bluuebunny/crossref_metadata_2025 huggingface dataset:
An Investigation Into the Syngas Production From Municipal Solid Waste (MSW) Gasification Under Various Pressures and CO2 Concentration Atmospheres
Authors: Kwon Eilhann , Westby Kelly J. , Castaldi Marco J.
Published: August 2009

The Municipal Solid Waste (MSW) gasification process is a promising candidate for both MSW disposal and syngas production. The MSW gasification process has been characterized thermo-gravimetrically under various experimental atmospheres in order to understand syngas production and char burnout. This preliminary data shows that with any concentration of carbon dioxide in the atmosphere the residual char is reduced about 20% of the original mass (in an inert atmosphere) to about 5%, corresponding to a significant amount of carbon monoxide production (0.7% of CO was produced from a 20mg sample with 100ml/min of purge gas at 825°C). Two main steps of thermal degradation have been observed. The first thermal degradation step occurs at temperatures between 280∼350°C and consists mainly of the decomposition of the biomass component into light C1–3-hydrocarbons. The second thermal degradation step occurs between 380∼450°C and is mainly attributed to polymer components, such as plastics and rubber, in MSW. The polymer component in MSW gave off significant amount of benzene derivatives such as styrene. In order to identify the optimal operating regime for MSW gasification, a series of tests covering a range of temperatures (280∼700°C), pressures (30∼45 Bar), and atmospheres (100% N2, 0∼20%CO2+Bal. N2 with/without steam) have been done and the results are presented here.
Elements of a Successful Waste-to-Energy Boiler Upgrade
Authors: Pethe Samit J. , Dayton Chris , Berz Marcel D. , Peterson Tim
Published: August 2009

Great River Energy operates a waste-to-energy plant in Elk River, Minnesota. The plant burns 850 tons per day of refuse derived fuel (RDF) in three boilers, and its three steam turbines can produce 32 MW of electricity. In the largest of the three units, the No. 3 Boiler, steam generation was restricted by carbon monoxide (CO) and nitrogen oxides (NOx) emission limits. The plant had an interest in improving the combustion performance of the unit, thereby allowing higher average RDF firing rates while staying within emissions compliance. The project was initiated by an engineering site visit and evaluation. The boiler had a history of unstable burning on the stoker grate, which required periodic natural gas co-firing to reduce CO levels. As an outcome to the evaluation, it was decided to install a new overfire air (OFA) system to improve burnout of combustible gases above the grate. Current and new OFA arrangements were evaluated via Computational Fluid Dynamics (CFD) modeling. The results illustrated the limitations of the original OFA system (comprised of multiple rows of small OFA ports on the front and rear furnace walls), which generated inadequate mixing of air and combustible gases in the middle of the boiler. The modeling illustrated the advantages of large and fewer OFA nozzles placed on the side walls in an interlaced pattern, a configuration that has given excellent performance on over 45 biomass-fired boilers of similar design upgraded by Jansen Combustion and Boiler Technologies, Inc. (JANSEN). Installation of the new OFA system was completed in April of 2008. Subsequent testing of the No. 3 Boiler showed that it could reliably meet the state emission levels for CO and NOx (200 ppm and 250 ppm, respectively, corrected to 7% dry flue gas oxygen) while generating 24% more steam than a representative five month period prior to the upgrade. This paper describes the elements that led to a successful project, including: data collection, engineering analyses, CFD modeling, system design, equipment supply, installation, operator training, and startup assistance.
Data Pipeline From CAD to AR Based Assembly Instructions
Authors: Salonen Tapio , Sa¨a¨ski Juha , Woodward Charles , Korkalo Otto , Marstio Ilari , Rainio Kari
Published: August 2009

One of the main challenges of introducing Augmented Reality technology into industrial applications is fast, reliable, low-cost authoring of animated AR content of product data created in 3D CAD systems. In this paper we present a product data information pipeline from industry used commercial CAD systems to a marker-based augmented reality system. The pipeline utilizes ISO 10303 (STEP) data protocol, DFA-Tool (Design For Assembly), and VTT’s proprietary content creation and augmenting software. The pipeline is verified with a real industrial application.
An Immersive VR Application for Interactive Product Concept Generation and Qualitative Evaluation
Authors: Noon Christian , Zhang Ruqin , Winer Eliot , Oliver Jim , Gilmore Brian , Duncan Jerry
Published: August 2009

Currently, new product concepts are evaluated by developing detailed virtual models with Computer Aided Design (CAD) tools followed by evaluation analyses (e.g., finite element analysis, computational fluid dynamics, etc.). Due to the complexity of these evaluation methods, it is generally not possible to model and analyze each of the ideas generated throughout the conceptual design phase of the design process. Thus, promising ideas may be eliminated based solely on insufficient time to model and assess them. Additionally, the analysis performed is usually of much higher detail than needed for such early assessment. By eliminating the time-consuming CAD complexity, engineers could spend more time evaluating additional concepts. To address these issues, a software framework, the Advanced Systems Design Suite (ASDS), was created. The ASDS incorporates a PC user interface with an immersive virtual reality (VR) environment to ease the creation and assessment of conceptual design prototypes individually or collaboratively in a VR environment. Assessment tools incorporate metamodeling approximations and immersive visualization to evaluate the validity of each concept. In this paper, the ASDS framework and interface along with specifically designed immersive VR assessment tools such as state saving, dynamic viewpoint creation, and animation playback are presented alongside a test case example of redesigning a Boeing 777 in the conceptual design phase.
Assembly Planning and Motion Study Using Virtual Reality
Authors: Sung Raymond C. W. , Ritchie James M. , Lim Theodore , Medellin Hugo
Published: August 2009

