bluuebunny/crossref_metadata_2025 huggingface dataset:
Taking Turns Sending and Receiving
Authors: Gough Nancy R.
Published: November 2009

Inverse oscillatory recruitment of two signaling components to interacting Neurospora germling cells prevents cells from self-stimulation.
Intrapulmonary Pharmacokinetics of S-013420, a Novel Bicyclolide Antibacterial, in Healthy Japanese Subjects
Authors: Furuie Hidetoshi , Saisho Yutaka , Yoshikawa Takayoshi , Shimada Jingoro
Published: November 2009

S-013420 (EDP-420) is a novel bicyclolide (bridged bicyclic macrolide) antibacterial currently under development for the treatment of respiratory tract infections. The objective of the present study was to determine the plasma and intrapulmonary pharmacokinetic parameters of orally administered S-013420 in healthy volunteers. Twenty-eight healthy Japanese male subjects who never smoked were randomly allocated to seven groups of four subjects each who underwent bronchoalveolar lavage (BAL) at different times after dosing (2, 4, 6, 8, 10, 12, or 24 h). Blood samples were also taken at 0, 0.5, 1, 2, 4, 6, 8, 10, 12, 24, 48, and 72 h after dosing. The S-013420 concentrations in plasma, epithelial lining fluid (ELF), and alveolar macrophages (AMs) were measured by using a combined high-performance liquid chromatography-mass spectrometric technique. A pharmacokinetic analysis of the plasma, ELF, and AM S-013420 concentration profiles was performed. S-013420 was rapidly absorbed in plasma, and the mean time to the maximum concentration in plasma was 2.27 h. S-013420 was rapidly distributed to the ELF and was slowly distributed to AMs. The areas under the concentration-time curves from time zero to 24 h (AUC0-24) for S-013420 were 20.3 times higher in ELF than in plasma and 244.6 times higher in AMs than in plasma. The mean maximum concentration in plasma was higher in ELF than in plasma and was much higher in AM than in plasma. Furthermore, pharmacodynamic calculations were done by using the AUC0-24/MIC90ratio for common pneumonia pathogens (Staphylococcus aureus,Streptococcus pneumoniae,Haemophilus influenzae, andMoraxella catarrhalis). The AUC0-24for plasma/MIC90s for these four organisms were 41.8, 83.6, 1.3, and 20.9, respectively. The AUC0-24for ELF/MIC90s were 849.6, 1,699.2, 26.6, and 424.8, respectively. Considering the good efficacy shown in a subsequent phase 2 study (S. Kohno, K. Yamaguchi, Y. Tanigawara, A. Watanabe, A. Aoki, Y. Niki, and J. Fujita, Abstr. 47th Intersci. Conf. Antimicrob. Agents Chemother., abstr. L-485), the good distribution of S-013420 in AMs and ELF observed in the present study is predictive of the good efficacy of S-013420 against respiratory pathogens.
Polyphyletic Emergence of Linezolid-Resistant Staphylococci in the United States
Authors: Wong Agnes , Reddy Shilpa P. , Smyth Davida S. , Aguero-Rosenfeld Maria E. , Sakoulas George , Robinson D. Ashley
Published: November 2009

Since the year 2000, linezolid has been used in the United States to treat infections caused by antimicrobial-resistant Gram-positive cocci. At present, linezolid-resistant (Lin
r
)
Staphylococcus aureus
and
Staphylococcus epidermidis
strains are rare and the diversity of their genetic backgrounds is unknown. We performed sequence-based strain typing and resistance gene characterization of 46 Lin
r
isolates that were collected from local and national sources between the years 2004 and 2007. Resistance was found to occur in at least three clonal complexes (CCs; lineages) of
S. aureus
and in at least four subclusters of a predominant, phylogenetically unstable CC of
S. epidermidis
. New candidate resistance mutations in 23S rRNA and the L4 riboprotein were identified among the
S. epidermidis
isolates. These findings suggest that linezolid resistance has emerged independently in multiple clones of
S. aureus
and with a variety of ribosomal mutations in multiple clones of
S. epidermidis
.
Differential Patterns of Liver Proteins in Experimental Murine Hepatosplenic Schistosomiasis
Authors: Manivannan B. , Rawson P. , Jordan T. W. , Secor W. E. , La Flamme A. C.
Published: November 2009

Schistosoma mansonieggs produced by adult worms in the mesenteric vasculature become trapped in the liver, where they induce granulomatous lesions and strong immune responses. Infected individuals suffer from intestinal schistosomiasis (INT) in 90% of cases, whereas the remaining 10% present with severe hepatosplenic schistosomiasis (HS). The CBA/J mouse model mimics human disease, with 20% of infected mice developing hypersplenomegaly syndrome (HSS) that resembles HS and 80% developing moderate splenomegaly syndrome (MSS) similar to INT. We studied differential patterns of protein expression in livers of 20-week-infected CBA/J mice with MSS or HSS to understand the molecular changes that underlie these two disease forms. Using differential in-gel electrophoresis to identify differentially expressed protein spots, we found 80 protein spots significantly changed with infection and 35 changes specific to severe disease. In particular, the abundances of prohibitin 2, transferrin isoforms, and major urinary protein isoforms were significantly altered in HSS mice. Furthermore, annexin 5, glutathioneS-transferase pi class, andS. mansoniphosphoenolpyruvate carboxykinase expression levels changed significantly with schistosome infection. Additionally, levels of major urinary protein decreased and levels of transferrin increased significantly in the sera of HSS mice compared to levels in sera of MSS or control mice, and these differences correlated to the degree of splenomegaly. These findings indicate that the liver protein abundances differ between MSS and HSS mice and may be used for the development of diagnostic markers for the early detection of hepatosplenic schistosomiasis.
Yersinia pestisTwo-Component Gene Regulatory Systems Promote Survival in Human Neutrophils
Authors: O'Loughlin Jason L. , Spinner Justin L. , Minnich Scott A. , Kobayashi Scott D.
Published: November 2009

