bluuebunny/crossref_metadata_2025 huggingface dataset:
Elucidation of Essential and Nonessential Genes in the
Haemophilus influenzae
Rd Cell Wall Biosynthetic Pathway by Targeted Gene Disruption
Authors: Trepod Catherine M. , Mott John E.
Published: January 2005

Targeted gene disruption by in vitro transposon mutagenesis has been used to identify the genes required for biosynthesis of the
Haemophilus influenzae
Rd cell wall under standard cultivation conditions. Of the 28 genes known to be associated with the cell wall biosynthetic pathway, 14 were determined to be essential.
Distribution of Subclasses
mefA
and
mefE
of the
mefA
Gene among Clinical Isolates of Macrolide-Resistant (M-Phenotype)
Streptococcus pneumoniae
, Viridans Group Streptococci, and
Streptococcus pyogenes
Authors: Ardanuy Carmen , Tubau Fe , Liñares Josefina , Domínguez María Angeles , Pallarés Román , Martín Rogelio
Published: January 2005

The distribution of subclasses
mefA
and
mefE
of the
mefA
gene among 116 M-phenotype streptococci was as follows: pneumococci (38 strains had
mefE
and 4
mefA
), viridans streptococci (49
mefE
and 1
mefA
), and
Streptococcus pyogenes
(24
mefA
). Spain
9V
-3-14 and England
14
-9 clones of serotype 14 were dominant among pneumococci.
Mutations in
pfmdr1
Modulate the Sensitivity of
Plasmodium falciparum
to the Intrinsic Antiplasmodial Activity of Verapamil
Authors: Hayward Rhys , Saliba Kevin J. , Kirk Kiaran
Published: January 2005

As well as having the ability to reverse chloroquine resistance in the human malaria parasite
Plasmodium falciparum
, verapamil has itself an innate antiplasmodial activity. We show here that mutations in Pgh1, the product of the malaria parasite's
pfmdr1
gene, influence the parasite's susceptibility to the toxic effects of verapamil.
Effects of Cetylpyridinium Chloride Resistance and Treatment on Fluconazole Activity versus
Candida albicans
Authors: Edlind Merritt P. , Smith W. Lamar , Edlind Thomas D.
Published: January 2005

Mouthwash antiseptic cetylpyridinium chloride (CPC) has potent activity against
Candida albicans
; however, two of five azole-resistant strains showed reduced CPC susceptibility. To further examine the potential for cross-resistance, CPC-resistant mutants were selected in vitro and their fluconazole susceptibility was tested. MICs were unchanged, and trailing growth generally decreased. With CPC-fluconazole combinations, both antagonism and synergism were observed, which can be explained, in part, by
CDR1
-
CDR2
multidrug transporter upregulation.
Modeling In Vivo Pharmacokinetics and Pharmacodynamics of Moxifloxacin Therapy forMycobacterium tuberculosisInfection by Using a Novel Cartridge System
Authors: Ginsburg Amy Sarah , Lee Jin , Woolwine Samuel C. , Grosset Jacques H. , Hamzeh Fayez M. , Bishai William R.
Published: January 2005

To study the efficacy of moxifloxacin treatment for tuberculosis, we utilized a novel cartridge system to simulate in vivo pharmacokinetics. We found this system to be a robust method for modeling in vivo pharmacokinetics and present data supporting the utility of intermittent moxifloxacin treatment as a component of antituberculosis chemotherapy.
Hyposmotic activation of ICl,swell in rabbit nonpigmented ciliary epithelial cells involves increased ClC-3 trafficking to the plasma membrane
Authors: Vessey John P , Shi Chanjuan , Jollimore Christine AB , Stevens Kelly T , Coca-Prados Miguel , Barnes Steven , Kelly Melanie EM
Published: January 2005

In mammalian nonpigmented ciliary epithelial (NPE) cells, hyposmotic stimulation leading to cell swelling activates an outwardly rectifying Cl conductance (ICl,swell), which, in turn, results in regulatory volume decrease. The aim of this study was to determine whether increased trafficking of intracellular ClC-3 Cl channels to the plasma membrane could contribute to the ICl,swell following hyposmotic stimulation. Our results demonstrate that hyposmotic stimulation reversibly activates an outwardly rectifying Cl current that is inhibited by phorbol-12-dibutyrate and niflumic acid. Transfection with ClC-3 antisense, but not sense, oligonucleotides reduced ClC-3 expression as well as ICl,swell. Intracellular dialysis with 2 different ClC-3 antibodies abolished activation of ICl,swell. Immunofluorescence microscopy showed that hyposmotic stimulation increased ClC-3 immunoreactivity at the plasma membrane. To determine whether this increased expression of ClC-3 at the plasma membrane could be due to increased vesicular trafficking, we examined membrane dynamics with the fluorescent membrane dye FM1-43. Hyposmotic stimulation rapidly increased the rate of exocytosis, which, along with ICl,swell, was inhibited by the phosphoinositide-3-kinase inhibitor wortmannin and the microtubule disrupting agent, nocodazole. These findings suggest that ClC-3 channels contribute to ICl,swell following hyposmotic stimulation through increased trafficking of channels to the plasma membrane.Key words: ClC-3, NPE, cell swelling, membrane trafficking, ciliary body epithelium.
New ways to skin a kap: mechanisms for controlling nuclear transport
Authors: Lusk C Patrick , Makhnevych Taras , Wozniak Richard W
Published: January 2005

