bluuebunny/crossref_metadata_2025 huggingface dataset:
Response of forest soil Acari to prescribed fire following stand structure manipulation in the southern Cascade RangeThis article is one of a selection of papers from the Special Forum on Ecological Studies in Interior Ponderosa Pine — First Findings from Blacks Mountain Interdisciplinary Research.
Authors: Camann Michael A. , Gillette Nancy E. , Lamoncha Karen L. , Mori Sylvia R.
Published: May 2008

We studied responses of Acari, especially oribatid mites, to prescribed low-intensity fire in an east side pine site in the southern Cascade Range in California. We compared oribatid population and assemblage responses to prescribed fire in stands that had been selectively logged to enhance old growth characteristics, in logged stands to minimize old growth characteristics, and in undisturbed forest reference stands. Low-intensity prescribed fire altered habitat characteristics within the organic layer of forest soil. Acarine populations declined following prescribed fire, and oribatid losses accounted for two thirds of that decline. Individual oribatid species responded differently to prescribed fire, with a few populations increasing after fire but most declining. The prescribed fire also altered oribatid assemblages, reducing species richness and species diversity and modifying assemblage dominance relationships. We also identified several oribatid taxa that were potential indicator species of fire effects upon forest soil fauna. Finally, our results suggested that oribatid responses to fire were intensified by stand alteration and especially by removal of old growth structural characteristics. Decline in oribatid abundance, species richness and diversity, and loss of equilibrium dominance relationships was greatest in the low structural diversity plots.
Stability of the large tree component in treated and untreated late-seral interior ponderosa pine standsThis article is one of a selection of papers from the Special Forum on Ecological Studies in Interior Ponderosa Pine — First Findings from Blacks Mountain Interdisciplinary Research.
Authors: Ritchie Martin W. , Wing Brian M. , Hamilton Todd A.
Published: May 2008

Ponderosa pine ( Pinus ponderosa Dougl. ex P. & C. Laws.) stands with late-seral features are found infrequently, owing to past management activities throughout western North America. Thus, management objectives often focus on maintaining existing late-seral stands. Observations over a 65 year period of stands with no past history of harvest showed substantial ingrowth in the smaller diameter classes and elevated rates of mortality among the largest mature trees in the stand. Adjacent stands, with combinations of thinning and prescribed fire, had far fewer high-risk mature trees and generally lower rates of mortality after treatment. Forecasts using individual-tree diameter growth and mortality models suggest that observed declines in these stands with remaining old trees and a dense understory will continue in the absence of any treatment. Increased vigor in thinned stands appeared to be offset by an increase in mortality of large trees when thinning was followed by prescribed fire.
Blacks Mountain Experimental Forest: bark beetle responses to differences in forest structure and the application of prescribed fire in interior ponderosa pineThis article is one of a selection of papers from the Special Forum on Ecological Studies in Interior Ponderosa Pine — First Findings from Blacks Mountain Interdisciplinary Research.
Authors: Fettig Christopher J. , Borys Robert R. , McKelvey Stephen R. , Dabney Christopher P.
Published: May 2008

Mechanical thinning and the application of prescribed fire are commonly used tools in the restoration of fire-adapted forest ecosystems. However, few studies have explored their effects on subsequent amounts of bark beetle caused tree mortality in interior ponderosa pine, Pinus ponderosa Dougl. ex P. & C. Laws. var. ponderosa. In this study, we examined bark beetle responses to creation of midseral (low diversity) and late-seral stages (high diversity) and the application of prescribed fire on 12 experimental units ranging in size from 76 to 136 ha. A total of 9500 (5.0% of all trees) Pinus and Abies trees died 2 years after treatment of which 28.8% (2733 trees) was attributed to bark beetle colonization. No significant difference in the mean percentage of trees colonized by bark beetles was found between low diversity and high diversity. The application of prescribed fire resulted in significant increases in bark beetle caused tree mortality (all species) and for western pine beetle, Dendroctonus brevicomis LeConte, mountain pine beetle, Dendroctonus ponderosae Hopkins, Ips spp., and fir engraver, Scolytus ventralis LeConte, individually. Approximately 85.6% (2339 trees) of all bark beetle caused tree mortality occurred on burned split plots. The implications of these and other results to sustainable forest management are discussed.
Response of ground-dwelling spider assemblages to prescribed fire following stand structure manipulation in the southern Cascade RangeThis article is one of a selection of papers from the Special Forum on Ecological Studies in Interior Ponderosa Pine — First Findings from Blacks Mountain Interdisciplinary Research.
Authors: Gillette Nancy E. , Vetter Richard S. , Mori Sylvia R. , Rudolph Carline R. , Welty Dessa R.
Published: May 2008

