bluuebunny/crossref_metadata_2025 huggingface dataset:
Data space-oriented tiling for enhancing locality
Authors: Kadayif I. , Kandemir M.
Published: August 2005

Improving locality of data references is becoming increasingly important due to increasing gap between processor cycle times and off-chip memory access latencies. Improving data locality not only improves effective memory access time but also reduces memory system energy consumption due to data references. An optimizing compiler can play an important role in enhancing data locality in array-intensive embedded media applications with regular data access patterns.This paper presents a compiler-based data space-oriented tiling approach (DST). In this strategy, the data space (e.g., an array of signals) is logically divided into chunks (called data tiles) and each data tile is processed in turn. In processing a data tile, our approach traverses the entire iteration space of all nests in the code and executes all iterations (potentially coming from different nests) that access the data tile being processed. In doing so, it also takes data dependences into account. Since a data space is common across all nests that access it, DST can potentially achieve better results than traditional iteration space (loop) tiling by exploiting internest data locality.We also present an example application of DST for improving the effectiveness of a scratch pad memory (SPM) for data accesses. SPMs are alternatives to conventional cache memories in embedded computing world. These small on-chip memories, like caches, provide fast and low-power access to data; but, they differ from conventional data caches in that their contents are managed by compiler instead of hardware. We have implemented DST in a source-to-source translator and quantified its benefits using a simulator. Our preliminary results with several array-intensive applications and varying input sizes show that our approach outperforms classical iteration space-oriented tiling as well as a data-oriented approach that considers each nest in isolation.
Practical parallel algorithms for personalized communication and integer sorting
Authors: Bader David A. , Helman David R. , JáJá Joseph
Published: August 2005

A fundamental challenge for parallel computing is to obtain high-level, architecture independent, algorithms which efficiently execute on general-purpose parallel machines. With the emergence of message passing standards such as MPI, it has become easier to design efficient and portable parallel algorithms by making use of these communication primitives. While existing primitives allow an assortment of collective communication routines, they do not handle an important communication event when most or all processors have non-uniformly sized personalized messages to exchange with each other. We focus in this paper on the h-relation personalized communication whose efficient implementation will allow high performance implementations of a large class of algorithms. While most previous h-relation algorithms use randomization, this paper presents a new deterministic approach for h-relation personalized communication with asymptotically optimal complexity for

h>p
2

. As an application, we present an efficient algorithm for stable integer sorting.

The algorithms presented in this paper have been coded in Split-C and run on a variety of platforms, including the Thinking Machines CM-5, IBM SP-1 and SP-2, Cray Research T3D, Meiko Scientific CS-2, and the Intel Paragon. Our experimental results are consistent with the theoretical analysis and illustrate the scalability and efficiency of our algorithms across different platforms. In fact, they seem to outperform all similar algorithms known to the authors on these platforms.
Experimental analysis of dynamic algorithms for the single source shortest paths problem
Authors: Frigioni Daniele , Ioffreda Mario , Nanni Umberto , Pasqualone Giulio
Published: August 2005

In this paper we propose the first experimental study of the fully dynamic single-source shortest-paths problem on directed graphs with positive real edge weights. In particular, we perform an experimental analysis of three different algorithms: Dijkstra's algorithm, and the two output bounded algorithms proposed by Ramalingam and Reps in [30] and by Frigioni, Marchetti-Spaccamela and Nanni in [18], respectively. The main goal of this paper is to provide a first experimental evidence for: (a) the effectiveness of dynamic algorithms for shortest paths with respect to a traditional static approach to this problem; (b) the validity of the theoretical model of output boundedness to analyze dynamic graph algorithms. Beside random generated graphs, useful to capture the "asymptotic" behavior of the algorithms, we also developed experiments by considering a widely used graph from the real world, i.e., the Internet graph.
International learning in an international world
Authors: Martinez Margaret
Published: August 2005

How do we support successful, lifelong learners and performers and help them competently respond to rapidly changing opportunities in the 21st century. The answer to this question lies in how well we understand audiences differentiated by key learning differences and consider how these differentiations influence winning learning and performance. Historically, cognitive-rich explanations have tended to underplay the dominant impact of affective and conative factors on thinking and learning. Recently, these dimensions have gained considerable importance as contemporary multidisciplinary research has begun to demonstrate how intentions and emotions can influence, guide, and, at times, override our thinking and other cognitive processes. More importantly, research suggests that intentions and emotions are a dominant, powerful influence on learner success.
CoRR
Authors: Halpern Joseph Y.
Published: August 2005

This paper describes the decisions by which teh Association for Computing Machinery integrated good features from the Los Alamos e-print (physics) archive and from Cornell University's Networked Computer Science Technical Reference Library to form their own open, permanent, online “computing research repository” (CoRR). Submitted papers are not refereed and anyone can browse and extract CoRR material for free, so Corr's eventual success could revolutionize computer science publishing. But several serious challenges remain: some journals forbid online preprints, teh CoRR user interface is cumbersome, submissions are only self-indexed, (no professional library staff manages teh archive) and long-term funding is uncertain.
Hybrid tree reconstruction methods
Authors: Huson D. , Nettles S. , Rice K. , Warnow T. , Yooseph S.
Published: August 2005

