bluuebunny/crossref_metadata_2025 huggingface dataset:
Cooperating knowledge-based assistants for the office
Authors: Kaye A. Roger , Karam Gerald M.
Published: July 2002

This paper presents an approach to high-level support of office workers by embedding office knowledge in a network of distributed cooperating knowledge-based or expert “assistants” and servers. These knowledge-based systems incorporate both factual and procedural knowledge and are capable of making use of existing conventional office technology. They constitute a form of computer-supported cooperative work. We describe a common architecture for our assistants and servers that incorporates several key features. Our systems are capable of supporting concurrent multiple consultations or tasks and have facilities for the interruption and resumption of consultations as appropriate. The various assistants and servers, which may reside on different machines, cooperate in solving problems or completing tasks by passing messages. We propose a taxonomy of the general office knowledge normally used by office workers, together with a frame and rule-based knowledge representation scheme. We also describe an experimental system, written in PROLOG, that incorporates the above design principles.
Multiple-query optimization
Authors: Sellis Timos K.
Published: July 2002

Some recently proposed extensions to relational database systems, as well as to deductive database systems, require support for multiple-query processing. For example, in a database system enhanced with inference capabilities, a simple query involving a rule with multiple definitions may expand to more than one actual query that has to be run over the database. It is an interesting problem then to come up with algorithms that process these queries together instead of one query at a time. The main motivation for performing such an interquery optimization lies in the fact that queries may share common data. We examine the problem of multiple-query optimization in this paper. The first major contribution of the paper is a systematic look at the problem, along with the presentation and analysis of algorithms that can be used for multiple-query optimization. The second contribution lies in the presentation of experimental results. Our results show that using multiple-query processing algorithms may reduce execution cost considerably.
Optimal design and use of retry in fault-tolerant computer systems
Authors: Lee Yann-Heng , Shin Kang G.
Published: July 2002

In this paper, a new method is presented for (i) determining an
optimal retry policy
and (ii) using retry for
fault characterization
, which is defined as classification of the fault type and determination of fault durations. First, an optimal retry policy is derived for a given fault characteristic, which determines the maximum allowable retry durations so as to minimize the total task completion time. Then, the
combined
fault characterization and retry decision, in which the characteristic of a fault is estimated simultaneously with the determination of the optimal retry policy, are carried out. Two solution approaches are developed: one is based on point estimation and the other on Bayes sequential decision analysis.

Numerical examples are presented in which all the durations associated with faults (i.e., active, benign, and interfailure durations) have monotone hazard rate functions (e.g., exponential Weibull and gamma distributions). These are standard distributions commonly used for modeling and analyses of faults.
Implementing ranking strategies using text signatures
Authors: Croft W. Bruce , Savino Pasquale
Published: July 2002

Signature files provide an efficient access method for text in documents, but retrieval is usually limited to finding documents that contain a specified Boolean pattern of words. Effective retrieval requires that documents with similar meanings be found through a process of plausible inference. The simplest way of implementing this retrieval process is to rank documents in order of their probability of relevance. In this paper techniques are described for implementing probabilistic ranking strategies with sequential and bit-sliced signature tiles and the limitations of these implementations with regard to their effectiveness are pointed out. A detailed comparison is made between signature-based ranking techniques and ranking using term-based document representatives and inverted files. The comparison shows that term-based representations are at least competitive (in terms of efficiency) with signature files and, in some situations, superior.
Computing in higher education: the Athena experience
Authors: Balkovich Edward , Lerman Steven , Parmelee Richard P.
Published: July 2002

Project Athena at MIT is an experiment to explore the potential uses of advanced computer technology in the university curriculum. About 60 different educational development projects, spanning virtually all of MIT's academic departments, are already in progress.
Abstraction mechanisms in hypertext
Authors: Garg Pankaj,K.
Published: July 2002

Abstraction is the means by which information can be stored and retrieved from an information structure at different levels of detail and from different perspectives. As such, abstraction mechanisms in hypertext are interesting to evaluate from a theoretical perspective as they become various first-order logic formulae.
Optimal design of synchronous circuits using software pipelining techniques
Authors: Boyer François R. , Aboulhamid El Mostapha , Savaria Yvon , Boyer Michel
Published: July 2002

We present a method to optimize clocked circuits by relocating and changing the time of activation of registers to maximize the throughput. Our method is based on a modulo scheduling algorithm for software pipelining, instead of retiming. It optimizes the circuit without the constraint on the clock phases that retiming has, which permits to always achieve the optimal clock period. The two methods have the same overall time complexity, but we avoid the computation of all pair-shortest paths, which is a heavy burden regarding both space and time. From the optimal schedule found, registers are placed in the circuit without looking at where the original registers were. The resulting circuit is a multi-phase clocked circuit, where all the clocks have the same period and the phases are automatically determined by the algorithm. Edge-triggered flip-flops are used where the combinational delays exactly match that period, whereas level-sensitive latches are used elsewhere, improving the area occupied by the circuit. Experiments on existing and newly developed benchmarks show a substantial performance improvement compared to previously published work.
Mobile telephony in a connected life
Authors: Palen Leysia
Published: July 2002

