bluuebunny/crossref_metadata_2025 huggingface dataset:
A New College
Science
Prize
Authors: Alberts Bruce
Published: January 2011

To start the New Year,
Science
is pleased to announce the “
Science
prize for Inquiry-Based Instruction” to highlight outstanding “modules” for teaching introductory college science courses that can readily spread to other settings and schools. Therefore, a unit can neither be unusually expensive nor require highly specialized expertise. To be eligible, a module must provide a coherent piece of coursework in a field such as biology, chemistry, physics, or earth sciences and require 8 to 50 hours of student effort. It should also be free-standing: that is, suitable for teaching as a discrete unit, independent of other modules in the course. How do inquiry-based science modules differ from other science lessons, and why does
Science
care enough about them to create a special prize?
The Battle Over the 2011 Budget: What's at Stake for Research
Authors: Mervis Jeffrey
Published: January 2011

How will Congress play the 2011 budget card? The answer could shape U.S. science for years to come.
A Slimy Invader Blooms in the Rivers of Patagonia
Authors: Segura Patricio
Published: January 2011

In 2010, to the dismay of naturalists and Chile's tourism industry, the alga
Didymosphenia geminata
gained a foothold in Patagonia. Officials in Chile have launched a massive effort to halt it, but its propagation may be unstoppable.
Was North Africa the Launch Pad for Modern Human Migrations?
Authors: Balter Michael
Published: January 2011

A growing number of researchers suspect that long-neglected North Africa was the original home of the modern humans who first trekked out of the continent.
The Power of One
Authors: Leslie Mitch
Published: January 2011

Rather than probe masses of cells all at once, scientists are now applying new research techniques to individual cells.
Meeting for Peer Review at a Resort That's Virtually Free
Authors: Bohannon John
Published: January 2011

More than 19,000 scientists travel to NSF headquarters each year to take part in grant evaluation panels. Could their avatars do the job as well?
Development and Validation of a Multiplex Microsphere-Based Assay for Detection of Domestic Cat (
Felis catus
) Cytokines
Authors: Wood Britta A. , O'Halloran Kevin P. , VandeWoude Sue
Published: January 2011

Cytokines are essential signaling molecules that mediate the innate immune response, and therefore their presence can be of diagnostic, prognostic, and pathogenic significance. Microsphere-based immunoassays allow rapid and accurate evaluation of cytokine levels in several species, including humans, dogs, and mice; however, technology to evaluate domestic cat (
Felis catus
) cytokines has been limited to single-analyte enzyme-linked immunosorbent assays (ELISAs). Microsphere-based immunoassays provide an attractive alternative technology for detecting and quantifying multiple analytes in a single assay using as little as 50 μl of sample. We describe the development and validation of a microsphere-based assay for three commonly analyzed domestic cat cytokines (gamma interferon, interleukin-10, and interleukin-12/interleukin-23 p40) using reagents from commercially available ELISAs. The assay was optimized for capture and detection antibody concentrations, streptavidin-phycoerythrin concentration, and number of microspheres. The validated lower and upper quantitation limits were 31 and 1,000 pg/ml for gamma interferon, 63 and 2,000 pg/ml for interleukin-10, and 39 and 625 pg/ml for interleukin-12/interleukin-23 p40. Cytokine concentrations in peripheral blood mononuclear cell supernatants were measured, and results obtained by the microsphere assay were correlated with values obtained with commercially available ELISA kits. This technology is a convenient and reproducible assay to evaluate domestic cat cytokine responses elicited by a variety of diseases.
Prevalence of Antibodies against Seasonal Influenza A and B Viruses in Children in Netherlands
Authors: Bodewes R. , de Mutsert G. , van der Klis F. R. M. , Ventresca M. , Wilks S. , Smith D. J. , Koopmans M. , Fouchier R. A. M. , Osterhaus A. D. M. E. , Rimmelzwaan G. F.
Published: January 2011