Human polymorphonuclear leukocytes (PMNs, or neutrophils) are the most abundant innate immune cell and kill most invading bacteria through combined activities of reactive oxygen species (ROS) and antimicrobial granule constituents. Pathogens such asYersinia pestisresist destruction by the innate immune system and are able to survive in macrophages and neutrophils. The specific molecular mechanisms used byY. pestisto survive following phagocytosis by human PMNs are incompletely defined. To gain insight into factors that governY. pestisintracellular survival in neutrophils, we inactivated 25 two-component gene regulatory systems (TCSs) with known or inferred function and assessed susceptibility of these mutant strains to human PMN granule extracts.Y. pestisstrains deficient for PhoPQ, KdpED, CheY, CvgSY, and CpxRA TCSs were selected for further analysis, and all five strains were altered for survival following interaction with PMNs. Of these five strains, onlyY. pestisΔphoPQdemonstrated global sensitivity to a panel of seven individual neutrophil antimicrobial peptides and serine proteases. Notably,Y. pestisΔphoPQwas deficient for intracellular survival in PMNs. Iterative analysis withY. pestisstrains lacking the PhoP-regulated genesugdandpmrKindicated that the mechanism most likely responsible for increased resistance to killing is 4-amino-4-deoxy-l-arabinose modification of lipid A. Together, the data provide new information aboutY. pestisevasion of the innate immune system.
Protease-Activated Receptor 2 Has Pivotal Roles in Cellular Mechanisms Involved in Experimental Periodontitis
Authors: Wong David M. , Tam Vivian , Lam Roselind , Walsh Katrina A. , Tatarczuch Liliana , Pagel Charles N. , Reynolds Eric C. , O'Brien-Simpson Neil M. , Mackie Eleanor J. , Pike Robert N.
Published: November 2009

The tissue destruction seen in chronic periodontitis is commonly accepted to involve extensive upregulation of the host inflammatory response. Protease-activated receptor 2 (PAR-2)-null mice infected withPorphyromonas gingivalisdid not display periodontal bone resorption in contrast to wild-type-infected and PAR-1-null-infected mice. Histological examination of tissues confirmed the lowered bone resorption in PAR-2-null mice and identified a substantial decrease in mast cells infiltrating the periodontal tissues of these mice. T cells fromP. gingivalis-infected or immunized PAR-2-null mice proliferated less in response to antigen than those from wild-type animals. CD90 (Thy1.2) expression on CD4+and CD8+T-cell-receptor β (TCRβ) T cells was significantly (P< 0.001) decreased in antigen-immunized PAR-2-null mice compared to sham-immunized PAR-2-null mice; this was not observed in wild-type controls. T cells from infected or antigen-immunized PAR-2-null mice had a significantly different Th1/inflammatory cytokine profile from wild-type cells: in particular, gamma interferon, interleukins (interleukin-2, -3, and -17), granulocyte-macrophage colony-stimulating factor, and tumor necrosis factor alpha demonstrated lower expression than wild-type controls. The absence of PAR-2 therefore appears to substantially decrease T-cell activation and the Th1/inflammatory response. Regulation of such proinflammatory mechanisms in T cells and mast cells by PAR-2 suggests a pivotal role in the pathogenesis of the disease.
Transitions in Oral and Intestinal Microflora Composition and Innate Immune Receptor-Dependent Stimulation during Mouse Development
Authors: Hasegawa Mizuho , Osaka Toshifumi , Tawaratsumida Kazuki , Yamazaki Takashi , Tada Hiroyuki , Chen Grace Y. , Tsuneda Satoshi , Núñez Gabriel , Inohara Naohiro
Published: November 2009

Commensal bacteria possess immunostimulatory activities that can modulate host responses to affect development and homeostasis in the intestine. However, how different populations of resident bacteria stimulate the immune system remains largely unknown. We characterized here the ability of intestinal and oral microflora to stimulate individual pattern recognition receptors (PRRs) in bone marrow-derived macrophages and mesothelial cells. The intestinal but not oral microflora elicited age- and cell type-specific immunostimulation. The immunostimulatory activity of the intestinal microflora varied among individual mice but was largely mediated via Toll-like receptor 4 (TLR4) during breast-feeding, whereas it became TLR4 independent after weaning. This transition was associated with a change from a microflora rich in TLR4-stimulatory proteobacteria to one dominated by
Bacteroidales
and/or
Clostridiales
that poorly stimulate TLR4. The major stimulatory activity of the intestinal microflora was still intact in NOD1-, NOD2-, TLR2-, TLR4-, TLR5-, TLR9-, TLR11-, ASC-, or RICK-deficient cells but still relied on the adaptor MyD88. These studies demonstrate a transition in the intestinal microflora accompanied by a dynamic change of its ability to stimulate different PRRs which control intestinal homeostasis.
Critical Roles of Complement and Antibodies in Host Defense Mechanisms againstNeisseria meningitidisas Revealed by Human Complement Genetic Deficiencies
Authors: Hellerud Bernt Christian , Aase Audun , Herstad Tove Karin , Næss Lisbeth Meyer , Kristiansen Lisa Høyem , Trøseid Anne-Marie Siebke , Harboe Morten , Lappegård Knut Tore , Brandtzæg Petter , Høiby E. Arne , Mollnes Tom Eirik
Published: November 2009

