based materials are particularly good examples, highlighted by the fascinating quantum properties of, for example, nanotubes or graphene. Here, we demonstrate the synthesis and application of ultrapure isotopically controlled single-crystal chemical vapour deposition (CVD) diamond with a remarkably low concentration of paramagnetic impurities. The content of nuclear spins associated with the (13)C isotope was depleted to 0.3% and the concentration of other paramagnetic defects was measured to be <10(13) cm(-3). Being placed in such a spin-free lattice, single electron spins show the longest room-temperature spin dephasing times ever observed in solid-state systems (T2=1.8 ms). This benchmark will potentially allow observation of coherent coupling between spins separated by a few tens of nanometres, making it a versatile material for room-temperature quantum information processing devices. We also show that single electron spins in the same isotopically engineered CVD diamond can be used to detect external magnetic fields with a sensitivity reaching 4 nT Hz(-1/2) and subnanometre spatial resolution.

Anger Is an Approach-Related Affect: Evidence and Implications.

Abstract: The authors review a range of evidence concerning the motivational underpinnings of anger as an affect, with particular reference to the relationship between anger and anxiety or fear. The evidence supports the view that anger relates to an appetitive or approach motivational system, whereas anxiety relates to an aversive or avoidance motivational system. This evidence appears to have 2 implications. One implication concerns the nature of anterior cortical asymmetry effects. The evidence suggests that such asymmetry reflects direction of motivational engagement (approach vs. withdrawal) rather than affective valence. The other implication concerns the idea that affects form a purely positive dimension and a purely negative dimension, which reflect the operation of appetitive and aversive motivational systems, respectively. The evidence reviewed does not support that view. The evidence is, however, consistent with a discrete-emotions view (which does not rely on dimensionality) and with an alternative dimensional approach.

Modern electric, hybrid electric, and fuel cell vehicles : fundamentals, theory, and design

Abstract: Environmental Impact and History of Modern Transportation Air Pollution Global Warming Petroleum Resources Induced Costs Importance of Different Transportation Development Strategies to Future Oil Supply History of EVs History of HEVs History of Fuel Cell Vehicles Fundamentals of Vehicle Propulsion and Brake General Description of Vehicle Movement Vehicle Resistance Dynamic Equation Tire-Ground Adhesion and Maximum Tractive Effort Power Train Tractive Effort and Vehicle Speed Vehicle Power Plant and Transmission Characteristics Vehicle Performance Operating Fuel Economy Brake Performance Internal Combustion Engines 4S, Spark-Ignited IC Engines 4S, Compression-Ignition IC Engines 2S Engines Wankel Rotary Engines Stirling Engines Gas Turbine Engines Quasi-Isothermal Brayton Cycle Engines Electric Vehicles Configurations of EVs Performance of EVs Tractive Effort in Normal Driving Energy Consumption Hybrid Electric Vehicles Concept of Hybrid Electric Drive Trains Architectures of Hybrid Electric Drive Trains Electric Propulsion Systems DC Motor Drives Induction Motor Drives Permanent Magnetic BLDC Motor Drives SRM Drives Design Principle of Series (Electrical Coupling) Hybrid Electric Drive Train Operation Patterns Control Strategies Design Principles of a Series (Electrical Coupling) Hybrid Drive Train Design Example Parallel (Mechanically Coupled) Hybrid Electric Drive Train Design Drive Train Configuration and Design Objectives Control Strategies Parametric Design of a Drive Train Simulations Design and Control Methodology of Series-Parallel (Torque and Speed Coupling) Hybrid Drive Train Drive Train Configuration Drive Train Control Methodology Drive Train Parameters Design Simulation of an Example Vehicle Design and Control Principles of Plug-In Hybrid Electric Vehicles Statistics of Daily Driving Distance Energy Management Strategy Energy Storage Design Mild Hybrid Electric Drive Train Design Energy Consumed in Braking and Transmission Parallel Mild Hybrid Electric Drive Train Series-Parallel Mild Hybrid Electric Drive Train Peaking Power Sources and Energy Storages Electrochemical Batteries Ultracapacitors Ultra-High-Speed Flywheels Hybridization of Energy Storages Fundamentals of Regenerative Breaking Braking Energy Consumed in Urban Driving Braking Energy versus Vehicle Speed Braking Energy versus Braking Power Braking Power versus Vehicle Speed Braking Energy versus Vehicle Deceleration Rate Braking Energy on Front and Rear Axles Brake System of EV, HEV, and FCV Fuel Cells Operating Principles of Fuel Cells Electrode Potential and Current-Voltage Curve Fuel and Oxidant Consumption Fuel Cell System Characteristics Fuel Cell Technologies Fuel Supply Non-Hydrogen Fuel Cells Fuel Cell Hybrid Electric Drive Train Design Configuration Control Strategy Parametric Design Design Example Design of Series Hybrid Drive Train for Off-Road Vehicles Motion Resistance Tracked Series Hybrid Vehicle Drive Train Architecture Parametric Design of the Drive Train Engine/Generator Power Design Power and Energy Design of Energy Storage Appendices Index