Mobile phones help manage and grant instant access to users' dispersed social networks but risk violating the age-old social conventions of face-to-face relationships.
Statistical profile estimation in database systems
Authors: Mannino Michael V. , Chu Paicheng , Sager Thomas
Published: July 2002

A statistical profile summarizes the instances of a database. It describes aspects such as the number of tuples, the number of values, the distribution of values, the correlation between value sets, and the distribution of tuples among secondary storage units. Estimation of database profiles is critical in the problems of query optimization, physical database design, and database performance prediction. This paper describes a model of a database of profile, relates this model to estimating the cost of database operations, and surveys methods of estimating profiles. The operators and objects in the model include build profile, estimate profile, and update profile. The estimate operator is classified by the relational algebra operator (select, project, join), the property to be estimated (cardinality, distribution of values, and other parameters), and the underlying method (parametric, nonparametric, and ad-hoc). The accuracy, overhead, and assumptions of methods are discussed in detail. Relevant research in both the database and the statistics disciplines is incorporated in the detailed discussion.
Garbarge collection for Prolog based on WAM
Authors: Appleby Karen , Carlsson Mats , Haridi Seif , Sahlin Dan
Published: July 2002

The Warren abstract machine (WAM) has become a generally accepted standard Prolog implementation technique. Garbage collection is an important aspect in the implementation of any Prolog system. A synopsis of the WAM is presented and then marking and compaction algorithms are shown that take advantage of WAM's unique use of the data areas. Marking and compaction are performed on both the heap and the trail; both use pointer reversal techniques, which obviate the need for extra stack space. However, two bits for every pointer on the heap are reserved for the garbage collection algorithm. The algorithm can work on segments of the heap, which may lead to a significant reduction of the total garbage collection time. The time of the algorithms are linear in the size of the areas.
Computation of cyclic redundancy checks via table look-up
Authors: Sarwate D. V.
Published: July 2002

Cyclic Redundancy Check (CRC) codes provide a simple yet powerful method of error detection during digital data transmission. Use of a table look-up in computing the CRC bits will efficiently implement these codes in software.
A state transition model for distributed query processing
Authors: Lafortune Stéphane , Wong Eugene
Published: July 2002

A state transition model for the optimization of query processing in a distributed database system is presented. The problem is parameterized by means of a state describing the amount of processing that has been performed at each site where the database is located. A state transition occurs each time a new join or semijoin is executed. Dynamic programming is used to compute recursively the costs of the states and the globally optimal solution, taking into account communication and local processing costs. The state transition model is general enough to account for the possibility of parallel processing among the various sites, as well as for redundancy in the database. The model also permits significant reductions of the necessary computations by taking advantage of simple additivity and site-uniformity properties of a cost model, and of clever strategies that improve on the basic dynamic programming algorithm.
Decentralizing a global naming service for improved performance and fault tolerance
Authors: Cheriton D. R. , Mann T. P.
Published: July 2002

Naming is an important aspect of distributed system design. A naming system allows users and programs to assign character-string names to objects, and subsequently use the names to refer to those objects. With the interconnection of clusters of computers by wide-area networks and internetworks, the domain over which naming systems must function is growing to encompass the entire world.

In this paper we address the problem of a global naming system, proposing a three-level naming architecture that consists of global, administrational, and managerial naming mechanisms, each optimized to meet the performance, reliability, and security requirements at its own level. We focus in particular on a decentralized approach to the lower levels, in which naming is handled directly by the managers of the named objects. Client-name caching and multicast are exploited to implement name mapping with almost optimum performance and fault tolerance. We also show how the naming system can be made secure. Our conclusions are bolstered by experience with an implementation in the V distributed operating system.
Initializing generalized feedback shift register pseudorandom number generators
Authors: Collings Bruce Jay , Hembree G. Barry
Published: July 2002

The generalized feedback shift register pseudorandom number generators proposed by Lewis and Payne provide a very attractive method of random number generation. Unfortunately, the published initialization procedure can be extremely time consuming. This paper considers an alternative method of initialization based on a natural polynomial representation for the terms of a feedback shift register sequence that results in substantial improvements in the initialization process.
Partitioned two-phase locking
Authors: Hsu Meichun , Chan Arvola
Published: July 2002

In a large integrated database, there often exists an “information hierarchy,” where both raw data and derived data are stored and used together. Therefore, among update transactions, there will often be some that perform only read accesses from a certain (i.e., the “raw” data) portion of the database and write into another (i.e., the “derived” data) portion. A conventional concurrency control algorithm would have treated such transactions as regular update transactions and subjected them to the usual protocols for synchronizing update transactions. In this paper such transactions are examined more closely. The purpose is to devise concurrency control methods that allow the computation of derived information to proceed without interfering with the updating of raw data.