Certain complement defects are associated with an increased propensity to contractNeisseria meningitidisinfections. We performed detailed analyses of complement-mediated defense mechanisms againstN. meningitidis44/76 with whole blood and serum from two adult patients who were completely C2 or C5 deficient. The C5-deficient patient and the matched control were also deficient in mannose-binding lectin (MBL). The proliferation of meningococci incubated in freshly drawn whole blood was estimated by CFU and quantitative DNA real-time PCR. The serum bactericidal activity and opsonophagocytic activity by granulocytes were investigated, including heat-inactivated postvaccination sera, to examine the influence of antimeningococcal antibodies. The meningococci proliferated equally in C2- and C5-deficient blood, with a 2 log10increase of CFU and 4- to 5-log10increase in DNA copies. Proliferation was modestly decreased in reconstituted C2-deficient and control blood. After reconstitution of C5-deficient blood, all meningococci were killed, which is consistent with high antibody titers being present. The opsonophagocytic activity was strictly C2 dependent, appeared with normal serum, and increased with postvaccination serum. Serum bactericidal activity was strictly dependent on C2, C5, and high antibody titers. MBL did not influence any of the parameters observed. Complement-mediated defense against meningococci was thus dependent on the classical pathway. Some opsonophagocytic activity occurred despite low levels of antimeningococcal antibodies but was more efficient with immune sera. Serum bactericidal activity was dependent on C2, C5, and immune sera. MBL did not influence any of the parameters observed.
Fenugreek seeds reduce atherogenic diet-induced cholesterol gallstone formation in experimental mice
Authors: Reddy R.L.R. , Srinivasan K.
Published: November 2009

Dietary hypocholesterolemic adjuncts may have a beneficial role in the prevention and treatment of cholesterol gallstones (CGS). In this investigation, fenugreek (Trigonella foenum-graecum) seed was evaluated for this potential on the experimental induction of CGS in laboratory mice. CGS was induced by maintaining mice on a lithogenic diet (0.5% cholesterol) for 10 weeks. Fenugreek seed powder was included at 5%, 10%, and 15% of this lithogenic diet. Dietary fenugreek significantly lowered the incidence of CGS in these mice; the incidence was 63%, 40%, and 10% in the 5%, 10%, and 15% fenugreek groups, respectively, compared with 100% in the lithogenic control. The antilithogenic influence of fenugreek is attributable to its hypocholesterolemic effect. Serum cholesterol level was decreased by 26%–31% by dietary fenugreek, while hepatic cholesterol was lowered by 47%–64% in these high cholesterol-fed animals. Biliary cholesterol was 8.73–11.2 mmol/L as a result of dietary fenugreek, compared with 33.6 mmol/L in high-cholesterol feeding without fenugreek. Cholesterol saturation index in bile was reduced to 0.77–0.99 in fenugreek treatments compared with 2.57 in the high-cholesterol group. Thus, fenugreek seed offers health-beneficial antilithogenic potential by virtue of its favourable influence on cholesterol metabolism.
Alteration of perivascular adipose tissue function in angiotensin II-induced hypertension
Authors: Lee Robert M.K.W. , Ding Lili , Lu Chao , Su Li-Ying , Gao Yu-Jing
Published: November 2009

We studied the role of perivascular adipose tissue (PVAT) in the control of vascular function in an in vivo experimental model of hypertension produced by angiotensin II infusion by osmotic minipump in adult male Wistar rats. Two weeks after infusion with angiotensin II, blood pressure in treated rats was significantly elevated but heart rate was reduced compared with control rats infused with physiological saline. Contraction of aorta from the 2 groups of rats in response to phenylephrine or serotonin was significantly attenuated by the presence of PVAT in both the presence and absence of endothelium. This attenuation effect on contraction to phenylephrine was higher, however, in vessels from control rats than in vessels from hypertensive rats in the absence of endothelium. In the mesenteric resistance arteries, lumen diameter was larger in both hypertensive and control vessels with intact PVAT than in vessels with PVAT removed. The medial wall was thicker in arteries from hypertensive rats. The presence of PVAT potentiated the contraction induced by KCl in mesenteric arteries from control rats, but not in hypertensive rats. PVAT also attenuated the contraction of mesenteric arteries in response to phenylephrine or serotonin in both hypertensive and control groups. Mesenteric arteries from hypertensive rats were more responsive to stimulation by serotonin than those from control rats. We conclude that the increased blood pressure of Wistar rats that occurred after infusion with angiotensin II was associated with changes in the functions of PVAT in the aorta and mesenteric arteries and in the structure and function of resistance arteries.
Inhibitory effects of dauricine on early afterdepolarizations and L-type calcium current
Authors: Liu Qiang-Ni , Zhang Li , Gong Pei-Li , Yang Xiao-Yan , Zeng Fan-Dian
Published: November 2009