We assessed spider (Arachnida: Araneae) responses to prescribed fire following stand structure treatments in ponderosa pine ( Pinus ponderosa Dougl. ex P. & C. Laws.) stands in the Cascade Range of California. Stands were logged or left untreated to create three levels of structural diversity. We logged one treatment to minimize old-growth characteristics (low diversity) and one to enhance old-growth characteristics (high diversity) and we used unlogged Research Natural Areas (RNAs) as old-growth, highest-diversity reference stands. We conducted low-intensity prescribed fire on half of each plot following harvest. Spider assemblages in unburned, logged stands were similar to one another but diverged from those in RNAs, with increased abundance, species richness, and diversity in more structurally diverse stands. Prescribed fire, which altered habitat in the organic soil layer where many spiders forage, resulted in altered spider assemblages and population declines in most plots. Fire generally reduced spider species richness, evenness, and diversity. Several taxa were potential indicators of fire and old-growth structure, and we discovered one species and one genus that were previously unknown. There was evidence that old-growth characteristics intensified the effects of fire on spider abundance. This outcome probably results from the deep litter layers in high-diversity stands and RNAs, which constituted greater fuel loads than low-diversity stands.
GENERALIZED UNCERTAINTY PRINCIPLE AND THERMODYNAMIC QUANTITIES OF THE ACHUCARRO–ORTIZ BLACK HOLE
Authors: ZHAO REN , WU YUE-QIN , ZHANG LI-CHUN
Published: May 2008

Recently, there has been much attention devoted to resolving the quantum corrections to the Bekenstein–Hawking entropy of a black hole. In this paper, we calculate the correction value of thermodynamic quantities of the Achucarro–Oritz black hole motivated by utilizing the generalized uncertainty principle. We obtain the Cardy–Verlinde formula after considering the correction.
UNIQUENESS OF THE McVITTIE SOLUTION AS PLANE SYMMETRIC SOURCELESS ELECTROMAGNETIC FIELD SPACETIMES
Authors: FEROZE TOOBA , QADIR ASGHAR , ZIAD M.
Published: May 2008

It is proved that plane symmetric Lorentzian manifolds representing a sourceless electromagnetic field admit only a four-dimensional maximal symmetry group and consist of only the McVittie5 spacetime and its non-static analogue.4
ON THE CONSTRAINT ALGEBRA STRUCTURE FOR SYSTEMS WITH GAUGE TRANSFORMATIONS DEPENDING ON HIGHER ORDER TIME DERIVATIVES OF THE GAUGE PARAMETERS
Authors: STOILOV M. N.
Published: May 2008

In the Hamiltonian approach to the gauge models, the constraints on the one hand and the Hamiltonian and constraints on the other hand have to form closed algebras with respect to the Poisson brackets. We investigate the consequences of this requirement when the dynamical system is invariant under gauge transformations with higher order time derivatives of the gauge parameter. It is demonstrated that the required algebraic structure leads to rigid relations in the constraint algebra.
BRANE INDUCED GRAVITY: CODIMENSION-2
Authors: KALOPER NEMANJA
Published: May 2008

We review the results of arXiv:hep-th/0703190, on brane induced gravity (BIG) in 6D. Among a large diversity of regulated codimension-2 branes, we find that for near-critical tension branes live inside very deep throats which efficiently compactify the angular dimension. In there, 4D gravity first changes to 5D, and only later to 6D. The crossover from 4D to 5D is independent of the tension, but the crossover from 5D to 6D is not. This shows how the vacuum energy problem manifests in BIG: instead of tuning vacuum energy to adjust the 4D curvature, generically one must tune it to get the desired crossover scales and the hierarchy between the scales governing the 4D → 5D → 6D transitions. In the near-critical limit, linearized perturbation theory remains under control below the crossover scale, and we find that linearized gravity around the vacuum looks like a scalar–tensor theory.
CHRONOMETRIC INVARIANCE AND STRING THEORY
Authors: POLLOCK M. D.
Published: May 2008

The Einstein–Hilbert Lagrangian R is expressed in terms of the chronometrically invariant quantities introduced by Zel'manov for an arbitrary four-dimensional metric gij. The chronometrically invariant three-space is the physical space γαβ = -gαβ+e2ϕ γαγβ, where e 2ϕ = g00 and γα = g0α/g00, and whose determinant is h. The momentum canonically conjugate to γαβ is [Formula: see text], where [Formula: see text] and ∂t≡ e -ϕ∂0 is the chronometrically invariant derivative with respect to time. The Wheeler–DeWitt equation for the wave function Ψ is derived. For a stationary space-time, such as the Kerr metric, παβ vanishes, implying that there is then no dynamics. The most symmetric, chronometrically-invariant space, obtained after setting ϕ = γα = 0, is [Formula: see text], where δαβ is constant and has curvature k. From the Friedmann and Raychaudhuri equations, we find that λ is constant only if k=1 and the source is a perfect fluid of energy-density ρ and pressure p=(γ-1)ρ, with adiabatic index γ=2/3, which is the value for a random ensemble of strings, thus yielding a three-dimensional de Sitter space embedded in four-dimensional space-time. Furthermore, Ψ is only invariant under the time-reversal operator [Formula: see text] if γ=2/(2n-1), where n is a positive integer, the first two values n=1,2 defining the high-temperature and low-temperature limits ρ ~ T±2, respectively, of the heterotic superstring theory, which are thus dual to one another in the sense T↔1/2π2α′T.
APSIS: AN ARTIFICIAL PLANETARY SYSTEM IN SPACE TO PROBE EXTRA-DIMENSIONAL GRAVITY AND MOND
Authors: SAHNI VARUN , SHTANOV YURI
Published: May 2008