Transport between the nucleus and the cytoplasm occurs through large macromolecular assemblies called nuclear pore complexes (NPCs). The NPC is traditionally viewed as a passive structure whose primary role is to provide an interface for the soluble transport machinery, the karyopherins and their cargos, to move molecules between these compartments. Recent work has challenged this view of the NPC and provides support for a dynamic structure that can modify its architecture to actively regulate nuclear transport.Key words: nuclear transport, nuclear pore complex, karyopherin, nucleoporin.
Regulation of G protein-coupled receptor endocytosis by ARF6 GTP-binding proteins
Authors: Claing Audrey
Published: January 2005

The function of G protein-coupled receptors is regulated by a broad variety of membrane-bound and intracellular proteins. These act in concert to activate signaling pathways that will lead to the desensitization of activated receptors and, for most receptor types, their trafficking to intracellular compartments. This review focuses mainly on the endocytic pathways used by a G protein-coupled receptor and on the proteins that play an essential role in the regulation of the internalization process, most specifically the ADP-ribosylation factors. This family of proteins has been shown to be important for vesicle trafficking between different cellular membranes. The latest findings regarding the molecular mechanisms that regulate internalization of an agonist-stimulated receptor are presented here. Finally, a perspective on how ARF6 proteins might regulate the internalization process is also proposed.Key words: G protein-coupled receptors, endocytosis, ADP-ribosylation factor.
Wiring diagrams of MAPK regulation by MEKK1, 2, and 3
Authors: Uhlik Mark T , Abell Amy N , Cuevas Bruce D , Nakamura Kazuhiro , Johnson Gary L
Published: January 2005

Mitogen-activated protein kinase (MAPK) pathways are activated by a plethora of stimuli. The literature is filled with papers describing the activation of different MAPKs by almost any stimulus or insult imaginable to cells. In this review, we use signal transduction wiring diagrams to illustrate putative upstream regulators for the MAPK kinase kinases, MEKK1, 2, and 3. Targeted gene disruption of MEKK1, 2, or 3 defined phenotypes for each MEKK associated with loss of specific MAPK regulation. Genetic analysis of MEKK function clearly defines specific components of the wiring diagram that require MEKK1, 2, or 3 for physiological responses. We propose that signal transduction network wiring diagrams are valuable tools for hypothesis building and filtering physiologically relevant phenotypic responses from less connected protein relations in the regulation of MAPK pathways.Key words: MAPK pathways, MEKKs, signaling hubs, connections map.
Signaling and regulation of G-protein coupled receptors encoded by cytomegaloviruses
Authors: Stropes Melissa P. M , Miller William E
Published: January 2005

Cytomegaloviruses (CMVs) are species-specific β-herpesviruses whose replicative success is largely due to establishment of novel mechanisms for altering the host immune response. CMV encodes 3 families of putative G-protein coupled receptors (GPCRs) likely pirated from the host cell. While the functions of these virally encoded GPCRs remain unclear, the receptors possess potent signaling abilities. Understanding the molecular regulation of these GPCRs will provide important insight into CMV pathogenesis.Key words: GPCRs, HCMV, GRKs, β-arrestin, US28.
Order or chaos? An evaluation of the regulation of protein kinase CK2
Authors: Olsten Mary Ellen K , Litchfield David W
Published: January 2005

CK2 is a highly conserved, ubiquitously expressed protein serine/threonine kinase present in all eukaryotes. Circumscribed as having a vast array of substrates located in a number of cellular compartments, CK2 has been implicated in critical cellular processes such as proliferation, apoptosis, differentiation, and transformation. Despite advances in elucidating its substrates and involvement in cellular regulation, its precise mode of regulation remains poorly defined. In this respect, there are currently conflicting views as to whether CK2 is constitutively active or modulated in response to specific stimuli. Perhaps an important consideration in resolving these apparent discrepancies is recognition of the existence of many discrete CK2 subpopulations that are distinguished from one another by localization or association with distinct cellular components. The existence of these subpopulations brings to light the possibility of each population being regulated independently rather than the entire cellular CK2 content being regulated globally. Logically, each local population may then be regulated in a distinct manner to carry out its precise function(s). This review will examine those mechanisms including regulated expression and assembly of CK2 subunits, phosphorylation of CK2, and interactions with small molecules or cellular proteins that could contribute to the local regulation of distinct CK2 populations.Key words: protein kinase CK2, regulation, phosphorylation, protein-protein interactions, HIKE domains, regulatory interactions, CKIP-1, signal transduction.
Signaling in glial development: differentiation migration and axon guidance
Authors: Parker Robert J , Auld Vanessa J
Published: January 2005

