bluuebunny/crossref_metadata_2025 huggingface dataset:
Routing through a rectangle
Authors: Mehlhorn K. , Preparata F. P.
Published: July 2002

In this paper an
O
(
N
log
N
) algorithm for routing through a rectangle is presented. Consider an
n
-by-
m
rectangular grid and a set of
N
two-terminal nets. A net is a pair of points on the boundary of the rectangle. A layout is a set of edge-disjoint paths, one for each net. Our algorithm constructs a layout, if there is one, in
O
(
N
log
N
) time; this contrasts favorably with the area of the layout that might be as large as
N
2
. The layout constructed can be wired using four layers of interconnect with only
O
(
N
) contact cuts. A partial extension to multiterminal nets is also discussed.
A matrix-algebraic solution to two

K
m

servers in a loop
Authors: van de Liefvoort Appie , Lipsky Lester
Published: July 2002

An explicit steady-state solution is given for any queuing loop made up of two general servers, whose distribution functions have rational Laplace transforms. The solution is in matrix geometric form over a vector space that is itself a direct or Kronecker product of the internal state spaces of the two servers. The algebraic properties of relevant entities in this space are given in an appendix. The closed-form solution yields simple recursive relations that in turn lead to an efficient algorithm for calculating various performance measures such as queue length and throughput. A computational-complexity analysis shows that the algorithm requires at least an order of magnitude less computational effort than any previously reported algorithm.
An algorithm for the multiplication of symmetric polynomials
Authors: Garavelli John S.
Published: July 2002

Although the cycle index polynomial for a permutation group can often be easily determined, expansion of the figure counting series in a Po´lya enumeration presents computational difficulties for object sets with higher degrees of symmetry and more than modest size. An algorithm that does not require algebraic symbol manipulation is derived for multiplying symmetric polynomials represented by partitions. Because the repetitive identification and collection of common terms are eliminated and storage requirements reduced, this algorithm is useful in rapidly expanding the figure counting series in such Po´lya enumeration problems as the counting of chemical isomers.
Algorithm 665: Machar: a subroutine to dynamically determined machine parameters
Authors: Cody W. J.
Published: July 2002

Numerical software written in high-level languages often relies on machine-dependent parameters to improve portability. MACHAR is an evolving FORTRAN subroutine for dynamically determining thirteen fundamental parameters associated with a floating-point arithmetic system. The version presented here operates correctly on a large number of different floating-point systems, including those implementing the new IEEE Floating-Point Standard.
Admediation
Authors: Gopal Ram D. , Walter Zhiping , Tripathi Arvind K.
Published: July 2002

Using incentive-based approaches to match interested buyers and sellers.
On the fundamental limitations of transformational design
Authors: Voeten Jeroen
Published: July 2002

The completeness of a collection of design transformations is an important aspect in transformational design. Completeness guarantees that any correct design can in principle be explored using the transformation system. In the field of transformational design the problem of incompleteness is not well understood and it is often believed that complete transformation systems can be constructed. In this article, we show, using a formal framework based on the theory of computation, that this is not the case if the transformation system is based on an expressive general-purpose design language such as VHDL. Only when restrictions are imposed on the design language and correctness relation, a transformation system can be made complete in theory, but this is expected to result in serious practical problems. It is shown that the incompleteness problem in transformational design is closely related to the syntactic variance problem in high-level synthesis and that this latter problem is not solvable in general either.
Using complete-1-distinguishability for FSM equivalence checking
Authors: Ashar Pranav , Gupta Aarti , Malik Sharad
Published: July 2002

This article introduces the notion of a Complete-1-Distinguishability (C-1-D) property for simplifying equivalence checking of finite state machines (FSMs). When a specification machine has the C-1-D property, the traversal of the product machine can be eliminated. Instead, a much simpler check suffices. The check consists of first obtaining a 1-equivalence mapping between the individually reachable states of the specification and the implementation machines, and then checking that it is a bisimulation relation. The C-1-D property can be used directly for specification machines on which it naturally holds---a condition that has not been exploited thus far in FSM verification. We also show how this property can be enforced on an arbitrary FSM by exposing some of its latch outputs as pseudo-primary outputs during synthesis and verification. In this sense, our synthesis/verification methodology provides another point in the trade-off curve between constraints-on-synthesis versus complexity-of-verification. Practical experiences with this methodology have resulted in success with several examples for which it is not possible to complete verification using existing implicit state space traversal techniques.
Stodgy by design, and the notion of `dumbing up'
Authors: Glass Robert L.
Published: July 2002

Depending on your career roots, it seems editorial preferences may focus less on what is said and more on how it's said.
Creating e-commerce courses with regional intent
Authors: Zhang Qing Bian , Chau Patrick Y. K.
Published: July 2002

How one university in China created and incorporated e-commerce courses with due speed and native reference tools.
Question and answer
Authors: Seiden Joshua
Published: July 2002

Have you found yourself using standard design features simply because they are standards? I know I have. We assume that a feature has become standard for a good reason, and we may follow it without much consideration. Josh Seiden urges us to change our approach, restrain our impulse to use the standard answer to a design problem, and look deeper to see if it really does meet our users' needs.
---Elizabeth Buie