We have previously reported that dauricine exerted antiarrhythmic effects on various experimental arrhythmias. To further clarify its mechanism, the effects of dauricine on action potential duration (APD), early afterdepolarizations (EADs), triangulation, which is defined as the repolarization time from APD at 30% level (APD30) to APD at 90% level (APD90), and L-type calcium current (ICa-L) were studied using standard microelectrode techniques on rabbit papillary muscles and whole-cell patch clamp techniques on single myocytes isolated from rabbits by enzymatic digestion, respectively. Cardiac hypertrophy was induced by coarctating the abdominal aorta of rabbits. The results showed that in papillary muscles of hypertrophied rabbits, 1 µmol/L dofetilide, a selective IKr blocker, prolonged APD50 and APD90 and induced EADs (4/6, p < 0.01) with hypokalemia ([K+]o = 2.7 mmol/L). Dauricine inhibited EADs (p < 0.01) and shortened the prolonged APD (p < 0.01). In single myocytes, dauricine also inhibited EADs induced by dofetilide, hypokalemia, and hypomagnesaemia. Dauricine decreased the triangulation and reduced the peak amplitude of ICa-L at all potentials tested. Dauricine shifted the steady-state activation curves to the right and steady-state inactivation curves to the left and prolonged the τ value of the recovery curve. These results suggest that dauricine inhibits EADs and this effect may be associated with its blockade of ICa-L.
THE EXTENDED ALGEBRA OF OBSERVABLES FOR DIRAC FIELDS AND THE TRACE ANOMALY OF THEIR STRESS-ENERGY TENSOR
Authors: DAPPIAGGI CLAUDIO , HACK THOMAS-PAUL , PINAMONTI NICOLA
Published: November 2009

We discuss from scratch the classical structure of Dirac spinors on an arbitrary globally hyperbolic, Lorentzian spacetime, their formulation as a locally covariant quantum field theory, and the associated notion of a Hadamard state. Eventually, we develop the notion of Wick polynomials for spinor fields, and we employ the latter to construct a covariantly conserved stress-energy tensor suited for back-reaction computations. We shall explicitly calculate its trace anomaly in particular.
GAUGE-EQUIVARIANT HILBERT BIMODULES AND CROSSED PRODUCTS BY ENDOMORPHISMS
Authors: VASSELLI EZIO
Published: November 2009

C*-endomorphisms arising from superselection structures with nontrivial center define a 'rank' and a 'first Chern class'. Crossed products by such endomorphisms involve the Cuntz–Pimsner algebra of a vector bundle having the above-mentioned rank, first Chern class and can be used to construct a duality for abstract (nonsymmetric) tensor categories versus group bundles acting on (nonsymmetric) Hilbert bimodules. Existence and unicity of the dual object (i.e. the 'gauge' group bundle) are not ensured: we give a description of this phenomenon in terms of a certain moduli space associated with the given endomorphism. The above-mentioned Hilbert bimodules are noncommutative analogs of gauge-equivariant vector bundles in the sense of Nistor–Troitsky.
FROM QUASI-ENTROPY TO SKEW INFORMATION
Authors: PETZ D. , SZABÓ V. E. S.
Published: November 2009

This paper gives an overview about particular quasi-entropies, generalized quantum covariances, quantum Fisher informations, skew informations and their relations. The point is the dependence on operator monotone functions. It is proven that a skew information is the Hessian of a quasi-entropy. The skew information and some inequalities are extended to a von Neumann algebra setting.
LANGMUIR–BLODGETT FILMS AND MOLECULAR ELECTRONICS
Authors: HUSSAIN SYED-ARSHAD , BHATTACHARJEE D.
Published: November 2009

Molecular electronics is a new, exciting and interdisciplinary field of research. The main concern of the subject is to exploit the organic materials in electronic and optoelectronic devices. On the other hand, the Langmuir–Blodgett (LB) film deposition technique is one of the best among few methods used to manipulate materials at the molecular level. In this article, the LB film preparation technique is discussed briefly with an emphasis on its application towards molecular electronics.
RECONFIRMATION OF THE THREE-DOMAIN CLASSIFICATION OF LIFE BY CLUSTER ANALYSIS OF PROTEIN LENGTH DISTRIBUTIONS
Authors: LI DIRSON JIAN , ZHANG SHENGLI
Published: November 2009

The classification of life should be based on the intrinsic mechanism in the evolution of life. We found new methods to classify life into Archaea, Bacteria and Eucarya based on the correlation analysis and spectral analysis of protein length distributions. We show that there is rich evolutionary information stored in the fluctuations of protein length distributions. The intrinsic mechanism of diversification of life is revealed by the properties of protein length distributions.
SUPER INTEGRABLE HIERARCHY AND SUPER HAMILTONIAN STRUCTURES ASSOCIATED WITH GUO HIERARCHY
Authors: ZHANG NING , DONG HUANHE
Published: November 2009

A Lie superalgebra is constructed from which establishes an isospectral problems. By solving the zero curvature equation, a resulting super hierarchies of the Guo hierarchy are obtained. By making use of the super identity, the Hamiltonian structures of the above super integrable hierarchies are generated, this method can be used to other superhierarchy.
DESTABILIZING EFFECTS OF IMPULSE IN DELAYED BAM NEURAL NETWORKS
Authors: LI CHUANDONG , LI CHAOJIE , LIU CHAO
Published: November 2009

