bluuebunny/crossref_metadata_2025 huggingface dataset:
Investigation on the Effect of Immune Selection on Resistance to Bactericidal Antibodies to Group B Meningococci In Vitro
Authors: Santos George F. , Giuliani Marzia , Santini Laura , Adu-Bobie Jeanette , Pizza Mariagrazia , Rappuoli Rino , Wacknov William , Donnelly John
Published: August 2009

The induction of resistance by immune selective pressure to bactericidal antibodies from humans immunized with Novartis recombinant meningococcal group B vaccines was assessed. Serum bactericidal antibody titers against selected bacteria were within assay variability through a selection event frequency of 1 in 10
−5
. No change in antigen expression was observed by Western blotting.
Interaction between Host Cells and SepticemicSalmonella entericaSerovar Typhimurium Isolates from Pigs
Authors: Bergeron Nadia , Corriveau Jonathan , Letellier Ann , Daigle France , Lessard Louise , Quessy Sylvain
Published: August 2009

Salmonella entericaserovar Typhimurium is an important pathogen in swine and is also a frequently reported zoonotic agent. The objective of this study was to characterize isolates ofS. entericaserovar Typhimurium associated with septicemia in swine and to compare them to isolates recovered from clinically healthy pigs. We were particularly interested in comparing the two groups of isolates for their ability to adhere to and invade host cells, to be phagocytized and survive in monocyte cells, to induce apoptosis, and to adhere to intestinal mucus. Their surface properties were also evaluated by interactions with solvents. The isolates recovered from diseased animals were shown to invade intestinal epithelial cell lines at a higher rate (P= 0.003) than isolates from healthy pigs. Septicemic isolates were phagocytized by human monocytes at a higher rate than isolates from healthy pigs (P= 0.009). The mean percentages of phagocytosis were significantly lower for human monocytes than for porcine monocytes (P= 0.02 andP= 0.008, respectively) for isolates from both diseased and healthy animals. Healthy animal isolates were phagocytized more by porcine monocytes at 15 min (P= 0.02) than septicemic isolates. No difference between isolates from septicemic pigs and isolates from healthy pigs was detected for other tested parameters. These results suggest that septicemic isolates have a particular pattern of invasion.
Improved Multiple-Locus Variable-Number Tandem-Repeat Assay for
Staphylococcus aureus
Genotyping, Providing a Highly Informative Technique Together with Strong Phylogenetic Value
Authors: Pourcel Christine , Hormigos Katia , Onteniente Lucie , Sakwinska Olga , Deurenberg Ruud H. , Vergnaud Gilles
Published: August 2009

We describe an improved
m
ultiple-
l
ocus
v
ariable-
n
umber
t
andem-
r
epeat (VNTR)
a
nalysis (MLVA) scheme for genotyping
Staphylococcus aureus
. We compare its performance to those of
m
ulti
l
ocus
s
equence
t
yping (MLST) and
spa
typing in a survey of 309 strains. This collection includes 87 epidemic methicillin-resistant
S. aureus
(MRSA) strains of the Harmony collection, 75 clinical strains representing the major MLST clonal complexes (CCs) (50 methicillin-sensitive
S. aureus
[MSSA] and 25 MRSA), 135 nasal carriage strains (133 MSSA and 2 MRSA), and 13 published
S. aureus
genome sequences. The results show excellent concordance between the techniques' results and demonstrate that the discriminatory power of MLVA is higher than those of both MLST and
spa
typing. Two hundred forty-two genotypes are discriminated with 14 VNTR loci (diversity index, 0.9965; 95% confidence interval, 0.9947 to 0.9984). Using a cutoff value of 45%, 21 clusters are observed, corresponding to the CCs previously defined by MLST. The variability of the different tandem repeats allows epidemiological studies, as well as follow-up of the evolution of CCs and the identification of potential ancestors. The 14 loci can conveniently be analyzed in two steps, based upon a first-line simplified assay comprising a subset of 10 loci (panel 1) and a second subset of 4 loci (panel 2) that provides higher resolution when needed. In conclusion, the MLVA scheme proposed here, in combination with available on-line genotyping databases (including
http://mlva.u-psud.fr/
), multiplexing, and automatic sizing, can provide a basis for almost-real-time large-scale population monitoring of
S. aureus
.
Comparison of the Xpert Methicillin-Resistant
Staphylococcus aureus
(MRSA) Assay, BD GeneOhm MRSA Assay, and Culture for Detection of Nasal and Cutaneous Groin Colonization by MRSA
Authors: Kelley P. G. , Grabsch E. A. , Howden B. P. , Gao W. , Grayson M. L.
Published: August 2009

Detection of methicillin (meticillin)-resistant
Staphylococcus aureus
colonization was assessed using combined nose and groin swabs in two commercial PCR assays (the Xpert MRSA assay and the BD GeneOhm MRSA assay). Compared to routine culture, both had similar sensitivities (87.0% versus 84.8%, respectively) and specificities (93.8% versus 92.7%, respectively). Combined PCR assays provide a rapid and more-complete assessment of colonization at a cost similar to that of single-site analysis.
Cross-Sectional and Longitudinal Multilocus Sequence Typing of
Pseudomonas aeruginosa
in Cystic Fibrosis Sputum Samples
Authors: Waine David J. , Honeybourne David , Smith E. Grace , Whitehouse Joanna L. , Dowson Chris G.
Published: August 2009