P.S. When I conceived "Whiteboard," I envisioned a provocative, opinionated, informal, and humorous column. What I did not insist on was that I agree with its contributors' views. This installment was difficult for me to edit---not for its main point (challenging assumptions can be a very good thing) but because I question some of its specific recommendations (I certainly want to know in which folder my file is being stored!) and also because I am involved in standards development. It was an interesting exercise in maintaining my detachment, and I have Josh to thank for the opportunity.
On fault classes and error detection capability of specification-based testing
Authors: Tsuchiya Tatsuhiro , Kikuno Tohru
Published: July 2002

In a previous paper, Kuhn [1999] showed that faults in Boolean specifications constitute a hierarchy with respect to detectability, and drew the conclusion that missing condition faults should be hypothesized to generate tests. However this conclusion was premature, since the relationships between missing condition faults and faults in other classes have not been sufficiently analyzed. In this note, we investigate such relationships, aiming to complement the work of Kuhn. As a result, we obtain an extended hierarchy of fault classes and reach a different conclusion.
Computer science: the science of and about information and computation
Authors: Bajcsy Ruzena , Reynolds Craig
Published: July 2002

New computing paradigms present serious challenges for system architecture.
Microarchitectural synthesis of performance-constrained, low-power VLSI designs
Authors: Goodby Laurence , Orailoğlu Alex , Chau Paul M.
Published: July 2002

New portable signal-processing applications such as mobile telephony, wireless computing, and personal digital assistants place stringent power consumption limits on their constituent components. Substantial power savings can be realized if 5 V designs are translated to use the new lower supply voltage standards. This conversion, however, is not achieved easily: a design originally targeted for implementation in a 5 V technology will typically require significant rework to meet timing and throughput requirements at the lower operating voltage. In this paper we describe a high-level synthesis system which assists the designer in performing this task, minimizing the need for manual redesign. Techniques employed in this work include pipelining and a new approach to module selection that minimizes power consumption subject to timing constraints. Using these and other high-level synthesis techniques to target designs to 3.3 V libraries, we show that it is possible to reduce power consumption by as much as 56% as compared to the original 5 V implementation, while meeting specified minimum throughput and maximum latency constraints.
What's in a word?
Authors: Allen Bruce G. , Buie Elizabeth
Published: July 2002

When you say something is
intuitive
, do you mean that absolutely everybody understands it right away? If you say a program is
logical
, what help is that to a user? Does
user-friendly
mean anything these days? (Did it ever?)
Motivo
Authors: Abbott Robert , Litfin Bill
Published: July 2002

Motivo
is an award-winning interactive design firm that blends strategic information design, appropriate technology, and meaningful visual communication to achieve the goal of innovation. Every day, we solve complex interaction and communication problems for national and international clientele by extending brands, empowering experience, and enabling commerce.
An optimal minimum spanning tree algorithm
Authors: Pettie Seth , Ramachandran Vijaya
Published: July 2002

We establish that the algorithmic complexity of the minimum
spanning tree problem is equal to its decision-tree complexity.
Specifically, we present a deterministic algorithm to find a
minimum spanning tree of a graph with
n
vertices and
m
edges that runs in time
O
(
T
*
(
m,n
)) where
T
*
is the minimum number of edge-weight
comparisons needed to determine the solution. The algorithm is
quite simple and can be implemented on a pointer machine.Although
our time bound is optimal, the exact function describing it is not
known at present. The current best bounds known for
T
*
are
T
*
(
m,n
) =
Ω(
m
) and
T
*
(
m,n
) =
O
(
m
∙ α(
m,n
)), where α is a
certain natural inverse of Ackermann's function.Even under the
assumption that
T
*
is superlinear, we show that
if the input graph is selected from
G

n,m

,
our algorithm runs in linear time with high probability, regardless
of
n
,
m
, or the permutation of edge weights. The
analysis uses a new martingale for
G

n,m

similar to the edge-exposure martingale for
G

n,p

.
Building big, reliable web sites, (part 1)
Authors: Treese Win
Published: July 2002

In the early days of the Web, most users were not terribly concerned with performance or reliability. Sometimes Web sites were slow, sometimes they did not respond, but that was to be expected. Besides, many users had slow connections to the network, so they hardly noticed if the server was slow. A popular server might be overloaded for a while, but then it would recover.
The use of memory in text processing
Authors: Lebowitz Michael
Published: July 2002

The performance of a natural language processing system should improve as it reads more and more texts. This is true both for systems intended as cognitive models and for practical text processing systems. Permanent long-term memory should be useful during all stages of text understanding. For example, if, while reading a patent abstract about a new disk drive, a system can retrieve information about similar objects from memory, processing should be simplified. However, most natural language programs do not exhibit such learning behavior. We describe in this article how RESEARCHER, a program that reads, remembers and generalizes from patent abstracts, makes use of its automatically generated memory to assist in low-level text processing, primarily involving disambiguation that could be accomplished no other way. We describe both RESEARCHER's basic understanding methods and the integration of memory access. Included is an extended example of RESEARCHER processing a patent abstract by using information about several other abstracts already in memory.
Whiteboards: a graphical database tool
Authors: Donahue James , Widom Jennifer
Published: July 2002

