bluuebunny/crossref_metadata_2025 huggingface dataset:
Efficient Virus Extinction by Combinations of a Mutagen and Antiviral Inhibitors
Authors: Pariente Nonia , Sierra Saleta , Lowenstein Pedro R. , Domingo Esteban
Published: July 2002

The effect of combinations of the mutagenic base analog 5-fluorouracil (FU) and the antiviral inhibitors guanidine hydrochloride (G) and heparin (H) on the infectivity of foot-and-mouth disease virus (FMDV) in cell culture has been investigated. Related FMDV clones differing up to 10
6
-fold in relative fitness in BHK-21 cells have been compared. Systematic extinction of intermediate fitness virus was attained with a combination of FU and G but not with the mutagen or the inhibitor alone. Systematic extinction of high-fitness FMDV required the combination of FU, G, and H. FMDV showing high relative fitness in BHK-21 cells but decreased replicative ability in CHO cells behaved as a low-fitness virus with regard to extinction mutagenesis in CHO cells. This confirms that relative fitness, rather than a specific genomic sequence, determines the FMDV response to enhanced mutagenesis. Mutant spectrum analysis of several genomic regions from a preextinction population showed a statistically significant increase in the number of mutations compared with virus passaged in parallel in the absence of FU and inhibitors. Also, in a preextinction population the types of mutations that can be attributed to the mutagenic action of FU were significantly more frequent than other mutation types. The results suggest that combinations of mutagenic agents and antiviral inhibitors can effectively drive high-fitness virus into extinction.
Human T-Cell Leukemia Virus Type 1 Tax Protein Binds to Assembled Nuclear Proteasomes and Enhances Their Proteolytic Activity
Authors: Hemelaar Joris , Bex Françoise , Booth Bruce , Cerundolo Vincenzo , McMichael Andrew , Daenke Susan
Published: July 2002

The human T-cell leukemia virus type 1 (HTLV-1) Tax protein activates the HTLV-1 long terminal repeat and key regulatory proteins involved in inflammation, activation, and proliferation and may induce cell transformation. Tax is also the immunodominant target antigen for cytotoxic T cells in HTLV-1 infection. We found that Tax bound to assembled nuclear proteasomes, but Tax could not be detected in the cytoplasm. Confocal microscopy revealed a partial colocalization of Tax with nuclear proteasomes. As Tax translocated into the nucleus very quickly after synthesis, this process probably takes place prior to and independent of proteasome association. Tax mutants revealed that both the Tax N and C termini play a role in proteasome binding. We also found that proteasomes from Tax-transfected cells had enhanced proteolytic activity on prototypic peptide substrates. This effect was not due to the induction of the LMP2 and LMP7 proteasome subunits. Furthermore, Tax appeared to be a long-lived protein, with a half-life of around 15 h. These data suggest that the association of Tax with the proteasome and the enhanced proteolytic activity do not target Tax for rapid degradation and may not determine its immunodominance.
Exercise dependence, social physique anxiety, and social support in experienced and inexperienced bodybuilders and weightlifters
Authors: Hurst Richard , Hale Bruce , Smith David , Collins David
Published: July 2002

Objectives—To investigate psychological correlates of exercise dependence in experienced and inexperienced bodybuilders and weightlifters. Secondary objectives included measuring social physique anxiety, bodybuilding identity, and social support among bodybuilders and weightlifters.

Methods—Thirty five experienced bodybuilders, 31 inexperienced bodybuilders, and 23 weightlifters completed the bodybuilding dependence scale, a bodybuilding version of the athletic identity measurement scale, the social physique anxiety scale, and an adapted version of the social support survey-clinical form.

Results—A between subjects multivariate analysis of variance was calculated on the scores of the three groups of lifters for the four questionnaires. UnivariateFtests and follow up tests indicated that experienced bodybuilders scored significantly higher than inexperienced bodybuilders and weightlifters on bodybuilding dependence (p<0.001), social identity and exclusivity subscales of bodybuilding identity (p<0.001), and social support scales (p<.001), and significantly lower on social physique anxiety (p<0.001).

Conclusion—Experienced bodybuilders exhibit more exercise dependence, show greater social support behaviour, and experience less social physique anxiety than inexperienced bodybuilders and weightlifters.
The first 20 years (1978-1979 to 1998–1999) of ice-wedge growth at the Illisarvik experimental drained lake site, western Arctic coast, Canada
Authors: Mackay J Ross , Burn C R
Published: July 2002