The Genome Sequence of Taurine Cattle: A Window to Ruminant Biology and Evolution

Abstract: To understand the biology and evolution of ruminants, the cattle genome was sequenced to about sevenfold coverage. The cattle genome contains a minimum of 22,000 genes, with a core set of 14,345 orthologs shared among seven mammalian species of which 1217 are absent or undetected in noneutherian (marsupial or monotreme) genomes. Cattle-specific evolutionary breakpoint regions in chromosomes have a higher density of segmental duplications, enrichment of repetitive elements, and species-specific variations in genes associated with lactation and immune responsiveness. Genes involved in metabolism are generally highly conserved, although five metabolic genes are deleted or extensively diverged from their human orthologs. The cattle genome sequence thus provides a resource for understanding mammalian evolution and accelerating livestock genetic improvement for milk and meat production.

Unified Hybridization of Discontinuous Galerkin, Mixed, and Continuous Galerkin Methods for Second Order Elliptic Problems

Abstract: We introduce a unifying framework for hybridization of finite element methods for second order elliptic problems. The methods fitting in the framework are a general class of mixed-dual finite element methods including hybridized mixed, continuous Galerkin, nonconforming, and a new, wide class of hybridizable discontinuous Galerkin methods. The distinctive feature of the methods in this framework is that the only globally coupled degrees of freedom are those of an approximation of the solution defined only on the boundaries of the elements. Since the associated matrix is sparse, symmetric, and positive definite, these methods can be efficiently implemented. Moreover, the framework allows, in a single implementation, the use of different methods in different elements or subdomains of the computational domain, which are then automatically coupled. Finally, the framework brings about a new point of view, thanks to which it is possible to see how to devise novel methods displaying very localized and simple mortaring techniques, as well as methods permitting an even further reduction of the number of globally coupled degrees of freedom.

Arginine metabolism and nutrition in growth, health and disease

Abstract: l-Arginine (Arg) is synthesised from glutamine, glutamate, and proline via the intestinal-renal axis in humans and most other mammals (including pigs, sheep and rats). Arg degradation occurs via multiple pathways that are initiated by arginase, nitric-oxide synthase, Arg:glycine amidinotransferase, and Arg decarboxylase. These pathways produce nitric oxide, polyamines, proline, glutamate, creatine, and agmatine with each having enormous biological importance. Arg is also required for the detoxification of ammonia, which is an extremely toxic substance for the central nervous system. There is compelling evidence that Arg regulates interorgan metabolism of energy substrates and the function of multiple organs. The results of both experimental and clinical studies indicate that Arg is a nutritionally essential amino acid (AA) for spermatogenesis, embryonic survival, fetal and neonatal growth, as well as maintenance of vascular tone and hemodynamics. Moreover, a growing body of evidence clearly indicates that dietary supplementation or intravenous administration of Arg is beneficial in improving reproductive, cardiovascular, pulmonary, renal, gastrointestinal, liver and immune functions, as well as facilitating wound healing, enhancing insulin sensitivity, and maintaining tissue integrity. Additionally, Arg or l-citrulline may provide novel and effective therapies for obesity, diabetes, and the metabolic syndrome. The effect of Arg in treating many developmental and health problems is unique among AAs, and offers great promise for improved health and wellbeing of humans and animals.