The “Whiteboards” system is intended to be an electronic equivalent of the whiteboards and corkboards that we have in our offices. A Whiteboard database has similar qualities of storing disparate collections of data and saving their spatial location in a window to help with organization. A Whiteboard database can contain references to arbitrary entities: text files, notes, programs, tools, pictures, etc. Whiteboards runs as an application in the Cedar programming environment developed at the Xerox Palo Alto Research Center.
Complexity and parallel processing: an interview with Richard Karp
Authors: Frenkel Karen A. , Karp Richard
Published: July 2002

In the following interview, which took place at ACM 85 in Denver, Karp discusses the relation of his work to leading-edge computing topics like parallel processing and artificial intelligence. Tracing his experience as a pioneer in highly theoretical computer science, Karp describes how the decision to go against established wisdom led to the work for which he is best known and how a colleague's findings led him to see links between two previously unrelated areas. Throughout, he stresses the exchange of ideas with colleagues that helped yield fundamental insights.
The structure of microcomputer file systems
Authors: Golden Donald , Pechura Michael
Published: July 2002

With an understanding of the structure of microcomputer file systems and what causes incompatibilities between them, it is possible to write software that will enable one system to read files written by another—provided they have physically compatible hardware.
Variable-depth trie index optimization: theory and experimental results
Authors: Ramesh R. , Babu A. J. G. , Kincaid J. Peter
Published: July 2002

We develop an efficient approach to Trie index optimization. A
Trie
is a data structure used to index a file having a set of attributes as record identifiers. In the proposed methodology, a file is horizontally partitioned into subsets of records using a Trie index whose depth of indexing is allowed to vary. The retrieval of a record from the file proceeds by “stepping through” the index to identify a subset of records in the file in which a binary search is performed. This paper develops a taxonomy of optimization problems underlying variable-depth Trie index construction. All these problems are solvable in polynomial time, and their characteristics are studied. Exact algorithms and heuristics for their solution are presented. The algorithms are employed in CRES-an expert system for editing written narrative material, developed for the Department of the Navy. CRES uses several large-to-very-large dictionary files for which Trie indexes are constructed using these algorithms. Computational experience with CRES shows that search and retrieval using variable-depth Trie indexes can be as much as six times faster than pure binary search. The space requirements of the Tries are reasonable. The results show that the variable-depth Tries constructed according to the proposed algorithms are viable and efficient for indexing large-to-very-large files by attributes in practical applications.
Size-time complexity of Boolean networks for prefix computations
Authors: Bilardi G. , Preparata F. P.
Published: July 2002

The prefix problem consists of computing all the products
x
0
x
1
…

x
j

(
j
= 0, … ,
N
- 1), given a sequence x = (
x
0
,
x
1
, … ,
x

N-
1

) of elements in a semigroup. In this paper we completely characterize the size-time complexity of computing prefixes with Boolean networks, which are synchronized interconnections of Boolean gates and one-bit storage devices. This complexity crucially depends upon two properties of the underlying semigroup, which we call cycle-freedom (no cycle of length greater than one in the Cayley graph of the semigroup), and memory-induciveness (arbitrarily long products of semigroup elements are true functions of all their factors). A nontrivial characterization is given of non-memory-inducive semigroups as those whose recurrent subsemigroup (formed by the elements with self-loops in the Cayley graph) is the direct product of a left-zero semigroup and a right-zero semigroup. Denoting by
S
and
T
size and computation time, respectively, we have S = Θ((
N
/
T
)log(
N
/
T
)) for memory-inducive non-cycle-free semigroups, and S = Θ(
N
/
T
) for all other semigroups. We have
T
ε [Ω(log
N
), Ο(
N
)] for all semigroups, with the exception of those whose recurrent subsemigroup is a right-zero semigroup, for which
T
ε [Ω(1), Ο(
N
)]. The preceding results are also extended to the VLSI model of computation. Area-time optimal circuits are obtained for both boundary and nonboundary I/O protocols.
Self-timing programs and the quantum scheduler
Authors: Guthery S. B.
Published: July 2002

Using an internally generated program clock in conjunction with a quantum scheduler creates self-timing programs that are useful in building deterministic computer systems.
The Department of Defense software initiative—a status report
Authors: Lieblein Edward
Published: July 2002

The Initiative is a comprehensive effort to address major software engineering issues in both the military and private industry.
Self-assessment procedure XV: a self-assessment procedure dealing with file processing
Authors: Solomon Martin K. , Bickel Riva Wenig
Published: July 2002

A self-assessment procedure dealing with file processing
On driving many long wires in a VLSI layout
Authors: Ramachandran Vijaya
Published: July 2002

