bluuebunny/crossref_metadata_2025 huggingface dataset:
A Positive Regulatory Loop Controls Expression of the Locus of Enterocyte Effacement-Encoded Regulators Ler and GrlA
Authors: Barba Jeannette , Bustamante Víctor H. , Flores-Valdez Mario A. , Deng Wanyin , Finlay B. Brett , Puente José L.
Published: November 2005

The formation of attaching and effacing (A/E) lesions on intestinal epithelial cells is an essential step in the pathogenesis of human enteropathogenic and enterohemorrhagicEscherichia coliand of the mouse pathogenCitrobacter rodentium. The genes required for the development of the A/E phenotype are located within a pathogenicity island known as thelocus ofenterocyteeffacement (LEE). The LEE-encoded transcriptional regulators Ler, an H-NS-like protein, and GrlA, a member of a novel family of transcriptional activators, positively control the expression of the genes located in the LEE and their corresponding virulence. In this study, we usedC. rodentiumas a model to study the mechanisms controlling the expression of Ler and GrlA. By deletion analysis of thelerandgrlRAregulatory regions and complementation experiments, negative and positivecis-acting regulatory motifs were identified that are essential for the regulation of both genes. This analysis confirmed that GrlA is required for the activation ofler, but it also showed that Ler is required for the expression ofgrlRA, revealing a novel regulatory loop controlling the optimal expression of virulence genes in A/E pathogens. Furthermore, our results indicate that Ler and GrlA induce the expression of each other by, at least in part, counteracting the repression mediated by H-NS. However, whereas GrlA is still required for the optimal expression oflereven in the absence of H-NS, Ler is not needed for the expression ofgrlRAin the absence of H-NS. This type of transcriptional positive regulatory loop represents a novel mechanism in pathogenic bacteria that is likely required to maintain an appropriate spatiotemporal transcriptional response during infection.
Identification and Characterization of a Novel Outer Membrane Protein (OMP J) of
Moraxella catarrhalis
That Exists in Two Major Forms
Authors: Hays John P. , van Selm Saskia , Hoogenboezem Theo , Estevão Silvia , Eadie Kimberly , van Veelen Peter , Tommassen Jan , van Belkum Alex , Hermans Peter W. M.
Published: November 2005

Moraxella catarrhalis
is a common commensal of the human respiratory tract that has been associated with a number of disease states, including acute otitis media in children and exacerbations of chronic obstructive pulmonary disease in adults. During studies to investigate the outer membrane proteins of this bacterium, two novel major proteins, of approximately 19 kDa and 16 kDa (named OMP J1 and OMP J2, respectively), were identified. Further analysis indicated that these two proteins possessed almost identical gene sequences, apart from two insertion/deletion events in predicted external loops present within the putative barrel-like structure of the proteins. The development of a PCR screening strategy found a 100% (96/96) incidence for the genes encoding the OMP J1 and OMP J2 proteins within a set of geographically diverse
M. catarrhalis
isolates, as well as a significant association of OMP J1/OMP J2 with both the genetic lineage and the complement resistance phenotype (Fisher's exact test;
P
< 0.01). Experiments using two Δ
ompJ2
mutants (one complement resistant and the other complement sensitive) indicated that both were less easily cleared from the lungs of mice than were their isogenic wild-type counterparts, with a significant difference in bacterial clearance being observed for the complement-resistant isolate but not for its isogenic Δ
ompJ2
mutant (unpaired Student's
t
test;
P
< 0.001 and
P
= 0.32). In this publication, we characterize a novel outer membrane protein of
Moraxella catarrhalis
which exists in two variant forms associated with particular genetic lineages, and both forms are suggested to contribute to bacterial clearance from the lungs.
Molecular Analysis and Organization of the σ
B
Operon in
Staphylococcus aureus
Authors: Senn Maria Magdalena , Giachino Philipp , Homerova Dagmar , Steinhuber Andrea , Strassner Jochen , Kormanec Jan , Flückiger Ursula , Berger-Bächi Brigitte , Bischoff Markus
Published: November 2005

