bluuebunny/crossref_metadata_2025_split huggingface dataset:
Permissible symmetries of coupled cell networks
Authors: Ashwin Peter , Stork Peter 
Published: November 2008

AbstractWe consider coupled sets of identical cells and address the problem of which symmetries are permissible in such networks. For example, n linearly coupled cells with one independent variable in each cell cannot be constructed with the symmetry group An, the alternating group on n symbols. Using a graphical technique, we show that it is possible to construct cell networks with any desired finite group of symmetries. In particular, we show that any subgroup of Sn can be realized as the symmetries of a group of n cells. Special forms of coupling (especially low order polynomial coupling) are shown to restrict the possible symmetries. We give some upper and lower bounds for the degree of polynomial required to realize several classes of subgroups of Sn.
Quartic curves in characteristic 2
Authors: Wall C. T. C. 
Published: November 2008

Simple singularities in positive characteristicSimple singularities in positive characteristic have been discussed by many authors, and the article [5] in particular establishes the subject on a firm footing. In it a simple, or ‘ADE’ singularity is defined by a list of normal forms and it is shown that the following conditions on a singularity are equivalent: (i) it is simple, (ii) it has finite deformation type, (iii) it has finite Cohen-Macaulay module type. Moreover, the normal forms for surface singularities coincide with the earlier list of Artin [1] and those for curves with the list of [9]: in those papers further characterizations were obtained.
Discrete coactions on Hilbert C*-modules
Authors: Ng Chi-Keung 
Published: November 2008

In this paper, we will investigate discrete coactions on Hilbert C*-modules. In particular, we obtain a one-to-one correspondence between Hilbert C*-modules with discrete coactions and Hilbert C*-modules over the crossed products of the original C*-algebras which satisfies some nice properties (see 3·6 and 3·7). Then we will give some applications of this correspondence in the last three sections.In Section 2, we give some results about discrete coactions on Hilbert C*-modules which mainly correspond to those about discrete coactions on C*-algebras (see [7]).
Dehn surgery and essential annuli
Authors: Hayashi Chuichiro 
Published: November 2008

In this paper we consider Dehn surgery and essential annuli whose two boundary components are in distinct components of the boundary of a 3-manifold.Let Nl be an orientable 3-manifold with boundary, Kl a knot in Nl, and N2 the 3-manifold obtained by performing γ-Dehn surgery Kl. In detail, let Vl be a regular neighbourhood Kl, X = Nl − int Vl the exterior of Kl, T the toral component ∂Vl of ∂X, and γ a slope on T. Then we obtain the 3-manifold N2 by attaching a solid torus V2 to X so that γ bounds a disc in V2. Let K2 be the core of V2. Let π be the slope of a meridian loop of Kl, and Δ the distance between the slopes π and γ, i.e. the minimal number of intersection points of the two slopes on T. Suppose for i = 1 and 2 that Ni contains a proper annulus Ai such that the two components of ∂Ai are essential loops on distinct incompressible components of ∂Ni. Then note that Ai is essential, i.e. incompressible and ∂-incompressible in Ni.
A harmonic quadrature formula characterizing open strips
Authors: Armitage D. H. , Nelson C. S. 
Published: November 2008

Let γn denote n-dimensional Lebesgue measure. It follows easily from the well-known volume mean value property of harmonic functions that if h is an integrable harmonic function on an open ball B of centre ξ0 in ℝn, where n ≥ 2, thenA converse of this result is due to Kuran [8]: if D is an open subset of ℝn such that γn(D) < + ∞ and if there exists a point ξo∈D such thatfor every integrable harmonic function h on D, then D is a ball of centre ξ0. Armitage and Goldstein [2], theorem 1, showed that the same conclusion holds under the weaker hypothesis that (1·2) holds for all positive integrable harmonic functions h on D.
A mathematical model for long waves generated by wavemakers in non-linear dispersive systems
Authors: Bona J. L. , Bryant P. J. 
Published: November 2008

An initial-boundary-value problem for the equationis considered for x, t ≥ 0. This system is a model for long water waves of small but finite amplitude, generated in a uniform open channel by a wavemaker at one end. It is shown that, in contrast to an alternative, more familiar model using the Korteweg–deVries equation, the solution of (a) has good mathematical properties: in particular, the problem is well set in Hadamard's classical sense that solutions corresponding to given initial data exist, are unique, and depend continuously on the specified data.
Efficient self-interpretation in lambda calculus
Authors: Mogensen Torben Æ. 
Published: November 2008