A major computational problem in biology is the reconstruction of evolutionary trees for species sets, and accuracy is measured by comparing the topologies of the reconstructed tree and the model tree. One of the major debates in the field is whether large evolutionary trees can be even approximately accurately reconstructed from biomolecular sequences of realistically bounded lengths (up to about 2000 nucleotides) using standard techniques (polynomial-time distance methods, and heuristics for NP-hard optimization problems). Using both analytical and experimental techniques, we show that on large trees, the two most popular methods in systematic biology, Neighbor-Joining and Maximum Parsimony heuristics, as well as two promising methods introduced by theoretical computer scientists, are all likely to have significant errors in the topology reconstruction of the model tree. We also present a new general technique for combining outputs of different methods (thus producing hybrid methods), and show experimentally how one such hybrid method has better performance than its constituent parts.
Fast priority queues for cached memory
Authors: Sanders Peter
Published: August 2005

The cache hierarchy prevalent in todays high performance processors has to be taken into account in order to design algorithms that perform well in practice. This paper advocates the adaption of external memory algorithms to this purpose. This idea and the practical issues involved are exemplified by engineering a fast priority queue suited to external memory and cached memory that is based on k-way merging. It improves previous external memory algorithms by constant factors crucial for transferring it to cached memory. Running in the cache hierarchy of a workstation the algorithm is at least two times faster than an optimized implementation of binary heaps and 4-ary heaps for large inputs.
Implementing weighted b-matching algorithms
Authors: Müller-Hannemann Matthias , Schwartz Alexander
Published: August 2005

We present an experimental study of an implementation of weighted perfect b-matching based on the primal-dual blossom algorithm. Although this problem is well-understood in theory and efficient algorithms are known, only little experience with implementations is available. In this paper several algorithmic variants are compared on synthetic and application problem data of very sparse graphs. This study was motivated by the practical need for an efficient b-matching solver for the latter application, namely as a subroutine in our approach to a mesh refinement problem in computer-aided design (CAD).Linear regression and operation counting is used to analyze code variants. The experiments confirm that a fractional jump-start speeds up the algorithm, they indicate that a variant based on pairing heaps is slightly superior to a k-heap variant, and that scaling of large b-values is not necessary, whereas a delayed blossom shrinking heuristic significantly improves running times only for graphs with average degree two. The fastest variant of our implementation appears to be highly superior to a code by Miller and Pekny (1995).
Little machines
Authors: Johnson-Eilola Johndan
Published: August 2005

This paper questions the ubiquitous practice of supplying minimalist information to users, of making that information functional only, of assuming that the Shannon-Weaver communication model should govern online systems, and of ignoring the social implications of such a stance. Help systems that provide fast, temporary solutions without providing any background information lead to the danger of users completing tasks that they do not understand at all. (Word will help us write a legal pleading, even if we have no idea what one is.) As a result, we have help systems that attempt to be invisible and to provide tool instruction but not conceptual instruction. Such a system presents itself as a neutral tool, but it is actually an incomplete environment, denying both the complexity and alternative (and possibly improved) modes of thinking about the subject at hand.
The metaphysics of information quality
Authors: Weiss Edmond H.
Published: August 2005

The expressed promise in the title of Producing Quality Technical Information is that following its prescriptions will yield "quality" technical information. This commentary asks what the term quality means here and whether the manual delivers on its promise. In other words, which of the several senses of quality is intended in the title, and the does the publication deliver as promised? That is, which of the major quality schemes corresponds to the rationale of the text: legalistic quality, in which quality is conformity to a long list of detailed regulations and specifications (as in ISO 9000); principle-based quality, in which quality is the result of working according to a small set of broad precepts; or mystical quality, in which quality is an indefinable property or spiritual construct, toward which virtuous people should aspire.
Energy management for battery-powered embedded systems
Authors: Rakhmatov Daler , Vrudhula Sarma
Published: August 2005

Portable embedded computing systems require energy autonomy. This is achieved by batteries serving as a dedicated energy source. The requirement of portability places severe restrictions on size and weight, which in turn limits the amount of energy that is continuously available to maintain system operability. For these reasons, efficient energy utilization has become one of the key challenges to the designer of battery-powered embedded computing systems.In this paper, we first present a novel analytical battery model, which can be used for the battery lifetime estimation. The high quality of the proposed model is demonstrated with measurements and simulations. Using this battery model, we introduce a new "battery-aware" cost function, which will be used for optimizing the lifetime of the battery. This cost function generalizes the traditional minimization metric, namely the energy consumption of the system. We formulate the problem of battery-aware task scheduling on a single processor with multiple voltages. Then, we prove several important mathematical properties of the cost function. Based on these properties, we propose several algorithms for task ordering and voltage assignment, including optimal idle period insertion to exercise charge recovery.This paper presents the first effort toward a formal treatment of battery-aware task scheduling and voltage scaling, based on an accurate analytical model of the battery behavior.
Planar point location for large data sets
Authors: Vahrenhold Jan , Hinrichs Klaus H.
Published: August 2005

