bluuebunny/crossref_metadata_2025 huggingface dataset:
RACE/ETHNICITY, PERCEIVED DISCRIMINATION, AND BELIEFS ABOUT THE MEANING OF AN OBAMA PRESIDENCY
Authors: Hunt Matthew O. , Wilson David C.
Published: July 2009

This paper explores how race/ethnicity and perceptions of racial discrimination and inequality shape beliefs about the implications of an Obama presidency for U.S. race relations. Specifically, using data from a June/July 2008 Gallup/USA Todaysurvey, we examine how African Americans, Hispanics, and Whites differ in their perceptions of the importance of an Obama victory and in beliefs about the implications of such for race relations, racial progress, and opportunities for Blacks in their careers and in national politics. We also examine how perceptions of the extent and nature of racial discrimination and inequality shape these outcomes (overall and by race/ethnicity). Results show that African Americans, relative to Whites and Hispanics, are especially likely to see an Obama victory as important and meaningful in terms of relatively abstract notions of racial change. In contrast, Hispanics are more likely than African Americans and Whites to believe that an Obama win will translate into concrete societal changes, such as expanded opportunities for Blacks in work and politics. In addition, perceived discrimination and inequality positively shape all of the outcomes under study (more perceived discrimination equals more importance and optimism attached to an Obama win), though this association is especially strong amongWhites—a pattern possibly rooted in divergentmeaningsattached to perceived discrimination and inequality by race/ethnicity. Overall, our findings suggest that African Americans view an Obama victory as meaningful primarily because of its symbolic significance, rather than because they believe it will result in substantive racial progress. We conclude by offering some speculation and selected questions for future research on race and U.S. politics.
Climatic circulation in the Gulf of Trieste (northern Adriatic)
Authors: Malačič V. , Petelin B.
Published: July 2009

The climatic circulation of the Gulf of Trieste, which is a shallow semienclosed basin in the closed northeastern end of the northern Adriatic, is studied with a numerical model. In all seasons there is a general inflow into the Gulf of Trieste at its lower, deeper part. This inflow makes a cyclonic turn centered in the southern part during average winter conditions. This turn is enhanced during spring and closes in an elongated cyclonic gyre during average summer conditions. In spring and summer, the cyclonic gyre is coupled with an anticyclonic gyre near the closed eastern part of the gulf. A “dome”‐like density profile across the gulf's axis in the inner part of the gulf above the bottom appears with this circulation during spring and summer. In climatic autumn there is a smaller anticyclonic gyre on its southern side. Near the sea surface there is an outflow during winter, which is driven by the dominant “bora” wind blowing along the gulf's axis. This outflow, however, is detached from the southern coastline to the right, and crosses the gulf diagonally, merging with the belt of freshwater outflow along the northern coastline. This is shown to be a consequence of the balance between the pressure gradient force caused by elevation piled up in the direction out of the gulf, the Coriolis force, and vertical friction between layers near the sea surface. During the stratified season the surface of the gulf is occupied by an anticyclonic gyre due to the inertial plume of the Isonzo River.
Impulse regime CRLH resonator for tunable pulse rate multiplication
Authors: Gómez‐Díaz J. S. , Alvarez‐Melcon A. , Gupta S. , Caloz C.
Published: July 2009

A novel tunable microwave broadband resonator, inspired from optical laser systems, is presented. In contrast to usual harmonic resonators, the proposed device is based on broadband composite right/left handed metamaterial lines. This line, configured as a resonator, provides nonuniform spectral resonances due to the nonlinear nature of its dispersion curve. This is exploited in the impulse regime, where the input pulse spectrum is discretized inside the resonator, with different spectral separation as a function of the carrier frequency. This discretization leads to a pulse periodicity in time, with a tunable output time period. On the basis of the new broadband resonator features, a pulse rate multiplication device is proposed. This device provides an increase in the repetition rate of a periodic input pulse, with the additional advantage of repetition rate tunability.
Contributions of thermal expansion of monuments and nearby bedrock to observed GPS height changes
Authors: Yan Haoming , Chen Wu , Zhu Yaozhong , Zhang Weimin , Zhong Min
Published: July 2009

Long‐term continuous Global Positioning System (GPS) observations have become an important tool for studying the various geodynamic processes. To fully study the geodynamic processes at GPS stations, the temporal movements of GPS monuments and nearby bedrock induced by thermal expansion need to be considered. In this paper, we extend a theoretical model to estimate the thermal expansions of GPS monuments and nearby bedrock for 86 globally distributed GPS stations based upon measurements of surface air temperatures. The results show that annual temperature variations are the dominant contributors for the thermal expansion of GPS monuments and nearby bedrock. The contributions of thermal expansion to GPS height changes display largely spatial variations and can reach to a few millimeters.
Aerosol effect on cloud droplet size as monitored from surface‐based remote sensing over East China Sea region
Authors: Pandithurai G. , Takamura T. , Yamaguchi J. , Miyagi K. , Takano T. , Ishizaka Y. , Dipu S. , Shimizu A.
Published: July 2009