A proposal is made to test Newton's inverse-square law using the perihelion shift of test masses (planets) in free fall within a spacecraft located at the Earth–Sun L2 point. Such an artificial planetary system in space (APSIS) will operate in a drag-free environment with controlled experimental conditions and minimal interference from terrestrial sources of contamination. We demonstrate that such a space experiment can probe the presence of a "hidden" fifth dimension on the scale of a micron, if the periapsis shift of a "planet" can be measured to sub-arc-second accuracy. Some suggestions for spacecraft design are made.
NON-NEWTONIAN BEHAVIOR IN WEAK FIELD GENERAL RELATIVITY FOR EXTENDED ROTATING SOURCES
Authors: BALASIN H. , GRUMILLER D.
Published: May 2008

Exact stationary axially symmetric solutions to the four-dimensional Einstein equations with corotating pressureless perfect fluid sources are studied. A particular solution with an approximately flat rotation curve is discussed in some detail. We find that simple Newtonian arguments overestimate the amount of matter needed to explain such curves by more than 30%. The crucial insight gained by this model is that the Newtonian approximation breaks down in an extended rotating region, even though it is valid locally everywhere. No conflict with solar system tests arises.
THE ROLE OF THE PLANCK SCALE IN BLACK HOLE RADIANCE
Authors: AGULLÓ IVÁN , NAVARRO-SALAS JOSÉ , OLMO GONZALO J. , PARKER LEONARD
Published: May 2008

Lorentz invariance plays a pivotal role in the derivation of the Hawking effect, which crucially requires an integration in arbitrarily small distances or, equivalently, in unbounded energies. New physics at the Planck scale could, therefore, potentially modify the emission spectrum. We argue, however, that the kinematic invariance can be deformed in such a way that the thermal spectrum remains insensitive to trans-Planckian physics.
THE RETURN OF THE MEMBRANE PARADIGM? BLACK HOLES AND STRINGS IN THE WATER TAP
Authors: CARDOSO VITOR , DIAS ÓSCAR J. C. , GUALTIERI LEONARDO
Published: May 2008

Several general arguments indicate that the event horizon behaves as a stretched membrane. We propose using this relation to understand the gravity and dynamics of black objects in higher dimensions. We provide evidence that:

(i) The gravitational Gregory–Laflamme instability has a classical counterpart in the Rayleigh–Plateau instability of fluids. Each known feature of the gravitational instability can be accounted for in the fluid model. These features include threshold mode, dispersion relation, time evolution and critical dimension of certain phase transitions. Thus, we argue that black strings break in much the same way as water from a faucet breaks up into small droplets.

(ii) General rotating black holes can also be understood with this analogy. In particular, instability and bifurcation diagrams for black objects can easily be inferred.

This correspondence can and should be used as a guiding tool for understanding and exploring the physics of gravity in higher dimensions.
SYMMETRIES, SINGULARITIES AND THE DE-EMERGENCE OF SPACE
Authors: DAMOUR THIBAULT , NICOLAI HERMANN
Published: May 2008

Recent work has revealed intriguing connections between a Belinsky–Khalatnikov–Lifshitz-type analysis of spacelike singularities in general relativity and certain infinite-dimensional Lie algebras, particularly the "maximally extended" hyperbolic Kac–Moody algebra E10. In this essay we argue that these results may lead to an entirely new understanding of the (quantum) nature of space(–time) at the Planck scale, and hence — via an effective "de-emergence" of space near the singularity — to a novel mechanism for achieving background independence in quantum gravity.
GRAVITATIONAL ANOMALIES: A RECIPE FOR HAWKING RADIATION
Authors: DAS SAURYA , ROBINSON SEAN P. , VAGENAS ELIAS C.
Published: May 2008

We explore the method of Robinson and Wilczek for deriving the Hawking temperature of a black hole. In this method, the Hawking radiation restores general covariance in an effective theory of near-horizon physics which otherwise exhibits a gravitational anomaly at the quantum level. The method has been shown to work for broad classes of black holes in arbitrary space–time dimensions. These include static black holes, accreting or evaporating black holes, charged black holes, rotating black holes, and even black rings. In the cases of charged and rotating black holes, the expected superradiant current is also reproduced.
BLACK HOLE NONEXTENSIVE ENTROPY: FORMATION PROCESSES SIGNALIZED BY GRAVITATIONAL WAVE EMISSION
Authors: DE OLIVEIRA H. P. , SOARES I. DAMIÃO
Published: May 2008

We show that gravitational wave emission, both in the linear approximation and in the full nonlinear regime of general relativity, gives a hint of black hole thermodynamic processes by which a black hole evolves emitting part of its perturbation in the form of gravitational waves and absorbing the remnant, reaching a final configuration with a larger entropy. The partition of energy in this process is constrained by the maximum entropy principle, and the final entropy obtained numerically is given as a distribution function of the efficiency of the process. The distribution function is in the realm of nonextensive thermostatistics with entropic index q ≃ 1/2, a result that is validated analytically by the linear approximation.
HOLOGRAPHY FROM LOOP QUANTUM GRAVITY
Authors: GAMBINI RODOLFO , PULLIN JORGE
Published: May 2008