Pulmonary Passage is a Major Obstacle for Intravenous Stem Cell Delivery: The Pulmonary First-Pass Effect

Abstract: Intravenous (IV) stem cell delivery for regenerative tissue therapy has been increasingly used in both experimental and clinical trials. However, recent data suggest that the majority of administered stem cells are initially trapped in the lungs. We sought to investigate variables that may affect this pulmonary first-pass effect. In anesthetized Sprague-Dawley rats, silicone tubing catheters were placed in the left internal jugular vein and common carotid artery. We investigated four different cell types: mesenchymal stromal cells (MSC), multipotent adult progenitor cells (MAPCs), bone marrow-derived mononuclear cells (BMMC), and neural stem cells (NSC). Cells were co-labeled with Qtracker 655 (for flow cytometry) and Qtracker 800 (for infrared imaging) and infused intravenously with continual arterial sample collection. Samples were analyzed via flow cytometry to detect labeled cells reaching the arterial circulation. Following sampling and exsanguination, heart, lungs, spleen, kidney, and liver were harvested and placed on an infrared imaging system to identify the presence of labeled cells. The majority of MSCs were trapped inside the lungs following intravenous infusion. NSC and MAPC pulmonary passage was 2-fold and BMMC passage was 30-fold increased as compared to MSCs. Inhibition of MSC CD49d significantly increased MSC pulmonary passage. Infusion via two boluses increased pulmonary MSC passage as compared to single bolus administration. Infrared imaging revealed stem cells evenly distributed over all lung fields. Larger stem and progenitor cells are initially trapped inside the lungs following intravenous administration with a therapeutically questionable number of cells reaching the arterial system acutely.

Multi-site assessment of the precision and reproducibility of multiple reaction monitoring–based measurements of proteins in plasma

Abstract: Verification of candidate biomarkers relies upon specific, quantitative assays optimized for selective detection of target proteins, and is increasingly viewed as a critical step in the discovery pipeline that bridges unbiased biomarker discovery to preclinical validation. Although individual laboratories have demonstrated that multiple reaction monitoring (MRM) coupled with isotope dilution mass spectrometry can quantify candidate protein biomarkers in plasma, reproducibility and transferability of these assays between laboratories have not been demonstrated. We describe a multilaboratory study to assess reproducibility, recovery, linear dynamic range and limits of detection and quantification of multiplexed, MRM-based assays, conducted by NCI-CPTAC. Using common materials and standardized protocols, we demonstrate that these assays can be highly reproducible within and across laboratories and instrument platforms, and are sensitive to low mug/ml protein concentrations in unfractionated plasma. We provide data and benchmarks against which individual laboratories can compare their performance and evaluate new technologies for biomarker verification in plasma.

A benchmark study on the thermal conductivity of nanofluids

Abstract: This article reports on the International Nanofluid Property Benchmark Exercise, or INPBE, in which the thermal conductivity of identical samples of colloidally stable dispersions of nanoparticles or “nanofluids,” was measured by over 30 organizations worldwide, using a variety of experimental approaches, including the transient hot wire method, steady-state methods, and optical methods. The nanofluids tested in the exercise were comprised of aqueous and nonaqueous basefluids, metal and metal oxide particles, near-spherical and elongated particles, at low and high particle concentrations. The data analysis reveals that the data from most organizations lie within a relatively narrow band (±10% or less) about the sample average with only few outliers. The thermal conductivity of the nanofluids was found to increase with particle concentration and aspect ratio, as expected from classical theory. There are (small) systematic differences in the absolute values of the nanofluid thermal conductivity among the various experimental approaches; however, such differences tend to disappear when the data are normalized to the measured thermal conductivity of the basefluid. The effective medium theory developed for dispersed particles by Maxwell in 1881 and recently generalized by Nan et al. [J. Appl. Phys. 81, 6692 (1997)], was found to be in good agreement with the experimental data, suggesting that no anomalous enhancement of thermal conductivity was achieved in the nanofluids tested in this exercise.

Dark matter search results from the CDMS II experiment.