To gain insight into the age at which children become infected with influenza viruses for the first time, we analyzed the seroprevalence of antibodies against influenza viruses in children 0 to 7 years of age in the Netherlands. Serum samples were collected during a cross-sectional population-based study in 2006 and 2007 and were tested for the presence of antibodies against influenza A/H1N1, A/H3N2, and B viruses representative of viruses present in previous influenza seasons using the hemagglutination inhibition assay. The seroprevalence of antibodies to influenza virus was higher in children 1 to 6 months of age than in children 7 to 12 months of age, which likely reflects the presence of maternally derived antibodies. The proportion of study subjects >1 year of age with detectable antibodies against influenza viruses gradually increased with age until they reached the age of 6 years, when they all had antibodies to at least one influenza A virus. These findings may have implications for the development of vaccination strategies aiming at the protection of young children against seasonal and/or pandemic influenza virus infection.
Molecular Epidemiology of Mycobacterium avium subsp. paratuberculosis in a Longitudinal Study of Three Dairy Herds
Authors: Pradhan Abani K. , Mitchell Rebecca M. , Kramer Aagje J. , Zurakowski Michael J. , Fyock Terry L. , Whitlock Robert H. , Smith Julia M. , Hovingh Ernest , Van Kessel Jo Ann S. , Karns Jeffrey S. , Schukken Ynte H.
Published: January 2011

The objective of this study was to evaluate whether cows that were low shedders ofMycobacterium aviumsubsp.paratuberculosiswere passively shedding or truly infected withM. aviumsubsp.paratuberculosis. We also investigated whether it is possible that theseM. aviumsubsp.paratuberculosis-infected animals could have been infected as adults by contemporary high-shedding animals (supershedders). TheM. aviumsubsp.paratuberculosisisolates were obtained from a longitudinal study of three dairy herds in the northeastern United States. Isolates were selected from fecal samples and tissues at slaughter from all animals that were culture positive at the same time that supershedders were present in the herds. Shedding levels (CFU ofM. aviumsubsp.paratuberculosis/g of feces) for the animals at each culture-positive occasion were determined. Using a multilocus short-sequence-repeat technique, we found 15 different strains ofM. aviumsubsp.paratuberculosisfrom a total of 142 isolates analyzed. Results indicated herd-specific infection patterns; there was a clonal infection in herd C, with 89% of isolates from animals sharing the same strain, whereas herds A and B showed several different strains infecting the animals at the same time. Tissues from 80% of cows with at least one positive fecal culture (other than supershedders) were culture positive, indicating a trueM. aviumsubsp.paratuberculosisinfection. The results ofM. aviumsubsp.paratuberculosisstrain typing and observed shedding levels showed that at least 50% of low shedders have the same strain as that of a contemporary supershedder. Results of this study suggest that in a dairy herd, more of the low-shedding cows are truly infected withM. aviumsubsp.paratuberculosisthan are passively sheddingM. aviumsubsp.paratuberculosis. The sharing of strains between low shedders and the contemporary supershedders suggests that low shedders may have been infected by environmental exposure ofM. aviumsubsp.paratuberculosis.
Ribosomal RNA Sequence Analysis of Brucella Infection Misidentified as Ochrobactrum anthropi Infection
Authors: Horvat Rebecca T. , El Atrouni Wissam , Hammoud Kassem , Hawkinson Dana , Cowden Scott
Published: January 2011

A
Brucella
isolate was identified from purulent material collected during a hip surgery. Two previous blood cultures from the same patient yielded
Ochrobactrum anthropi
. After rRNA sequencing, all the isolates were identified as
Brucella
species and subsequently serotyped as
Brucella suis
. Misidentification of
Brucella
species remains a problem with bacterial identification systems.
Comparison of Bruker Biotyper Matrix-Assisted Laser Desorption Ionization–Time of Flight Mass Spectrometer to BD Phoenix Automated Microbiology System for Identification of Gram-Negative Bacilli
Authors: Saffert Ryan T. , Cunningham Scott A. , Ihde Sherry M. , Monson Jobe Kristine E. , Mandrekar Jayawant , Patel Robin
Published: January 2011