We show that holography follows directly from the basic structure of spherically symmetric loop quantum gravity. The result is not dependent on detailed assumptions about the dynamics of the theory being considered. It ties strongly the amount of information contained in a region of space to the tight mathematical underpinnings of loop quantum geometry.
A COVARIANT ROAD TO SPATIAL AVERAGING IN COSMOLOGY: SCALAR CORRECTIONS TO THE COSMOLOGICAL EQUATIONS
Authors: PARANJAPE ASEEM
Published: May 2008

A consistent approach to cosmology requires an explicit averaging of the Einstein equations, to describe a homogeneous and isotropic geometry. Such an averaging will in general modify the Einstein equations. The averaging procedure due to Buchert has attracted considerable attention recently since it offers the tantalizing hope of explaining the phenomenon of dark energy through such corrections. This approach has been criticized, however, on the grounds that its effects may be gauge artifacts. We apply the fully covariant formalism of Zalaletdinov's macroscopic gravity and show that, after making some essential gauge choices, the cosmological equations receive space–time scalar corrections which are therefore observable in principle, and further, that the broad structure of these corrections is identical to those derived by Buchert.
THE INEVITABLE NONLINEARITY OF QUANTUM GRAVITY FALSIFIES THE MANY-WORLDS INTERPRETATION OF QUANTUM MECHANICS
Authors: SINGH T. P.
Published: May 2008

There are fundamental reasons why there should exist a reformulation of quantum mechanics which does not refer to a classical space–time manifold. It follows that quantum mechanics as we know it is a limiting case of a more general nonlinear quantum theory, with the nonlinearity becoming significant at the Planck mass/energy scale. This nonlinearity is responsible for a dynamically induced collapse of the wave function, during a quantum measurement, and it hence falsifies the many-worlds interpretation of quantum mechanics. We illustrate this conclusion using a mathematical model based on a generalized Doebner–Goldin equation. The non-Hermitian part of the Hamiltonian in this norm-preserving, nonlinear, Schrödinger equation dominates during a quantum measurement, and leads to a breakdown of linear superposition.
A NEW LOOK AT THE BIG BANG
Authors: WESSON PAUL S.
Published: May 2008

We give a mathematically exact and physically faithful embedding of curved 4D cosmology in a flat 5D space, thereby enabling visualization of the big bang in a new and informative way. In fact, in unified theories of fields and particles with real extra dimensions, it is possible to dispense with the initial singularity.
DARK ENERGY: A UNIFYING VIEW
Authors: ZIMDAHL WINFRIED
Published: May 2008

Different models of the cosmic substratum which pretend to describe the present stage of accelerated expansion of the Universe, like the ΛCDM model or the Chaplygin gas, can be seen as special realizations of a holographic dark energy cosmology if the option of an interaction between pressureless dark matter and dark energy is taken seriously. The corresponding interaction strength parameter plays the role of a cosmological constant. Differences occur at the perturbative level. In particular, the pressure perturbations are intrinsically nonadiabatic.
SYMMETRIES, HORIZONS AND BLACK HOLE ENTROPY
Authors: CARLIP S.
Published: May 2008

Black holes behave as thermodynamic systems, and a central task of any quantum theory of gravity is to explain these thermal properties. A statistical-mechanical description of black hole entropy once seemed remote, but today we suffer an embarrassment of riches: despite counting very different states, many inequivalent approaches to quantum gravity obtain identical results. Such "universality" may reflect an underlying two-dimensional conformal symmetry near the horizon, which can be powerful enough to control the thermal characteristics independent of other details of the theory. This picture suggests an elegant description of the relevant degrees of freedom as Goldstone-boson-like excitations arising from symmetry breaking by the conformal anomaly.
HOW BLACK HOLES FORM IN HIGH ENERGY COLLISIONS
Authors: KALOPER NEMANJA , TERNING JOHN
Published: May 2008

We elucidate how black holes form in trans-Planckian collisions. In the rest frame of one of the incident particles, the gravitational field of the other, which is rapidly moving, looks like a gravitational shock wave. The shock wave focuses the target particle down to a much smaller impact parameter. In turn, the gravitational field of the target particle captures the projectile when the resultant impact parameter is smaller than its own Schwarzschild radius, forming a black hole. One can deduce this by referring to the original argument of escape velocities exceeding the speed of light, which Michell and Laplace used to discover the existence of black holes.
HEAVY ION COLLISIONS AND BLACK HOLE DYNAMICS
Authors: GUBSER STEVEN S.
Published: May 2008

Relativistic heavy ion collisions create a strongly coupled quark–gluon plasma. Some of the plasma's properties can be approximately understood in terms of a dual black hole. These properties include shear viscosity, thermalization time, and drag force on heavy quarks. They are hard to calculate from first principles in QCD.

