bluuebunny/crossref_metadata_2025 huggingface dataset:
Development of a screening tool to assess the suitability of people with a disability for oral care under sedation or general anesthesia
Authors: Prabhu Neeta T. , Nunn June H. , Evans D.J. , Girdler N.M.
Published: July 2008

The aim of this study was to develop a screening tool to assess the suitability of people with disabilities for oral care in different settings. The objectives were to investigate retrospectively the uptake of general anesthetic (GA) services and use this information to develop a composite tool.

One hundred cases referred for GA were reviewed to generate data for a Delphi Panel. Patients with disabilities were the subject of a tool, devised by the Delphi Panel, to appropriately allocate patients to the most suitable care, including the patients' medical, behavioral, and social status as well as planned dental treatment complexity. A total of 124 patients, between the ages of 4 and 75 years, in seven centers were treated under sedation or GA, according to the tool. Agreement on behavior assessment between dentists and anesthesiologists was poor.

The tool has the potential to identify which people with disabilities can be effectively allocated for treatment under sedation or GA.
Development of polymorphic microsatellite markers for Cryptococcus neoformans
Authors: KARAOGLU HAYDAR , LEE CRYSTAL MAN YING , CARTER DEE , MEYER WIELAND
Published: July 2008

Cryptococcus neoformans is a haploid basidiomycetous yeast that causes life‐threatening infections in patients with and without impaired immune function. Present typing systems for C. neoformans are limited by either poor standardization or high cost. We present eleven microsatellite loci that were developed from the published genomes of C. neoformans var. neoformans, and are applicable to the varieties and hybrids within C. neoformans.
Polymorphic microsatellite markers for the Mojave desert tortoise, Gopherus agassizii
Authors: HAGERTY B. E. , PEACOCK M. M. , KIRCHOFF V. S. , TRACY C. R.
Published: July 2008

We describe primers and polymerase chain reaction (PCR) conditions to amplify 14 tri‐ and tetranucleotide microsatellite loci for the Mojave desert tortoise (Gopherus agassizii). Across three populations (87 individuals) located in the Mojave Desert, USA, the markers yielded a range of four to 33 alleles and an average observed heterozygosity of 0.733 (range 0.433 to 0.933). We neither detected linkage disequilibrium between any pair of loci nor did we find a consistent pattern of deviation from Hardy–Weinberg equilibrium. These microsatellites are designed for PCR multiplexing, and provide higher throughput capacity to aid in conservation genetics studies for this threatened species.
Isolation and characterization of microsatellite markers in Acca sellowiana (Berg) Burret
Authors: SANTOS K. L. , SANTOS M. O. , LABORDA P. R. , SOUZA A. P. , PERONI N. , NODARI R. O.
Published: July 2008

Acca sellowiana has commercial potential because of the quality and the unique flavor of its fruit. Conservation of natural populations and management of breeding programmes would benefit from the availability of molecular markers that could be used to characterize levels and distribution of genetic variability. Thus, 13 microsatellite markers were developed from an enriched genomic library of A. sellowiana. They were characterized using 40 samples. The expected and observed heterozygosities ranged from 0.513 to 0.913 and from 0.200 to 0.889, respectively. These are the first microsatellite loci characterized from A. sellowiana that will contribute to improve researches on the genetic conservation, characterization and breeding.
A large panel of novel microsatellite markers for the bank vole (Myodes glareolus)
Authors: RIKALAINEN K. , GRAPPUTO A. , KNOTT E. , KOSKELA E. , MAPPES T.
Published: July 2008

We describe a set of 66 highly polymorphic microsatellite loci isolated from the bank vole, Myodes (Clethrionomys) glareolus. These microsatellites were characterized for a long‐term study on periodically fluctuating density of the bank vole population in Central Finland. We detected six to 38 alleles per locus in the population sampled at two different density phases, and the levels of observed and expected heterozygosities varied between 0.17 and 1.00, and between 0.72 and 0.95, respectively. This microsatellite panel serves as an informative tool for population and molecular genetic studies.
Antiphospholipid syndrome: a systemic and multidisciplinary disease
Authors: PAGALAVAN L.
Published: July 2008

Antiphospholipid syndrome (APS) was first described by Hughes and colleagues in 1983. Since the first few initial descriptions of the syndrome, almost every organ in the body has been reported to be involved in APS. The ‘Sapporo’ criteria which has been used as the diagnostic criteria since 1999 was recently revised in Sydney before the 11th International Congress on antiphospholipid antibodies in 2006. Over the last 24 years it has evolved into a systemic and multidisciplinary disease. This article looks into the extensive multidisciplinary involvement and presentation of APS including neurology, nephrology, cardiology, respiratory medicine, obstetrics and gynecology, endocrinology, hematology, ophthalmology, dermatology, otorhinolaryngology, gastroenterology, and orthopaedics.
Effect of aquatic respiratory exercise‐based program in patients with fibromyalgia
Authors: IDE Maiza Ritomy , LAURINDO Iêda Maria Magalhães , RODRIGUES‐JÚNIOR Antônio Luiz , TANAKA Clarice
Published: July 2008

Objective:  This study assessed the effects of an aquatic respiratory exercise‐based program in patients with fibromyalgia (FMS).

Methods:  Forty women, aged between 20 and 60 years, were randomly assigned into two groups of 20 patients: the aquatic respiratory exercise‐based program (ARG) and the control group (CTL). The ARG group performed the exercise program for 1 h, four times a week, for 4 weeks which included: (i) warming‐up; (ii) respiratory exercises, consisting of five different breathing patterns, along with upper, lower limbs and trunk movements (45 min); and (iii) relaxation exercises. Both groups were included in supervised recreational activities of 1 h, once a week, for 4 weeks. Questionnaires were applied before and after intervention to assess quality of life and functional capacity (SF‐36, Fibromyalgia Impact Questionnaire [FIQ]), anxiety (Hamilton Anxiety Scale [HAS]), and quality of sleep (Pittsburg Sleep Quality Index [PSQI]). Number of tender points and pain (Visual Analogue Scale [VAS]) were also evaluated.