AbstractWe start by giving a compact representation schema for λ-terms, and show how this leads to an exceedingly small and elegant self-interpreter. We then define the notion of aself-reducer, and show how this too can be written as a small λ-term. Both the self-interpreter and the self-reducer are proved correct. We finally give a constructive proof for the second fixed point theorem for the representation schema. All the constructions have been implemented on a computer, and experiments verify their correctness. Timings show that the self-interpreter and self-reducer are quite efficient, being about 35 and 50 times slower than direct execution using a call-by-need reductions strategy
Dynamic typing in polymorphic languages
Authors: Abadi M. , Cardelli L. , Pierce B. , Rémy D. 
Published: November 2008

AbstractThere are situations in programming where some dynamic typing is needed, even in the presence of advanced static type systems. We investigate the interplay of dynamic types with other advanced type constructions, discussing their integration into languages with explicit polymorphism (in the style of system F), implicit polymorphism (in the style of ML), abstract data types, and subtyping.
Semantics directed program execution monitoring
Authors: Kishon Amir , Hudak Paul 
Published: November 2008

AbstractMonitoring semanticsis a formal model of program execution which captures ‘monitoring activity’ as found in profilers, tracers, debuggers, etc. Beyond its theoretical interest, this formalism provides a new methodology for implementing a large family of source-level monitoring activities for sequential deterministic programming languages. In this article we explore the use of monitoring semantics in the specification and implementation of a variety of monitors: profilers, tracers, collecting interpreters, and, most importantly, interactive source-level debuggers. Although we consider such monitors only for (both strict and non-strict) functional languages, the methodology extends easily to imperative languages, since it begins with a continuation semantics specification.In addition, using standard partial evaluation techniques as an optimization strategy, we show that the methodology forms a practical basis for building real monitors. Our system can be optimized at two levels of specialization: specializing the interpreter with respect to a monitor specification automatically yields an instrumented interpreter; further specializing this instrumented interpreter with respect to a source program yields an instrumented program, i.e. one in which the extra code to perform monitoring has been automatically embedded into the program.
The Communicative Effectiveness Survey: Preliminary Evidence of Construct Validity
Authors: Donovan Neila J. , Kendall Diane L. , Young Mary Ellen , Rosenbek John C. 
Published: October 2008

PurposeTo provide preliminary evidence of the construct validity of the Communicative Effectiveness Survey (CES) for individuals with dysarthria and idiopathic Parkinson’s disease (PD).MethodIn a prospective, quasi-experimental design, 25 participants each were assigned to 3 groups (N= 75): PD and dysarthria, non-PD and no dysarthria, and PD significant others (SOs). Mean CES ratings were used to test for significant differences between the PD and non-PD group, and PD and SO rating of PD’s communicative effectiveness. Multiple linear regression tested for significant predictors of CES ratings for PD group only using sentence intelligibility and spontaneous speech intelligibility scores as predictor variables.ResultsThe PD group rated their CES significantly lower than did the non-PD group. The PD group rated their CES significantly higher than their SOs rated them. Neither speech intelligibility score was a significant predictor of CES ratings. In follow-up analysis, the Hoehn and Yahr PD staging accounted for 47% of the variability in CES ratings for the PD group participants.ConclusionsThis study provides preliminary evidence of the CES’s construct validity. Clinicians and researchers who assess and treat individuals with PD may consider adding an additional assessment to the traditional clinical measures (i.e., speech intelligibility) by obtaining a measure of communicative effectiveness.
Update on a Clinical Measure for the Assessment of Problem Solving
Authors: Marshall Robert C. , Karow Colleen M. 
Published: October 2008

Purpose
The Rapid Assessment of Problem Solving test (RAPS) is a clinical measure of problem solving based on the 20 Questions Test. This article updates clinicians on the RAPS, addresses questions raised about the test in an earlier article (R. C. Marshall, C. M. Karow, C. Morelli, K. Iden, & J. Dixon, 2003a), and discusses the clinical utility of the RAPS.

Method
The RAPS was administered to 373 normal adults. Tests were analyzed to assess the impact of demographic, psychometric, and other factors on performance on the RAPS. To determine the effects of strategy selection on test scores, participants were assigned to novel, category-focused, or mixed strategy groups based on the types of first questions asked.

