bluuebunny/crossref_metadata_2025 huggingface dataset:
Using a two‐phase sowing approach in restoration: sowing foundation species to restore, and subordinate species to evaluate restoration success
Authors: Coiffait‐Gombault Clémentine , Buisson Elise , Dutoit Thierry
Published: January 2012

Questions

Is it possible to restore a target herbaceous plant community on ex‐arable land by sowing foundation species? What is the impact of sheep grazing on the restoration of this ecosystem? How can we rapidly evaluate the success of restoration methods?

Location

Nature reserve of the plain of La Crau, southeast France (43° 31′ N, 4° 50′ E)

Methods

In an ex‐arable field, we sowed an indigenous species mix in 2007. This was composed of two perennial species dominant in the reference grassland ecosystem (Brachypodium retusum, Thymus vulgaris) and one annual species (Trifolium subterraneum) also found on the reference grassland and which is well‐known for its ability to quickly cover bare soil. These three species are called foundation species as they play an essential role in structuring the restored ecosystem community. To investigate the significances of the foundation species on community dynamics, four subordinate species were sown 1 yr later: Taeniatherum caput‐medusae, Linum strictum, Evax pygmaea and Asphodelus ayardii. The subordinate species are typical plants of the reference grassland which describe well this vegetation type.

Results

Sowing foundation species was an effective means of reintroducing them. Their presence in the ex‐arable field very rapidly promoted establishment of grassland species and impeded establishment of weeds. When grazing was excluded, the foundation species covered the ground, particularly with Trifolium subterraneum, which reached 54% ground cover. Subordinate species established better on the foundation species sown treatment and on the grazed treatment.

Conclusion

In the short term, sowing indigenous foundation species and maintaining grazing seems to be a good method to restore grassland plant communities that have a poor ability to re‐establish spontaneously. This study also demonstrates that sowing and monitoring of subordinate species is an effective method to rapidly test whether a particular restoration protocol will have a positive effect on community assembly and development.
Disaster triage tags: Is one better than another?
Authors: Varshney Kavita , Mallows James , Hamd Mohind
Published: January 2012

Objective: To determine which of the disaster triage tag systems in use in Australia and New Zealand is better in terms of the time taken to complete the triage and the ease of use.

Methods: A disaster scenario was created. Mock patients were provided with clinical information to allow them to be triaged in a disaster sieve. Six different triage tag systems available in Australia and New Zealand were trialled. Participants triaged 10 patients with each triage tag system. The 10 patients used were different for each of the tag systems and were standardized for acuity and triage category. The time to complete the triage of the 10 patients with each different tag system was measured. The participants then completed a questionnaire with regards to the ease of use of the different tags and were asked to nominate their most preferred tag.

Results: The Victorian cruciate fold up tag was the quickest to complete, with an average of 6.6 min to triage 10 patients, compared with an average time for all systems of 7.8 min. New Zealand tags were found to be the easiest to use, easiest to fill in and were considered the most preferred tag.

Conclusion: The Victorian style of tag was found to be the most efficient in terms of the time to complete a triage. The New Zealand tags were the easiest to use, easiest to fill in and the most preferred tag by the participants. We recommend that one of these tags be adapted for use as a nationwide system.
Calabi‐Yau manifolds and their degenerations
Authors: Tosatti Valentino
Published: January 2012

Calabi‐Yau manifolds are geometric objects of central importance in several branches of mathematics, including differential geometry, algebraic geometry, and mathematical physics. In this paper, we give a brief introduction to the subject aimed at a general mathematical audience and present some of our results that shed some light on the possible ways in which families of Calabi‐Yau manifolds can degenerate.
The effect of galectins on leukocyte trafficking in inflammation: sweet or sour?
Authors: Cooper Dianne , Iqbal Asif J. , Gittens Beatrice R. , Cervone Carmela , Perretti Mauro
Published: January 2012

The trafficking of leukocytes from the blood stream to the surrounding tissue is a fundamental feature of an inflammatory response. Although many of the adhesion molecules and chemokines that direct leukocyte trafficking have been identified, there is still much to be discovered, particularly with regard to the persistence of leukocyte infiltrates in chronic inflammation. Elucidating the molecular mechanisms involved in this process is critical to understanding and treating inflammatory pathologies. Recent studies have identified members of the galectin family as immunoregulatory proteins. Included among the actions of galectins are modulatory effects, both positive and negative, on leukocyte recruitment. The focus of this review is to summarize current knowledge on the role of galectins in leukocyte trafficking during inflammation. A better understanding of the function of this family of endogenous lectins will open new avenues for innovative drug discovery.
DisseminatedScedosporium prolificansinfection in a German Shepherd dog
Authors: Haynes SM , Hodge PJ , Tyrrell D , Abraham LA
Published: January 2012

DisseminatedScedosporium prolificansinfection in a 1‐year‐old female spayed German Shepherd dog is described. Clinical signs were predominantly associated with fungal pyelonephritis and the organism was cultured from the urine. The dog was treated with itraconazole and later, terbinafine was added. Subsequent antifungal susceptibility testing of the isolate showed it to be resistant to all available antifungal drugs. The dog was euthanased because of acute abdominal haemorrhage and associated clinical deterioration. Postmortem examination revealed extensive pyogranulomas containing fungal organisms in the renal parenchyma, myocardium, bone marrow, skeletal muscle, liver, lung, spleen, multiple lymph nodes and pancreas.
Transection of the lateral and long digital extensor tendons in racehorses
Authors: Elliott CRB , Vasey JR , Russell TM
Published: January 2012

Objective To report on the outcome of wounds to the hindlimb of racehorses, and horses with the intended use of racing, where both the long digital extensor (LoDE) and lateral digital extensor (LaDE) tendons had been completely transected.