We present an algorithm for external memory planar point location that is both effective and easy to implement. The base algorithm is an external memory variant of the bucket method by Edahiro, Kokubo and Asano that is combined with Lee and Yang's batched internal memory algorithm for planar point location. Although our algorithm is not optimal in terms of its worst-case behavior, we show its efficiency for both batched and single-shot queries by experiments with real-world data. The experiments show that the algorithm benefits from the mainly sequential disk access pattern and significantly outperforms the fastest algorithm for internal memory. Due to its simple concept, the algorithm can take advantage of multiple disks and processors in a rather straightforward yet efficient way.
I/O-Efficient Algorithms for Problems on Grid-Based Terrains
Authors: Arge Lars , Toma Laura , Vitter Jeffrey Scott
Published: August 2005

The potential and use of Geographic Information Systems is rapidly increasing due to the increasing availability of massive amounts of geospatial data from projects like NASA's Mission to Planet Earth. However, the use of these massive datasets also exposes scalability problems with existing GIS algorithms. These scalability problems are mainly due to the fact that most GIS algorithms have been designed to minimize internal computation time, while I/O communication often is the bottleneck when processing massive amounts of data. In this paper, we consider I/O-efficient algorithms for problems on grid-based terrains.Detailed grid-based terrain data is rapidly becoming available for much of the earth's surface. We describe [EQUATION] I/O algorithms for several problems on [EQUATION] grids for which only O(N) algorithms were previously known. Here
M
denotes the size of the main memory and
B
the size of a disk block.We demonstrate the practical merits of our work by comparing the empirical performance of our new algorithm for the
flow accumulation
problem with that of the previously best known algorithm. Flow accumulation, which models flow of water through a terrain, is one of the most basic hydrologic attributes of a terrain. We present the results of an extensive set of experiments on real-life terrain datasets of different sizes and characteristics. Our experiments show that while our new algorithm scales nicely with dataset size, the previously known algorithm "breaks down" once the size of the dataset becomes bigger than the available main memory. For example, while our algorithm computes the flow accumulation for the Appalachian Mountains in about three hours, the previously known algorithm takes several weeks.
Adapting Radix Sort to the Memory Hierarchy
Authors: Rahman Naila , Raman Rajeev
Published: August 2005

We demonstrate the importance of reducing misses in the translation-lookaside buffer (TLB) for obtaining good performance on modern computer architectures. We focus on least-significantbit first (LSB) radix sort, standard implementations of which make many TLB misses. We give three techniques which simultaneously reduce cache and TLB misses for LSB radix sort: reducing working set size, explicit block transfer and pre-sorting. We note that: • All the techniques above yield algorithms whose implementations outperform optimised cache-tuned implementations of LSB radix sort and comparison-based sorting algorithms. The fastest running times are obtained by the pre-sorting approach and these are over twice as fast as optimised cache-tuned implementations of LSB radix sort and quicksort. Even the simplest optimisation, using the TLB size to guide the choice of radix in standard implementations of LSB radix sort, gives good improvements over cache-tuned algorithms. • One of the pre-sorting algorithms and explicit block transfer make few cache and TLB misses in the worst case. This is not true of standard implementations of LSB radix sort.We also apply these techniques to the problem of permuting an array of integers, and obtain gains of over 30% relative to the naive algorithm by using explicit block transfer.
The Effect of Flexible Parsing for Dynamic Dictionary-Based Data Compression
Authors: Matias Yossi , Rajpoot Nasir , Sahinalp Cenk
Published: August 2005

We report on the performance evaluation of greedy parsing with a
single step lookahead (which we call flexible Parsing or
FP
as an alternative to the commonly used greedy parsing (with
no-lookaheads) scheme. Greedy parsing is the basis of most popular
compression programs including
UNIX compress
and
gzip
, however it usually results in far from optimal
parsing/compression with regard to the dictionary construction
scheme in use. Flexible parsing, however, is optimal [MS99], i.e.
partitions any given input to the smallest number of phrases
possible, for dictionary construction schemes which satisfy the
prefix property throughout their execution.