The first part of the paper presents a proof method for correctness of concurrency control algorithms in a hierarchically decomposed database. The proof method provides a framework for understanding the intricacies in dealing with hierarchically decomposed databases. The second part of the paper is an application of the proof method to show the correctness of a two-phase-locking- based algorithm, called partitioned two-phase locking, for hierarchically decomposed databases. This algorithm is a natural extension to the Version Pool method proposed previously in the literature.
Conception, evolution, and application of functional programming languages
Authors: Hudak Paul
Published: July 2002

The foundations of functional programming languages are examined from both historical and technical perspectives. Their evolution is traced through several critical periods: early work on lambda calculus and combinatory calculus, Lisp, Iswim, FP, ML, and modern functional languages such as Miranda
1
and Haskell. The fundamental premises on which the functional programming methodology stands are critically analyzed with respect to philosophical, theoretical, and pragmatic concerns. Particular attention is paid to the main features that characterize modern functional languages: higher-order functions, lazy evaluation, equations and pattern matching, strong static typing and type inference, and data abstraction. In addition, current research areas—such as parallelism, nondeterminism, input/output, and state-oriented computations—are examined with the goal of predicting the future development and application of functional languages.
Simultaneous WRITES of parallel random access machines do not help to compute simple arithmetic functions
Authors: Reischuk Rüdiger
Published: July 2002

The ability of the strongest parallel random access machine model WRAM is investigated. In this model different processors may simultaneously try to write into the same cell of the common memory. It has been shown that a parallel RAM without this option (PRAM), even with arbitrarily many processors, can almost never achieve sublogarithmic time. On the contrary, every function with a small domain like binary values in case of Boolean functions can be computed by a WRAM in constant time. The machine makes fast table look-ups using its simultaneous write ability. The main result of this paper implies that in general this is the “only way” to perform such fast computations and that a domain of small size is necessary. Otherwise simultaneous writes do not give an advantage. Functions with large domains for which any change of one of the
n
arguments also changes the result are considered, and a logarithmic lower time bound for WRAMs is proved. This bound can be achieved by machines that do not perform simultaneous writes. A simple example of such a function is the sum of
n
natural numbers.
On the design of some systolic algorithms
Authors: van de Snepscheut Jan L. A. , Swenker Johan B.
Published: July 2002

The design of systolic algorithms is discussed, that is, algorithms that may efficiently be executed by a synchronous array of cells that perform local communications only. Systolic algorithms are designed through techniques developed in the context of sequential programming. Heuristics are given that guide the programmer in the design of a variety of efficient solutions.
Multicast tree construction in bus-based networks
Authors: McKinley Philip K. , Liu Jane W. S.
Published: July 2002

Because of the multiple-access property of the media, the problem of constructing multicast trees in bus-based networks differs fundamentally from that in point-to-point networks. This article investigates the multicast tree construction for both general and specific network topologies.
Cube structures for multiprocessors
Authors: Padmanabhan Krishnan
Published: July 2002

The exact structural relationship between the hypercube and multistage interconnection networks for multiprocessors is characterized here. By varying the node architecture, structures other than these two interconnection schemes can be derived.
Lower bounds for orthogonal range searching: I. The reporting case
Authors: Chazelle Bernard
Published: July 2002

We establish lower bounds on the complexity of orthogonal range reporting in the static case. Given a collection of
n
points in
d
-space and a box [
a
1
,
b
1
] X … X [

a
d

,

b
d

], report every point whose
i
th coordinate lies in [

a
i
, b
i

], for each
i
= l, … ,
d
. The collection of points is fixed once and for all and can be preprocessed. The box, on the other hand, constitutes a query that must be answered online. It is shown that on a pointer machine a query time of
O
(
k
+ polylog(
n
)), where
k
is the number of points to be reported, can only be achieved at the expense of Ω(
n
(log
n
/log log
n
)

d
-1

) storage. Interestingly, these bounds are optimal in the pointer machine model, but they can be improved (ever so slightly) on a random access machine. In a companion paper, we address the related problem of adding up weights assigned to the points in the query box.
A relational information resource dictionary system
Authors: Dolk Daniel R , Kirsch Robert A.
Published: July 2002

A relational implementation of IRDS using SQL demonstrates how the flexibility of the relational environment enhances the extensibility of the IRDS while at the same time providing more powerful dictionary capabilities than are typically found in relational systems.
“Topologies”—distributed objects on multicomputers
Authors: Schwan Karsten , Bo Win
Published: July 2002

Application programs written for large-scale multicomputers with interconnection structures known to the programmer (e.g., hypercubes or meshes) use complex communication structures for connecting the applications' parallel tasks. Such structures implement a wide variety of functions, including the exchange of data or control information relevant to the task computations and/or the communications required for task synchronization, message forwarding/filtering under program control, and so on.Topologyis a programming and operating system construct that allows programmers to describe and efficiently implement such functionality as distributed objects with well-defined operational interfaces. As with abstract data types, topologies may be reused by any application desiring their functionality. However, in contrast to other research in parallel or distributed object-based operating systems, internally, a topology may be an entirely distributed implementation of the object's functionality, consisting of a communication graph and type-specific computations, which are triggered by messages traversing the graph. Sample computations may perform additions or minimizations of the values traversing a topology, thereby computing a global sum or minimum. Similarly, computations may concatenate or filter messages in order to implement program monitoring, I/O, file storage, or virtual terminal services.

