bluuebunny/crossref_metadata_2025 huggingface dataset:
Asphaltene Near-well-bore Formation Damage Modeling
Authors: Leontaritis Kosta J.
Published: August 2005

When during oil production the thermodynamic conditions within the near-well-bore formation lie inside the asphaltene deposition envelope of the reservoir fluid, the flocculated asphaltenes cause formation damage. Mathematically, formation damage is a reduction in the hydrocarbon effective mobility, λ, λ=ko∕μo=kkro∕μo. Three possible mechanisms of asphaltene-induced formation damage have been discussed in the literature. Asphaltenes can reduce the hydrocarbon effective mobility by a) blocking pore throats thus reducing the rock permeability, k, b) adsorbing onto the rock and altering the formation wettability from water-wet to oil-wet thus diminishing the effective permeability to oil, ko, and c) increasing the reservoir fluid viscosity, μo, by nucleating water-in-oil emulsions. In the most frequently encountered case of asphaltene-induced formation damage where under-saturated oil is being produced without water, the most dominant damage mechanism is blockage of pore throats by asphaltene particles causing a reduction in rock permeability k. This paper presents a rather simple, yet realistic way of modeling asphaltene-induced near-well formation damage caused by blockage of pore throats by asphaltene particles. The model utilizes both macroscopic and microscopic concepts to represent the pore throat blockages. It also utilizes the Thermodynamic-Colloidal Model of Asphaltene, TCModelSM, an existing AsphWax asphaltene phase behavior model capable of simulating the asphaltene particle size distribution as a function of the thermodynamics of the system. The new asphaltene near-well formation damage model is applied in one case where it is used to track the degree of formation damage as a function of time and the effect it has on near-well-bore and well-bore hydraulics. Similarly the model can be used to study a priori the economics of developing a reservoir known to contain under-saturated asphaltenic oil.
Formation Sand Liquefaction: A Mechanism for Explaining Fines Migration and Well Sanding
Authors: Hayatdavoudi A.
Published: August 2005

To understand the basic relationship between the rising water-cut, well sanding, and migration of fines, the author’s work led him to examine the mechanism of well sanding due to sand liquefaction in cases where the storm chokes in offshore wells were activated and when the production platform separator lines froze due to sudden cold weather. The author found that as the original water-oil contact plane rose above the original plane of contact, it caused a drastic change in water saturation and relative permeability. We show the increased water saturation decreases the resistance of the formation to stress by as much as 50%. This is one of the causes of sand liquefaction at or near the perforation cavities. The parameters affecting the process most are the fine-particle buoyancy, changes in the effective stress and the bulk density of the sand, the pore pressure buildup and changes in porosity near the perforation cavities, the induced transient shear stress resulting from the water-hammer total pressure wave, and the lack of adequate cohesive cement or interlocking contacts between the grains of the unconsolidated sand. The simple model calculations pointed to the conclusion that if the grains of the unconsolidated sand or the fine particles accelerated above the threshold limit of 0.19000g, the chances for fines migration and sand liquefaction were high. Furthermore, if, at the free face of the washed-out perf tunnels or the cavernous cavities of the unconsolidated sand, the total pressure wave magnitude exceeded the shear resistance of the sand, then sand liquefaction was certain to occur. The obvious outcome of this process is nothing but serious formation damage. Based on his models, the author’s recommendation for alleviating this type of damage, includes but is not limited to selective perforation, oriented perforation, gravel packing, frac packing, filter packing, trajectory planning for well reentries, and controlled drawdown.
On Predicting Softening Effects in Hard Turned Surfaces—Part II: Finite Element Modeling and Verification
Authors: Shi Jing , Liu C. Richard
Published: August 2005

A material softening model based on thermal activation energy has been successfully established through tempering experiments in the first part of this study. To apply the model to predicting material softening in hard turned surfaces, the thermal history of work material is needed. In this part, a three-dimensional finite element (FE) model of machining hardened 52100 steel is constructed, and coupled thermal-stress analysis is performed to obtain the material thermal history. Then the material softening model uses the computed thermal history as input to predict the material hardness profiles along the depth into the machined surfaces. Overall, the prediction precisely catches the trend of hardness change along depth and agrees reasonably well with the hardness measurement. What’s more, the sensitivity of material softening to cutting parameters is investigated both quantitatively and qualitatively. Within the investigation range, it is observed that the increase of tool flank wear and feed rate produces severe material softening and a deeper softened layer, while the increase of cutting speed causes significant softening to the surface material but hardly changes the softened depth.
Ductile Regime Nanomachining of Single-Crystal Silicon Carbide
Authors: Patten John , Gao Wei , Yasuto Kudo
Published: August 2005

We have demonstrated the ability to perform a ductile material removal operation, via single-point diamond turning, on single-crystal silicon carbide (6H). To our knowledge, this is the first reported work on the ductile machining of single-crystal silicon carbide (SiC). SiC experiences a ductile-to-brittle transition similar to other nominally brittle materials such as silicon, germanium, and silicon nitride. It is believed that the ductility of SiC during machining is due to the formation of a high-pressure phase at the cutting edge, which encompasses the chip formation zone and its associated material volume. This high-pressure phase transformation mechanism is similar to that found with other semiconductors and ceramics, leading to a plastic response rather than brittle fracture at small size scales.
A Scratch Intersection Model of Material Removal During Chemical Mechanical Planarization (CMP)
Authors: Che Wei , Guo Yongjin , Chandra Abhijit , Bastawros Ashraf
Published: August 2005