We focus on the application of
FP
in the context of the
LZW variant of the Lempel-Ziv'78 dictionary construction method
[Wel84, ZL78], which is of considerable practical interest. We
implement two compression algorithms which use (1)
FP
with
LZW dictionary (LZW-
FP
), and (2)
FP
with an
alternative flexible dictionary (FPA as introduced in [Hor95]). Our
implementations are based on novel on-line data structures enabling
us to use linear time and space. We test our implementations on a
collection of input sequences which includes textual files, DNA
sequences, medical images, and pseudorandom binary files, and
compare our results with two of the most popular compression
programs
UNIX compress
and
gzip
. Our results
demonstrate that flexible parsing is especially useful for
non-textual data, on which it improves over the compression rates
of
compress
and
gzip
by up to 20% and 35%,
respectively.
Educating via entertainment media
Authors: Revelle Glenda L.
Published: August 2005

Sesame Workshop was founded 35 years ago to investigate whether entertainment media could be used to educate children. At that time the medium in question was television. As the Sesame Street television show prepares to celebrate its 35th year on the air, the television programming schedule now includes a wide variety of other educational programming for young children, and researchers are in almost universal agreement that television can be used successfully for educational purposes. In recent years, the Workshop has faced the same challenge with a variety of interactive entertainment media (including videogames, DVD, and interactive television); i.e., these media all might have potential for educating children, but neither the platforms themselves nor the typical programming for these media are being planned with any particular thought toward education. This paper describes how the Sesame Street "experiment" has been continued and extended, by adapting interactive media platforms designed for entertainment so that they can be used to deliver educational experiences to young children. The paper also outlines Sesame Workshop's educational philosophy and approach, as applied in the interactive arena, and identifies some of the challenges and solutions in designing interfaces and interactive educational experiences that can be used and enjoyed by preschool-age children. Two specific research projects are described as examples of this approach: one details the development of an adapted software interface to make console videogame systems accessible to young children and the other evaluates a new approach to creating interactive television programming for young children on a DVD platform.
Coding of Tactile Response Properties in the Rat Deep Cerebellar Nuclei
Authors: Rowland Nathan C. , Jaeger Dieter
Published: August 2005

In the lateral hemispheres of the cerebellar cortex, somatosensory responses are represented in a finely grained fractured somatotopy. It is unclear, however, how these responses contribute to the ultimate output of the cerebellum from the deep cerebellar nuclei (DCN). Robust responses of DCN neurons to somatosensory stimuli have been described, but a detailed examination of their somatotopic arrangement and stimulus coding properties is lacking. To address these questions, we recorded extracellular, single-unit activity in the DCN of ketamine-anesthetized rats in response to air-puff stimuli aimed at six different orofacial and forelimb locations. In additional experiments, the duration and intensity of air-puff stimuli to the ipsilateral upper lip were systematically varied. Overall, we found that DCN neuron responses to air puff stimuli showed combinations of three distinct response components: a short-latency spike response, a pronounced inhibition, and a long-latency increase in firing. Individual neurons responsive to air-puff stimulation exhibited any combination of just one, two, or all three of these response components. The inhibitory response was most common and frequently consisted of a complete cessation of spiking despite a high spontaneous rate of baseline firing. In contrast to published findings from cerebellar cortical recordings, the receptive fields of all responsive neurons in the DCN were large. In fact, the receptive field of most neurons covered the ipsi- and contralateral face as well as forepaws. Response properties of individual neurons did not reliably indicate stimulus intensity or duration, although as a population DCN neurons showed significantly increasing response amplitudes as air-puff intensity or duration increased. Overall, the responses were characterized by a distinct temporal profile in each neuron, which remained unchanged with changes in stimulus condition. We conclude that the responses in the DCN of rats to air-puff stimuli differ substantially from cerebellar cortical responses in their receptive field properties and do not provide a robust code of tactile stimulus properties. Rather, the characteristic temporal response profile of each neuron may be tuned to control the timing of a specific task to which its output is linked.
Characterizations of fixed points of nonexpansive mappings
Authors: Suzuki Tomonari
Published: July 2005

Using the notion of Banach limits, we discuss the characterization
of fixed points of nonexpansive mappings in Banach spaces. Indeed, we prove that the two sets of fixed points of a nonexpansive mapping and some mapping generated by a Banach limit coincide. In our discussion, we may not assume the strict convexity of the Banach space.
Brain‐like functor control machine for general humanoidbiodynamics
Authors: Ivancevic Vladimir , Beagley Nicholas
Published: July 2005

A novel, brain‐like, hierarchical (affine‐neuro‐fuzzy‐topological)
control for biomechanically realistic humanoid‐robot biodynamics (HB), formulated previously in [15, 16], is proposed in the form of a tensor‐invariant, “meta‐cybernetic” functor machine. It represents a physiologically inspired, three‐level, nonlinear feedback controller of muscular‐like joint actuators. On the
spinal level, nominal joint‐trajectory tracking is formulated as an affine Hamiltonian control system, resembling the spinal (autogenetic‐reflex) “motor servo.” On the cerebellar level, a feedback‐control map is proposed in the form of self‐organized,
oscillatory, neurodynamical system, resembling the associative interaction of excitatory granule cells and inhibitory Purkinje cells. On the cortical level, a topological “hyper‐joystick” command space is formulated with a fuzzy‐logic feedback‐control map defined on it, resembling the regulation of locomotor conditioned reflexes. Finally, both the cerebellar and the cortical control systems are extended to provide translational force control for moving 6‐degree‐of‐freedom chains of inverse kinematics.
A necessary and sufficient condition for global existence for a quasilinear reaction‐diffusion system
Authors: Lair Alan V.
Published: July 2005

