bluuebunny/crossref_metadata_2025_split huggingface dataset:
HIV-1 Vpr Oligomerization but Not That of Gag Directs the Interaction between Vpr and Gag
Authors: Fritz Joëlle V. , Dujardin Denis , Godet Julien , Didier Pascal , De Mey Jan , Darlix Jean-Luc , Mély Yves , de Rocquigny Hugues 
Published: November 2009

ABSTRACT

During HIV-1 assembly, the viral protein R (Vpr) is incorporated into newly made viral particles
via
an interaction with the C-terminal domain of the Gag polyprotein precursor Pr55
Gag
. Vpr has been implicated in the nuclear import of newly made viral DNA and subsequently in its transcription. In addition, Vpr can affect the cell physiology by causing G
2
/M cell cycle arrest and apoptosis. Vpr can form oligomers, but their roles have not yet been investigated. We have developed fluorescence lifetime imaging microscopy-fluorescence resonance energy transfer-based assays to monitor the interaction between Pr55
Gag
and Vpr in HeLa cells. To that end, we used enhanced green fluorescent protein-Vpr that can be incorporated into the virus and tetracysteine (TC)-tagged Pr55
Gag
-TC. This TC motif is tethered to the C terminus of Pr55
Gag
and does not interfere with Pr55
Gag
trafficking and the assembly of virus-like particles (VLPs). Results show that the Pr55
Gag
-Vpr complexes accumulated mainly at the plasma membrane. In addition, results with Pr55
Gag
-TC mutants confirm that the
41
LXXLF domain of Gag-p6 is essential for Pr55
Gag
-Vpr interaction. We also report that Vpr oligomerization is crucial for Pr55
Gag
recognition and its accumulation at the plasma membrane. On the other hand, Pr55
Gag
-Vpr complexes are still formed when Pr55
Gag
carries mutations impairing its multimerization. These findings suggest that Pr55
Gag
-Vpr recognition and complex formation occur early during Pr55
Gag
assembly.
The Major Determinant for Addition of Tegument Protein pUL48 (VP16) to Capsids in Herpes Simplex Virus Type 1 Is the Presence of the Major Tegument Protein pUL36 (VP1/2)
Authors: Ko Debbie H. , Cunningham Anthony L. , Diefenbach Russell J. 
Published: November 2009

ABSTRACT

In this study a number of herpes simplex virus type 1 (HSV-1) proteins were screened, using a yeast-two-hybrid assay, for interaction with the tegument protein pUL48 (VP16). This approach identified interactions between pUL48 and the capsid proteins pUL19 (VP5), pUL38 (VP19C), and pUL35 (VP26). In addition, the previously identified interaction of pUL48 with the major tegument protein pUL36 (VP1/2) was confirmed. All of these interactions, except that of pUL35 and pUL48, could be confirmed using an
in vitro
pulldown assay. A subsequent pulldown assay with intact
in vitro
-assembled capsids, consisting of pUL19, pUL38, and pUL18 (VP23) with or without pUL35, showed no binding of pUL48, suggesting that the capsid/pUL48 interactions initially identified were more then likely not biologically relevant. This was confirmed by using a series of HSV-1 mutants lacking the gene encoding either pUL35, pUL36, or pUL37. For each HSV-1 mutant, analysis of purified deenveloped C capsids indicated that only in the absence of pUL36 was there a complete loss of capsid-bound pUL48, as well as pUL37. Collectively, this study shows for the first time that pUL36 is a major factor for addition of both pUL48 and pUL37, likely through a direct interaction of both with nonoverlapping sites in pUL36, to unenveloped C capsids during assembly of HSV-1.
The U24 Protein from Human Herpesvirus 6 and 7 Affects Endocytic Recycling
Authors: Sullivan Brian M. , Coscoy Laurent 
Published: November 2009

