bluuebunny/crossref_metadata_2025 huggingface dataset:
Supporting presence in collaborative environments by haptic force feedback
Authors: Sallnäs Eva-Lotta , Rassmus-Gröhn Kirsten , Sjöström Calle
Published: July 2002

An experimental study of interaction in a collaborative desktop virtual environment is described. The aim of the experiment was to investigate if added haptic force feedback in such an environment affects
perceived virtual presence, perceived social presence, perceived task performance, and task performance. A between-group design was employed, where seven pairs of subjects used an interface with graphic representation of the environment, audio connection, and haptic force feedback. Seven other pairs of subjects used an interface without haptic force feedback, but with identical features otherwise. The PHANToM, a one-point haptic device, was used for the haptic force feedback, and a program especially developed for the purpose provided the virtual environment. The program enables for two individuals placed in different locations to simultaneously feel and manipulate dynamic objects in a shared desktop virtual environment. Results show that haptic force feedback significantly improves task performance, perceived task performance, and pereceived virtual presence in the collaborative distributed environment. The results suggest that haptic force feedback increases perceived social presence, but the difference is not significant.
Object-focused interaction in collaborative virtual environments
Authors: Hindmarsh Jon , Fraser Mike , Heath Christian , Benford Steve , Greenhalgh Chris
Published: July 2002

This paper explores and evaluates the support for object-focused interaction provided by a desktop Collaborative Virtual Environment. An experimental “design” task was conducted, and video recordings of the participants' activities facilitated an observational analysis of interaction in, and through, the virtual world. Observations include: problems due to “fragmented” views of embodiments in relation to shared objects; participants compensating with spoken accounts of their actions; and difficulties in understanding others' perspectives. Implications and proposals for the design of CVEs drawn from these observations are: the use of semidistorted views to support peripheral awareness; more explicit or exaggerated representations of actions than are provided by pseudohumanoid avatars; and navigation techniques that are sensitive to the actions of others. The paper also presents some examples of the ways in which these proposals might be realized.
Data manipulation and programming problems in automatic information retrieval
Authors: Salton G.
Published: July 2002

Automatic information retrieval programs require the manipulation of a variety of different data structures, including linear text, sparse matrices, and tree or list structures. The main data manipulations to be performed in automatic information systems are first briefly reviewed. A variety of data representations which have been used to describe structured information are then examined, and the characteristics of various processing languages are outlined in the light of the procedures requiring implementation. Advantages and disadvantages of these programming languages for the retrieval application are examined, and suggestions are made for the design of programming facilities to aid in information retrieval.
A new policy for algorithms?
Authors: Perlis A. J.
Published: July 2002

Debate is under way concerning the Algorithms section of the
Communications
. Specifically, there is considerable sentiment in favor of also publishing algorithms in languages other than ALGOL.
Triangular walk pattern for the down-hill method of solving a transcendental equation
Authors: Onoe Morio
Published: July 2002

The down-hill method by Ward is a numerical method for determining a complex root of ƒ(
z
) = 0 and suitable for machine computation [1]. It is based on a theorem that
W
(
z
) = |Re(ƒ)| + |Im(ƒ)| (1) has minimum value, actually zero, at and only at a root of ƒ and seeks to minimize
W
by non-random walk from a starting point over the complex plane.
Dynamic structures in modeling and simulation
Authors: Uhrmacher A. M.
Published: July 2002

As the number of flexible, adaptable systems grows so does the need for specification and analysis tools that support adaptable system structures. The increasing number of simulation tools that equip models with the capability of changing their behavior patterns, composition, and interactions raises the desire for a theoretical and methodological approach. A formalism is introduced based on DEVS which emphasizes the reflective nature of variable structure models. The proposed formalism and DEVS are shown to be bisimilar, which emphasizes the role of variable structure models as an agency of modularization. The formalism is used to reveal general problems and solutions in implementing variable structure models.
Environmental and institutional models of system development: a national criminal history system
Authors: Laudon Kenneth C.
Published: July 2002

This article tests two competing theories of system development referred to here as environmental and institutional models. These models form the basis for most explanations of why systems are developed and utilized. We will examine both models in detail and apply them to a single set of data concerned with the emerging national computerized criminal history system (CCH). A hybrid model, which combines elements of environmental and institutional approaches, is also developed and tested. A substantive result of this new model will alter our understanding of why a national CCH system is being developed. At the theoretical level, we conclude that a hybrid model is more powerful than either an environmental or an institutional model taken separately and that future research must take this into account.
A review of recent developments in solving ODEs
Authors: Gupta Gopal K. , Sacks-Davis Ron , Tescher Peter E.
Published: July 2002

Mathematical models when simulating the behavior of physical, chemical, and biological systems often include one or more ordinary differential equations (ODEs). To study the system behavior predicted by a model, these equations are usually solved numerically.

Although many of the current methods for solving ODEs were developed around the turn of the century, the past 15 years or so has been a period of intensive research. The emphasis of this survey is on the methods and techniques used in software for solving ODEs.