In August 1978, a large tundra lake was drained to study the aggradation of permafrost into newly exposed lake-bottom sediments. Ice-wedge growth, which started in the first winter following drainage, had ceased in most of the lake bottom within about twelve years. The gradual cessation of thermal contraction cracking can be attributed to rapid vegetation growth, snow entrapment, an increase in winter ground temperatures, and a decrease in the linear coefficient of thermal contraction associated with freezethaw consolidation of the initially saturated lake-bottom sediments. The tilt and separation of markers in the active layer revealed gradual convergence towards the troughs even after ice-wedge growth had ceased. For the first few years the ice-wedge growth rate was up to 3 cm/a as determined by excavation, drilling, separation of the bottoms of benchmarks installed into permafrost, and divergence of free-floating inductance coils placed on the sides of ice wedges well below the bottom of the active layer. The vertical extent of most ice wedges was probably about 2 m, as deduced from the depths of ice-wedge cracks and the geometries of the wedge tops. Many thermal contraction cracks propagated upward to the ground surface from the tops of the ice wedges rather than downward from the ground surface. Small, upward facing, horizontal steps and vertical slickensided surfaces in permafrost on both sides of an excavated ice wedge near its top indicated that the adjacent permafrost had moved upward, relative to the wedge, from thermal expansion during the warming period.
Construction over organic soils in an urban environment: four case histories
Authors: Gould R A , Bedell Philip R , Muckle J G
Published: July 2002

Four case histories relating to construction over organic soils in an urban environment are reported. Three of the cases can be classified as failures; buildings were unwittingly constructed over organic soils and the subsequent performance of the buildings was unsatisfactory. The presence of peat was recognized in the fourth case, but the design was carried out to accommodate the resulting settlements. Case history 1 deals with a small industrial mall that was founded in fill and was partially located over a peat-filled pocket. The building experienced large differential settlements, and extensive repairs consisting of piled foundations in the affected area were required. Case histories 2 and 3 concern single-family houses that were founded in fill overlying organic soils. Differential settlement caused severe damage to the houses. Repairs were required and consisted of levelling the structures on the original foundations and reducing the loads to minimize future settlements. In addition, a unique method of foundation wall reinforcement was employed in case history 2. Case history 4 documents the performance of a municipal roadway and sanitary sewer constructed over a deposit of organic materials. This sewer was designed with a flexible pipe to float within the fill over the compressible material, with provision being made for future settlement. Settlements of the road surface have been monitored. The information presented should assist the design engineer in mitigating the effects of having compressible, organic subsoils beneath structures.Key words: organic soils, peat, case histories, settlement.
SCALING ALGEBRAS AND RENORMALIZATION GROUP IN ALGEBRAIC QUANTUM FIELD THEORY
Authors: BUCHHOLZ DETLEV , VERCH RAINER
Published: July 2002

For any given algebra of local observables in Minkowski space an associated scaling algebra is constructed on which renormalization group (scaling) transformations act in a canonical manner. The method can be carried over to arbitrary space-time manifolds and provides a framework for the systematic analysis of the short distance properties of local quantum field theories. It is shown that every theory has a (possibly non-unique) scaling limit which can be classified according to its classical or quantum nature. Dilation invariant theories are stable under the action of the renormalization group. Within this framework the problem of wedge (Bisognano-Wichmann) duality in the scaling limit is discussed and some of its physical implications are outlined.
YET ANOTHER CHAOTIC ATTRACTOR
Authors: CHEN GUANRONG , UETA TETSUSHI
Published: July 2002

This Letter reports the finding of a new chaotic at tractor in a simple three-dimensional autonomous system, which resembles some familiar features from both the Lorenz and Rossler at tractors.
ON THE CLOSURE OF MASS BALANCE MODELS FOR TUMOR GROWTH
Authors: AMBROSI D. , PREZIOSI L.
Published: July 2002

Mass balance equations typically adopted to describe tumor growth are to be closed by introducing a suitable velocity field. The first part of this paper is devoted to a critical review of some approaches devised to this aim in the relevant literature. In the second part we start from the observation that the phenomenological description of a tumor spheroid suggests to model it as a growing and deformable porous material. The concept of volume fraction and the essentials of the mechanics of multicomponent continua are then introduced and applied to the problem at hand. The system of equations regulating such a system is stated and its validity is then discussed at the light of numerical simulations.
LOGISTIC REGRESSION MODELING OF SOFTWARE QUALITY
Authors: KHOSHGOFTAAR TAGHI M. , ALLEN EDWARD B.
Published: July 2002

Reliable software is mandatory for complex mission-critical systems. Classifying modules as fault-prone, or not, is a valuable technique for guiding development processes, so that resources can be focused on those parts of a system that are most likely to have faults.

Logistic regression offers advantages over other classification modeling techniques, such as interpretable coefficients. There are few prior applications of logistic regression to software quality models in the literature, and none that we know of account for prior probabilities and costs of misclassification. A contribution of this paper is the application of prior probabilities and costs of misclassification to a logistic regression-based classification rule for a software quality model.

This paper also contributes an integrated method for using logistic regression in software quality modeling, including examples of how to interpret coefficients, how to use prior probabilities, and how to use costs of misclassifications. A case study of a major subsystem of a military, real-time system illustrates the techniques.
The interdisciplinary study of coordination
Authors: Malone Thomas W. , Crowston Kevin
Published: July 2002

This survey characterizes an emerging research area, sometimes called
coordination theory
, that focuses on the interdisciplinary study of coordination. Research in this area uses and extends ideas about coordination from disciplines such as computer science, organization theory, operations research, economics, linguistics, and psychology.