Extracting predictions about quark–gluon plasmas from dual black holes mostly involves solving Einstein's equations and classical string equations of motion. AdS/CFT provides a translation from gravitational calculations to gauge theory predictions. The gauge theory to which the predictions apply is [Formula: see text] super-Yang–Mills theory. QCD is different in many respects from super-Yang–Mills, but it seems that its high temperature properties are similar enough for us to make some meaningful comparisons.
HOW MANY BLACK HOLES FIT ON THE HEAD OF A PIN?
Authors: DENEF FREDERIK , MOORE GREGORY W.
Published: May 2008

The Bekenstein–Hawking entropy of certain black holes can be computed microscopically in string theory by mapping the elusive problem of counting microstates of a strongly gravitating black hole to the tractable problem of counting microstates of a weakly coupled D-brane system, which has no event horizon, and indeed comfortably fits on the head of a pin. We show here that, contrary to widely held beliefs, the entropy of spherically symmetric black holes can easily be dwarfed by that of stationary multi-black-hole "molecules" of the same total charge and energy. Thus, the corresponding pin-sized D-brane systems do not even approximately count the microstates of a single black hole, but rather those of a zoo of entropically dominant multicentered configurations.
GETTING AWAY FROM NUMBERS: USING QUALITATIVE OBSERVATION FOR AGENT-BASED MODELING
Authors: YANG LU , GILBERT NIGEL
Published: May 2008

Although in many social sciences there is a radical division between studies based on quantitative (e.g. statistical) and qualitative (e.g. ethnographic) methodologies and their associated epistemological commitments, agent-based simulation fits into neither camp, and should be capable of modelling both quantitative and qualitative data. Nevertheless, most agent-based models (ABMs) are founded on quantitative data. This paper explores some of the methodological and practical problems involved in basing an ABM on qualitative participant observation and proposes some advice for modelers.
HISTORICAL SIMULATION: A STUDY OF CIVIL SERVICE EXAMINATIONS, THE FAMILY LINE AND CULTURAL CAPITAL IN CHINA
Authors: KURAHASHI SETSUYA , TERANO TAKAO
Published: May 2008

In this study, we investigate what would happen in a Chinese historical family line. We have analyzed a particular family line which had a great many candidates who passed the very tough examinations for Chinese government officials over 500 years. First, we studied the genealogical records Zokufu in China. Second, based on the study, we implemented an agent-based model with the family line network as an adjacency matrix, and the personal profile data as an attribution matrix. Third, using the "inverse simulation" technique, we optimized the agent-based model in order to fit the simulation profiles to the real profile data. From the intensive experiments, we have found that both grandfather and mother have a profound impact within a family in (1) transmitting cultural capital to the children, and (2) maintaining the norm system of the family. We conclude that advanced agent-based models are able to contribute to the discovery of new knowledge in the fields of historical science.
A MULTIAGENT SIMULATION OF A STYLIZED FRENCH LABOR MARKET: EMERGENCES AT THE MICRO LEVEL
Authors: LEWKOVICZ ZACH , KANT JEAN-DANIEL
Published: May 2008

The aim of this work is to design a multiagent system (MAS) simulation to model the French labor market. We departed from an economic model proposed by Cahuc and Carcillo to model the introduction of a new job contract into the labor market. We designed a specific methodology to convert this equation-based model to an agent-based model, and calibrated our MAS to reproduce the data found in the economic simulations. As we observed the same tendencies found in the former model, a new dimension emerged from the agent-based simulation: an increase of oscillations for the characteristic rates, revealing an increase of precariousness (job instability) due to the new type of contract. Moreover, our simulation enabled us to detect and correct some flaws of the Cobb–Douglas type of matching function. These encouraging results led us to continue in that direction, where several extensions of our model can be proposed, including the move to a large-scale simulation framework.
MARKET DIMENSIONALITY AND THE PROLIFERATION OF SMALL-SCALE FIRMS
Authors: GARCÍA-DÍAZ CÉSAR , VAN WITTELOOSTUIJN ARJEN , PÉLI GÁBOR
Published: May 2008

We build an agent-based computational model to study how the changing number of active product variants in a two-dimensional product space affects the performance of different firm types (i.e. large-scale and small-scale enterprises). We use an alternative approach to measure product space dimensionality, considering that dimensions may be a fraction of the Euclidean measure. The results confirm that high dimensionality gives advantage to small-scale firms. Additionally, we find that large-scale firms may also benefit from initial increasing dimensionality, since it allows a small degree of product differentiation and price discrimination.
USING ASSOCIATIVE NETWORKS TO REPRESENT ADOPTERS' BELIEFS IN A MULTIAGENT MODEL OF INNOVATION DIFFUSION
Authors: THIRIOT SAMUEL , KANT JEAN-DANIEL
Published: May 2008

A lot of agent-based models were built to study diffusion of innovations. In most of these models, beliefs of individuals about the innovation were not represented at all, or in a highly simplified way. In this paper, we argue that representing beliefs could help to tackle problematics identified for diffusion of innovations, like misunderstanding of information, which can lead to diffusion failure, or diffusion of linked inventions. We propose a formalization of beliefs and messages as associative networks. This representation allows one to study the social representations of innovations and to validate diffusion models against real data. It could also make models usable to analyze diffusion prior to the product launch. Our approach is illustrated by a simulation of iPod™ diffusion.
GROWINGQAWM: AN EVIDENCE-DRIVEN DECLARATIVE MODEL OF AFGHAN POWER STRUCTURES
Authors: GELLER ARMANDO , MOSS SCOTT
Published: May 2008