ABSTRACTModulation of T-cell receptor expression and signaling is essential to the survival of many viruses. The U24 protein expressed by human herpesvirus 6A, a ubiquitous human pathogen, has been previously shown to downregulate the T-cell receptor. Here, we show that U24 also mediates cell surface downregulation of a canonical early endosomal recycling receptor, the transferrin receptor, indicating that this viral protein acts by blocking early endosomal recycling. We present evidence that U24 is a C-tail-anchored protein that is dependent for its function on TRC40/Asna-1, a component of a posttranslational membrane insertion pathway. Finally, we find that U24 proteins from other roseoloviruses have a similar genetic organization and a conserved function that is dependent on a proline-rich motif. Inhibition of a basic cellular process by U24 has interesting implications not only for the pathogenicity of roseoloviruses but also for our understanding of the biology of endosomal transport.
Newcastle Disease Virus-Vectored Vaccines Expressing the Hemagglutinin or Neuraminidase Protein of H5N1 Highly Pathogenic Avian Influenza Virus Protect against Virus Challenge in Monkeys
Authors: DiNapoli Joshua M. , Nayak Baibaswata , Yang Lijuan , Finneyfrock Brad W. , Cook Anthony , Andersen Hanne , Torres-Velez Fernando , Murphy Brian R. , Samal Siba K. , Collins Peter L. , Bukreyev Alexander 
Published: November 2009

ABSTRACTH5N1 highly pathogenic avian influenza virus (HPAIV) causes periodic outbreaks in humans, resulting in severe infections with a high (60%) incidence of mortality. The circulating strains have low human-to-human transmissibility; however, widespread concerns exist that enhanced transmission due to mutations could lead to a global pandemic. We previously engineered Newcastle disease virus (NDV), an avian paramyxovirus, as a vector to express the HPAIV hemagglutinin (HA) protein, and we showed that this vaccine (NDV/HA) induced a high level of HPAIV-specific mucosal and serum antibodies in primates when administered through the respiratory tract. Here we developed additional NDV-vectored vaccines expressing either HPAIV HA in which the polybasic cleavage site was replaced with that from a low-pathogenicity strain of influenza virus [HA(RV)], in order to address concerns of enhanced vector replication or genetic exchange, or HPAIV neuraminidase (NA). The three vaccine viruses [NDV/HA, NDV/HA(RV), and NDV/NA] were administered separately to groups of African green monkeys by the intranasal/intratracheal route. An additional group of animals received NDV/HA by aerosol administration. Each of the vaccine constructs was highly restricted for replication, with only low levels of virus shedding detected in respiratory secretions. All groups developed high levels of neutralizing antibodies against homologous and heterologous strains of HPAIV and were protected against challenge with 2 × 107PFU of homologous HPAIV. Thus, needle-free, highly attenuated NDV-vectored vaccines expressing either HPAIV HA, HA(RV), or NA have been developed and demonstrated to be individually immunogenic and protective in a primate model of HPAIV infection. The finding that HA(RV) was protective indicates that it would be preferred for inclusion in a vaccine. The study also identified NA as an independent protective HPAIV antigen in primates. Furthermore, we demonstrated the feasibility of aerosol delivery of NDV-vectored vaccines.
Mutations in Classical Swine Fever Virus NS4B Affect Virulence in Swine
Authors: Fernandez-Sainz I. , Gladue D. P. , Holinka L. G. , O'Donnell V. , Gudmundsdottir I. , Prarat M. V. , Patch J. R. , Golde W. T. , Lu Z. , Zhu J. , Carrillo C. , Risatti G. R. , Borca M. V. 
Published: November 2009

ABSTRACT
NS4B is one of the nonstructural proteins of classical swine fever virus (CSFV), the etiological agent of a severe, highly lethal disease of swine. Protein domain analysis of the predicted amino acid sequence of the NS4B protein of highly pathogenic CSFV strain Brescia (BICv) identified a putative Toll/interleukin-1 receptor (TIR)-like domain. This TIR-like motif harbors two conserved domains, box 1 and box 2, also observed in other members of the TIR superfamily, including Toll-like receptors (TLRs). Mutations within the BICv NS4B box 2 domain (V2566A, G2567A, I2568A) produced recombinant virus NS4B.VGIv, with an altered phenotype displaying enhanced transcriptional activation of TLR-7-induced genes in swine macrophages, including a significant sustained accumulation of interleukin-6 (IL-6) mRNA. Transfection of swine macrophages with the wild-type NS4B gene partially blocked the TLR-7-activating effect of imiquimod (R837), while transfection with the NS4B gene harboring mutations in either of the putative boxes displayed decreased blocking activity. NS4B.VGIv showed an attenuated phenotype in swine, displaying reduced replication in the oronasal cavity and limited spread from the inoculation site to secondary target organs. Furthermore, the level and duration of IL-6 production in the tonsils of pigs intranasally inoculated with NS4B.VGIv were significantly higher than those for animals infected with BICv. The peak of IL-6 production in infected animals paralleled the ability of animals infected with NS4B.VGIv to resist challenge with virulent BICv. Interestingly, treatment of peripheral blood mononuclear cell cultures with recombinant porcine IL-6 results in a significant decrease in BICv replication.
CALCULATING THE CARBON FOOTPRINT OF A CHEMICAL PLANT: A CASE STUDY OF AKZONOBEL
Authors: STEIN MICHAEL , KHARE ANSHUMAN 
Published: November 2009