A key insight of the framework presented here is that coordination can be seen as the process of
managing dependencies
among activities. Further progress, therefore, should be possible by characterizing different kinds of dependencies and identifying the coordination processes that can be used to manage them. A variety of processes are analyzed from this perspective, and commonalities across disciplines are identified. Processes analyzed include those for managing
shared resources, producer/consumer relationships, simultaneity constraints
, and
task/subtask dependencies
.

Section 3 summarizes ways of applying a coordination perspective in three different domains:(1) understanding the effects of information technology on human organizations and markets, (2) designing cooperative work tools, and (3) designing distributed and parallel computer systems. In the final section, elements of a research agenda in this new area are briefly outlined.
Semiring-based constraint satisfaction and optimization
Authors: Bistarelli Stefano , Montanari Ugo , Rossi Francesca
Published: July 2002

We introduce a general framework for constraint satisfaction and optimization where classical CSPs, fuzzy CSPs, weighted CSPs, partial constraint satisfaction, and others can be easily cast. The framework is based on a semiring structure, where the set of the semiring specifies the
values to be associated with each tuple of values of the variable domain, and the two semiring operations (+ and X) model constraint projection and combination respectively. Local consistency algorithms, as usually used for classical CSPs, can be exploited in this general framework as well, provided that certain conditions on the semiring operations are satisfied. We then show how this framework can be used to model both old and new constraint solving and optimization schemes, thus allowing one to both formally justify many informally taken choices in existing schemes, and to prove that local consistency techniques can be used also in newly defined schemes.
Approximate graph coloring by semidefinite programming
Authors: Karger David , Motwani Rajeev , Sudan Madhu
Published: July 2002

We consider the problem of coloring
k
-colorable graphs with the fewest possible colors. We present a randomized polynomial time algorithm that colors a 3-colorable graph on
n
vertices with min{
O
(Δ
1/3
log
1/2
Δ log
n
),
O
(
n
1/4
log
1/2
n
)} colors where Δ is the maximum degree of any vertex. Besides giving the best known approximation ratio in terms of
n
, this marks the first nontrivial approximation result as a function of the maximum degree Δ. This result can be generalized to
k
-colorable graphs to obtain a coloring using min{
O
(Δ

1-2/
k

log
1/2
Δ log
n
),
O
(
n

1−3/(
k
+1)

log
1/2
n
)} colors. Our results are inspired by the recent work of Goemans and Williamson who used an algorithm for
semidefinite optimization problems
, which generalize linear programs, to obtain improved approximations for the MAX CUT and MAX 2-SAT problems. An intriguing outcome of our work is a duality relationship established between the value of the optimum solution to our semidefinite program and the Lovász θ-function. We show lower bounds on the gap between the optimum solution of our semidefinite program and the actual chromatic number; by duality this also demonstrates interesting new facts about the θ-function.
Private information retrieval
Authors: Chor Benny , Kushilevitz Eyal , Goldreich Oded , Sudan Madhu
Published: July 2002

Publicly accessible databases are an indispensable resource for retrieving up-to-date information. But they also pose a significant risk to the privacy of the user, since a curious database operator can follow the user's queries and infer what the user is after. Indeed, in cases where the users' intentions are to be kept secret, users are often cautious about accessing the database. It can be shown that when accessing a single database, to completely guarantee the privacy of the user, the whole database should be down-loaded; namely
n
bits should be communicated (where
n
is the number of bits in the database).

In this work, we investigate whether by replicating the database, more efficient solutions to the private retrieval problem can be obtained. We describe schemes that enable a user to access
k
replicated copies of a database (
k
≥2) and
privately
retrieve information stored in the database. This means that each individual server (holding a replicated copy of the database) gets no information on the identity of the item retrieved by the user. Our schemes use the replication to gain substantial saving. In particular, we present a two-server scheme with communication complexity
O(n
1/3
).
An
O
(log
n
) expected rounds randomized byzantine generals protocol
Authors: Bracha Gabriel
Published: July 2002

Byzantine Generals protocols enable processes to broadcast messages reliably in the presence of faulty processes. These protocols are run in a system that consists of
n
processes,
t
of which are faulty. The protocols are conducted in synchronous rounds of message exchange. It is shown that, in the absence of eavesdropping, without using cryptography, for any ε > 0 and
t
=
n
/(3 + ε), there is a randomized protocol with
O
(log
n
) expected number of rounds. If cryptographic methods are allowed, then, for ε > 0 and
t
=
n
/(2 + ε), there is a randomized protocol with
O
(log
n
) expected number of rounds. This is an improvement on the lower bound of
t
+ 1 rounds required for deterministic protocols, and on a previous result of
t
/log
n
expected number of rounds for randomized noncryptographic protocols.
Making abstract interpretations complete
Authors: Giacobazzi Roberto , Ranzato Francesco , Scozzari Francesca
Published: July 2002