Multilocus sequence typing (MLST) is a genetic typing tool designed to provide information about the relatedness of isolates at the core genome level. The utility of MLST in regard to cystic fibrosis (CF)-related infection with
Pseudomonas aeruginosa
is unknown. The molecular clock speed of the MLST genes was studied using 219 colonies isolated longitudinally from 49 patients with CF. A cross-sectional study examining 27 to 46 colonies per sputum sample for samples from 16 patients was also undertaken. The molecular clock speed was estimated to be 2.05 × 10
−5
(upper 95% confidence limit) or 4.75 × 10
−6
(50% confidence limit) point mutations per nucleotide per year. In the cross-sectional study, 50% of patients were infected with more than one sequence type. There was evidence of point mutations, recombination events, and coinfection with epidemic and unique strains. A clonal complex that was highly genetically distinct from the rest of the
P. aeruginosa
population was identified. The MLST scheme uses genes with an appropriate clock speed and provides useful information about the genetic variation of
P. aeruginosa
within and between patients with CF.
Comparison of Fingerprinting Methods for Typing Methicillin-ResistantStaphylococcus aureusSequence Type 398
Authors: Rasschaert G. , Vanderhaeghen W. , Dewaele I. , Janež N. , Huijsdens X. , Butaye P. , Heyndrickx M.
Published: August 2009

This study evaluates the multiple-locus variable-number tandem-repeat assay (MLVA) and pulsed-field gel electrophoresis (PFGE) when using restriction enzymes BstZI, SacII, and ApaI to fingerprint a diverse collection of methicillin (meticillin)-resistantStaphylococcus aureus(MRSA) sequence type 398 (ST398) isolates. These isolates had been characterized previously by multilocus sequence typing,spatyping, and staphylococcal cassette chromosomemec(SCCmec) typing. Typeability and discriminatory power were analyzed, and the concordance between the various methods was determined. All MRSA ST398 isolates were typeable by the MLVA and PFGE using BstZI, SacII, and ApaI. With each method, the MRSA ST398 isolates formed a separate group from the two non-ST398 MRSA strains. PFGE, performed with any of the three restriction enzymes, had the most discriminatory power, followed by MLVA,spatyping, and SCCmectyping. The MLVA showed the highest concordance with PFGE using ApaI andspatyping. As further expressed by the Wallace coefficient, the MLVA type was poorly predicted byspatyping, whereas thespatype was well predicted by MLVA. PFGE, using a combination of all three restriction enzymes, had the highest concordance with the MLVA but had a low probability of being predicted by MLVA. PFGE, using a combination of all three restriction enzymes, was able to predict SCCmectype and MLVA type completely and had a high probability of predictingspatype. Both the MLVA and PFGE could be used to discriminate among the MRSA ST398 isolates. Although the MLVA is a faster technique, PFGE had more discriminatory power than the MLVA, especially when a combination of restriction enzymes was used.
Population Structure Dynamics of
Mycobacterium tuberculosis
Beijing Strains during Past Decades in Japan
Authors: Iwamoto Tomotada , Fujiyama Riyo , Yoshida Shiomi , Wada Takayuki , Shirai Chika , Kawakami Yasuto
Published: August 2009

We used 909 strains to compare the population structures of the
Mycobacterium tuberculosis
Beijing family between different birth-year cohorts in Japan. The results revealed that the spread of a modern sublineage that has high transmissibility is currently increasing, while the spread of an ancient sublineage, STK, has significantly decreased in younger generations.
Immediate Incubation of Blood Cultures Outside Routine Laboratory Hours of Operation Accelerates Antibiotic Switching
Authors: Kerremans J. J. , van der Bij A. K. , Goessens W. , Verbrugh H. A. , Vos M. C.
Published: August 2009

The aim of this prospective randomized controlled clinical trial was to assess the impact of immediate incubation of blood cultures delivered to the laboratory outside its hours of operation on turnaround times, antibiotic prescription practices, and patient outcomes. A continuously monitoring blood culture incubator was placed outside the laboratory, which was switched on (intervention arm) and off (control arm) in a randomized manner. Included were new bacteremia episodes of patients older than 18 years. During the 30-week study period, the first positive blood culture specimen of an episode had to be brought to the laboratory outside its hours of operation. The median time from specimen collection until growth detection was reduced by 10.1 h in the intervention arm (
P
< 0.001). For 46 of 66 (70%) episodes in the intervention arm and for 51 of 85 (60%) episodes in the control arm, the antibiotic regimen was changed (not significant). The median time until the first change in the antibiotic regimen was 42.8 h in the intervention arm and 64.0 h in the control arm (
P
, 0.024). There was no difference in length of stay or hospital mortality. Immediate incubation of blood cultures outside laboratory hours reduces turnaround times and accelerates antibiotic switching.
Implanted-Port-Catheter-Related Sepsis Caused byAcidovorax avenaeand Methicillin-SensitiveStaphylococcus aureus
Authors: Malkan Alpin D. , Strollo Wendy , Scholand Stephen J. , Dudrick Stanley J.
Published: August 2009

Acidovorax avenaeis a gram-negative rod in the familyComamonadaceaeand a phytopathogen found in the environment. Human infections caused by members of theComamonadaceaeare extremely rare. We report a case of implanted-port-catheter-related sepsis caused byAcidovorax avenaeand methicillin (meticillin)-sensitiveStaphylococcus aureus(MSSA).
In Vitro Susceptibility of Clinical Isolates of
Aspergillus
spp. to Anidulafungin, Caspofungin, and Micafungin: a Head-to-Head Comparison Using the CLSI M38-A2 Broth Microdilution Method
Authors: Pfaller M. A. , Boyken L. , Hollis R. J. , Kroeger J. , Messer S. A. , Tendolkar S. , Diekema D. J.
Published: August 2009