Design Retrospective case series.

Methods Records of all horses admitted with hindlimb lacerations between 2002 and 2009 were examined for cases where both the LoDE and LaDE tendons in the hindlimb had been severed, and specifically in horses intended to be used for racing. Outcome was assessed via retrieval of race records and via telephone questioning of the owners.

Results In total, 589 records were retrieved and 34 horses met the inclusion criteria: 26 horses (76%) had proximal wounds that severed both the LoDE and LaDE tendons and 8 (24%) had more distal wounds, where the tendons were severed below the point at which they join; 14 horses (41%) were euthanased prior to discharge. Of the 20 horses discharged, 6 (30%) raced and 12 (60%) did not; 2 (10%) of the treated horses, both Thoroughbred colts, were in race training and showing no signs of lameness at the time of the study. Of the 34 horses presented for treatment, 18% went on to race.

Conclusions The prognosis for racing after transection of both hindlimb extensor tendons is poor. Clinicians may wish to consider these findings when formulating advice for clients regarding this injury in racehorses.
Leucopenia associated with abalone viral ganglioneuritis
Authors: Hooper C , Slocombe R , Day R , Crawford S
Published: January 2012

Objective  To compare microscopic lesion severity with circulating total haemocyte counts (THC) in abalone affected by abalone viral ganglioneuritis (AVG).

Results  A herpes‐like virus led to severe mortality in a number of Australian abalone farms in 2006. The infection was associated with severe necrotising ganglioneuritis. The microscopic lesions were well demarcated, affecting the neural tissue almost exclusively and were characterised by necrosis and increased cellularity in affected ganglia and nerves. On two farms, the presence or absence of typical AVG pathology was compared with THC. Those abalone with microscopic lesions of AVG had significantly lower haemocyte counts. The mean THC in abalone with no evidence of AVG from both farms was 4.6 × 106/mL (±0.3 SE). The THC in AVG‐affected abalone in farm 1 was 2.8 × 106/mL (±0.5 SE) and farm 2 was 0.98 × 106/mL (±0.4 SE).

Conclusions  Severe AVG is associated with leucopenia in affected abalone.
Validating the return period of rainfall thresholds used for Extreme Rainfall Alerts by linking rainfall intensities with observed surface water flood events
Authors: Hurford A.P. , Parker D.J. , Priest S.J. , Lumbroso D.M.
Published: January 2012

In 2008, the Environment Agency and the Meteorological Office launched a pilot Extreme Rainfall Alert (ERA) service as a first step towards providing a warning for surface water flooding. An ERA is based on rainfall intensity thresholds of an average of 1‐in‐30 year storms, to represent rainfall thought likely to cause severe surface water flooding in urban areas. This research investigates whether this return period is appropriate for warning of surface water flooding by examining the intensity and return period of rainfall associated with observed surface water flood (SWF) events. Data from rainfall gauges and flood events were analysed which showed that most of the SWF events were associated with rainfall intensities of less than 1‐in‐10 year return period. Improvements in data recording could provide flood magnitudes and durations, which would facilitate better understanding of the relationship between flood magnitude and rainfall intensity and allow more informed debate about SWF warning thresholds.
Synovial fluid chondroitin sulphate indicates abnormal joint metabolism in asymptomatic osteochondritic horses
Authors: MACHADO T. S. L. , CORREIA da SILVA L. C. L. , BACCARIN R. Y. A. , MICHELACCI Y. M.
Published: January 2012

Reasons for performing study:Alternative methods to evaluate the joint condition in asymptomatic osteochondrosis dissecans (OCD) and other joint diseases may be useful.

Objectives:To investigate possible changes in synovial fluid composition that may lead to joint conditions in asymptomatic OCD, in mature horses.

Methods:Animals aged >2 years, of different breeds, with OCD in the intermediate ridge of distal tibia, symptomatic or not, were studied. Synovial fluid samples (10 healthy; 11 asymptomatic OCD; 25 symptomatic OCD) were collected by arthroscopy from 29 horses. Glycosaminoglycans (GAGs) were analysed by a combination of agarose gel electrophoresis and enzymatic degradation with specific GAG lyases. The viscosity, white blood cell (WBC) count, protein concentration and hyaluronic acid (HA) molecular weight were also determined.

Results:The method used here to analyse synovial fluid GAGs is reliable, reproducible and specific. The main synovial fluid GAGs are HA and chondroitin sulphate (CS), 93% and 7% respectively in normal horses. In symptomatic OCD, the concentrations of both increased (expressed as GAG/urea ratios), but CS increased more. The CS increased also in asymptomatic OCD. An inflammatory reaction was suggested by the increased WBC counts in OCD. The molecular weight of the synovial fluid HA was reduced in OCD, explaining the lower viscosity observed.

Conclusions:The increased CS in synovial fluid of OCD joints in mature horses suggests that the synovial fluid CS and the WBC count are good markers of the joint conditions, allowing the identification of pathological phase in joint diseases.