Completeness is an ideal, although uncommon, feature of abstract interpretations, formalizing the intuition that, relatively to the properties encoded by the underlying abstract domains, there is no loss of information accumulated in abstract computations. Thus, complete abstract interpretations can be rightly understood as optimal. We deal with both pointwise completeness, involving generic semantic operations, and (least) fixpoint completeness. Completeness and fixpoint completeness are shown to be properties that depend on the underlying abstract domains only. Our primary goal is then to solve the problem of making abstract interpretations complete by minimally extending or restricting the underlying abstract domains. Under the weak and reasonable hypothesis of dealing with continuous semantic operations, we provide constructive characterizations for the least complete extensions and the greatest complete restrictions of abstract domains. As far as fixpoint completeness is concerned, for merely monotone semantic operators, the greatest restrictions of abstract domains are constructively characterized, while it is shown that the existence of least extensions of abstract domains cannot be, in general, guaranteed, even under strong hypotheses. These methodologies, which in finite settings give rise to effective algorithms, provide advanced formal tools for manipulating and comparing abstract interpretations, useful both in static program analysis and in semantics design. A number of examples illustrating these techniques are given.
Analyzing bounding boxes for object intersection
Authors: Suri Subhash , Hubbard Philip M. , Hughes John F.
Published: July 2002

Heuristics that exploit bouning boxes are common in algorithms for rendering, modeling, and animation. While experience has shown that bounding boxes improve the performance of these algorithms in practice, the previous theoretical analysis has concluded that bounding boxes perform poorly in the worst case. This paper reconciles this discrepancy by analyzing intersections amongngeometric objects in terms of two parameters: α an upper bound on theaspect ratioor elongatedness of each object; and σ an upper bound on thescale factoror size disparity between the largest and smallest objects. LettingKoandKbbe the number of intersecting object pairs and bounding box pairs, respectively, we analyze a ratio measure of the bounding boxes' efficiency, ρ =Kb/ (n + K0). The analysis proves thatρ = O(α√σlog2σ)andρ = Ω(α√σ).

One important consequence is that if α and σ are small constants (as is often the case in practice), thenKb=O(Ko)+O(n, so an algorithm that uses bounding boxes has time complexity proportional to the number of actual object intersections. This theoretical result validates the efficiency that bounding boxes have demonstrated in practice. Another consequence of our analysis is a proof of the output-sensitivity of an algorithm for reporting all intersecting pairs in a set ofnconvex polyhedra with constant α and σ. The algorithm takes timeO(nlogd-1n+Kologd-1n) for dimensiond= 2, 3. This running time improves on the performance of previous algorithms, which make no assumptions about α and σ.
Charting past, present, and future research in ubiquitous computing
Authors: Abowd Gregory D. , Mynatt Elizabeth D.
Published: July 2002

The proliferation of computing into the physical world promises more than the ubiquitous availability of computing infrastructure; it suggest new paradigms of interaction inspired by constant access to information and computational capabilities. For the past decade, application-driven research on abiquitous computing (ubicomp) has pushed three interaction themes:natural interfaces, context-aware applications,andautomated capture and access. To chart a course for future research in ubiquitous computing, we review the accomplishments of these efforts and point to remaining research challenges. Research in ubiquitious computing implicitly requires addressing some notion of scale, whether in the number and type of devices, the physical space of distributed computing, or the number of people using a system. We posit a new area of applications research,everyday computing,focussed on scaling interaction with respect to time. Just as pushing the availiability of computing away from the traditional desktop fundamentally changes the relationship between humans and computers, providing continuous interaction moves computing from a localized tool to a constant companion. Designing for continous interaction requires addressing interruption and reumption of intreaction, representing passages of time and providing associative storage models. Inherent in all of these interaction themes are difficult issues in thesocial implicationsof ubiquitous computing and the challenges ofevaluating>ubiquitious computing research. Although cumulative experience points to lessons in privacy, security, visibility, and control, there are no simple guidelines for steering research efforts. Akin to any efforts involving new technologies, evaluation strategies form a spectrum from technology feasibility efforts to long-term use studies—but a user-centric perspective is always possible and necessary
A comparison of next-fit, first-fit, and best-fit
Authors: Bays Carter
Published: July 2002

“Next-fit” allocation differs from first-fit in that a first-fit allocator commences its search for free space at a fixed end of memory, whereas a next-fit allocator commences its search wherever it previously stopped searching. This strategy is called “modified first-fit” by Shore [2] and is significantly faster than the first-fit allocator. To evaluate the relative efficiency of next-fit (as well as to confirm Shore's results) a simulation was written in Basic Plus on the PDP-11, using doubly linked lists to emulate the memory structure of the simulated computer. The simulation was designed to perform essentially in the manner described in [2]. The results of the simulation of the three methods show that the efficiency of next-fit is decidedly inferior to first-fit and best-fit when the mean size of the block requested is less than about 1/16 the total memory available. Beyond this point all three allocation schemes have similar efficiencies.
Ethernet
Authors: Metcalfe Robert M. , Boggs David R.
Published: July 2002