Carrying out assembly process planning tasks manually is both time-consuming and requires a lot of effort. Due to this, a great deal of research has been carried out on computer-aided process planning (CAPP) and computer-aided assembly planning (CAAP) systems. This paper presents two virtual tools called COSTAR (Cable Organisation System Through Alternative Reality) and HAMMS (Haptic Assembly, Manufacturing and Machining System) that both have an assembly planning capability. To gain an insight into the processes that occur during a design and assembly task, two time and motion study methods called therbligs and chronocyclegraphs have been utilised in both virtual tools to carry out the investigation. In addition, a brief investigation has been carried out to examine the time savings of using the virtual tools in comparison with the traditional manual method.
Evaluating the Impact of Virtual Reality on Mechanical Design Education
Authors: Peruzzini Margherita , Mengoni Maura , Germani Michele
Published: August 2009

The promise of Virtual Reality in design environments is to facilitate the interaction with digital models and to enhance the results of design activity. Design education is one of the most recent and interesting applications. Thanks to technological advances in human-computer interfaces, Virtual Reality represents a new way to stimulate design students and to develop innovative teaching methods. The paper explores the impact of Virtual Reality technologies on design learning, with particular attention to mechanical product design. It is focused on the analysis of cognitive and technical aspects of learning processes and the definition of a proper evaluation protocol. The protocol is based on the classification of the most meaningful activities in mechanical engineering teaching and the identification of a set of metrics that enable to objectively evaluate the learning process. Assessing how VR supports design education, an experimental study is proposed. It is based on the comparison of three different approaches performed by two-dimensional drawings, by 3D CAD models and, finally, by virtual reality technologies.
Force Models and GPU-Based Computation for Fluid Interactions in Surgical Simulation Design
Authors: Rianto Sugeng , Li Ling
Published: August 2009

In this paper, we solve the force model and 3D fluid dynamics solver for surgical simulation designs by taking a combination of a cubic interpolated fluid solver and the advantage of the parallelism and programmability of GPU. In comparison to other methods, we present innovation in tree aspects. First, force models in haptic for fluid interactions is generated by GPU-CPU message passing scheme to get rapid development of haptic feedback modes for fluid dynamic data. Second, rapid solution in fluid dynamic solvers is developed by applying cubic interpolated propagation method. This method only split Navier-Stokes equations (NSEs) into advection and non-advection equation to generate immediate fluid dynamic solvers. To get more acceleration in the computation, we pack these equations into channels of texels. Third, beside we take advantage of the parallelism and programmability of the GPU where computation models are performed on pixels that can be considered to be a grid of cells, the CPU-GPU balancing is included; therefore, despite of the complexity of the anatomical geometry, processing on multiple vertices and pixels can be done simultaneously in parallel. The data are also passed to CPU to control the haptic in providing kinesthetic interaction and felling. These strategies provide effective enough to simulate fluid dynamic model for real-time interaction in 3D computer graphic for PC platform. Our experimental tests prove that fluid flowing on various obstacles with haptic interactions on the human anatomical model can be effectively and efficiently simulated on the reasonable frame rate with a realistic synthetic visualization.
Flourishing After the End-Permian Mass Extinction
Authors: Marshall Charles R. , Jacobs David K.
Published: August 2009

Cephalopods, which live in the water column, recovered much faster from the end-Permian mass extinction than did bottom-dwelling fauna.
Coupling Strongly, Discretely
Authors: Hone James , Deshpande Vikram V.
Published: August 2009

Mechanical systems acting as electronic quantum dots can be tuned at the level of single electrons.
Unpersuasive Thoughts and Unhelpful Ideas
Authors: Wolpert Lewis
Published: August 2009

Science, Truth, and Democracy
. Philip Kitcher. Oxford University Press, New York, 2001. 233 pp. $29.95. ISBN 0-19-514583-6.

Building on his earlier work, especially through a consideration of molecular genetics, Kitcher argues for a philosophy that recognizes scientific truth but "permits social consensus to determine which avenues to investigate."
Sequencing 40 Silkworm Genomes Unravels History of Cultivation
Authors: Normile Dennis
Published: August 2009

In a
paper
published online this week by
Science
, a research team of primarily Chinese scientists reports on the use of modern genomic analyses to probe the domestication of the silkworm.
Warning: Don't Let Your Elders Brainwash You
Authors: Bhattacharjee Yudhijit
Published: August 2009

Catherine Cesarsky, the departing president of the International Astronomical Union, warns against the dangers of excessive planning in astronomy.
How to Make a Collider
Authors: Cho Adrian
Published: August 2009

A synchrotron circulates particles in one direction, so it takes some extra work to make one into a collider.
Yersinia pestisCan Bypass Protective Antibodies to LcrV and Activation with Gamma Interferon To Survive and Induce Apoptosis in Murine Macrophages
Authors: Noel Betty L. , Lilo Sarit , Capurso Daniel , Hill Jim , Bliska James B.
Published: August 2009