Potential relevance:The analysis of synovial fluid GAGs shows that cartilage damage occurs even in asymptomatic OCD, implying that arthroscopic removal of osteochondral fragments should be performed even in asymptomatic OCD.
A recess intervention to promote moderate‐to‐vigorous physical activity
Authors: Howe C. A. , Freedson P. S. , Alhassan S. , Feldman H. A. , Osganian S. K.
Published: January 2012

Background

Schools provide a prime environment for interventions that attempt to increase physical activity and prevent obesity.

Objective

This study examined the effect of a 30‐min, structured recess using 22 games of known energy expenditure on moderate‐to‐vigorous physical activity when compared to free play implemented with third graders from two elementary schools over 9 weeks.

Methods

Moderate‐to‐vigorous physical activity and other cardiovascular risk factors were assessed pre‐ and post‐intervention in 27 children.

Results

Moderate‐to‐vigorous physical activity during recess increased significantly in intervention school children from 6.9 ± 0.8 to 14.9 ± 0.9 min pre‐ and post‐intervention, respectively (adjusted mean change 8.0 ± 1.1; P < 0.0001), with no differences by gender or body mass index (BMI). In‐school, moderate‐to‐vigorous physical activity also increased significantly more for intervention compared to control children (adjusted mean change 14 ± 4 min vs. 3 ± 3 min; P = 0.014, respectively).

Conclusion

There was no significant difference in BMI and cardiovascular risk factors. A structured recess is feasible to implement and can significantly increase moderate‐to‐vigorous physical activity.
Cylindrical Shell Control With Center- and Corner-Placed Photostrictive Skew-Quad Actuator Systems
Authors: Jiang J. , Yue H. H. , Deng Z. Q. , Tzou H. S.
Published: January 2012

Light-driven photostrictive actuators can induce control actions for wireless non-contact actuation and control of precision structures and systems. Conventional distributed actuators laminated on shells and plates usually only introduce uniform control forces and moments. Structural actuation and control based on uniform control forces and moments have been investigated for over two decades. This paper is to exploit a new photostrictive actuator design, i.e., a skew-quad (SQ) actuator system. This new distributed SQ actuator system laminated on shells and plates can introduce non-uniform control forces and moments. The new SQ actuator system is composed of four pieces of photostrictive materials and the inner two edges of each piece are bonded to a cross fixture. Under the irradiation of high-energy lights, each piece generates non-uniform control forces and moments, due to its uneven non-symmetrical boundary conditions. Modal actuation characteristics of a cylindrical shell coupled with the center-placed and corner-placed SQ actuator systems are evaluated respectively. A paired-design regulating positive/negative control forces of each actuator region is also proposed and evaluated to improve the control effectiveness of the center-located SQ actuator system. Parametric analysis proves improved control effectiveness of unsymmetrical shell modes.
Reliable and Evolvable Vibration Suppression by Self-Powered Digital Vibration Control
Authors: Takeuchi Shinsuke , Makihara Kanjuro , Onoda Junjiro
Published: January 2012

A reliable and evolvable vibration suppression technique using a digital processor powered by energy harvested from a piezoelectric element was developed and investigated. This technique, called a self-powered digital vibration control, benefits from both the sophisticated control logic of the digital processor and a reliable self-powered semiactive element. A system embodying this technique consists of a circuit outline, CPU, and DC/DC converter. Two experiments emulating the synchronized switch damping on inductor (SSDI) technique demonstrated its effectiveness for steady inputs as well as transient ones.
Lower Bound Limit Load Estimation Using a Linear Elastic Analysis
Authors: Manoj Simha C. Hari , Adibi-Asl R.
Published: January 2012

We present a scheme that utilizes one elastic stress field (no iterations) to compute lower bound limit load multipliers of structures that collapse through gross (or localized) plasticity. A criterion to distinguish between these collapse modes is presented. For structures that collapse through gross plasticity, we demonstrate that the m′ multiplier proposed by Mura et al. (1965, Extended Theorems of Limit Analysis,” Q. Appl. Math., 23(2), pp. 171–179) is a lower bound in the context of deformation theory. For structures that undergo plastic localization at collapse, we present a criterion that identifies (approximately) the subvolumes of the structure that participate in the collapse. Multiplier m′ is computed over the selected subvolumes, denoted as m'S, and demonstrated to be a lower bound multiplier in the context of deformation theory. We consider numerical examples of structures that collapse by localized or gross plasticity and show that our proposed multiplier is lower than the corresponding multiplier obtained through elastic–plastic analysis and the proposed multiplier is not overly conservative.
Modeling the Flow and Heat Transfer in a Packed Bed High Temperature Gas-Cooled Reactor in the Context of a Systems CFD Approach
Authors: du Toit C. G. , Rousseau P. G.
Published: January 2012

Engineers are faced with two major challenges when carrying out the thermal-fluid design of a complex system consisting of many interacting components. The first challenge is to predict the performance of all the individual thermal-fluid components. The second challenge is to predict the performance of the integrated plant consisting of all its subsystems. The complexity associated with the thermal-fluid design of complex systems requires the use of a variety of analysis techniques and simulation tools. These range from simple one-dimensional models that do not capture all the significant physical phenomena, to large-scale three-dimensional computational fluid dynamics (CFD) codes that, for practical reasons, cannot simulate the entire plant as a single integrated model. In the systems CFD approach, a network code serves as the framework to link the models of the various components together and to control the solution. The models of the components can be of varying degrees of complexity. These can range from simple lumped models to complex fully three-dimensional CFD models. This paper gives a brief overview of the systems CFD (SCFD) approach and an overview of the model of the pebble bed nuclear reactor that was developed in the context of the SCFD approach.
Whole-Body Human Thermal Modeling, an Alternative to Immersion in Cold Water and Other Unpleasant Endeavors
Authors: Wissler Eugene H.
Published: January 2012