Ethernet is a branching broadcast communication system for carrying digital data packets among locally distributed computing stations. The packet transport mechanism provided by Ethernet has been used to build systems which can be viewed as either local computer networks or loosely coupled multiprocessors. An Ethernet's shared communication facility, its Ether, is a passive broadcast medium with no central control. Coordination of access to the Ether for packet broadcasts is distributed among the contending transmitting stations using controlled statistical arbitration. Switching of packets to their destinations on the Ether is distributed among the receiving stations using packet address recognition. Design principles and implementation are described based on experience with an operating Ethernet of 100 nodes along a kilometer of coaxial cable. A model for estimating performance under heavy loads and a packet protocol for error controlled communication are included for completeness.
The UNIX time-sharing system
Authors: Ritchie Dennis M. , Thompson Ken
Published: July 2002

UNIX is a general-purpose, multi-user, interactive operating system for the Digital Equipment Corporation PDP-11/40 and 11/45 computers. It offers a number of features seldom found even in larger operating systems, including: (1) a hierarchical file system incorporating demountable volumes; (2) compatible file, device, and inter-process I/O; (3) the ability to initiate asynchronous processes; (4) system command language selectable on a per-user basis; and (5) over 100 subsystems including a dozen languages. This paper discusses the nature and implementation of the file system and of the user command interface.
Design and evaluation of a wide-area event notification service
Authors: Carzaniga Antonio , Rosenblum David S. , Wolf Alexander L.
Published: July 2002

The components of a loosely coupled system are typically designed to operate by generating and responding to asynchronous events. An
event notification service
is an application-independent infrastructure that supports the construction of event-based systems, whereby generators of events publish event notifications to the infrastructure and consumers of events subscribe with the infrastructure to receive relevant notifications. The two primary services that should be provided to components by the infrastructure are notification selection (i. e., determining which notifications match which subscriptions) and notification delivery (i.e., routing matching notifications from publishers to subscribers). Numerous event notification services have been developed for local-area networks, generally based on a centralized server to select and deliver event notifications. Therefore, they suffer from an inherent inability to scale to wide-area networks, such as the Internet, where the number and physical distribution of the service's clients can quickly overwhelm a centralized solution. The critical challenge in the setting of a wide-area network is to maximize the expressiveness in the selection mechanism without sacrificing scalability in the delivery mechanism. This paper presents SIENA, an event notification service that we have designed and implemented to exhibit both expressiveness and scalability. We describe the service's interface to applications, the algorithms used by networks of servers to select and deliver event notifications, and the strategies used to optimize performance. We also present results of simulation studies that examine the scalability and performance of the service.
Searching the Web
Authors: Arasu Arvind , Cho Junghoo , Garcia-Molina Hector , Paepcke Andreas , Raghavan Sriram
Published: July 2002

We offer an overview of current Web search engine design. After introducing a generic search engine architecture, we examine each engine component in turn. We cover crawling, local Web page storage, indexing, and the use of link analysis for boosting search performance. The most common design and implementation techniques for each of these components are presented. For this presentation we draw from the literature and from our own experimental search engine testbed. Emphasis is on introducing the fundamental concepts and the results of several performance analyses we conducted to compare different designs.
Consensus in the presence of partial synchrony
Authors: Dwork Cynthia , Lynch Nancy , Stockmeyer Larry
Published: July 2002

The concept of partial synchrony in a distributed system is introduced. Partial synchrony lies between the cases of a synchronous system and an asynchronous system. In a synchronous system, there is a known fixed upper bound Δ on the time required for a message to be sent from one processor to another and a known fixed upper bound Φ on the relative speeds of different processors. In an asynchronous system no fixed upper bounds Δ and Φ exist. In one version of partial synchrony, fixed bounds Δ and Φ exist, but they are not known a priori. The problem is to design protocols that work correctly in the partially synchronous system regardless of the actual values of the bounds Δ and Φ. In another version of partial synchrony, the bounds are known, but are only guaranteed to hold starting at some unknown time
T
, and protocols must be designed to work correctly regardless of when time
T
occurs. Fault-tolerant consensus protocols are given for various cases of partial synchrony and various fault models. Lower bounds that show in most cases that our protocols are optimal with respect to the number of faults tolerated are also given. Our consensus protocols for partially synchronous processors use new protocols for fault-tolerant “distributed clocks” that allow partially synchronous processors to reach some approximately common notion of time.
The P
2
algorithm for dynamic calculation of quantiles and histograms without storing observations
Authors: Jain Raj , Chlamtac Imrich
Published: July 2002