A scratch intersection based material removal mechanism for CMP processes is proposed in this paper. The experimentally observed deformation pattern by SEM and the trends of the measured force profiles (Che et al., 2003) reveal that, for an isolated shallow scratch, the material is mainly plowed sideway along the track of the abrasive particle with no net material removal. However, it is observed that material is detached close to the intersection zone of two scratches. Motivated by this observation, it is speculated that the deformation mechanism changes from ploughing mode to shear-segmentation mode as the abrasive particle approaches the intersection of two scratches under small indentation depth for ductile metals. The proposed mechanistic material removal rate (MRR) model yields Preston constant similar to those observed experimentally for CMP processes. The proposed model also reveals that the nature of the slurry-pad interaction mechanism, and its associated force partitioning mechanism, is important for determining the variation of MRR with particle size and concentration. It is observed that under relatively soft pads, small particles and low particle concentration, the pad undergoes local deformation, yielding an increased MRR with increasing particle size and concentration. At the other extreme, the intact walls of the surface cells and the connecting cell walls between the surface pores deform globally, resembling a beam or a plate, and a decreasing trend in MRR is observed with increasing particle size and concentration. The predicted MRR trends are compared to existing experimental observations.
A Comparative Study of Single-Phase AC and Multiphase DC Resistance Spot Welding
Authors: Li Wei , Cerjanec Daniel , Grzadzinski Gerald A.
Published: August 2005

This paper presents a comparative study of the AC and MFDC resistance spot welding process. Both experiments and finite element simulation were conducted to compare the weld size and energy consumption. The experiments were performed on two identical spot welding machines, one with a single phase ac and the other with a mid-frequency DC weld control. The machines were instrumented such that both the primary and secondary voltage and current signals could be collected for energy calculation. The finite element simulation model was developed to understand the underlying mechanisms of the difference between the ac and MFDC processes. The effect of the current waveform was investigated by using the actual process measurements as an input to the simulation model. It is shown that the MFDC process generally produces larger welds than the AC process with the same root-mean-square welding current. However, this difference is more prominent when the welding current is relatively low. Overall, the AC welding process consumes more energy to make a same sized weld than the MFDC process. The larger the welding current is used, the less efficient the AC welding process will become. The differences between the two welding processes are caused by the contact resistance behavior and the electrical inductance in the AC welding process.
The Bacteriophage P1hotGene Product Can Substitute for theEscherichia coliDNA Polymerase III θ Subunit
Authors: Chikova Anna K. , Schaaper Roel M.
Published: August 2005

The θ subunit (holEgene product) ofEscherichia coliDNA polymerase (Pol) III holoenzyme is a tightly bound component of the polymerase core. Within the core (α-ε-θ), the α and ε subunits carry the DNA polymerase and 3′ proofreading functions, respectively, while the precise function of θ is unclear.holEhomologs are present in genomes of other enterobacteriae, suggestive of a conserved function. Putative homologs have also been found in the genomes of bacteriophage P1 and of certain conjugative plasmids. The presence of these homologs is of interest, because these genomes are fully dependent on the host replication machinery and contribute few, if any, replication factors themselves. To study the role of these θ homologs, we have constructed anE. colistrain in whichholEis replaced by the P1 homolog,hot. We show thathotis capable of substituting forholEwhen it is assayed for its antimutagenic action on the proofreading-impaireddnaQ49mutator, which carries a temperature-sensitive ε subunit. The ability ofhotto substitute forholEwas also observed with other, although not all,dnaQmutator alleles tested. The data suggest that the P1hotgene product can substitute for the θ subunit and is likely incorporated in the Pol III complex. We also show that overexpression of either θ or Hot further suppresses thednaQ49mutator phenotype. This suggests that the complexing ofdnaQ49-ε with θ is rate limiting for its ability to proofread DNA replication errors. The possible role ofhotfor bacteriophage P1 is discussed.
Swine and Poultry Pathogens: the Complete Genome Sequences of Two Strains ofMycoplasma hyopneumoniaeand a Strain ofMycoplasma synoviae
Authors: Vasconcelos Ana Tereza R. , Ferreira Henrique B. , Bizarro Cristiano V. , Bonatto Sandro L. , Carvalho Marcos O. , Pinto Paulo M. , Almeida Darcy F. , Almeida Luiz G. P. , Almeida Rosana , Alves-Filho Leonardo , Assunção Enedina N. , Azevedo Vasco A. C. , Bogo Maurício R. , Brigido Marcelo M. , Brocchi Marcelo , Burity Helio A. , Camargo Anamaria A. , Camargo Sandro S. , Carepo Marta S. , Carraro Dirce M. , de Mattos Cascardo Júlio C. , Castro Luiza A. , Cavalcanti Gisele , Chemale Gustavo , Collevatti Rosane G. , Cunha Cristina W. , Dallagiovanna Bruno , Dambrós Bibiana P. , Dellagostin Odir A. , Falcão Clarissa , Fantinatti-Garboggini Fabiana , Felipe Maria S. S. , Fiorentin Laurimar , Franco Gloria R. , Freitas Nara S. A. , Frías Diego , Grangeiro Thalles B. , Grisard Edmundo C. , Guimarães Claudia T. , Hungria Mariangela , Jardim Sílvia N. , Krieger Marco A. , Laurino Jomar P. , Lima Lucymara F. A. , Lopes Maryellen I. , Loreto Élgion L. S. , Madeira Humberto M. F. , Manfio Gilson P. , Maranhão Andrea Q. , Martinkovics Christyanne T. , Medeiros Sílvia R. B. , Moreira Miguel A. M. , Neiva Márcia , Ramalho-Neto Cicero E. , Nicolás Marisa F. , Oliveira Sergio C. , Paixão Roger F. C. , Pedrosa Fábio O. , Pena Sérgio D. J. , Pereira Maristela , Pereira-Ferrari Lilian , Piffer Itamar , Pinto Luciano S. , Potrich Deise P. , Salim Anna C. M. , Santos Fabrício R. , Schmitt Renata , Schneider Maria P. C. , Schrank Augusto , Schrank Irene S. , Schuck Adriana F. , Seuanez Hector N. , Silva Denise W. , Silva Rosane , Silva Sérgio C. , Soares Célia M. A. , Souza Kelly R. L. , Souza Rangel C. , Staats Charley C. , Steffens Maria B. R. , Teixeira Santuza M. R. , Urmenyi Turan P. , Vainstein Marilene H. , Zuccherato Luciana W. , Simpson Andrew J. G. , Zaha Arnaldo
Published: August 2005