We show that the reaction‐diffusion system ut = Δφ(u) + f(v), vt = Δψ(v) + g(u), with homogeneous Neumann boundary conditions, has a positive global solution on Ω × [0, ∞) if and only if
(or, equivalently, ), where and . The domain Ω⊆ℝN(N ≥ 1) is bounded with smooth boundary. The functions φ, ψ, f, and g are nondecreasing, nonnegative C([0, ∞)) functions satisfying φ(s)ψ(s)f(s)g(s) > 0 for s > 0 and φ(0) = ψ(0) = 0. Applied to the special case f(s) = sp and g(s) = sq, p > 0, q > 0, our result proves that the system has a global solution if and only if pq ≤ 1.
Intrathoracic Impedance Monitoring in Patients With Heart Failure
Authors: Yu Cheuk-Man , Wang Li , Chau Elaine , Chan Raymond Hon-Wah , Kong Shun-Ling , Tang Man-Oi , Christensen Jill , Stadler Robert W. , Lau Chu-Pak
Published: August 2005

Background—

Patients with heart failure are frequently hospitalized for fluid overload. A reliable method for chronic monitoring of fluid status is therefore desirable. We evaluated an implantable system capable of measuring intrathoracic impedance to identify potential fluid overload before heart failure hospitalization and to determine the correlation between intrathoracic impedance and standard measures of fluid status during hospitalization.

Methods and Results—

Thirty-three patients with NYHA class III and IV heart failure were implanted with a special pacemaker in the left pectoral region and a defibrillation lead in the right ventricle. Intrathoracic impedance was regularly measured and recorded between the lead and the pacemaker case. During hospitalizations, pulmonary capillary wedge pressure and fluid status were monitored. Ten patients were hospitalized for fluid overload 25 times over 20.7±8.4 months. Intrathoracic impedance decreased before each admission by an average of 12.3±5.3% (
P
<0.001) over an average of 18.3±10.1 days. Impedance reduction began 15.3±10.6 days (
P
<0.001) before the onset of worsening symptoms. There was an inverse correlation between intrathoracic impedance and pulmonary capillary wedge pressure (
r
=−0.61,
P
<0.001) and between intrathoracic impedance and net fluid loss (
r
=−0.70,
P
<0.001) during hospitalization. Automated detection of impedance decreases was 76.9% sensitive in detecting hospitalization for fluid overload, with 1.5 false-positive (threshold crossing without hospitalization) detections per patient-year of follow-up.

Conclusions—

Intrathoracic impedance is inversely correlated with pulmonary capillary wedge pressure and fluid balance and decreased before the onset of patient symptoms and before hospital admission for fluid overload. Regular monitoring of impedance may provide early warning of impending decompensation and diagnostic information for titration of medication.
Differential Influence of Chemokine Receptors CCR2 and CXCR3 in Development of Atherosclerosis In Vivo
Authors: Veillard Niels R. , Steffens Sabine , Pelli Graziano , Lu B. , Kwak Brenda R. , Gerard Craig , Charo Israel F. , Mach François
Published: August 2005

Background—

Recruitment of mononuclear leukocytes within atherosclerotic lesions is a critical step in atherogenesis. Mice lacking the chemokine receptor CCR2, highly expressed on macrophages but also on T lymphocytes, show a striking reduction of atherosclerotic lesion formation. The chemokine receptor CXCR3 is a marker of activated T helper type 1 lymphocytes, the principal T lymphocyte type detected within atheroma. We investigated whether the deletion of both of these 2 important receptors expressed on the principal inflammatory cells present in atheroma would further affect atherogenesis in vivo.

Methods and Results—

We crossed ApoE
−/−
mice with either CCR2
−/−
or CXCR3
−
mice and crossed ApoE
−/−
CCR2
−/−
mice with the ApoE
−/−
CXCR3
−
mice to generate a triple knockout strain. Analysis of atherosclerosis development after 10 weeks of high-cholesterol diet revealed differential effects on early atherosclerotic lesions in the abdominal aorta and on advanced lesions in aortic roots. ApoE
−/−
CXCR3
−
mice, but not the triple knockout mice, displayed significantly reduced atherosclerotic lesion development within abdominal aortas compared with ApoE
−/−
CCR2
−/−
and ApoE
−/−
mice. This reduction of lesion formation correlated with an upregulation of antiinflammatory molecules such as interleukin-10, interleukin-18BP, and endothelial nitric oxide synthase and with an increased number of regulatory T lymphocytes within atherosclerotic lesions. In contrast, lesion size development within the aortic roots was more enhanced in ApoE
−/−
and ApoE
−/−
CXCR3
−
mice compared with ApoE
−/−
CCR2
−/−
and triple knockout mice.