Yersinia pestis, the agent of plague, uses a type III secretion injectisome to deliver Yop proteins into macrophages to counteract phagocytosis and induce apoptosis. Additionally, internalizedY. pestiscan survive in the phagosomes of naïve or gamma interferon (IFN-γ)-activated macrophages by blocking vacuole acidification. TheY. pestisLcrV protein is a target of protective antibodies. The binding of antibodies to LcrV at the injectisome tip results in neutralization of the apoptosis ofY. pestis-infected macrophages and is used as an in vitro correlate of protective immunity. The cytokines IFN-γ and tumor necrosis factor alpha can cooperate with anti-LcrV to promote protection against lethalY. pestisinfection in mice. It is not known if these phagocyte-activating cytokines cooperate with anti-LcrV to increase the killing of the pathogen and decrease apoptosis in macrophages. We investigated how anti-LcrV and IFN-γ impact bacterial survival and apoptosis in cultured murine macrophages infected withY. pestisKIM5.Y. pestisKIM5 opsonized with polyclonal or monoclonal anti-LcrV was used to infect macrophages treated with or without IFN-γ. The phagocytosis and survival of KIM5 and the apoptosis of macrophages were measured at different time points postinfection. The results show that anti-LcrV reduced apoptosis at an early time point (5 h) but not at a later time point (24 h). Polyclonal anti-LcrV was unable to inhibit apoptosis at either time point in IFN-γ-activated macrophages. Additionally, anti-LcrV was ineffective at promoting the killing of KIM5 in naïve or activated macrophages. We conclude thatY. pestiscan bypass protective antibodies to LcrV and activation with IFN-γ to survive and induce apoptosis in murine macrophages.
Variation in T-SPOT.
TB
Spot Interpretation between Independent Observers from Different Laboratories
Authors: Franken Willeke P. J. , Thijsen Steven , Wolterbeek Ron , Bouwman John J. M. , el Bannoudi Hanane , Kik Sandra V. , van Dissel Jaap T. , Arend Sandra M.
Published: August 2009

T-SPOT.
TB
is a specific assay for the diagnosis of tuberculosis. The assay needs to be performed with freshly isolated cells, and interpretation requires training. T-SPOT.
TB
has been used in various clinical-epidemiological settings, but so far no studies have evaluated the effect of interobserver variation in test reading. Our aim was to evaluate variation between different observers in reading T-SPOT.
TB
results. The study was nested within an ongoing cohort study, in which part of the T-SPOT.
TB
had been performed with frozen material. Culture plates were read visually by four different observers from two laboratories and by two automated readers. Of 313 T-SPOT.
TB
assays, 235 were performed with fresh cells and 78 were performed with frozen cells. No significant difference was found between results obtained with fresh cells and those obtained with frozen cells. The percentage of positive results varied between readers by maximally 15%; five/six raters were within a 6% difference in positive results. Analysis of the observed interrater differences showed that some individuals systematically counted more spots than others did. Because test interpretation includes subtraction of background values, this systematic variance had little influence on interindividual differences. The test result as positive or negative varied between independent raters, mainly due to samples with values around the cutoff. This warrants further study regarding determinants affecting the reading of T-SPOT.
TB
.
homB
Status of
Helicobacter pylori
as a Novel Marker To Distinguish Gastric Cancer from Duodenal Ulcer
Authors: Jung Sung Woo , Sugimoto Mitsushige , Graham David Y. , Yamaoka Yoshio
Published: August 2009

The
hom
family of
Helicobacter pylori
outer-membrane proteins, especially the
homB
gene, has been suggested as a novel virulence factor; however, the clinical association and function of this gene are still unclear. We evaluated the presence of the
homA
,
homB
, and
cagA
genes in 286 strains isolated from patients in the U.S. and Colombian populations (126 with gastritis, 96 with duodenal ulcer, and 64 with gastric cancer) by PCR. The results were compared with the clinical presentation and gastric injury. The prevalence of the
homB
gene was significantly higher in strains isolated from gastric-cancer patients (71.9%) than in those from duodenal ulcer patients (52.1%) (
P
= 0.012). In a multivariate analysis, the presence of the
cagA
gene significantly increased the risk for developing gastric cancer and duodenal ulcer, with the presence of the
homB
gene acting as a factor that could distinguish gastric cancer from duodenal ulcer (adjusted odds ratio, 3.033; 95% confidence interval, ∼1.37 to ∼6.73).
cagA
status was correlated with
homB
status (
r
= 0.323;
P
< 0.01). A histological analysis showed that
cagA
status was associated with inflammation and atrophy both in the antrum and in the corpus, while
homB
status was associated with inflammation and atrophy in the corpus.
homB
gene status might be susceptible to gastric-cancer development such that the
homB
gene is used as a factor for discriminating the risk of gastric cancer from that of duodenal ulcer.
Monoclonal Antibodies to VP1 Recognize a Broad Range of Enteroviruses
Authors: Miao Lynn Yihong , Pierce Christina , Gray-Johnson Jennifer , DeLotell Jill , Shaw Carl , Chapman Nate , Yeh Elaine , Schnurr David , Huang Yung T.
Published: August 2009

Enteroviruses (EVs) are common seasonal viruses that are associated with a variety of diseases. High-quality monoclonal antibodies (MAbs) are needed to improve the accuracy of EV diagnosis in clinical laboratories. In the present study, the full-length VP1 genes of poliovirus 1 (Polio 1) and coxsackievirus B3 (Cox B3) were cloned, and the encoded proteins were expressed and used as antigens in an attempt to raise broad-spectrum MAbs to EVs. Two pan-EV MAbs were isolated: one raised against Polio 1 VP1 and the other against Cox B3 VP1. The binding sites of both pan-EV MAbs were mapped to an amino acid sequence within a conserved region in the N terminus of Polio 1 VP1 by peptide and competition enzyme-linked immunosorbent assay. Two additional MAbs, an EV70-specific MAb and an EV71/Cox A16-bispecific MAb, developed against EV70 and 71 VP1 proteins, were pooled with the two pan-EV MAbs (pan-EV MAb mix) and tested for their sensitivity and specificity in the staining of various virus-infected cells. The pan-EV MAb mix detected all 40 prototype EVs tested and showed no cross-reactivity to 18 different non-EV human viruses. Compared with two commercially available EV tests, the pan-EV MAb mix exhibited higher specificity than one test and broader spectrum reactivity than the other. Thus, our study demonstrates that full-length Polio 1 VP1 and Cox B3 VP1 can serve as effective antigens for developing a pan-EV MAb and that the pan-EV MAb mix can be used for the laboratory diagnosis of a wide range of EV infections.
Validation of Vitek 2 Nonfermenting Gram-Negative Cards and Vitek 2 Version 4.02 Software for Identification and Antimicrobial Susceptibility Testing of Nonfermenting Gram-Negative Rods from Patients with Cystic Fibrosis
Authors: Otto-Karg Ines , Jandl Stefanie , Müller Tobias , Stirzel Beate , Frosch Matthias , Hebestreit Helge , Abele-Horn Marianne
Published: August 2009