The alternative sigma factor σ
B
of
Staphylococcus aureus
controls the expression of a variety of genes, including virulence determinants and global regulators. Genetic manipulations and transcriptional start point (TSP) analyses showed that the
sigB
operon is transcribed from at least two differentially controlled promoters: a putative σ
A
-dependent promoter, termed
sigB
p1
, giving rise to a 3.6-kb transcript covering sa2059
-
sa2058
-rsbU-rsbV-rsbW-sigB
, and a σ
B
-dependent promoter,
sigB
p3
, initiating a 1.6-kb transcript covering
rsbV-rsbW-sigB
. TSP and promoter-reporter gene fusion experiments indicated that a third promoter, tentatively termed
sigB
p2
and proposed to lead to a 2.5-kb transcript, including
rsbU-rsbV-rsbW-sigB
, might govern the expression of the
sigB
operon. Environmental stresses, such as heat shock and salt stress, induced a rapid response within minutes from promoters
sigB
p1
and
sigB
p3
. In vitro, the
sigB
p1
promoter was active in the early growth stages, while the
sigB
p2
and
sigB
p3
promoters produced transcripts throughout the growth cycle, with
sigB
p3
peaking around the transition state between exponential growth and stationary phase. The amount of
sigB
transcripts, however, did not reflect the concentration of σ
B
measured in cell extracts, which remained constant over the entire growth cycle. In a guinea pig cage model of infection,
sigB
transcripts were as abundant 2 and 8 days postinoculation as values found in vitro, demonstrating that
sigB
is indeed transcribed during the course of infection. Physical interactions between staphylococcal RsbU-RsbV, RsbV-RsbW, and RsbW-σ
B
were inferred from a yeast (
Saccharomyces cerevisiae
) two-hybrid approach, indicating the presence of a partner-switching mechanism in the σ
B
activation cascade similar to that of
Bacillus subtilis
. The finding that overexpression of RsbU was sufficient to trigger an immediate and strong activation of σ
B
, however, signals a relevant difference in the regulation of σ
B
activation between
B. subtilis
and
S. aureus
in the cascade upstream of RsbU.
Comparative Analysis of Two Classes of Quorum-Sensing Signaling Systems That Control Production of Extracellular Proteins and Secondary Metabolites inErwinia carotovoraSubspecies
Authors: Chatterjee Asita , Cui Yaya , Hasegawa Hiroaki , Leigh Nathan , Dixit Vaishali , Chatterjee Arun K.
Published: November 2005

InErwinia carotovorasubspecies,N-acyl homoserine lactone (AHL) controls the expression of various traits, including extracellular enzyme/protein production and pathogenicity. We report here thatE. carotovorasubspecies possess two classes of quorum-sensing signaling systems defined by the nature of the major AHL analog produced as well as structural and functional characteristics of AHL synthase (AhlI) and AHL receptor (ExpR). Class I strains represented byE. carotovorasubsp.atrosepticastrain Eca12 andE. carotovorasubsp.carotovorastrains EC153 and SCC3193 produce 3-oxo-C8-HL (N-3-oxooctanoyl-l-homoserine lactone) as the major AHL analog as well as low but detectable levels of 3-oxo-C6-HL (N-3-oxohexanoyl-l-homoserine lactone). In contrast, the members of class II (i.e.,E. carotovorasubsp.betavasculorumstrain Ecb168 andE. carotovorasubsp.carotovorastrains Ecc71 and SCRI193) produce 3-oxo-C6-HL as the major analog. ExpR species of both classes activatersmA(Rsm, repressor of secondary metabolites) transcription and bindrsmADNA. Gel mobility shift assays with maltose-binding protein (MBP)-ExpR71and MBP-ExpR153fusion proteins show that both bind a 20-mer sequence present inrsmA. The two ExpR functions (i.e.,expR-mediated activation ofrsmAexpression and ExpR binding withrsmADNA) are inhibited by AHL. The AHL effects are remarkably specific in thatexpReffect of EC153, a strain belonging to class I, is counteracted by 3-oxo-C8-HL but not by 3-oxo-C6-HL. Conversely, theexpReffect of Ecc71, a strain belonging to class II, is neutralized by 3-oxo-C6-HL but not by 3-oxo-C8-HL. The AHL responses correlated withexpR-mediated inhibition of exoprotein and secondary metabolite production.
Genome-Wide Transcriptional Analysis of the Phosphate Starvation Stimulon ofBacillus subtilis
Authors: Allenby Nicholas E. E. , O'Connor Nicola , Prágai Zoltán , Ward Alan C. , Wipat Anil , Harwood Colin R.
Published: November 2005

Bacillus subtilisresponds to phosphate starvation stress by inducing the PhoP and SigB regulons. While the PhoP regulon provides a specific response to phosphate starvation stress, maximizing the acquisition of phosphate (Pi) from the environment and reducing the cellular requirement for this essential nutrient, the SigB regulon provides nonspecific resistance to stress by protecting essential cellular components, such as DNA and membranes. We have characterized the phosphate starvation stress response ofB. subtilisat a genome-wide level using DNA macroarrays. A combination of outlier and cluster analyses identified putative new members of the PhoP regulon, namely,yfkN(2′,3′ cyclic nucleotide 2′-phosphodiesterase),yurI(RNase),yjdB(unknown), andvpr(extracellular serine protease). YurI is thought to be responsible for the nonspecific degradation of RNA, while the activity of YfkN on various nucleotide phosphates suggests that it could act on substrates liberated by YurI, which produces 3′ or 5′ phosphoribonucleotides. The putative new PhoP regulon members are either known or predicted to be secreted and are likely to be important for the recovery of inorganic phosphate from a variety of organic sources of phosphate in the environment.
Characterization of Temporal Protein Production in
Pseudomonas aeruginosa
Biofilms
Authors: Southey-Pillig Christopher J. , Davies David G. , Sauer Karin
Published: November 2005