ODEs can be classified as stiff or nonstiff, and may be stiff for some parts of an interval and nonstiff for others. We discuss stiff equations, why they are difficult to solve, and methods and software for solving both nonstiff and stiff equations. We conclude this review by looking at techniques for dealing with special problems that may arise in some ODEs, for example, discontinuities.

Although important theoretical developments have also taken place, we report only those developments which have directly affected the software and provide a review of this research. We present the basic concepts involved but assume that the reader has some background in numerical computing, such as a first course in numerical methods.
Optimal simulations between mesh-connected arrays of processors
Authors: Kosaraju S. Rao , Atallah Mikhail J.
Published: July 2002

Let
G
and
H
be two mesh-connected arrays of processors, where
G
=
g
1
, X
g
2
X … X
g
1
,
H
=
h
1
x
h
2
x … x

h
d

, and
g
1
…

g
1

≤
h
1
…

h
d

. The problem of simulating
G
by
H
is considered and the best possible simulation in terms of the

g
i

's and

h
i

's is characterized by giving such a simulation and proving its optimality in the worst-case sense. Also the same bound on the average cost of encoding the edges of
G
as distinct paths in
H
is established.
Access to, usage of, and outcomes from an electronic messaging system
Authors: Rice Ronald E. , Shook Douglas E.
Published: July 2002

This study examines relationships among perceived accessibility to an electronic messaging system (EMS), computer-monitored and reported usage of the system by approximately 100 employees of one division of an aerospace firm, user's job type, perceived appropriateness of the EMS, and reported outcomes such as changes in effectiveness and use of paper-based media. Greater accessibility resulted in more usage and reported increases in effectiveness. Physical distance to a terminal affects the associations of other aspects of accessibility with usage and has a greater influence on these associations earlier in one's adoption process. Differences in job type showed statistically significant associations with usage, independent of the influence of accessibility. Computer-monitored and reported usage measures were only moderately correlated and were differentially associated with the access measures and with the two outcomes. The article ends by discussing implications for implementation and evaluation of computer-based communication systems, theories of media characteristics and information value, and methodological issues in using computer-monitored usage data.
Evaluating ontological decisions with OntoClean
Authors: Guarino Nicola , Welty Christopher
Published: July 2002

Explosing common misuses of the subsumption relationship and the formal basis for why they are wrong.
Diversity in the use of electronic mail: a preliminary inquiry
Authors: Mackay Wendy E.
Published: July 2002

This paper describes a series of interviews that examine the ways that professional office workers use electronic mail to manage their daily work. The purpose is to generate hypotheses for future research. A number of implications for the design of flexible mail systems are discussed.

Two principal claims are made. First, the use of electronic mail is strikingly diverse, although not infinitely so. Individuals vary both in objective measures of mail use and in preferred strategies for managing work electronically. Feelings of control are similarly diverse and are related to the size of the user's inbox, numbers of folders, and subscriptions to distribution lists. This diversity implies that one's own experiences with electronic mail are unlikely to provide sufficient understanding of other's uses of mail. Mail designers should thus seek flexible primitives that capture the important dimensions of use and provide flexibility for a wide range of users.

The second claim is that electronic mail is more than just a communication system. Users archive messages for subject retrieval, prioritize messages to sequence work activities, and delegate tasks via mail. A taxonomy of work management is proposed in which mail is used for information management, time management, and task management activities. Directions for future research are suggested.
Algorithm 671: FARB-E-2D: fill area with bicubics on rectangles—a contour plot program
Authors: Preusser A.
Published: July 2002

An algorithm plotting contour lines for discrete values

z
ij

, given at the nodes of a rectangular mesh is described. A bicubic Hermite polynomial
f
(
x
,
y
) is determined for every rectangle of the mesh, interpolating the

z
ij

and the derivatives

z
x

,

z
y

, and

z
xy

. The derivatives are optionally computed by the algorithm. The contours found are normally smooth curves. They consist of polygons approximating intersections with the bicubics. It is possible to fill the areas between them with certain colors or patterns. This is done with a piecewise technique rectangle by rectangle. The method for finding the points of the polygons is shortly reviewed, and some numerical problems are pointed out. The algorithm has a flexible, easy-to-use interface and is easily installed with all plotting systems, provided that a fill-area command is available. A GKS interface may be used.
Characterizing computer performance with a single number
Authors: Smith J. E.
Published: July 2002

The controversy surrounding single number performance reduction is examined and solutions are suggested through a comparison of measures.
Automatic verification of database transaction safety
Authors: Sheard Tim , Stemple David
Published: July 2002

Maintaining the integrity of databases is one of the promises of database management systems. This includes assuring that integrity constraints are invariants of database transactions. This is very difficult to accomplish efficiently in the presence of complex constraints and large amounts of data. One way to minimize the amount of processing required to maintain database integrity over transaction processing is to prove at compile-time that transactions cannot, if run atomically, disobey integrity constraints. We report on a system that performs such verification for a robust set of constraint and transaction classes. The system accepts database schemas written in a more or less traditional style and accepts programs in a high-level programming language. Automatic verification fast enough to be effective on current workstation hardware is performed.
Algorithm 676: ODRPACK: software for weighted orthogonal distance regression
Authors: Boggs Paul T. , Donaldson Janet R. , Byrd Richaard h. , Schnabel Robert B.
Published: July 2002