Analysis of heat transfer in the human involves different scales ranging from countercurrent heat transfer between small arteries and veins to the whole-body, which is the principal subject of this paper. Important applications of whole-body human thermal models are predicting comfort under various conditions, such as riding in an air-conditioned automobile on a hot day, and predicting the probability of survival under life-threatening conditions, such as accidental immersion is cold water. This paper is arranged in three parts. In the first part, the evolution of human thermal models is discussed. Then, aspects of human physiology fundamental to thermoregulation are discussed, and finally we discuss a practical application derived from an Arctic survival project with which the author is involved.
Crystallization of Ge in SiO2 matrix by femtosecond laser processing
Authors: Salihoglu Omer , Kürüm Ulaş , Yaglioglu Halime Gul , Elmali Ayhan , Aydinli Atilla
Published: January 2012

Germanium nanocrystals embedded in a siliconoxide matrix has been fabricated by single femtosecond laser pulse irradiation of germanium doped SiO2 thin films deposited with plasma enhanced chemical vapor deposition. SEM and AFM are used to analyze surface modification induced by laser irradiation. Crystallization of Ge in the oxide matrix is monitored with the optic phonon at 300 cm−1 as a function of laser fluence. Both the position the linewidth of the phonon provides clear signature for crystallization of Ge. In PL experiments, strong luminescence around 600 nm has been observed.
Visualizing Gas Molecules Interacting with Supported Nanoparticulate Catalysts at Reaction Conditions
Authors: Yoshida Hideto , Kuwauchi Yasufumi , Jinschek Joerg R. , Sun Keju , Tanaka Shingo , Kohyama Masanori , Shimada Satoshi , Haruta Masatake , Takeda Seiji
Published: January 2012

Tracking Reaction Surfaces

Gold becomes a remarkably active catalyst for CO oxidation when it is dispersed as nanoparticles on the surface of reducible metal oxides such as ceria, so much so that the reaction proceeds at room temperature.

Yoshida
et al.

(p.
317
) used an aberration-corrected, environmental transmission electron microscope to follow the changes in both ceria-supported gold nanoparticles and the adsorbed species for this reaction.
Demonstration of Blind Quantum Computing
Authors: Barz Stefanie , Kashefi Elham , Broadbent Anne , Fitzsimons Joseph F. , Zeilinger Anton , Walther Philip
Published: January 2012

Quantum Blindness

While quantum computers offer speed advantages over their classical counterparts, the technological challenges facing their eventual realization suggest that they will need to be located in specialized facilities. Thus, interaction would then need to be on a quantum client:quantum server basis.

Barz
et al.

(p.
303
; see the Perspective by

Vedral

) implemented a proof-of-principle protocol that illustrates complete security in such a setup—for both the client and the server. In this blind quantum computing protocol, the client maintains the security of their data and the specifics of the calculation they want to perform, and the server cannot access the data or calculation of the client.
Bird-Brained Illusionists
Authors: Anderson Barton L.
Published: January 2012

The bowers constructed by great bowerbirds to attract mates create optical size and distance illusions.
Sowing the Seeds of Centromeres
Authors: Jansen Lars E. T.
Published: January 2012

How can a centromere relocate to a new chromosomal position?
Clingfish Stick Like Geckos
Authors: Pennisi Elizabeth
Published: January 2012

An undergraduate reported at the meeting that
Gobiesox maeandricus
adhered to eight surfaces mimicking the range of sandpaper grades with an average force 180 times their body weight.
Phenotypic Screening of Carbapenemases and Associated β-Lactamases in Carbapenem-Resistant Enterobacteriaceae
Authors: Birgy André , Bidet Philippe , Genel Nathalie , Doit Catherine , Decré Dominique , Arlet Guillaume , Bingen Edouard
Published: January 2012

Dissemination of carbapenem resistance among
Enterobacteriaceae
poses a considerable threat to public health. Carbapenemase gene detection by molecular methods is the gold standard but is available in only a few laboratories. The aim of this study was to test phenotypic methods for the detection of metallo-β-lactamase (MBL)- or
Klebsiella pneumoniae
carbapenemase (KPC)-producing
Enterobacteriaceae
and associated mechanisms of β-lactam resistance against a panel of 30 genotypically characterized carbapenem-resistant
Enterobacteriaceae
: 9 MBL, 7 KPC, 6 OXA-48, and 8 extended-spectrum β-lactamase (ESBL) or AmpC β-lactamases associated with decreased permeability. We used carbapenemase inhibitor-impregnated agar to test for carbapenem-resistant strains. Differences in the inhibition zone sizes of the meropenem, imipenem, ertapenem, and doripenem disks were measured between control and inhibitor (EDTA or phenylboronic acid [PBA] with or without cloxacillin)-impregnated Mueller-Hinton agar with a cutoff of 10 mm. All 9 MBL- and 7 KPC-producing
Enterobacteriaceae
were identified from the differences in zone size in the presence and absence of specific inhibitors, regardless of the carbapenem MICs and including isolates with low-level resistance to carbapenems. We also detected their associated β-lactam resistance mechanisms (11 ESBL-type and 5 class A β-lactamase 2b). No differences in zone size were observed for OXA-48-producing strains or other carbapenem resistance mechanisms such as ESBL and decreased permeability. We propose a new strategy to detect carbapenemases (MBL- and KPC-type) and associated mechanisms of β-lactam resistance (ESBL or class A β-lactamase 2b) by the use of inhibitor-impregnated agar. A rapid phenotypic detection of resistance mechanisms is important for epidemiological purposes and for limiting the spread of resistant strains by implementing specific infection control measures.
Phenotypic, Biochemical, and Molecular Techniques for Detection of Metallo-β-Lactamase NDM in Acinetobacter baumannii
Authors: Bonnin Rémy A. , Naas Thierry , Poirel Laurent , Nordmann Patrice
Published: January 2012