Reduction of greenhouse gas emissions is one of the key requirements for sustainable production and consumption, but while the Canadian chemical industry has been very successful in reducing emissions to water and air, and while non- CO2 greenhouse gas emissions have been minimised as well, reduction of CO2 emissions has been less successful. The industry itself forecasts that further reduction of CO2 emissions will be minimal. On the other hand concerns about global warming are increasing, while at the same time the chemical industry increases its commitment to sustainability. Determining the carbon footprint of a chemical plant and of its products will help to identify more emissions reduction possibilities and is a necessary step for the further reduction of the chemical industry's environmental impact. Carbon footprint determination is a corporate goal for AkzoNobel, an international coatings and specialty chemicals company, but the carbon footprint is not yet established for many products, and the information available from the chemical industry is scarce. This paper presents a case study of AkzoNobel's Saskatoon Plant and its attempt to calculate and analyse the carbon footprint of the plant and its main products which are used in the potash industry.
Lack of outcome benefit and clopidogrel “resistance”
Authors: Serebruany Victor 
Published: November 2009

SummaryImpaired response to clopidogrel, or “resistance” is a cornerstone concept for justification of more aggressive antiplatelet regimens, and development of new more potent drugs. There are over 1,000 citations (although predominantly reviews, or case reports) in MEDLINE related to clopidogrel “resistance”, while about 100 of them attempted to link low response to adverse clinical outcomes. However, most of these studies are woefully small, and not randomised. The TRITON trial assessed head-to-head novel antiplatelet agent prasugrel versus clopidogrel in patients with acute coronary syndromes. This study was the first in a decade to challenge clopidogrel monopoly, and to indirectly test the “resistance” hypothesis. The primary endpoint was the rate of cardiovascular death, non-fatal myocardial infarction, or stroke, and occurred in 12.1% of patients treated with clopidogrel, and 9.9% of patients randomised to prasugrel, suggesting impressive vascular outcome benefit of prasugrel over clopidogrel. However, the Food and Drug Administration (FDA) presented more balanced, and realistic outlook on TRITON. While very early periprocedural benefit exists, long-term prasugrel therapy yielded identical to clopidogrel vascular outcomes among 13,608 TRITON patients challenging the postulate that clopidogrel “resistance” phenomenon is clinically relevant. Despite the fact that prasugrel 10 mg/daily cause 2.5 times more potent platelet inhibition than conventional clopidogrel 75 mg/daily, with fewer patients exhibiting broad response variability, and/or antiplatelet “resistance”, the vascular benefit beyond acute phase was identical. Keeping in mind growing over time bleeding, cancer, and mortality risks associated with chronic prasugrel use, small observational studies should be judged with skepticism as hypothesis-generating, pending confirmation in randomised trials.
Convolutional Networks Can Learn to Generate Affinity Graphs for Image Segmentation
Authors: Turaga Srinivas C. , Murray Joseph F. , Jain Viren , Roth Fabian , Helmstaedter Moritz , Briggman Kevin , Denk Winfried , Seung H. Sebastian 
Published: November 2009

Many image segmentation algorithms first generate an affinity graph and then partition it. We present a machine learning approach to computing an affinity graph using a convolutional network (CN) trained using ground truth provided by human experts. The CN affinity graph can be paired with any standard partitioning algorithm and improves segmentation accuracy significantly compared to standard hand-designed affinity functions. We apply our algorithm to the challenging 3D segmentation problem of reconstructing neuronal processes from volumetric electron microscopy (EM) and show that we are able to learn a good affinity graph directly from the raw EM images. Further, we show that our affinity graph improves the segmentation accuracy of both simple and sophisticated graph partitioning algorithms. In contrast to previous work, we do not rely on prior knowledge in the form of hand-designed image features or image preprocessing. Thus, we expect our algorithm to generalize effectively to arbitrary image types.
A Reanalysis System for the Generation of Mesoscale Climatographies
Authors: Hahmann Andrea N. , Rostkier-Edelstein Dorita , Warner Thomas T. , Vandenberghe Francois , Liu Yubao , Babarsky Richard , Swerdlin Scott P. 
Published: November 2009