We determined the in vitro activities of anidulafungin, caspofungin, and micafungin against 526 isolates of
Aspergillus
spp. (64
A. flavus
, 391
A. fumigatus
, 46
A. niger
, and 25
A. terreus
isolates) collected from over 60 centers worldwide from 2001 through 2007. Susceptibility testing was performed according to the CLSI M38-A2 method. All three echinocandins—anidulafungin (50% minimum effective concentration [MEC
50
], 0.007 μg/ml; MEC
90
, 0.015 μg/ml), caspofungin (MEC
50
, 0.015 μg/ml; MEC
90
, 0.03 μg/ml), and micafungin (MEC
50
, 0.007 μg/ml; MEC
90
, 0.015 μg/ml)—were very active against
Aspergillus
spp. More than 99% of all isolates were inhibited by ≤0.06 μg/ml of all three agents.
Bimolecular Complementation of Paramyxovirus Fusion and Hemagglutinin-Neuraminidase Proteins Enhances Fusion: Implications for the Mechanism of Fusion Triggering
Authors: Connolly Sarah A. , Leser George P. , Jardetzky Theodore S. , Lamb Robert A.
Published: August 2009

For paramyxoviruses, entry requires a receptor-binding protein (hemagglutinin-neuraminidase [HN], H, or G) and a fusion protein (F). Like other class I viral fusion proteins, F is expressed as a prefusion metastable protein that undergoes a refolding event to induce fusion. HN binding to its receptor triggers F refolding by an unknown mechanism. HN may serve as a clamp that stabilizes F in its prefusion state until HN binds the target cell (the “clamp model”). Alternatively, HN itself may undergo a conformational change after receptor binding that destabilizes F and causes F to trigger (the “provocateur model”). To examine F-HN interactions by bimolecular fluorescence complementation (BiFC), the cytoplasmic tails of parainfluenza virus 5 (PIV5) F and HN were fused to complementary fragments of yellow fluorescent protein (YFP). Coexpression of the BiFC constructs resulted in fluorescence; however, coexpression with unrelated BiFC constructs also produced fluorescence. The affinity of the two halves of YFP presumably superseded the F-HN interaction. Unexpectedly, coexpression of the BiFC F and HN constructs greatly enhanced fusion in multiple cell types. We hypothesize that the increase in fusion occurs because the BiFC tags bring F and HN together more frequently than occurs in a wild-type (wt) scenario. This implies that normally much of wt F is not associated with wt HN, in conflict with the clamp model for activation. Correspondingly, we show that wt PIV5 fusion occurs in an HN concentration-dependent manner. Also inconsistent with the clamp model are the findings that BiFC F does not adopt a postfusion conformation when expressed in the absence of HN and that HN coexpression does not provide resistance to the heat-induced triggering of F. In support of a provocateur model of F activation, we demonstrate by analysis of the morphology of soluble F trimers that the hyperfusogenic mutation S443P has a destabilizing effect on F.
Foot-and-Mouth Disease Virus Assembly: Processing of Recombinant Capsid Precursor by Exogenous Protease Induces Self-Assembly of Pentamers In Vitro in a Myristoylation-Dependent Manner
Authors: Goodwin Stewart , Tuthill Tobias J. , Arias Armando , Killington Richard A. , Rowlands David J.
Published: August 2009

The assembly of foot-and-mouth disease virus (FMDV) particles is poorly understood. In addition, there are important differences in the antigenic and receptor binding properties of virus assembly and dissociation intermediates, and these also remain unexplained. We have established an experimental model in which the antigenicity, receptor binding characteristics, and in vitro assembly of capsid precursor can be studied entirely from purified components. Recombinant capsid precursor protein (P1 region) was expressed inEscherichia colias myristoylated or unmyristoylated protein. The protein sedimented in sucrose gradients at 5S and reacted with monoclonal antibodies which recognize conformational or linear antigen determinants on the virion surface. In addition, it bound the integrin αvβ6, a cellular receptor for FMDV, indicating that unprocessed recombinant capsid precursor is both structurally and antigenically similar to native virus capsid. These characteristics were not dependent on the presence of 2A at the C terminus but were altered by N-terminal myristoylation and in mutant precursors which lacked VP4. Proteolytic processing of myristoylated precursor by recombinant FMDV 3Cproin vitro induced a shift in sedimentation from 5S to 12S, indicating assembly into pentameric capsid subunits. Nonmyristoylated precursor still assembled into higher-order structures after processing with 3Cpro, but these particles sedimented in sucrose gradients at approximately 17S. In contrast, mutant precursors lacking VP4 were antigenically distinct, were unable to form pentamers, and had reduced capacity for binding integrin receptor. These studies demonstrate the utility of recombinant capsid precursor protein for investigating the initial stages of assembly of FMDV and other picornaviruses.
Analysis of Protein Levels of 24 Cytokines in Scrapie Agent-Infected Brain and Glial Cell Cultures from Mice Differing in Prion Protein Expression Levels
Authors: Tribouillard-Tanvier Déborah , Striebel James F. , Peterson Karin E. , Chesebro Bruce
Published: August 2009