This paper further studies the global exponential stability of the equilibrium point of the delayed bidirectional associative memory (DBAM) neural networks with impulse effects. Several results characterizing the aggregated effects of impulse and dynamical property of the impulse-free DBAM on the exponential stability of the considered DBAM have been established. It is shown that the impulsive DBAM will preserve the global exponential stability of the impulse-free DBAM even if the impulses have enlarging effects on the states of neurons.
A NEW METHOD TO ANALYZE ACOUSTO-OPTIC TUNABLE FILTER
Authors: LI HONG-YU , LI HENG-WEN , HAN BAO-KUN , XU LE-NIAN
Published: November 2009

A method based on the acoustics is developed to analyze the acousto-optic tunable filter (AOTF). A design of AOTF is provided to improve the performance of AOTF based on the method. And the experiment confirms the design.
OPTIMIZATION OF MACHINE LOCATION: AN IMPROVED HEURISTIC SOLUTION APPROACH
Authors: DAS BIMAN
Published: November 2009

An improvement in Wimmert's heuristic solution was developed for the optimization of machine location. This was accomplished by ordering the cells of the load-distance matrix on the basis of the product of "load × distance" values for eliminating less desirable load-distance combinations. The methodology is explained with four machines, four locations and five products for which Wimmert's method of diagonal elimination fails, while the improved method produces an optimal solution.
ALTERNATIVE METHODS FOR MULTI-ROBOT TASK ALLOCATION
Authors: CHOUDHURY B. B. , BISWAL B. B.
Published: November 2009

One of the most important aspects in the design of multi-robot systems (MRS) is the allocation of tasks among the robots in a productive and efficient manner. This paper presents an empirical study on task allocation strategies in multirobot environment. In general, optimal solutions are found through an exhaustive search, but because there are n × m ways in which m tasks can be assigned to n robots, an exhaustive search is often not possible with increased number of tasks. Task allocation methodologies for multirobot systems are developed by considering their capability in terms of time and space. The present work adopts a two-phase methodology to allocate tasks optimally amongst the candidate robots. The allocation cost of the robots is determined during the first phase and alternate algorithms are used in the second phase for optimizing the allocation. The work considers systems of practical sizes and the results obtained through this are helpful in recommending appropriate techniques to the users of MRS for increasing producibility and robot utilization. Three different approaches using Linear programming, Hungarian Algorithm and Knapsack Algorithm are presented and their results are analyzed for the suitability of the methods for an allocation problem. Simulation results are presented and compared for the benefit of the users.
A COMPARATIVE STUDY OF TAIWANESE PRODUCTION MANAGEMENT SYSTEM WITH DIFFERENT OUTSOURCING STRATEGY
Authors: WEE HUI-MING , PENG SHU-YUN , YANG CHING-CHOW
Published: November 2009

Through an appropriate process design and outsourcing decision, enterprises are able to control critical factors and performance indices to maintain flexibility and robustness. This study uses an empirical research to investigate the performance of Taiwanese production management systems. We analyze and compare the differences between the production management system with low, middle and high outsourcing rate strategies through questionnaires. There are four critical factors which influence customer satisfaction, of which flexible capability is the most influential. Satisfied suppliers will promote a good performance within SCM, and it will improve customer services. Enterprises should cooperate with their suppliers closely in their business collaborations. The middle outsourcing rate strategy has better flexibility in product and process change. These findings give enterprises managerial insights to achieve good performance and production management objectives.
Kode ViciousBroken builds
Authors: Neville-Neil George V.
Published: November 2009

Frequent broken builds could be symptomatic of deeper problems within a development project.
ViewpointA "smart" cyberinfrastructure for research
Authors: Parastatidis Savas , Viegas Evelyne , Hey Tony
Published: November 2009

A view of semantic computing and its role in research.
What DNS is not
Authors: Vixie Paul
Published: November 2009

DNS is many things to many people---perhaps too many things to too many people.
Future Tense: Mightier than the pen
Authors: Haldeman Joe
Published: November 2009

Future Tense, one of the revolving features on this page, presents stories and essays from the intersection of computational science and technological speculation, their boundaries limited only by our ability to imagine what will and could be.

The computer reconfigures me.
Space-time tradeoffs for approximate nearest neighbor searching
Authors: Arya Sunil , Malamatos Theocharis , Mount David M.
Published: November 2009

Nearest neighbor searching is the problem of preprocessing a set of
n
point points in
d
-dimensional space so that, given any query point
q
, it is possible to report the closest point to
q
rapidly. In approximate nearest neighbor searching, a parameter ε > 0 is given, and a multiplicative error of (1 + ε) is allowed. We assume that the dimension
d
is a constant and treat
n
and ε as asymptotic quantities. Numerous solutions have been proposed, ranging from low-space solutions having space
O
(
n
) and query time
O
(log
n
+ 1/ε

d
−1

) to high-space solutions having space roughly
O
((
n
log
n
)/ε

d

) and query time
O
(log (
n
/ε)).

We show that there is a single approach to this fundamental problem, which both improves upon existing results and spans the spectrum of space-time tradeoffs. Given a tradeoff parameter γ, where 2 ≤ γ ≤ 1/ε, we show that there exists a data structure of space
O
(
n
γ

d
−1

log(1/ε)) that can answer queries in time
O
(log(
n
γ) + 1/(εγ)

(
d
−1)/2

. When γ = 2, this yields a data structure of space
O
(
n
log (1/ε)) that can answer queries in time
O
(log
n
+ 1/ε

(
d
−1)/2

). When γ = 1/ε, it provides a data structure of space
O
((
n
/ε

d
−1

)log(1/ε)) that can answer queries in time
O
(log(
n
/ε)).