In this paper, we describe ODRPACK, a software package for the weighted orthogonal distance regression problem. This software is an implementation of the algorithm described in [2] for finding the parameters that minimize the sum of the squared weighted orthogonal distances from a set of observations to a curve or surface determined by the parameters. It can also be used to solve the ordinary nonlinear least squares problem. The weighted orthogonal distance regression procedure application to curve and surface fitting and to measurement error models in statistics. The algorithm implemented is an efficient and stable trust region (Levenberg-Marquardt) procedure that exploits the structure of the problem so that the computational cost per iteration is equal to that for the same type of algorithm applied to the ordinary nonlinear least squares problem. The package allows a general weighting scheme, provides for finite difference derivatives, and contains extensive error checking and report generating facilities.
Integer programming vs. expert systems: an experimental comparison
Authors: Dhar Vasant , Ranganathan Nicky
Published: July 2002

Expert system and integer programming formulations of an NP-complete constraint satisfaction problem are contrasted in terms of performance, ability to encode complex preferences, control of reasoning, and supporting incremental modification of solutions in response to changing input data.
A logic of authentication
Authors: Burrows Michael , Abadi Martin , Needham Roger
Published: July 2002

Authentication protocols are the basis of security in many distributed systems, and it is therefore essential to ensure that these protocols function correctly. Unfortunately, their design has been extremely error prone. Most of the protocols found in the literature contain redundancies or security flaws. A simple logic has allowed us to describe the beliefs of trustworthy parties involved in authentication protocols and the evolution of these beliefs as a consequence of communication. We have been able to explain a variety of authentication protocols formally, to discover subtleties and errors in them, and to suggest improvements. In this paper we present the logic and then give the results of our analysis of four published protocols, chosen either because of their practical importance or because they serve to illustrate our method.
Algorithm 681: INTBIS, a portable interval Newton/bisection package
Authors: Kearfott R. Baker , Novoa Manuel
Published: July 2002

We present a portable software package for finding all real roots of a system of nonlinear equations within a region defined by bounds on the variables. Where practical, the package should find all roots with mathematical certainty. Though based on interval Newton methods, it is self-contained. It allows various control and output options and does not require programming if the equations are polynomials; it is structured for further algorithmic research. Its practicality does not depend in a simple way on the dimension of the system or on the degree of nonlinearity.
A Theory of Communicating Sequential Processes
Authors: Brookes S. D. , Hoare C. A. R. , Roscoe A. W.
Published: July 2002

A mathematical model for communicating sequential processes is
given, and a number of its interesting and useful properties are
stated and proved. The possibilities of nondetermimsm are fully
taken into account.
Table-driven implementation of the logarithm function in IEEE floating-point arithmetic
Authors: Tang Ping-Tak Peter
Published: July 2002

Algorithms and implementation details for the logarithm functions in both single and double precision of IEEE 754 arithmetic are presented here. With a table of moderate size, the implementation need only working- precision arithmetic and are provably accurate to within 0.57 ulp.
NAGPRA IS FOREVER: Osteology and the Repatriation of Skeletons
Authors: Rose Jerome C. , Green Thomas J. , Green Victoria D.
Published: July 2002

▪ Abstract  The 1990 Native American Graves Protection and Repatriation Act requires universities, museums, and federal agencies to inventory their archeological collections to prepare for the repatriation of skeletons to their Native American descendants. The loss of these collections will be a detriment to the study of North American osteology, but the inventory and repatriation process has increased the number of skeletons studied from about 30% to nearly 100%. The availability of funds stimulated by this law produced osteological data collection and systematization unprecedented in the history of osteology. The possibility of forming partnerships between Native Americans and osteologists has the potential of producing a vibrant future for North American osteology and the new bioarcheology.
ROLE AND REGULATION OF SUCROSE-PHOSPHATE SYNTHASE IN HIGHER PLANTS
Authors: Huber Steven C. , Huber Joan L.
Published: July 2002

▪ Abstract  Sucrose-phosphate synthase (SPS; E.C. 2.4.1.14) is the plant enzyme thought to play a major role in sucrose biosynthesis. In photosynthetic and nonphotosynthetic tissues, SPS is regulated by metabolites and by reversible protein phosphorylation. In leaves, phosphorylation modulates SPS activity in response to light/dark signals and end-product accumulation. SPS is phosphorylated on multiple seryl residues in vivo, and the major regulatory phosphorylation site involved is Ser158 in spinach leaves and Ser162 in maize leaves. Regulation of the enzymatic activity of SPS appears to involve calcium, metabolites, and novel “coarse” control of the protein phosphatase that activates SPS. Activation of SPS also occurs during osmotic stress of leaf tissue in darkness, which may function to facilitate sucrose formation for osmoregulation. Manipulation of SPS expression in vivo confirms the role of this enzyme in the control of sucrose biosynthesis.
BIOSYNTHESIS AND ACTION OF JASMONATES IN PLANTS
Authors: Creelman Robert A. , Mullet John E.
Published: July 2002