We compared the BD Phoenix automated microbiology system to the Bruker Biotyper (version 2.0) matrix-assisted laser desorption ionization–time of flight (MALDI-TOF) mass spectrometry (MS) system for identification of Gram-negative bacilli, using biochemical testing and/or genetic sequencing to resolve discordant results. The BD Phoenix correctly identified 363 (83%) and 330 (75%) isolates to the genus and species level, respectively. The Bruker Biotyper correctly identified 408 (93%) and 360 (82%) isolates to the genus and species level, respectively. The 440 isolates were grouped into common (308) and infrequent (132) isolates in the clinical laboratory. For the 308 common isolates, the BD Phoenix and Bruker Biotyper correctly identified 294 (95%) and 296 (96%) of the isolates to the genus level, respectively. For species identification, the BD Phoenix and Bruker Biotyper correctly identified 93% of the common isolates (285 and 286, respectively). In contrast, for the 132 infrequent isolates, the Bruker Biotyper correctly identified 112 (85%) and 74 (56%) isolates to the genus and species level, respectively, compared to the BD Phoenix, which identified only 69 (52%) and 45 (34%) isolates to the genus and species level, respectively. Statistically, the Bruker Biotyper overall outperformed the BD Phoenix for identification of Gram-negative bacilli to the genus (
P
< 0.0001) and species (
P
= 0.0005) level in this sample set. When isolates were categorized as common or infrequent isolates, there was statistically no difference between the instruments for identification of common Gram-negative bacilli (
P
> 0.05). However, the Bruker Biotyper outperformed the BD Phoenix for identification of infrequently isolated Gram-negative bacilli (
P
< 0.0001).
High Rate of Exophiala dermatitidis Recovery in the Airways of Patients with Cystic Fibrosis Is Associated with Pancreatic Insufficiency
Authors: Kondori Nahid , Gilljam Marita , Lindblad Anders , Jönsson Bodil , Moore Edward R. B. , Wennerås Christine
Published: January 2011

The black-pigmented fungusExophiala dermatitidisis considered to be a harmless colonizer of the airways of cystic fibrosis (CF) patients. The aim of this study was to establish the recovery rate ofE. dermatitidisin respiratory specimens from CF patients, transplant recipients, and subjects with other respiratory disorders in Sweden. Second, we wished to determine if particular clinical traits were associated withE. dermatitidiscolonization of the airways and the antifungal susceptibility profiles ofExophialastrains. Sputum and bronchoalveolar lavage samples (n= 492) derived from 275 patients were investigated.E. dermatitidiswas isolated in respiratory specimens from 19% (18/97) of the CF patients but in none of the other patient categories. All isolates were recovered after 6 to 25 days of incubation on erythritol-chloramphenicol agar (ECA) medium. Morphological and genetic analyses confirmed species identity. Pancreatic insufficiency was positively associated with the presence ofE. dermatitidisin sputum samples (P= 0.0198). Antifungal susceptibility tests demonstrated that voriconazole and posaconazole had the lowest MICs againstE. dermatitidis. In conclusion,E. dermatitidisis a frequent colonizer of the respiratory tract in CF patients in Sweden and appears to be associated with more advanced disease. WhetherE. dermatitidisis pathogenic remains to be elucidated.
Aminoglycoside-Resistant Aeromonas hydrophila as Part of a Polymicrobial Infection following a Traumatic Fall into Freshwater
Authors: Shak Joshua R. , Whitaker Jennifer A. , Ribner Bruce S. , Burd Eileen M.
Published: January 2011