This work reports the results of analyses of three complete mycoplasma genomes, a pathogenic (7448) and a nonpathogenic (J) strain of the swine pathogenMycoplasma hyopneumoniaeand a strain of the avian pathogenMycoplasma synoviae; the genome sizes of the three strains were 920,079 bp, 897,405 bp, and 799,476 bp, respectively. These genomes were compared with other sequenced mycoplasma genomes reported in the literature to examine several aspects of mycoplasma evolution. Strain-specific regions, including integrative and conjugal elements, and genome rearrangements and alterations in adhesin sequences were observed in theM. hyopneumoniaestrains, and all of these were potentially related to pathogenicity. Genomic comparisons revealed that reduction in genome size implied loss of redundant metabolic pathways, with maintenance of alternative routes in different species. Horizontal gene transfer was consistently observed betweenM. synoviaeandMycoplasma gallisepticum. Our analyses indicated a likely transfer event of hemagglutinin-coding DNA sequences fromM. gallisepticumtoM. synoviae.
Localization of SpoVAD to the Inner Membrane of Spores of
Bacillus subtilis
Authors: Vepachedu Venkata Ramana , Setlow Peter
Published: August 2005

The products of the hexacistronic
spoVA
operon of
Bacillus subtilis
may be involved in the transport of dipicolinic acid into the forespore during sporulation and its release during spore germination. The major hydrophilic coding region of
B. subtilis spoVAD
was cloned, the protein was expressed in
Escherichia coli
as a His tag fusion protein, and a rabbit antiserum was raised against the purified protein. Western blot analyses of fractions from
B. subtilis
spores showed that SpoVAD is an integral inner membrane protein present at levels >50-fold higher than those of the spore's nutrient germinant receptors that are also present in the inner membrane. SpoVAD also persisted in outgrowing spores.
Biochemical Characterization of RssA-RssB, a Two-Component Signal Transduction System Regulating Swarming Behavior in
Serratia marcescens
Authors: Wei Jun-Rong , Tsai Yu-Huan , Soo Po-Chi , Horng Yu-Tze , Hsieh Shang-Chen , Ho Shen-Wu , Lai Hsin-Chih
Published: August 2005

Our previous study had identified a pair of potential two-component signal transduction proteins, RssA-RssB, involved in the regulation of
Serratia marcescens
swarming. When mutated, both
rssA
and
rssB
mutants showed precocious swarming phenotypes on LB swarming agar, whereby swarming not only occurred at 37°C but also initiated on a surface of higher agar concentration and more rapidly than did the parent strain at 30°C. In this study, we further show that the predicted sensor kinase RssA and the response regulator RssB bear characteristics of components of the phosphorelay signaling system. In vitro phosphorylation and site-directed mutagenesis assays showed that phosphorylated RssA transfers the phosphate group to RssB and that histidine 248 and aspartate 51 are essential amino acid residues involved in the phosphotransfer reactions in RssA and RssB, respectively. Accordingly, while wild-type
rssA
could, the mutated
rssA
(H248A) in
trans
could not complement the precocious swarming phenotype of the
rssA
mutant. Although RssA-RssB regulates expressions of
shlA
and
ygfF
of
S. marcescens
(

ygfF
Sm

), in vitro DNA-binding assays showed that the phosphorylated RssB did not bind directly to the promoter regions of these two genes but bound to its own
rssB
promoter. Subsequent assays located the RssB binding site within a 63-bp
rssB
promoter DNA region and confirmed a direct negative autoregulation of the RssA-RssB signaling pathway. These results suggest that when activated, RssA-RssB acts as a negative regulator for controlling the initiation of
S. marcescens
swarming.
Regulation of
finP
Transcription by DNA Adenine Methylation in the Virulence Plasmid of
Salmonella enterica
Authors: Camacho Eva M. , Serna Ana , Madrid Cristina , Marqués Silvia , Fernández Raúl , de la Cruz Fernando , Juárez Antonio , Casadesús Josep
Published: August 2005