The effect of increased aerosol concentrations on the low‐level, non‐precipitating, ice‐free stratus clouds is examined using a suite of surface‐based remote sensing systems. Cloud droplet effective radius and liquid water path are retrieved using cloud radar and microwave radiometer. Collocated measurements of aerosol scattering coefficient, size distribution and cloud condensation nuclei (CCN) concentrations were used to examine the response of cloud droplet size and optical thickness to increased CCN proxies. During the episodic events of increase in aerosol accumulation‐mode volume distribution, the decrease in droplet size and increase in cloud optical thickness is observed. The indirect effect estimates are made for both droplet effective radius and cloud optical thickness for different liquid water path ranges and they range 0.02–0.18 and 0.005–0.154, respectively. Data are also categorized into thin and thick clouds based on cloud geometric thickness (Δz) and estimates show IE values are relatively higher for thicker clouds.
Links between fluid circulation, temperature, and metamorphism in subducting slabs
Authors: Spinelli G. A. , Wang K.
Published: July 2009

The location and timing of metamorphic reactions in subducting lithosphere are influenced by thermal effects of fluid circulation in the ocean crust aquifer. Fluid circulation in subducting crust extracts heat from the Nankai subduction zone, causing the crust to pass through cooler metamorphic facies than if no fluid circulation occurs. This fluid circulation shifts the basalt‐to‐eclogite transition and the associated slab dehydration 14 km deeper (35 km farther landward) than would be predicted with no fluid flow. For most subduction zones, hydrothermal cooling of the subducting slab will delay eclogitization relative to estimates made without considering fluid circulation.
Particle dynamics description of “BGK collisions” as a Poisson process
Authors: Milla Marco , Kudeki Erhan
Published: July 2009

The Gordeyev integral for plasma particles colliding with neutrals is obtained using a particle dynamics formalism in which the collisions are modeled as a discrete Poisson process. The result leads to an electron density fluctuation spectrum model for partially ionized plasmas which is identical with the spectral model obtained from BGK plasma kinetic equations. This isomorphism between the Poisson process and the BGK operator is analogous to a similar relation between the Brownian motion process and the Fokker‐Planck operator with constant coefficients. We take advantage of this analogy to derive a collisional ISR spectrum model that takes into account collisions with both neutrals and charged species.
Identifying chaos from heart rate: The right task?
Authors: Freitas Ubiratan , Roulin Elise , Muir Jean-François , Letellier Christophe
Published: July 2009

Providing a conclusive answer to the question “is this dynamics chaotic?” remains very challenging when experimental data are investigated. We showed that such a task is actually a difficult problem in the case of heart rates. Nevertheless, an appropriate dynamical analysis can discriminate healthy subjects from patients.
Biofuel contribution to mitigate fossil fuel CO2 emissions: Comparing sugar cane ethanol in Brazil with corn ethanol and discussing land use for food production and deforestation
Authors: Rosa Luiz Pinguelli , Pires de Campos Christiano , Muylaert de Araujo Maria Silvia
Published: July 2009

This paper compares the use of sugar cane and corn for the production of ethanol, with a focus on global warming and the current international debate about land use competition for food and biofuel production. The indicators used to compare the products are CO2 emissions, energy consumption, sugar cane coproducts, and deforestation. The life cycle emission inventory as a methodological tool is taken into account. The sustainability of socioeconomic development and the developing countries’ need to overcome barriers form the background against which the Brazilian government energy plans are analyzed.
Stochastic vagal modulation of cardiac pacemaking may lead to erroneous identification of cardiac “chaos”
Authors: Zhang J. Q. , Holden A. V. , Monfredi O. , Boyett M. R. , Zhang H.
Published: July 2009

Fluctuations in the time interval between two consecutive R-waves of electrocardiogram during normal sinus rhythm may result from irregularities in the autonomic drive of the pacemaking sinoatrial node (SAN). We use a biophysically detailed mathematical model of the action potentials of rabbit SAN to quantify the effects of fluctuations in acetylcholine (ACh) on the pacemaker activity of the SAN and its variability. Fluctuations in ACh concentration model the effect of stochastic activity in the vagal parasympathetic fibers that innervate the SAN and produce varying rates of depolarization during the pacemaker potential, leading to fluctuations in cycle length (CL). Both the estimated maximal Lyapunov exponent and the noise limit of the resultant sequence of fluctuating CLs suggest chaotic dynamics. Apparently chaotic heart rate variability (HRV) seen in sinus rhythm can be produced by stochastic modulation of the SAN. The identification of HRV data as chaotic by use of time series measures such as a positive maximal Lyapunov exponent or positive noise limit requires both caution and a quantitative, predictive mechanistic model that is fully deterministic.
Delays in the human heartbeat dynamics
Authors: Alvarez-Ramirez Jose , Rodriguez Eduardo , Echeverría Juan Carlos
Published: July 2009

This paper explores the possibility of applying statistical nonlinear physics methods to elucidate the underlying mechanisms controlling the heart rate. In particular, the presence of delays in RR interval dynamics is studied by using a lagged detrended fluctuation analysis. The results indicate that patients with congestive heart failure (CHF) have a prolonged time delay in the baroreflex response. Some implications of large delays for the functioning of autonomic control in subjects with CHF are discussed.
Characterizing heart rate variability by scale-dependent Lyapunov exponent
Authors: Hu Jing , Gao Jianbo , Tung Wen-wen
Published: July 2009