▪ Abstract  Jasmonic acid and its derivatives can modulate aspects of fruit ripening, production of viable pollen, root growth, tendril coiling, and plant resistance to insects and pathogens. Jasmonate activates genes involved in pathogen and insect resistance, and genes encoding vegetative storage proteins, but represses genes encoding proteins involved in photosynthesis. Jasmonic acid is derived from linolenic acid, and most of the enzymes in the biosynthetic pathway have been extensively characterized. Modulation of lipoxygenase and allene oxide synthase gene expression in transgenic plants raises new questions about the compartmentation of the biosynthetic pathway and its regulation. The activation of jasmonic acid biosynthesis by cell wall elicitors, the peptide systemin, and other compounds will be related to the function of jasmonates in plants. Jasmonate modulates gene expression at the level of translation, RNA processing, and transcription. Promoter elements that mediate responses to jasmonate have been isolated. This review covers recent advances in our understanding of how jasmonate biosynthesis is regulated and relates this information to knowledge of jasmonate modulated gene expression.
LEAF DEVELOPMENT IN ANGIOSPERMS
Authors: Sinha Neelima
Published: July 2002

▪ Abstract  Leaves are produced in succession on the shoot apical meristem (SAM) of a plant. The three landmark stages in leaf morphogenesis include initiation, acquisition of suborgan identities, and tissue differentiation. The expression of various genes relative to these steps in leaf morphogenesis is described. KNOTTED-like homeobox (KNOX) genes, FLO/LFY, and floral homeotic genes may be involved in generation of leaf shape and complexity. The differences between compound leaves and simple leaves in gene expression characteristics and morphogenetic patterns are discussed.
PLANTCELLULAR ANDMOLECULARRESPONSES TOHIGHSALINITY
Authors: Hasegawa Paul M. , Bressan Ray A. , Zhu Jian-Kang , Bohnert Hans J.
Published: July 2002

▪ Abstract  Plant responses to salinity stress are reviewed with emphasis on molecular mechanisms of signal transduction and on the physiological consequences of altered gene expression that affect biochemical reactions downstream of stress sensing. We make extensive use of comparisons with model organisms, halophytic plants, and yeast, which provide a paradigm for many responses to salinity exhibited by stress-sensitive plants. Among biochemical responses, we emphasize osmolyte biosynthesis and function, water flux control, and membrane transport of ions for maintenance and re-establishment of homeostasis. The advances in understanding the effectiveness of stress responses, and distinctions between pathology and adaptive advantage, are increasingly based on transgenic plant and mutant analyses, in particular the analysis of Arabidopsis mutants defective in elements of stress signal transduction pathways. We summarize evidence for plant stress signaling systems, some of which have components analogous to those that regulate osmotic stress responses of yeast. There is evidence also of signaling cascades that are not known to exist in the unicellular eukaryote, some that presumably function in intercellular coordination or regulation of effector genes in a cell-/tissue-specific context required for tolerance of plants. A complex set of stress-responsive transcription factors is emerging. The imminent availability of genomic DNA sequences and global and cell-specific transcript expression data, combined with determinant identification based on gain- and loss-of-function molecular genetics, will provide the infrastructure for functional physiological dissection of salt tolerance determinants in an organismal context. Furthermore, protein interaction analysis and evaluation of allelism, additivity, and epistasis allow determination of ordered relationships between stress signaling components. Finally, genetic activation and suppression screens will lead inevitably to an understanding of the interrelationships of the multiple signaling systems that control stress-adaptive responses in plants.
MODEL ATMOSPHERES OF VERY LOW MASS STARS AND BROWN DWARFS
Authors: Allard France , Hauschildt Peter H. , Alexander David R. , Starrfield Sumner
Published: July 2002

▪ Abstract  As progressively cooler stellar and substellar objects are discovered, the presence first of molecules and then of condensed particulates greatly complicates the understanding of their physical properties. Accurate model atmospheres that include these processes are the key to establishing their atmospheric parameters. They play a crucial role in determining structural characteristics by setting the surface conditions of model interiors and providing transformations to the various observational planes. They can reveal the spectroscopic properties of brown dwarfs and help establish their detectability. In this paper, we review the current state-of-the-art theory and modeling of the atmospheres of very low mass stars, including the coolest known M dwarfs, M subdwarfs, and brown dwarfs, i.e. Teff≤ 4,000 K and −4.0 ≤ [M/H] ≤ +0.0. We discuss ongoing efforts to incorporate molecular and grain opacities in cool stellar spectra, as well as the latest progress in (a) deriving the effective temperature scale of M dwarfs, (b) reproducing the lower main sequences of metal-poor subdwarfs in the halo and globular clusters, and (c) results of the models related to the search for brown dwarfs.
Dusty Circumstellar Disks
Authors: Zuckerman B.
Published: July 2002