DNA adenine methylase (Dam
−
) mutants of
Salmonella enterica
serovar Typhimurium contain reduced levels of FinP RNA encoded on the virulence plasmid. Dam methylation appears to regulate
finP
transcription, rather than FinP RNA stability or turnover. The
finP
promoter includes canonical −10 and −35 modules and depends on the σ
70
factor. Regulation of
finP
transcription by Dam methylation does not require DNA sequences upstream from the −35 module, indicating that Dam acts at the promoter itself or downstream. Unexpectedly, a GATC site overlapping with the −10 module is likewise dispensable for Dam-mediated regulation. These observations indicate that Dam methylation regulates
finP
transcription indirectly and suggest the involvement of a host factor(s) responsive to the Dam methylation state of the cell. We provide evidence that one such factor is the nucleoid protein H-NS, which acts as a repressor of
finP
transcription in a Dam
−
background. H-NS also restrains transcription of the overlapping
traJ
gene, albeit in a Dam-independent fashion. Hence, the decreased FinP RNA content found in Dam
−
hosts of
S. enterica
appears to result from H-NS-mediated repression of
finP
transcription.
Phylogenetic Analysis of
Pasteuria penetrans
by Use of Multiple Genetic Loci
Authors: Charles Lauren , Carbone Ignazio , Davies Keith G. , Bird David , Burke Mark , Kerry Brian R. , Opperman Charles H.
Published: August 2005

Pasteuria penetrans
is a gram-positive, endospore-forming eubacterium that apparently is a member of the
Bacillus-Clostridium
clade. It is an obligate parasite of root knot nematodes (
Meloidogyne
spp.) and preferentially grows on the developing ovaries, inhibiting reproduction. Root knot nematodes are devastating root pests of economically important crop plants and are difficult to control. Consequently,
P. penetrans
has long been recognized as a potential biocontrol agent for root knot nematodes, but the fastidious life cycle and the obligate nature of parasitism have inhibited progress on mass culture and deployment. We are currently sequencing the genome of the
Pasteuria
bacterium and have performed amino acid level analyses of 33 bacterial species (including
P. penetrans
) using concatenation of 40 housekeeping genes, with and without insertions/deletions (indels) removed, and using each gene individually. By application of maximum-likelihood, maximum-parsimony, and Bayesian methods to the resulting data sets,
P. penetrans
was found to cluster tightly, with a high level of confidence, in the
Bacillus
class of the gram-positive, low-G+C-content eubacteria. Strikingly, our analyses identified
P. penetrans
as ancestral to
Bacillus
spp. Additionally, all analyses revealed that
P. penetrans
is surprisingly more closely related to the saprophytic extremophile
Bacillus haladurans
and
Bacillus subtilis
than to the pathogenic species
Bacillus anthracis
and
Bacillus cereus
. Collectively, these findings strongly imply that
P. penetrans
is an ancient member of the
Bacillus
group. We suggest that
P. penetrans
may have evolved from an ancient symbiotic bacterial associate of nematodes, possibly as the root knot nematode evolved to be a highly specialized parasite of plants.
Rickettsial
metK
-Encoded Methionine Adenosyltransferase Expression in an
Escherichia coli metK
Deletion Strain
Authors: Driskell Lonnie O. , Tucker Aimee M. , Winkler Herbert H. , Wood David O.
Published: August 2005

The obligate intracellular bacterium
Rickettsia prowazekii
has recently been shown to transport the essential metabolite
S
-adenosylmethionine (SAM). The existence of such a transporter would suggest that the
metK
gene, coding for the enzyme that synthesizes SAM, is unnecessary for rickettsial growth. Genome sequencing has revealed that this is the case for the
metK
genes of the spotted fever group and the Madrid E strain of
R. prowazekii
, which contain recognizable inactivating mutations. However, several strains of the typhus group rickettsiae possess
metK
genes lacking obvious mutations. In order to determine if these genes code for a product that retains MAT function, an
Escherichia coli metK
deletion mutant was constructed in which individual rickettsial
metK
genes were tested for the ability to complement the methionine adenosyltransferase deficiency. Both the
R. prowazekii
Breinl and
R. typhi
Wilmington
metK
genes complemented at a level comparable to that of an
E. coli metK
control, demonstrating that the typhus group rickettsiae have the capability of synthesizing as well as transporting SAM. However, the appearance of mutations that affect the function of the
metK
gene products (a stop codon in the Madrid E strain and a 6-bp deletion in the Breinl strain) provides experimental support for the hypothesis that these typhus group genes, like the more degenerate spotted fever group orthologs, are in the process of gene degradation.
Regulation of Excision Genes of theBacteroidesConjugative Transposon CTnDOT
Authors: Moon Kyung , Shoemaker Nadja B. , Gardner Jeffrey F. , Salyers Abigail A.
Published: August 2005