It is assumed that long wires represent large capacitive loads, and the effect on the area of a VLSI layout when drivers are introduced along many long wires in the layout is investigated. A layout is presented for which the introduction of
standard
drivers along long wires squares the area of the layout; it is shown, however, that the increase in area is never greater than the layout's area squared if the driver can be laid out in a square region. This paper also shows an area-time trade-off for the driver of a single long wire of length / by which the area of the driver from Θ(
l
), to Θ(

l
q

),
q
< l, can be reduced if a delay of Θ(
l
l-q
) rather than Θ(log
l
) can be tolerated. Tight bounds are also obtained on the worst-case area increase in general layouts having these drivers.
ALGORITHM 643
Authors: Mehta Cyrus R. , Patel Nitin R.
Published: July 2002

The computer code for Mehta and Patel's (1983) network algorithm for Fisher's exact test on unordered
r×c
contingency tables is provided. The code is written in double precision FORTRAN 77. This code provides the fastest currently available method for executing Fisher's exact test, and is shown to be orders of magnitude superior to any other available algorithm. Many important details of data structures and implementation that have contributed crucially to the success of the network algorithm are recorded here.
Iterated interpolation using a systolic array
Authors: McKeown G. P.
Published: July 2002

An implementation using systolic array logic of Aitken's method of iterated interpolation is described. The proposed design has a simple, linear topology, requires no clock, and makes only modest demands on the host computer. By overlapping the computation of successive function values, a processing element utilization of approximately 1/2 is achieved. The paper illustrates how “mathematical hardware” packages, as well as software library routines, may be part of the mathematical problem solver's tool kit in the future.
New lower bounds for parallel computation
Authors: Li Ming , Yesha Yaacov
Published: July 2002

Lower bounds are proven on the parallel-time complexity of several basic functions on the most powerful concurrent-read concurrent-write PRAM with unlimited shared memory and unlimited power of individual processors (denoted by PRIORITY(∞)):

It is proved that with a number of processors polynomial in
n
, Ω (log
n
) time is needed for addition, multiplication or bitwise OR of
n
numbers, when each number has
n
' bits. Hence even the
bit complexity
(i.e., the time complexity as a function of the total number of bits in the input) is logarithmic in this case. This improves a beautiful result of Meyer auf der Heide and Wigderson [22]. They proved a log
n
lower bound using Ramsey-type techniques. Using Ramsey theory, it is possible to get an upper bound on the number of bits in the inputs used. However, for the case of polynomially many processors, this upper bound is more than a polynomial in
n
.

An Ω (log
n
) lower bound is given for PRIORITY(∞) with
n
o(1)
processors on a function with inputs from {0, 1}, namely for the function ƒ(
x
1
, … ,

x
n

,) = Σ

n

l
- 1

x
l
a
i

where
a
is fixed and

x
i

ε {0, 1}.

Finally, by a new efficient simulation of PRIORITY(∞) by unbounded fan-in circuits, that with less than exponential number of processors, it is proven a PRIORITY(∞) cannot compute PARITY in constant time, and with

n
O(1)

processors Ω(√log
n
) time is needed. The simulation technique is of independent interest since it can serve as a general tool to translate circuit lower bounds into PRAM lower bounds.

Further, the lower bounds in (1) and (2) remain valid for probabilistic or nondeterministic concurrent-read concurrent-write PRAMS.
The
five color
concurrency control protocol: non-two-phase locking in general databases
Authors: Dasgupta Partha , Kedem Zvi M.
Published: July 2002

Concurrency control protocols based on two-phase locking are a popular family of locking protocols that preserve serializability in general (unstructured) database systems. A concurrency control algorithm (for databases with no inherent structure) is presented that is practical, non two-phase, and allows varieties of serializable logs not possible with any commonly known locking schemes. All transactions are required to predeclare the data they intend to read or write. Using this information, the protocol anticipates the existence (or absence) of possible conflicts and hence can allow non-two-phase locking.

It is well known that serializability is characterized by acyclicity of the conflict graph representation of interleaved executions. The two-phase locking protocols allow only
forward
growth of the paths in the graph. The
Five Color
protocol allows the conflict graph to grow in any direction (avoiding two-phase constraints) and prevents cycles in the graph by maintaining transaction access information in the form of data-item markers. The read and write set information can also be used to provide relative immunity from deadlocks.
Asymptotic expansion for large closed queuing networks
Authors: Knessl Charles , Tier Charles
Published: July 2002

In this paper, a new asymptotic method is developed for analyzing closed BCMP queuing networks with a single class (chain) consisting of a large number of customers, a single infinite server queue, and a large number of single server queues with fixed (state-independent) service rates. Asymptotic approximations are computed for the normalization constant (partition function) starting directly from a recursion relation of Buzen. The approach of the authors employs the ray method of geometrical optics and the method of matched asymptotic expansions. The method is applicable when the servers have nearly equal relative utilizations or can be divided into classes with nearly equal relative utilizations. Numerical comparisons are given that illustrate the accuracy of the asymptotic approximations.
An investigation of curvature variations over recursively generated B-spline surfaces
Authors: Ball A. A. , Storry D. J. T.
Published: July 2002