Phenotypic and genetic evidence supporting the notion of biofilm formation as a developmental process is growing. In the present work, we provide additional support for this hypothesis by identifying the onset of accumulation of biofilm-stage specific proteins during
Pseudomonas aeruginosa
biofilm maturation and by tracking the abundance of these proteins in planktonic and three biofilm developmental stages. The onset of protein production was found to correlate with the progression of biofilms in developmental stages. Protein identification revealed that proteins with similar function grouped within similar protein abundance patterns. Metabolic and housekeeping proteins were found to group within a pattern separate from virulence, antibiotic resistance, and quorum-sensing-related proteins. The latter were produced in a progressive manner, indicating that attendant features that are characteristic of biofilms such as antibiotic resistance and virulence may be part of the biofilm developmental process. Mutations in genes for selected proteins from several protein production patterns were made, and the impact of these mutations on biofilm development was evaluated. The proteins cytochrome
c
oxidase, a probable chemotaxis transducer, a two-component response regulator, and MexH were produced only in mature and late-stage biofilms. Mutations in the genes encoding these proteins did not confer defects in growth, initial attachment, early biofilm formation, or twitching motility but were observed to arrest biofilm development at the stage of cell cluster formation we call the maturation-1 stage. The results indicated that expression of theses genes was required for the progression of biofilms into three-dimensional structures on abiotic surfaces and the completion of the biofilm developmental cycle. Reverse transcription-PCR analysis confirmed the detectable change in expression of the respective genes
ccoO
, PA4101, and PA4208. We propose a possible mechanism for the role of these biofilm-specific proteins in biofilm formation.
Isolation and Characterization of New Thiamine-Deregulated Mutants of
Bacillus subtilis
Authors: Schyns Ghislain , Potot Sébastien , Geng Yi , Barbosa Teresa M. , Henriques Adriano , Perkins John B.
Published: November 2005

In bacteria, thiamine pyrophosphate (TPP) is an essential cofactor that is synthesized de novo. Thiamine, however, is not an intermediate in the biosynthetic pathway but is salvaged from the environment and phosphorylated to TPP. We have isolated and characterized new mutants of
Bacillus subtilis
that deregulate thiamine biosynthesis and affect the export of thiamine products from the cell. Deletion of the
ydiA
gene, which shows significant similarity to the thiamine monophosphate kinase gene of
Escherichia coli
(
thiL
), did not generate the expected thiamine auxotroph but instead generated a thiamine bradytroph that grew to near-wild-type levels on minimal medium. From this Δ
thiL
deletion mutant, two additional ethyl methanesulfonate-induced mutants that derepressed the expression of a
thiC-lacZ
transcriptional reporter were isolated. One mutant, Tx1, contained a nonsense mutation within the
B. subtilis yloS
(
thiN
) gene that encodes a thiamine pyrophosphokinase, a result which confirmed that
B. subtilis
contains a single-step, yeast-like thiamine-to-TPP pathway in addition to the bacterial TPP de novo pathway. A second mutant, strain Tx26, was shown to contain two lesions. Genetic mapping and DNA sequencing indicated that the first mutation affected
yuaJ
, which encodes a thiamine permease. The second mutation was located within the
ykoD
cistron of the
ykoFEDC
operon, which putatively encodes the ATPase component of a unique thiamine-related ABC transporter. Genetic and microarray studies indicated that both the mutant
yuaJ
and
ykoD
genes were required for the derepression of thiamine-regulated genes. Moreover, the combination of the four mutations (the Δ
thiL
,
thiN
,
yuaJ
, and
ykoD
mutations) into a single strain significantly increased the production and excretion of thiamine products into the culture medium. These results are consistent with the proposed “riboswitch” mechanism of thiamine gene regulation (W. C. Winkler, A. Nahvi, and R. R. Breaker, Nature
419:
952-956, 2002).
Homodimeric Hexaprenyl Pyrophosphate Synthase from the Thermoacidophilic Crenarchaeon
Sulfolobus solfataricus
Displays Asymmetric Subunit Structures
Authors: Sun Han-Yu , Ko Tzu-Ping , Kuo Chih-Jung , Guo Rey-Ting , Chou Chia-Cheng , Liang Po-Huang , Wang Andrew H.-J.
Published: November 2005

Hexaprenyl pyrophosphate synthase (HexPPs) from
Sulfolobus solfataricus
catalyzes the synthesis of
trans
-C
30
-hexaprenyl pyrophosphate (HexPP) by reacting two isopentenyl pyrophosphate molecules with one geranylgeranyl pyrophosphate. The crystal structure of the homodimeric C
30
-HexPPs resembles those of other
trans
-prenyltransferases, including farnesyl pyrophosphate synthase (FPPs) and octaprenyl pyrophosphate synthase (OPPs). In both subunits, 10 core helices are arranged about a central active site cavity. Leu164 in the middle of the cavity controls the product chain length. Two protein conformers are observed in the
S. solfataricus
HexPPs structure, and the major difference between them occurs in the flexible region of residues 84 to 100. Several helices (αI, αJ, αK, and part of αH) and the associated loops have high-temperature factors in one monomer, which may be related to the domain motion that controls the entrance to the active site. Different side chain conformations of Trp136 in two HexPPs subunits result in weaker hydrophobic interactions at the dimer interface, in contrast to the symmetric π-π stacking interactions of aromatic side chains found in FPPs and OPPs. Finally, the three-conformer switched model may explain the catalytic process for HexPPs.
A Degenerate Type III Secretion System from Septicemic
Escherichia coli
Contributes to Pathogenesis
Authors: Ideses Diana , Gophna Uri , Paitan Yossi , Chaudhuri Roy R. , Pallen Mark J. , Ron Eliora Z.
Published: November 2005