Results:  At baseline there was no difference between the two groups, including number of tender points and questionnaire responses. After intervention, the ARG group, compared with the CTL group, showed improvement in SF‐36 scores (physical functioning P = 0.001, bodily pain P = 0.001, vitality P = 0.009, social functioning P = 0.001, emotional role P = 0.001), in FIQ (total score P = 0.049, work missed P = 0.036, fatigue P = 0.013, morning tiredness P = 0.007) plus in VAS‐pain (P = 0.029), VAS‐dyspnea (P = 0.04), anxiety (HAS P = 0.005) and quality of sleep (PSQI P = 0.004).

Conclusions:  The short‐term aquatic respiratory exercise‐based program improved pain, quality of life, functional capacity, anxiety and quality of sleep in patients with FMS and may be a relevant addition to the treatment of these patients.
TNF‐α polymorphisms in Korean adult‐onset Still's disease patients
Authors: SUNG Yoon‐Kyoung , SEONG Sang‐Seokg , WOO Jin‐Hyun , LEE Myung‐Ho , CHUNG Won‐Tae , CHOE Jeong‐Yoon , YOO Dae‐Hyun
Published: July 2008

Aim: To investigate the role ofTNF‐αpromoter polymorphisms in the pathogenesis of Korean adult‐onset Still's disease (AOSD) patients.

Methods: DNA was isolated from blood samples collected from 58 patients with AOSD meeting Yamaguchi's criteria and 105 healthy controls.TNF‐αpromoter polymorphisms at positions –1013, –863, –857, –308 were analysed by polymerase chain reaction‐restriction fragment length polymorphism method. Genotype, allele, and estimated haplotype frequencies were compared between the AOSD group and controls.

Results: The genotype, allele distributions, and estimated haplotype frequencies of theTNF‐αpolymorphism between AOSD patients and controls were not significantly different. In addition,TNF‐αpolymorphisms did not appear to have an effect on the disease course of the Korean AOSD patients.

Conclusion: Genetic polymorphisms ofTNF‐αdo not play a significant role in the development or in their course of Korean AOSD patients.
Seven wonders in the world of rheumatology: a short story of romance, reminiscences and renaissance
Authors: PISPATI Prakash
Published: July 2008

Genesis and evolution of contemporary rheumatology is many centuries old. The lessons of medical history, its triumphs and failures, its twists and turns, have all facilitated today's science. Even in the ancient era some rheumatic diseases have been described with vivid accuracy. Among these are gout, spinal afflictions, osteoporosis and rheumatoid arthritis, as we recognize them today. Ancient systems of medicine such as Ayurveda in India led to the introduction of gold salts. Invention of the microscope paved the way to the birth of microbiology, unfolding infective, and later inflammatory diseases, cellular pathology and immunology. Progress in therapeutics was slow and physicians and rheumatologists had to borrow drugs from other medical disciplines, for example antimalarials and cytotoxics. The Nobel Prize‐winning discovery and development of cortisone was a major landmark in medicine, while also treating rheumatoid arthritis. Thanks to the advent of molecular medicine, rapid strides have been accomplished, and we now have new agents of biotechnology research. Orthopedics with computer‐assisted and robotic surgeries, are becoming almost fail‐safe for specific indications. The nature of chronic rheumatic diseases, necessitating long‐term treatments, have led to the popularity of alternative medicines. Seven significant episodes are essayed herein. Rheumatology is on the threshold of exciting medical progress, enabling the majority of rheumatic patients to enjoy enhanced quality of life.
Internalist Foundationalism and the Problem of the Epistemic Regress*
Authors: ZALABARDO JOSÉ L.
Published: July 2008

I provide a construal of the epistemic regress problem and I take issue with the contention that a foundationalist solution is incompatible with an internalist account of warrant. I sketch a foundationalist solution to the regress problem that respects a plausible version of internalism. I end with the suggestion that the strategy that I have presented is not available only to the traditional versions of foundationalism that ascribe foundational status to experiential beliefs. It can also be used to generate a version of internalist foundationalism based on reliabilist principles.
A BIOECONOMIC APPROACH TO THE FAUSTMANN–HARTMAN MODEL: ECOLOGICAL INTERACTIONS IN MANAGED FOREST
Authors: TOUZA JULIA , TERMANSEN METTE , PERRINGS CHARLES
Published: July 2008

AbstractThis paper develops a bioeconomic forestry model that makes it possible to take ecosystem services that are independent of the age structure of trees into account. We derive the Faustmann–Hartman optimal harvesting strategy as a special case. The bioeconomic model is then extended to account for the fact that forest harvesting decisions impact on other ecological resources, which provide benefits for the wider community. The paper focuses on impacts associated with disturbance caused by logging operations and habitat destruction due to tree removal. This enables us to explore the interactions between forest management and the dynamics of ecological resources. The optimal rotation rule is obtained as a variation on the traditional Faustmann–Hartman equation, where an additional term captures the potential benefits derived from the growth of the ecological resource valued at its shadow price. The steady‐state solutions to the problem and sensitivity to model parameter are identified using numerical analysis.
THE EFFECTS OF DIFFERENT STRATEGIC VARIABLES IN NONCOOPERATIVE FISHERIES GAMES
Authors: EKERHOVD NILS‐ARNE
Published: July 2008