Accurate identification and antimicrobial susceptibility testing (AST) of nonfermenters from cystic fibrosis patients are essential for appropriate antimicrobial treatment. This study examined the ability of the newly designed Vitek 2 nonfermenting gram-negative card (NGNC) (new gram-negative identification card; bioMérieux, Marcy-l'Ètoile, France) to identify nonfermenting gram-negative rods from cystic fibrosis patients in comparison to reference methods and the accuracy of the new Vitek 2 version 4.02 software for AST compared to the broth microdilution method. Two hundred twenty-four strains for identification and 138 strains for AST were investigated. The Vitek 2 NGNC identified 211 (94.1%) of the nonfermenters correctly. Among morphologically atypical microorganisms, five strains were misidentified and eight strains were determined with low discrimination, requiring additional tests which raised the correct identification rate to 97.8%. Regarding AST, the overall essential agreement of Vitek 2 was 97.6%, and the overall categorical agreement was 92.9%. Minor errors were found in 5.1% of strains, and major and very major errors were found in 1.6% and 0.3% of strains, respectively. In conclusion, the Vitek NGNC appears to be a reliable method for identification of morphologically typical nonfermenters and is an improvement over the API NE system and the Vitek 2 GNC database version 4.01. However, classification in morphologically atypical nonfermenters must be interpreted with care to avoid misidentification. Moreover, the new Vitek 2 version 4.02 software showed good results for AST and is suitable for routine clinical use. More work is needed for the reliable testing of strains whose MICs are close to the breakpoints.
Cerebral Aspergillosis Caused by
Aspergillus granulosus
Authors: Sutton Deanna A. , Wickes Brian L. , Romanelli Anna M. , Rinaldi Michael G. , Thompson Elizabeth H. , Fothergill Annette W. , Dishop Megan K. , Elidemir Okan , Mallory George B. , Moonnamakal Siby P. , Adesina Adekunle M. , Schecter Marc G.
Published: August 2009

Disseminated disease by
Aspergillus granulosus
has been reported only once previously in a cardiac transplant recipient. We report a fatal central nervous system infection in a lung transplant recipient. Key features of this species in the section
Usti
include growth at 37°C and large, randomly spaced aggregates of variably shaped Hülle cells.
Comparison of Nine Commercially Available
Clostridium difficile
Toxin Detection Assays, a Real-Time PCR Assay for
C
.
difficile tcdB
, and a Glutamate Dehydrogenase Detection Assay to Cytotoxin Testing and Cytotoxigenic Culture Methods
Authors: Eastwood Kerrie , Else Patrick , Charlett André , Wilcox Mark
Published: August 2009

The continuing rise in the incidence of
Clostridium difficile
infection is a cause for concern, with implications for patients and health care systems. Laboratory diagnosis largely relies on rapid toxin detection kits, although assays detecting alternative targets, including glutamate dehydrogenase (GDH) and toxin genes, are now available. Six hundred routine diagnostic diarrheal samples were tested prospectively using nine commercial toxin detection assays, cytotoxin assay (CYT), and cytotoxigenic culture (CYTGC) and retrospectively using a GDH detection assay and PCR for the toxin B gene. The mean sensitivity and specificity for toxin detection assays were 82.8% (range, 66.7 to 91.7%) and 95.4% (range, 90.9 to 98.8%), respectively, in comparison with CYT and 75.0% (range, 60.0 to 86.4%) and 96.1% (91.4 to 99.4%), respectively, in comparison with CYTGC. The sensitivity and specificity of the GDH assay were 90.1% and 92.9%, respectively, compared to CYT and 87.6% and 94.3%, respectively, compared to CYTGC. The PCR assay had the highest sensitivity of all the tests in comparison with CYT (92.2%) and CYTGC (88.5%), and the specificities of the PCR assay were 94.0% and 95.4% compared to CYT and CYTGC, respectively. All kits had low positive predictive values (range, 48.6 to 86.8%) compared with CYT, assuming a positive sample prevalence of 10% (representing the hospital setting), which compromises the clinical utility of single tests for the laboratory diagnosis of
C
.
difficile
infection. The optimum rapid single test was PCR for toxin B gene, as this had the highest negative predictive value. Diagnostic algorithms that optimize test combinations for the laboratory diagnosis of
C
.
difficile
infection need to be defined.
Comparative Evaluation of a Commercially Available Automated System for Extraction of Viral DNA from Whole Blood: Application to Monitoring of Epstein-Barr Virus and Cytomegalovirus Load
Authors: Pillet Sylvie , Bourlet Thomas , Pozzetto Bruno
Published: August 2009

The NucliSENS easyMAG automated system was compared to the column-based Qiagen method for Epstein-Barr virus (EBV) or cytomegalovirus (CMV) DNA extraction from whole blood before viral load determination using the corresponding R-gene amplification kits. Both extraction techniques exhibited a total agreement of 81.3% for EBV and 87.2% for CMV.
Variability of Immediate-Early Gene 62 in German Varicella-Zoster Virus Wild-Type Strains
Authors: Sauerbrei A. , Bohn K. , Zell R. , Wutzler P.
Published: August 2009