Our results are based on a data structure called a (
t
,ε)-AVD, which is a hierarchical quadtree-based subdivision of space into cells. Each cell stores up to
t
representative points of the set, such that for any query point
q
in the cell at least one of these points is an approximate nearest neighbor of
q
. We provide new algorithms for constructing AVDs and tools for analyzing their total space requirements. We also establish lower bounds on the space complexity of AVDs, and show that, up to a factor of
O
(log (1/ε)), our space bounds are asymptotically tight in the two extremes, γ = 2 and γ = 1/ε.
On the union of fat tetrahedra in three dimensions
Authors: Ezra Esther , Sharir Micha
Published: November 2009

We show that the combinatorial complexity of the union of
n
“fat” tetrahedra in 3-space (i.e., tetrahedra all of whose solid angles are at least some fixed constant) of arbitrary sizes, is
O
(
n
2+ε
), for any ε > 0;the bound is almost tight in the worst case, thus almost settling a conjecture of Pach et al. [2003]. Our result extends, in a significant way, the result of Pach et al. [2003] for the restricted case of
nearly congruent cubes
. The analysis uses cuttings, combined with the Dobkin-Kirkpatrick hierarchical decomposition of convex polytopes, in order to partition space into subcells, so that, on average, the overwhelming majority of the tetrahedra intersecting a subcell Δ behave as fat
dihedral
wedges in Δ. As an immediate corollary, we obtain that the combinatorial complexity of the union of
n
cubes in R
3
, having arbitrary side lengths, is
O
(
n
2+ε
), for any ε > 0 (again, significantly extending the result of Pach et al. [2003]). Finally, our analysis can easily be extended to yield a nearly quadratic bound on the complexity of the union of arbitrarily oriented fat triangular prisms (whose cross-sections have arbitrary sizes) in R
3
.
Efficient and secure authenticated key exchange using weak passwords
Authors: Katz Jonathan , Ostrovsky Rafail , Yung Moti
Published: November 2009

Mutual authentication and authenticated key exchange are fundamental techniques for enabling secure communication over public, insecure networks. It is well known how to design secure protocols for achieving these goals when parties share
high-entropy
cryptographic keys in advance of the authentication stage. Unfortunately, it is much more common for users to share weak,
low-entropy
passwords which furthermore may be chosen from a known space of possibilities (say, a dictionary of English words). In this case, the problem becomes much more difficult as one must ensure that protocols are immune to
off-line dictionary attacks
in which an adversary exhaustively enumerates all possible passwords in an attempt to determine the correct one.

We propose a 3-round protocol for password-only authenticated key exchange, and provide a rigorous proof of security for our protocol based on the decisional Diffie-Hellman assumption. The protocol assumes only public parameters—specifically, a “common reference string”—which can be “hard-coded” into an implementation of the protocol; in particular, and in contrast to some previous work, our protocol does
not
require either party to pre-share a public key. The protocol is also remarkably efficient, requiring computation only (roughly) 4 times greater than “classical” Diffie-Hellman key exchange that provides no authentication at all. Ours is the first protocol for password-only authentication that is both
practical
and
provably-secure using standard cryptographic assumptions
.
Compressing and indexing labeled trees, with applications
Authors: Ferragina Paolo , Luccio Fabrizio , Manzini Giovanni , Muthukrishnan S.
Published: November 2009

Consider an ordered, static tree
T
where each node has a label from alphabet Σ. Tree
T
may be of arbitrary degree and shape. Our goal is designing a compressed storage scheme of
T
that supports basic
navigational
operations among the immediate neighbors of a node (i.e. parent,
i
th child, or any child with some label,…) as well as more sophisticated
path
-based search operations over its labeled structure.

We present a novel approach to this problem by designing what we call the XBW-transform of the tree in the spirit of the well-known Burrows-Wheeler transform for strings [1994]. The XBW-transform uses path-sorting to linearize the labeled tree
T
into
two
coordinated arrays, one capturing the structure and the other the labels. For the first time, by using the properties of the XBW-transform, our compressed indexes go beyond the information-theoretic lower bound, and support navigational and path-search operations over labeled trees within (near-)optimal time bounds and entropy-bounded space.

Our XBW-transform is simple and likely to spur new results in the theory of tree compression and indexing, as well as interesting application contexts. As an example, we use the XBW-transform to design and implement a compressed index for XML documents whose compression ratio is significantly better than the one achievable by state-of-the-art tools, and its query time performance is order of magnitudes faster.
Target tracking with binary proximity sensors
Authors: Shrivastava Nisheeth , Mudumbai Raghuraman , Madhow Upamanyu , Suri Subhash
Published: November 2009

We explore fundamental performance limits of tracking a target in a two-dimensional field of binary proximity sensors, and design algorithms that attain those limits while providing minimal descriptions of the estimated target trajectory. Using geometric and probabilistic analysis of an idealized model, we prove that the achievable spatial resolution in localizing a target's trajectory is of the order of 1/ρ
R
, where
R
is the sensing radius and ρ is the sensor density per unit area. We provide a geometric algorithm for computing an economical (in descriptive complexity) piecewise linear path that approximates the trajectory within this fundamental limit of accuracy. We employ analogies between binary sensing and sampling theory to contend that only a “lowpass” approximation of the trajectory is attainable, and explore the implications of this observation for estimating the target's velocity. We also consider nonideal sensing, employing particle filters to average over noisy sensor observations, and geometric geometric postprocessing of the particle filter output to provide an economical piecewise linear description of the trajectory. In addition to simulation results validating our approaches for both idealized and nonideal sensing, we report on lab-scale experiments using motes with acoustic sensors.
Ultra-low power data storage for sensor networks
Authors: Mathur Gaurav , Desnoyers Peter , Chukiu Paul , Ganesan Deepak , Shenoy Prashant
Published: November 2009