Results
Normal participants exhibited a range of performance levels on the RAPS. Participants in the novel strategy group performed significantly better than the participants in 2 other strategy groups.

Conclusions
The RAPS is a clinically useful tool to examine problem solving that is easy to administer and to score. Findings suggest clinicians can use the RAPS with greater confidence than was the case 4 years ago. The RAPS is now part of the public domain and may be used by clinicians to assess clients' problem-solving deficits.
Poisson approximation for significance in genome-wide ChIP-chip tiling arrays
Authors: Zhang Yu 
Published: October 2008

AbstractMotivation: A genome-wide ChIP-chip tiling array study requires millions of simultaneous comparisons of hybridization for significance. Controlling the false positive rate in genome-wide tiling array studies is very important, because the number of computationally identified regions can easily go beyond the capability of experimental verification. No accurate and efficient method exists for evaluating statistical significance in tiling arrays. The Bonferroni method is overly conservative and the permutation test is time consuming for genome-wide studies.Result: Motivated by the Poisson clumping heuristic, we propose an accurate and efficient method for evaluating statistical significance in genome-wide ChIP-chip tiling arrays. The method works accurately for any large number of multiple comparisons, and the computational cost for evaluating P-values does not increase with the total number of tests. Based on a moving window approach, we demonstrate how to combine results using various window sizes to increase the detection power while maintaining a specified type I error rate. We further introduce a new false discovery rate control that is more appropriate in measuring the false proportion of binding intervals in tiling array analysis. Our method is general and can be applied to many large-scale genomic and genetic studies.Availability: http://www.stat.psu.edu/~yuzhang/pass.tarContact: yuzhang@stat.psu.edu
Modularity of cellular networks shows general center-periphery polarization
Authors: Vinogradov Alexander E. 
Published: October 2008

Abstract
The modular biology is supposed to be a bridge from the molecular to the systems biology. Using a new approach, it is shown here that the protein interaction networks of yeast Saccharomyces cerevisiae and bacteria Escherichia coli consist of two large-scale modularity layers, central and peripheral, separated by a zone of depressed modularity. This finding based on the analysis of network topology is further supported by the discovery that there are many more Gene Ontology categories (terms) and KEGG biochemical pathways that are overrepresented in the central and peripheral layers than in the intermediate zone. The categories of the central layer are mostly related to nuclear information processing, regulation and cell cycle, whereas the peripheral layer is dealing with various metabolic and energetic processes, transport and cell communication. A similar center-periphery polarization of modularity is found in the protein domain networks (‘built-in interactome’) and in a powergrid (as a non-biological example). These data suggest a ‘polarized modularity’ model of cellular networks where the central layer seems to be regulatory and to use information storage of the nucleus, whereas the peripheral layer seems devoted to more specialized tasks and environmental interactions, with a complex ‘bus’ between the layers.
Contact: aevin@mail.cytspb.rssi.ru
Supplementary information: Supplementary data are available at Bioinformatics online.
AUGIST: inferring species trees while accommodating gene tree uncertainty
Authors: Oliver Jeffrey C. 
Published: October 2008

Abstract
Summary: AUGIST (accomodating uncertainty in genealogies while inferring species tress) is a new software package for inferring species trees while accommodating uncertainty in gene genealogies. It is written for the Mesquite software system and provides sampling procedures to incorporate uncertainty in gene tree reconstruction while providing confidence estimates for inferred species trees.
Availability: http://www.lycaenid.org/augist/
Contact: jeffrey.oliver@yale.edu
BASH: a tool for managing BeadArray spatial artefacts
Authors: Cairns J. M. , Dunning M. J. , Ritchie M. E. , Russell R. , Lynch A. G. 
Published: October 2008

Abstract
Summary: With their many replicates and their random layouts, Illumina BeadArrays provide greater scope fordetecting spatial artefacts than do other microarray technologies. They are also robust to artefact exclusion, yet there is a lack of tools that can perform these tasks for Illumina. We present BASH, a tool for this purpose. BASH adopts the concepts of Harshlight, but implements them in a manner that utilizes the unique characteristics of the Illumina technology. Using bead-level data, spatial artefacts of various kinds can thus be identified and excluded from further analyses.
Availability: The beadarray Bioconductor package (version 1.10 onwards), www.bioconductor.org
Contact: andy.lynch@cancer.org.uk
Supplementary information: Additional information and a vignette are included in the beadarray package.
CS-8958, a Prodrug of the New Neuraminidase Inhibitor R-125489, Shows Long-Acting Anti-Influenza Virus Activity
Authors: Yamashita Makoto , Tomozawa Takanori , Kakuta Masayo , Tokumitsu Akane , Nasu Hatsumi , Kubo Shuku 
Published: October 2008