Glial cells have diverse functions that are necessary for the proper development and function of complex nervous systems. During development, a variety of reciprocal signaling interactions between glia and neurons dictate all parts of nervous system development. Glia may provide attractive, repulsive, or contact-mediated cues to steer neuronal growth cones and ensure that neurons find their appropriate synaptic targets. In fact, both neurons and glia may act as migrational substrates for one another at different times during development. Also, the exchange of trophic signals between glia and neurons is essential for the proper bundling, fasciculation, and ensheathement of axons as well as the differentiation and survival of both cell types. The growing number of links between glial malfunction and human disease has generated great interest in glial biology. Because of its relative simplicity and the many molecular genetic tools available, Drosophila is an excellent model organism for studying glial development. This review will outline the roles of glia and their interactions with neurons in the embryonic nervous system of the fly.Key words: glia, axon guidance, migration, EGF receptor.
Performance differences in Pinus radiata progeny with differing site nutrient availability
Authors: Carson S D , Skinner M F , Lowe A T , Kimberley M O
Published: January 2005

Two intensive harvesting trials with contrasting nutrient capital were examined for genetic × environment interactions to age 5 years after planting. Treatments included differences in removal of organic matter and in site preparation and weed control, with each treatment having both fertilized and nonfertilized plots. Three harvest treatments (both fertilized and nonfertilized) were common to both sites, with two additional treatments at one site. There were four replicate plots of each treatment combination at each site, with two trees from each of three control seed lots and 47 open-pollinated families chosen to represent the range of performance for growth planted in each plot. Large differences among sites and among treatments in both growth and foliar nutrient concentration were observed. Genetic × site interactions and genetic × treatment within site interactions were seldom significant. Significant interactions did not appear to be related to changes in rankings of families, but rather to the differences in variance among families in different treatments. This study suggests that selection of specific radiata pine (Pinus radiata D. Don) families for better growth performance on nutrient-deficient sites in New Zealand would not result in substantial improvement over selection for growth on all sites disregarding nutrient availability.
Evaluation of three methods for predicting diameter distributions of black spruce (Picea mariana) plantations in central Canada
Authors: Liu Chuangmin , Zhang S Y , Lei Yuancai , Newton Peter F , Zhang Lianjun
Published: January 2005

The direct parameter prediction method (PPM), moment-based parameter recovery method (PRM), and percentile-based parameter recovery method (PCT) for estimating the parameters of the three-parameter Weibull probability density function were evaluated for their applicability in predicting the diameter distribution of unthinned black spruce (Picea mariana (Mill.) B.S.P.) plantations. Employing diameter frequency data derived from 267 permanent sample plots situated throughout central Canada, fit (n = 214) and validation (n = 53) data sets were created. Using stepwise regression analyses in combination with seemingly unrelated regression techniques, the three methods were calibrated using commonly measured prediction variables (stand age, dominant height, site index, and stand density). Results indicated that, although all three methods were successful in predicting the diameter frequency distributions within the sample stands, the PCT was superior in terms of prediction error. Specifically, the PCT had the lowest mean error index (80.98), followed by the PRM (82.73) and the PPM (83.98). Consequently, among the three methods assessed, the PCT was considered the most suitable for describing unimodal diameter distributions via the three-parameter Weibull probability density function within unthinned black spruce plantations.
Geographic allozyme variation in Atlantic white-cedar,Chamaecyparis thyoides(Cupressaceae)
Authors: Mylecraine Kristin A , Kuser John E , Smouse Peter E , Zimmermann George L
Published: January 2005

Chamaecyparis thyoides (L.) B.S.P. is an important wetland tree species occurring along the Atlantic and Gulf Coasts of the United States. Substantial decline over the past two centuries has led to interest in the geographic pattern of genetic variation of the species, as it affects both restoration and ongoing management. We examined the extent and distribution of allozyme variation among 31 populations throughout the species' range. Averaged across populations, the mean number of alleles per locus (A) was 1.94, the effective number of alleles per locus (Ae) was 1.31, expected heterozygosity (He) was 0.16, and the proportion of polymorphic loci (P) was 63.6%. Significant population differentiation was apparent, with FST= 0.085. Using analysis of molecular variance (AMOVA), we were able to ascribe 6% of the total variation to differences between varieties. We identified three main geographical regions: (1) Atlantic Coastal, (2) peninsular Florida, and (3) Gulf Coast. Within the Gulf Coast region, three subregions are apparent: central Florida panhandle, western Florida panhandle, and Mississippi. This geographic pattern may have resulted from three or more separate Pleistocene glacial refugia and suggests that propagules for regeneration and restoration activities should not be moved out of their region of origin.
Terrestrial movements of juvenile and adult tailed frogs in relation to timber harvest in coastal British Columbia
Authors: Wahbe Tanya R , Bunnell Fred L , Bury R Bruce
Published: January 2005