The first step in the transfer of theBacteroidesconjugative transposon CTnDOT is excision of the integrated element from the chromosome to form a circular transfer intermediate. Excision occurs only after the bacteria are exposed to tetracycline. Previously, four excision genes were identified. One was the integrase geneintDOT, which appeared to be expressed constitutively. Three other genes essential for excision (orf2c,orf2d, andexc) were found located in a cluster 13 kbp downstream ofintDOT. By usinguidAfusions and real-time reverse transcriptase PCR, we demonstrate here that the excision genesorf2c,orf2d, andexcare part of an operon that also contains open reading frameorf3, previously shown not to be essential for excision. We also show that operon expression is regulated at the transcriptional level in response to tetracycline. The transcript start site for the operon has been localized. Three CTnDOT regulatory genes are thought to be involved in tetracycline regulation of excision,rteA,rteB, andrteC. By placingrteCunder the control of a heterologous promoter, we found that RteC alone was sufficient for induction of theorf2coperon. If, however, therteCgene was under the control of its own promoter, it was not able to induceorf2coperon expression unlessrteAandrteBwere present. Thus, RteA and RteB participate in excision by stimulating transcription ofrteC. Using electrophoretic mobility shift analysis, we found that a purified His6-tagged form of RteC bound DNA upstream of the −33 region of the promoter. Changing the sequence in the region between bp −50 and −70 reduced the expression of theorf2coperon in vivo. Taken together, our results support the hypothesis that RteC acts as a DNA-binding protein that binds upstream of theorf2cpromoter and is responsible for tetracycline-regulated transcriptional regulation of theorf2coperon.
MONOTONE TRACE FUNCTIONS OF SEVERAL VARIABLES
Authors: HANSEN FRANK
Published: August 2005

We investigate monotone operator functions of several variables under a trace or a trace-like functional. In particular, we prove the inequality τ(x1⋯xn) ≤ τ(y1⋯yn) for a trace τ on a C*-algebra and abelian n-tuples (x1,…,xn) ≤ (y1,…,yn) of positive elements. We formulate and prove Jensen's inequality for expectation values, and we study matrix functions of several variables which are convex or monotone with respect to the weak majorization for matrices.
Parameterized object sensitivity for points-to analysis for Java
Authors: Milanova Ana , Rountev Atanas , Ryder Barbara G.
Published: August 2005

The goal of
points-to analysis
for Java is to determine the set of objects pointed to by a reference variable or a reference object field. We present
object sensitivity
, a new form of context sensitivity for flow-insensitive points-to analysis for Java. The key idea of our approach is to analyze a method separately for each of the object names that represent run-time objects on which this method may be invoked. To ensure flexibility and practicality, we propose a parameterization framework that allows analysis designers to control the tradeoffs between cost and precision in the object-sensitive analysis.
Side-effect analysis
determines the memory locations that may be modified by the execution of a program statement.
Def-use analysis
identifies pairs of statements that set the value of a memory location and subsequently use that value. The information computed by such analyses has a wide variety of uses in compilers and software tools. This work proposes new versions of these analyses that are based on object-sensitive points-to analysis.We have implemented two instantiations of our parameterized object-sensitive points-to analysis. On a set of 23 Java programs, our experiments show that these analyses have comparable cost to a context-insensitive points-to analysis for Java which is based on Andersen's analysis for C. Our results also show that object sensitivity significantly improves the precision of side-effect analysis and call graph construction, compared to (1) context-insensitive analysis, and (2) context-sensitive points-to analysis that models context using the invoking call site. These experiments demonstrate that object-sensitive analyses can achieve substantial precision improvement, while at the same time remaining efficient and practical.
Introduction
Authors: Streitz Norbert , Nixon Paddy
Published: August 2005

It seems like a paradox but it will soon become reality: The rate at which computers disappear will be matched by the rate at which information technology will increasingly permeate our environment and our lives.
Privacy and trust issues with invisible computers
Authors: Lahlou Saadi , Langheinrich Marc , Röcker Carsten
Published: August 2005

A set of designer guidelines from the European Union offers the first step in building privacy-aware systems.
Hybrid design creates innovative museum experiences
Authors: Bannon Liam , Benford Steve , Bowers John , Heath Christian
Published: August 2005

Assembling mixed media artifacts in order to create engaging museum environments.
The LOCKSS peer-to-peer digital preservation system
Authors: Maniatis Petros , Roussopoulos Mema , Giuli T. J. , Rosenthal David S. H. , Baker Mary
Published: August 2005

The LOCKSS project has developed and deployed in a world-wide test a peer-to-peer system for preserving access to journals and other archival information published on the Web. It consists of a large number of independent, low-cost, persistent Web caches that cooperate to detect and repair damage to their content by voting in “opinion polls.” Based on this experience, we present a design for and simulations of a novel protocol for voting in systems of this kind. It incorporates rate limitation and intrusion detection to ensure that even some very powerful adversaries attacking over many years have only a small probability of causing irrecoverable damage before being detected.
Link analysis ranking: algorithms, theory, and experiments
Authors: Borodin Allan , Roberts Gareth O. , Rosenthal Jeffrey S. , Tsaparas Panayiotis
Published: August 2005