Activation of microglia and astroglia is seen in many neurodegenerative diseases including prion diseases. Activated glial cells produce cytokines as a protective response against certain pathogens and as part of the host inflammatory response to brain damage. In addition, cytokines might also exacerbate tissue damage initiated by other processes. In the present work using multiplex assays to analyze protein levels of 24 cytokines in scrapie agent-infected C57BL/10 mouse brains, we observed elevation of CCL2, CCL5, CXCL1, CXCL10, granulocyte-macrophage colony-stimulating factor (GM-CSF), gamma interferon (IFN-γ), interleukin 1α (IL-1α), IL-1β, IL-6, and IL-12p40. Scrapie agent-infected wild-type mice and transgenic mice expressing anchorless prion protein (PrP) had similar cytokine responses in spite of extensive differences in neuropathology. Therefore, these responses may be primarily a reaction to brain damage induced by prion infection rather than specific inducers of a particular type of pathology. To study the roles of astroglia and microglia in these cytokine responses, primary glial cultures were exposed to scrapie agent-infected brain homogenates. Microglia produced only IL-12p40 and CXCL10, whereas astroglia produced these cytokines plus CCL2, CCL3, CCL5, CXCL1, G-CSF, IL-1β, IL-6, IL-12p70, and IL-13. Glial cytokine responses from wild-type mice and transgenic mice expressing anchorless PrP differed only slightly, but glia from PrP-null mice produced only IL-12p40, indicating that PrP expression was required for scrapie agent induction of other cytokines detected. The difference in cytokine response between microglia and astroglia correlated with 20-fold-higher levels of PrP expression in astroglia versus microglia, suggesting that high-level PrP expression on astroglia might be important for induction of certain cytokines.
Identification of RNA Helicase A as a New Host Factor in the Replication Cycle of Foot-and-Mouth Disease Virus
Authors: Lawrence Paul , Rieder Elizabeth
Published: August 2009

Foot-and-mouth disease virus (FMDV), as with other RNA viruses, recruits various host cell factors to assist in the translation and replication of the virus genome. In this study, we investigated the role of RNA helicase A (RHA) in the life cycle of FMDV. Immunofluorescent microscopy (IFM) showed a change in the subcellular distribution of RHA from the nucleus to the cytoplasm in FMDV-infected cells as infection progressed. Unlike nuclear RHA, the RHA detected in the cytoplasm reacted with an antibody that recognizes only the nonmethylated form of RHA. In contrast to alterations in the subcellular distribution of nuclear factors observed during infection with the related cardioviruses, cytoplasmic accumulation of RHA did not require the activity of the FMDV leader protein. Using IFM, we have found cytoplasmic RHA in proximity to the viral 2C and 3A proteins, which promotes the assembly of the replication complexes, as well as cellular poly(A) binding protein (PABP). Coimmunoprecipitation assays confirmed that these proteins are complexed with RHA. We have also identified a novel interaction between RHA and the S fragment in the FMDV 5′ nontranslated region. Moreover, a reduction in the expression of RHA, using RHA-specific small interfering RNA constructs, inhibited FMDV replication. These results indicate that RHA plays an essential role in the replication of FMDV and potentially other picornaviruses through ribonucleoprotein complex formation at the 5′ end of the genome and by interactions with 2C, 3A, and PABP.
Synthesis and properties of ladder-type 1,4-dihydro-1,4-phosphasilins
Authors: Ren Yi , Linder Thomas , Baumgartner Thomas
Published: August 2009

The synthesis and advanced characterization of a series of extended dithieno[2,3-b:3′,2′-e][1,4-dihydro-1,4]phosphasilins is reported, and their suitability as new building blocks for organic electronics is evaluated. Synthesis of basic, as well as benzo-extended dithienophosphasilins, can be achieved using appropriate 2,3-dibromothiophene precursors in a two-step protocol introducing the silicon and phosphorus centers subsequently. Both ladder-type materials show the typical reactivity of trivalent phosphorus species and can quantitatively be converted into the corresponding oxides or gold complexes, the latter exemplified with the basic dithienophosphasilin. Their optoelectronic properties were found to be inferior to those of related dithieno[3,2-b:2′,3′-d]phospholes, indicating a disruption of the π-conjugation in the molecular scaffold. X-ray crystallographic studies revealed that the molecular scaffold is planar in the oxidized benzo-extended material, whereas the basic dithieno materials show some small deviation from planarity. Density functional theory calculations suggest all materials to be planar, with the exception of the benzo-extended trivalent phosphasilin. This structure–property study illustrates that the disruption of the π-conjugation in the molecular scaffold of the extended phosphasilins is exclusively due to the presence of the silicon center and its electronic effects, rather than structural features.
Phenolic constituents of Phellodendron chinense bark
Authors: Li Xue-Hu , Zhang Wen-Juan , Qi Huan-Yang , Shi Yan-Ping
Published: August 2009

The bark of Phellodendron chinense is a very important herbal medicine in traditional Chinese medicine. In a detailed phytochemical investigation, a new phenolic lactone, 2β,3β-dihydroxy-3α-vanilloylmethyl-γ-lactone (named as phellolactone) (1), and nine known phenolic compounds (2–10) were isolated from the bark of P. chinense Schneid. Their structures were characterized by spectroscopic methods, including IR, UV, HR-ESI-MS, NMR, and chemical transformation analysis.
In situ high-pressure study of ammonia borane by Raman and IR spectroscopy
Authors: Xie Shuntai , Song Yang , Liu Zhenxian
Published: August 2009

Pressure-induced structural transformations of the ammonia borane complex (NH3·BH3) were investigated in diamond anvil cells by Raman spectroscopy and synchrotron IR spectroscopy up to 14 GPa at room temperature. Starting with a disordered tetragonal structure, NH3·BH3 is found to undergo several transformations upon compression as monitored by in situ Raman measurements. These transformations are indicated by the sequential changes of characteristic Raman modes as well as by the pressure dependence of these modes. Synchrotron IR absorption spectroscopy provided supplementary and consistent information about the structural evolution of NH3·BH3 under compression. Decompression measurements on NH3·BH3 suggest the pressure-induced transformations are reversible in the entire pressure region. The combined Raman and IR data allowed analysis of possible high-pressure structures of NH3·BH3. Our study significantly complements previous high-pressure Raman studies by providing new information on the structures and stabilities of NH3·BH3.
BURSTS OF LOW-ENERGY ELECTRON–POSITRON PAIRS IN TeV-RANGE COLLIDER PHYSICS
Authors: GIACOSA FRANCESCO , HOFMANN RALF
Published: August 2009