Tailed frog (Ascaphus truei Stejneger) populations are at risk in much of the Pacific Northwest, and recolonization of sites may be slow postlogging. To examine the terrestrial movements of Ascaphus in clearcuts and old growth, we employed pitfall traps and drift-fence arrays installed along streams and 100 m into upland habitat. In the fall, we captured frogs farther from streams in old growth than in clearcuts, and more frogs were captured ≤25 m from streams in clearcuts. Stronger stream affinity in clearcuts was most evident with juvenile frogs, which exhibited more upstream movements than adults. Compared with inland sites where frogs remained close to streams (e.g., 12 m), frogs at our coastal sites were captured at greater distances from streams (≥100 m), having lower stream affinity than frogs at inland sites. Long-distance overland movements appear more likely where forested stands are present. Aggregations of Ascaphus at individual streams may not represent distinct populations and should not be managed as distinct units. Preserving groups of interconnected streams within watersheds instead of individual streams will improve the conservation status of Ascaphus. Population monitoring can ensure conservation measures promote long-term persistence.
Genetic parameter estimates for wood stiffness, strength, internal checking, and resin bleeding for radiata pine
Authors: Kumar Satish
Published: January 2005

Data from two separate experiments were used to estimate genetic parameters for different wood properties of Pinus radiata D. Don in New Zealand. In experiment 1, 72 and 60 open-pollinated families were sampled at two sites, Kinleith and Paengaroa, respectively. Fifty-nine such families were common to both sites. In experiment 2, 62 and 29 pollen-parent families were sampled from a female-tester trial at two sites, Kaingaroa and Warrengong (the latter in Australia), respectively. Twenty-nine such families were common to both sites. Clearwood stiffness (MOE) and strength (MOR), wood density (DEN), acoustic stiffness on standing trees (IMLH), acoustic stiffness in 5-m logs (HITMAN), external resin bleeding (ERB), internal checking from discs taken at 1.3-m and 3.0-m height (CHEK_B and CHEK_U), and diameter at breast height (DBH) were assessed. Within-site narrow-sense heritability (h2) estimates of various wood properties were consistent, particularly within New Zealand. Across-sites estimates of h2 of HITMAN, CHEK_B, and DEN were, respectively, 0.24, 0.40, and 0.62 in experiment 1 and 0.21, 0.16, and 0.38 in experiment 2. Estimated type B genetic correlations were generally high for all traits except DBH. DEN showed strong positive genetic correlation with all direct and acoustic measures of stiffness (MOE, HITMAN, and IMLH). DEN and all measures of stiffness showed low to moderate negative genetic correlations with DBH.
Inferred summer precipitation for southern Ontario back to AD 610, as reconstructed from ring widths of Thuja occidentalis
Authors: Buckley Brendan M , Wilson Robert JS , Kelly Peter E , Larson Douglas W , Cook Edward R
Published: January 2005

We present a network of seven ring-width chronologies of eastern white-cedar (Thuja occidentalis L.) from the Niagara Escarpment in southern Ontario, Canada. Using principal component regression, a 350-year June-July precipitation reconstruction (SOR) is developed for the region. Prior to the 20th century, the SOR series shows reasonable coherence, particularly at the decadal scale, with an independent tree-ring-based reconstruction of the Palmer drought severity index (PDSI) for roughly the same region. A weakening of the tree-growth  climate relationship in recent decades results in a regression model explaining 21% of the variance in the original climate series when the recent data are used for calibration. We therefore compromise with a model, calibrated for the period 19001960, which explains 33% of the variance. The model, while not terribly strong, does pass verification tests, indicating some degree of predictive skill. The longest chronology in our network, the 2787-year Flowerpot Island (FLOW) chronology, also exhibits common variability with the PDSI reconstruction, particularly on decadal and longer time scales and was used to infer hydroclimatic conditions back to AD 610. The combined information of the SOR, PDSI, and FLOW series suggests that dry conditions existed for the periods 17001725, 17501800, and 18401900, and wet conditions for the periods 16751700, 17301750, and 18101840. Over longer time scales, the FLOW chronology shows that summer precipitation was particularly variable during the 7th, 9th, 13th, and 16th centuries.
Simulating the dynamics of linear forests in Great Plains agroecosystems under changing climates
Authors: Guo Qinfeng , Brandle J , Schoeneberger M , Buettner D
Published: January 2005

Most forest growth models are not suitable for the highly fragmented, linear (or linearly shaped) forests in the Great Plains agroecosystems (e.g., windbreaks, riparian forest buffers), where such forests are a minor but ecologically important component of the land mosaics. This study used SEEDSCAPE, a recently modified gap model designed for cultivated land mosaics in the Great Plains, to simulate the effects of climate change on the dynamics of such linear forests. We simulated the dynamics of windbreaks with different initial planting species richness and widths (light changes as the selected resulting factor) using current climate data and nested regional circulation models (RegCMs). Results indicated that (i) it took 7080 simulation years for the linear forests to reach a steady state under both normal (present-day) and warming climates; (ii) warming climates would reduce total aboveground tree biomass and the spatial variation in biomass, but increase dominance in the linear forests, especially in the upland forests; (iii) linear forests with higher planting species richness and smaller width produced higher aboveground tree biomass per unit area; and (iv) the same species performed very differently with different climate scenarios, initial planting diversity, and forest widths. Although the model still needs further improvements (e.g., the effects of understory species should be included), the model can serve as a useful tool in modeling the succession of linear forests in human-dominated land mosaics under changing climates and may also have significant practical implications in other systems.
There’s No Such Thing as a Free (Software) Lunch
Authors: Michaelson Jay
Published: January 2005