The explosive growth and the widespread accessibility of the Web has led to a surge of research activity in the area of information retrieval on the World Wide Web. The seminal papers of Kleinberg [1998, 1999] and Brin and Page [1998] introducedLink Analysis Ranking, where hyperlink structures are used to determine the relativeauthorityof a Web page and produce improved algorithms for the ranking of Web search results. In this article we work within the hubs and authorities framework defined by Kleinberg and we propose new families of algorithms. Two of the algorithms we propose use a Bayesian approach, as opposed to the usual algebraic and graph theoretic approaches. We also introduce a theoretical framework for the study of Link Analysis Ranking algorithms. The framework allows for the definition of specific properties of Link Analysis Ranking algorithms, as well as for comparing different algorithms. We study the properties of the algorithms that we define, and we provide an axiomatic characterization of the INDEGREE heuristic which ranks each node according to the number of incoming links. We conclude the article with an extensive experimental evaluation. We study the quality of the algorithms, and we examine how different structures in the graphs affect their performance.
Establishing pairwise keys in distributed sensor networks
Authors: Liu Donggang , Ning Peng , Li Rongfang
Published: August 2005

Pairwise key establishment is a fundamental security service in sensor networks; it enables sensor nodes to communicate securely with each other using cryptographic techniques. However, due to the resource constraints on sensor nodes, it is not feasible to use traditional key management techniques such as public key cryptography and key distribution center (KDC). A number of key predistribution techniques have been proposed for pairwise key establishment in sensor networks recently. To facilitate the study of novel pairwise key predistribution techniques, this paper develops a general framework for establishing pairwise keys between sensor nodes using bivariate polynomials. This paper then proposes two efficient instantiations of the general framework: a
random subset assignment
key predistribution scheme, and a
hypercube-based
key predistribution scheme. The analysis shows that both schemes have a number of nice properties, including high probability, or guarantee to establish pairwise keys, tolerance of node captures, and low storage, communication, and computation overhead. To further reduce the computation at sensor nodes, this paper presents an optimization technique for polynomial evaluation, which is used to compute pairwise keys. This paper also reports the implementation and the performance of the proposed schemes on MICA2 motes running TinyOS, an operating system for networked sensors. The results indicate that the proposed techniques can be applied efficiently in resource-constrained sensor networks.
A P2P genetic algorithm environment for the internet
Authors: Tan K. C. , Wang M. L. , Peng W.
Published: August 2005

Effectively utilizing distributed computational resources while hiding the complexity of the network programming.
Spam, spim, and spit
Authors: Cerf Vinton G.
Published: August 2005

Abolishing spam, and its morphing forms, will take more than public protest and current filtering and legislative quick fixes.
Introduction
Authors: Martinsons Maris G.
Published: August 2005

In the 19th century, Napoleon Bonaparte predicted "When China awakens, it will astonish the world." China's recent stirring from its centuries-old slumber has far-reaching implications for international business and politics, as well as for science and technology development.For much of the last two millennia, China was one of the world's greatest economies and most technologically advanced societies. In recent centuries, however, the Middle Kingdom stagnated as other parts of the world experienced the Enlightenment, the Industrial Revolution, and the emergence of computer-based IT. Since paramount leader Deng Xiaoping opened China's door to the outside world in 1979, an infusion of market economics, foreign capital, and modern technology has been restoring its historical prominence [8]. From a global perspective, the country has gone from near irrelevance during the 1960s to being quaint, exotic, and inscrutable before emerging as a heavyweight. The Beijing Olympic Games in 2008 will celebrate the country's latest rise and represent an important milestone in its transformation from isolated Maoist state to full-fledged member of the international community.
Computer-related technostress in China
Authors: Tu Qiang , Wang Kanliang , Shu Qin
Published: August 2005

Technostress has been defined as any negative effect on human attitudes, thoughts, behavior, and psychology that directly or indirectly results from technology [8]. With the recent widespread application of IT and the Internet throughout China, technostress has become a serious issue for both users and IT professionals due to its potential effect on users' mental health and on-the-job productivity. Chinese employees are surrounded, often overwhelmed, by modern technology. The top 100 largest Chinese enterprises, accounting for 25% of China's GDP, are investing heavily ($10--$15 billion annually) in new IT applications, including enterprise resource planning systems. A 2002 report by the Chinese Ministry of Information Industry stated that there are 380 million mobile phone subscribers in China, making the country the world's largest mobile phone market. And a survey conducted in 2004 by the China Internet Network Information Center found that 87 million Chinese frequently accessed the Internet in 2004, an increase of 19 million, or 27.9%, over 2003.
Regular expression types for XML
Authors: Hosoya Haruo , Vouillon Jérôme , Pierce Benjamin C.
Published: August 2005