The continuity properties of recursively generated B-spline surfaces over an arbitrary topology have been related to the eigenproperties of the local subdivision tranformation, and conditions have been established on the subdivision weightings for tangent plane continuity at extraordinary points. In this paper, curves through an extradordinary point, which align in both the tagent and binormal direction, are identified, and their curvatures are compared either side of the point. Further restrictions on the subdivision weightings are derived to optimize the curvature properties of the surface. In general continuity of curvature is not attained.
Federated database systems for managing distributed, heterogeneous, and autonomous databases
Authors: Sheth Amit P. , Larson James A.
Published: July 2002

A federated database system (FDBS) is a collection of cooperating database systems that are autonomous and possibly heterogeneous. In this paper, we define a reference architecture for distributed database management systems from system and schema viewpoints and show how various FDBS architectures can be developed. We then define a methodology for developing one of the popular architectures of an FDBS. Finally, we discuss critical issues related to developing and operating an FDBS.
Implementing fault-tolerant services using the state machine approach: a tutorial
Authors: Schneider Fred B.
Published: July 2002

The state machine approach is a general method for implementing fault-tolerant services in distributed systems. This paper reviews the approach and describes protocols for two different failure models—Byzantine and fail stop. Systems reconfiguration techniques for removing faulty components and integrating repaired components are also discussed.
The Four Careers of George and Louise Spindler: 1948-2000
Authors: Spindler George D.
Published: July 2002

▪ Abstract  This essay summarizes the four careers of George and Louise Spindler over a 50-year period—psychological anthropology, anthropology and education, teaching, and editing. Our relations with Indian tribes with which we worked are described. Special attention is given to illusions affecting the construction of education in American schools, to the use of projective techniques in studies among Native American communitites, and to studies in urbanizing German villages. The concept of cultural therapy is introduced. Publications from each of our four careers are sampled.
MOLECULAR BIOLOGY OF CATION TRANSPORT IN PLANTS
Authors: Fox Tama Christine , Guerinot Mary Lou
Published: July 2002

▪ Abstract  This review summarizes current knowledge about genes whose products function in the transport of various cationic macronutrients (K, Ca) and micronutrients (Cu, Fe, Mn, and Zn) in plants. Such genes have been identified on the basis of function, via complementation of yeast mutants, or on the basis of sequence similarity, via database analysis, degenerate PCR, or low stringency hybridization. Not surprisingly, many of these genes belong to previously described transporter families, including those encoding Shaker-type K+ channels, P-type ATPases, and Nramp proteins. ZIP, a novel cation transporter family first identified in plants, also seems to be ubiquitous; members of this family are found in protozoa, yeast, nematodes, and humans. Emerging information on where in the plant each transporter functions and how each is controlled in response to nutrient availability may allow creation of food crops with enhanced mineral content as well as crops that bioaccumulate or exclude toxic metals.
GENETIC ANALYSIS OF HORMONE SIGNALING
Authors: McCourt Peter
Published: July 2002

▪ Abstract  Phytohormones influence many diverse developmental processes ranging from seed germination to root, shoot, and flower formation. Recently, mutational analysis using the model plant Arabidopsis thaliana has been instrumental in determining the individual components of specific hormone signal transduction pathways. Moreover, epistasis and suppressor studies are beginning to explain how these genes and their products relate to one another. While no hormone transduction pathway is completely understood, the genes identified to date suggest that simple molecular rules can be established to explain how plant hormone signals are transduced. This review describes some of the shared characteristics of plant hormone signal transduction pathways and the properties for informational transfer common to many of the genes that specify the transduction of the signal.
RADIO EMISSION FROM SOLAR FLARES
Authors: Bastian T. S. , Benz A. O. , Gary D. E.
Published: July 2002

▪ Abstract  Radio emission from solar flares offers a number of unique diagnostic tools to address long-standing questions about energy release, plasma heating, particle acceleration, and particle transport in magnetized plasmas. At millimeter and centimeter wavelengths, incoherent gyrosynchrotron emission from electrons with energies of tens of kilo electron volts to several mega electron volts plays a dominant role. These electrons carry a significant fraction of the energy released during the impulsive phase of flares. At decimeter and meter wavelengths, coherent plasma radiation can play a dominant role. Particularly important are type III and type III–like radio bursts, which are due to upward- and downward-directed beams of nonthermal electrons, presumed to originate in the energy release site. With the launch of Yohkoh and the Compton Gamma-Ray Observatory, the relationship between radio emission and energetic photon emissions has been clarified. In this review, recent progress on our Dunderstanding of radio emission from impulsive flares and its relation to X-ray emission is discussed, as well as energy release in flare-like phenomena (microflares, nanoflares) and their bearing on coronal heating.
ALTERATION OF NUCLEOSOME STRUCTURE AS A MECHANISM OF TRANSCRIPTIONAL REGULATION
Authors: Workman J. L. , Kingston R. E.
Published: July 2002

The nucleosome, which is the primary building block of chromatin, is not a static structure: It can adopt alternative conformations. Changes in solution conditions or changes in histone acetylation state cause nucleosomes and nucleosomal arrays to behave with altered biophysical properties. Distinct subpopulations of nucleosomes isolated from cells have chromatographic properties and nuclease sensitivity different from those of bulk nucleosomes. Recently, proteins that were initially identified as necessary for transcriptional regulation have been shown to alter nucleosomal structure. These proteins are found in three types of multiprotein complexes that can acetylate nucleosomes, deacetylate nucleosomes, or alter nucleosome structure in an ATP-dependent manner. The direct modification of nucleosome structure by these complexes is likely to play a central role in appropriate regulation of eukaryotic genes.
Design and Selection of Novel Cys2His2 Zinc Finger Proteins
Authors: Pabo Carl O. , Peisach Ezra , Grant Robert A.
Published: July 2002