The licenses for most software are designed to take away your freedom to share and change it. By contrast, the GNU General Public License is intended to guarantee your freedom to share and change free software to make sure the software is free for all its users. So begins the GNU General Public License, or GPL, which has become the most widely used of open source software licenses. Freedom is the watchword; it’s no coincidence that the organization that wrote the GPL is called the Free Software Foundation and that open source developers everywhere proclaim, “Information wants to be free.”
Desktop Linux: Where Art Thou?
Authors: Decrem Bart
Published: January 2005

Linux on the desktop has come a long way - and it’s been a roller-coaster ride. At the height of the dot-com boom, around the time of Red Hat’s initial public offering, people expected Linux to take off on the desktop in short order. A few years later, after the stock market crash and the failure of a couple of high-profile Linux companies, pundits were quick to proclaim the stillborn death of Linux on the desktop.
TCP Offload to the Rescue
Authors: Currid Andy
Published: January 2005

In recent years, TCP/IP offload engines, known as TOEs, have attracted a good deal of industry attention and a sizable share of venture capital dollars. A TOE is a specialized network device that implements a significant portion of the TCP/IP protocol in hardware, thereby offloading TCP/IP processing from software running on a general-purpose CPU. This article examines the reasons behind the interest in TOEs and looks at challenges involved in their implementation and deployment.
A Conversation with Sam Leffler
Authors: Russell James
Published: January 2005

The seeds of Unix and open source were sown in the 1970s, and Sam Leffler was right in there doing some of the heaviest cultivating. He has been actively working with Unix since 1976 when he first encountered it at Case Western Reserve University, and he has been involved with what people now think of as open source, as he says, “long before it was even termed open source.” While working for the Computer Systems Research Group (CSRG) at the University of California at Berkeley, he helped with the 4.1BSD release and was responsible for the release of 4.2BSD. He has contributed to almost every aspect of BSD systems, most recently working (again) on the networking subsystem.
A Bigot by Any Other Name...
Authors: Coates Josh
Published: January 2005

I’ve been responsible for hiring many software engineers. I tend to ask lots of elaborate technical questions so I can really get to know how the candidate thinks and works with me while solving hard problems. QA engineers will appreciate this one (it’s a “negative test” for intellectual honesty): “Explain the relative strengths and weaknesses of FreeBSD, Windows NT, Solaris, and Linux.”
Blaster Revisited
Authors: Morrison Jim
Published: January 2005

What lessons can we learn from the carnage the Blaster worm created? The following tale is based upon actual circumstances from corporate enterprises that were faced with confronting and eradicating the Blaster worm, which hit in August 2003. The story provides views from many perspectives, illustrating the complexity and sophistication needed to combat new blended threats.
Security: The Root of the Problem
Authors: Ranum Marcus J
Published: January 2005

Security bug? My programming language made me do it! It doesn’t seem that a day goes by without someone announcing a critical flaw in some crucial piece of software or other. Is software that bad? Are programmers so inept? What the heck is going on, and why is the problem getting worse instead of better? One distressing aspect of software security is that we fundamentally don’t seem to “get it.” In the 15 years I’ve been working the security beat, I have lost track of the number of times I’ve seen (and taught) tutorials on “how to write secure code” or read books on that topic.
Network Forensics
Authors: Laurie Ben
Published: January 2005

The dictionary defines forensics as “the use of science and technology to investigate and establish facts in criminal or civil courts of law.” I am more interested, however, in the usage common in the computer world: using evidence remaining after an attack on a computer to determine how the attack was carried out and what the attacker did. The standard approach to forensics is to see what can be retrieved after an attack has been made, but this leaves a lot to be desired. The first and most obvious problem is that successful attackers often go to great lengths to ensure that they cover their trails. The second is that unsuccessful attacks often go unnoticed, and even when they are noticed, little information is available to assist with diagnosis.
The Insider, Naivety, and Hostility: Security Perfect Storm?
Authors: Thompson Herbert H , Ford Richard
Published: January 2005

Every year corporations and government installations spend millions of dollars fortifying their network infrastructures. Firewalls, intrusion detection systems, and antivirus products stand guard at network boundaries, and individuals monitor countless logs and sensors for even the subtlest hints of network penetration. Vendors and IT managers have focused on keeping the wily hacker outside the network perimeter, but very few technological measures exist to guard against insiders - those entities that operate inside the fortified network boundary. The 2002 CSI/FBI survey estimates that 70 percent of successful attacks come from the inside. Several other estimates place those numbers even higher.
From the Editors: The New Screen of Death
Authors: Grossman Edward
Published: January 2005