Topologies are implemented as an extension of the Intel iPSC hypercube's operating system kernel and have been used with several, large-scale parallel application programs.
Contention is no obstacle to shared-memory multiprocessing
Authors: Rettberg Randall , Thomas Robert
Published: July 2002

Contention in large-scale shared-memory systems is less of a concern than generally believed. Through careful engineering of a parallel system, the effects of contention can be controlled.
A formal protection model of security in centralized, parallel, and distributed systems
Authors: Benson Glenn S. , Akyildiz Ian F. , Appelbe William F.
Published: July 2002

One way to show that a system is not secure is to demonstrate that a malicious or mistake-prone user or program can break security by causing the system to reach a nonsecure state. A fundamental aspect of a security model is a proof that validates that every state reachable from a secure initial state is secure. A sequential security model assumes that every command that acts as a state transition executes sequentially, while a concurrent security model assumes that multiple commands execute concurrently. This paper presents a security model called the Centralized-Parallel-Distributed model (CPD model) that defines security for logically, or physically centralized, parallel, and distributed systems. The purpose of the CPD model is to define concurrency conditions that guarentee that a concurrent system cannot reach a state in which privileges are configured in a nonsecure manner. As an example, the conditions are used to construct a representation of a distributed system.
The impact of information systems on organizations and markets
Authors: Gurbaxani Vijay , Whang Seungjin
Published: July 2002

The adoption of information technology (IT) in organizations has been growing at a rapid pace. The use of the technology has evolved from the automation of structured processes to systems that are truly revolutionary in that they introduce change into fundamental business procedures. Indeed, it is believed that “More than being helped by computers, companies will live by them, shaping strategy and structure to fit new information technology [25].” While the importance of the relationship between information technology and organizational change is evidenced by the considerable literature on the subject,
1
there is a lack of comprehensive analysis of these issues from the economic perspective. The aim of this article is to develop an economic understanding of how information systems affect some key measures of organization structure.
THE CONSTRUCTION OF POVERTY AND HOMELESSNESS IN US CITIES
Authors: Susser I.
Published: July 2002

▪ Abstract  The review focuses on analyses of the creation of culture among poor populations in the United States whose lives have been structured by residing at the center of the global economy. Literature is examined concerning the changing construction of labor, space, time, and identity in the new poverty. Throughout, the review examines the generation of poverty and questions of gender, race, political mobilization, and resistance. This outline of current research provides a framework for an analysis of the violence and conflict generated by the lowering of wages and the reduction of leisure time.
THE COMPARATIVE DEMOGRAPHY OF PRIMATES: With Some Comments on the Evolution of Life Histories
Authors: Gage Timothy B.
Published: July 2002

▪ Abstract  This chapter reviews the current state of knowledge concerning the demography of primates. It compiles demographic systems (mortality and fertility estimates) for four broad grades of primates: New World monkeys, Old World monkeys, chimpanzees, and humans. The characteristics of each system, including its demographic stability, are presented and discussed. The environmentally induced variation in human and nonhuman primate vital rates are explored whenever possible. Findings include (a) that more data are needed particularly with respect to nonhuman primate fertility, (b) that human demographic systems are the least stable, and (c) that Pan troglodytes demography is probably evolutionarily derived from the general primate pattern.
PLANT TRANSCRIPTION FACTOR STUDIES
Authors: Schwechheimer C. , Zourelidou M. , Bevan M. W.
Published: July 2002

▪ Abstract  Major advances have been made in understanding the role of transcription factors in gene expression in yeast, Drosophila, and man. Transcription factor modification, synergistic events, protein-protein interactions, and chromatin structure have been successfully integrated into transcription factor studies in these organisms. While many putative transcription factors have been isolated from plants, most of them are only poorly characterized. This review summarizes examples where molecular biological techniques have been successfully employed to study plant transcription factors. The functional analysis of transcription factors is described as well as techniques for studying the interactions of transcription factors with other proteins and with DNA.
CRASSULACEAN ACID METABOLISM:Molecular Genetics
Authors: Cushman John C. , Bohnert Hans J.
Published: July 2002