Abstract: We report results from a blind analysis of the final data taken with the Cryogenic Dark Matter Search experiment (CDMS II) at the Soudan Underground Laboratory, Minnesota, USA. A total raw exposure of 612 kg-days was analyzed for this work. We observed two events in the signal region; based on our background estimate, the probability of observing two or more background events is 23%. These data set an upper limit on the Weakly Interacting Massive Particle (WIMP)-nucleon elastic-scattering spin-independent cross-section of 7.0 x 10{sup -44} cm{sup 2} for a WIMP of mass 70 GeV/c{sup 2} at the 90% confidence level. Combining this result with all previous CDMS II data gives an upper limit on the WIMP-nucleon spin-independent cross-section of 3.8 x 10{sup -44} cm{sup 2} for a WIMP of mass 70 GeV/c{sup 2}. We also exclude new parameter space in recently proposed inelastic dark matter models.

Tropical tropopause layer

Abstract: [1] Observations of temperature, winds, and atmospheric trace gases suggest that the transition from troposphere to stratosphere occurs in a layer, rather than at a sharp “tropopause.” In the tropics, this layer is often called the “tropical tropopause layer” (TTL). We present an overview of observations in the TTL and discuss the radiative, dynamical, and chemical processes that lead to its time-varying, three-dimensional structure. We present a synthesis definition with a bottom at 150 hPa, 355 K, 14 km (pressure, potential temperature, and altitude) and a top at 70 hPa, 425 K, 18.5 km. Laterally, the TTL is bounded by the position of the subtropical jets. We highlight recent progress in understanding of the TTL but emphasize that a number of processes, notably deep, possibly overshooting convection, remain not well understood. The TTL acts in many ways as a “gate” to the stratosphere, and understanding all relevant processes is of great importance for reliable predictions of future stratospheric ozone and climate.

A redetermination of the hubble constant with the hubble space telescope from a differential distance ladder

Abstract: This is the second of two papers reporting results from a program to determine the Hubble constant to ~5% precision from a refurbished distance ladder based on extensive use of differential measurements. Here we report observations of 240 Cepheid variables obtained with the Near-Infrared Camera and Multi-Object Spectrometer (NICMOS) Camera 2 through the F160W filter on the Hubble Space Telescope (HST). The Cepheids are distributed across six recent hosts of Type Ia supernovae (SNe Ia) and the maser galaxy NGC 4258, allowing us to directly calibrate the peak luminosities of the SNe Ia from the precise, geometric distance measurements provided by the masers. New features of our measurement include the use of the same instrument for all Cepheid measurements across the distance ladder and homogeneity of the Cepheid periods and metallicities, thus necessitating only a differential measurement of Cepheid fluxes and reducing the largest systematic uncertainties in the determination of the fiducial SN Ia luminosity. In addition, the NICMOS measurements reduce the effects of differential extinction in the host galaxies by a factor of ~5 over past optical data. Combined with a greatly expanded set of 240 SNe Ia at z < 0.1 which define their magnitude-redshift relation, we find H 0 = 74.2 ? 3.6 km s?1 Mpc?1, a 4.8% uncertainty including both statistical and systematic errors. To independently test the maser calibration, we use 10 individual parallax measurements of Galactic Cepheids obtained with the HST fine guidance sensor and find similar results. We show that the factor of 2.2 improvement in the precision of H 0 is a significant aid to the determination of the equation-of-state parameter of dark energy, w = P/(?c 2). Combined with the Wilkinson Microwave Anisotropy Probe five-year measurement of ? M h 2, we find w = ?1.12 ? 0.12 independent of any information from high-redshift SNe Ia or baryon acoustic oscillations (BAO). This result is also consistent with analyses based on the combination of high-redshift SNe Ia and BAO. The constraints on w(z) now including high-redshift SNe Ia and BAO are consistent with a cosmological constant and are improved by a factor of 3 due to the refinement in H 0 alone. We show that future improvements in the measurement of H 0 are likely and should further contribute to multi-technique studies of dark energy.