In this letter we investigate the possible emission of low-energy electron neutrinos and electron–positron pairs of anomalously large multiplicity in close-to-central pp collisions at LHC. The scenario is based on confining SU(2) Yang–Mills dynamics of Hagedorn temperature ~ me = 511 keV being responsible for the emergence of the lightest lepton family and the weak interactions of the Standard Model. Although cut off by LHC's detectors these electron–positron bursts would be seen indirectly by a large defect energy and thus an anomalously strong decrease of events with interesting high-energy secondaries for increasing [Formula: see text]. This is because the formation of superconducting (preconfining) SU(2) hot-spots "steals" a large fraction of [Formula: see text] subsequently transferring it to a thermal spectrum of electron neutrinos, electrons, and positrons liberated through evaporation. We thus propose the detection of electrons and positrons of kinetic energy ~ me and photons of energy ~ 2me.
A NEW ATTACK ON SCALE-FREE NETWORKS BASED ON CASCADING FAILURES
Authors: YU KAI , RONG LILI , WANG JIANWEI
Published: August 2009

In this paper, based on the local information about nodes, we propose a new attack strategy, considering the average degree of the node's neighboring nodes. Adopting the cascading model proposed in Chin. Phys. Lett.25(10) (2008) 3826, we investigate the effect of the new attack strategy for the robustness against cascading failures on a typical network, i.e. BA scale-free networks. Compared with two attacks on the nodes with the highest load or the lowest load, numerically we find that our presented attack is the most efficient way to destruct the BA scale-free networks in the case of α ≤ 0.6, where α is a tunable parameter and determines to the load strength of a node. In addition, we also find that the efficiency of the new attack strategy is more obvious near the parameter α = 0.5. We expect our findings to provide insights into the protection of the key nodes for real-life networks to avoid cascading-failure-induced disasters.
COHERENT BREMSSTRAHLUNG IN PERIODICALLY DEFORMED CRYSTALS WITH A COMPLEX BASE
Authors: MKRTCHYAN A. R. , SAHARIAN A. A. , PARAZIAN V. V.
Published: August 2009

In the present paper, we investigate coherent bremsstrahlung of high energy electrons moving in a periodically deformed single crystal with a complex base. The formula for corresponding differential cross-section is derived for an arbitrary deformation field. The conditions are discussed under which the influence of the deformation is important. The case is considered in detail when the electron enters into the crystal at small angles with respect to a crystallographic axis. It is shown that in dependence of the parameters, the presence of the deformation can either enhance or reduce the bremsstrahlung cross-section.
PHONON DYNAMICS AND THERMODYNAMICAL PROPERTIES OF ALKALI METAL DOPED C60 COMPOUNDS
Authors: VARSHNEY DINESH , JAIN RAJENDRA K. , RANJAN K. , DHARAMVIR KEYA , JINDAL V. K.
Published: August 2009

The present paper deals with the comprehensive studies of phonon dynamics in alkali metal (M) doped C 60 ( MC 60) solids in fcc phase using a rigid ion model with pairwise interionic interaction potential. The investigations include the computation of the phonon density of states, the specific heat, the Gruneisen parameters, thermal expansion and thermal expansion coefficient and the phonon-dispersion curves of RbC 60. The analysis incorporates the van der Waal's and Coulomb interactions for alkali metal– C 60 as well C 60– C 60 molecule and show fairly good agreement with reported inelastic neutron scattering results for RbC 60. We have found that thermal expansion coefficient at room temperature is in the range 4.3–6.2 × 10-5 K -1, which is of the order of pure C 60 solid (6.1 × 10-5 K -1). Comparing the thermal expansion coefficient of different alkali-doped solids, we conclude that doping decreases anharmonicity in general, and further it decreases with increase in size of the alkali metal. The results have been found to present an overall consistent interpretation of the available experimental data.
DETERMINING A SET OF MAXIMUM INSCRIBED RECTANGLES FOR LABEL PLACEMENT IN A REGION
Authors: GAVRILOVA MARINA L.
Published: August 2009

Driven by the industrial challenge of labeling maps for GIS applications, we investigate the problem of computing a map region P such that a rectangular axis-parallel label L of a given size can be placed in it. The map region to be labeled is in general a non-convex n-gon which may contain holes. We first derive a new practical algorithm based on the sweep-line technique that determines the com set of Maximum Inscribed Rectangles (MIRs) in P in O(nk), where k is the size of the output, for the case when the polygon sides have an axis-parallel orientation. After the set of MIRs has been found, any subsequent query on label L placement runs in only O(logn) time. We then provide an algorithm to convert the general case to the axis-parallel case. Extensive experimentation in both laboratory and industrial settings confirms that the developed method is practical and highly efficient for processing large GIS data sets.
GUARD PLACEMENT FOR MAXIMIZING L-VISIBILITY EXTERIOR TO A CONVEX POLYGON
Authors: BARDHAN DEBABRATA , ROY SANSANKA , DAS SANDIP
Published: August 2009