The type III secretion system (T3SS) is an important virulence factor used by several gram-negative bacteria to deliver effector proteins which subvert host cellular processes. Enterohemorrhagic
Escherichia coli
O157 has a well-defined T3SS involved in attachment and effacement (ETT1) and critical for virulence. A gene cluster potentially encoding an additional T3SS (ETT2), which resembles the SPI-1 system in
Salmonella enterica
, was found in its genome sequence. The ETT2 gene cluster has since been found in many
E. coli
strains, but its in vivo role is not known. Many of the ETT2 gene clusters carry mutations and deletions, raising the possibility that they are not functional. Here we show the existence in septicemic
E. coli
strains of an ETT2 gene cluster, ETT2
sepsis
, which, although degenerate, contributes to pathogenesis. ETT2
sepsis
has several premature stop codons and a large (5 kb) deletion, which is conserved in 11
E. coli
strains from cases of septicemia and newborn meningitis. A null mutant constructed to remove genes coding for the putative inner membrane ring of the secretion complex exhibited significantly reduced virulence. These results are the first demonstration of the importance of ETT2 for pathogenesis.
Four Unusual Two-Component Signal Transduction Homologs, RedC to RedF, Are Necessary for Timely Development inMyxococcus xanthus
Authors: Higgs Penelope I. , Cho Kyungyun , Whitworth David E. , Evans Lisa S. , Zusman David R.
Published: November 2005

We identified a cluster of four two-component signal transduction genes that are necessary for proper progression ofMyxococcus xanthusthrough development.redCtoredFmutants developed and sporulated early, resulting in small, numerous, and disorganized fruiting bodies. Yeast two-hybrid analyses suggest that RedCDEF act in a single signaling pathway. The previously identifiedespAgene displays a phenotype similar to that ofredCDEF. However, combined mutants defective inespA redCDEFexhibited a striking additive developmental phenotype, suggesting that EspA and RedC to RedF play independent roles in controlling developmental progression.
Vancomycin Stress Response in a Sensitive and a Tolerant Strain ofStreptococcus pneumoniae
Authors: Haas Wolfgang , Kaushal Deepak , Sublett Jack , Obert Caroline , Tuomanen Elaine I.
Published: November 2005

The vancomycin stress response was studied inStreptococcus pneumoniaestrains T4 (TIGR4) and Tupelo. Vancomycin affected the expression of 175 genes, including genes encoding transport functions and enzymes involved in aminosugar metabolism. The two-component systems TCS03, TCS11, and CiaRH also responded to antibiotic treatment. We hypothesize that the three regulons are an important part of the bacterium's response to vancomycin stress.
Iron-Responsive Regulation of Biofilm Formation in
Staphylococcus aureus
Involves Fur-Dependent and Fur-Independent Mechanisms
Authors: Johnson Miranda , Cockayne Alan , Williams Peter H. , Morrissey Julie A.
Published: November 2005

We have shown that
Staphylococcus aureus
biofilm production is induced in iron-restricted conditions and is repressed by iron via a Fur-independent mechanism, while Fur has both positive and negative regulatory roles in low iron. Furthermore, there is no significant increase in polymeric
N
-acetylglucosamine polysaccharide expression to account for induction of biofilms in low iron.
COMBINED MODEL-BASED 3D OBJECT RECOGNITION
Authors: KIM SUNGHO , JANG GIJEONG , LEE WANG-HEON , KWEON IN SO
Published: November 2005

This paper presents a combined model-based 3D object recognition method motivated by the robust properties of human vision. The human visual system (HVS) is very efficient and robust in identifying and grabbing objects, in part because of its properties of visual attention, contrast mechanism, feature binding, multiresolution and part-based representation. In addition, the HVS combines bottom-up and top-down information effectively using combined model representation. We propose a method for integrating these aspects under a Monte Carlo method. In this scheme, object recognition is regarded as a parameter optimization problem. The bottom-up process initializes parameters, and the top-down process optimizes them. Experimental results show that the proposed recognition model is feasible for 3D object identification and pose estimation.
COMPARATIVE ASSESSMENT OF CONTENT-BASED FACE IMAGE RETRIEVAL IN DIFFERENT COLOR SPACES
Authors: SHIH PEICHUNG , LIU CHENGJUN
Published: November 2005