Previous studies on heart rate variability (HRV) using chaos theory, fractal scaling analysis, and many other methods, while fruitful in many aspects, have produced much confusion in the literature. Especially the issue of whether normal HRV is chaotic or stochastic remains highly controversial. Here, we employ a new multiscale complexity measure, the scale-dependent Lyapunov exponent (SDLE), to characterize HRV. SDLE has been shown to readily characterize major models of complex time series including deterministic chaos, noisy chaos, stochastic oscillations, random 1/f processes, random Levy processes, and complex time series with multiple scaling behaviors. Here we use SDLE to characterize the relative importance of nonlinear, chaotic, and stochastic dynamics in HRV of healthy, congestive heart failure, and atrial fibrillation subjects. We show that while HRV data of all these three types are mostly stochastic, the stochasticity is different among the three groups.
Multifractality and heart rate variability
Authors: Sassi Roberto , Signorini Maria Gabriella , Cerutti Sergio
Published: July 2009

In this paper, we participate to the discussion set forth by the editor of Chaos for the controversy, “Is the normal heart rate chaotic?” Our objective was to debate the question, “Is there some more appropriate term to characterize the heart rate variability (HRV) fluctuations?” We focused on the ≈24 h RR series prepared for this topic and tried to verify with two different techniques, generalized structure functions and wavelet transform modulus maxima, if they might be described as being multifractal. For normal and congestive heart failure subjects, the hq exponents showed to be decreasing for increasing q with both methods, as it should be for multifractal signals. We then built 40 surrogate series to further verify such hypothesis. For most of the series (≈75%–80% of cases) multifractality stood the test of the surrogate data employed. On the other hand, series coming from patients in atrial fibrillation showed a small, if any, degree of multifractality. The population analyzed is too small for definite conclusions, but the study supports the use of multifractal series to model HRV. Also it suggests that the regulatory action of autonomous nervous system might play a role in the observed multifractality.
On the evolution of the cellular automaton of rule 150 from some simple initial states
Authors: Macfarlane A. J.
Published: July 2009

The evolution Eα in discrete time t of the cellular automaton CA150 of Wolfram rule 150 is studied for certain initial states ψα. The values of the cell variables in any state ψα considered are all zero outside a principal sequence (PS) of length k within which they take on values 1a2a3⋯ak−2ak−11, where a2=1,0,…. Powerful algebraic methods are used to develop formulas for the weight, Ωα(t), i.e., the total number of cell variables with value equal to 1 at time t, of the state of Eα at time t≥0, and of the sum Wα(N)=∑t=02N−1Ωα(t) of the weights of the first 2N states of the evolution of Eα in discrete time. The methods are described carefully. A selection of results, new here, is stated and proved for several initial states ψα with simple PSs of increasing lengths k>1. Many of them feature numbers in the Fibonacci, Lucas, and Jacobsthal sequences.
Heat transfer analysis for peripheral blood flow measurement system
Authors: Nagata Koji , Hattori Hideharu , Sato Nobuhiko , Ichige Yukiko , Kiguchi Masashi
Published: July 2009

Some disorders such as circulatory disease and metabolic abnormality cause many problems to peripheral blood flow condition. Therefore, frequent measurement of the blood flow condition is bound to contribute to precaution against those disorders and to control of conditions of the diseases. We propose a convenient means of blood flow volume measurement at peripheral part, such as fingertips. Principle of this measurement is based on heat transfer characteristics of peripheral part containing the blood flow. Transition response analysis of skin surface temperature has provided measurement model of the peripheral blood flow volume. We developed the blood flow measurement system based on that model and evaluated it by using artificial finger under various temperature conditions of ambience and internal fluid. The evaluation results indicated that proposed method could estimate the volume of the fluid regardless of temperature condition of them. Finally we applied our system to real finger testing and have obtained results correlated well with laser Doppler blood flow meter values.
Electrolysis of glycerol in subcritical water
Authors: Yuksel Asli , Koga Hiromichi , Sasaki Mitsuru , Goto Motonobu
Published: July 2009

Recently, there has been a rising interest for the disposal of biorelated components that cannot be treated easily by biological processes. Because of the development of biodiesel production, the production of by-products such as crude glycerol has increased dramatically. Presently, in many biodiesel plants with low capacity, the aqueous phase containing produced/left glycerol, which is an important molecule in the context of renewable biomass resources to provide hydrogen energy and chemical intermediates, methanol and salts as by-products, is discharged as wastewater. In this manner, both environmental pollution and economical losses are created. Therefore, we developed a new hydrothermal electrolysis system, by which these organics can be converted into value added chemicals, under high-temperature and high-pressure aqueous conditions. In this study, hydrothermal electrolysis reactions of glycerol with an alkali were investigated systematically to determine the intermediate products and current efficiency. We next studied the effects of electricity loading on the molecular transformation of glycerol through the comparison of the product distribution obtained by hydrothermal electrolysis with that by hydrothermal degradation under alkaline conditions. As a gaseous product, hydrogen gas was generated, whereas lactic acid was produced as the main liquid product. The yield of lactic acid increased to 34.7% at 280 °C with 50 mM NaOH after 90 min reaction time.
Quasiperiodic solutions for the cubic complex Ginzburg–Landau equation
Authors: Cong Hongzi , Liu Jianjun , Yuan Xiaoping
Published: July 2009