In the olden days (say, all the way back in 1995), the popular complaint about computers was that they crashed too often. And while stability remains a problem in which perhaps there’s still progress to be made, the blue screen of death has been eclipsed by the new screen of death: Security.
Grid Tools: Coming to a Cluster Near You
Authors: Wolfe Alex
Published: January 2005

A set of surprisingly mainstream software tools has come out of an unlikely source—a scientifically focused collective called the Gelato Federation. Formally launched in March 2002, the group seeks to apply open source Linux software running on Intel’s advanced Itanium processor as an enabling technology toward the goal of putting together large, highly scalable clusters of 64-bit systems. The Gelato group believes such scalability is the most significant trend in high-performance computing in the last 10 to 15 years. It marks a potent—and much cheaper—alternative to the Cray supercomputers that populated university labs in the 1980s and early 1990s.
The Reincarnation of Virtual Machines
Authors: Rosenblum Mendel
Published: January 2005

The term virtual machine initially described a 1960s operating system concept: a software abstraction with the looks of a computer system’s hardware (real machine). Forty years later, the term encompasses a large range of abstractions?for example, Java virtual machines that don’t match an existing real machine. Despite the variations, in all definitions the virtual machine is a target for a programmer or compilation system. In other words, software is written to run on the virtual machine.
Building Systems to Be Shared, Securely
Authors: Kamp Poul-Henning , Watson Robert
Published: January 2005

The history of computing has been characterized by continuous transformation resulting from the dramatic increases in performance and drops in price described by Moore’s law. Computing power has migrated from centralized mainframes/servers to distributed systems and the commodity desktop. Despite these changes, system sharing remains an important tool for computing. From the multitasking, file-sharing, and virtual machines of the desktop environment to the large-scale sharing of server-class ISP hardware in collocation centers, safely sharing hardware between mutually untrusting parties requires addressing critical concerns of accidental and malicious damage.
Simulators: Virtual Machines of the Past (and Future)
Authors: Supnik Bob
Published: January 2005

Simulators are a form of “virtual machine” intended to address a simple problem: the absence of real hardware. Simulators for past systems address the loss of real hardware and preserve the usability of software after real hardware has vanished. Simulators for future systems address the variability of future hardware designs and facilitate the development of software before real hardware exists.
Security is Harder than You Think
Authors: Viega John , Messier Matt
Published: January 2005

Many developers see buffer overflows as the biggest security threat to software and believe that there is a simple two-step process to secure software: switch from C or C++ to Java, then start using SSL (Secure Sockets Layer) to protect data communications. It turns out that this naïve tactic isn’t sufficient. In this article, we explore why software security is harder than people expect, focusing on the example of SSL.
A Conversation with James Gosling
Authors: Allman Eric
Published: January 2005

As a teenager, James Gosling came up with an idea for a little interpreter to solve a problem in a data analysis project he was working on at the time. Through the years, as a grad student and at Sun as creator of Java and the Java Virtual Machine, he has used several variations on that solution. “I came up with one answer once, and I have just been repeating it over and over again for a frightening number of years,” he says.
Experimental analysis of the fastest optimum cycle ratio and mean algorithms
Authors: Dasdan Ali
Published: January 2005

Optimum cycle ratio (OCR) algorithms are fundamental to the performance analysis of (digital or manufacturing) systems with cycles. Some applications in the computer-aided design field include cycle time and slack optimization for circuits, retiming, timing separation analysis, and rate analysis. There are many OCR algorithms, and since a superior time complexity in theory does not mean a superior time complexity in practice, or vice-versa, it is important to know how these algorithms perform in practice on real circuit benchmarks. A recent published study experimentally evaluated almost all the known OCR algorithms, and determined the fastest one among them. This article improves on that study in the following ways: (1) it focuses on the fastest OCR algorithms only; (2) it provides a unified theoretical framework and a few new results; (3) it runs these algorithms on the largest circuit benchmarks available; (4) it compares the algorithms in terms of many properties in addition to running times such as operation counts, convergence behavior, space requirements, generality, simplicity, and robustness; (5) it analyzes the experimental results using statistical techniques and provides asymptotic time complexity of each algorithm in practice; and (6) it provides clear guidance to the use and implementation of these algorithms together with our algorithmic improvements.
Cache optimization for embedded processor cores
Authors: Ghosh Arijit , Givargis Tony
Published: January 2005

Embedded microprocessor cores are increasingly being used in embedded and mobile devices. The software running on these embedded microprocessor cores is often a priori known; thus, there is an opportunity for customizing the cache subsystem for improved performance. In this work, we propose an efficient algorithm to directly compute cache parameters satisfying desired performance criteria. Our approach avoids simulation and exhaustive exploration, and, instead, relies on an exact algorithmic approach. We demonstrate the feasibility of our algorithm by applying it to a large number of embedded system benchmarks.
Jump map-based interactive texture synthesis
Authors: Zelinka Steve , Garland Michael
Published: January 2005