▪ Abstract  Dusty circumstellar disks in orbit around main-sequence stars were discovered in 1983 by the infrared astronomical satellite. It was the first time material that was not another star had been seen in orbit around a main-sequence star other than our Sun. Since that time, analyses of data from the infrared astronomical satellite, the infrared space observatory, and ground-based telescopes have enabled astronomers to paint a picture of dusty disks around numerous main-sequence and post–main-sequence stars. This review describes, primarily in an evolutionary framework, the properties of some dusty disks orbiting, first, pre–main-sequence stars, then main-sequence and post–main-sequence stars, and ending with white dwarfs.
MODIFIED OLIGONUCLEOTIDES: Synthesis and Strategy for Users
Authors: Verma Sandeep , Eckstein Fritz
Published: July 2002

Synthetic oligonucleotide analogs have greatly aided our understanding of several biochemical processes. Efficient solid-phase and enzyme-assisted synthetic methods and the availability of modified base analogs have added to the utility of such oligonucleotides. In this review, we discuss the applications of synthetic oligonucleotides that contain backbone, base, and sugar modifications to investigate the mechanism and stereochemical aspects of biochemical reactions. We also discuss interference mapping of nucleic acid–protein interactions; spectroscopic analysis of biochemical reactions and nucleic acid structures; and nucleic acid cross-linking studies.

The automation of oligonucleotide synthesis, the development of versatile phosphoramidite reagents, and efficient scale-up have expanded the application of modified oligonucleotides to diverse areas of fundamental and applied biological research. Numerous reports have covered oligonucleotides for which modifications have been made of the phosphodiester backbone, of the purine and pyrimidine heterocyclic bases, and of the sugar moiety; these modifications serve as structural and mechanistic probes. In this chapter, we review the range, scope, and practical utility of such chemically modified oligonucleotides. Because of space limitations, we discuss only those oligonucleotides that contain phosphate and phosphate analogs as internucleotidic linkages.
Vascular Tissue Engineering
Authors: Nerem Robert M. , Seliktar Dror
Published: July 2002

▪ Abstract  The development of a tissue-engineered blood vessel substitute has motivated much of the research in the area of cardiovascular tissue engineering over the past 20 years. Several methodologies have emerged for constructing blood vessel replacements with biological functionality. These include cell-seeded collagen gels, cell-seeded biodegradable synthetic polymer scaffolds, cell self-assembly, and acellular techniques. This review details the most recent developments, with a focus on core technologies and construct development. Specific examples are discussed to illustrate both the benefits and shortcomings of each methodology, as well as to underline common themes. Finally, a brief perspective on challenges for the future is presented.
RAMAN SPECTROSCOPY OF PROTEIN AND NUCLEIC ACID ASSEMBLIES
Authors: Thomas George J.
Published: July 2002

▪ Abstract  The Raman spectrum of a protein or nucleic acid consists of numerous discrete bands representing molecular normal modes of vibration and serves as a sensitive and selective fingerprint of three-dimensional structure, intermolecular interactions, and dynamics. Recent improvements in instrumentation, coupled with innovative approaches in experimental design, dramatically increase the power and scope of the method, particularly for investigations of large supramolecular assemblies. Applications are considered that involve the use of (a) time-resolved Raman spectroscopy to elucidate assembly pathways in icosahedral viruses, (b) polarized Raman microspectroscopy to determine detailed structural parameters in filamentous viruses, (c) ultraviolet-resonance Raman spectroscopy to probe selective DNA and protein residues in nucleoprotein complexes, and (d) difference Raman methods to understand mechanisms of protein/DNA recognition in gene regulatory and chromosomal complexes.
THE PROTEASOME
Authors: Bochtler Matthias , Ditzel Lars , Groll Michael , Hartmann Claudia , Huber Robert
Published: July 2002

▪ Abstract  Proteasomes are large multisubunit proteases that are found in the cytosol, both free and attached to the endoplasmic reticulum, and in the nucleus of eukaryotic cells. Their ubiquitous presence and high abundance in these compartments reflects their central role in cellular protein turnover. Proteasomes recognize, unfold, and digest protein substrates that have been marked for degradation by the attachment of a ubiquitin moiety. Individual subcomplexes of the complete 26S proteasome are involved in these different tasks: The ATP-dependent 19S caps are believed to unfold substrates and feed them to the actual protease, the 20S proteasome. This core particle appears to be more ancient than the ubiquitin system. Both prokaryotic and archaebacterial ancestors have been identified. Crystal structures are now available for the E. coli proteasome homologue and the T. acidophilum and S. cerevisiae 20S proteasomes. All three enzymes are cylindrical particles that have their active sites on the inner walls of a large central cavity. They share the fold and a novel catalytic mechanism with an N-terminal nucleophilic threonine, which places them in the family of Ntn (N terminal nucleophile) hydrolases. Evolution has added complexity to the comparatively simple prokaryotic prototype. This minimal proteasome is a homododecamer made from two hexameric rings stacked head to head. Its heptameric version is the catalytic core of archaebacterial proteasomes, where it is sandwiched between two inactive antichambers that are made up from a different subunit. In eukaryotes, both subunits have diverged into seven different subunits each, which are present in the particle in unique locations such that a complex dimer is formed that has six active sites with three major specificities that can be attributed to individual subunits. Genetic, biochemical, and high-resolution electron microscopy data, but no crystal structures, are available for the 19S caps. A first step toward a mechanistic understanding of proteasome activation and regulation has been made with the elucidation of the X-ray structure of the alternative, mammalian proteasome activator PA28.
A CONSERVED SIGNALING PATHWAY: The Drosophila Toll-Dorsal Pathway
Authors: Belvin Marcia P. , Anderson Kathryn V.
Published: July 2002