Seven NDM-positive
Acinetobacter baumannii
isolates of worldwide origin were studied to evaluate the best technique for their identification. Detection of carbapenemase producers based on the measurement of carbapenemase activity by UV spectrophotometry (as for
A. baumannii
strains producing other types of carbapenemase), or by the modified Hodge test, failed. Inhibition activity using EDTA was a sensitive technique but lacked specificity compared to molecular techniques, which remain the gold standard.
Evidence for N-Glycan Shielding of Antigenic Sites during Evolution of Human Influenza A Virus Hemagglutinin
Authors: Kobayashi Yuki , Suzuki Yoshiyuki
Published: January 2012

After the emergence of influenza A viruses in the human population, the number of N-glycosylation sites (NGS) in the globular head region of hemagglutinin (HA) has increased continuously for several decades. It has been speculated that the addition of NGS to the globular head region of HA has conferred selective advantages to the virus by preventing the binding of antibodies (Ab) to antigenic sites (AS). Here, the effect of N-glycosylation on the binding of Ab to AS in human influenza A virus subtype H3N2 (A/H3N2) was examined by inferring natural selection at AS and other sites (NAS) that are located close to and distantly from the NGS in the three-dimensional structure of HA through a comparison of the rates of synonymous (
d
S
) and nonsynonymous (
d
N
) substitutions. When positions 63, 122, 126, 133, 144, and 246 in the globular head region of HA were non-NGS, the
d
N
/
d
S
was >1 and positive selection was detected at the AS located near these positions. However, the
d
N
/
d
S
value decreased and the evidence of positive selection disappeared when these positions became NGS. In contrast,
d
N
/
d
S
at the AS distantly located from the positions mentioned above and at the NAS of any location were generally <1 and did not decrease when these positions changed from non-NGS to NGS. These results suggest that the attachment of N-glycans to the NGS in the globular head region of HA prevented the binding of Ab to AS in the evolutionary history of human A/H3N2 virus.
HIV Cell-to-Cell Transmission Requires the Production of Infectious Virus Particles and Does Not Proceed through Env-Mediated Fusion Pores
Authors: Monel Blandine , Beaumont Elodie , Vendrame Daniela , Schwartz Olivier , Brand Denys , Mammano Fabrizio
Published: January 2012

Direct cell-to-cell transmission of human immunodeficiency virus (HIV) is a more potent and efficient means of virus propagation than infection by cell-free virus particles. The aim of this study was to determine whether cell-to-cell transmission requires the assembly of enveloped virus particles or whether nucleic acids with replication potential could translocate directly from donor to target cells through envelope glycoprotein (Env)-induced fusion pores. To this end, we characterized the transmission properties of viruses carrying mutations in the matrix protein (MA) that affect the incorporation of Env into virus particles but do not interfere with Env-mediated cell-cell fusion. By use of cell-free virus, the infectivity of MA mutant viruses was below the detection threshold both in single-cycle and in multiple-cycle assays. Truncation of the cytoplasmic tail (CT) of Env restored the incorporation of Env into MA mutant viruses and rescued their cell-free infectivity to different extents. In cell-to-cell transmission assays, MA mutations prevented HIV transmission from donor to target cells, despite efficient Env-dependent membrane fusion. HIV transmission was blocked at the level of virus core translocation into the cytosol of target cells. As in cell-free assays, rescue of Env incorporation by truncation of the Env CT restored the virus core translocation and cell-to-cell infectivity of MA mutant viruses. These data show that HIV cell-to-cell transmission requires the assembly of enveloped virus particles. The increased efficiency of this infection route may thus be attributed to the high local concentrations of virus particles at sites of cellular contacts rather than to a qualitatively different transmission process.
Role for the Phosphatidylinositol 3-Kinase-Akt-TOR Pathway during Sindbis Virus Replication in Arthropods
Authors: Patel Rohini K. , Hardy Richard W.
Published: January 2012