Amikacin is a first-line treatment for
Aeromonas
infection due to high efficacy. There are few reports of aminoglycoside-resistant
Aeromonas
spp. We report a soft tissue infection containing multiple pathogens, including a strain of
Aeromonas hydrophila
resistant to amikacin, tobramycin, and multiple cephalosporins.
Rapid Stool-Based Diagnosis of Clostridium difficile Infection by Real-Time PCR in a Children's Hospital
Authors: Luna Ruth Ann , Boyanton Bobby L. , Mehta Seema , Courtney Ebony M. , Webb C. Renee , Revell Paula A. , Versalovic James
Published: January 2011

Clostridium difficile
is a major cause of nosocomial antibiotic-associated infectious diarrhea and pseudomembranous colitis. Detection of
C. difficile
by anaerobic bacterial culture and/or cytotoxicity assays has been largely replaced by rapid enzyme immunoassays (EIA). However, due to the lack of sensitivity of stool EIA, we developed a multiplex real-time PCR assay targeting the
C. difficile
toxin genes
tcdA
and
tcdB
. Stool samples from hospitalized pediatric patients suspected of having
C. difficile
-associated disease were prospectively cultured on cycloserine-cefoxitin-fructose agar following alcohol shock. Six testing modalities were evaluated, including stool EIA, culture EIA, and real-time PCR (
tcdA
and
tcdB
) of cultured isolates and stool samples. Real-time PCR detection was performed with
tcdA
and
tcdB
gene-specific primers and hydrolysis probes using the LightCycler platforms (Roche Diagnostics, Indianapolis, IN). A total of 157 samples from 96 pediatric patients were analyzed. The sensitivities of stool real-time PCR and stool EIA were 95% and 35%, respectively, with a specificity of 100% for both methods. The lower limit of detection of the stool real-time PCR was 30 CFU/ml of stool sample per reaction for
tcdA
and
tcdB
. This study highlights the poor performance of stool toxin EIAs in pediatric settings. Direct detection of
C. difficile
toxin genes in stool samples by real-time PCR showed sensitivity superior to that of stool and culture EIAs and performance comparable to that of real-time PCR assay of cultured isolates. Real-time PCR of DNA from stool samples is a rapid and cost-effective diagnostic modality for children that should facilitate appropriate patient management and halt the practice of serial testing by EIA.
Distribution of Putative Virulence Genes in Streptococcus mutans Strains Does Not Correlate with Caries Experience
Authors: Argimón Silvia , Caufield Page W.
Published: January 2011

Streptococcus mutans
, a member of the human oral flora, is a widely recognized etiological agent of dental caries. The cariogenic potential of
S. mutans
is related to its ability to metabolize a wide variety of sugars, form a robust biofilm, produce copious amounts of lactic acid, and thrive in the acid environment that it generates. The remarkable genetic variability present within the species is reflected at the phenotypic level, notably in the differences in the cariogenic potential between strains. However, the genetic basis of these differences is yet to be elucidated. In this study, we surveyed by PCR and DNA hybridization the distribution of putative virulence genes, genomic islands, and insertion sequences across a collection of 33 strains isolated from either children with severe early childhood caries (S-ECC) or those who were caries free (CF). We found this genetically diverse group of isolates to be remarkably homogeneous with regard to the distribution of the putative virulence genes and genetic elements analyzed. Our findings point to the role of other factors in the pathogenesis of S-ECC, such as uncharacterized virulence genes, differences in gene expression and/or enzymatic activity, cooperation between
S. mutans
strains or with other members of the oral biota, and host factors.
Comparison of Two Mycoplasma genitalium Real-Time PCR Detection Methodologies
Authors: Twin Jimmy , Taylor Nicole , Garland Suzanne M. , Hocking Jane S. , Walker Jennifer , Bradshaw Catriona S. , Fairley Christopher K. , Tabrizi Sepehr N.
Published: January 2011