Abstract In this paper, we use stock size, harvest quantity, and fishing effort as strategic variables. We model a two‐agent noncooperative fishery game, where the agents (nations) harvest a common fish stock. The planning horizon is infinite. The model is solved successively using one instrument at a time as the strategic variable in the game. The net present values of fishing and the escapement stock level from the three different models are compared to show how the choice of variables affects the results. The choice of strategic variable is not a trivial one, as the results are shown to be sensitive to the discounting, the stock's rate of growth, and the assumptions about the distribution of the fish in response to harvesting.
NOAH'S NONCONCAVITY: ON THE EXISTENCE OF NONTRIVIAL INTERIOR SOLUTIONS TO THE PROBLEM OF COST‐EFFECTIVE CONSERVATION PLANNING
Authors: HUNTER GREG
Published: July 2008

Abstract The idea that species loss diminishes future information flows is a cornerstone of arguments for conservation planning. In his seminal work entitled The Noah's Ark Problem, Weitzman [1998] examines the problem of cost‐effective conservation planning from a theoretical perspective accounting for the affect planning has on the expected size of the biosphere's informative potential. This paper extends Weitzman's analysis by examining how his conclusions are altered by the introduction of a conservation authority that considers the value of information contained in the biosphere. Introducing nonquasiconcave preferences for the information contained in each species substantially modifies the characterization of a cost‐effective conservation plan. In particular, I find that a cost‐effective plan generally includes partial funding for many species and funds no species completely. This investigation is motivated by theoretical contributions to the information economics literature, a laRadner and Stiglitz [1984], showing that the value function for information tends to exhibit increasing returns.
Efficacy of Oritavancin in a Murine Model of
Bacillus anthracis
Spore Inhalation Anthrax
Authors: Heine H. S. , Bassett J. , Miller L. , Bassett A. , Ivins B. E. , Lehoux D. , Arhin F. F. , Parr T. R. , Moeck G.
Published: July 2008

The inhaled form of
Bacillus anthracis
infection may be fatal to humans. The current standard of care for inhalational anthrax postexposure prophylaxis is ciprofloxacin therapy twice daily for 60 days. The potent in vitro activity of oritavancin, a semisynthetic lipoglycopeptide, against
B
.
anthracis
(MIC against Ames strain, 0.015 μg/ml) prompted us to test its efficacy in a mouse aerosol-anthrax model. In postexposure prophylaxis dose-ranging studies, a single intravenous (i.v.) dose of oritavancin of 5, 15, or 50 mg/kg 24 h after a challenge with 50 to 75 times the median lethal dose of Ames strain spores provided 40, 70, and 100% proportional survival, respectively, at 30 days postchallenge. Untreated animals died within 4 days of challenge, whereas 90% of control animals receiving ciprofloxacin at 30 mg/kg intraperitoneally twice daily for 14 days starting 24 h after challenge survived. Oritavancin demonstrated significant activity post symptom development; a single i.v. dose of 50 mg/kg administered 42 h after challenge provided 56% proportional survival at 30 days. In a preexposure prophylaxis study, a single i.v. oritavancin dose of 50 mg/kg administered 1, 7, 14, or 28 days before lethal challenge protected 90, 100, 100, and 20% of mice at 30 days; mice treated with ciprofloxacin 24 h or 24 and 12 h before challenge all died within 5 days. Efficacy in pre- and postexposure models of inhalation anthrax, together with a demonstrated low propensity to engender resistance, promotes further study of oritavancin pharmacokinetics and efficacy in nonhuman primate models.
Efficient Clearance of
Aspergillus fumigatus
in Murine Lungs by an Ultrashort Antimicrobial Lipopeptide, Palmitoyl-Lys-Ala-
d
Ala-Lys
Authors: Vallon-Eberhard Alexandra , Makovitzki Arik , Beauvais Anne , Latgé Jean-Paul , Jung Steffen , Shai Yechiel
Published: July 2008

Aspergillus fumigatus
is an opportunistic fungal pathogen responsible for invasive aspergillosis in immunocompromised individuals. The inefficiency of antifungal agents and high mortality rate resulting from invasive aspergillosis remain major clinical concerns. Recently, we reported on a new family of ultrashort cationic lipopeptides active in vitro against fungi. Mode of action studies supported a membranolytic or a detergent-like effect. Here, we screened several lipopeptides in vitro for their anti-
A. fumigatus
activity. To investigate the therapeutic properties of the selected peptides in vivo, we challenged immunosuppressed C57BL/6 wild-type mice intranasally with DsRed-labeled
A. fumigatus
conidia and subsequently treated the animals locally with the lipopeptides. Confocal microscopic analysis revealed the degradation of DsRed-labeled hyphal forms and residual conidia in the lungs of the mice. The most efficient peptide was tested further using a survival assay and was found to significantly prolong the life of the treated animals, whereas no mice survived with the current standard antifungal treatment with amphotericin B. Moreover, as opposed to the drug-treated lungs, the peptide-treated lungs did not display any toxicity of the peptide. Our results highlight the potential of this family of lipopeptides for the treatment of pulmonary invasive aspergillosis.
Identification and Biochemical Characterization of Small-Molecule Inhibitors of West Nile Virus Serine Protease by a High-Throughput Screen
Authors: Mueller Niklaus H. , Pattabiraman Nagarajan , Ansarah-Sobrinho Camilo , Viswanathan Prasanth , Pierson Theodore C. , Padmanabhan R.
Published: July 2008