We present techniques for accelerated texture synthesis from example images. The key idea of our approach is to divide the task into two phases: analysis, and synthesis. During the analysis phase, which is performed once per sample texture, we generate a jump map. Using the jump map, the synthesis phase is capable of synthesizing texture similar to the analyzed example at interactive rates. We describe two such synthesis phase algorithms: one for creating images, and one for directly texturing manifold surfaces. We produce texture images at rates comparable to the fastest alternative algorithms, and produce textured surfaces an order of magnitude faster than current alternative approaches. We further develop a new, faster patch-based algorithm for image synthesis, which improves the quality of our results on ordered textures. We show how controls used for specifying texture synthesis on surfaces may be used on images as well, allowing interesting new image-based effects, and highlight modelling applications enabled by the speed of our approach.
Lighting sensitive display
Authors: Nayar Shree K. , Belhumeur Peter N. , Boult Terry E.
Published: January 2005

Although display devices have been used for decades, they have functioned without taking into account the illumination of their environment. We present the concept of a lighting sensitive display (LSD)---a display that measures the incident illumination and modifies its content accordingly. An ideal LSD would be able to measure the 4D illumination field incident upon it and generate a 4D light field in response to the illumination. However, current sensing and display technologies do not allow for such an ideal implementation. Our initial LSD prototype uses a 2D measurement of the illumination field and produces a 2D image in response to it. In particular, it renders a 3D scene such that it always appears to be lit by the real environment that the display resides in. The current system is designed to perform best when the light sources in the environment are distant from the display, and a single user in a known location views the display.

The displayed scene is represented by compressing a very large set of images (acquired or rendered) of the scene that correspond to different lighting conditions. The compression algorithm is a lossy one that exploits not only image correlations over the illumination dimensions but also coherences over the spatial dimensions of the image. This results in a highly compressed representation of the original image set. This representation enables us to achieve high quality relighting of the scene in real time. Our prototype LSD can render 640 × 480 images of scenes under complex and varying illuminations at 15 frames per second using a 2 GHz processor. We conclude with a discussion on the limitations of the current implementation and potential areas for future research.
Variational normal meshes
Authors: Friedel Ilja , Schröder Peter , Khodakovsky Andrei
Published: January 2005

Hierarchical representations of surfaces have many advantages for digital geometry processing applications. Normal meshes are particularly attractive since their level-to-level displacements are in the local normal direction only. Consequently, they only require scalar coefficients to specify. In this article, we propose a novel method to approximate a given mesh with a normal mesh. Instead of building an associated parameterization on the fly, we assume a globally smooth parameterization at the beginning and cast the problem as one of perturbing this parameterization. Controlling the magnitude of this perturbation gives us explicit control over the range between fully constrained (only scalar coefficients) and unconstrained (3-vector coefficients) approximations. With the unconstrained problem giving the lowest approximation error, we can thus characterize the error cost of normal meshes as a function of the number of nonnormal offsets---we find a significant gain for little (error) cost. Because the normal mesh construction creates a geometry driven approximation, we can replace the difficult geometric distance minimization problem with a much simpler least squares problem. This variational approach reduces magnitude and structure (aliasing) of the error further. Our method separates the parameterization construction into an initial setup followed only by subsequent perturbations, giving us an algorithm which is far simpler to implement, more robust, and significantly faster.
Some simple but interesting results concerning the P ?=
NP
Problem
Authors: Ylikoski Antti
Published: January 2005

In this paper, I discuss some properties of two functions, which I call f1() and f2(), which are interesting from the point of view of the P ?= NP problem. The both functions f1() and f2() concern the problem of solving a nondeterministic polynomial-time problem deterministically in a polynomial time. Based on the results, I finally outline a research program to study the P ?= NP problem.
Etude on theme of Dijkstra
Authors: Shilova S. O. , Shilov N. V.
Published: January 2005

We present a tutorial for undergraduate students who are interested in different programming contests like National Programming Olympiads or regional ACM International Collegiate Programming Contests (ACM ICPC). It is based on a problem discussed by E. W. Dijkstra in a public lecture in 1994. The tutorial was a part of a special undergraduate course presented for students of Novosibirsk State University in 2003-04 academic year during their preparation for ACM ICPC Final at Prague (2004).

The original problem is how to couple N black and N white points on the plane by intervals without intersections. E. W. Dijkstra suggested a nice heuristic search algorithm and proved its termination and correctness by the method of R. W. Floyd. Unfortunately, the upper bound of his algorithm was exponential. Due to this reason, he suggested to audience investigation of the problem complexity and development of an efficient algorithm.