Abstract
The use of a mesoscale model–based four-dimensional data assimilation (FDDA) system for generating mesoscale climatographies is demonstrated. This dynamical downscaling method utilizes the fifth-generation Pennsylvania State University–National Center for Atmospheric Research Mesoscale Model (MM5), wherein Newtonian relaxation terms in the prognostic equations continually nudge the model solution toward surface and upper-air observations. When applied to a mesoscale climatography, the system is called Climate-FDDA (CFDDA). Here, the CFDDA system is used for downscaling eastern Mediterranean climatographies for January and July. The downscaling method performance is verified by using independent observations of monthly rainfall, Quick Scatterometer (QuikSCAT) ocean-surface winds, gauge rainfall, and hourly winds from near-coastal towers. The focus is on the CFDDA system’s ability to represent the frequency distributions of atmospheric states in addition to time means. The verification of the monthly rainfall climatography shows that CFDDA captures most of the observed spatial and interannual variability, although the model tends to underestimate rainfall amounts over the sea. The frequency distributions of daily rainfall are also accurately diagnosed for various regions of the Levant, except that very light rainfall days and heavy precipitation amounts are overestimated over Lebanon. The verification of the CFDDA against QuikSCAT ocean winds illustrates an excellent general correspondence between observed and modeled winds, although the CFDDA speeds are slightly lower than those observed. Over land, CFDDA- and the ECMWF-derived wind climatographies when compared with mast observations show similar errors related to their inability to properly represent the local orography and coastline. However, the diurnal variability of the winds is better estimated by CFDDA because of its higher horizontal resolution.
Radiation and Dissipation of Internal Waves Generated by Geostrophic Motions Impinging on Small-Scale Topography: Theory
Authors: Nikurashin Maxim , Ferrari Raffaele 
Published: November 2009

Abstract
Observations and inverse models suggest that small-scale turbulent mixing is enhanced in the Southern Ocean in regions above rough topography. The enhancement extends O(1) km above the topography, suggesting that mixing is supported by the breaking of gravity waves radiated from the ocean bottom. In this study, it is shown that the observed mixing rates can be sustained by internal waves generated by geostrophic motions flowing over bottom topography. Weakly nonlinear theory is used to describe the internal wave generation and the feedback of the waves on the zonally averaged flow. Vigorous inertial oscillations are driven at the ocean bottom by waves generated at steep topography. The wave radiation and dissipation at equilibrium is therefore the result of both geostrophic flow and inertial oscillations differing substantially from the classical lee-wave problem. The theoretical predictions are tested versus two-dimensional high-resolution numerical simulations with parameters representative of Drake Passage. This work suggests that mixing in Drake Passage can be supported by geostrophic motions impinging on rough topography rather than by barotropic tidal motions, as is commonly assumed.
High intertester reliability of the Cumulated Ambulation Score for the evaluation of basic mobility in patients with hip fracture
Authors: Kristensen Morten Tange , Andersen Lene , Bech-Jensen Rie , Moos Malene , Hovmand Bente , Ekdahl Charlotte , Kehlet Henrik 
Published: November 2009

Objective: To examine the intertester reliability of the three activities of the Cumulated Ambulation Score (CAS) and the total CAS, and to define limits for the smallest change in basic mobility that indicates a real change in patients with hip fracture. Design: An intertester reliability study. Setting: An acute 20-bed orthopaedic hip fracture unit. Subjects: Fifty consecutive patients with a median age of 83 (25—75% quartile, 68—86) years. Interventions: The CAS, which describes the patient’s independency in three activities — (1) getting in and out of bed, (2) sit to stand from a chair, and (3) walking ability — was assessed by two independent physiotherapists at postoperative median day 3. Each activity was assessed on a three-point ordinal scale from 0 (not able to) to 2 (independent of human assistance). The cumulated score for each activity provides a total CAS from 0 to 6, with 6 indicating independent ambulation. Main measures: Reliability was evaluated using weighted kappa statistics, the standard error of measurement (SEM) and the smallest real difference (SRD). Results: The kappa coefficient, the SEM and the SRD in the three activities and the total CAS were ≥0.92, ≤0.20 and ≤0.55 CAS points, respectively. Conclusions: The intertester reliability of the CAS is very high, and a change of more than 0.20 and 0.55 CAS points for the total CAS indicates a real change in basic mobility, at group level and for an individual patient, respectively.
Sulphur reduction in fluid catalytic cracking using a kaolin in situ crystallization catalyst modified with vanadium
Authors: Dai Ya-Li , Zheng Shu-Qin , Qian Dong 
Published: November 2009