Two points a and b are said to be L-visible among a set of polygonal obstacles if the length of the shortest path from a to b avoiding these obstacles is no more than L. For a given convex polygon P with n vertices, Gewali et al.1 addressed the guard placement problem on the boundary of P that covers the maximum area outside to the polygon under L-visibility with P as obstacle. Their proposed algorithm runs in O(n) time if [Formula: see text], where π(P) denotes the perimeter of P. They conjectured that if [Formula: see text], then the problem can be solved in subquadratic time. In this paper, we settle the conjecture in the affirmative sense, by proposing an easy to implement linear time algorithm for any arbitrary value of L.
Responses of Humid Tropical Trees to Rising CO2
Authors: Körner Christian
Published: August 2009

Although no mature tropical tree had ever been exposed to an experimentally CO2-enriched atmosphere, evidence from works with seedlings and saplings, theory, models, and proxy data suggest effects on biodiversity and enhanced forest dynamics. Tropical forest carbon stocking is unlikely to increase, given that carbon pool size is driven by tree and patch demography, with tree longevity unlikely to increase. Unlike epiphytes, tropical lianas are likely to play a more important role in a CO2-rich future.
The Role of Propagule Pressure in Biological Invasions
Authors: Simberloff Daniel
Published: August 2009

Although most studies of factors contributing to successful establishment and spread of non-native species have focused on species traits and characteristics (both biotic and abiotic), increasing empirical and statistical evidence implicates propagule pressure—propagule sizes, propagule numbers, and temporal and spatial patterns of propagule arrival—as important in both facets of invasion. Increasing propagule size enhances establishment probability primarily by lessening effects of demographic stochasticity, whereas propagule number acts primarily by diminishing impacts of environmental stochasticity. A continuing rain of propagules, particularly from a variety of sources, may erase or vitiate the expected genetic bottleneck for invasions initiated by few individuals (as most are), thereby enhancing likelihood of survival. For a few species, recent molecular evidence suggests ongoing propagule pressure aids an invasion to spread by introducing genetic variation adaptive for new areas and habitats. This phenomenon may also explain some time lags between establishment of a non-native species and its spread to become an invasive pest.
Learning in Financial Markets
Authors: Pastor Lubos , Veronesi Pietro
Published: August 2009

We survey the recent literature on learning in financial markets. Our main theme is that many financial market phenomena that appear puzzling at first sight are easier to understand once we recognize that parameters in financial models are uncertain and subject to learning. We discuss phenomena related to the volatility and predictability of asset returns, stock price bubbles, portfolio choice, mutual fund flows, trading volume, and firm profitability, among others.
Protection from diclofenac-induced small intestinal injury by the JNK inhibitor SP600125 in a mouse model of NSAID-associated enteropathy
Authors: Ramirez-Alcantara Veronica , LoGuidice Amanda , Boelsterli Urs A.
Published: August 2009

Small intestinal ulceration, bleeding, and inflammation are major adverse effects associated with the use of diclofenac (DCF) or other nonsteroidal anti-inflammatory drugs (NSAIDs). The underlying mechanisms of DCF enteropathy are poorly understood, but there is increasing evidence that topical effects are involved. The aim of this study was to explore the role of c-Jun- N-terminal kinase (JNK) in DCF-induced enterocyte death because JNK not only regulates mitochondria-mediated apoptosis but also is a key node where many of the proximal stress signals converge. Male C57BL/6J mice were injected intraperitoneally with DCF or vehicle (Solutol HS-15), and the extent of small intestinal ulceration was determined. A single dose of DCF (60 mg/kg) produced numerous ulcers in the third and fourth quartiles of the jejunum and ileum, with maximal effects after 18 h and extensive recovery after 48 h. To study the molecular pathways leading to enterocyte injury, we isolated villi-enriched mucosal fractions from DCF-treated mice. Immunoblot studies with a phosphospecific JNK antibody revealed that JNK1/2 (p46) was activated at 6 h, leading to phosphorylation of the downstream target c-Jun. The levels of the JNK-regulated proapoptotic transcription factor C/EBP homologous protein (CHOP) were also increased after DCF. The selective JNK inhibitor SP600125 (30 mg/kg ip), given both 1 h before and 1 h after DCF, blocked JNK kinase activity and afforded significant protection against DCF enteropathy. In conclusion, these data demonstrate that the JNK pathway is critically involved in the pathogenesis of DCF-induced enteropathy and suggest a potential application of JNK inhibitors in the prevention of NSAID-induced enteropathy.
Thermogenic activity of the Ca2+-ATPase from blue marlin heater organ: regulation by KCl and temperature
Authors: da Costa Danielly Cristiny Ferraz , Landeira-Fernandez Ana Maria
Published: August 2009

This work shows that vesicles derived from the blue marlin heater organ retain a sarcoplasmic reticulum (SR) Ca2+-ATPase that can interconvert different forms of energy. During the hydrolysis of ATP part of the energy is always converted into heat, and the other part can be converted into work (Ca2+transport) or heat, depending on the temperature and the presence of KCl in the reaction medium. At 15°C, where KCl stimulates the activity approximately threefold, measurements of the amount of heat released per mole of ATP hydrolyzed (ΔHcal) show similar values (approximately −11 kcal/mol) in the presence or absence of a Ca2+gradient. At 25°C, KCl activates the enzyme to the same extent as at 15°C, but inhibits the production of extra heat by SR Ca2+-ATPase when a Ca2+gradient is built up across the membrane. The ΔHcalvalues found in the presence of a Ca2+-gradient were −26.2 ± 2.9 kcal/mol ( n = 7) in control experiments and −16.1 ± 1.5 ( n = 14) in the presence of 100 mM KCl. At 35°C, KCl has a smaller effect (∼1.5-fold) on activating the enzyme. Similar to SR Ca2+-ATPase from mammals, at this temperature the enzyme produces almost twice the amount of heat per mole of ATP hydrolyzed in the presence of a Ca2+gradient and KCl has no effect at all on this increment. These data suggest that the marlin SR Ca2+-ATPase may play an important role in heater organ thermogenesis and that KCl has the potential for regulating the heat production catalyzed by the enzyme.
Transglutaminase-1 protects renal epithelial cells from hydrogen peroxide-induced apoptosis through activation of STAT3 and AKT signaling pathways
Authors: Ponnusamy Murugavel , Pang Maoyin , Annamaraju Pavan Kumar , Zhang Zhu , Gong Rujun , Chin Y. Eugene , Zhuang Shougang
Published: August 2009