▪ Abstract  The Toll-Dorsal pathway in Drosophila and the interleukin-1 receptor (IL-1R)-NF-κB pathway in mammals are homologous signal transduction pathways that mediate several different biological responses. In Drosophila, genetic analysis of dorsal-ventral patterning of the embryo has defined the series of genes that mediate the Toll-Dorsal pathway. Binding of extracellular ligand activates the transmembrane receptor Toll, which requires the novel protein Tube to activate the cytoplasmic serine/threonine kinase Pelle. Pelle activity controls the degradation of the Cactus protein, which is present in a cytoplasmic complex with the Dorsal protein. Once Cactus is degraded in response to signal, Dorsal is free to move into the nucleus where it regulates transcription of specific target genes. The Toll, tube, pelle, cactus, and dorsal genes also appear to be involved in Drosophila immune response. Because the IL-1R-NF-κB pathway plays a role in vertebrate innate immunity and because plant homologues of the Toll-Dorsal pathway are important in plant disease resistance, it is likely that this pathway arose before the divergence of plants and animals as a defense against pathogens.
GENETIC ANALYSIS OF THE ACTIN CYTOSKELETON IN THE DROSOPHILA OVARY
Authors: Robinson Douglas N. , Cooley Lynn
Published: July 2002

▪ Abstract  The Drosophila ovary provides a favorable model system in which to study cellular morphogenesis. The development of a mature egg involves a syncytium of 16 germline cells and over 1000 somatically derived follicle cells. Intercellular transport, stable intercellular bridges, cell migrations, cell shape changes, and specific subcellular localization of many embryonic patterning determinants contribute to egg development and require a dynamic cytoskeleton. We discuss many of the recent genetic and cell biological studies that have led to insights into how the actin cytoskeleton is assembled and regulated during the morphogenesis of the Drosophila egg.
NUCLEAR ASSEMBLY
Authors: Gant Tracey Michele , Wilson Katherine L.
Published: July 2002

▪ Abstract  We review old and new insights into the structure of the nuclear envelope and the components responsible for its dynamic reassembly during mitosis. New information is coming to light about several of the proteins that mediate nuclear reassembly. These proteins include the lamins and their emerging relationship with proteins such as otefin and the MAN antigens: peripheral proteins that might participate in lamina structure. There are four identified proteins localized to the inner nuclear membrane: the lamina-associated proteins LAP1 and LAP2, emerin, and the lamin B receptor (LBR). LBR can interact independently with lamin B and a chromodomain protein, Hp1, and appears to be a central player in targeting nuclear membranes to chromatin. Intermediates in the assembly of nuclear pore complexes (NPCs) can now be studied biochemically and visualized by high resolution scanning electron microscopy. We discuss the possibility that the filament-forming proteins Tpr/p270, NuMA, and perhaps actin may have roles in nuclear assembly.
The Role of Orphan Nuclear Receptors in the Regulation of Cholesterol Homeostasis
Authors: Repa Joyce J. , Mangelsdorf David J.
Published: July 2002

▪ Abstract  Cholesterol balance is maintained by a series of regulatory pathways that control the acquisition of cholesterol from endogenous and exogenous sources and the elimination of cholesterol, facilitated by its conversion to bile acids. Over the past decade, investigators have discovered that a family of membrane-bound transcription factors, sterol regulatory element-binding proteins (SREBPs), mediate the end-product repression of key enzymes of cholesterol biosynthesis. Recently orphan members of another family of transcription factors, the nuclear hormone receptors, have been found to regulate key pathways in bile acid metabolism, thereby controlling cholesterol elimination. The study of these orphan nuclear receptors suggests their potential as targets for new drug therapies.
CHANNEL NETWORKS
Authors: Rinaldo Andrea , Rodriguez-Iturbe Ignacio , Rigon Riccardo
Published: July 2002