▪ Abstract  Crassulacean acid metabolism (CAM) is an adaptation of photosynthesis to limited availability of water or CO2. CAM is characterized by nocturnal CO2fixation via the cytosolic enzyme PEP carboxylase (PEPC), formation of PEP by glycolysis, malic acid accumulation in the vacuole, daytime decarboxylation of malate and CO2re-assimilation via ribulose-1,5-bisphosphate carboxylase (RUBISCO), and regeneration of storage carbohydrates from pyruvate and/or PEP by gluconeogenesis. Within this basic framework, the pathway exhibits an extraordinary range of metabolic plasticity governed by environmental, developmental, tissue-specific, hormonal, and circadian cues. Characterization of genes encoding key CAM enzymes has shown that a combination of transcriptional, posttranscriptional, translational, and posttranslational regulatory events govern the expression of the pathway. Recently, this information has improved our ability to dissect the regulatory and signaling events that mediate the expression and operation of the pathway. Molecular analysis and sequence information have also provided new ways of assessing the evolutionary origins of CAM. Genetic and physiological analysis of transgenic plants currently under development will improve our further understanding of the molecular genetics of CAM.
PLANTPLASMAMEMBRANEH+-ATPases: Powerhouses for Nutrient Uptake
Authors: Palmgren Michael G
Published: July 2002

▪ Abstract  Most transport proteins in plant cells are energized by electrochemical gradients of protons across the plasma membrane. The formation of these gradients is due to the action of plasma membrane H+pumps fuelled by ATP. The plasma membrane H+-ATPases share a membrane topography and general mechanism of action with other P-type ATPases, but differ in regulatory properties. Recent advances in the field include the identification of the complete H+-ATPase gene family in Arabidopsis, analysis of H+-ATPase function by the methods of reverse genetics, an improved understanding of the posttranslational regulation of pump activity by 14-3-3 proteins, novel insights into the H+transport mechanism, and progress in structural biology. Furthermore, the elucidation of the three-dimensional structure of a related Ca2+pump has implications for understanding of structure-function relationships for the plant plasma membrane H+-ATPase.
REGULATION OF EUKARYOTIC PHOSPHATIDYLINOSITOL-SPECIFIC PHOSPHOLIPASE C AND PHOSPHOLIPASE D
Authors: Singer William D. , Brown H. Alex , Sternweis Paul C.
Published: July 2002

This review focuses on two phospholipase activities involved in eukaryotic signal transduction. The action of the phosphatidylinositol-specific phospholipase C enzymes produces two well-characterized second messengers, inositol 1,4,5-trisphosphate and diacylglycerol. This discussion emphasizes recent advances in elucidation of the mechanisms of regulation and catalysis of the various isoforms of these enzymes. These are especially related to structural information now available for a phospholipase C δ isozyme.

Phospholipase D hydrolyzes phospholipids to produce phosphatidic acid and the respective head group. A perspective of selected past studies is related to emerging molecular characterization of purified and cloned phospholipases D. Evidence for various stimulatory agents (two small G protein families, protein kinase C, aand phosphoinositides) suggests complex regulatory mechanisms, and some studies suggest a role for this enzyme activity in intracellular membrane traffic.
G PROTEIN–COUPLED RECEPTOR KINASES
Authors: Pitcher Julie A. , Freedman Neil J. , Lefkowitz Robert J.
Published: July 2002

G protein–coupled receptor kinases (GRKs) constitute a family of six mammalian serine/threonine protein kinases that phosphorylate agonist-bound, or activated, G protein–coupled receptors (GPCRs) as their primary substrates. GRK-mediated receptor phosphorylation rapidly initiates profound impairment of receptor signaling, or desensitization. This review focuses on the regulation of GRK activity by a variety of allosteric and other factors: agonist-stimulated GPCRs, βγ subunits of heterotrimeric GTP-binding proteins, phospholipid cofactors, the calcium-binding proteins calmodulin and recoverin, posttranslational isoprenylation and palmitoylation, autophosphorylation, and protein kinase C–mediated GRK phosphorylation. Studies employing recombinant, purified proteins, cell culture, and transgenic animal models attest to the general importance of GRKs in regulating a vast array of GPCRs both in vitro and in vivo.
Conus Peptides Targeted to Specific Nicotinic Acetylcholine Receptor Subtypes
Authors: McIntosh J. Michael , Santos Ameurfina D. , Olivera Baldomero M.
Published: July 2002