By means of evidence-driven and declaratively implemented social simulation, we grow qawm — solidarity networks in Afghanistan. The study of qawm lends insight into the structural and processual dynamics of Afghan society. In particular, we concentrate on the evolution of power structures. An agent-based computational model is presented whose ontology borrows from neopatrimonialism, a notion of power prevalent in contemporary conflicts. In this model, agents' structural arrangement, behavior and cognition are informed by qualitative data derived from case studies on Afghanistan. The simulation results suggest that the emergence of qawm and, hence, the fragmentation of Afghan society are systemic and lead to a constant drain of resources. Cross-validation between the simulated network and a target system network reveals that qawm exhibit small world characteristics.
PREDICTION OF CELL WALL SORTING SIGNALS IN GRAM-POSITIVE BACTERIA WITH A HIDDEN MARKOV MODEL: APPLICATION TO COMPLETE GENOMES
Authors: LITOU ZOI I. , BAGOS PANTELIS G. , TSIRIGOS KONSTANTINOS D. , LIAKOPOULOS THEODORE D. , HAMODRAKAS STAVROS J.
Published: May 2008

Surface proteins in Gram-positive bacteria are frequently implicated in virulence. We have focused on a group of extracellular cell wall-attached proteins (CWPs), containing an LPXTG motif for cleavage and covalent coupling to peptidoglycan by sortase enzymes. A hidden Markov model (HMM) approach for predicting the LPXTG-anchored cell wall proteins of Gram-positive bacteria was developed and compared against existing methods. The HMM model is parsimonious in terms of the number of freely estimated parameters, and it has proved to be very sensitive and specific in a training set of 55 experimentally verified LPXTG-anchored cell wall proteins as well as in reliable data sets of globular and transmembrane proteins. In order to identify such proteins in Gram-positive bacteria, a comprehensive analysis of 94 completely sequenced genomes has been performed. We identified, in total, 860 LPXTG-anchored cell wall proteins, a number that is significantly higher compared to those obtained by other available methods. Of these proteins, 237 are hypothetical proteins according to the annotation of SwissProt, and 88 had no homologs in the SwissProt database — this might be evidence that they are members of newly identified families of CWPs. The prediction tool, the database with the proteins identified in the genomes, and supplementary material are available online at .
ANALYSIS OF NONLINEAR RELATIONS BETWEEN EXPRESSION PROFILES BY THE PRINCIPAL CURVES OF ORIENTED-POINTS APPROACH
Authors: HUERTA MARIO , CEDANO JUAN , QUEROL ENRIQUE
Published: May 2008

DNA microarray technology enables high-throughput gene expression analysis and allows researchers to test the activity of thousands of genes at one time in multiple cellular conditions. This approach is based on principal curves of oriented points (PCOP) analysis and minimum spanning trees to analyze temporal and nontemporal series data to relate the genes. PCOP is a very suitable method, non–hypothesis-driven, for nonlinear relationship recognition between multivariable sets of data. Initially, a gene-relations tree is generated from the correlation between each pair of genes, calculated by PCOP analysis. Next, the researcher can introduce the query genes to be studied into the zoom-in operation, and the system selects the genes which connect the previously provided ones, beyond the activation pathways, using the minimum spanning tree. Thus, this zoom-in operation generates the nonlinear pattern of the intraset expression behavior for the new gene set. This inner expression pattern relates the query and selected genes to study their mutual interdependence in detail. This detailed information is especially useful in the biomedical environment, where such information is not possible to obtain by applying the current analytical methods.
TESTING DIFFERENTIAL EXPRESSION IN NONOVERLAPPING GENE PAIRS: A NEW PERSPECTIVE FOR THE EMPIRICAL BAYES METHOD
Authors: KLEBANOV LEV , QIU XING , YAKOVLEV ANDREI
Published: May 2008

The currently practiced methods of significance testing in microarray gene expression profiling are highly unstable and tend to be very low in power. These undesirable properties are due to the nature of multiple testing procedures, as well as extremely strong and long-ranged correlations between gene expression levels. In an earlier publication, we identified a special structure in gene expression data that produces a sequence of weakly dependent random variables. This structure, termed the δ-sequence, lies at the heart of a new methodology for selecting differentially expressed genes in nonoverlapping gene pairs. The proposed method has two distinct advantages: (1) it leads to dramatic gains in terms of the mean numbers of true and false discoveries, and in the stability of the results of testing; and (2) its outcomes are entirely free from the log-additive array-specific technical noise. We demonstrate the usefulness of this approach in conjunction with the nonparametric empirical Bayes method. The proposed modification of the empirical Bayes method leads to significant improvements in its performance. The new paradigm arising from the existence of the δ-sequence in biological data offers considerable scope for future developments in this area of methodological research.
Liposomes: Technologies and Analytical Applications
Authors: Jesorka Aldo , Orwar Owe
Published: May 2008

Liposomes are structurally and functionally some of the most versatile supramolecular assemblies in existence. Since the beginning of active research on lipid vesicles in 1965, the field has progressed enormously and applications are well established in several areas, such as drug and gene delivery. In the analytical sciences, liposomes serve a dual purpose: Either they are analytes, typically in quality-assessment procedures of liposome preparations, or they are functional components in a variety of new analytical systems. Liposome immunoassays, for example, benefit greatly from the amplification provided by encapsulated markers, and nanotube-interconnected liposome networks have emerged as ultrasmall-scale analytical devices. This review provides information about new developments in some of the most actively researched liposome-related topics.
Surface-Enhanced Raman Spectroscopy
Authors: Stiles Paul L. , Dieringer Jon A. , Shah Nilam C. , Van Duyne Richard P.
Published: May 2008