Individual Power Distance Orientation and Follower Reactions to Transformational Leaders: A Cross-Level, Cross-Cultural Examination

Abstract: Using 560 followers and 174 leaders in the People's Republic of China and United States, we found that individual follower's “power distance” orientation and their group's shared perceptions of tra...

Conceptualizing Corporate Entrepreneurship Strategy

Abstract: Our knowledge of corporate entrepreneurship (CE) continues to expand. However, this knowledge remains quite fragmented and non–cumulative. Herein, we conceptualize CE strategy as a useful focal poi...

You Say Illegal, I Say Legitimate: Entrepreneurship in the Informal Economy

Abstract: The entrepreneurial process drives economic activities in the formal economy; however, little is known theoretically about how the entrepreneurial process works in the informal economy. To address this theoretical gap, we employ a multilevel perspective integrating entrepreneurship theory (microlevel) with institutional (macrolevel) and collective identity (mesolevel) theories to examine the role institutions and collective identity play in the recognition and exploitation of opportunities in the informal economy. Additionally, we explore factors that influence the transition to the formal economy.

You Say Illegal, I Say Legitimate: Entrepreneurship in the Informal Economy

Abstract: The entrepreneurial process drives economic activities in the formal economy; however, little is known theoretically about how the entrepreneurial process works in the informal economy. To address this theoretical gap, we employ a multi-level perspective integrating entrepreneurship theory (micro-level) with institutional (macro-level) and collective identity (meso-level) theories to examine the role institutions and collective identity play in the recognition and exploitation of opportunities in the informal economy. Additionally, we explore factors that influence transition to the formal economy.

Systematic measurements of identified particle spectra in pp, d+Au, and Au+Au collisions at the star detector.

Abstract: Identified charged-particle spectra of pi(+/-), K(+/-), p, and (p) over bar at midrapidity (vertical bar y vertical bar < 0.1) measured by the dE/dx method in the STAR (solenoidal tracker at the BNL Relativistic Heavy Ion Collider) time projection chamber are reported for pp and d + Au collisions at root s(NN) = 200 GeV and for Au + Au collisions at 62.4, 130, and 200 GeV. Average transverse momenta, total particle production, particle yield ratios, strangeness, and baryon production rates are investigated as a function of the collision system and centrality. The transverse momentum spectra are found to be flatter for heavy particles than for light particles in all collision systems; the effect is more prominent for more central collisions. The extracted average transverse momentum of each particle species follows a trend determined by the total charged-particle multiplicity density. The Bjorken energy density estimate is at least several GeV/fm(3) for a formation time less than 1 fm/c. A significantly larger net-baryon density and a stronger increase of the net-baryon density with centrality are found in Au + Au collisions at 62.4 GeV than at the two higher energies. Antibaryon production relative to total particle multiplicity is found to be constant over centrality, but increases with the collision energy. Strangeness production relative to total particle multiplicity is similar at the three measured RHIC energies. Relative strangeness production increases quickly with centrality in peripheral Au + Au collisions, to a value about 50% above the pp value, and remains rather constant in more central collisions. Bulk freeze-out properties are extracted from thermal equilibrium model and hydrodynamics-motivated blast-wave model fits to the data. Resonance decays are found to have little effect on the extracted kinetic freeze-out parameters because of the transverse momentum range of our measurements. The extracted chemical freeze-out temperature is constant, independent of collision system or centrality; its value is close to the predicted phase-transition temperature, suggesting that chemical freeze-out happens in the vicinity of hadronization and the chemical freeze-out temperature is universal despite the vastly different initial conditions in the collision systems. The extracted kinetic freeze-out temperature, while similar to the chemical freeze-out temperature in pp, d + Au, and peripheral Au + Au collisions, drops significantly with centrality in Au + Au collisions, whereas the extracted transverse radial flow velocity increases rapidly with centrality. There appears to be a prolonged period of particle elastic scatterings from chemical to kinetic freeze-out in central Au + Au collisions. The bulk properties extracted at chemical and kinetic freeze-out are observed to evolve smoothly over the measured energy range, collision systems, and collision centralities.