West Nile virus and dengue virus are mosquito-borne flaviviruses that cause a large number of human infections each year. No vaccines or chemotherapeutics are currently available. These viruses encode a serine protease that is essential for polyprotein processing, a required step in the viral replication cycle. In this study, a high-throughput screening assay for the West Nile virus protease was employed to screen ∼32,000 small-molecule compounds for identification of inhibitors. Lead inhibitor compounds with three distinct core chemical structures (1 to 3) were identified. In a secondary screening of selected compounds, two compounds, belonging to the 8-hydroxyquinoline family (compounds A and B) and containing core structure 1, were identified as potent inhibitors of the West Nile virus protease, with
K

i

values of 3.2 ± 0.3 μM and 3.4 ± 0.6 μM, respectively. These compounds inhibited the dengue virus type 2 protease with
K

i

values of 28.6 ± 5.1 μM and 30.2 ± 8.6 μM, respectively, showing some selectivity in the inhibition of these viral proteases. However, the compounds show no inhibition of cellular serine proteases, trypsin, or factor Xa. Kinetic analysis and molecular docking of compound B onto the known crystal structure of the West Nile virus protease indicate that the inhibitor binds in the substrate-binding cleft. Furthermore, compound B was capable of inhibiting West Nile virus RNA replication in cultured Vero cells (50% effective concentration, 1.4 ± 0.4 μM; selectivity index, 100), presumably by inhibition of polyprotein processing.
PCR Detection of Type I Polyketide Synthase Genes in Myxobacteria
Authors: Komaki Hisayuki , Fudou Ryosuke , Iizuka Takashi , Nakajima Daisuke , Okazaki Koei , Shibata Daisuke , Ojika Makoto , Harayama Shigeaki
Published: July 2008

The diversity of type I modular polyketide synthase (PKS) was explored by PCR amplification of DNA encoding ketosynthase and acyltransferase domains in myxobacteria. The sequencing of the amplicons revealed that many PKS genes were distantly related to the published sequences. Thus, myxobacteria may be excellent resources for novel and diverse polyketides.
Probiotic
Lactobacillus plantarum
299v Does Not Counteract Unfavorable Phytohemagglutinin-Induced Changes in the Rat Intestinal Microbiota
Authors: Gross Gabriele , Wildner Jessica , Schonewille Arjan , Rademaker Jan L. W. , van der Meer Roelof , Snel Johannes
Published: July 2008

Application of phytohemagglutinin (PHA) in weaning feed has been suggested to stimulate intestinal epithelium maturation. In this study, PHA strongly affected the fecal bacterial population structure of rats.
Escherichia coli
overgrowth was not prevented by probiotic mannose-adhering
Lactobacillus plantarum
299v. Therefore, use of PHA in weaning feed deserves careful evaluation.
Biological Enrichment of Mycoplasma Agents by Cocultivation with Permissive Cell Cultures
Authors: Volokhov Dmitriy V. , Kong Hyesuk , George Joseph , Anderson Christine , Chizhikov Vladimir E.
Published: July 2008

In this study, we describe our results on the evaluation of the ability of different permissive mammalian cell lines to support the biological enrichment of mycoplasma species known to be bacterial contaminants of cell substrates. The study showed that this approach is able to significantly improve the efficiency of mycoplasma detection based on nucleic acid testing or biochemical technologies (e.g., MycoAlert mycoplasma detection). Of 10 different cell lines (Vero, MDBK, HEK-293, Hep-G2, CV-1, EBTr, WI-38, R9ab, MDCK, and High Five) used in the study, only MDCK cell culture was found to support the efficient growth of all the tested mycoplasmas (
Mycoplasma arginini
,
M. bovis
,
M. fermentans
,
M. gallinaceum
,
M. gallisepticum
,
M. synoviae
,
M. hominis
,
M. hyorhinis
,
M. orale
,
M. salivarium
, and
Acholeplasma laidlawii
) known to be most frequently associated with contamination of cell substrates and cell lines in research laboratories or manufacturing facilities. The infection of MDCK cells with serial dilutions of each mycoplasma species demonstrated that these common cell line contaminants can be detected reliably after 7-day enrichment in MDCK cell culture at contamination levels of 0.05 to 0.25 CFU/ml. The High Five insect cell line was also found to be able to support the efficient growth of most mycoplasma species tested, except for
M. hyorhinis
strain DBS1050. However, mycoplasma growth in insect cell culture was demonstrated to be temperature dependent, and the most efficient growth was observed when the incubation temperature was increased from 28°C to between 35 and 37°C. We believe that this type of mycoplasma enrichment is one of the most promising approaches for improving the purity and safety testing of cell substrates and other cell-derived biologics and pharmaceuticals.
Broad-Host-Range Expression Vectors with Tightly Regulated Promoters and Their Use To Examine the Influence of TraR and TraM Expression on Ti Plasmid Quorum Sensing
Authors: Khan Sharik R. , Gaines Jennifer , Roop R. Martin , Farrand Stephen K.
Published: July 2008