The efficient transmission of alphaviruses requires the establishment of a persistent infection in the arthropod vector; however, the nature of the virus-arthropod host interaction is not well understood. The phosphatidylinositol 3-kinase (PI3K)-Akt-TOR pathway is a signaling pathway with which viruses interact to manipulate cellular functions. The viral activation of this pathway can enhance translation and inhibit apoptosis, potentially promoting viral replication; conversely, repression can enhance cell death. Using a system to study Sindbis virus RNA replication in
Drosophila melanogaster
, we found that the overexpression of Akt enhanced Sindbis virus replication. In contrast, a decrease in viral replication was observed for flies hypomorphic for the Akt gene. Infection of cultured
Drosophila
cells led to the phosphorylation and activation of Akt. The chemical inhibition of PI3K, Akt, and TOR in mosquito cells reduced virus replication, suggesting that this pathway is proviral. Early after infection, there was an increase in the TOR-dependent phosphorylation of 4E-BP1 in mosquito cells and a consequent increase in the translation of a capped reporter mRNA. In contrast, no change in 4E-BP1 phosphorylation was seen in mammalian cells, and the level of translation of the reporter decreased following infection. Finally, we found that the increase in the phosphorylation of 4E-BP1 was stimulated by replicon RNA but not by UV-inactivated virus. Our data indicate that Sindbis virus replication complex formation in mosquito cells activates the PI3K-Akt-TOR pathway, causing the phosphorylation of 4E-BP1 and increasing the formation of eukaryotic initiation factor 4F (eIF4F), which promote cap-dependent translation. This virus-induced increase in cap-dependent translation allows the efficient translation of viral mRNA while minimizing the burden on the cell.
Enterovirus 71 Disrupts Interferon Signaling by Reducing the Level of Interferon Receptor 1
Authors: Lu Jing , Yi Lina , Zhao Jin , Yu Jun , Chen Ying , Lin Marie C. , Kung Hsiang-Fu , He Ming-Liang
Published: January 2012

The recent outbreak of enterovirus 71 (EV71) infected millions of children and caused over 1,000 deaths. To date, neither an effective vaccine nor antiviral treatment is available for EV71 infection. Interferons (IFNs) have been successfully applied to treat patients with hepatitis B and C viral infections for decades but have failed to treat EV71 infections. Here, we provide the evidence that EV71 antagonizes type I IFN signaling by reducing the level of interferon receptor 1 (IFNAR1). We show that the host cells could sense EV71 infection and stimulate IFN-β production. However, the induction of downstream IFN-stimulated genes is inhibited by EV71. Also, only a slight interferon response and antiviral effects could be detected in cells treated with recombinant type I IFNs after EV71 infection. Further studies reveal that EV71 blocks the IFN-mediated phosphorylation of STAT1, STAT2, Jak1, and Tyk2 by reducing IFNAR1. Finally, we identified the 2A protease encoded by EV71 as an antagonist of IFNs and show that the protease activity is required for reducing IFNAR1 levels. Taken together, our study for the first time uncovers a mechanism used by EV71 to antagonize type I IFN signaling and provides new targets for future antiviral strategies.
The 3A Protein from Multiple Picornaviruses Utilizes the Golgi Adaptor Protein ACBD3 To Recruit PI4KIIIβ
Authors: Greninger Alexander L. , Knudsen Giselle M. , Betegon Miguel , Burlingame Alma L. , DeRisi Joseph L.
Published: January 2012

The activity of phosphatidylinositol 4-kinase class III beta (PI4KIIIβ) has been shown to be required for the replication of multiple picornaviruses; however, it is unclear whether a physical association between PI4KIIIβ and the viral replication machinery exists and, if it does, whether association is necessary. We examined the ability of the 3A protein from 18 different picornaviruses to form a complex with PI4KIIIβ by affinity purification of Strep-Tagged transiently transfected constructs followed by mass spectrometry and Western blotting for putative interacting targets. We found that the 3A proteins of Aichi virus, bovine kobuvirus, poliovirus, coxsackievirus B3, and human rhinovirus 14 all copurify with PI4KIIIβ. Furthermore, we found that multiple picornavirus 3A proteins copurify with the Golgi adaptor protein acyl coenzyme A (acyl-CoA) binding domain protein 3 (ACBD3/GPC60), including those from Aichi virus, bovine kobuvirus, human rhinovirus 14, poliovirus, and coxsackievirus B2, B3, and B5. Affinity purification of ACBD3 confirmed interaction with multiple picornaviral 3A proteins and revealed the ability to bind PI4KIIIβ in the absence of 3A. Mass-spectrometric analysis of transiently expressed Aichi virus, bovine kobuvirus, and human klassevirus 3A proteins demonstrated that the N-terminal glycines of these 3A proteins are myristoylated. Alanine-scanning mutagenesis along the entire length of Aichi virus 3A followed by transient expression and affinity purification revealed that copurification of PI4KIIIβ could be eliminated by mutation of specific residues, with little or no effect on recruitment of ACBD3. One mutation at the N terminus, I5A, significantly reduced copurification of both ACBD3 and PI4KIIIβ. The dependence of Aichi virus replication on the activity of PI4KIIIβ was confirmed by both chemical and genetic inhibition. Knockdown of ACBD3 by small interfering RNA (siRNA) also prevented replication of both Aichi virus and poliovirus. Point mutations in 3A that eliminate PI4KIIIβ association sensitized Aichi virus to PIK93, suggesting that disruption of the 3A/ACBD3/PI4KIIIβ complex may represent a novel target for therapeutic intervention that would be complementary to the inhibition of the kinase activity itself.
Expression of Dicer and Drosha in triple-negative breast cancer
Authors: Passon Nadia , Gerometta Anna , Puppin Cinzia , Lavarone Elisa , Puglisi Fabio , Tell Gianluca , Di Loreto Carla , Damante Giuseppe
Published: January 2012

Aims

Dicer and Drosha are components of the miRNA-producing machinery and their altered expression may play a role in cancer progression. The main purpose of this study was a detailed investigation of Dicer and Drosha expression and localisation in triple-negative breast cancers.