We propose
regular expression types
as a foundation for statically typed XML processing languages. Regular expression types, like most schema languages for XML, introduce regular expression notations such as repetition (*), alternation (|), etc., to describe XML documents. The novelty of our type system is a semantic presentation of subtyping, as inclusion between the sets of documents denoted by two types. We give several examples illustrating the usefulness of this form of subtyping in XML processing.The decision problem for the subtype relation reduces to the inclusion problem between tree automata, which is known to be EXPTIME-complete. To avoid this high complexity in typical cases, we develop a practical algorithm that, unlike classical algorithms based on determinization of tree automata, checks the inclusion relation by a top-down traversal of the original type expressions. The main advantage of this algorithm is that it can exploit the property that type expressions being compared often share portions of their representations. Our algorithm is a variant of Aiken and Murphy's set-inclusion constraint solver, to which are added several new implementation techniques, correctness proofs, and preliminary performance measurements on some small programs in the domain of typed XML processing.
The science of deriving dense linear algebra algorithms
Authors: Bientinesi Paolo , Gunnels John A. , Myers Margaret E. , Quintana-Ortí Enrique S. , Geijn Robert A. van de
Published: August 2005

In this article we present a systematic approach to the derivation of families of high-performance algorithms for a large set of frequently encountered dense linear algebra operations. As part of the derivation a constructive proof of the correctness of the algorithm is generated. The article is structured so that it can be used as a tutorial for novices. However, the method has been shown to yield new high-performance algorithms for well-studied linear algebra operations and should also be of interest to those who wish to produce best-in-class high-performance codes.
Parallel out-of-core computation and updating of the QR factorization
Authors: Gunter Brian C. , Van De Geijn Robert A.
Published: August 2005

This article discusses the high-performance parallel implementation of the computation and updating of QR factorizations of dense matrices, including problems large enough to require out-of-core computation, where the matrix is stored on disk. The algorithms presented here are scalable both in problem size and as the number of processors increases. Implementation using the Parallel Linear Algebra Package (PLAPACK) and the Parallel Out-of-Core Linear Algebra Package (POOCLAPACK) is discussed. The methods are shown to attain excellent performance, in some cases attaining roughly 80% of the “realizable” peak of the architectures on which the experiments were performed.
Algorithm 841: BHESS: Gaussian reduction to a similar banded Hessenberg form
Authors: Howell Gary W. , Diaa Nadia
Published: August 2005

BHESS uses Gaussian similarity transformations to reduce a general real square matrix to similar upper Hessenberg form. Multipliers are bounded in root mean square by a user-supplied parameter. If the input matrix is not highly nonnormal and the user-supplied tolerance on multipliers is of a size greater than ten, the returned matrix usually has small upper bandwidth. In such a case, eigenvalues of the returned matrix can be determined by the bulge-chasing BR iteration or by Rayleigh quotient iteration. BHESS followed by BR iteration determines a complete spectrum in about one-fifth the time required for orthogonal reduction to Hessenberg form followed by QR iterations. The FORTRAN 77 code provided for BHESS runs efficiently on a cache-based architecture.
From linear time to branching time
Authors: Kupferman Orna , Vardi Moshe Y.
Published: August 2005

Model checking is a method for the verification of systems with respect to their specifications. Symbolic model-checking, which enables the verification of large systems, proceeds by calculating fixed-point expressions over the system's set of states. The μ-calculus is a branching-time temporal logic with fixed-point operators. As such, it is a convenient logic for symbolic model-checking tools. In particular, the alternation-free fragment of μ-calculus has a restricted syntax, making the symbolic evaluation of its formulas computationally easy. Formally, it takes time that is linear in the size of the system. On the other hand, specifiers find the μ-calculus inconvenient. In addition, specifiers often prefer to use linear-time formalisms. Such formalisms, however, cannot in general be translated to the alternation-free μ-calculus, and their symbolic evaluation involves nesting of fixed-points, resulting in time complexity that is quadratic in the size of the system. In this article, we characterize linear-time properties that can be specified in the alternation-free μ-calculus. We show that a linear-time property can be specified in the alternation-free μ-calculus iff it can be recognized by a deterministic Büchi automaton. We study the problem of deciding whether a linear-time property, specified by either an automaton or an LTL formula, can be translated to an alternation-free μ-calculus formula, and describe the translation, when possible.
Comparisons and computation of well-founded semantics for disjunctive logic programs
Authors: Wang Kewen , Zhou Lizhu
Published: August 2005

Much work has been done on extending the well-founded semantics to general disjunctive logic programs and various approaches have been proposed. However, these semantics are different from each other and no consensus is reached about which semantics is the most intended. In this article, we look at disjunctive well-founded reasoning from different angles. We show that there is an intuitive form of the well-founded reasoning in disjunctive logic programming which can be characterized by slightly modifying some existing approaches to defining disjunctive well-founded semantics, including program transformations, argumentation, unfounded sets (and resolution-like procedure). By employing the techniques developed by Brass and Dix in their transformation-based approach, we also provide a bottom-up procedure for this semantics. The significance of our work is not only in clarifying the relationship among different approaches, but also shed some light on what is an intended well-founded semantics for disjunctive logic programs.
Minimum model semantics for logic programs with negation-as-failure
Authors: Rondogiannis Panos , Wadge William W.
Published: August 2005