▪ Abstract  The venoms of predatory cone snails represent a rich combinatorial-like library of evolutionarily selected, neuropharmacologically active peptides. A major fraction of the venom components are conotoxins—small, disulfide-rich peptides that potently and specifically target components of the neuromuscular system, particularly ligand- and voltage-gated ion channels. This review focuses on Conus peptides, which act at nicotinic acetylcholine receptors. These nicotinic antagonist peptides from Conus are broadly divided into two groups: those that act at the neuromuscular junction and those that act at subtypes of neuronal nicotinic acetylcholine receptors. The latter include peptides specific for the α7, α3β2, and α3β4 nicotinic receptor subtypes. The degree of specificity exhibited by these peptides is remarkable, particularly given their relatively small size. As a group the nicotinic acetylcholine receptor-targeted Conus peptides represent an increasingly well-defined set of tools for probing the structure, function, and physiological role of nicotinic acetylcholine receptors.
STRUCTURAL AND MECHANISTIC DETERMINANTS OF AFFINITY AND SPECIFICITY OF LIGANDS DISCOVERED OR ENGINEERED BY PHAGE DISPLAY
Authors: Katz Bradley A.
Published: July 2002

▪ Abstract  The scope and utility of phage display is reviewed with emphasis on medical applications and structure-based ligand and drug design, from literature mostly after 1994. General principles by which phage-displayed peptides achieve affinity and selectivity for targets are described, along with selected structural or mechanistic studies of the binding of peptides or proteins discovered or engineered by phage display. Such engineered proteins whose wild-type or mutant crystal or 2D-NMR structures yield insight about the basis for enhanced affinity or altered specificity include antibodies, zinc fingers, human growth hormone, protein A, and atrial natriuretic peptide. Structures of complexes of de novo phage-discovered peptide ligands with targets such as the Src SH3 domain, streptavidin, and erythropoietin receptor reveal the structural basis for receptor-peptide recognition in these systems.
CALCIUM IN CLOSE QUARTERS:Microdomain Feedback in Excitation-Contraction Coupling and Other Cell Biological Phenomena
Authors: Ríos Eduardo , Stern Michael D.
Published: July 2002

▪ Abstract  Researchers have made good progress in unraveling the molecular mechanisms of excitation-contraction (EC) coupling in striated muscle. Despite this progress, paradoxes abound. In skeletal muscle, the existence of a mechanical coupling between membrane charge movement and activation of sarcoplasmic reticulum (SR) release channels is essentially established, but the contribution of Ca2+-induced Ca2+ release (CICR) to the transient and steady-state components of Ca2+ release remains controversial. In cardiac muscle, the role of CICR as the primary mechanism of EC coupling is well established, but the stability and tight coupling between membrane Ca2+ current and release are paradoxical. Answers may lie in microdomain issues, and in the examination of discrete elementary release events, although quantitative treatments are needed. This review explores the theoretical and experimental methods used and the observations made in the study of microdomain Ca2+.
RNA RECOGNITION BY RNP PROTEINS DURING RNA PROCESSING
Authors: Varani Gabriele , Nagai Kiyoshi
Published: July 2002

▪ Abstract  The ribonucleoprotein (RNP) domain is one of the most common eukaryotic protein folds. Proteins containing RNP domains function in important steps of posttranscriptional regulation of gene expression by directing the assembly of multiprotein complexes on primary transcripts, mature mRNAs, and stable ribonucleoprotein components of the RNA processing machinery. The diverse functions performed by these proteins depend on their dual ability to recognize RNA and to interact with other proteins, often utilizing specialized auxiliary domains. Crystallographic and NMR structures of several RNP domains and a handful of structures of RNA-protein complexes have begun to reveal the molecular basis for RNP-RNA recognition.
ROTATIONAL COUPLING IN THE F0F1 ATP SYNTHASE
Authors: Nakamoto Robert K. , Ketchum Christian J. , Al-Shawi Marwan K.
Published: July 2002

▪ Abstract  The F0F1 ATP synthase is a large multisubunit complex that couples translocation of protons down an electrochemical gradient to the synthesis of ATP. Recent advances in structural analyses have led to the demonstration that the enzyme utilizes a rotational catalytic mechanism. Kinetic and biochemical evidence is consistent with the expected equal participation of the three catalytic sites in the α3β3 hexamer, which operate in sequential, cooperative reaction pathways. The rotation of the core γ subunit plays critical roles in establishing the conformation of the sites and the cooperative interactions. Mutational analyses have shown that the rotor subunits are responsible for coupling and in doing so transmit specific conformational information between transport and catalysis.
The Structural Biology of Molecular Recognition by Vancomycin
Authors: Loll Patrick J. , Axelsen Paul H.
Published: July 2002

▪ Abstract  Vancomycin is the archetype among naturally occurring compounds known as glycopeptide antibiotics. Because it is a vital therapeutic agent used worldwide for the treatment of infections with gram-positive bacteria, emerging bacterial resistance to vancomycin is a major public health threat. Recent investigations into the mechanisms of action of glycopeptide antibiotics are driven by a need to understand their detailed mechanism of action so that new agents can be developed to overcome resistance. These investigations have revealed that glycopeptide antibiotics exhibit a rich array of complex cooperative phenomena when they bind target ligands, making them valuable model systems for the study of molecular recognition.
Theoretical and Empirical Examination of Density-Dependent Selection
Authors: Mueller Laurence D.
Published: July 2002