Genome-Wide Survey of SNP Variation Uncovers the Genetic Structure of Cattle Breeds

Abstract: The imprints of domestication and breed development on the genomes of livestock likely differ from those of companion animals. A deep draft sequence assembly of shotgun reads from a single Hereford female and comparative sequences sampled from six additional breeds were used to develop probes to interrogate 37,470 single-nucleotide polymorphisms (SNPs) in 497 cattle from 19 geographically and biologically diverse breeds. These data show that cattle have undergone a rapid recent decrease in effective population size from a very large ancestral population, possibly due to bottlenecks associated with domestication, selection, and breed formation. Domestication and artificial selection appear to have left detectable signatures of selection within the cattle genome, yet the current levels of diversity within breeds are at least as great as exists within humans.

First-Year Sloan Digital Sky Survey-II Supernova Results: Hubble Diagram and Cosmological Parameters

Abstract: We present measurements of the Hubble diagram for 103 Type Ia supernovae (SNe) with redshifts 0.04 < z < 0.42, discovered during the first season (Fall 2005) of the Sloan Digital Sky Survey-II (SDSS-II) Supernova Survey. These data fill in the redshift "desert" between low- and high-redshift SN Ia surveys. Within the framework of the MLCS2K2 light-curve fitting method, we use the SDSS-II SN sample to infer the mean reddening parameter for host galaxies, RV = 2.18 ± 0.14stat ± 0.48syst, and find that the intrinsic distribution of host-galaxy extinction is well fitted by an exponential function, P(AV ) = exp(–AV /τV), with τV = 0.334 ± 0.088 mag. We combine the SDSS-II measurements with new distance estimates for published SN data from the ESSENCE survey, the Supernova Legacy Survey (SNLS), the Hubble Space Telescope (HST), and a compilation of Nearby SN Ia measurements. A new feature in our analysis is the use of detailed Monte Carlo simulations of all surveys to account for selection biases, including those from spectroscopic targeting. Combining the SN Hubble diagram with measurements of baryon acoustic oscillations from the SDSS Luminous Red Galaxy sample and with cosmic microwave background temperature anisotropy measurements from the Wilkinson Microwave Anisotropy Probe, we estimate the cosmological parameters w and ΩM, assuming a spatially flat cosmological model (FwCDM) with constant dark energy equation of state parameter, w. We also consider constraints upon ΩM and ΩΛ for a cosmological constant model (ΛCDM) with w = –1 and non-zero spatial curvature. For the FwCDM model and the combined sample of 288 SNe Ia, we find w = –0.76 ± 0.07(stat) ± 0.11(syst), ΩM = 0.307 ± 0.019(stat) ± 0.023(syst) using MLCS2K2 and w = –0.96 ± 0.06(stat) ± 0.12(syst), ΩM = 0.265 ± 0.016(stat) ± 0.025(syst) using the SALT-II fitter. We trace the discrepancy between these results to a difference in the rest-frame UV model combined with a different luminosity correction from color variations; these differences mostly affect the distance estimates for the SNLS and HST SNe. We present detailed discussions of systematic errors for both light-curve methods and find that they both show data-model discrepancies in rest-frame U band. For the SALT-II approach, we also see strong evidence for redshift-dependence of the color-luminosity parameter (β). Restricting the analysis to the 136 SNe Ia in the Nearby+SDSS-II samples, we find much better agreement between the two analysis methods but with larger uncertainties: w = –0.92 ± 0.13(stat)+0.10 –0.33(syst) for MLCS2K2 and w = –0.92 ± 0.11(stat)+0.07 –0.15 (syst) for SALT-II.

Genome sequence, comparative analysis, and population genetics of the domestic horse.

Abstract: We report a high-quality draft sequence of the genome of the horse (Equus caballus). The genome is relatively repetitive but has little segmental duplication. Chromosomes appear to have undergone few historical rearrangements: 53% of equine chromosomes show conserved synteny to a single human chromosome. Equine chromosome 11 is shown to have an evolutionary new centromere devoid of centromeric satellite DNA, suggesting that centromeric function may arise before satellite repeat accumulation. Linkage disequilibrium, showing the influences of early domestication of large herds of female horses, is intermediate in length between dog and human, and there is long-range haplotype sharing among breeds.