AbstractSulphur reduction catalysts represent a viable option for S reduction in the fluid catalytic cracking (FCC) process. In this paper, a kaolin in situ crystallization catalyst was modified with vanadium and evaluated in a fixed fluid bed (FFB) reactor. The relation between the acidity of the catalyst, the S reduction rate and the catalyst activity is discussed. The results show that increasing weak Lewis acid acidity favours S reduction in the FCC process. Increasing the V content enhances the weak Lewis acidity, so causing the S reduction rate to increase. The kaolin in situ crystallization catalyst modified with 0.6 wt.% of V leads to a 34.5% reduction in the S content of the liquid product. Comprehensive evaluation of the FFB results and the S reduction ability indicates that the catalyst modified with 0.45 wt.% V provided the best performance.
Copper substitution alone and in the presence of chromium, zinc, cadmium and lead in goethite (α-FeOOH)
Authors: Kaur N. , Singh B. , Kennedy B. J. 
Published: November 2009

AbstractA series of Cu-substituted goethites, single and co-substituted with Cr, Zn, Cd and/or Pb was prepared, having molar ratios equal to 2.00, 3.33 and 5.00 mol%. All the samples contained only goethite, except Cu-, (Cu,Zn)- and (Cu,Pb)-samples synthesized at 5.00 mol% where hematite was also formed. The presence of Cr/Cd suppressed the hematite-forming effects of Cu. The general sequence of metal entry into the single-metal-substituted goethites was Zn = Cr > Cd > Cu > Pb and in di- (5.00 mol%) and tri- (3.33 mol%) metal-substituted goethites was Cu > Zn > Cd > Cr >> Pb. Cu incorporation increased all the unit-cell parameters in single-metal-substituted goethite, and these parameters increased in combination with other metals as follows: Cd > Zn > Cr > Pb in the multimetal-substituted goethites. The Cu-substituted goethite dissolved faster than pure goethite. Co substitutions of Cr/Pb reduced the dissolution rate (kFe), while substitutions of Cd/Zn increased kFe.
Mechano-chemical effects on surface properties and molybdate exchange on hydrotalcite
Authors: Bonifacio-Martínez J. , Serrano-Gómez J. , Del Carmen López-Reyes Ma. , Granados-Correa F. 
Published: November 2009

AbstractThe effects of mechano-chemical treatment on the surface characteristics and sorption properties of hydrotalcite were studied. Non-milled (crushed) and milled samples were characterized by X-ray diffraction (XRD), scanning electron microscopy (SEM), particle size analysis and specific area. A milling time of 2 h decreased the particle size of the hydrotalcite samples from 21 to 8.0 nm, the specific area from 97 to 5.7 m2g–1and the total pore volume from 0.41 to 0.01 cm3. After the crushed and milled samples had been separately calcined at 500ºC, they were agitated with 10–2M Na2MoO4aqueous solutions for 48 h. The molybdate ion content in the regenerated non-milled hydrotalcite samples (HTc-MoO4) was found to be 6.0 meq g–1while in the milled hydrotalcite (HTm-MoO4) samples this content was 2.5 meq g–1. The lower molybdate content was thought to be a result of compaction and, hence, reduced reactivity of the milled HT samples.
Cis/trans-but-2-ene adsorption on natural and modified clinoptilolite
Authors: Faghihian H. , Pirouzi M. 
Published: November 2009

AbstractAdsorption of cis-2-butene and trans-2-butene on clinoptilolite-rich tuff and ion-exchanged forms was investigated. Clinoptilolite samples were characterized by X-ray diffraction (XRD), Fourier-transform infrared (FTIR) spectroscopy, chemical analysis and nitrogen adsorption techniques. Adsorption isotherms for cis and trans 2-butene on purified clinoptilolite (Cp) and modified forms (Na-Cp, K-Cp, Ca-Cp and Mg-Cp) were obtained at pressures up to 2.7 atm. and at 25ºC. The results show that natural clinoptilolite has a considerable potential for separation of the two hydrocarbons. Mg-Cp samples showed maximal uptake of both cis-2-butene and trans-2-butene.