Varicella-zoster virus strains of European genotypes have developed a high variability of open reading frame (ORF) 62 during their occurrence over many years in Germany. M1 strains in Germany display a uniform ORF 62 pattern, suggesting that these strains were introduced from Africa and/or Asia via few sources during the last years.
Carriage Rate of
Enterocytozoon bieneusi
in an Orphanage in Bangkok, Thailand
Authors: Pagornrat Watcharee , Leelayoova Saovanee , Rangsin Ram , Tan-Ariya Peerapan , Naaglor Tawee , Mungthin Mathirut
Published: August 2009

This study was performed to evaluate the incidence of and risk factors for
E
nterocytozoon bieneusi
carriage in an orphanage in Bangkok, Thailand.
E. bieneusi
has been identified by PCR every 2 consecutive months since June 2003. The incidence ranged between 0.6 and 4.7/100 person-months. Person-to-person transmission was indicated by risk factor analysis and genotyping information.
Analysis of Nucleotide Sequences of Human Parvovirus B19 Genome Reveals Two Different Modes of Evolution, a Gradual Alteration and a Sudden Replacement: a Retrospective Study in Sapporo, Japan, from 1980 to 2008
Authors: Suzuki Masashi , Yoto Yuko , Ishikawa Aki , Tsutsumi Hiroyuki
Published: August 2009

There have been no long-term systematic analyses of the molecular epidemiology of human parvovirus B19 (B19V). We investigated the variations of nucleotide sequences of B19V strains collected in Sapporo, Japan, from 1980 to 2008. In that period, six outbreaks of erythema infectiosum occurred regularly at 5-year intervals. The B19V strains collected successively, regardless of the outbreak, were analyzed for nucleotide variation in the subgenomic NS1-VP1u junction. The isolated strains can be classified into 10 subgroups. Two patterns of change of endemic strains were observed. One was a dynamic replacement of strains that occurred almost every 10 years, and the other was a gradual change consisting of an accumulation of point mutations.
The Epstein-Barr Virus Protein Kinase BGLF4 and the Exonuclease BGLF5 Have Opposite Effects on the Regulation of Viral Protein Production
Authors: Feederle Regina , Mehl-Lautscham Anja M. , Bannert Helmut , Delecluse Henri-Jacques
Published: August 2009

The Epstein-Barr virus BGLF4 and BGLF5 genes encode a protein kinase and an alkaline exonuclease, respectively. Both proteins were previously found to regulate multiple steps of virus replication, including lytic DNA replication and primary egress. However, while inactivation of BGLF4 led to the downregulation of several viral proteins, the absence of BGLF5 had the opposite effect. Using recombinant viruses that lack both viral enzymes, we confirm and extend these initial observations, e.g., by showing that both BGLF4 and BGLF5 are required for proper phosphorylation of the DNA polymerase processivity factor BMRF1. We further found that neither BGLF4 nor BGLF5 is required for baseline viral protein production. Complementation with BGLF5 downregulated mRNA levels and translation of numerous viral genes, though to various degrees, whereas BGLF4 had the opposite effect. BGLF4 and BGLF5 influences on viral expression were most pronounced for BFRF1 and BFLF2, two proteins essential for nuclear egress. For most viral genes studied, cotransfection of BGLF4 and BGLF5 had only a marginal influence on their expression patterns, showing that BGLF4 antagonizes BGLF5-mediated viral gene shutoff. To be able to exert its functions on viral gene expression, BGLF4 must be able to escape BGLF5's shutoff activities. Indeed, we found that BGLF5 stimulated the BGLF4 gene's transcription through an as yet uncharacterized molecular mechanism. The BGLF4/BGLF5 enzyme pair builds a regulatory loop that allows fine-tuning of virus protein production, which is required for efficient viral replication.
Involvement of SSRP1 in Latent Replication of Kaposi's Sarcoma-Associated Herpesvirus
Authors: Hu Jianhong , Liu Eugene , Renne Rolf
Published: August 2009

Kaposi's sarcoma-associated herpesvirus (also named human herpesvirus 8) is a γ-herpesvirus that undergoes both lytic and latent infection. During latent infection, two viral elements are required: latency-associated nuclear antigen (LANA), which functions as an origin binding protein, and the latent origin, which resides within the terminal repeats (TRs) of the viral genome. Previously, we identified two
cis
-elements within the TRs which are required for latent DNA replication: two LANA binding sites (LBS1 and LBS2 [LBS1/2]) and a GC-rich replication element (RE) upstream of LBS1/2. To further characterize the RE, we constructed a 71-bp minimal replicon (MR) and performed a detailed mutational analysis. Our data indicate that the first 8 nucleotides within the RE are critical for replication. Moreover, both the position and the distance between the RE and LBS1/2 can affect origin replication activity, suggesting that the RE may function as a loading pad for cellular proteins involved in replication. Using biotinylated DNA fragments of wild-type or mutant MRs as probes, we identified 30 proteins that preferentially bind to the origin. Among these proteins, structure-specific recognition protein 1 (SSRP1), a subunit of the FACT complex, and telomeric repeat binding factor 2 (TRF2) formed complexes with LANA at the MR region. Furthermore, the small interfering RNA-based knockdown of SSRP1, but not the dominant-negative-based knockdown of TRF2, significantly decreased the efficiency of LANA-dependent DNA replication. These results indicate that SSRP1 is a novel cellular protein involved in LANA-dependent DNA replication.
Murine Gammaherpesvirus 68 Infection of Gamma Interferon-Deficient Mice on a BALB/c Background Results in Acute Lethal Pneumonia That Is Dependent on Specific Viral Genes
Authors: Lee Katherine S. , Cool Carlyne D. , van Dyk Linda F.
Published: August 2009