The development of theory on density-dependent natural selection has seen a transition from very general, logistic growth-based models to theories that incorporate details of specific life histories. This transition has been justified by the need to make predictions that can then be tested experimentally with specific model systems like bacteria or Drosophila. The most general models predict that natural selection should increase density-dependent rates of population growth. When trade-offs exist, those genotypes favored in low-density environments will show reduced per capita growth rates under crowded conditions and vice versa for evolution in crowded environments. This central prediction has been verified twice in carefully controlled experiments with Drosophila. Empirical research in this field has also witnessed a major transition from field-based observations and conjecture to carefully controlled laboratory selection experiments. This change in approach has permitted crucial tests of theories of density-dependent natural selection and a deeper understanding of the mechanisms of adaptation to different levels of population crowding. Experimental research with Drosophila has identified several phenotypes important to adaptation, especially at high larval densities. This same research revealed that an important trade-off occurs between competitive ability and energetic efficiency.
Dissecting Global Diversity Patterns: Examples from the Ordovician Radiation
Authors: Miller Arnold I.
Published: July 2002

Although the history of life has been characterized by intermittent episodes of radiation that can be recognized in global compilations of biodiversity, it does not necessarily follow that these episodes are caused by processes that occurred uniformly around the world. Major diversity increases could be generated by the cumulative effects of different mechanisms operating simultaneously at several geographic or environmental scales. The purpose of this review is to describe ongoing research on the manifestations, at several scales, of the Ordovician Radiation, which was among the most extensive intervals of diversification in the history of life. Through much of the period, diversity was concentrated most heavily near regions of active mountain building and volcanism; differences in diversity patterns from continent to continent, and among regions within continents, reflect this overprint. While this suggests a linkage of the Radiation and tectonic activity, this is by no means the only mediating agent. Outcrop-based research in North America has demonstrated that tectonic activity was detrimental to some biotic elements, in contrast to its effects on other organisms. Moreover, in the Great Basin of North America where the local stratigraphic record is of particularly high quality, biotic transitions characteristic of the period occurred far more rapidly than observed in global compilations of diversity, suggesting that the global rate of transition may represent the aggregate sum of transitions that occurred abruptly, but at different times, around the world. Finally, it has been demonstrated that, in concert with an increase in average age, the environmental and geographic ranges of Ordovician genera both increased significantly through the period, indicating a role for intrinsic factors in producing Ordovician biotic patterns.
EARLY EVOLUTION OF LAND PLANTS: Phylogeny, Physiology, and Ecology of the Primary Terrestrial Radiation
Authors: Bateman Richard M. , Crane Peter R. , DiMichele William A. , Kenrick Paul R. , Rowe Nick P. , Speck Thomas , Stein William E.
Published: July 2002

▪ Abstract  The Siluro-Devonian primary radiation of land biotas is the terrestrial equivalent of the much-debated Cambrian “explosion” of marine faunas. Both show the hallmarks of novelty radiations (phenotypic diversity increases much more rapidly than species diversity across an ecologically undersaturated and thus low-competition landscape), and both ended with the formation of evolutionary and ecological frameworks analogous to those of modern ecosystems. Profound improvements in understanding early land plant evolution reflect recent liberations from several research constraints: Cladistic techniques plus DNA sequence data from extant relatives have prompted revolutionary reinterpretations of land plant phylogeny, and thus of systematics and character-state acquisition patterns. Biomechanical and physiological experimental techniques developed for extant plants have been extrapolated to fossil species, with interpretations both aided and complicated by the recent knowledge that global landmass positions, currents, climates, and atmospheric compositions have been profoundly variable (and thus nonuniformitarian) through the Phanerozoic. Combining phylogenetic and paleoecological data offers potential insights into the identity and function of key innovations, though current evidence suggests the importance of accumulating within lineages a critical mass of phenotypic character. Challenges to further progress include the lack of sequence data and paucity of phenotypic features among the early land plant clades, and a fossil record still inadequate to date accurately certain crucial evolutionary and ecological events.
Cenozoic Mammalian Herbivores From the Americas: Reconstructing Ancient Diets and Terrestrial Communities
Authors: MacFadden Bruce J.
Published: July 2002

▪ Abstract  Herbivory first evolved in terrestrial mammals during the late Cretaceous, ∼100 million years ago (Mya). Of the ∼35 ordinal-level clades of extinct or extant eutherian mammals from the New World, ∼24 have been adapted to herbivory in one form or another. Dental adaptations for specialized terrestrial browsing are first recognized during the early Cenozoic (Paleocene-Eocene). Mammalian herbivores adapted for grazing did not become widespread in the New World until the middle Cenozoic; it seems that this adaptation and the spread of grasslands occurred during the late Oligocene (30 Mya) in South America ∼10 million years earlier than in North America (20 Mya). Carbon isotopic evidence from fossil herbivore teeth indicates that C3 plants predominated until the late Miocene (∼8 Mya). Thereafter, C3 and C4 terrestrial communities diversified. Late Pleistocene extinctions ∼10,000 years ago decimated the diversity of mammalian herbivores, particularly those of larger body size.
BIOLOGICAL MEDIATORS OF INSECT IMMUNITY
Authors: Gillespie and Jeremy P. , Kanost Michael R. , Trenczek Tina
Published: July 2002