We demonstrate that the problem is decidable in cubic time by quadratic reduction to the classical assignment problem. We also discuss how to solve the coupling problem in pure geometric/topological way. We also present some examples of utility of the coupling problem.
Review of "Reasoning about Uncertainty by Joseph Y. Halpern." The MIT Press, 2003.
Authors: Zhao Wenzhong
Published: January 2005

Dealing with uncertain and imprecise information has been one of the major issues in almost all intelligent systems. Uncertainty is a fundamental and unavoidable feature of our daily life. It arises because agents almost never have access to the whole truth about their environment. It can also occur when the agents have incomplete and/or incorrect information about the properties of their environment.
Review of "Learning Kernel Classifiers: Theory and Algorithms by Ralf Herbrich." MIT Press, Cambridge, Mass., 2002. ISBN 026208306X, 384 pages; and Review of "Learning with Kernels: Support Vector Machines, Regularization Optimization and Beyond by Bernhard Scholkopf and Alexander J. Smola." IT Press, Cambridge, Mass., 2002, ISBN 0262194759, 644 pages.
Authors: Wille Luc T.
Published: January 2005

Pattern recognition is arguably the critical first step in intelligence - be it natural or artificial. Science could not exist if humans were not able to spot regularities. Only subsequently do we analyze and classify them, and ultimately come up with underlying descriptions, some of which eventually make it to the lofty status of natural laws. Of course evolution did NOT ENDOw humans (or animals for that matter) with the ability to recognize patterns so we could build grandiose scientific edifices, rather we need that ability at the most elementary level. Humans simply cannot function in everyday life without pattern recognition capabilities and when those capabilities are impaired, as in patients with Alzheimer's disease for example, the result is nothing less than tragic.
Review of "Essentials of Constraint Programming by T. Fruhwirth and S. Abdennadher." Springer-Verlag.
Authors: Oliveira Carlos
Published: January 2005

Constraint programming (CP) is an area of computer science in which the considered problems can be expressed as a set of logical rules, also known as constraints. This results in a huge class of problems, encompassing domains such as logic programming, mathematical programming, and optimization.
Computational geometry column 46
Authors: O'Rourke Joseph
Published: January 2005

The old problem of determining the chromatic number of the plane is revisited.

The question of the chromatic number of the Euclidean plane E2 has been unresolved for over fifty years. Informally, the question asks: How many colors are needed to paint the plane so that no two points a unit distance apart are painted the same color? If the same question is asked of the line, the answer is 2: Coloring [0,1) red, [1,2) blue, etc., ensures that no two unit-separated points have the same color. Here I report on a few new developments, and some related open problems that are perhaps easier.

One can view the question as asking for the chromatic number X(E2) of the infinite unit-distance graph G, with every point in the plane a node, and an are between two nodes if they are separated by a unit distance. Erdös and de Bruijn showed [EdB51] that the chromatic number of the plane is attained for some finite subgraph of G. This result led to narrowing the answer to 4 ≤ X(E2) ≤7. For example, the lower bound of 4 is established by the "Moser graph" shown in Fig. 1, which needs 4 colors.
SIGACT news online algorithms column 4
Authors: Chrobak Marek
Published: January 2005

From the editor: This issue's column contains an expository article by Leah Eppstein and Rob Van Stee on models and algorithms for buffer management in QofS networks. This area has seen a flurry of activity in the last four years. In spite of good progress, several fundamental, easy-to-state problems remain open. Many thanks to Leah and Rob for this timely contribution.
Analysis of lexical signatures for improving information persistence on the World Wide Web
Authors: Park Seung-Taek , Pennock David M. , Giles C. Lee , Krovetz Robert
Published: January 2005

A lexical signature (LS) consisting of several key words from a Web document is often sufficient information for finding the document later, even if its URL has changed. We conduct a large-scale empirical study of nine methods for generating lexical signatures, including Phelps and Wilensky's original proposal (PW), seven of our own static variations, and one new dynamic method. We examine their performance on the Web over a 10-month period, and on a TREC data set, evaluating their ability to both (1) uniquely identify the original (possibly modified) document, and (2) locate other relevant documents if the original is lost. Lexical signatures chosen to minimize document frequency (DF) are good at unique identification but poor at finding relevant documents. PW works well on the relatively small TREC data set, but acts almost identically to DF on the Web, which contains billions of documents. Term-frequency-based lexical signatures (TF) are very easy to compute and often perform well, but are highly dependent on the ranking system of the search engine used. The term-frequency inverse-document-frequency- (TFIDF-) based method and hybrid methods (which combine DF with TF or TFIDF) seem to be the most promising candidates among static methods for generating effective lexical signatures. We propose a dynamic LS generator called Test & Select (TS) to mitigate LS conflict. TS outperforms all eight static methods in terms of both extracting the desired document and finding relevant information, over three different search engines. All LS methods show significant performance degradation as documents in the corpus are edited.
Fast phrase querying with combined indexes
Authors: Williams Hugh E. , Zobel Justin , Bahle Dirk
Published: January 2005

Search engines need to evaluate queries extremely fast, a challenging task given the quantities of data being indexed. A significant proportion of the queries posed to search engines involve phrases. In this article we consider how phrase queries can be efficiently supported with low disk overheads. Our previous research has shown that phrase queries can be rapidly evaluated using nextword indexes, but these indexes are twice as large as conventional inverted files. Alternatively, special-purpose phrase indexes can be used, but it is not feasible to index all phrases. We propose combinations of nextword indexes and phrase indexes with inverted files as a solution to this problem. Our experiments show that combined use of a partial nextword, partial phrase, and conventional inverted index allows evaluation of phrase queries in a quarter the time required to evaluate such queries with an inverted file alone; the additional space overhead is only 26% of the size of the inverted file.