Gamma interferon (IFN-γ) is critical for the control of chronic infection with murine gammaherpesvirus 68 (γHV68). Current data indicate that IFN-γ has a lesser role in the control of acute replication of γHV68. Here, we show that IFN-γ-deficient mice on the BALB/c genetic background poorly control acute viral replication and succumb to early death by acute pneumonia. Notably, this acute, lethal pneumonia was dependent not only on the viral dose, but also on specific viral genes including the viral cyclin gene, previously identified to be important in promoting optimal chronic infection and reactivation from latency.
Dynamin- and Lipid Raft-Dependent Entry of Decay-Accelerating Factor (DAF)-Binding and Non-DAF-Binding Coxsackieviruses into Nonpolarized Cells
Authors: Patel Kunal P. , Coyne Carolyn B. , Bergelson Jeffrey M.
Published: August 2009

Group B coxsackieviruses (CVB) use the CVB and adenovirus receptor (CAR) to enter and infect cells. Some CVB also bind to decay-accelerating factor (DAF), but that interaction alone is insufficient for infection. We previously found that CVB3 entry into polarized human intestinal cells (Caco-2) occurs by a caveolin-dependent but dynamin-independent mechanism that requires DAF-mediated tyrosine kinase signals. In this study, we examined how CVB enter and infect nonpolarized HeLa cells and how DAF binding affects these processes. Using immunofluorescence microscopy and a combination of dominant-negative proteins, small interfering RNAs, and drugs targeting specific endocytic pathways, we found that both DAF-binding and non-DAF-binding virus isolates require dynamin and lipid rafts to enter and infect cells. Unlike what we observed in Caco-2 cells, CVB3 entered HeLa cells with CAR. We found no role for clathrin, endosomal acidification, or caveolin. Inhibition of tyrosine kinases blocked an early event in infection but did not prevent entry of virus into the cell. These results indicate that CVB3 entry into nonpolarized HeLa cells differs significantly from entry into polarized Caco-2 cells and is not influenced by virus binding to DAF.
Mutational Analysis Reveals a Noncontractile but Interactive Role of Actin and Profilin in Viral RNA-Dependent RNA Synthesis
Authors: Harpen Mary , Barik Tiasha , Musiyenko Alla , Barik Sailen
Published: August 2009

As obligatory parasites, viruses co-opt a variety of cellular functions for robust replication. The expression of the nonsegmented negative-strand RNA genome of respiratory syncytial virus (RSV), a significant pediatric pathogen, absolutely requires actin and is stimulated by the actin-regulatory protein profilin. As actin is a major contractile protein, it was important to determine whether the known functional domains of actin and profilin were important for their ability to activate RSV transcription. Analyses of recombinant mutants in a reconstituted RSV transcription system suggested that the divalent-cation-binding domain of actin is critically needed for binding to the RSV genome template and for the activation of viral RNA synthesis. In contrast, the nucleotide-binding domain and the N-terminal acidic domain were needed neither for template binding nor for transcription. Specific surface residues of actin, required for actin-actin contact during filamentation, were also nonessential for viral transcription. Unlike actin, profilin did not directly bind to the viral template but was recruited by actin. Mutation of the interactive residues of actin or profilin, resulting in the loss of actin-profilin binding, also abolished profilin's ability to stimulate viral transcription. Together, these results suggest that actin acts as a classical transcription factor for the virus by divalent-cation-dependent binding to the viral template and that profilin acts as a transcriptional cofactor, in part by associating with actin. This essential viral role of actin is independent of its contractile cellular role.
Gene Mapping and Phylogenetic Analysis of the Complete Genome from 30 Single-Stranded RNA Male-Specific Coliphages (Family
Leviviridae
)
Authors: Friedman Stephanie D. , Genthner Fred J. , Gentry Jennifer , Sobsey Mark D. , Vinjé Jan
Published: August 2009

Male-specific single-stranded RNA (FRNA) coliphages belong to the family
Leviviridae
. They are classified into two genera (
Levivirus
and
Allolevivirus
), which can be subdivided into four genogroups (genogroups I and II in
Levivirus
and genogroups III and IV in
Allolevivirus
). Relatively few strains have been completely characterized, and hence, a detailed knowledge of this virus family is lacking. In this study, we sequenced and characterized the complete genomes of 19 FRNA strains (10
Levivirus
strains and 9
Allolevivirus
strains) and compared them to the 11 complete genome sequences available in GenBank. Nucleotide similarities among strains of
Levivirus
genogroups I and II were 75% to 99% and 83 to 94%, respectively, whereas similarities among strains of
Allolevivirus
genogroups III and IV ranged from 70 to 96% and 75 to 95%, respectively. Although genogroup I strain fr and genogroup III strains MX1 and M11 share only 70 to 78% sequence identity with strains in their respective genogroups, phylogenetic analyses of the complete genome and the individual genes suggest that strain fr should be grouped in
Levivirus
genogroup I and that the MX1 and M11 strains belong in
Allolevivirus
genogroup III. Strains within each genus share >50% sequence identity, whereas between the two genera, strains have <40% nucleotide sequence identity. Overall, amino acid composition, nucleotide similarities, and replicase catalytic domain location contributed to phylogenetic assignments. A conserved eight-nucleotide signature at the 3′ end of the genome distinguishes leviviruses (5′ ACCACCCA 3′) from alloleviviruses (5′ TCCTCCCA 3′).
Ruthenium-catalyzed efficient routes to oxindole derivatives
Authors: Tabatabaeian Khalil , Mamaghani Manouchehr , Mahmoodi Nosratollah , Khorshidi Alireza
Published: August 2009