▪ Abstract  Cys2His2 zinc finger proteins offer a stable and versatile framework for the design of proteins that recognize desired target sites on double-stranded DNA. Individual fingers from these proteins have a simple ββα structure that folds around a central zinc ion, and tandem sets of fingers can contact neighboring subsites of 3–4 base pairs along the major groove of the DNA. Although there is no simple, general code for zinc finger–DNA recognition, selection strategies have been developed that allow these proteins to be targeted to almost any desired site on double-stranded DNA. The affinity and specificity of these new proteins can also be improved by linking more fingers together or by designing proteins that bind as dimers and thus recognize an extended site. These new proteins can then be modified by adding other domains—for activation or repression of transcription, for DNA cleavage, or for other activities. Such designer transcription factors and other new proteins will have important applications in biomedical research and in gene therapy.
MOLECULAR MECHANISM OF PHOTOSIGNALING BY ARCHAEAL SENSORY RHODOPSINS
Authors: Hoff Wouter D. , Jung Kwang-Hwan , Spudich John L.
Published: July 2002

▪ Abstract  Two sensory rhodopsins (SRI and SRII) mediate color-sensitive phototaxis responses in halobacteria. These seven-helix receptor proteins, structurally and functionally similar to animal visual pigments, couple retinal photoisomerization to receptor activation and are complexed with membrane-embedded transducer proteins (HtrI and HtrII) that modulate a cytoplasmic phosphorylation cascade controlling the flagellar motor. The Htr proteins resemble the chemotaxis transducers from Escherichia coli. The SR-Htr signaling complexes allow studies of the biophysical chemistry of signal generation and relay, from the photobiophysics of initial excitation of the receptors to the final output at the level of the flagellar motor switch, revealing fundamental principles of sensory transduction and more broadly the nature of dynamic interactions between membrane proteins. We review here recent advances that have led to new insights into the molecular mechanism of signaling by these membrane complexes.
Signaling and Subcellular Targeting by Membrane-Binding Domains
Authors: Hurley James H. , Misra Saurav
Published: July 2002

▪ Abstract  Protein kinase C homology-1 and -2, FYVE, and pleckstrin homology domains are ubiquitous in eukaryotic signal transduction and membrane-trafficking proteins. These domains regulate subcellular localization and protein function by binding to lipid ligands embedded in cell membranes. Structural and biochemical analysis of these domains has shown that their molecular mechanisms of membrane binding depend on a combination of specific and nonspecific interactions with membrane lipids. In vivo studies of green fluorescent protein fusions have highlighted the key roles of these domains in regulating protein localization to plasma and internal membranes in cells.
Ethylene: A Gaseous Signal Molecule in Plants
Authors: Bleecker Anthony B. , Kende Hans
Published: July 2002

▪ Abstract  Ethylene regulates a multitude of plant processes, ranging from seed germination to organ senescence. Of particular economic importance is the role of ethylene as an inducer of fruit ripening. Ethylene is synthesized from S-adenosyl-L-methionine via 1-aminocyclopropane-1-carboxylic acid (ACC). The enzymes catalyzing the two reactions in this pathway are ACC synthase and ACC oxidase. Environmental and endogenous signals regulate ethylene biosynthesis primarily through differential expression of ACC synthase genes. Components of the ethylene signal transduction pathway have been identified by characterization of ethylene-response mutants in Arabidopsis thaliana. One class of mutations, exemplified by etr1, led to the identification of the ethylene receptors, which turned out to be related to bacterial two-component signaling systems. Mutations that eliminate ethylene binding to the receptor yield a dominant, ethylene-insensitive phenotype. CTR1 encodes a Raf-like Ser/Thr protein kinase that acts downstream from the ethylene receptor and may be part of a MAP kinase cascade. Mutants in CTR1 exhibit a constitutive ethylene-response phenotype. Both the ethylene receptors and CTR1 are negative regulators of ethylene responses. EIN2 and EIN3 are epistatic to CTR1, and mutations in either gene lead to ethylene insensitivity. Whereas the function of EIN2 in ethylene transduction is not known, EIN3 is a putative transcription factor involved in regulating expression of ethylene-responsive genes. Biotechnological modifications of ethylene synthesis and of sensitivity to ethylene are promising methods to prevent spoilage of agricultural products such as fruits, whose ripening is induced by ethylene.
Cajal Bodies: The First 100 Years
Authors: Gall Joseph G.
Published: July 2002