Our recent studies showed that transglutaminase-1 (TGase-1) is uniquely expressed in mouse renal proximal tubular cells (RPTC) and mediates cell proliferation. In this study, we investigated the role of TGase-1 in cell survival and the survival signaling pathways regulated by TGase-1 in RPTC following oxidant injury. Exposure of RPTC to hydrogen peroxide (H2O2) resulted in apoptosis and an increase in TGase activity. Inhibition of TGase activity with monodansylcadervine (MDC), a TGase inhibitor, or knockdown of TGase-1 with small interference (si)RNA enhanced apoptosis and decreased cell survival in H2O2-treated RPTC. Conversely, overexpression of TGase-1 rendered RPTC more resistant to H2O2toxicity and MDC treatment blocked this response. Concurrent with RPTC apoptosis, phosphorylation of AKT, signal transducer and activator of transcription-3 (STAT3), and glucogen synthase kinase-3β (GSK-3β) were observed. Pretreatment of cells with MDC or TGase-1 siRNA inhibited phosphorylation of all these molecules. Inhibition of either the AKT or STAT3 pathway potentiated H2O2-induced cell death and increased GSK-3β activity by dephosphorylation at serine 9. Furthermore, treatment with GSK-3β inhibitors reduced H2O2-induced apoptosis and abolished the death-promoting effect of AKT and STAT3 inhibition. Therefore, we have identified TGase-1 as a novel survival factor in renal epithelial cells and it contributes to cell survival through activation of the AKT and STAT3 signaling pathways following oxidant injury.
Changing the “When” and “What” of Intended Actions
Authors: Obhi Sukhvinder S. , Matkovich Shannon , Chen Robert
Published: August 2009

Humans often have to modify the timing and/or type of their planned actions on the basis of new sensory information. In the present experiments, participants planned to make a right index finger keypress 3 s after a warning stimulus but on some trials were interrupted by a temporally unpredictable auditory tone prompting the same action ( experiment 1) or a different action ( experiment 2). In experiment 1, by comparing the reaction time (RT) to tones presented at different stages of the preparatory period to RT in a simple reaction time condition, we determined the cost of switching from an internally generated mode of response production to an externally triggered mode in situations requiring only a change in when an action is made (i.e., when the tone prompts the action at a different time from the intended time of action). Results showed that the cost occurred for interruption tones delivered 200 ms after a warning stimulus and remained relatively stable throughout most of the preparatory period with a reduction in the magnitude of the cost during the last 200 ms prior to the intended time of movement. In experiment 2, which included conditions requiring a change in both when and what action is produced on the tone, results show a larger cost when the switched to action is different from the action being prepared. We discuss our results in the light of neurophysiological experiments on motor preparation and suggest that intending to act is accompanied by a general inhibitory mechanism preventing premature motor output and a specific excitatory process pertaining to the intended movement. Interactions between these two mechanisms could account for our behavioral results.
Question of Reference Frames: Visual Direction-Selective Neurons in the Accessory Optic System of Goldfish
Authors: Masseck Olivia Andrea , Hoffmann Klaus-Peter
Published: August 2009

We investigated if visual direction-selective neurons in the pretectal area (APT) of goldfish ( Carassius auratus auratus) preferred visual stimuli resulting from rotations around axes corresponding to the best responsive axes of the semicircular canals [optic flow that is consistent to a maximal activation of the horizontal canal pair (yaw), to a maximal activation of the right anterior/left posterior semicircular canal pair (RALP), and to a maximal activation of the left anterior/right posterior semicircular canal pair (LARP)]. Our sample of neurons recorded in the left pretectum had two preferred axes of rotation: first, rotation around the yaw axis and second, rotation around the RALP axis. Both axes of rotation correspond to best responsive axes of the semicircular canals. For this reason, coding in a reference frame defined by the vestibular system or the pulling direction of the eye muscles is suggested. In our population of recorded APT neurons, we did not find segregation of different preferred axes of rotation into different anatomical structures. Furthermore in all axes no bias for clockwise or counterclockwise rotations was obvious. This is particularly noteworthy for the yaw axis because preference for temporo-nasal and naso-temporal rotations was found at the same recording side. Hence we conclude that in fish the accessory optic system may consist of one nucleus on each side of the midbrain only, the APT. Segregation into different nuclei coding for different axes and different senses of rotation probably first developed in amphibians.
Transient Firing of Dorsal Raphe Neurons Encodes Diverse and Specific Sensory, Motor, and Reward Events
Authors: Ranade Sachin P. , Mainen Zachary F.
Published: August 2009