The existence of two-dimensional Kolmogorov–Arnold–Moser invariant tori is proved for cubic complex Ginzburg–Landau equation of higher spatial dimension. As a consequence, the equation possesses a Cantorian branch of nontraveling-wave quasiperiodic solutions of two-dimensional frequency vector.
Minimum free-energy path of homogenous nucleation from the phase-field equation
Authors: Iwamatsu Masao
Published: July 2009

The minimum free-energy path (MFEP) is the most probable route of the nucleation process on the multidimensional free-energy surface. In this study, the phase-field equation is used as a mathematical tool to deduce the MFEP of homogeneous nucleation. We use a simple square-gradient free-energy functional with a quartic local free-energy function as an example and study the time evolution of a single nucleus placed within a metastable environment. The time integration of the phase-field equation is performed using the numerically efficient cell-dynamics method. By monitoring the evolution of the size of the nucleus and the free energy of the system simultaneously, we can easily deduce the free-energy barrier as a function of the size of the sub- and the supercritical nucleus along the MFEP.
Interaction between electromagnetic waves and plasma waves in motional plasma
Authors: Chen S. Y. , Gao M. , Tang C. J. , Peng X. D.
Published: July 2009

The electromagnetic wave (EM wave) behavior and the electromagnetic instability caused by the interaction between an EM wave and a plasma wave in motional plasma are studied. The dispersion relation of EM waves and the dielectric tensor of motional plasma are derived by magnetohydrodynamics, and the wave phenomenon in motional plasma is displayed. As a result, the electromagnetic instability, which is excited by the interaction between the EM waves and the plasma waves, is revealed. The mechanism of the instability is the coupling between high frequency electromagnetic field and the transverse electron oscillation derived from the deflection of longitudinal electron oscillation due to self-magnetic field. The present research is useful with regard to the new type of plasma radiation source, ion-focusing accelerator, and plasma diagnostic technique.
Superconducting device helps probe glasslike dynamics in solid helium
Authors: Miller Johanna
Published: July 2009

Accurate measurements over a wide range of conditions may unravel some of the mysteries of the apparently flowing solid.
Population genetics and range expansions
Authors: Hallatschek Oskar , Nelson David R.
Published: July 2009

On a molecular level and at the frontiers of expanding habitats, large stochastic fluctuations can obscure signals of Darwinian evolution.
The dichotomous history of diffusion
Authors: Narasimhan T. N.
Published: July 2009

Nearly a century after the equations of physical diffusion and stochastic diffusion were formulated, Albert Einstein united the observable and the abstract to establish a molecular–kinetic theory of heat.
Janus particles
Authors: Granick Steve , Jiang Shan , Chen Qian
Published: July 2009

What if one could see under a microscope how molecules fit together? Tiny Janus spheres, whose chemical makeup differs between two sides, represent an exciting step in that direction.
What is science?
Authors: Quinn Helen
Published: July 2009

Helen Quinn is a theoretical particle physicist at SLAC. Throughout her career, she has been passionately involved in science education and public understanding of science.
Infectious tolerance via the consumption of essential amino acids and mTOR signaling
Authors: Cobbold Stephen P. , Adams Elizabeth , Farquhar Claire A. , Nolan Kathleen F. , Howie Duncan , Lui Kathy O. , Fairchild Paul J. , Mellor Andrew L. , Ron David , Waldmann Herman
Published: July 2009

Infectious tolerance describes the process of CD4
+
regulatory T cells (Tregs) converting naïve T cells to become additional Tregs. We show that antigen-specific Tregs induce, within skin grafts and dendritic cells, the expression of enzymes that consume at least 5 different essential amino acids (EAAs). T cells fail to proliferate in response to antigen when any 1, or more, of these EAAs are limiting, which is associated with a reduced mammalian target of rapamycin (mTOR) signaling. Inhibition of the mTOR pathway by limiting EAAs, or by specific inhibitors, induces the Treg-specific transcription factor forkhead box P3, which depends on both T cell receptor activation and synergy with TGF-β.
Ethical perspective on quality of care: the nature of ethical dilemmas identified by new graduate and experienced speech pathologists
Authors: Kenny Belinda J. , Lincoln Michelle , Blyth Katrina , Balandin Susan
Published: July 2009

Background: Speech pathologists are confronted by ethical issues when they need to make decisions about client care, address team conflict, and fulfil the range of duties and responsibilities required of health professionals. However, there has been little research into the specific nature of ethical dilemmas experienced by speech pathologists and whether the nature of ethical conflict changes as they acquire experience in the professional workforce. Speech pathologists' perceptions of ethical issues provide insight into factors impacting upon quality of care in contemporary healthcare settings.