A heuristic algorithm is proposed for dynamic calculation of the median and other quantiles. The estimates are produced dynamically as the observations are generated. The observations are not stored; therefore, the algorithm has a very small and fixed storage requirement regardless of the number of observations. This makes it ideal for implementing in a quantile chip that can be used in industrial controllers and recorders. The algorithm is further extended to histogram plotting. The accuracy of the algorithm is analyzed.
Deciding first-order properties of locally tree-decomposable structures
Authors: Frick Markus , Grohe Martin
Published: July 2002

We introduce the concept of a class of graphs, or more generally, relational structures, being
locally tree-decomposable
. There are numerous examples of locally tree-decomposable classes, among them the class of planar graphs and all classes of bounded valence or of bounded tree-width. We also consider a slightly more general concept of a class of structures having
bounded local tree-width
.We show that for each property ϕ of structures that is definable in first-order logic and for each locally tree-decomposable class C of structures, there is a linear time algorithm deciding whether a given structure
A
∈ C has property ϕ. For classes C of bounded local tree-width, we show that for every
k
≥ 1 there is an algorithm solving the same problem in time
O
(
n

1+(1/
k
)

) (where
n
is the cardinality of the input structure).
Mixin layers
Authors: Smaragdakis Yannis , Batory Don
Published: July 2002

A "refinement" is a functionality addition to a software project that can affect multiple dispersed implementation entities (functions, classes, etc.). In this paper, we examine large-scale refinements in terms of a fundamental object-oriented technique called collaboration-based design. We explain how collaborations can be expressed in existing programming languages or can be supported with new language constructs (which we have implemented as extensions to the Java language). We present a specific expression of large-scale refinements called
mixin layers
, and demonstrate how it overcomes the scalability difficulties that plagued prior work. We also show how we used mixin layers as the primary implementation technique for building an extensible Java compiler, JTS.
Understanding the effectiveness of computer graphics for decision support: a cumulative experimental approach
Authors: Dickson Gary W. , DeSanctis Gerardine , McBride D. J.
Published: July 2002

A total of 840 junior and senior-level undergraduate business students particpated in three experiments that compared computer-generated graphical forms of data presentation to traditional tabular reports. The first experiment compared tables and bar charts for their effects on readability, interpretation accuracy, and decision making. No differences in interpretation accuracy or decision quality were observed for the two groups, although tabular reports were rated as "easier to read and understand" than graphical reports. The second experiment compared line plots to tables for their effects on interpretation accuracy and decision quality. Subjects with graphical reports outperformed those with tables. There were no meaningful differences in interpretation accuracy across treatment groups. The third experiment compared graphical and tabular reports for their ability to convey a "message" to the reader. Only in situations in which a vast amount of information was presented and relatively simple impressions were to be made, did subjects given graphs outperform those using tables.

This program of cumulative experiments indicates that generalized claims of superiority of graphic presentation are unsupported, at least for decision-related activities. In fact, the experiments suggest that the effectiveness of the data display format is largely a function of the characteristics of the task at hand, and that impressions gleaned from "one shot" studies of the effectiveness of the use of graphs may be nothing more than situationally dependent artifacts.
CULTURE IN NONHUMAN PRIMATES?
Authors: McGrew W. C.
Published: July 2002

▪ Abstract  Cultural primatology is hypothesized on the basis of social learning of group-specific behavior by nonhuman primates, especially in nature. Scholars ask different questions in testing this idea: what? (anthropologists), how? (psychologists), and why? (zoologists). Most evidence comes from five genera: Cebus (capuchin monkeys), Macaca (macaque monkeys), Gorilla (gorilla), Pongo (orangutan), and Pan (chimpanzees). Two species especially, Japanese monkey (Macaca fuscata) and chimpanzee (Pan troglodytes), show innovation, dissemination, standardization, durability, diffusion, and tradition in both subsistence and nonsubsistence activities, as revealed by decades of longitudinal study.
OXYGEN DEFICIENCY AND ROOT METABOLISM: Injury and Acclimation Under Hypoxia and Anoxia
Authors: Drew Malcolm C.
Published: July 2002

▪ Abstract  Oxygen deficiency in the rooting zone occurs with poor drainage after rain or irrigation, causing depressed growth and yield of dryland species, in contrast with native wetland vegetation that tolerates such conditions. This review examines how roots are injured by O2 deficiency and how metabolism changes during acclimation to low concentrations of O2.