We give a purely model-theoretic characterization of the semantics of logic programs with negation-as-failure allowed in clause bodies. In our semantics, the meaning of a program is, as in the classical case, the unique
minimum
model in a program-independent ordering. We use an expanded truth domain that has an uncountable linearly ordered set of truth values between
False
(the minimum element) and
True
(the maximum), with a
Zero
element in the middle. The truth values below
Zero
are ordered like the countable ordinals. The values above
Zero
have exactly the reverse order. Negation is interpreted as reflection about
Zero
followed by a step towards
Zero
; the only truth value that remains unaffected by negation is
Zero
. We show that every program has a unique minimum model
M
P
, and that this model can be constructed with a
T
P
iteration which proceeds through the countable ordinals. Furthermore, we demonstrate that
M
P
can alternatively be obtained through a construction that generalizes the well-known model intersection theorem for classical logic programming. Finally, we show that by collapsing the true and false values of the infinite-valued model
M
P
to (the classical)
True
and
False
, we obtain a three-valued model identical to the well-founded one.
An efficient normalized maximum likelihood algorithm for DNA sequence compression
Authors: Korodi Gergely , Tabus Ioan
Published: August 2005

This article presents an efficient algorithm for DNA sequence compression, which achieves the best compression ratios reported over a test set commonly used for evaluating DNA compression programs. The algorithm introduces many refinements to a compression method that combines: (1) encoding by a simple normalized maximum likelihood (NML) model for discrete regression, through reference to preceding approximate matching blocks, (2) encoding by a first order context coding and (3) representing strings in clear, to make efficient use of the redundancy sources in DNA data, under fast execution times. One of the main algorithmic features is the constraint on the matching blocks to include reasonably long contiguous matches, which not only reduces significantly the search time, but also can be used to modify the NML model to exploit the constraint for getting smaller code lengths. The algorithm handles the changing statistics of DNA data in an adaptive way and by predictively encoding the matching pointers it is successful in compressing long approximate matches. Apart from comparison with previous DNA encoding methods, we present compression results for the recently published human genome data.
Historical spatio-temporal aggregation
Authors: Tao Yufei , Papadias Dimitris
Published: August 2005

Spatio-temporal databases store information about the positions of individual objects over time. However, in many applications such as traffic supervision or mobile communication systems, only summarized data, like the number of cars in an area for a specific period, or phone-calls serviced by a cell each day, is required. Although this information can be obtained from operational databases, its computation is expensive, rendering online processing inapplicable. In this paper, we present specialized methods, which integrate spatio-temporal indexing with pre-aggregation. The methods support dynamic spatio-temporal dimensions for the efficient processing of historical aggregate queries without a priori knowledge of grouping hierarchies. The superiority of the proposed techniques over existing methods is demonstrated through a comprehensive probabilistic analysis and an extensive experimental evaluation.
Predicting human interruptibility with sensors
Authors: Fogarty James , Hudson Scott E. , Atkeson Christopher G. , Avrahami Daniel , Forlizzi Jodi , Kiesler Sara , Lee Johnny C. , Yang Jie
Published: August 2005

A person seeking another person's attention is normally able to quickly assess how interruptible the other person currently is. Such assessments allow behavior that we consider natural, socially appropriate, or simply polite. This is in sharp contrast to current computer and communication systems, which are largely unaware of the social situations surrounding their usage and the impact that their actions have on these situations. If systems could model human interruptibility, they could use this information to negotiate interruptions at appropriate times, thus improving human computer interaction.This article presents a series of studies that quantitatively demonstrate that simple sensors can support the construction of models that estimate human interruptibility as well as people do. These models can be constructed without using complex sensors, such as vision-based techniques, and therefore their use in everyday office environments is both practical and affordable. Although currently based on a demographically limited sample, our results indicate a substantial opportunity for future research to validate these results over larger groups of office workers. Our results also motivate the development of systems that use these models to negotiate interruptions at socially appropriate times.
Lineage retrieval for scientific data processing: a survey
Authors: Bose Rajendra , Frew James
Published: August 2005

Scientific research relies as much on the dissemination and exchange of data sets as on the publication of conclusions. Accurately tracking the lineage (origin and subsequent processing history) of scientific data sets is thus imperative for the complete documentation of scientific work. Researchers are effectively prevented from determining, preserving, or providing the lineage of the computational data products they use and create, however, because of the lack of a definitive model for lineage retrieval and a poor fit between current data management tools and scientific software. Based on a comprehensive survey of lineage research and previous prototypes, we present a metamodel to help identify and assess the basic components of systems that provide lineage retrieval for scientific data products.
Trade-offs for fully dynamic transitive closure on DAGs: breaking through the
O
(
n
2
barrier
Authors: Demetrescu Camil , Italiano Giuseppe F.
Published: August 2005

We present an algorithm for directed acyclic graphs that breaks through the
O
(
n
2
) barrier on the single-operation complexity of fully dynamic transitive closure, where
n
is the number of edges in the graph. We can answer queries in
O
(
n
ε
) worst-case time and perform updates in
O
(
n
ω(1,ε,1)−ε
+
n
1+ε
) worst-case time, for any ε∈[0,1], where ω(1,ε,1) is the exponent of the multiplication of an
n
×
n
ε
matrix by an
n
ε
×
n
matrix. The current best bounds on ω(1,ε,1) imply an
O
(
n
0.575
) query time and an
O
(
n
1.575
) update time in the worst case. Our subquadratic algorithm is randomized, and has one-sided error. As an application of this result, we show how to solve single-source reachability in
O
(
n
1.575
) time per update and constant time per query.