▪ Abstract  This review proceeds from Luna Leopold's and Ronald Shreve's lasting accomplishments dealing with the study of random-walk and topologically random channel networks. According to the random perspective, which has had a profound influence on the interpretation of natural landforms, nature's resiliency in producing recurrent networks and landforms was interpreted to be the consequence of chance. In fact, central to models of topologically random networks is the assumption of equal likelihood of any tree-like configuration. However, a general framework of analysis exists that argues that all possible network configurations draining a fixed area are not necessarily equally likely. Rather, a probability P (s) is assigned to a particular spanning tree configuration, say s, which can be generally assumed to obey a Boltzmann distribution: P(s) ∝ e−H(s)/τ, where τ is a parameter and H (s) is a global property of the network configuration s related to energetic characters, i.e. its Hamiltonian. One extreme case is the random topology model where all trees are equally likely, i.e. the limit case for τ → ∞. The other extreme case is τ → ∞, and this corresponds to network configurations that tend to minimize their total energy dissipation to improve their likelihood. Networks obtained in this manner are termed optimal channel networks (OCNs). Observational evidence suggests that the characters of real river networks are reproduced extremely well by OCNs. Scaling properties of energy and entropy of OCNs suggest that large network development is likely to effectively occur at zero temperature (i.e. minimizing its Hamiltonian). We suggest a corollary of dynamic accessibility of a network configuration and speculate towards a thermodynamics of critical self-organization. We thus conclude that both chance and necessity are equally important ingredients for the dynamic origin of channel networks—and perhaps of the geometry of nature.
WESTERN UNITED STATES EXTENSION: How the West was Widened
Authors: Sonder Leslie J. , Jones Craig H.
Published: July 2002

▪ Abstract  Cenozoic extension in the western United States presents a complex interrelation of extension, volcanism, and plate boundary tectonics that defeats simple notions of “active” or “passive” rifting. Forces driving extension can originate at plate boundaries, through basal traction, basal normal forces, or from buoyancy forces internal to the crust and lithospheric mantle. The latter two are most responsible for driving extension where it is observed in the Basin and Range. The complex evolution of the northern Basin and Range probably represents removal or alteration of mantle lithosphere interacting with buoyancy stored in the crust. In contrast, crustal buoyancy forces combined with a divergent plate boundary between about 28 and 16 Ma to drive extension in the southern Basin and Range. The central Basin and Range most likely extended as a result of boundary forces external to itself but arising from buoyancy forces elsewhere in the western United States.
Preserving the Information Content of Species: Genetic Diversity, Phylogeny, and Conservation Worth
Authors: Crozier R. H.
Published: July 2002

A variety of phylogenetic measures have been proposed to quantify distinctiveness, often held to mark species of high conservation worth. However, distinctiveness of species and their numbers have different implications for conservation policy, depending on whether moral, esthetic, or utilitarian reasons are accepted as justifying conservation. The utilitarian position values species according to increasing numbers, and as they are more, as opposed to less, distinctive. The view is taken that conservation should seek to maximize the preserved information of the planet's biota, best expressed in terms of genetic information held in genes and not in portions of the genome of uncertain or no function. Gene number is thus an important component of assessing conservation value. Phylogenetic measures are better indicators of conservation worth than species richness, and measures using branch-lengths are better than procedures relying solely on topology. Distance measures estimating the differences between genomes are preferable to substitution distances. Higher-taxon richness is a promising surrogate for branch-length measures. Complete enumeration of biotas in terms of phylogeny is desirable to avoid uncertainties in the use of indicator groups, and this is achievable now for bacteria. Phylogenetic measures are already important for management of sets of populations within species and are applicable for sets of species. Measures incorporating extinction probabilities and decision costs are being developed, and these, in conjunction with the use of confidence limits on the conservation worth of alternative reserves, are vital for conservation decision-making.
Evolution of Diversity in Warning Color and Mimicry: Polymorphisms, Shifting Balance, and Speciation
Authors: Mallet James , Joron Mathieu
Published: July 2002

▪ Abstract  Mimicry and warning color are highly paradoxical adaptations. Color patterns in both Müllerian and Batesian mimicry are often determined by relatively few pattern-regulating loci with major effects. Many of these loci are “supergenes,” consisting of multiple, tightly linked epistatic elements. On the one hand, strong purifying selection on these genes must explain accurate resemblance (a reduction of morphological diversity between species), as well as monomorphic color patterns within species. On the other hand, mimicry has diversified at every taxonomic level; warning color has evolved from cryptic patterns, and there are mimetic polymorphisms within species, multiple color patterns in different geographic races of the same species, mimetic differences between sister species, and multiple mimicry rings within local communities. These contrasting patterns can be explained, in part, by the shape of a “number-dependent” selection function first modeled by Fritz Müller in 1879: Purifying selection against any warning-colored morph is very strong when that morph is rare, but becomes weak in a broad basin of intermediate frequencies, allowing opportunities for polymorphisms and genetic drift. This Müllerian explanation, however, makes unstated assumptions about predator learning and forgetting which have recently been challenged. Today's “receiver psychology” models predict that classical Müllerian mimicry could be much rarer than believed previously, and that “quasi-Batesian mimicry,” a new type of mimicry intermediate between Müllerian and Batesian, could be common. However, the new receiver psychology theory is untested, and indeed it seems to us unlikely; alternative assumptions could easily lead to a more traditional Müllerian/Batesian mimicry divide.
Streams in Mediterranean Climate Regions: Abiotic Influences and Biotic Responses to Predictable Seasonal Events
Authors: Gasith Avital , Resh Vincent H.
Published: July 2002