The ability to control the size, shape, and material of a surface has reinvigorated the field of surface-enhanced Raman spectroscopy (SERS). Because excitation of the localized surface plasmon resonance of a nanostructured surface or nanoparticle lies at the heart of SERS, the ability to reliably control the surface characteristics has taken SERS from an interesting surface phenomenon to a rapidly developing analytical tool. This article first explains many fundamental features of SERS and then describes the use of nanosphere lithography for the fabrication of highly reproducible and robust SERS substrates. In particular, we review metal film over nanosphere surfaces as excellent candidates for several experiments that were once impossible with more primitive SERS substrates (e.g., metal island films). The article also describes progress in applying SERS to the detection of chemical warfare agents and several biological molecules.
Mass Spectrometry for Rapid Characterization of Microorganisms
Authors: Demirev Plamen A. , Fenselau Catherine
Published: May 2008

Advances in instrumentation, proteomics, and bioinformatics have contributed to the successful applications of mass spectrometry (MS) for detection, identification, and classification of microorganisms. These MS applications are based on the detection of organism-specific biomarker molecules, which allow differentiation between organisms to be made. Intact proteins, their proteolytic peptides, and nonribosomal peptides have been successfully utilized as biomarkers. Sequence-specific fragments for biomarkers are generated by tandem MS of intact proteins or proteolytic peptides, obtained after, for instance, microwave-assisted acid hydrolysis. In combination with proteome database searching, individual biomarker proteins are unambiguously identified from their tandem mass spectra, and from there the source microorganism is also identified. Such top-down or bottom-up proteomics approaches permit rapid, sensitive, and confident characterization of individual microorganisms in mixtures and are reviewed here. Examples of MS-based functional assays for detection of targeted microorganisms, e.g., Bacillus anthracis, in environmental or clinically relevant backgrounds are also reviewed.
Fundamentals of Protein Separations: 50 Years of Nanotechnology, and Growing
Authors: Egas David A. , Wirth Mary J.
Published: May 2008

The separation of proteins in biology samples has long been recognized as an important and daunting endeavor that continues to have enormous impact on human health. Today's technology for protein separations has its origins in the early nanotechnology of the 1950s and 1960s, and the methods include immunoassays and other affinity extractions, electrophoresis, and chromatography. What is different today is the need to resolve and identify many low-abundance proteins within complex biological matrices. Multidimensional separations are the rule, high speed is needed, and the separations must be able to work with mass spectrometry for protein identification. Hybrid approaches that combine disparate separation tools (including recognition, electrophoresis, and chromatography) take advantage of the fact that no single class of separation can resolve the proteins in a biological matrix. Protein separations represent a developing area technologically, and understanding the principles of protein separations from a molecular and nanoscale viewpoint will enable today's researchers to invent tomorrow's technology.
Formation and Characterization of Organic Monolayers on Semiconductor Surfaces
Authors: Hamers Robert J.
Published: May 2008

Organic-semiconductor interfaces are playing increasingly important roles in fields ranging from electronics to nanotechnology to biosensing. The continuing decrease in microelectronic device feature sizes is raising an especially great interest in understanding how to integrate molecular systems with conventional, inorganic microelectronic materials, particularly silicon. The explosion of interest in the biological sciences has provided further impetus for learning how to integrate biological molecules and systems with microelectronics to form true bioelectronic systems. Organic monolayers present an excellent opportunity for surmounting many of the practical barriers that have hindered the full integration of microelectronics technology with organic and biological systems. Of all the semiconductor materials, silicon and diamond stand out as unique. This review focuses upon the preparation and characterization of organic and biomolecular layers on semiconductor surfaces, with special emphasis on monolayers formed on silicon and diamond.
Functional and Spectroscopic Measurements with Scanning Tunneling Microscopy
Authors: Moore Amanda M. , Weiss Paul S.
Published: May 2008

Invented as a surface analytical technique capable of imaging individual atoms and molecules in real space, scanning tunneling microscopy (STM) has developed and advanced into a technique able to measure a variety of structural, functional, and spectroscopic properties and relationships at the single-molecule level. Here, we review basic STM operation and image interpretation, techniques developed to manipulate single atoms and molecules with the STM to measure functional properties of surfaces, local spectroscopies used to characterize atoms and molecules at the single-molecule level, and surface perturbations affecting surface coverage and surface reactions. Each section focuses on determining the identity and function of chemical species so as to elucidate information beyond topography with STM.
High-Resolution Mass Spectrometers
Authors: Marshall Alan G. , Hendrickson Christopher L.
Published: May 2008

Over the past decade, mass spectrometry has been revolutionized by access to instruments of increasingly high mass-resolving power. For small molecules up to ∼400 Da (e.g., drugs, metabolites, and various natural organic mixtures ranging from foods to petroleum), it is possible to determine elemental compositions (CcHhNnOoSsPp…) of thousands of chemical components simultaneously from accurate mass measurements (the same can be done up to 1000 Da if additional information is included). At higher mass, it becomes possible to identify proteins (including posttranslational modifications) from proteolytic peptides, as well as lipids, glycoconjugates, and other biological components. At even higher mass (∼100,000 Da or higher), it is possible to characterize posttranslational modifications of intact proteins and to map the binding surfaces of large biomolecule complexes. Here we review the principles and techniques of the highest-resolution analytical mass spectrometers (time-of-flight and Fourier transform ion cyclotron resonance and orbitrap mass analyzers) and describe some representative high-resolution applications.
Plasma Diagnostics for Unraveling Process Chemistry
Authors: Stillahn Joshua M. , Trevino Kristina J. , Fisher Ellen R.
Published: May 2008