In the root apical meristem, cell survival is important for the future development; metabolic changes under anoxia help maintain cell survival by generating ATP anaerobically and minimizing the cytoplasmic acidosis associated with cell death. Behind the apex, where cells are fully expanded, ethylene-dependent death and lysis occurs under hypoxia to form continuous, gas-filled channels (aerenchyma) conveying O2 from the leaves. This selective sacrifice of cells may resemble programmed cell death and is distinct from cell death caused by anoxia. Evidence concerning alternative possible mechanisms of anoxia tolerance and avoidance is presented.
Functions of Cell Surface Heparan Sulfate Proteoglycans
Authors: Bernfield Merton , Götte Martin , Park Pyong Woo , Reizes Ofer , Fitzgerald Marilyn L. , Lincecum John , Zako Masahiro
Published: July 2002

▪ Abstract  The heparan sulfate on the surface of all adherent cells modulates the actions of a large number of extracellular ligands. Members of both cell surface heparan sulfate proteoglycan families, the transmembrane syndecans and the glycosylphosphoinositide-linked glypicans, bind these ligands and enhance formation of their receptor-signaling complexes. These heparan sulfate proteoglycans also immobilize and regulate the turnover of ligands that act at the cell surface. The extracellular domains of these proteoglycans can be shed from the cell surface, generating soluble heparan sulfate proteoglycans that can inhibit interactions at the cell surface. Recent analyses of genetic defects in Drosophila melanogaster, mice, and humans confirm most of these activities in vivo and identify additional processes that involve cell surface heparan sulfate proteoglycans. This chapter focuses on the mechanisms underlying these activities and on the cellular functions that they regulate.
Cyclooxygenases: Structural, Cellular, and Molecular Biology
Authors: Smith William L. , DeWitt David L. , Garavito R. Michael
Published: July 2002

▪ Abstract  The prostaglandin endoperoxide H synthases-1 and 2 (PGHS-1 and PGHS-2; also cyclooxygenases-1 and 2, COX-1 and COX-2) catalyze the committed step in prostaglandin synthesis. PGHS-1 and 2 are of particular interest because they are the major targets of nonsteroidal anti-inflammatory drugs (NSAIDs) including aspirin, ibuprofen, and the new COX-2 inhibitors. Inhibition of the PGHSs with NSAIDs acutely reduces inflammation, pain, and fever, and long-term use of these drugs reduces fatal thrombotic events, as well as the development of colon cancer and Alzheimer's disease. In this review, we examine how the structures of these enzymes relate mechanistically to cyclooxygenase and peroxidase catalysis, and how differences in the structure of PGHS-2 confer on this isozyme differential sensitivity to COX-2 inhibitors. We further examine the evidence for independent signaling by PGHS-1 and PGHS-2, and the complex mechanisms for regulation of PGHS-2 gene expression.
Platelet-Activating Factor and Related Lipid Mediators
Authors: Prescott Stephen M. , Zimmerman Guy A. , Stafforini Diana M. , McIntyre Thomas M.
Published: July 2002

▪ Abstract  Platelet-activating factor (PAF) is a phospholipid with potent, diverse physiological actions, particularly as a mediator of inflammation. The synthesis, transport, and degradation of PAF are tightly regulated, and the biochemical basis for many of these processes has been elucidated in recent years. Many of the actions of PAF can be mimicked by structurally related phospholipids that are derived from nonenzymatic oxidation, because such compounds can bind to the PAF receptor. This process circumvents much of the biochemical control and presumably is regulated primarily by the rate of degradation, which is catalyzed by PAF acetylhydrolase. The isolation of cDNA clones encoding most of the key proteins involved in regulating PAF has allowed substantial recent progress and will facilitate studies to determine the structural basis for substrate specificity and the precise role of PAF in physiological events.
PEROXISOME PROLIFERATOR-ACTIVATED RECEPTORS: A Nuclear Receptor Signaling Pathway in Lipid Physiology
Authors: Lemberger Thomas , Desvergne Béatrice , Wahli Walter
Published: July 2002

▪ Abstract  Peroxisome proliferator-activated receptors (PPARs) are lipid-activated transcription factors that belong to the steroid/thyroid/retinoic acid receptor superfamily. All their characterized target genes encode proteins that participate in lipid homeostasis. The recent finding that antidiabetic thiazolidinediones and adipogenic prostanoids are ligands of one of the PPARs reveals a novel signaling pathway that directly links these compounds to processes involved in glucose homeostasis and lipid metabolism including adipocyte differentiation. A detailed understanding of this pathway could designate PPARs as targets for the development of novel efficient treatments for several metabolic disorders.
Cell Polarity in Yeast
Authors: Chant John
Published: July 2002

▪ Abstract  Subcellular asymmetry, cell polarity, is fundamental to the diverse specialized functions of eukaryotic cells. In yeast, cell polarization is essential to division and mating. As a result, this highly accessible experimental system serves as a paradigm for deciphering the molecular mechanisms underlying the generation of polarity. Beyond yeast, cell polarity is essential to the partitioning of cell fate in embryonic development, the generation of axons and their guidance during neuronal development, and the intimate communication between lymphocytes within the immune system. The polarization of yeast cells shares many features with that of these more complex examples, including regulation by both intrinsic and extrinsic cues, conserved regulatory molecules such as Cdc42 GTPase, and asymmetry of the cytoskeleton as its centerpiece. This review summarizes the molecular pathways governing the generation of cell polarity in yeast.
Cooperation Between Microtubule- and Actin-Based Motor Proteins
Authors: Brown Susan S.
Published: July 2002