ABSTRACT

Two neuraminidase (NA) inhibitors, zanamivir (Relenza) and oseltamivir phosphate (Tamiflu), have been licensed for the treatment of and prophylaxis against influenza. In this paper, the new potent NA inhibitor R-125489 is reported for the first time. R-125489 inhibited the NA activities of various type A and B influenza viruses, including subtypes N1 to N9 and oseltamivir-resistant viruses. The survival effect of R-125489 was shown to be similar to that of zanamivir when administered intranasally in a mouse influenza virus A/Puerto Rico/8/34 infection model. Moreover, we found that the esterified form of R-125489 showed improved efficacy compared to R-125489 and zanamivir, depending on the acyl chain length, and that 3-(
O
)-octanoyl R-125489 (CS-8958) was the best compound in terms of its life-prolonging effect (
P
< 0.0001, compared to zanamivir) in the same infection model. A prolonged survival effect was observed after a single administration of CS-8958, even if it was given 7 days before infection. It is suggested that intranasally administered CS-8958 works as a long-acting NA inhibitor and shows in vivo efficacy as a result of a single intranasal administration.
Polysorbate 80 Inhibition ofPseudomonas aeruginosaBiofilm Formation and Its Cleavage by the Secreted Lipase LipA
Authors: Toutain-Kidd Christine M. , Kadivar Samoneh C. , Bramante Carolyn T. , Bobin Stephen A. , Zegans Michael E. 
Published: October 2008

ABSTRACTSurface-associated bacterial communities known as biofilms are an important source of nosocomial infections. Microorganisms such asPseudomonas aeruginosacan colonize the abiotic surfaces of medical implants, leading to chronic infections that are difficult to eradicate. Our study demonstrates that polysorbate 80 (PS80), a surfactant commonly added to food and medicines, is able to inhibit biofilm formation byP. aeruginosaon a variety of surfaces, including contact lenses. Many clinical isolates ofP. aeruginosa, as well as gram-negative and gram-positive clinical isolates, were also inhibited in their ability to form biofilms in the presence of PS80. AP. aeruginosamutant able to form biofilms in the presence of this surfactant was identified and characterized, and it was revealed that this mutant overexpresses a lipase, LipA. Surfactants such as PS80 can be cleaved by lipases, and we demonstrate that PS80 is cleaved by LipA at its ester bond. Finally, polyethoxylated(20) oleyl alcohol, a chemical with a structure that is similar to that of PS80 but that lacks the ester bond of PS80, can inhibit the biofilm formation ofP. aeruginosastrains, including the mutant overexpressing LipA. Our results demonstrate that surfactants such as PS80 can inhibit bacterial biofilm formation on medically relevant materials at concentrations demonstrated to be safe in humans and suggest that the understanding of the mechanisms of bacterial resistance to such surfactants will be important in developing clinically effective derivatives.
The Electricidal Effect: Reduction of
Staphylococcus
and
Pseudomonas
Biofilms by Prolonged Exposure to Low-Intensity Electrical Current
Authors: del Pozo Jose L. , Rouse Mark S. , Mandrekar Jayawant N. , Steckelberg James M. , Patel Robin 
Published: October 2008