Content-based face image retrieval is concerned with computer retrieval of face images (of a given subject) based on the geometric or statistical features automatically derived from these images. It is well known that color spaces provide powerful information for image indexing and retrieval by means of color invariants, color histogram, color texture, etc. This paper assesses comparatively the performance of content-based face image retrieval in different color spaces using a standard algorithm, the Principal Component Analysis (PCA), which has become a popular algorithm in the face recognition community. In particular, we comparatively assess 12 color spaces (RGB, HSV, YUV, YCbCr, XYZ, YIQ, L*a*b*, U*V*W*, L*u*v*, I1I2I3, HSI, and rgb) by evaluating seven color configurations for every single color space. A color configuration is defined by an individual or a combination of color component images. Take the RGB color space as an example, possible color configurations are R, G, B, RG, RB, GB and RGB. Experimental results using 600 FERET color images corresponding to 200 subjects and 456 FRGC (Face Recognition Grand Challenge) color images of 152 subjects show that some color configurations, such as YV in the YUV color space and YI in the YIQ color space, help improve face retrieval performance.
The General Determinants of Share Returns: An Empirical Investigation on the Dhaka Stock Exchange
Authors: Mobarek Asma , Mollah A. Sabur
Published: November 2005

This paper investigates the underlying factors that determine share returns on the Dhaka Stock Exchange. The empirical analysis does not support the critical condition of the Capital Asset Pricing Model of a positive relationship between share return and beta. However, it shows that variables such as size, price to book, volume of shares traded, earnings yield and cash flow yield have a significant influence on share returns. The degree and direction of relationship among the variables are similar to other emerging markets, but are not always consistent with developed markets perhaps due to lack of homogeneous expectations regarding risk return characteristics and different market microstructure.
Expectations and Equilibrium in High-Grade Australian Bond Markets
Authors: In Francis , Batten Jonathan A.
Published: November 2005

This paper examines the equilibrium implications of the Expectations Hypothesis of term structure to different maturities of high-grade Australian dollar denominated Eurobonds and Australian Government bonds (AGBs) using the Canonical Cointegrating Regression (CCR) technique developed by Econometrica 60 (1992) 119. Our findings provide evidence only for equilibrium relationships between each group of bonds based on credit class, but not between any of the subsets of AGBs and the Eurobonds. Furthermore, the error correction model supports theory with the most liquid, long-term 10-year AGB driving the AGB term structure, with short-term yields adjusting to movements in the long-run yields, though the opposite is true for Eurobonds. The lesson for markets is to simplify the risk management task.

Managers are advised to treat portfolios of equivalent credit class separately for hedging and risk management.
Does Mutual Fund Management in India Correspond to its Investment Objective Classification?
Authors: Agudo Luis Ferruz , Lázaro Cristina Ortiz
Published: November 2005

The aim of this article is to investigate the mutual fund market in India and verify whether or not the fund classification obtained from the name given to identify them corresponds to that which would be obtained were prior management to be taken into account. This industry has undergone spectacular growth in recent years, making this study extremely interesting, not least because institutional control could be less in times of expansion. The methodologies employed in the study are factor analysis and cluster analysis. The former determines that risk would clearly identify two groups of funds in the same manner as public classification of the funds. Cluster analysis, on the other hand, identifies funds that are, in fact, very close to one another, when for the bulk of investors they are not.
Visualization for security
Authors: Ma Kwan-Liu
Published: November 2005

We have all become more security conscious because our daily life may be greatly affected by the unpredictable terrorism and nonstop cyber attacks. A rapidly growing effort is being made to address these security problems at different levels by collecting and analyzing vast amounts of information from diverse sources. As demonstrated in many other data analysis problems, visualization can be very useful when massive data is involved. For example, it is generally easier to understand the Internet connectivity and traffic or complex relations among people and events that are presented as a graph rather than as a table of descriptive information. Even more powerful is interactive visualization, which facilitates exploration in the data space.
Focus on ACM SIGGRAPH Canadian chapters
Authors: Woo Andrew
Published: November 2005

There are currently four active ACM SIGGRAPH chapters in Canada. We decided to get together to write up a review of our respective ACM SIGGRAPH chapter activities, because these activities may be of interest to the Canadian and overall ACM SIGGRAPH community. The Canadian chapters include:
Atlantic

Heather Fowler: Chair

http://atlantic-canadian.siggraph.org
Montreal

Myriam Côté, Chair

http://montreal.siggraph.org
Toronto

Adele Newton, Chair

http://toronto.siggraph.org
Vancouver

Andrew Woo, Chair

http://vancouver.siggraph.org
If you are interested in being a volunteer or a speaker (especially if you are from out of town), please contact the appropriate chapters (see addresses above), and we will be more than happy to talk to you. We hope you enjoy the review of the ACM SIGGRAPH Canadian chapters!
Visual learning in science and engineering
Authors: Brown Judy
Published: November 2005

Visual learning is the use of graphics, images and animations to enable and enhance learning in science and engineering.
Learning through computer-generated visualization
Authors: Spencer Stephen N.
Published: November 2005

Regular readers of this column are accustomed to the Editor's thoughts, words and requests of the community. For this issue and the next, however, you'll have another's voice: I'm Stephen Spencer, ACM SIGGRAPH Director for Publications, and though I've been involved with ACM SIGGRAPH for many years, it's not often that I've had (or taken) the opportunity to speak with you in this forum.
Designing augmented reality interfaces
Authors: Billinghurst Mark , Grasset Raphael , Looser Julian
Published: November 2005

Most interactive computer graphics appear on a screen separate from the real world and the user's surroundings. However this does not always have to be the case. In augmented reality (AR) interfaces, three-dimensional virtual images appear superimposed over real objects. AR applications typically use head-mounted or handheld displays to make computer graphics appear in the user's environment.
Toward new grounds in visualization
Authors: Hauser Helwig
Published: November 2005