Experiments requiring strong repression and precise control of cloned genes can be difficult to conduct because of the relatively high basal level of expression of currently employed promoters. We report the construction of a family of vectors that contain a reengineered
lacI
q
-
lac
promoter-operator complex in which cloned genes are strongly repressed in the absence of inducer. The vectors, all based on the broad-host-range plasmid pBBR1, are mobilizable and stably replicate at moderate copy number in representatives of the alpha- and gammaproteobacteria. Each vector contains a versatile multiple cloning site that includes an NdeI site allowing fusion of the cloned gene to the initiation codon of
lacZ
α. In each tested bacterium, a
uidA
reporter fused to the promoter was not expressed at a detectable level in the absence of induction but was inducible by 10- to 100-fold, depending on the bacterium. The degree of induction was controllable by varying the concentration of inducer. When the vector was tested in
Agrobacterium tumefaciens
, a cloned copy of the
traR
gene, the product of which is needed at only a few copies per cell, did not confer activity under noninducing conditions. We used this attribute of very tight and variably regulatable control to assess the relative amounts of TraR required to activate the Ti plasmid conjugative transfer system. We identified levels of induction that gave wild-type transfer frequencies, as well as levels that induced correspondingly lower frequencies of transfer. We also used this system to show that the antiactivator TraM sets the level of intracellular TraR required for
tra
gene activation.
Gene Silencing by RNA Interference in the White Rot Fungus
Phanerochaete chrysosporium
Authors: Matityahu Avi , Hadar Yitzhak , Dosoretz Carlos G. , Belinky Paula A.
Published: July 2008

The effectiveness of RNA interference (RNAi) is demonstrated in the lignin-degrading fungus
Phanerochaete chrysosporium
. The manganese-containing superoxide dismutase gene (
MnSOD1
) was used as the target for RNAi. The plasmid constructed for gene silencing contained a transcriptional unit for hairpin RNA expression. Significantly lower
MnSOD
expression at both the mRNA and protein activity levels was detected in RNAi transformants. Furthermore, even though
P. chrysosporium
possesses three copies of the
MnSOD
gene, this RNAi construct was sufficient to decrease the enzymatic activity by as much as 70% relative to control levels. Implementation of the RNAi technique in
P. chrysosporium
provides an alternative genetic tool for studies of gene function, particularly of essential genes or gene families.
Schizosaccharomyces pombe
Noc3 Is Essential for Ribosome Biogenesis and Cell Division but Not DNA Replication
Authors: Houchens Christopher R. , Perreault Audrey , Bachand François , Kelly Thomas J.
Published: July 2008

The initiation of eukaryotic DNA replication is preceded by the assembly of prereplication complexes (pre-RCs) at chromosomal origins of DNA replication. Pre-RC assembly requires the essential DNA replication proteins ORC, Cdc6, and Cdt1 to load the MCM DNA helicase onto chromatin.
Saccharomyces cerevisiae
Noc3 (ScNoc3), an evolutionarily conserved protein originally implicated in 60S ribosomal subunit trafficking, has been proposed to be an essential regulator of DNA replication that plays a direct role during pre-RC formation in budding yeast. We have cloned
Schizosaccharomyces pombe noc3
+
(Sp
noc3
+
), the
S. pombe
homolog of the budding yeast Sc
NOC3
gene, and functionally characterized the requirement for the SpNoc3 protein during ribosome biogenesis, cell cycle progression, and DNA replication in fission yeast. We showed that fission yeast SpNoc3 is a functional homolog of budding yeast ScNoc3 that is essential for cell viability and ribosome biogenesis. We also showed that SpNoc3 is required for the normal completion of cell division in fission yeast. However, in contrast to the proposal that ScNoc3 plays an essential role during DNA replication in budding yeast, we demonstrated that fission yeast cells do enter and complete S phase in the absence of SpNoc3, suggesting that SpNoc3 is not essential for DNA replication in fission yeast.
Evolution of theRhodococcus equi vapPathogenicity Island Seen through Comparison of Host-AssociatedvapAandvapBVirulence Plasmids
Authors: Letek Michal , Ocampo-Sosa Alain A. , Sanders Mandy , Fogarty Ursula , Buckley Tom , Leadon Desmond P. , González Patricia , Scortti Mariela , Meijer Wim G. , Parkhill Julian , Bentley Stephen , Vázquez-Boland José A.
Published: July 2008

The pathogenic actinomyceteRhodococcus equiharbors different types of virulence plasmids associated with specific nonhuman hosts. We determined the complete DNA sequence of avapB+plasmid, typically associated with pig isolates, and compared it with that of the horse-specificvapA+plasmid type. pVAPB1593, a circular 79,251-bp element, had the same housekeeping backbone as thevapA+plasmid but differed over an ≈22-kb region. This variable region encompassed thevappathogenicity island (PAI), was clearly subject to selective pressures different from those affecting the backbone, and showed major genetic rearrangements involving thevapgenes. The pVAPB1593 PAI harbored five differentvapgenes (vapBandvapJto -M, withvapKpresent in two copies), which encoded products differing by 24 to 84% in amino acid sequence from the six full-lengthvapA+plasmid-encoded Vap proteins, consistent with a role for the specificvapgene complement inR. equihost tropism. Sequence analyses, including interpolated variable-order motifs for detection of alien DNA and reconstruction of Vap family phylogenetic relationships, suggested that thevapPAI was acquired by an ancestor plasmid via lateral gene transfer, subsequently evolving byvapgene duplication and sequence diversification to give different (host-adapted) plasmids. TheR. equivirulence plasmids belong to a new family of actinobacterial circular replicons characterized by an ancient conjugative backbone and a horizontally acquired niche-adaptive plasticity region.
DISCONTINUOUS GALERKIN SCHEMES FOR ISOTHERMAL LATTICE BOLTZMAN MODELS IN ONE DIMENSION
Authors: SOFONEA VICTOR
Published: July 2008

Discontinuous Galerkin schemes are introduced in an isothermal Lattice Boltzmann model in one dimension. Simulation of diffusion phenomena in a two-component system shows the reduction of the numerical diffusivity.
BOUND STATES OF THE KLEIN–GORDON EQUATION FOR WOODS–SAXON POTENTIAL WITH POSITION DEPENDENT MASS
Authors: ARDA ALTUĞ , SEVER RAMAZAN
Published: July 2008