▪ Abstract  Organelle transport has been proposed to proceed in two steps: long-range transport along microtubules and local delivery via actin filaments. This model is supported by recent studies of pigment transport in several cell types and transport in neurons, and in several cases, class V myosin has been implicated as the actin-based motor. Mutations in mice (dilute) and yeast (myo2) have also implicated this class of myosin in organelle transport, and genetic interactions in yeast have indicated that a kinesin-related protein (Smy1p) plays a supporting role. This link between members of two different motor superfamilies has now taken a surprising turn: There is evidence for a physical interaction between class V myosins and kinesin or Smy1p in both mice and yeast.
MELTING TEMPERATURE OF THE EARTH'S MANTLE AND CORE: Earth's Thermal Structure
Authors: Boehler Reinhard
Published: July 2002

▪ Abstract  Although the temperature at the top of the lower mantle is well constrained by phase equilibrium data for the transformation of transition zone minerals to the denser perovskite polymorphs, the temperature distribution in the lower mantle is poorly known. Models depend strongly on the assumptions of the amount of internal heating and the viscosity profile. New melting data on iron to pressures of the outer core (2 Mbar) and the observed strong decrease of eutectic melting depression in the Fe-FeO-FeS system with increasing pressure, however, tightly constrain the temperature at the inner-core boundary to slightly less than 5000 K. This estimate can be reconciled with all recent static melting measurements on iron and lays within the uncertainty of shock temperature measurements. The resulting temperature at the core-mantle boundary of about 4000 K then requires a large temperature gradient at the bottom of the lower mantle of about 1500 K. Recent findings of the very high melting temperatures of the major lower-mantle materials Mg-Si-perovskite and magnesiowüstite indicate that this increase in temperature does not cause melting in the lower mantle.
SEDIMENT BACTERIA: Who's There, What Are They Doing, and What's New?
Authors: Nealson Kenneth H.
Published: July 2002

▪ Abstract  The prokaryotes (bacteria) comprise the bulk of the biomass and chemical activity in sediments. They are well suited to their role as sediment chemists, as they are the right size and have the required metabolic versatility to oxidize the organic carbon in a variety of different ways. The characteristic vertical nutrient (electron donor and electron acceptor) profiles seen in sediments are produced as a result of microbial activities, with each nutrient a product or reactant of one or more metabolic groups. Thus, understanding the mechanisms by which the chemical environment of a sediment is generated and stabilized requires a knowledge of resident populations, something that has been very difficult to obtain, given the techniques available to microbiologists. However, the new approaches of molecular biology, which have added insights into the phylogenetic relationships of the prokaryotes, have also provided tools whereby sedimentary populations can be examined without the need for culturing the organisms. These techniques, in concert with new methods of microscopy, isolation of new metabolic groups, and the study of new ecosystems, suggest that there is much that will be learned about the microbiology of sedimentary environments in the coming years.
MAJOR PATTERNS IN THE HISTORY OF CARNIVOROUS MAMMALS
Authors: Van Valkenburgh Blaire
Published: July 2002

▪ Abstract  The history of carnivorous mammals is characterized by a series of rise-and-fall patterns of diversification in which declining clades are replaced by phylogenetically distinct but functionally similar clades. Seven such examples from the last 46 million years are described for North America and Eurasia. In three of the seven turnover events, competition with replacement taxa may have driven the decline of formerly dominant taxa. In the remaining four this is less likely because inferred functional similarity was minimal during the interval of temporal overlap between clades. However, competition still may have been important in producing the rise-and-fall pattern through suppression of evolution within replacement taxa; as long as the large carnivore ecospace was filled, the radiation of new taxa into that ecospace was limited, only occurring after the extinction of the incumbents. The apparently inevitable decline of incumbent taxa may reflect the tendency for clades of large carnivorous mammals to produce more specialized species as they mature, leading to increased vulnerability to extinction when environments change.
RECRUITMENT AND THE LOCAL DYNAMICS OF OPEN MARINE POPULATIONS
Authors: Caley M. J. , Carr M. H. , Hixon M. A. , Hughes T. P. , Jones G. P. , Menge B. A.
Published: July 2002

▪ Abstract  The majority of marine populations are demographically open; their replenishment is largely or exclusively dependent on a supply of juveniles from the plankton. In spite of much recent research, no consensus has yet been reached regarding the importance of recruitment relative to other demographic processes in determining local population densities. We argue 1. that demographic theory suggests that, except under restrictive and unlikely conditions, recruitment must influence local population density to some extent. Therefore, 2. the question as to whether the size of a particular population is limited by recruitment is misguided. Finally, 3. the effect of recruitment on population size can be difficult to detect but is nonetheless real. A major weakness of most existing studies is a lack of attention to the survival of recruits over appropriate scales of time and space. Acknowledgment of the multifactorial determination of population density should guide the design of future experimental studies of the demography of open populations.