▪ Abstract  Infection in insects stimulates a complex defensive response. Recognition of pathogens may be accomplished by plasma or hemocyte proteins that bind specifically to bacterial or fungal polysaccharides. Several morphologically distinct hemocyte cell types cooperate in the immune response. Hemocytes attach to invading organisms and then isolate them by phagocytosis, by trapping them in hemocyte aggregates called nodules, or by forming an organized multicellular capsule around large parasites. These responses are often accompanied by proteolytic activation of the phenoloxidase zymogen that is present in the hemolymph. A component of insect immune responses to bacteria is the synthesis by fat body and hemocytes of a variety of antibacterial proteins and peptides, which are secreted into the hemolymph. These molecules attack bacteria by several mechanisms. Inducible antifungal proteins have also been recently discovered in insect hemolymph. The promoters for several antibacterial protein genes in insects are regulated by transcription factors similar to those involved in mammalian acute phase responses.
Arthropod Allergens and Human Health
Authors: Arlian Larry G.
Published: July 2002

▪ Abstract  Many species of arthropods are the sources of potent allergens that sensitize and induce IgE-mediated allergic reactions in humans. Most of these arthropod allergens are proteins, and the allergic response mechanism to these allergens is the same as it is for allergens from other sources such as plant pollens, molds, and foods. Aside from ingestion of crustaceans (shrimp, lobster), among arthropods, humans have the greatest contact with insects and mites, and as a result allergies to these two groups of arthropods have been the most frequently reported. Because of the large number of people affected by allergic reactions to stinging insects, cockroaches, and dust mites, many allergens of these organisms have been extensively studied, purified, and immunobiochemically characterized and for some recombinant allergens, produced. Cocktails of these recombinant allergens have the potential for use in diagnosis and immunotherapy. In this chapter, we review the insects and mites that induce allergic reactions. Where the information exists, the immunobiochemical characterization of the allergens and the frequency of sensitivity or clinical reactivity in the human population are also reviewed. As background, the beginning of this review includes sections that define allergens, explain the allergic reaction mechanism, and describe the methods for naming allergens.
EXPERIMENTS ON THERMOCAPILLARY INSTABILITIES
Authors: Schatz Michael F , Neitzel G Paul
Published: July 2002

▪ Abstract  This review summarizes recent experimental studies of instabilities in free-surface flows driven by thermocapillarity. Two broad classes are considered, depending upon whether the imposed temperature gradient is perpendicular (Marangoni-convection instability) or parallel (thermocapillary-convection instability) to the free surface. Both steady and time-dependent instabilites are reviewed in experiments employing both large- and small-aspect-ratio geometries of various symmetries.
RECOGNITION AND SILENCING OF REPEATED DNA
Authors: Hsieh Jenny , Fire Andrew
Published: July 2002

▪ Abstract  Mechanisms for repetition of DNA pose both opportunities and challenges to a functional genome: opportunities for increasing gene expression by amplification of useful sequences, and challenges of controlling amplification by unwanted sequences such as transposons and viruses. Experiments in numerous organisms have suggested the likely existence of a general mechanism for recognition of repeated character in DNA. This review focuses (a) on the nature of these recognition mechanisms, and (b) on types of chromatin modification and gene silencing that are used to control repeated DNA.
MOLECULAR MECHANISMS FOR CONSTITUTIONAL CHROMOSOMAL REARRANGEMENTS IN HUMANS
Authors: Shaffer Lisa G. , Lupski James R.
Published: July 2002

▪ Abstract  Cytogenetic imbalance in the newborn is a frequent cause of mental retardation and birth defects. Although aneuploidy accounts for the majority of imbalance, structural aberrations contribute to a significant fraction of recognized chromosomal anomalies. This review describes the major classes of constitutional, structural cytogenetic abnormalities and recent studies that explore the molecular mechanisms that bring about their de novo occurrence. Genomic features flanking the sites of recombination may result in susceptibility to chromosomal rearrangement. One such substrate for recombination is low-copy region-specific repeats. The identification of genome architectural features conferring susceptibility to rearrangements has been accomplished using methods that enable investigation of regions of the genome that are too small to be visualized by traditional cytogenetics and too large to be resolved by conventional gel electrophoresis. These investigations resulted in the identification of previously unrecognized structural cytogenetic anomalies, which are associated with genetic syndromes and allowed for the molecular basis of some chromosomal rearrangements to be delineated.