Established in-house quantitative PCR (qPCR) assays to detect the
Mycoplasma genitalium
adhesion protein (MgPa) and the 16S rRNA gene were found to be comparable for screening purposes, with a kappa value of 0.97 (95% confidence interval [CI], 0.94 to 1.01) and no difference in bacterial load quantified (
P
= 0.4399).
Comparison of the Broth Microdilution Methods of the European Committee on Antimicrobial Susceptibility Testing and the Clinical and Laboratory Standards Institute for Testing Itraconazole, Posaconazole, and Voriconazole against Aspergillus Isolates
Authors: Pfaller M. , Boyken L. , Hollis R. , Kroeger J. , Messer S. , Tendolkar S. , Diekema D.
Published: January 2011

We compared EUCAST and CLSI antifungal susceptibility testing methods for itraconazole, posaconazole, and voriconazole by testing 245
Aspergillus
clinical isolates. The essential agreement (EA) between methods was excellent: 100% (itraconazole), 98.4% (posaconazole), and 99.6% (voriconazole) assessing EA at ±2 dilutions and 99.6% (itraconazole), 87.7% (posaconazole), and 96.3% (voriconazole) at ±1 dilution.
Methicillin-Resistant Staphylococcus aureus Colonization at Different Body Sites: a Prospective, Quantitative Analysis
Authors: Mermel Leonard A. , Cartony Jennifer M. , Covington Pauline , Maxey Gail , Morse Dan
Published: January 2011

We quantified methicillin-resistantStaphylococcus aureus(MRSA) carriage. The greater the log10count in samples from the nares, the greater the likelihood that other body sites had been colonized. Log10counts among body sites were correlated. The greatest sensitivity value (98%) was determined for the combined results from 2 sites: the nares and the groin.
Roscovitine Inhibits EBNA1 Serine 393 Phosphorylation, Nuclear Localization, Transcription, and Episome Maintenance
Authors: Kang Myung-Soo , Lee Eun Kyung , Soni Vishal , Lewis Timothy A. , Koehler Angela N. , Srinivasan Viswanathan , Kieff Elliott
Published: January 2011

Latent Epstein-Barr virus (EBV) infection causes human lymphomas and carcinomas. EBV usually persists as an episome in malignant cells. EBV episome persistence, replication, and gene expression are dependent on EBNA1 binding to multiple cognate sites in oriP. To search for inhibitors of EBNA1- and oriP-dependent episome maintenance or transcription, a library of 40,550 small molecules was screened for compounds that inhibit EBNA1- and oriP-dependent transcription and do not inhibit EBNA1- and oriP-independent transcription. This screening identified roscovitine, a selective inhibitor of cyclin-dependent kinase 1 (CDK1), CDK2, CDK5, and CDK7. Based on motif predictions of EBNA1 serine 393 as a CDK phosphorylation site and486RALL489and580KDLVM584as potential cyclin binding domains, we hypothesized that cyclin binding to EBNA1 may enable CDK1, -2, -5, or -7 to phosphorylate serine 393. We found thatEscherichia coli-expressed EBNA1 amino acids 387 to 641 were phosphorylatedin vitroby CDK1-, -2-, -5-, and -7/cyclin complexes and serine 393 phosphorylation was roscovitine inhibited. Further, S393A mutation abrogated phosphorylation. S393A mutant EBNA1 was deficient in supporting EBNA1- and oriP-dependent transcription and episome persistence, and roscovitine had little further effect on the diminished S393A mutant EBNA1-mediated transcription or episome persistence. Immunoprecipitated FLAG-EBNA1 was phosphorylatedin vitro, and roscovitine inhibited this phosphorylation. Moreover, roscovitine decreased nuclear EBNA1 and often increased cytoplasmic EBNA1, whereas S393A mutant EBNA1 was localized equally in the nucleus and cytoplasm and was unaffected by roscovitine treatment. These data indicate that roscovitine effects are serine 393 specific and that serine 393 is important in EBNA1- and oriPCp-dependent transcription and episome persistence.
Transcription of Preintegrated HIV-1 cDNA Modulates Cell Surface Expression of Major Histocompatibility Complex Class I via Nef
Authors: Sloan Richard D. , Kuhl Björn D. , Donahue Daniel A. , Roland André , Bar-Magen Tamara , Wainberg Mark A.
Published: January 2011