Local storage is required in many sensor network applications, both for archival of detailed event information, as well as to overcome sensor platform memory constraints. Recent gains in energy efficiency of new-generation NAND flash storage have strengthened the case for in-network storage by data-centric sensor network applications. We argue that current storage solutions offering a simple file system abstraction are inadequate for sensor applications to exploit storage. Instead, we propose Capsule—a rich, flexible and portable object storage abstraction that offers stream, file, array, queue and index storage objects for data storage and retrieval. Further, Capsule supports checkpointing and rollback of object state for fault tolerance. Our experiments demonstrate that Capsule provides platform independence, greater functionality and greater energy efficiency than existing storage solutions.
On meeting lifetime goals and providing constant application quality
Authors: Lachenmann Andreas , Herrmann Klaus , Rothermel Kurt , Marrón Pedro José
Published: November 2009

Most work in sensor networks tries to maximize network lifetime. However, for many applications the required lifetime is known in advance. Therefore, application quality should rather be maximized for that given time.
Levels
, the approach presented in this article, is a programming abstraction for energy-aware sensor network applications that helps to meet such a user-defined lifetime goal by deactivating optional functionality.

With this programming abstraction, the application developer defines so-called
energy levels
. Functionality in energy levels is deactivated if the required lifetime cannot be met otherwise. The runtime system uses data about the energy consumption of different levels to compute an optimal level assignment that maximizes each node's quality for the time remaining.

As described in this paper,
Levels
includes a completely distributed coordination algorithm that balances energy level assignments and keeps the application quality of the network roughly constant over time. In this approach, each node computes its schedule based on those of its neighbors.

As the evaluation shows, applications using
Levels
can accurately meet given lifetime goals with only small fluctuations in application quality. In addition, the runtime overhead both for computation and for communication is negligible.
MARIA
Authors: Paterno' Fabio , Santoro Carmen , Spano Lucio Davide
Published: November 2009

One important evolution in software applications is the spread of service-oriented architectures in ubiquitous environments. Such environments are characterized by a wide set of interactive devices, with interactive applications that exploit a number of functionalities developed beforehand and encapsulated in Web services. In this article, we discuss how a novel model-based UIDL can provide useful support both at design and runtime for these types of applications. Web service annotations can also be exploited for providing hints for user interface development at design time. At runtime the language is exploited to support dynamic generation of user interfaces adapted to the different devices at hand during the user interface migration process, which is particularly important in ubiquitous environments.
KNIME - the Konstanz information miner
Authors: Berthold Michael R. , Cebron Nicolas , Dill Fabian , Gabriel Thomas R. , Kötter Tobias , Meinl Thorsten , Ohl Peter , Thiel Kilian , Wiswedel Bernd
Published: November 2009

The Konstanz Information Miner is a modular environment, which enables easy visual assembly and interactive execution of a data pipeline. It is designed as a teaching, research and collaboration platform, which enables simple integration of new algorithms and tools as well as data manipulation or visualization methods in the form of new modules or nodes. In this paper we describe some of the design aspects of the underlying architecture, briey sketch how new nodes can be incorporated, and highlight some of the new features of version 2.0.
Efficient deployment of predictive analytics through open standards and cloud computing
Authors: Guazzelli Alex , Stathatos Kostantinos , Zeller Michael
Published: November 2009

Over the past decade, we have seen tremendous interest in the application of data mining and statistical algorithms, first in research and science and, more recently, across various industries. This has translated into the development of a myriad of solutions by the data mining community that today impact scientific and business applications alike. However, even in this scenario, interoperability and open standards still lack broader adoption among data miners and modelers.

In this article we highlight the use of the Predictive Model Markup Language (PMML) standard, which allows for models to be easily exchanged between analytic applications. With a focus on interoperability and PMML, we also discuss here emerging trends in cloud computing and Software as a Service, which have already started to play a critical role in promoting a more effective implementation and widespread application of predictive models.

As an illustration of how the benefits of open standards and cloud computing can be combined, we describe a predictive analytics scoring engine platform that leverages these elements to deliver an efficient deployment process for statistical models.
Development and user experiences of an open source data cleaning, deduplication and record linkage system
Authors: Christen Peter
Published: November 2009

Record linkage, also known as database matching or entity resolution, is now recognised as a core step in the KDD process. Data mining projects increasingly require that information from several sources is combined before the actual mining can be conducted. Also of increasing interest is the deduplication of a single database. The objectives of record linkage and deduplication are to identify, match and merge all records that relate to the same real-world entities. Because real-world data is commonly 'dirty', data cleaning is an important first step in many deduplication, record linkage, and data mining project.