Conclusions—

Blocking chemokine signaling in vivo through deletion of the chemokine receptors CCR2 and CXCR3 has differential effects during atherogenesis. In addition, our results point to an important role of regulatory T lymphocytes during early atherogenesis.
The Seduction of Authenticity: "The Story of Yingying"
Authors: Luo Manling
Published: July 2005

This paper explores the notion of authenticity and its implications in the Tang classical tale "The Story of Yingying" from the perspective of literati discourse formation. By constructing a problematic "authentic" romance and its public, the story succeeds in turning romance into a "reality." Signifying the symbolic entry of romance into the domestic space, the story reveals sophisticated strategies for adapting, validating, and expanding the Tang literati discourse on romance.
Barry Saltzman and the Theory of Climate
Authors: Maasch K. A. , Oglesby R. J. , Fournier A.
Published: August 2005

Barry Saltzman was a giant in the fields of meteorology and climate science. A leading figure in the study of weather and climate for over 40 yr, he has frequently been referred to as the “father of modern climate theory.” Ahead of his time in many ways, Saltzman made significant contributions to our understanding of the general circulation and spectral energetics budget of the atmosphere, as well as climate change across a wide spectrum of time scales. In his endeavor to develop a unified theory of how the climate system works, he played a role in the development of energy balance models, statistical dynamical models, and paleoclimate dynamical models. He was a pioneer in developing meteorologically motivated dynamical systems, including the progenitor of Lorenz’s famous chaos model. In applying his own dynamical-systems approach to long-term climate change, he recognized the potential for using atmospheric general circulation models in a complimentary way. In 1998, he was awarded the Carl-Gustaf Rossby medal, the highest honor of the American Meteorological Society “for his life-long contributions to the study of the global circulation and the evolution of the earth’s climate.” In this paper, the authors summarize and place into perspective some of the most significant contributions that Barry Saltzman made during his long and distinguished career. This short review also serves as an introduction to the papers in this special issue of the Journal of Climate dedicated to Barry’s memory.
Siple Coast Ice Streams in a General Antarctic Ice Sheet Model
Authors: Verbitsky Mikhail
Published: August 2005

In an earlier paper by Verbitsky and Saltzman, a vertically integrated, high-resolution, nonlinearly viscous, nonisothermal ice sheet model was presented to calculate the “present-day” equilibrium regime of the Antarctic ice sheet. Steady-state solutions for the ice topography and thermodynamics, represented by the extent of the areas of basal melting, were shown to be in good agreement with both observations and results obtained from other three-dimensional thermodynamical equations. The solution for the basal temperature field of the West Antarctic Siple Coast produced areas at the pressure melting point separated by strips of frozen-to-bed ice, the structure of which looks very similar to ice streams A–E. Since the possible response of the Siple Coast basal temperature pattern to global warming and to associated changes in the snowfall rate is not obvious, a special sensitivity study was conducted. Results of such a study suggest that increased precipitation rate and associated intensification of ice advection can effectively “shut down” West Antarctic ice streams.
Reducing Climatology Bias in an Ocean–Atmosphere CGCM with Improved Coupling Physics
Authors: Luo Jing-Jia , Masson Sebastien , Roeckner Erich , Madec Gurvan , Yamagata Toshio
Published: August 2005

The cold tongue in the tropical Pacific extends too far west in most current ocean–atmosphere coupled GCMs (CGCMs). This bias also exists in the relatively high-resolution SINTEX-F CGCM despite its remarkable performance of simulating ENSO variations. In terms of the importance of air–sea interactions to the climatology formation in the tropical Pacific, several sensitivity experiments with improved coupling physics have been performed in order to reduce the cold-tongue bias in CGCMs.

By allowing for momentum transfer of the ocean surface current to the atmosphere [full coupled simulation (FCPL)] or merely reducing the wind stress by taking the surface current into account in the bulk formula [semicoupled simulation (semi-CPL)], the warm-pool/cold-tongue structure in the equatorial Pacific is simulated better than that of the control simulation (CTL) in which the movement of the ocean surface is ignored for wind stress calculation. The reduced surface zonal current and vertical entrainment owing to the reduced easterly wind stress tend to produce a warmer sea surface temperature (SST) in the western equatorial Pacific. Consequently, the dry bias there is much reduced. The warming tendency of the SST in the eastern Pacific, however, is largely suppressed by isopycnal diffusion and meridional advection of colder SST from south of the equator due to enhanced coastal upwelling near Peru. The ENSO signal in the western Pacific and its global teleconnection in the North Pacific are simulated more realistically.