Although transcription from unintegrated human immunodeficiency virus type 1 (HIV-1) DNA can occur inside infected cells, yielding all classes of viral mRNA transcripts, the translation of viral proteins is very limited. One of the proteins made is Nef, but it is unclear whether Nef produced in this way is able to play a role in immune evasion as occurs with integrated virus. We therefore asked whether transcription from preintegrated HIV-1 cDNAs could result in Nef-mediated modulation of cell surface major histocompatibility complex class I (MHC-I) expression. We infected a Rev-CEM green fluorescent protein (GFP) reporter cell line with virus and blocked integration though use of either an inactive integrase or the integrase inhibitor raltegravir. Infected cells were assayed by flow cytometry for cell surface expression of the HLA-A, HLA-B, and HLA-C allotypes (HLA-ABC), HLA-A31, and HLA-E. Viral RNA and DNA products were assayed via quantitative PCR (qPCR). The prevention of integration had no effect, relative to productively infected cells, on levels of expression of multiply spliced viral mRNA transcripts and Nef protein. Downregulation of HLA-ABC and HLA-A31 also occurred at levels similar to those seen in cells in which integration had occurred. Parallel experiments assaying cell surface HLA-ABC expression in infected activated primary CD4+T cells produced a similar pattern of results. Hence, the capacity of HIV-1 to modulate MHC-I is not linked to its ability to integrate. Thus, Nef-mediated evasion of host immune responsiveness might be attributable, in part at least, to transcription from unintegrated viral DNA.
Receptor Tyrosine Kinase Inhibitors Block Multiple Steps of Influenza A Virus Replication
Authors: Kumar Naveen , Liang Yuhong , Parslow Tristram G. , Liang Yuying
Published: January 2011

Host signaling pathways play important roles in the replication of influenza virus, but their functional effects remain to be characterized at the molecular level. Here we identify two receptor tyrosine kinase inhibitors (RTKIs) of the tyrphostin class that exhibit robust antiviral activity against influenza A virus replication in cultured cells. One of these (AG879) is a selective inhibitor of the nerve growth factor receptor and human epidermal growth factor receptor 2 (TrkA/HER2) signaling; the other, tyrphostin A9 (A9), inhibits the platelet-derived growth factor receptor (PDGFR) pathway. We find that each inhibits at least three postentry steps of the influenza virus life cycle: AG879 and A9 both strongly inhibit the synthesis of all three influenza virus RNA species, block Crm1-dependent nuclear export, and also prevent the release of viral particles through a pathway that is modulated by the lipid biosynthesis enzyme farnesyl diphosphate synthase (FPPS). Tests of short hairpin RNA (shRNA) knockdown and additional small-molecule inhibitors confirmed that interventions targeting TrkA can suppress influenza virus replication. Our study suggests that host cell receptor tyrosine kinase signaling is required for maximal influenza virus RNA synthesis, viral ribonucleoprotein (vRNP) nuclear export, and virus release and that specific RTKIs hold promise as novel anti-influenza virus therapeutics.
Kaposi's Sarcoma-Associated Herpesvirus ORF57 Promotes Escape of Viral and Human Interleukin-6 from MicroRNA-Mediated Suppression
Authors: Kang Jeong-Gu , Pripuzova Natalia , Majerciak Vladimir , Kruhlak Michael , Le Shu-Yun , Zheng Zhi-Ming
Published: January 2011