The effective mass Klein–Gordon equation in one dimension for the Woods–Saxon potential is solved by using the Nikiforov–Uvarov method. Energy eigenvalues and the corresponding eigenfunctions are computed. Results are also given for the constant mass case.
QUANTUM ENTANGLEMENT OF THREE ATOMS INDUCED BY FOCK STATE
Authors: WANG XIUWU , ZHANG XIAOHONG
Published: July 2008

In this paper, we study the quantum entanglement of three two-level atoms under the action of Fock state of a single-mode quantized radiation field. Milburn model is considered. Concurrence of the two atoms is given explicitly. As is expected, because of the intrinsic decoherence, Concurrence comes to a stationary value. A rule is summarized between this value and entanglement sudden death. As for the potential measurement of multi-particle entanglement, spin squeezing parameter is calculated.
ROBUSTNESS IN SCALE-FREE NETWORKS: COMPARING DIRECTED AND UNDIRECTED NETWORKS
Authors: EMMERT-STREIB FRANK , DEHMER MATTHIAS
Published: July 2008

In this paper, scale-free networks and their functional robustness with respect to structural perturbations of the network are studied. Two types of perturbations are distinguished: random perturbations and attacks. The robustness of directed and undirected scale-free networks is studied numerically for two different measures and the obtained results are compared. For random perturbations, the results indicate that the strength of the perturbation plays a crucial role. In general, directed scale-free networks are more robust than undirected scale-free networks.
From privacy methods to a privacy toolbox
Authors: Iachello Giovanni , Abowd Gregory D.
Published: July 2008

We describe the two-year-long development and evaluation of the Proportionality Method, a design method intended to aid HCI practitioners in designing advanced IT applications with complex privacy implications. The method is inspired by Data Protection Authorities' (DPA) and Courts' practice and proposes to balance the impact on privacy of IT applications with their usefulness. We discuss the results of an evaluation of the design method to verify its usability, usefulness and effectiveness vis-à-vis other design methods proposed in the HCI literature to address similar issues. Results suggest that different design methods for privacy highlight different sets of issues and a combination of methods should be employed in a comprehensive design process. We propose to judge design methods based on their overall quantitative and qualitative merits, including the type of application and technology for which they are most fit and their methodological approach. We finally propose to develop a privacy toolbox, that is, a set of heuristic methods that designers can choose from with knowledge and understanding of their relative advantages and limitations.
Static analysis tools for security checking in code at Motorola
Authors: Krishnan R , Nadworny Margaret , Bharill Nishil
Published: July 2008

As part of an overall initiative to improve the security aspects in the software used in Motorola's products, training and secure coding standards were developed. The goal is to decrease the number of security vulnerabilities introduced during the coding phase of the software development process. This paper describes the creation of the secure coding standards and the efforts to automate as many of the standards as possible.

Originally, the efforts focused on the
Inforce
tool from Klocwork, as many Motorola business units already used the tool for quality but without the security flags activated. This paper describes the efforts to evaluate, extend, and create the coverage for the secure coding standards with Klocwork. More recently, an opportunity arose which allowed a team to evaluate other static analysis tools as well. This paper also describes the findings from that evaluation.
Gem #2: Limited types in Ada 2005 --- <> notation in aggregates
Authors: Duff Bob
Published: July 2008

Ada Gem #2 --- The <> notation may be used in aggregates to request the default value for certain components.
Gem #5: Key-based searching in set containers
Authors: Heaney Matthew
Published: July 2008

Ada Gem #5 --- Sets are containers of elements. Like all containers, they are searchable, and given an element value you can find the element in the set equivalent to that value. For some applications, element equivalence is determined by just a part of the element (its "key" part), and it is often necessary to find an element given only a key value. A technique is presented here for key-based searching of elements in set containers.
Gem #7: The beauty of numeric literals in Ada
Authors: Gasperoni Franco
Published: July 2008

Ada Gem #7 --- Did you know that the marvels of Ada extend to integer and real numbers (numeric literals really). Read on to learn about this Ada gem.
Gem #8: Factory functions
Authors: Heaney Matthew
Published: July 2008

Ada Gem #8 --- A factory function is a technique for constructing an object from one class given only an object in some other class. The technique is used to implement assignment for objects having a class-wide type, such that tag-mismatch exceptions cannot occur.
Theory research at Google
Authors: Aggarwal Gagan , Ailon Nir , Constantin Florin , Even-Dar Eyal , Feldman Jon , Frahling Gereon , Henzinger Monika R. , Muthukrishnan S. , Nisan Noam , Pál Martin , Sandler Mark , Sidiropoulos Anastasios
Published: July 2008

Through the history of Computer Science, new technologies have emerged and generated fundamental problems of interest to theoretical computer scientists. From the era of telecommunications to computing and now, the Internet and the web, there are many such examples. This article is derived from the emergence of web search and associated technologies, and focuses on the problems of research interest to theoretical computer scientists that arise, in particular at Google.
On distributed computing principles in systems research
Authors: Keidar Idit
Published: July 2008

Distributed systems are increasingly deployed in the real world nowadays. Concepts like high-availability, disaster recovery, service-oriented architectures, grid computing, and peer-to-peer are now a standard part of a software engineer's vocabulary. Data is often stored on remote servers or disks, and redundancy is employed for fault-tolerance and high availability. Even computations on a single machine are becoming increasingly parallel due to the advent of multi-core architectures, as discussed in the previous Distributed Computing Column.
Distributed computing in SOSP and OSDI
Authors: Clement Allen
Published: July 2008