Methods

Thirty-one triple-negative breast cancers and several breast cancer cell lines were investigated. Expression of Dicer and Drosha was evaluated at the mRNA level by quantitative reverse transcription PCR and at the protein level by immunohistochemistry or western blot.

Results

Compared with normal breast tissues, a wide variation of Dicer and Drosha mRNA levels was detected in triple-negative breast cancers. As a group, Drosha mRNA levels in triple-negative breast cancers were significantly higher than those in normal breast tissues. Immunohistochemical data confirmed higher expression of Drosha protein in triple-negative breast cancers. In normal breast tissues Dicer was detectable predominantly in the cytoplasm of basal/myoepithelial cells only. In contrast, in the majority of triple-negative breast cancers, intense Dicer staining was detectable also in the nuclear compartment. Detection of Dicer and Drosha mRNA and protein levels in breast cancer cell lines confirmed the nuclear localisation of Dicer, suggesting, in addition, that the steady-state protein levels could be controlled by post-mRNA regulatory events.

Conclusions

These findings indicate that Dicer and Drosha expression is deregulated in triple-negative breast cancers.
Nearly frictionless states of ultra-high temperature amorphous matter
Authors: Chu Zotin Kwang-Hua
Published: January 2012

The almost frictionless transport of very high-temperature amorphous matter that resembles colored glass condensate (possibly having much of its origin in the RHIC heavy ion collisions) in a confined annular tube with transverse corrugations is investigated using the verified transition-rate model and boundary perturbation method. We found that for certain activation volume and energy there exist possible frictionless states that might be associated with perfect fluid formation during the early expansion stage in RHIC Au+Au collisions. We also address the possible similar scenario in LHC Pb+Pb collisions considering possible perfect fluid formation in ultra-high temperature transport of amorphous matter.
Optical properties of anatase TiO2 films modified by N ion implantation
Authors: Xiang X. , Chang D. , Jiang Y. , Liu C.M. , Zu X.T.
Published: January 2012

Anatase TiO2 thin films are deposited on K9 glass samples at different substrate temperatures by radio frequency magnetron sputtering. N ion implantation is performed in the as-deposited TiO2 thin films at ion fluences of 5 × 1016, 1 × 1017, and 5 × 1017 ions/cm2. X-ray diffraction, atomic force microscope, X-ray photoelectron spectroscopy (XPS), and UV–visible spectrophotometer are used to characterize the films. With increasing N ion fluences, the absorption edges of anatase TiO2 films shift to longer wavelengths and the absorbance increases in the visible light region. XPS results show that the red shift of TiO2 films is due to the formation of N–Ti–O compounds. As a result, photoactivity is enhanced with increasing N ion fluence.
Logarithmic entropy corrected holographic dark energy with nonminimal kinetic coupling
Authors: Amani Ali R. , Sadeghi J. , Farajollahi H. , Pourali M.
Published: January 2012

In this study, we have considered a cosmological model with nonminimal kinetic coupling terms and investigated its cosmological implications with respect to logarithmic entropy corrected holographic dark energy (LECHDE). The correspondence between LECHDE in flat Friedmann–Robertson–Walker cosmology and the phantom dark energy model is also examined with the aim of interpreting the current universe acceleration.
Analysis of temperature-dependent Schottky barrier parameters of Cu–Au Schottky contacts to n-InP
Authors: Devi V. Lakshmi , Jyothi I. , Reddy V. Rajagopal
Published: January 2012

In this work, we have investigated the electrical characteristics of Au–Cu–n-InP Schottky contacts by current–voltage (I–V) and capacitance–voltage (C–V) measurements in the temperature range 260–420 K in steps of 20 K. The diode parameters, such as the ideality factor, n, and zero-bias barrier height, Φb0, have been found to be strongly temperature dependent. It has been found that the zero-bias barrier height, Φb0(I–V), increases and the ideality factor, n, decreases with an increase in temperature. The forward I–V characteristics are analyzed on the basis of standard thermionic emission (TE) theory and the assumption of gaussian distribution of barrier heights, due to barrier inhomogeneities that prevail at the metal–semiconductor interface. The zero-bias barrier height Φb0 versus 1/2kT plot has been drawn to obtain the evidence of a gaussian distribution of the barrier heights. The corresponding values are Φb0 = 1.16 eV and σ0 = 159 meV for the mean barrier height and standard deviation, respectively. The modified Richardson plot has given mean barrier height, Φb0, and Richardson constant, A**, as 1.15 eV and 7.34 Acm−2K−2, respectively, which is close to the theoretical value of 9.4 Acm−2K−2. Barrier heights obtained from C–V measurements are higher than those obtained from I–V measurements. This inconsistency between Schottky barrier heights (SBHs) obtained from I–V and C–V measurements was also interpreted. The temperature dependence of the I–V characteristics of the Au–Cu–n-InP Schottky diode has been explained on the basis of TE mechanism with gaussian distribution of the SBHs.
Differences between scalar field and scalar density field solutions
Authors: Pirinççiog˜lu Nurettin , Sert Ilker
Published: January 2012