At the IEEE Visualization Conference 2004 in Austin, Texas, there was much discussion about the future of visualization research, especially about the future of scientific visualization. The fact that two visualization communities (SciVis and InfoVis) develop almost parallel to each other (instead of interweaving a bit) also raised questions, especially on the SciVis side.
Doing "neat stuff"
Authors: Greenfield Gary R.
Published: November 2005

"How come you get to do such neat stuff?" I'm constantly being asked. I like to think it is because I am passionate about learning and because my day-to-day activities are focused on pursuing that passion and imparting it to my students. But it wasn't always that way and it took some effort...
Inventing the future down under
Authors: Billinghurst Mark , Grasset Raphaël , Green Richard , Haller Michael
Published: November 2005

As computers become invisible, the interface between human and machine is increasingly important. The proliferation of computing and communication devices with improved capabilities creates a wealth of opportunities for new types of human computer interaction. However many companies have little experience in building intuitive interfaces. Thus there is a need for research organizations that can develop next generation computer interfaces.
Getting to the “graphics” in a graphics exercise
Authors: Schweitzer Dino , Northrop Linda
Published: November 2005

An "algorithms" course in Computer Graphics relies heavily upon programming exercises to teach students the intricacies of graphics techniques. Such exercises should be substantial enough to avoid "trivializing" the problem and, at the same time, be interesting to the student. Unfortunately, substantial exercises also introduce a lot of overhead not directly related to the central graphics concepts being demonstrated. Overhead such as complex data structure definition and manipulation, external file input and output, low-level user interfaces, and graphics device drivers add a significant programming burden to the student. This overhead also detracts from the desired learning experience of the exercise. Various alternatives for solving this problem while maintaining the complexity of the exercise include: 1) designing the exercise to allow previous solution reusability, 2) providing a conceptual solution, 3) supplying actual code, both "white box" and "black box", and 4) making development tools and aids available, This paper will describe these different approaches, examine their advantages and disadvantages, and summarize our experience in the graphics course at the Air Force Academy.
Discovery through experimentation
Authors: Crawley Dennis , Sachter Judy , Sutton Carol , Ursyn Anna , White Jackie , Abshere Kim
Published: November 2005

Secondary schools now offer computer graphics courses which meld the disciplines of the arts and sciences. Students are demanding more than the required computer literacy courses and are challenging their teachers to incorporate graphics into their specific area(s) of interest. Many courses are offered through their art departments and with specialized courses in science and math. Cooperative learning is beneficial since facilities, equipment and resources are major impediments. Students sharing computers and teaching one another have become commonplace.This panel of secondary school educators will share their experiences with curriculum, research, administrative support and examples of student work. Each panel member brings to this endeavor enthusiasm and personal pride in their research and individual school programs.
Virtual reality learning environments: potentials and challenges
Authors: Bricken Meredith
Published: November 2005

This paper addresses the unique characteristics of emerging Virtual Reality (VR) technology and the potential of virtual worlds as learning environments. I describe several key attributes of VR environments and discuss them in relationship to educational theory and pedagogical practice. I then identify three challenges that must be met before VR can be integrated into educational settings: cost, usability, and fear of the technology.
ACM SIGGRAPH education committee activities for computer graphics educators
Authors: Owen G. Scott
Published: November 2005

ACM SIGGRAPH supports computer graphics educators and students through the activities and projects of its education committee. These include curriculum studies, publication of informational materials and support of projects with educational value, plus many ACM SIGGRAPH conference-related activities. This paper discusses these activities and the associated resources that the education committee is making available for computer graphics educators.
Motion without movement
Authors: Freeman William T. , Adelson Edward H. , Heeger David J.
Published: November 2005

We describe a technique for displaying patterns that appear to move continuously without changing their positions. The method uses a quadrature pair of oriented filters to vary the local phase, giving the sensation of motion. We have used this technique in various computer graphic and scientific visualization applications.
Making radiosity usable
Authors: Baum Daniel R. , Mann Stephen , Smith Kevin P. , Winget James M.
Published: November 2005

Generating accurate radiosity solutions of real world environments is user-intensive and requires significant knowledge of the method. As a result, few end-users such as architects and designers use it. The output of most commercial modeling packages must be substantially "cleaned up" to satisfy the geometrical and topological criteria imposed by radiosity solution algorithms. Furthermore, the mesh used as the basis of the radiosity computation must meet several additional requirements for the solution to be accurate.A set of geometrical and topological requirements is formalized that when satisfied yields an accurate radiosity solution. A series of algorithms is introduced that automatically processes raw model databases to meet these requirements. Thus, the end-user can concentrate on the design rather than on the details of the radiosity solution process. These algorithms are generally independent of the radiosity solution technique used, and thus apply to all mesh based radiosity methods.
Trichromatic approximation for computer graphics illumination models
Authors: Borges Carlos F.
Published: November 2005