Aims: To describe, compare, and contrast the nature of ethical dilemmas identified by new graduate and experienced speech pathologists.

Methods & Procedures: A narrative methodology was used to explore the ethical dilemmas that participants experienced in the professional work place. Primary data were collected through in‐depth interviews with ten new graduate and ten experienced speech pathologists in their work settings. During these interviews, participants were asked to ‘tell the story’ of ethical dilemmas they identified at work.

Outcomes & Results: An ethical story was constructed for each participant based upon keywords and concepts from interview transcripts. These keywords and concepts were coded into group themes that reflected the nature of ethical dilemmas experienced by new graduate versus experienced speech pathologists. Comparing the results of thematic analysis for both groups of participant revealed similarities and differences in ethical dilemmas identified by new graduate and experienced health professionals.

Conclusions & Implications: Participants identified ethical dilemmas in the professional practice areas of client management, professional relationships, service delivery, and personal/professional identity. Themes from new graduates' ethical dilemmas included: making safe choices; avoiding conflict, following service delivery rules, and building professional identity. Experienced speech pathologists' themes included: life choices, adapting policies, and professional status. Supporting client autonomy, managing risk taking, adopting fair service delivery policies, and supporting health professionals' ethical practice are part of ethical quality care. The results support the need for an increased focus on ethical practice in the workplace and further support for speech pathologists experiencing ethical conflict in response to service delivery policies.
Auditory processing disorder in relation to developmental disorders of language, communication and attention: a review and critique
Authors: Dawes Piers , Bishop Dorothy
Published: July 2009

Background: Auditory Processing Disorder (APD) does not feature in mainstream diagnostic classifications such as the Diagnostic and Statistical Manual of Mental Disorders, 4th Edition (DSM‐IV), but is frequently diagnosed in the United States, Australia and New Zealand, and is becoming more frequently diagnosed in the United Kingdom.

Aims: To familiarize readers with current controversies surrounding APD, with an emphasis on how APD might be conceptualized in relation to language and reading problems, attentional problems and autistic spectrum disorders.

Methods & Procedures: Different conceptual and diagnostic approaches adopted by audiologists and psychologists can lead to a confusing picture whereby the child who is regarded as having a specific learning disability by one group of experts may be given an APD diagnosis by another. While this could be indicative of co‐morbidity, there are concerns that different professional groups are using different labels for the same symptoms.

Conclusions & Implications: APD, as currently diagnosed, is not a coherent category, but that rather than abandoning the construct, we need to develop improved methods for assessment and diagnosis, with a focus on interdisciplinary evaluation.
The primary divisions of life: a phylogenomic approach employing composition-heterogeneous methods
Authors: Foster Peter G. , Cox Cymon J. , Embley T. Martin
Published: July 2009

The three-domains tree, which depicts eukaryotes and archaebacteria as monophyletic sister groups, is the dominant model for early eukaryotic evolution. By contrast, the ‘eocyte hypothesis’, where eukaryotes are proposed to have originated from within the archaebacteria as sister to the Crenarchaeota (also called the eocytes), has been largely neglected in the literature. We have investigated support for these two competing hypotheses from molecular sequence data using methods that attempt to accommodate the across-site compositional heterogeneity and across-tree compositional and rate matrix heterogeneity that are manifest features of these data. When ribosomal RNA genes were analysed using standard methods that do not adequately model these kinds of heterogeneity, the three-domains tree was supported. However, this support was eroded or lost when composition-heterogeneous models were used, with concomitant increase in support for the eocyte tree for eukaryotic origins. Analysis of combined amino acid sequences from 41 protein-coding genes supported the eocyte tree, whether or not composition-heterogeneous models were used. The possible effects of substitutional saturation of our data were examined using simulation; these results suggested that saturation is delayed by among-site rate variation in the sequences, and that phylogenetic signal for ancient relationships is plausibly present in these data.
The not so universal tree of life
or
the place of viruses in the living world
Authors: Brüssow Harald
Published: July 2009

Darwin provided a great unifying theory for biology; its visual expression is the universal tree of life. The tree concept is challenged by the occurrence of horizontal gene transfer and—as summarized in this review—by the omission of viruses. Microbial ecologists have demonstrated that viruses are the most numerous biological entities on earth, outnumbering cells by a factor of 10. Viral genomics have revealed an unexpected size and distinctness of the viral DNA sequence space. Comparative genomics has shown elements of vertical evolution in some groups of viruses. Furthermore, structural biology has demonstrated links between viruses infecting the three domains of life pointing to a very ancient origin of viruses. However, presently viruses do not find a place on the universal tree of life, which is thus only a tree of cellular life. In view of the polythetic nature of current life definitions, viruses cannot be dismissed as non-living material. On earth we have therefore at least two large DNA sequence spaces, one represented by capsid-encoding viruses and another by ribosome-encoding cells. Despite their probable distinct evolutionary origin, both spheres were and are connected by intensive two-way gene transfers.
Gene and genome trees conflict at many levels
Authors: Haggerty Leanne S. , Martin Fergal J. , Fitzpatrick David A. , McInerney James O.
Published: July 2009