Ruthenium-catalyzed preparation of oxindoles from one-pot trimerization of indoles under oxidative conditions and from electrophilic substitution reaction of indoles with isatins or isatin-derived imines under very mild reaction conditions is reported.
Dammarane triterpenoid saponins from Bacopa monnieri
Authors: Bhandari Pamita , Kumar Neeraj , Singh Bikram , Kaur Inderjeet
Published: August 2009

Bacopa monnieri is a well-known Ayurvedic Indian medicinal plant traditionally used as a memory enhancer. Its memory-enhancing effect is mainly attributed to dammarane triterpenoid saponins. In the present study, two new dammarane-type triterpenoid saponins, bacopaside-XI (1) and bacopaside-XII (2), together with known compounds, bacopaside IV, bacopaside V, and apigenin, were isolated from the aerial parts of the B. monnieri . The structures of the new saponins were elucidated as 3-O-[α-L-arabinofuranosyl(1→3)]-6-O-sulfonyl-β-D-glucopyranosyl pseudojujubogenin (1) and 3-O-{β-D-glucopyranosyl(1→3)[α-L-arabinofuranosyl(1→2)]-β-D-glucopyranosyl}-20-O-α-L-arabinopyranosyl pseudojujubogenin (2) on the basis of extensive investigations of 1D and 2D NMR (HMQC and HMBC), ESI-QTOF-MS/MS spectroscopic methods, and chemical evidences.
Rhodium(I)–(N-heterocyclic carbene)–diphosphine complexes
Authors: Sun Hongsui , Yu Xiao-Yan , Marcazzan Paolo , Patrick Brian O. , James Brian R.
Published: August 2009

Reactions of [RhCl(COE)(IPr)]2 (1) and [RhCl(COE)(IMes)]2 (2) (COE = cyclooctene; IPr = N,N′-bis(2,6-diisopropylphenyl)imidazolin-2-ylidene; IMes = N,N′-bis(2,4,6-trimethylphenyl)imidazolin-2-ylidene) with the diphosphines Ph2P(CH2)nPPh2 and 1,2-bis(diphenylphosphino)benzene (dppbz) give the N-heterocyclic carbene (NHC) – diphosphine – rhodium(I) complexes: RhCl(NHC)[Ph2P(CH2)nPPh2] [NHC = IPr, n = 1 (3); NHC = IMes, n = 1 (4); NHC = IPr, n = 2 (5); NHC = IMes, n = 2 (6); NHC = IPr, n = 4 (7); NHC = IMes, n = 4 (8)] and RhCl(NHC)(dppbz) [NHC = IPr (9); NHC = IMes (10)]. All the complexes are characterized by 1H, 31P{1H}, and 13C{1H} NMR spectroscopy, elemental analysis, and mass spectrometry. Complexes 3, 7, and 9 are also characterized crystallographically. In benzene solution, the complexes decompose in the presence of O2 with formation of the diphosphine dioxide, whereas reaction with CO leads to replacement of the NHC ligand to give known carbonyl–diphosphine complexes.
RARE TOP DECAYS IN THE SMALLEST HIGGS MODEL WITH T-PARITY
Authors: YANG HUI-DI , YUE CHONG-XING , WEN JIA , WANG YONG-ZHI
Published: August 2009

We consider the rare top decays t → qh and [Formula: see text] (q = u or c) in the context of the smallest Higgs model with T-parity (called the LHT model). We find that the LHT model can significantly enhance the values of the branching ratios Br (t → qh) and [Formula: see text] with respect to those predicted by the standard model (SM).
CHIRAL COLOR SYMMETRY AND POSSIBLE G′-BOSON EFFECTS AT THE TEVATRON AND LHC
Authors: MARTYNOV M. V. , SMIRNOV A. D.
Published: August 2009

A gauge model with chiral color symmetry is considered and possible effects of the color G′-boson octet predicted by this symmetry are investigated in dependence on two free parameters, the mixing angle θG and G′ mass mG′. The allowed region in the mG'–θG plane is found from the Tevatron data on the cross section [Formula: see text] and forward–backward asymmetry [Formula: see text] of the [Formula: see text] production. The mass limits for the G′-boson are shown to be stronger than those for the axigluon. A possible effect of the G′-boson on the [Formula: see text] production at the LHC is discussed and the mass limits providing for the G′-boson evidence at the LHC are estimated in dependence on θG.
HOW IS TRANSVERSITY RELATED TO HELICITY FOR QUARKS AND ANTIQUARKS INSIDE THE PROTON?
Authors: BOURRELY CLAUDE , BUCCELLA FRANCO , SOFFER JACQUES
Published: August 2009

We consider the quark and antiquark transversity distributions inside a polarized proton and study how they are expected to be related to the corresponding helicity distributions, both in sign and magnitude. Our considerations lead to simple predictions in good agreement with their first determination for light quarks from experimental data. We also give our predictions for the light antiquarks transversity distributions, so far unknown.
STUDIES OF THE SPIN-HAMILTONIAN PARAMETERS AND OPTICAL SPECTRUM BAND POSITIONS FOR THE Yb3+ ION IN Tm3Al5O12 CRYSTALS
Authors: LIU HONG-GANG , ZHENG WEN-CHEN , FENG WEN-LIN , YANG WEI-QING
Published: August 2009