The complexity of computer graphics illumination models and the associated need to find ways of reducing evaluation time has led to the use of two methods for simplifying the spectral data needed for an exact solution. The first method, where spectral data is sampled at a number of discrete points, has been extensively investigated and bounds for the error are known. Unfortunately, the second method, where spectral data is replaced with tristimulus values (such as RGB values), is very little understood even though it is widely used. In this paper we examine the error incurred by the use of this method by investigating the problem of approximating the tristimulus coordinates of light reflected from a surface from those of the source and the surface. A variation on a well known and widely used approximation is presented. This variation used the XYZ primaries which have unique properties that yield straightforward analytic bounds for the approximation error. This analysis is important because it gives a sound mathematical footing to the widely used method of trichromatic approximation. The error bounds will give some insights into the factors that affect accuracy and will indicate why this method often works quite well in practice.
Automated generation of intent-based 3D Illustrations
Authors: Seligmann Dorée Duncan , Feiner Steven
Published: November 2005

This paper describes an automated intent-based approach to illustration. An
illustrution
is a picture that is designed to fulfill a communicative intent such as showing the location of an object or showing how an object is manipulated. An illustration is generated by implementing a set of stylistic decisions, ranging from determining the way in which an individual object is lit, to deciding the general composition of the illustration. The design of an illustration is treated as a goal-driven process within a system of constraints. The goal is to achieve communicative intent; the constraints are the illustrative techniques an illustrator can apply.We have developed IBIS (Intent-Based Illustration System), a system that puts these ideas into practice. IBIS designs illustrations using a generate-and-test approach, relying upon a rule-based system of methods and evaluators. Methods are rules that specify how to accomplish visual effects, while evaluators are rules that specify how to determine how well a visual effect is accomplished in an illustration. Examples of illustrations designed by IBIS are included.
A new simple and efficient antialiasing with subpixel masks
Authors: Schilling Andreas
Published: November 2005

Antialiasing of edges is often performed with the help of subpixel masks that indicate which parts of the pixel are covered by the object that has to be drawn. For this purpose, subpixel masks have to be generated during the scan conversion of an image. This paper introduces a new algorithm for creating subpixel masks that avoids some problems of traditional algorithms, like aliasing of high frequencies or blinking of small moving objects. The new algorithms can be implemented by lookup tables that make use of the inherent symmetry of the algorithm. The results are compared with conventional supersampling. A hardware implementation is described.
Spectrally optimal sampling for distribution ray tracing
Authors: Mitchell Don P.
Published: November 2005

Nonuniform sampling of images is a useful technique in computer graphics, because a properly designed pattern of samples can make aliasing take the form of high-frequency random noise. In this paper, the technique of nonuniform sampling is extended from two dimensions to include the extra parameter dimensions of distribution ray tracing. A condition for optimality is suggested, and algorithms for approximating optimal sampling are developed. The technique is demonstrated at low sampling densities, so the characteristics of aliasing noise are clearly visible. At supersampling rates, this technique should move noise into frequencies above the passband of the pixel-reconstruction filter.
Geometrically deformed models
Authors: Miller James V. , Breen David E. , Lorensen William E. , O'Bara Robert M. , Wozny Michael J.
Published: November 2005

We propose a new approach to the problem of generating a simple topologically-closed geometric model from a point-sampled volume data set. We call such a model a Geometrically Deformed Model or GDM. A GDM is created by placing a 'seed' model in the volume data set. The model is then deformed by a relaxation process that minimizes a set of constraints that provides a measure of how well the model fits the features in the data. Constraints are associated with each vertex in the model that control local deformation, interaction between the model and the data set, and the shape and topology of the model. Once generated, a GDM can be used for visualization, shape recognition, geometric measurements, or subjected to a series of geometric operations. This technique is of special importance because of the advent of nondestructive sensing equipment (CT, MRI) that generates point samples of true three-dimensional objects.
Volumetric shape description of range data using “Blobby Model”
Authors: Muraki Shigeru
Published: November 2005

Recently in the field of computer vision, there have been many attempts to obtain a symbolic shape description of an object by fitting simple primitives to the range data of the object. In this paper, we introduce the "
Blobby Model
" for automatically generating a shape description from range data. This model can express a 3D surface as an isosurface of a scalar field which is produced by a number of field generating primitives. The fields from many primitives are blended with each other and can form a very complicated shape. To determine the number and distribution of primitives required to adequately represent a complex 3D surface, an energy function is minimized which measures the shape difference between the range data and the "
Blobby Model
". We start with a single primitive and introduce more primitives by splitting each primitive into two further primitives so as to reduce the energy value. In this manner, the shape of the 3D object is slowly recovered as the isosurface produced by many primitives. We have successfully applied this method to human face range data and typical results are shown. The method herein does not require any prior range segmentation.
Specifying gestures by example
Authors: Rubine Dean
Published: November 2005

Gesture-Based interfaces offer an alternative to traditional keyboard, menu, and direct manipulation interfaces. The ability to specify objects, an operation, and additional parameters with a single intuitive gesture appeals to both novice and experienced users. Unfortunately, gesture-based interfaces have not been extensively researched, partly because they are difficult to create. This paper describes GRANDMA, a toolkit for rapidly adding gestures to direct manipulation interfaces. The trainable single-stroke gesture recognizer used by GRANDMA is also described.
Animation of dynamic legged locomotion
Authors: Raibert Marc H. , Hodgins Jessica K.
Published: November 2005