▪ Abstract  Cajal bodies are small nuclear organelles first described nearly 100 years ago by Ramón y Cajal in vertebrate neural tissues. They have since been found in a variety of animal and plant nuclei, suggesting that they are involved in basic cellular processes. Cajal bodies contain a marker protein of unknown function, p80-coilin, and many components involved in transcription and processing of nuclear RNAs. Among these are the three eukaryotic RNA polymerases and factors required for transcribing and processing their respective nuclear transcripts: mRNA, rRNA, and pol III transcripts. A model is discussed in which Cajal bodies are the sites for preassembly of transcriptosomes, unitary particles involved in transcription and processing of RNA. A parallel is drawn to the nucleolus and the preassembly of ribosomes, which are unitary particles involved in translation of proteins.
NON-CO2 GREENHOUSE GASES IN THE ATMOSPHERE
Authors: Khalil M. A. K.
Published: July 2002

▪ Abstract  Although global warming is generally linked to increasing levels of carbon dioxide, there are many other gases produced from industrial, agricultural, and energy-generating sources that can also cause the Earth's temperature to rise. Individually these gases are not likely to make a significant contribution, but, taken together, it is believed that they can rival the effects of carbon dioxide. This paper reviews the current trends of the most abundant or the most effective of these non-CO2 greenhouse gases. Methane, nitrous oxide, and the major chlorofluorocarbons (F-11 and F-12) have been the most notable greenhouse gases other than CO2. Although these gases will continue to play a role in global warming, new compounds are likely to become increasingly important. These include the fluorocarbon replacement compounds in the hydrofluorocarbon and the hydrochlorofluorocarbon groups and gases that are nearly inert in the atmosphere, persisting for thousands of years, such as the perfluorocarbons and sulfur hexafluoride.
WINDPOWER: A Turn of the Century Review
Authors: McGowan Jon G. , Connors Stephen R.
Published: July 2002

▪ Abstract  The 1990s saw a resurgence in the windpower industry, with installed grid-connected capacity expanding more than five-fold between 1990 and 2000. Most of this increase occurred in Europe, where governmental policies aimed at developing domestic energy supplies and reducing pollutant emissions provided a sheltered market for renewable energy generation. The 1990s were also marked by a return to large, megawatt-sized wind turbines, a reduction and consolidation of wind turbine manufacturers, and increased interest in offshore windpower. This article reviews recent trends in the windpower industry, including some of the fundamental engineering principles of wind turbine design. Technological impediments and advances are discussed in the context of changes in the global electricity markets and environmental performance.
Differential Gene Expression in Insects: Transcriptional Control
Authors: Harshman Lawrence G. , James Anthony A.
Published: July 2002

▪ Abstract  Studies on transcriptional control of gene expression play a pivotal role in many areas of biology. In non-Drosophilid insects, the cuticle, chorion, immune response, silk gland, storage proteins, and vitellogenin are foci for advances in basic research on promoter elements and transcription factors. Insects offer other advantages for gene regulation studies, including the availability of applied problems. In non-Drosophilid insects, the most serious problem for transcriptional control studies is the lack of homologous in vivo expression systems. Once this deficiency is addressed, the full impact of research on transcription control will be realized throughout the field of entomology.
Life History and Production of Stream Insects
Authors: Huryn Alexander D. , Wallace J. Bruce
Published: July 2002

▪ Abstract  Studies of the production of stream insects are now numerous, and general factors controlling the secondary production of stream communities are becoming evident. In this review we focus on how life-history attributes influence the production dynamics of stream insects and other macroinvertebrates. Annual production of macroinvertebrate communities in streams world-wide ranges from approximately 100to 103g dry mass m−2. High levels are reported for communities dominated by filter feeders in temperate streams. Filter feeding enables the accrual and support of high biomass, which drives the very highest production. Frequently disturbed communities in warm-temperate streams are also highly productive. Biomass accrual by macroinvertebrates is limited in these streams, and production is driven by rapid growth rates rather than high biomass. The lowest production, reported for macroinvertebrate communities of cool-temperate and arctic streams, is due to the constraints of low seasonal temperatures and nutrient or food limitation. Geographical bias, paucity of community-wide studies, and limited knowledge of the effects of biotic interactions limit current understanding of mechanisms controlling stream productivity.
Iron Metabolism in Insects
Authors: Nichol Helen , Law John H. , Winzerling Joy J.
Published: July 2002

▪ Abstract  Like other organisms, insects must balance two properties of ionic iron, that of an essential nutrient and a potent toxin. Iron must be acquired to provide catalysis for oxidative metabolism, but it must be controlled to avoid destructive oxidative reactions. Insects have evolved distinctive forms of the serum iron transport protein, transferrin, and the storage protein, ferritin. These proteins may serve different functions in insects than they do in other organisms. A form of translational control of protein synthesis by iron in insects is similar to that of vertebrates. The Drosophila melanogaster genome contains many genes that may encode other proteins involved in iron metabolism.
PHYLOGENETIC ANALYSIS IN MOLECULAR EVOLUTIONARY GENETICS
Authors: Nei Masatoshi
Published: July 2002