Differences between scalar field and scalar density solutions are explored using a Robertson–Walker (RW) metric, and a nonrelativistic Hamiltonian is derived for a scalar density field in the post-newtonian approximation. The results are compared with those of a scalar field. The expanding universe in a RW metric and a post-newtonian solution of the Klein–Gordon equation are discussed separately.
IMPROVED EFFICIENT ROUTING STRATEGY ON SCALE-FREE NETWORKS
Authors: JIANG ZHONG-YUAN , LIANG MAN-GUI
Published: January 2012

Since the betweenness of nodes in complex networks can theoretically represent the traffic load of nodes under the currently used routing strategy, we propose an improved efficient (IE) routing strategy to enhance to the network traffic capacity based on the betweenness centrality. Any node with the highest betweenness is susceptible to traffic congestion. An efficient way to improve the network traffic capacity is to redistribute the heavy traffic load from these central nodes to non-central nodes, so in this paper, we firstly give a path cost function by considering the sum of node betweenness with a tunable parameter β along the actual path. Then, by minimizing the path cost, our IE routing strategy achieved obvious improvement on the network transport efficiency. Simulations on scale-free Barabási–Albert (BA) networks confirmed the effectiveness of our strategy, when compared with the efficient routing (ER) and the shortest path (SP) routing.
STATISTICAL ANISOTROPY AND THE VECTOR CURVATON PARADIGM
Authors: DIMOPOULOS KONSTANTINOS
Published: January 2012

The vector curvaton paradigm is reviewed. The mechanism allows a massive vector boson field to contribute to or even generate the curvature perturbation in the Universe. Contribution of vector bosons is likely to generate statistical anisotropy in the spectrum and bispectrum of the curvature perturbation, which will soon be probed observationally. Two specific models for the generation of superhorizon spectra for the components of an Abelian vector field are analyzed. Emphasis is put on the observational signatures of the models when the vector fields play the role of vector curvatons. If future observations support the vector curvaton mechanism this will open a window into the gauge field content of theories beyond the standard model.
VECTOR-FIELD MODEL WITH COMPENSATED COSMOLOGICAL CONSTANT AND RADIATION-DOMINATED FRW PHASE
Authors: EMELYANOV V. , KLINKHAMER F. R.
Published: January 2012

A special model of a massless-vector-field is presented, which has an extra modified-gravity-type interaction term in the action. The cosmology of the model is studied with standard noninteracting relativistic matter added. It is found that this cosmology can have an early phase where the vector-field starts to compensate a (Planck-scale) cosmological constant and a late Friedmann–Robertson–Walker (FRW) phase where the relativistic-matter energy density dominates the dynamic vacuum energy density.
STRUCTURE FLUCTUATIONS AND CONFORMATIONAL CHANGES IN PROTEIN BINDING
Authors: RUVINSKY ANATOLY M. , KIRYS TATSIANA , TUZIKOV ALEXANDER V. , VAKSER ILYA A.
Published: January 2012

Structure fluctuations and conformational changes accompany all biological processes involving macromolecules. The paper presents a classification of protein residues based on the normalized equilibrium fluctuations of the residue centers of mass in proteins and a statistical analysis of conformation changes in the side-chains upon binding. Normal mode analysis and an elastic network model were applied to a set of protein complexes to calculate the residue fluctuations and develop the residue classification. Comparison with a classification based on normalized B-factors suggests that the B-factors may underestimate protein flexibility in solvent. Our classification shows that protein loops and disordered fragments are enriched with highly fluctuating residues and depleted with weakly fluctuating residues. Strategies for engineering thermostable proteins are discussed. To calculate the dihedral angles distribution functions, the configuration space was divided into cells by a cubic grid. The effect of protein association on the distribution functions depends on the amino acid type and a grid step in the dihedral angles space. The changes in the dihedral angles increase from the near-backbone dihedral angle to the most distant one, for most residues. On average, one fifth of the interface residues change the rotamer state upon binding, whereas the rest of the interface residues undergo local readjustments within the same rotamer.
PRACTICALITY AND TIME COMPLEXITY OF A SPARSIFIED RNA FOLDING ALGORITHM
Authors: DIMITRIEVA SLAVICA , BUCHER PHILIPP
Published: January 2012

Commonly used RNA folding programs compute the minimum free energy structure of a sequence under the pseudoknot exclusion constraint. They are based on Zuker's algorithm which runs in time O(n3). Recently, it has been claimed that RNA folding can be achieved in average time O(n2) using a sparsification technique. A proof of quadratic time complexity was based on the assumption that computational RNA folding obeys the "polymer-zeta property". Several variants of sparse RNA folding algorithms were later developed. Here, we present our own version, which is readily applicable to existing RNA folding programs, as it is extremely simple and does not require any new data structure. We applied it to the widely used Vienna RNAfold program, to create sibRNAfold, the first public sparsified version of a standard RNA folding program. To gain a better understanding of the time complexity of sparsified RNA folding in general, we carried out a thorough run time analysis with synthetic random sequences, both in the context of energy minimization and base pairing maximization. Contrary to previous claims, the asymptotic time complexity of a sparsified RNA folding algorithm using standard energy parameters remains O(n3) under a wide variety of conditions. Consistent with our run-time analysis, we found that RNA folding does not obey the "polymer-zeta property" as claimed previously. Yet, a basic version of a sparsified RNA folding algorithm provides 15- to 50-fold speed gain. Surprisingly, the same sparsification technique has a different effect when applied to base pairing optimization. There, its asymptotic running time complexity appears to be either quadratic or cubic depending on the base composition. The code used in this work is available at: http://sibRNAfold.sourceforge.net/ .