The approach as adopted in the FCPL run is able to generate a correct zonal SST slope and efficiently reduce the cold-tongue bias in the equatorial Pacific. The surface easterly wind itself in the FCPL run is weakened, reducing the easterly wind stress further. This is related with a weakened zonal Walker cell in the atmospheric boundary layer over the eastern Pacific and a new global angular momentum balance of the atmosphere associated with reduced westerly wind stress over the southern oceans.
The Variability of the Atlantic Meridional Overturning Circulation, the North Atlantic Oscillation, and the El Niño–Southern Oscillation in the Bergen Climate Model
Authors: Mignot Juliette , Frankignoul Claude
Published: August 2005

The link between the interannual to interdecadal variability of the Atlantic meridional overturning circulation (AMOC) and the atmospheric forcing is investigated using 200 yr of a control simulation of the Bergen Climate Model, where the mean circulation cell is rather realistic, as is also the location of deep convection in the northern North Atlantic. The AMOC variability has a slightly red frequency spectrum and is primarily forced by the atmosphere. The maximum value of the AMOC is mostly sensitive to the deep convection in the Irminger Sea, which it lags by about 5 yr. The latter is mostly forced by a succession of atmospheric patterns that induce anomalous northerly winds over the area. The impact of the North Atlantic Oscillation on deep convection in the Labrador and Greenland Seas is represented realistically, but its influence on the AMOC is limited to the interannual time scale and is primarily associated with wind forcing. The tropical Pacific shows a strong variability in the model, with too strong an influence on the North Atlantic. However, its influence on the tropical Atlantic is realistic. Based on lagged correlations and the release of fictitious Lagrangian drifters, the tropical Pacific seems to influence the AMOC with a time lag of about 40 yr. The mechanism is as follows: El Niño events induce positive sea surface salinity anomalies in the tropical Atlantic that are advected northward, circulate in the subtropical gyre, and then subduct. In the ocean interior, part of the salinity anomaly is advected along the North Atlantic current, eventually reaching the Irminger and Labrador Seas after about 35 yr where they destabilize the water column and favor deep convection.
Closing the Time-Varying Mass and Heat Budgets for Large Ocean Areas: The Tasman Box
Authors: Roemmich Dean , Gilson John , Willis Josh , Sutton Philip , Ridgway Ken
Published: August 2005

The role of oceanic advection in seasonal-to-interannual balances of mass and heat is studied using a 12-yr time series of quarterly eddy-resolving expendable bathythermograph (XBT) surveys around the perimeter of a region the authors call the Tasman Box in the southwestern Pacific. The region contains the South Pacific’s subtropical western boundary current system and associated strong mesoscale variability. Mean geostrophic transport in the warm upper ocean (temperature greater than 12°C) is about 3.8 Sv (1 Sv ≡ 106 m3 s−1) southward into the box across the Brisbane, Australia–Fiji northern edge. Net outflows are 3.3 Sv eastward across the Auckland, New Zealand–Fiji edge, and 2.7 Sv southward across Sydney, Australia–Wellington, New Zealand. Mean Ekman convergence of 2.2 Sv closes the mass budget. Net water mass conversions in the upper ocean consist of inflow of waters averaging about 26°C and 35.4 psu balanced by outflow at about 18°C and 35.7 psu, and reflect the net evaporation and heat loss in the formation of South Pacific Subtropical Mode Water. The mean heat balance shows good agreement between ocean heat flux convergence (42.3 W m−2), heat loss to the atmosphere from the NCEP–NCAR reanalysis (39.2 W m−2), and heat storage calculated from data in the box interior (1.3 W m−2). On interannual time scales, volume transport through the box ranges from about 1 to 9 Sv, with heat flux convergence ranging from about 20 to 60 W m−2. An interannual balance in the heat budget of the warm layer is achieved to within about 10 W m−2 (or 6 W m−2 for the upper 100 m alone). Maxima in the advective heat flux convergence occurred in 1993, 1997, and 1999–2000, and corresponded to maxima in air–sea heat loss. The evolution of surface-layer temperature in the region is the residual of nearly equal and opposing effects of ocean heat flux convergence and air–sea exchange. Hence, ocean circulation is a key element in the interannual heat budget of the air–sea climate system in the western boundary current region.
The National Institute Density Forecasts of Inflation
Authors: Mitchell James
Published: July 2005

This paper has three aims. First, we summarise and thereby make readily available the historical time-series of quarterly density forecasts of year ahead RPIX (RPI excluding mortgage payments) inflation made by the National Institute for the period 1994Q1–2004Q4. Previous work has focused on those forecasts made in Q4 only. Secondly, we evaluate the quality of these density forecasts. Thirdly, with the benefit of hindsight we draw lessons for the future production and use of density forecasts.
Detection of reactive oxygen species in isolated, perfused lungs by electron spin resonance spectroscopy
Authors: Weissmann Norbert , Kuzkaya Nermin , Fuchs Beate , Tiyerili Vedat , Schäfer Rolf U , Schütte Hartwig , Ghofrani Hossein A , Schermuly Ralph T , Schudt Christian , Sydykov Akylbek , Egemnazarow Bakytbek , Seeger Werner , Grimminger Friedrich
Published: August 2005

Background

The sources and measurement of reactive oxygen species (ROS) in intact organs are largely unresolved. This may be related to methodological problems associated with the techniques currently employed for ROS detection. Electron spin resonance (ESR) with spin trapping is a specific method for ROS detection, and may address some these technical problems.

Methods

We have established a protocol for the measurement of intravascular ROS release from isolated buffer-perfused and ventilated rabbit and mouse lungs, combining lung perfusion with the spin probe l-hydroxy-3-carboxy-2,2,5,5-tetramethylpyrrolidine (CPH) and ESR spectroscopy. We then employed this technique to characterize hypoxia-dependent ROS release, with specific attention paid to NADPH oxidase-dependent superoxide formation as a possible vasoconstrictor pathway.