SOSP, the
ACM Symposium on Operating Systems Principles
, and OSDI, the
USENIX Symposium no Operating System Design and Implementation
, are "the world's premier forum for researches, developers, programmers, vendors, and teachers of operating systems technology" according to the SOSP home page. While it may seem odd to discuss operating systems conferences in a column dedicated to distributed computing, the proceedings of the last few SOSP and OSDI's have included numerous papers focused on topics more traditionally associated with distributed computing---primarily transactions, Byzantine fault tolerance, and large distributed systems. In this article we highlight papers from the last 3 years of SOSP and OSDI that are especially relevant to the distributed computing community, identifying areas where the distributed computing community was clearly ahead of its time and others where it was not.
Modularity
Authors: Friedman Roy , Kermarrec Anne-Marie , Raynal Michel
Published: July 2008

Decomposing distributed systems into modules, each with a precise interface and a functional implementation independent specification, is highly effective both from a software engineering point of view and for theoretical purposes. The usefulness of this approach has been demonstrated in the past in several areas of distributed computing. Yet, despite its attractiveness, so far work on peer to peer systems failed to do so. This paper argues in favor of this approach and advocates such a decomposition for peer to peer systems. This allows designers to understand and explain both what a system does and how it does it.
Vancomycin-Induced DRESS Syndrome in a Female Patient
Authors: Vauthey Laetitia , Uçkay Ilker , Abrassart Sophie , Bernard Louis , Assal Mathieu , Ferry Tristan , Djordjevic Marina , Roussos Constantinos , Vaudaux Pierre
Published: July 2008

Background: DRESS syndrome (drug rash with eosinophilia and systemic symptoms) is a hypersensitivity reaction with skin rashes, eosinophilia, fever, lymph node enlargement and internal organ involvement. Case Report: A 60-year-old diabetic woman was hospitalized at the University Hospitals of Geneva for mid-leg amputation due to peripheral arterial occlusive disease. No drug allergy was reported. Because of a wound infection by methicillin-resistant Staphylococcus aureus, treatment with vancomycin (2 g/day) in continuous perfusion was initiated. Approximately 2 weeks later, she developed a toxidermia with fever, a progressive maculopapular skin rash, eosinophilia and acute renal insufficiency. The skin biopsy revealed a necrosis with lymphocytic and eosinophilic infiltrations, supporting the suspicion of DRESS syndrome. A cure was achieved by the withdrawal of vancomycin and the administration of methylprednisolone (1 g/day), antihistaminics and topical mometasone, without the introduction of other antibiotics. Conclusion: Vancomycin can be a cause of DRESS syndrome. A high index of suspicion is warranted in order not to miss this potentially lethal disease.
Metastatic Squamous Cell Carcinoma of the Ankle in Long-Standing Untreated Acrodermatitis Chronica Atrophicans
Authors: Leverkus M. , Finner A.M. , Pokrywka A. , Franke I. , Gollnick H.
Published: July 2008

Acrodermatitis chronica atrophicans (ACA) represents the persistent late stage of borreliosis in which Borrelia species may survive for decades. Occasionally, B-cell lymphoma may develop in these patients, and additional neoplastic complications such as basal cell carcinoma or squamous cell carcinoma (SCC) have been reported once each over the past 60 years. Here we describe, to the best of our knowledge, the first case of metastatic SCC in a European patient with long-standing ACA caused by Borrelia burgdorferi sensu stricto. Our case highlights a potential pathophysiological connection of untreated Borrelia infection with the initiation or progression of SCC and should alert dermatologists to this rare complication.
Mechanisms of Preejection and Postejection Velocity Spikes in Left Ventricular Myocardium
Authors: Remme Espen W. , Lyseggen Erik , Helle-Valle Thomas , Opdahl Anders , Pettersen Eirik , Vartdal Trond , Ragnarsson Asgrimur , Ljosland Morten , Ihlen Halfdan , Edvardsen Thor , Smiseth Otto A.
Published: July 2008

Background—

Normal left ventricular myocardium demonstrates distinct spikes in the velocity trace before and after left ventricular ejection. We tested the hypothesis that the preejection and postejection velocity spikes reflect early systolic shortening and late systolic lengthening that are interrupted by mitral and aortic valve closure, respectively.

Methods and Results—

In 11 anesthetized dogs, timing of valve closure was determined by pressure variables; left ventricular dimensions were determined by sonomicrometry. Myocardial shortening started 20±10 ms (mean±SD;
P
<0.001) before mitral valve closure and was interrupted at the time of mitral valve closure (time difference, 4±7 ms). Similarly, myocardial lengthening started 31±15 ms (
P
<0.001) before aortic valve closure and was interrupted at the time of aortic valve closure (time difference, 0±3 ms). Prevention of mitral (n=4) and aortic (n=4) valve closure by stenting the valves abolished the preejection and postejection velocity spikes, respectively. Echocardiographic measurements of patients (n=15) with severe mitral regurgitation showed that the preejection velocity spike was reduced after prosthetic valve replacement (43±25 versus 32±15 mm/s;
P
=0.036), indicating that preejection shortening was larger with a leaking valve. Similarly, late systolic lengthening was reduced in patients (n=15) with severe aortic regurgitation after prosthetic valve replacement; minimum postejection velocity spike was increased from −32±11 to −17±11 mm/s;
P
=0.0003). Asynchronous onset of contraction/relaxation and atrioventricular interaction were investigated as alternative mechanisms of the velocity spikes in dogs and patient groups but were found implausible.