ABSTRACT

The activity of electrical current against planktonic bacteria has previously been demonstrated. The short-term exposure of the bacteria in biofilms to electrical current in the absence of antimicrobials has been shown to have no substantial effect; however, longer-term exposure has not been studied. A previously described in vitro model was used to determine the effect of prolonged exposure (i.e., up to 7 days) to low-intensity (i.e., 20-, 200-, and 2,000-microampere) electrical direct currents on
Pseudomonas aeruginosa
,
Staphylococcus aureus
, and
Staphylococcus epidermidis
biofilms. Dose- and time-dependent killing was observed. A maximum of a 6-log
10
-CFU/cm
2
reduction was observed when
S. epidermidis
biofilms were exposed to 2,000 microamperes for at least 2 days. A 4- to 5-log
10
-CFU/cm
2
reduction was observed when
S. aureus
biofilms were exposed to 2,000 microamperes for at least 2 days. Finally, a 3.5- to 5-log
10
-CFU/cm
2
reduction was observed when
P. aeruginosa
biofilms were exposed to electrical current for 7 days. A higher electrical current intensity correlated with greater decreases in viable bacteria at all time points studied. In conclusion, low-intensity electrical current substantially reduced the numbers of viable bacteria in staphylococcal or
Pseudomonas
biofilms, a phenomenon we have labeled the “electricidal effect.”
GRL-02031, a Novel Nonpeptidic Protease Inhibitor (PI) Containing a Stereochemically Defined Fused Cyclopentanyltetrahydrofuran Potent against Multi-PI-Resistant Human Immunodeficiency Virus Type 1 In Vitro
Authors: Koh Yasuhiro , Das Debananda , Leschenko Sofiya , Nakata Hirotomo , Ogata-Aoki Hiromi , Amano Masayuki , Nakayama Maki , Ghosh Arun K. , Mitsuya Hiroaki 
Published: October 2008

ABSTRACT

We generated a novel nonpeptidic protease inhibitor (PI), GRL-02031, by incorporating a stereochemically defined fused cyclopentanyltetrahydrofuran (Cp-THF) which exerted potent activity against a wide spectrum of human immunodeficiency virus type 1 (HIV-1) isolates, including multidrug-resistant HIV-1 variants. GRL-02031 was highly potent against laboratory HIV-1 strains and primary clinical isolates, including subtypes A, B, C, and E (50% effective concentration [EC
50
] range, 0.015 to 0.038 μM), with minimal cytotoxicity (50% cytotoxic concentration, >100 μM in CD4
+
MT-2 cells), although it was less active against two HIV-2 strains (HIV-2
EHO
and HIV-2
ROD
) (EC
50
, ∼0.60 μM) than against HIV-1 strains. GRL-02031 at relatively low concentrations blocked the infection and replication of each of the HIV-1
NL4-3
variants exposed to and selected by up to 5 μM of saquinavir, amprenavir, indinavir, nelfinavir, or ritonavir and 1 μM of lopinavir or atazanavir (EC
50
range, 0.036 to 0.14 μM). GRL-02031 was also potent against multi-PI-resistant clinical HIV-1 variants isolated from patients who had no response to the conventional antiretroviral regimens that then existed, with EC
50
s ranging from 0.014 to 0.042 μM (changes in the EC
50
s were less than twofold the EC
50
for wild-type HIV-1). Upon selection of HIV-1
NL4-3
in the presence of GRL-02031, mutants carrying L10F, L33F, M46I, I47V, Q58E, V82I, I84V, and I85V in the protease-encoding region and G62R (within p17), L363M (p24-p2 cleavage site), R409K (within p7), and I437T (p7-p1 cleavage site) in the
gag
-encoding region emerged. GRL-02031 was potent against a variety of HIV-1
NL4-3
-based molecular infectious clones containing a single primary mutation reported previously or a combination of such mutations, although it was slightly less active against HIV-1 variants containing consecutive amino acid substitutions: M46I and I47V or I84V and I85V. Structural modeling analysis demonstrated a distinct bimodal binding of GRL-02031 to protease, which may provide advantages to GRL-02031 in blocking the replication of a wide spectrum of HIV-1 variants resistant to PIs and in delaying the development of resistance of HIV-1 to GRL-02031. The present data warrant the further development of GRL-02031 as a potential therapeutic agent for the treatment of infections with primary and multidrug-resistant HIV-1 variants.
OPT-80 Eliminates
Clostridium difficile
and Is Sparing of
Bacteroides
Species during Treatment of
C. difficile
Infection
Authors: Louie Thomas J. , Emery Judy , Krulicki Walter , Byrne Brendan , Mah Manuel 
Published: October 2008

ABSTRACT

During a 10-day treatment for
Clostridium difficile
infection, OPT-80 and vancomycin were comparably effective in reducing
C. difficile
counts.
Bacteroides fragilis
group counts appeared unaffected with increasing dosages of OPT-80, whereas vancomycin was markedly suppressive. Retention of components of the normal microflora might lower the risk of recurrent disease.