The spin-Hamiltonian parameters (g factors gi and hyperfine structure constants Ai, where i = x, y, z) and optical spectrum band positions of the Yb 3+ ion in the rhombically-distorted Tm 3+ site of Tm 3 Al 5 O 12 garnet crystal are calculated by a complete diagonalization (of the energy matrix) method, in which the Zeeman and hyperfine interaction terms are also included in the conventional Hamiltonian. From the calculations, the observed spin-Hamiltonian parameters of Tm 3 Al 5 O 12: Yb 3+ are explained reasonably and the optical spectrum band positions are suggested. The rationality of these suggested optical spectrum band positions is discussed by comparing them with the observed values of Yb 3+ ions in similar aluminum garnet ( Yb 3 Al 5 O 12, Y 3 Al 5 O 12 and Lu 3 Al 5 O 12) crystals.
MULTI-SCHEME FOR TELEPORTING AN UNKNOWN N-PARTICLE STATE
Authors: ZHA XIN-WEI , SONG HAI-YANG
Published: August 2009

By a transformation operator, we find that the transformation operator is not related to the unknown N-particle state. Here, we propose a multi-scheme for the teleportation of an arbitrary and unknown N-particle state by using the method of transformation operator. The proper transformation operator depends on the quantum channel and the measurement basis. The theoretical explanations of some quantum channels are given by transformation operators. Furthermore, we give the analysis for teleporting an arbitrary and unknown N-particle state.
AMPLIFYING CHARACTERISTICS OF Er3+/Yb3+ CODOPED SERIES-CASCADED DOUBLE-MICRORING RESONATORS
Authors: WANG YUHAI , MA CHUNSHENG , YAN XIN , ZHANG DAMING
Published: August 2009

Formulas for the transfer function and the output power gain are presented for an Er 3+/ Yb 3+ codoped series-cascaded double microring resonator (MRR). Around the pumping wavelength of 974 nm and the central signal wavelength of 1530 nm, the effects of the pump power, signal power, Er 3+/ Yb 3+ dopant concentrations and amplitude coupling ratios on the signal output spectrum are analyzed. The computed results show that the device can possess both the filtering and amplifying functions for the signal light. In the case of the amplitude coupling ratio between the microring and the channel being 0.17, and that between two microrings being 0.012, the device can produce more than 10.13 dB signal power gain.
MODE COMPETITION IN A TWO-MODE LASER SYSTEM SUBJECT TO BOTH PUMP NOISE AND QUANTUM NOISE
Authors: XIANG YOULIN , MEI DONGCHENG
Published: August 2009

The laser intensity Langevin equations for a two-mode ring laser subject to both pump noise and quantum noise have been obtained by a phase-locking method. By means of stochastic simulation, the mode competition between two modes for different combinations of the strength of the pump noise, the coupling constant and the difference of pump parameters have been investigated. The results show the following. (i) The pump noise dramatically affects the mode competition. (ii) The mode competition is quite sensitive to changing of the coupling constant near the line center. (iii) The mode competition gets stronger and stronger with increasing absolute value of the difference of pump parameters.
ON RECTANGULAR COVERING PROBLEMS
Authors: PORSCHEN STEFAN
Published: August 2009

Many applications like image processing, data compression or pattern recognition require a covering of a set of n points most often located in the (discrete) plane by rectangles due to specific cost constraints. In this paper we provide exact dynamic programming algorithms for covering point sets by regular rectangles, that have to obey certain boundary conditions, namely all rectangles must have lengths of at least k, which is a prescribed problem parameter. The concrete objective function underlying our optimization problem is the sum of area, circumference and a constant over all rectangles forming a covering. This objective function can be motivated by requirements of numerically solving PDE's by discretization over (adaptive multi-)grids.

More precisely, we propose exact deterministic algorithms for such problems based on a (set theoretic) dynamic programming approach yielding a time bound of O(n23n). In a second step this bound is (asymptotically) decreased to O(n62n) by exploiting some structural features. Finally, a generalization of the problem and its solution methods is discussed for the case of arbitrary (finite) space dimension.
Abundant Genetic Variation + Strong Selection = Multivariate Genetic Constraints: A Geometric View of Adaptation
Authors: Walsh Bruce , Blows Mark W.
Published: August 2009

Evolutionary biology has struggled to explain the coexistence of two basic observations: Genetic variation is found in almost all traits in the presence of strong natural and sexual selection in natural populations. These two observations are in direct conflict as such selection should deplete genetic variation. Furthermore, the presence of genetic variation in a trait, and selection acting on that trait, is often not sufficient for the trait to respond to selection. Here, we bring together geometric perspectives on mutation, selection, and genetic variation and show how the perceived incompatibility between these two observations is a consequence of taking a trait-by-trait approach to the multivariate problem of genetic variation and selection. We conclude that the simultaneous presence of widespead genetic variation in, and strong selection on, individual traits indicates that substantial multivariate genetic constraints are likely to be present in natural populations.
Nongenetic Inheritance and Its Evolutionary Implications
Authors: Bonduriansky Russell , Day Troy
Published: August 2009

Modern evolutionary biology is founded on the Mendelian-genetic model of inheritance, but it is now clear that this model is incomplete. Empirical evidence shows that environment (encompassing all external influences on the genome) can impose transgenerational effects and generate heritable variation for a broad array of traits in animals, plants, and other organisms. Such effects can be mediated by the transmission of epigenetic, cytoplasmic, somatic, nutritional, environmental, and behavioral variation. Building on the work of many authors, we outline a general framework for conceptualizing nongenetic inheritance and its evolutionary implications. This framework shows that, by decoupling phenotypic change from the genotype, nongenetic inheritance can circumvent the limitations of genetic inheritance and thereby influence population dynamics and alter the fitness landscape. The weight of theory and empirical evidence indicates that nongenetic inheritance is a potent factor in evolution that can engender outcomes unanticipated under the Mendelian-genetic model.