This paper is about the use of control algorithms to animate dynamic legged locomotion. Control could free the animator from specifying the details of joint and limb motion while producing both physically realistic and natural looking results. We implemented computer animations of a biped robot, a quadruped robot, and a kangaroo. Each creature was modeled as a linked set of rigid bodies with compliant actuators at its joints. Control algorithms regulated the running speed, organized use of the legs, and maintained balance. All motions were generated by numerically integrating equations of motion derived from the physical models. The resulting behavior included running at various speeds, traveling with several gaits (run, trot, bound, gallop, and hop), jumping, and traversing simple paths. Whereas the use of control permitted a variety of physically realistic animated behavior to be generated with limited human intervention, the process of designing the control algorithms was not automated: the algorithms were "tweaked" and adjusted for each new creature.
Convolution surfaces
Authors: Bloomenthal Jules , Shoemake Ken
Published: November 2005

Smoothly blended articulated models are often difficult to construct using current techniques. Our solution in this paper is to extend the surfaces introduced by Blinn [Blinn 1982] by using three-dimensional convolution with skeletons composed of polygons or curves. The resulting convolution surfaces permit fluid topology changes, seamless part joins, and efficient implementation.
A coherent projection approach for direct volume rendering
Authors: Wilhelms Jane , Van Gelder Allen
Published: November 2005

Direct volume rendering offers the opportunity to visualize all of a three-dimensional sample volume in one image. However, processing such images can be very expensive and good quality high-resolution images are far from interactive. Projection approaches to direct volume rendering process the volume region by region as opposed to ray-casting methods that process it ray by ray. Projection approaches have generated interest because they use coherence to provide greater speed than ray casting and generate the image in a layered, informative fashion. This paper discusses two topics: First, it introduces a projection approach for directly rendering rectilinear, parallel-projected sample volumes that takes advantage of coherence across cells and the identical shape of their projection. Second, it considers the repercussions of various methods of integration in depth and interpolation across the scan plane. Some of these methods take advantage of Gouraud-shading hardware, with advantages in speed but potential disadvantages in image quality.
Navigating the video maze
Authors: Myerson Terry , Rhyne Theresa
Published: November 2005

The technology required to produce professional video and audio presentations from a desktop computing environment is now available and is supported by many companies. The hardware to support this technology, however, is offered in widely varying forms and at a broad range of prices. This article provides an introductory perspective on the current video technology and includes commercial hardware products currently available for producing video productions from a computing environment.Recording a computer graphics animation to videotape is a complicated task. The heart of the difficulty lies in the fact that video monitors, such as standard televisions, and computer monitors both use the same Cathode Ray Tube (CRT) technology, but they require different signals for display. In 1941, the National Television Standards Committee, NTSC, established a standard for broadcast video in North America. This standard signal is still in use today and consists of a composite, interlaced, 525 line signal, scanning at 30 frames per second (30 Hz.) In contrast to this antiquated standard, today's high-quality monitors display a component red, green, and blue (RGB), non-interlaced, 1280 x 1024 signal, scanning at 75 Hz. The art of producing a video signal can be summed up as translating today's technology to meet yesterday's NTSC standard, with a minimal loss of quality. Although only NTSC signal needs are specifically addressed in this article, most of the equipment is equally compatible with the European broadcast standards: Phase Alternate Line (PAL) and Sequential Color and Memory (SECAM).A video production can be produced from an animation on either a low-end personal computer or a high-end workstation, and most of the hardware discussed can be used interchangeably with any platform. However, choosing the proper system for your needs can still be a formidable task. The vast array of available products presents an endless maze, rather than an easy solution.
A survey of algorithms for volume visualization
Authors: Elvins T. Todd
Published: November 2005

Many computer graphics programmers are working in the area of scientific visualization. One of the most interesting and fast-growing areas in scientific visualization is volume visualization. Volume visualization systems are used to create high-quality images from scalar and vector datasets defined on multidimensional grids, usually for the purpose of gaining insight into a scientific problem. Most volume visualization techniques are based on one of about five foundation algorithms. These algorithms, and the background necessary to understand them, are described here. Pointers to more detailed descriptions, further reading, and advanced techniques are also given.
The U.S. Environmental Protection Agency Scientific Visualization Center
Authors: Rhyne Theresa , Petterson Lynne
Published: November 2005

Visualization has come of age. It is in use as an analytical tool at an increasing number of campuses, research institutions, and government agencies, and in an increasing number of disciplines.This section consists of articles from a number of centers using visualization in innovative ways. It provides a look at the history and structure of some of the visualization centers themselves. It also illustrates the wide variety of fields to which the techniques of visualization are being successfully applied. We hope you enjoy and profit from it.
Scientific Visualization at the University of Leeds
Authors: Earnshaw R. A.
Published: November 2005

This article summarises the current plans and activities of the Scientific Visualization Group at the University. It also provides a brief report of an open seminar at the University of Leeds on 22 January 1992, that was attended by 150 people.