Results

While perfusing lungs with CPH over a range of inspired oxygen concentrations (1–21 %), the rate of CP• formation exhibited an oxygen-dependence, with a minimum at 2.5 % O2. Addition of superoxide dismutase (SOD) to the buffer fluid illustrated that a minor proportion of this intravascular ROS leak was attributable to superoxide. Stimulation of the lungs by injection of phorbol-12-myristate-13-acetate (PMA) into the pulmonary artery caused a rapid increase in CP• formation, concomitant with pulmonary vasoconstriction. Both the PMA-induced CPH oxidation and the vasoconstrictor response were largely suppressed by SOD. When the PMA challenge was performed at different oxygen concentrations, maximum superoxide liberation and pulmonary vasoconstriction occurred at 5 % O2. Using a NADPH oxidase inhibitor and NADPH-oxidase deficient mice, we illustrated that the PMA-induced superoxide release was attributable to the stimulation of NADPH oxidases.

Conclusion

The perfusion of isolated lungs with CPH is suitable for detection of intravascular ROS release by ESR spectroscopy. We employed this technique to demonstrate that 1) PMA-induced vasoconstriction is caused "directly" by superoxide generated from NADPH oxidases and 2) this pathway is pronounced in hypoxia. NADPH oxidases thus may contribute to the hypoxia-dependent regulation of pulmonary vascular tone.
Expressed sequence tags from the oomycete fish pathogen Saprolegnia parasitica reveal putative virulence factors
Authors: Torto-Alalibo Trudy , Tian Miaoying , Gajendran Kamal , Waugh Mark E , van West Pieter , Kamoun Sophien
Published: August 2005

Background

The oomycete Saprolegnia parasitica is one of the most economically important fish pathogens. There is a dramatic recrudescence of Saprolegnia infections in aquaculture since the use of the toxic organic dye malachite green was banned in 2002. Little is known about the molecular mechanisms underlying pathogenicity in S. parasitica and other animal pathogenic oomycetes. In this study we used a genomics approach to gain a first insight into the transcriptome of S. parasitica.

Results

We generated 1510 expressed sequence tags (ESTs) from a mycelial cDNA library of S. parasitica. A total of 1279 consensus sequences corresponding to 525944 base pairs were assembled. About half of the unigenes showed similarities to known protein sequences or motifs. The S. parasitica sequences tended to be relatively divergent from Phytophthora sequences. Based on the sequence alignments of 18 conserved proteins, the average amino acid identity between S. parasitica and three Phytophthora species was 77% compared to 93% within Phytophthora. Several S. parasitica cDNAs, such as those with similarity to fungal type I cellulose binding domain proteins, PAN/Apple module proteins, glycosyl hydrolases, proteases, as well as serine and cysteine protease inhibitors, were predicted to encode secreted proteins that could function in virulence. Some of these cDNAs were more similar to fungal proteins than to other eukaryotic proteins confirming that oomycetes and fungi share some virulence components despite their evolutionary distance

Conclusion

We provide a first glimpse into the gene content of S. parasitica, a reemerging oomycete fish pathogen. These resources will greatly accelerate research on this important pathogen. The data is available online through the Oomycete Genomics Database [1].
A molecular analysis by gene expression profiling reveals Bik/NBK overexpression in sporadic breast tumor samples of Mexican females
Authors: García Normand , Salamanca Fabio , Astudillo-de la Vega Horacio , Curiel-Quesada Everardo , Alvarado Isabel , Peñaloza Rosenda , Arenas Diego
Published: August 2005

Background

Breast cancer is one of the most frequent causes of death in Mexican women over 35 years of age. At molecular level, changes in many genetic networks have been reported as associated with this neoplasia. To analyze these changes, we determined gene expression profiles of tumors from Mexican women with breast cancer at different stages and compared these with those of normal breast tissue samples.

Methods

32P-radiolabeled cDNA was synthesized by reverse transcription of mRNA from fresh sporadic breast tumor biopsies, as well as normal breast tissue. cDNA probes were hybridized to microarrays and expression levels registered using a phosphorimager. Expression levels of some genes were validated by real time RT-PCR and immunohistochemical assays.

Results

We identified two subgroups of tumors according to their expression profiles, probably related with cancer progression. Ten genes, unexpressed in normal tissue, were turned on in some tumors. We found consistent high expression of Bik gene in 14/15 tumors with predominant cytoplasmic distribution.

Conclusion

Recently, the product of the Bik gene has been associated with tumoral reversion in different neoplasic cell lines, and was proposed as therapy to induce apoptosis in cancers, including breast tumors. Even though a relationship among genes, for example those from a particular pathway, can be observed through microarrays, this relationship might not be sufficient to assign a definitive role to Bik in development and progression of the neoplasia. The findings herein reported deserve further investigation.