▪ Abstract  Streams in mediterranean-climate regions (areas surrounding the Mediterranean Sea, parts of western North America, parts of west and south Australia, southwestern South Africa and parts of central Chile) are physically, chemically, and biologically shaped by sequential, predictable, seasonal events of flooding and drying over an annual cycle. Correspondingly, aquatic communities undergo a yearly cycle whereby abiotic (environmental) controls that dominate during floods are reduced when the discharge declines, which is also a time when biotic controls (e.g. predation, competition) can become important. As the dry season progresses, habitat conditions become harsher; environmental pressures may again become the more important regulators of stream populations and community structure. In contrast to the synchronous input of autumn litterfall in forested temperate streams, riparian input to mediterranean-type streams is more protracted, with fall and possibly spring peaks occurring in streams in the Northern Hemisphere and a summer peak existing in their Southern Hemisphere counterparts. We present 25 testable hypotheses that relate to the influence of the stream hydrograph on faunal richness, abundance, and diversity; species coexistence; seasonal changes in the relative importance of abiotic and biotic controls on the biotic structure; riparian inputs and the relative importance of heterotrophy compared to autotrophy; and the impact of human activities on these seasonally water-stressed streams. Population increases in mediterranean-climate regions (particularly in fertile regions) result in an intensification of the competition for water among different users; consequently, water abstraction, flow regulation, increased salinity, and pollution severely limit the ability of the streams to survive as sustainable, self-regulated systems.
ENERGY IN THETWENTIETHCENTURY: Resources, Conversions, Costs, Uses, and Consequences
Authors: Smil Vaclav
Published: July 2002

▪ Abstract  Civilization's advances during the twentieth century are closely bound with an unprecedented rise of energy consumption in general, and of hydrocarbons and electricity in particular. Substantial improvements of all key nineteenth-century energy techniques and introduction of new extraction and transportation means and new prime movers resulted in widespread diffusion of labor-saving and comfort-providing conversions and in substantially declining energy prices. Although modern societies could not exist without large and incessant flows of energy, there are no simple linear relationships between the inputs of fossil fuels and electricity and a nation's economic performance and social accomplishments. International comparisons show a variety of consumption patterns and a continuing large disparity between affluent and modernizing nations. The necessity of minimizing environmental impacts of energy use, particularly those with potentially worrisome global effects, is perhaps the greatest challenge resulting from the twentieth century's energy advances.
CHEMICAL ECOLOGY OF PHYTOPHAGOUS SCARAB BEETLES
Authors: Leal Walter Soares
Published: July 2002

▪ Abstract  Sex pheromones have been characterized only for species in the subfamilies Rutelinae and Melolonthinae; aggregation pheromones have been identified for two species in the Dynastinae. Melolonthines utilize mainly amino acid derivatives and terpenoid compounds, but sex pheromones of rutelines are fatty acid derivatives. Various other species utilize japonilure-type lactones that are produced by desaturation of fatty acids, followed by hydroxylation, chain shortening, and cyclization. In marked contrast to melolonthine sex pheromone glands that are everted from the abdominal tip, ruteline sex pheromone glands consist of epithelial cells that line the inner surfaces of the pygidium and two apical sternites. Some species that are geographically and/or seasonally isolated utilize the same sex pheromone system, but chirality plays an important role in the isolation of the communication channels of two ruteline species, where one enantiomer is utilized as sex pheromone and the other is a behavioral antagonist. Olfactory receptor neurons (ORNs) are specifically tuned to these enantiomeric pheromones. It is unlikely that the specificity of these ORNs is achieved only by odorant-binding proteins. Pheromone-degrading enzymes are present in scarab beetle antennae and show considerable substrate specificity.
GENETIC AND PHYSICAL MAPPING IN MOSQUITOES: Molecular Approaches
Authors: Severson David W. , Brown Susan E. , Knudson Dennis L.
Published: July 2002

▪ Abstract  The genetic background of individual mosquito species and populations within those species influences the transmission of mosquito-borne pathogens to humans. Technical advances in contemporary genomics are contributing significantly to the detailed genetic analysis of this mosquito-pathogen interaction as well as all other aspects of mosquito biology, ecology, and evolution. A variety of DNA-based marker types are being used to develop genetic maps for a number of mosquito species. Complex phenotypic traits such as vector competence are being dissected into their discrete genetic components, with the intention of eventually using this information to develop new methods to prevent disease transmission. Both genetic- and physical-mapping techniques are being used to define and compare genome architecture among and within mosquito species. The integration of genetic- and physical-map information is providing a sound framework for map-based positional cloning of target genes of interest. This review focuses on advances in genome-based analysis and their specific applications to mosquitoes.