▪ Abstract  Recent developments of statistical methods in molecular phylogenetics are reviewed. It is shown that the mathematical foundations of these methods are not well established, but computer simulations and empirical data indicate that currently used methods such as neighbor joining, minimum evolution, likelihood, and parsimony methods produce reasonably good phylogenetic trees when a sufficiently large number of nucleotides or amino acids are used. However, when the rate of evolution varies extensively from branch to branch, many methods may fail to recover the true topology. Solid statistical tests for examining the accuracy of trees obtained by neighbor joining, minimum evolution, and least-squares method are available, but the methods for likelihood and parsimony trees are yet to be refined. Parsimony, likelihood, and distance methods can all be used for inferring amino acid sequences of the proteins of ancestral organisms that have become extinct.
TRANSCRIPTION OF EUKARYOTIC PROTEIN-CODING GENES
Authors: Lee Tong Ihn , Young Richard A.
Published: July 2002

▪ Abstract  The past decade has seen an explosive increase in information about regulation of eukaryotic gene transcription, especially for protein-coding genes. The most striking advances in our knowledge of transcriptional regulation involve the chromatin template, the large complexes recruited by transcriptional activators that regulate chromatin structure and the transcription apparatus, the holoenzyme forms of RNA polymerase II involved in initiation and elongation, and the mechanisms that link mRNA processing with its synthesis. We describe here the major advances in these areas, with particular emphasis on the modular complexes associated with RNA polymerase II that are targeted by activators and other regulators of mRNA biosynthesis.
The Role of the Thymus in Immune Reconstitution in Aging, Bone Marrow Transplantation, and HIV-1 Infection
Authors: Haynes Barton F. , Markert M. Louise , Sempowski Gregory D. , Patel Dhavalkumar D. , Hale Laura P.
Published: July 2002

The human thymus is a complex chimeric organ comprised of central (thymic epithelial space) and peripheral (perivascular space) components that functions well into adult life to produce naive T lymphocytes. Recent advances in identifying thymic emigrants and development of safe methods to study thymic function in vivo in adults have provided new opportunities to understand the role that the human thymus plays in immune reconstitution in aging, in bone marrow transplantation, and in HIV-1 infection. The emerging concept is that there are age-dependent contributions of thymic emigrants and proliferation of postthymic T cells to maintain the peripheral T cell pool and to contribute to T cell regeneration, with the thymus contributing more at younger ages and peripheral T cell expansion contributing more in older subjects. New studies have revealed a dynamic interplay between postnatal thymus output and peripheral T cell pool proliferation, which play important roles in determining the nature of immune reconstitution in congenital immunodeficiency diseases, in bone marrow transplantation, and in HIV-1 infection. In this paper, we review recent data on human postnatal thymus function that, taken together, support the notion that the human thymus is functional well into the sixth decade and plays a role throughout life to optimize human immune system function.
SCANNING SQUID MICROSCOPY
Authors: Kirtley John R. , Wikswo John P.
Published: July 2002

▪ Abstract  The scanning SQUID microscope (SSM) is a powerful tool for imaging magnetic fields above sample surfaces. It has the advantage of high sensitivity and bandwidth and the disadvantages of relatively modest spatial resolution and the requirement of a cooled SQUID sensor. We describe the various implementations of this type of instrument and discuss a number of applications, including magnetic imaging of short circuits in integrated circuits, corrosion currents in aluminum, and trapped flux in superconductors.
CELLULAR AND MOLECULAR BIOLOGY OF ALZHEIMER'S DISEASE AND ANIMAL MODELS
Authors: Price, M.D Donald L. , Sisodia, Ph.D Sangram S.
Published: July 2002

▪ Abstract  Alzheimer's disease (AD), the most common dementing disorder of late life, is a major cause of disability and death in the elderly. Neurobiological, genetic, and molecular studies have defined the vulnerable neural systems, abnormalities in cytoskeletal proteins in neurons, the biology of the β-amyloid precursor protein (APP) and β-amyloid (Aβ, βA4), and several APP mutations linked to the disease. More recently, investigators have begun to develop animal models essential for delineating pathogenetic mechanisms and for developing and testing new therapies for treating AD in humans. This review focuses primarily on recent progress in investigation of animal models of AD (including aged nonhuman primates and transgenic mice), which have begun to clarify some of the questions raised by investigation of the disease in humans.
COMPLICATIONS OF LAPAROSCOPIC CHOLECYSTECTOMY
Authors: Jones, M.D Daniel B. , Soper, M.D. F.A.C.S Nathaniel J.
Published: July 2002

▪ Abstract  Video technology allows surgeons to offer patients operations through small incisions. While these minimally invasive techniques have been employed for a wide range of operations for many years, only recently has a laparoscopic cholecystectomy been possible. Compared to the same operation performed via laparotomy, it is deemed the “gold standard.” Overall mortality after laparoscopic cholecystectomy ranges from 0–1%, and the rate of major complications is less than 5%. As a group, general surgeons are beyond their initial learning curve for laparoscopic cholecystectomy, but the majority of iatrogenic injuries can be successfully avoided by appreciating the limitations and pitfalls of laparoscopic surgery, and by carefully dissecting the hepatocystic triangle before dividing any structure. Early identification and management of complications will minimize potentially devastating complications of small, unrecognized injuries. Physicians need to accurately advise patients of the proposed advantages and potential problems of laparoscopic cholecystectomy before referring them to a surgeon.