Conclusions—

This study supports the hypothesis that normal left ventricular preejection and postejection velocity spikes are attributed to valve closures that interrupt early systolic shortening and late systolic lengthening, respectively.
Proteinase Activity and Receptor Cleavage
Authors: DeLano Frank A. , Schmid-Schönbein Geert W.
Published: July 2008

Arterial hypertension is associated with organ dysfunctions, but the mechanisms are uncertain. We hypothesized that enhanced proteolytic activity in the microcirculation of spontaneously hypertensive rats (SHRs) may be a pathophysiological mechanism causing cell membrane receptor cleavage and examine this for 2 different receptors. Immunohistochemistry of matrix-degrading metalloproteinases (matrix metalloproteinase [MMP]-9) protein shows enhanced levels in SHR microvessels, mast cells, and leukocytes compared with normotensive Wistar-Kyoto rats. In vivo microzymography shows cleavage by MMP-1 and -9 in SHRs that colocalizes with MMP-9 and is blocked by metal chelation. SHR plasma also has enhanced protease activity. We demonstrate with an antibody against the extracellular domain that the insulin receptor-α density is reduced in SHRs, in line with elevated blood glucose levels and glycohemoglobin. There is also cleavage of the binding domain of the leukocyte integrin receptor CD18 in line with previously reported reduced leukocyte adhesion. Blockade of MMPs with a broad-acting inhibitor (doxycycline, 5.4 mg/kg per day) reduces protease activity in plasma and microvessels; blocks the proteolytic cleavage of the insulin receptor, the reduced glucose transport; normalizes blood glucose levels and glycohemoglobin levels; and reduces blood pressure and enhanced microvascular oxidative stress of SHRs. The results suggest that elevated MMP activity leads to proteolytic cleavage of membrane receptors in the SHR, eg, cleavage of the insulin receptor-binding domain associated with insulin resistance.
Marked Regional Left Ventricular Heterogeneity in Hypertensive Left Ventricular Hypertrophy Patients
Authors: Biederman Robert W.W. , Doyle Mark , Young Alistair A. , Devereux Richard B. , Kortright Eduardo , Perry Gilbert , Bella Jonathan N. , Oparil Suzanne , Calhoun David , Pohost Gerald M. , Dell'Italia Louis J.
Published: July 2008

Concentric hypertensive left ventricular (LV) hypertrophy is presumed to be a symmetrical process. Using MRI-derived intramyocardial strain, we sought to determine whether segmental deformation was also symmetrical, as suggested by echocardiography. High echocardiographic LV relative wall thickness in hypertensive LV hypertrophy allows preserved endocardial excursion despite depressed LV midwall shortening (MWS). Depressed MWS is an adverse prognostic indicator, but whether this is related to global or regional myocardial depression is unknown. We prospectively compared MWS derived from linear echocardiographic dimensions with MR strain(∈) in septal and posterior locations in 27 subjects with ECG LV hypertrophy in the Losartan Intervention for Endpoint Reduction in Hypertension Study. Although MRI-derived mass was higher in patients than in normal control subjects (124.0±38.6 versus 60.5±13.2g/m
2
;
P
<0.001), fractional shortening (30±5% versus 33±3%) and end-systolic stress (175±22 versus 146±28 g/cm
2
) did not differ between groups. However, mean MR(∈) was decreased in patients versus normal control subjects (13.9±6.8% versus 22.4±3.5%), as was echo MWS (13.4±2.8% versus 18.2±1.4%; both
P
<0.001). For patients versus normal control subjects, posterior wall(∈) was not different (17.8±7.1% versus 21.6±4.0%), whereas septal(∈) was markedly depressed (10.1±6.6% versus 23.2±3.4%;
P
<0.001). Although global MWS by echocardiography or MRI is depressed in hypertensive LV hypertrophy, MRI tissue tagging demonstrates substantial regional intramyocardial strain(∈) heterogeneity, with most severely depressed strain patterns in the septum. Although posterior wall 2D principal strain was inversely related to radius of curvature, septal strain was not, suggesting that factors other than afterload are responsible for pronounced myocardial strain heterogeneity in concentric hypertrophy.
Area-Specific Differences in Transmitter Release in Central Catecholaminergic Neurons of Spontaneously Hypertensive Rats
Authors: Teschemacher Anja G. , Wang Sheng , Raizada Mohan K. , Paton Julian F.R. , Kasparov Sergey
Published: July 2008

The link among blood pressure, sympathetic output, and brain neurons producing catecholamines is well documented. Nevertheless, their intrinsic properties and any alterations in signaling characteristics between normotensive and hypertensive phenotypes remain unknown. Here, we directly compared neurophysiological properties of catecholamine release of C1 and A2 neurons of the spontaneously hypertensive rat and Wistar rat in organotypic slices. C1 and A2 areas were studied because both are widely implicated in the pathophysiology of hypertension. Catecholaminergic neurons were visualized using viral vectors to express green fluorescent protein. Microamperometry revealed that C1 axonal varicosities of spontaneously hypertensive but not normotensive Wistar rats release a transmitter predominantly (≈86%) in very large quanta, comparable in catecholamine load to adrenal chromaffin granules. Because quantal size affects the spread of transmitter in the extracellular space, this may enhance the impact of C1 varicosities on their downstream targets and increase sympathetic drive in the hypertensive rat. Electrophysiological properties and Ca
2+
handling were studied using patch clamp and confocal imaging. Although overall electrophysiological characteristics of C1 and A2 neurons were comparable between strains, the characteristic angiotensin-II–induced Ca
2+
mobilization was reduced in A2 neurons of the spontaneously hypertensive rat. Because A2 neurons are a part of a homeostatic antihypertensive circuit, this could reduce their restraining influence on blood pressure. Thus, we have revealed an increased quantal size in C1 varicosities and a reduced responsiveness of A2 neurons of the spontaneously hypertensive rat to angiotensin II. Both effects could contribute to elevated sympathetic activity and blood pressure in the spontaneously hypertensive rat.