Horizontal gene transfer (HGT) plays a significant role in microbial evolution. It can accelerate the adaptation of an organism, it can generate new metabolic pathways and it can completely remodel an organism's genome. We examine 27 closely related genomes from the YESS group of gamma proteobacteria and a variety of four-taxon datasets from a diverse range of prokaryotes in order to explore the kinds of effects HGT has had on these organisms.
Egalitarian recruitment of localized mRNAs: Figure 1.
Authors: Nashchekin Dmitry , St Johnston Daniel
Published: July 2009

Bicaudal-D (Bic-D) and Egalitarian (Egl) are required for the dynein-dependent localization of many mRNAs in Drosophila, but the mRNAs show no obvious sequence similarities, and the RNA-binding proteins that recognize them and link them to dynein are not known. In this issue of Genes & Development, Dienstbier and colleagues (pp. 1546–1558) present evidence that the elusive RNA-binding protein is Egl itself. As well as linking mRNA to dynein, they show that Egl also activates dynein motility by binding Bic-D and the dynein light chain.
Multiplicity of DNA end resection machineries in chromosome break repair
Authors: Niu Hengyao , Raynard Steven , Sung Patrick
Published: July 2009

DNA end resection is critical for chromosome break repair by homologous recombination and influences the efficiency of repair by nonhomologous DNA end joining. An elegant study by Sinha and colleagues (pp. 1423–1437) published in the June 15, 2009, issue of Genes & Development identified a novel mycobacterial DNA end resection protein complex, AdnAB, that harbors dual DNA motor and dual nuclease functions. Sinha and colleagues also demonstrated that the DNA end-binding protein complex Ku regulates the activity of AdnAB.
Comparing Programs and Methods to Use for Global Multiple Sequence Alignment
Authors: Mount David W.
Published: July 2009

INTRODUCTION

It is difficult to find a global optimal alignment of more than two sequences (and, especially, more than three) that includes matches, mismatches, and gaps and that takes into account the degree of variation in all of the sequences at the same time. Thus, approximate methods are used, such as progressive global alignment, iterative global alignment, alignments based on locally conserved patterns found in the same order in the sequences, statistical methods that generate probabilistic models of the sequences, and multiple sequence alignments produced by graph-based methods. When 10 or more sequences are being compared, it is common to begin by determining sequence similarities between all pairs of sequences in the set. A variety of methods are then available to cluster the sequences into the most related groups or into a phylogenetic tree. This article discusses several of these methods and provides data that compare their utility under various conditions.
Phenotypic Analysis of Arabidopsis Mutants: Bacterial Pathogens
Authors: Weigel Detlef , Glazebrook Jane
Published: July 2009

INTRODUCTION

The most commonly used bacterial pathogen of Arabidopsis is Pseudomonas syringae, pathovar tomato strain DC3000 or pathovar maculicola strain ES4326. Plants used for infection with P. syringae should be grown on a short-day light cycle, so that they develop large leaves. For consistent results, it is important that the plants are watered well and do not experience any abiotic stresses. The plants should be grown and tested in a temperature- and humidity-controlled growth chamber, because the extent of bacterial growth is highly dependent on both factors. Gene-for-gene resistance to P. syringae is usually accompanied by the hypersensitive response (HR), a form of localized cell death that occurs in response to pathogen challenge. P. syringae strains carrying one of the avirulence genes avrRpt2, avrRpm1, avrB, avrPphB, and avrRps4 trigger the HR in wild-type Columbia. Other ecotypes may lack one or more of the R genes needed for recognition of these avirulence genes. Bacterial growth can be monitored by grinding up infected tissue, plating serial dilutions on King’s B medium, and counting colonies. This protocol describes methods for preparing bacterial cultures, inoculating plants, testing the HR, and assessing bacterial growth.
Collecting Live Ant Specimens (Colony Sampling)
Authors: Smith Chris R. , Tschinkel Walter R.
Published: July 2009

INTRODUCTION

Because of the great diversity of ants, it is difficult to give a single protocol for the collection of live specimens. Ant body size can be very small or extremely large; the ants can be hard or soft, sting or spray toxic chemicals, live in the open or in hard-to-reach places; and colony size can range from tens of individuals to millions. Thus, collection techniques must be tailored to each particular species. In particular, caution must always be taken when dealing with stinging species, and symptoms and basic first-aid measures, especially for the treatment of anaphylactic shock, should be reviewed before beginning fieldwork. Nonetheless, many species are collectable as whole colonies. This protocol reviews some basic techniques for collecting ground-nesting species and describes how to collect whole live colonies (with queens), which are necessary for long-term laboratory studies and addressing questions of social organization and ecology.
Ecological Sampling of Ants: Competition and Biodiversity
Authors: Smith Chris R.
Published: July 2009