Serotonin (5-hydroxytryptamine [5-HT]) is known to influence a wide range of behaviors and physiological processes, but relatively little is known about events that trigger 5-HT release. To address this issue, we recorded from neurons in the dorsal raphe nucleus (DRN) in rats performing an odor-guided spatial decision task. A large fraction of DRN neurons showed transient firing time locked to behavioral events on timescales as little as 20 ms. DRN transients were sometimes correlated with reward parameters, but also encoded specific sensorimotor events, including stimulus identity and response direction. These behavioral correlates were diverse but showed no apparent relationship with waveform or other firing properties indicative of neurochemical identity. These results suggest that the 5-HT system does not encode a unitary signal and that it will broadcast specific information to the forebrain with speed and precision sufficient not only to modulate but also to dynamically sculpt ongoing information processing.
Beyond the Reward Pathway: Coding Reward Magnitude and Error in the Rat Subthalamic Nucleus
Authors: Lardeux Sylvie , Pernaud Remy , Paleressompoulle Dany , Baunez Christelle
Published: August 2009

It was recently shown that subthalamic nucleus (STN) lesions affect motivation for food, cocaine, and alcohol, differentially, according to either the nature of the reward or the preference for it. The STN may thus code a reward according to its value. Here, we investigated how the firing of subthalamic neurons is modulated during expectation of a predicted reward between two possibilities (4 or 32% sucrose solution). The firing pattern of neurons responding to predictive cues and to reward delivery indicates that STN neurons can be divided into subpopulations responding specifically to one reward and less or giving no response to the other. In addition, some neurons (“oops” neurons) specifically encode errors as they respond only during error trials. These results reveal that the STN plays a critical role in ascertaining the value of the reward and seems to encode that value differently depending on the magnitude of the reward. These data highlight the importance of the STN in the reward circuitry of the brain.
Investigation of the Variability of Cloud Condensation Nuclei Concentrations at the Surface in Western North Dakota
Authors: Detwiler Andrew , Langerud Darin , Depue Tracy
Published: August 2009

Daily observations of cloud condensation nuclei (CCN) were made for three summer months in 2005 at a site in rural western North Dakota. The goal was to define the natural background CCN population characteristics and to lay the groundwork for investigating the potential impact of intentionally modifying clouds in this region using hygroscopic cloud-seeding techniques. Concentrations of CCN active at ∼0.5% supersaturation, averaged over several midday hours on each day, ranged from less than 200 to more than 1700 cm−3. This is similar to variability in CCN concentrations that have been observed in past studies in other rural areas of the central and northern high plains of the United States. At this site, only 2 out of 17 days with active convection at that site were characterized by concentrations of less than 300 cm−3 active at 0.5% supersaturation, indicating that the region is characterized by typically continental CCN populations on most convective days. Operational seeding might be more effectively conducted if CCN population characteristics could be forecast based on source regions for air forecast to arrive in a particular region on a particular day. However, back-trajectory calculations were found to have limited use for predicting CCN concentrations based on prior history of the air arriving at this observation site during this period.
Simulations of Polarimetric Radar Signatures of a Supercell Storm Using a Two-Moment Bulk Microphysics Scheme
Authors: Jung Youngsun , Xue Ming , Zhang Guifu
Published: August 2009

A new general polarimetric radar simulator for nonhydrostatic numerical weather prediction (NWP) models has been developed based on rigorous scattering calculations using the T-matrix method for reflectivity, differential reflectivity, specific differential phase, and copolar cross-correlation coefficient. A continuous melting process accounts for the entire spectrum of varying density and dielectric constants. This simulator is able to simulate polarimetric radar measurements at weather radar frequency bands and can take as input the prognostic variables of high-resolution NWP model simulations using one-, two-, and three-moment microphysics schemes. The simulator was applied at 10.7-cm wavelength to a model-simulated supercell storm using a double-moment (two moment) bulk microphysics scheme to examine its ability to simulate polarimetric signatures reported in observational studies. The simulated fields exhibited realistic polarimetric signatures that include ZDR and KDP columns, ZDR arc, midlevel ZDR and ρhυ rings, hail signature, and KDP foot in terms of their general location, shape, and strength. The authors compared the simulation with one employing a single-moment (SM) microphysics scheme and found that certain signatures, such as ZDR arc, midlevel ZDR, and ρhυ rings, cannot be reproduced with the latter. It is believed to be primarily caused by the limitation of the SM scheme in simulating the shift of the particle size distribution toward larger/smaller diameters, independent of mixing ratio. These results suggest that two- or higher-moment microphysics schemes should be used to adequately describe certain important microphysical processes. They also demonstrate the utility of a well-designed radar simulator for validating numerical models. In addition, the simulator can also serve as a training tool for forecasters to recognize polarimetric signatures that can be reproduced by advanced NWP models.
Mesoscale Eddy–Internal Wave Coupling. Part II: Energetics and Results from PolyMode
Authors: Polzin Kurt L.
Published: August 2009

The issue of internal wave–mesoscale eddy interactions is revisited. Previous observational work identified the mesoscale eddy field as a possible source of internal wave energy. Characterization of the coupling as a viscous process provides a smaller horizontal transfer coefficient than previously obtained, with vh ≅ 50 m2 s−1 in contrast to νh ≅ 200–400 m2 s−1, and a vertical transfer coefficient bounded away from zero, with νυ + ( f 2/N 2)Kh ≅ 2.5 ± 0.3 × 10−3 m2 s−1 in contrast to νυ + ( f 2/N 2)Kh = 0 ± 2 × 10−2 m2 s−1. Current meter data from the Local Dynamics Experiment of the PolyMode field program indicate mesoscale eddy–internal wave coupling through horizontal interactions (i) is a significant sink of eddy energy and (ii) plays an O(1) role in the energy budget of the internal wave field.