In this paper, an overview of the Febrl (Freely Extensible Biomedical Record Linkage) system is provided, and the results of a recent survey of Febrl users is discussed. Febrl includes a variety of functionalities required for data cleaning, deduplication and record linkage, and it provides a graphical user interface that facilitates its application for users who do not have programming experience.
Challenging research issues in data mining, databases and information retrieval
Authors: Varde Aparna S.
Published: November 2009

Data mining research along with related fields such as databases and information retrieval poses challenging problems, especially for doctoral students. The research spreads over a variety of topics such as text mining, semantic web, multilingual information analysis, heterogeneous data management, database learning, digital libraries and more. Much of this research cuts across multiple fields and presents interesting issues for discussion at conferences with a confluence of several tracks. The ACM Conference on Information and Knowledge Management provides an excellent environment for presenting such research problems spanning the three tracks of database systems, information retrieval and knowledge management. This article provides an overview of the dissertation problems presented at a Ph.D. workshop in the ACM Conference on Information and Knowledge Management. The goal of such workshops is to allow students to showcase their creative ideas at an early stage. This enables experts to critique their work and also gives the students an opportunity to exchange their thoughts with each other, besides providing excellent networking opportunities with industry and academia. This article provides an overview of the papers presented at the Ph.D workshop. It serves as a motivation for researchers to delve deeper into the innovative dissertation problems summarized here and the related work in these areas.
Adaptive learning and mining for data streams and frequent patterns
Authors: Bifet Albert
Published: November 2009

This thesis is devoted to the design of data mining algorithms for evolving data streams and for the extraction of closed frequent trees. First, we deal with each of these tasks separately, and then we deal with them together, developing classification methods for data streams containing items that are trees.

In the data stream model, data arrive at high speed, and the algorithms that must process them have very strict constraints of space and time. In the first part of this thesis we propose and illustrate a framework for developing algorithms that can adaptively learn from data streams that change over time. Our methods are based on using change detectors and estimator modules at the right places. We propose an adaptive sliding window algorithm ADWIN for detecting change and keeping updated statistics from a data stream, and use it as a black-box in place or counters or accumulators in algorithms initially not designed for drifting data. Since ADWIN has rigorous performance guarantees, this opens the possibility of extending such guarantees to learning and mining algorithms. We test our methodology with several learning methods as Naíve Bayes, clustering, decision trees and ensemble methods. We build an experimental framework for data stream mining with concept drift, based on the MOA framework, similar to WEKA, so that it will be easy for researchers to run experimental data stream benchmarks.

Trees are connected acyclic graphs and they are studied as link-based structures in many cases. In the second part of this thesis, we describe a rather formal study of trees from the point of view of closure-based mining. Moreover, we present efficient algorithms for subtree testing and for mining ordered and unordered frequent closed trees. We include an analysis of the extraction of association rules of full condence out of the closed sets of trees, and we have found there an interesting phenomenon: rules whose propositional counterpart is nontrivial are, however, always implicitly true in trees due to the peculiar combinatorics of the structures.

And finally, using these results on evolving data streams mining and closed frequent tree mining, we present high performance algorithms for mining closed unlabeled rooted trees adaptively from data streams that change over time. We introduce a general methodology to identify closed patterns in a data stream, using Galois Lattice Theory. Using this methodology, we then develop an incremental one, a sliding-window based one, and finally one that mines closed trees adaptively from data streams. We use these methods to develop classification methods for tree data streams.
Computational intelligence marketing
Authors: Kordon Arthur
Published: November 2009

Research marketing relies on capturing the attention of the targeted audience with inspiring messages and attractive presentations. Simple nontechnical language, interesting stories, and informative visualization are a must in this process. Humor is another significant factor for success and is widely used in many forms.
Pyevolve
Authors: Perone Christian S.
Published: November 2009

Pyevolve is an open-source framework for genetic algorithms. The initial long-term goal of the project was to create a complete and multi-platform framework for genetic algorithms in pure Python. However, the most recent developmental versions currently support also Genetic Programming (GP)[3]; accordingly, Pyevolve now aims at becoming a pure Python framework for evolutionary algorithms.
Association of Interleukin-8 with Cachexia from Patients with Low-Third Gastric Cancer
Authors: Song Bo , Zhang Dianliang , Wang Shuchun , Zheng Hongmei , Wang Xinxiang
Published: November 2009

Background. Interleukin (IL)-8 has been implicated in the development of cancer cachexia. The polymorphism of IL-8 gene, which may affect the production level of IL-8, may be associated with cancer cachexia.Methods. The serum IL-8 level in our study was examined by radioimmunoassay. We also analyzed single nucleotide polymorphisms (SNPs) −251 A/T and +781 C/T of IL-8 gene, using polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP).Results. The serum levels of IL-8 were significantly elevated in patients with low-third gastric cancer compared with controls, and were further up-regulated in patients with cachexia than those without (Z=−3.134,P=.002). A significantly increased frequency of +781 T allele was noted in patients with cachexia (OR=2.247, 95% CI: 1.351–3.737,P=.002). The +781 TT genotype was observed to be associated with a significantly increased risk of cachexia (OR=3.167, 95% CI: 1.265–7.929,P=.011), and with odds ratio of 3.033 (95% CI: 1.065–8.639,P=.038) for cachexia after adjusting for potential confounding factors. Meanwhile, haplotype analysis indicated a borderline positive association betweenT251T781haplotype and cachexia as compared with theT251C781haplotype (OR=4.92, 95% CI: 1.00–24.28;,P=.053).Conclusions. IL-8 appears to be associated with cachexia from patients with low-third gastric cancer.