INTRODUCTION

Ants are among the most dominant taxa in terrestrial ecosystems, despite their small individual size. Furthermore, they are a hyperdiverse family with an estimated 20,000 species. Together, these two properties make ants a model for ecological interactions (specifically competition) and biodiversity estimation. Although there are many means of measuring diversity, the two most common among myrmecologists are baiting and pitfall trapping. Pitfall traps provide an almost unbiased estimate of the ground foraging community, whereas baiting allows the estimation of ecological dominance and the competitive outcomes between species. This protocol describes an approach to assay both abundance (pitfall traps) and ecological interactions (baits) in the same community.
Stable Isotope and Elemental Analysis in Ants: Figure 1.
Authors: Smith Chris R. , Tillberg Chadwick V.
Published: July 2009

INTRODUCTION

Over the past 20 yr, the use of stable isotopes to infer feeding ecology and the examination of how energetic and elemental exchanges are affected by and affect life (ecological stoichiometry) have gained momentum. The ecological diversity of ants makes them interesting models to explore dietary ecology and their role in food webs. Moreover, their ecological dominance in most habitats facilitates sampling. The protocol described here will produce samples adequate for submission to most labs that specialize in high-throughput analysis of stable isotopes; one should check with any particular lab for specific submission instructions. Note, however, that this protocol is designed specifically for the quantification of the natural abundance of stable isotopes; it does not cover the preparation of trace samples.
Ant Fat Extraction with a Soxhlet Extractor: Figure 1.
Authors: Smith Chris R. , Tschinkel Walter R.
Published: July 2009

INTRODUCTION

Stored fat can be informative about the relative age of an ant, its nutritional status, and the nutritional status of the colony. Several methods are available for the quantification of stored fat. Before starting a project involving fat extraction, investigators should weigh the advantages and disadvantages of different methods in order to choose the one that is best suited to the question being addressed. This protocol, although not as accurate as some alternatives, facilitates the rapid quantification of many individuals.
Juvenile Hormone Extraction, Purification, and Quantification in Ants
Authors: Brent Colin , Dolezal Adam
Published: July 2009

INTRODUCTION

Juvenile hormone (JH) is an important insect hormone known to have many effects on development, reproduction, and behavior in both solitary and social insects. A number of questions using ants as a model involve JH. This procedure allows for quantification of circulating levels of JH III, which can be an important factor in many questions relating to insect research. The JH III is extracted from a subject, purified, and converted to a d3-methoxyhydrin derivative that can be quantified by gas chromatography-mass spectrometry (GC-MS). The major advantages of this protocol are its high resolution, and its ability to quantify significant differences between relatively small quantities of the hormone. Its major limitations are the time necessary to process samples, its relatively high cost, and maintaining the sensitivity of the equipment.
Ant Ecdysteroid Extraction and Radioimmunoassay
Authors: Brent Colin , Dolezal Adam
Published: July 2009

INTRODUCTION

Ecdysteroids are a group of steroid compounds present in many plant and invertebrate species. In arthropods, they function primarily as hormones involved in the regulation of molting. This protocol describes how to extract ecdysteroid hormones from ant specimens and subsequently quantify circulating levels of the hormone. The hormone can be extracted from hemolymph or from whole-body homogenates of insects and quantified by radioimmunoassay.
Phase-Unknown Linkage Mapping in Ants: Figure 1.
Authors: Gadau Jürgen
Published: July 2009

INTRODUCTION

To create a genetic linkage map of an ant genome, the phase of a marker (i.e., which marker/allele came from the grandmother and which came from the grandfather of the individuals used for linkage mapping) must be known. However, field colonies contain only two generations: the queen(s) and their offspring. Normally, virgin queens disperse from their nest, mate with one or multiple males who die after mating, and start a new colony. A new reproductive brood (i.e., virgin queens and males) is usually produced after colony establishment, which can take from 6 mo to 3-5 yr. Hence, determining the phase of markers from field samples is impossible because the grandparents of a reproductive queen are no longer available for genetic analysis. Ants raised in the laboratory are likewise unsuitable for such analyses, because most ants cannot be bred regularly in the laboratory, and attempts to inseminate ant queens artificially have not been successful. However, three features facilitate “phase-unknown” linkage mapping for any ant (or other social hymenopteran) species, which is described here: (1) Mature colonies usually produce many reproductive offspring during a short period of time, which allows for the collection of a good-sized mapping population (>100 males) from a field colony; (2) Ants have a haplodiploid sex determination system (i.e., males are haploid and females diploid); (3) Queens produce males parthenogenetically. Thus, because they have no father, only those markers for which the queen is heterozygous are expected to segregate 1:1 in her male offspring.
Preparation of High-Molecular-Weight DNA from Drosophila Embryos: Figure 1.
Authors: Karpen Gary H.
Published: July 2009

INTRODUCTION

Standard methods for extracting DNA from cells or organisms (e.g., phenol extraction and ethanol precipitation) produce fragments with an average size of 50-200 kb under optimal conditions. The shearing forces that are applied to DNA in solution during mechanical vortexing or mixing and pipetting produce frequent double-stranded breaks. To prepare high-molecular-weight (HMW) DNA, it is necessary to guard against such damaging forces by performing all extractions and manipulations on DNA that is embedded within a protective matrix. Preparation of HMW DNA from Drosophila embryos is described in detail here because, in our hands, it is the simplest and most reliable protocol and can be used for large- or small-scale preparations. The overall strategy is to purify nuclei, gently embed them in molten agarose, and then extract proteins and perform other enzymatic reactions by transferring the solidified agarose block into the appropriate solutions. Salts, soaps, and enzymes act on the DNA by diffusing through the agarose matrix, while the matrix protects the DNA from shearing forces.
Using Hidden Markov Models to Align Multiple Sequences
Authors: Mount David W.
Published: July 2009