This review focuses on the use of diagnostic tools to examine plasma processing chemistry, primarily plasma species energetics, dynamics, and molecule-surface reactions. We describe the use of optical diagnostic tools, mass spectrometry, and Langmuir probes in measuring species densities, rotational and kinetic energies, and plasma-surface reactions. Molecule-surface interactions for MXn species (M = C, Si, N; X = H, F, Cl) are presented and interpreted with respect to the molecule's electronic configuration and dipole moments.
Novel Detection Schemes of Nuclear Magnetic Resonance and Magnetic Resonance Imaging: Applications from Analytical Chemistry to Molecular Sensors
Authors: Harel Elad , Schröder Leif , Xu Shoujun
Published: May 2008

Nuclear magnetic resonance (NMR) is a well-established analytical technique in chemistry. The ability to precisely control the nuclear spin interactions that give rise to the NMR phenomenon has led to revolutionary advances in fields as diverse as protein structure determination and medical diagnosis. Here, we discuss methods for increasing the sensitivity of magnetic resonance experiments, moving away from the paradigm of traditional NMR by separating the encoding and detection steps of the experiment. This added flexibility allows for diverse applications ranging from lab-on-a-chip flow imaging and biological sensors to optical detection of magnetic resonance imaging at low magnetic fields. We aim to compare and discuss various approaches for a host of problems in material science, biology, and physics that differ from the high-field methods routinely used in analytical chemistry and medical imaging.
Spectroscopic and Statistical Techniques for Information Recovery in Metabonomics and Metabolomics
Authors: Lindon John C. , Nicholson Jeremy K.
Published: May 2008

Methods for generating and interpreting metabolic profiles based on nuclear magnetic resonance (NMR) spectroscopy, mass spectrometry (MS), and chemometric analysis methods are summarized and the relative strengths and weaknesses of NMR and chromatography-coupled MS approaches are discussed. Given that all data sets measured to date only probe subsets of complex metabolic profiles, we describe recent developments for enhanced information recovery from the resulting complex data sets, including integration of NMR- and MS-based metabonomic results and combination of metabonomic data with data from proteomics, transcriptomics, and genomics. We summarize the breadth of applications, highlight some current activities, discuss the issues relating to metabonomics, and identify future trends.
Analysis of Atmospheric Aerosols
Authors: Prather Kimberly A. , Hatch Courtney D. , Grassian Vicki H.
Published: May 2008

Aerosols represent an important component of the Earth's atmosphere. Because aerosols are composed of solid and liquid particles of varying chemical complexity, size, and phase, large challenges exist in understanding how they impact climate, health, and the chemistry of the atmosphere. Only through the integration of field, laboratory, and modeling analysis can we begin to unravel the roles atmospheric aerosols play in these global processes. In this article, we provide a brief review of the current state of the science in the analysis of atmospheric aerosols and some important challenges that need to be overcome before they can become fully integrated. It is clear that only when these areas are effectively bridged can we fully understand the impact that atmospheric aerosols have on our environment and the Earth's system at the level of scientific certainty necessary to design and implement sound environmental policies.
Time-Resolved Microdialysis for In Vivo Neurochemical Measurements and Other Applications
Authors: Schultz Kristin N. , Kennedy Robert T.
Published: May 2008

Monitoring changes in chemical concentrations over time in complex environments is typically performed using sensors and spectroscopic techniques. Another approach is to couple sampling methods, such as microdialysis, with chromatographic, electrophoretic, or enzymatic assays. Recent advances of such coupling have enabled improvements in temporal resolution, multianalyte capability, and automation. In a sampling and analysis method, the temporal resolution is set by the mass sensitivity of the analytical method, analysis time, and zone dispersion during sampling. Coupling methods with high speed and mass sensitivity to microdialysis sampling help to reduce some of these contributions to yield methods with temporal resolution of seconds. These advances have been primarily used in monitoring neurotransmitters in vivo. This review covers the problems associated with chemical monitoring in the brain, recent advances in using microdialysis for time-resolved in vivo measurements, sample applications, and other potential applications of the technology such as determining reaction kinetics and process monitoring.
Peptides in the Brain: Mass Spectrometry–Based Measurement Approaches and Challenges
Authors: Li Lingjun , Sweedler Jonathan V.
Published: May 2008

The function and activity of almost every circuit in the human brain are modified by the signaling peptides (SPs) surrounding the neurons. As the complement of peptides can vary even in adjacent neurons and their physiological actions can occur over a broad range of concentrations, the required figures of merit for techniques to characterize SPs are surprisingly stringent. In this review, we describe the formation and catabolism of SPs and highlight a range of mass spectrometric techniques used to characterize SPs. Approaches that supply high chemical information content, direct tissue profiling, spatially resolved data, and temporal information on peptide release are also described. Because of advances in measurement technologies, our knowledge of SPs has greatly increased over the last decade, and SP discoveries will continue as the capabilities of modern measurement approaches improve.