INTRODUCTION

A hidden Markov model (HMM) is a probabilistic model of a multiple sequence alignment (msa) of proteins. In the model, each column of symbols in the alignment is represented by a frequency distribution of the symbols (called a “state”), and insertions and deletions are represented by other states. One moves through the model along a particular path from state to state in a Markov chain (i.e., random choice of next move), trying to match a given sequence. The next matching symbol is chosen from each state, recording its probability (frequency) and also the probability of going to that state from a previous one (the transition probability). State and transition probabilities are multiplied to obtain a probability of the given sequence. The hidden nature of the HMM is due to the lack of information about the value of a specific state, which is instead represented by a probability distribution over all possible values. This article discusses the advantages and disadvantages of HMMs in msa and presents algorithms for calculating an HMM and the conditions for producing the best HMM.
Using Multiple Sequence Alignment Editors and Formatters: Figure 1.
Authors: Mount David W.
Published: July 2009

INTRODUCTION

Sequence alignment editors enable the user to manually edit a multiple sequence alignment (msa) in order to obtain a more reasonable or expected alignment. Editors allow sequences to be reordered and/or modified using the computer’s cut and paste commands. They are designed to accept various msa formats and to provide the output file in a suitable user-designated format. Sequence formatters provide various output formatting options, such as color and shading schemes to enhance visualization of residue alignments. The formatters can output files in Postscript, EPS, RTF, and other widely recognized formats, while accepting the standard input formats, such as MSF, ALN, and FASTA. This article introduces a number of sequence alignment editors and formatters, and provides links to sites where they can be found.
The PLASTID DIVISION1 and 2 Components of the Chloroplast Division Machinery Determine the Rate of Chloroplast Division in Land Plant Cell Differentiation
Authors: Okazaki Kumiko , Kabeya Yukihiro , Suzuki Kenji , Mori Toshiyuki , Ichikawa Takanari , Matsui Minami , Nakanishi Hiromitsu , Miyagishima Shin-ya
Published: July 2009

In most algae, the chloroplast division rate is held constant to maintain the proper number of chloroplasts per cell. By contrast, land plants evolved cell and chloroplast differentiation systems in which the size and number of chloroplasts change along with their respective cellular function by regulation of the division rate. Here, we show that PLASTID DIVISION (PDV) proteins, land plant–specific components of the division apparatus, determine the rate of chloroplast division. Overexpression of PDV proteins in the angiosperm Arabidopsis thaliana and the moss Physcomitrella patens increased the number but decreased the size of chloroplasts; reduction of PDV levels resulted in the opposite effect. The level of PDV proteins, but not other division components, decreased during leaf development, during which the chloroplast division rate also decreased. Exogenous cytokinins or overexpression of the cytokinin-responsive transcription factor CYTOKININ RESPONSE FACTOR2 increased the chloroplast division rate, where PDV proteins, but not other components of the division apparatus, were upregulated. These results suggest that the integration of PDV proteins into the division machinery enabled land plant cells to change chloroplast size and number in accord with the fate of cell differentiation.
Wettability of Silica Substrates by Silver–Copper Based Brazing Alloys inVacuo
Authors: López‐Cuevas Jorge , Jones Howard , Atkinson Helen V.
Published: July 2009

The sessile drop method has been used to determine the time dependence of the contact angle at 850°C in vacuo for Ag–28 wt% Cu, Ag–35 wt% Cu–1.5 wt% Ti, and Ag–27 wt% Cu–12 wt% In–2 wt% Ti on vitreous and devitrified fused quartz substrates. Nonwetting behavior (θ > 90°) was observed for Ag–28 wt% Cu on both substrates with no evident effect of time at temperature. The silica substrate structure, whether crystalline or amorphous, as well as its surface condition, whether smooth or rough, made no significant difference. In contrast, with Ag–35 wt% Cu–1.5 wt% Ti and Ag–27 wt% Cu–12 wt% In–2 wt% Ti the contact angle continuously decreased with time for both silica substrates, and the structure and surface condition of the substrates had a negligible effect in the case of Ag–27 wt% Cu–12 wt% In–2 wt% Ti, which produced essentially the same contact angles on both silica substrates at a given time of hold at 850°C. The contact angles produced by Ag–35 wt% Cu–1.5 wt% Ti on devitrified fused quartz were consistently higher than those produced on the vitreous substrates, with increasing holding time at 850°C. This is attributable to the presence of extensive cracks in the α‐cristobalite layer at the surface of the devitrified substrates, which obstruct wetting and spreading. These results, when correlated with the wettability of preoxidized silicon carbide by the same alloys reported in previous work, could account for the adverse effect on wetting of the high‐temperature silica films formed on the surface of the SiC in that work.