Kaposi's sarcoma-associated herpesvirus (KSHV) lytic infection increases the expression of viral and human interleukin-6 (vIL-6 and hIL-6, respectively), an important factor for cell growth and pathogenesis. Here, we report genome-wide analysis of viral RNA targets of KSHV ORF57 by a novel UV-cross-linking and immunoprecipitation (CLIP) assay. We identified 11 viral transcripts as putative ORF57 targets and demonstrate that vIL-6 mRNA is an authentic target of ORF57. Disrupting the ORF57 gene in the KSHV genome leads to inefficient expression of vIL-6. With transient transfection, the expression of vIL-6 could be enhanced greatly in the presence of ORF57 in a dose-dependent manner. We found that the open reading frame (ORF) region of vIL-6 RNA contains an MRE (MTA [ORF57]-responsive element) composed of two motifs, MRE-A and MRE-B, and binding of ORF57 to these two motifs stabilizes vIL-6 RNA and promotes vIL-6 translation. We demonstrate that vIL-6 MRE-B bears an miR-1293 binding site and that, mechanistically, ORF57 competes with miR-1293 for the same binding site to interact with vIL-6 RNA, thereby preventing vIL-6 RNA from association with the miR-1293-specified RNA-induced silencing complex (RISC). Consistent with this, ORF57 also interacts with an miR-608 binding site in the hIL-6 ORF and prevents miR-608 repression of hIL-6. Collectively, our results identify a novel function of ORF57 in being responsible for stabilization of viral and human IL-6 RNAs and the corresponding enhancement of RNA translation. In addition, our data provide the first evidence that a tumor virus may use a viral protein to interfere with microRNA (miRNA)-mediated repression of an miRNA target to induce cell proliferation and tumorigenesis during virus infection.
A Comprehensive Structure-Function Comparison of Hepatitis C Virus Strain JFH1 and J6 Polymerases Reveals a Key Residue Stimulating Replication in Cell Culture across Genotypes
Authors: Schmitt Melanie , Scrima Nathalie , Radujkovic Danijela , Caillet-Saguy Célia , Simister Philip C. , Friebe Peter , Wicht Oliver , Klein Rahel , Bartenschlager Ralf , Lohmann Volker , Bressanelli Stéphane
Published: January 2011

The hepatitis C virus (HCV) genotype 2a isolate JFH1 represents the only cloned HCV wild-type sequence capable of efficient replication in cell culture as well as
in vivo
. Previous reports have pointed to NS5B, the viral RNA-dependent RNA polymerase (RdRp), as a major determinant for efficient replication of this isolate. To understand the contribution of the JFH1 NS5B gene at the molecular level, we aimed at conferring JFH1 properties to NS5B from the closely related J6 isolate. We created intragenotypic chimeras in the NS5B regions of JFH1 and J6 and compared replication efficiency in cell culture and RdRp activity of the purified proteins
in vitro
, revealing more than three independent mechanisms conferring the role of JFH1 NS5B in efficient RNA replication. Most critical was residue I405 in the thumb domain of the polymerase, which strongly stimulated replication in cell culture by enhancing overall
de novo
RNA synthesis. A structural comparison of JFH1 and J6 at high resolution indicated a clear correlation of a closed-thumb conformation of the RdRp and the efficiency of the enzyme at
de novo
RNA synthesis, in accordance with the proposal that I405 enhances
de novo
initiation. In addition, we identified several residues enhancing replication independent of RdRp activity
in vitro
. The functional properties of JFH1 NS5B could be restored by a few single-nucleotide substitutions to the J6 isolate. Finally, we were able to enhance the replication efficiency of a genotype 1b isolate with the I405 mutation, indicating that this mechanism of action is conserved across genotypes.
Budding Capability of the Influenza Virus Neuraminidase Can Be Modulated by Tetherin
Authors: Yondola Mark A. , Fernandes Fiona , Belicha-Villanueva Alan , Uccelini Melissa , Gao Qinshan , Carter Carol , Palese Peter
Published: January 2011

We have determined that, in addition to its receptor-destroying activity, the influenza virus neuraminidase is capable of efficiently forming virus-like particles (VLPs) when expressed individually from plasmid DNA. This observation applies to both human subtypes of neuraminidase, N1 and N2. However, it is not found with every strain of influenza virus. Through gain-of-function and loss-of-function analyses, a critical determinant within the neuraminidase ectodomain was identified that contributes to VLP formation but is not sufficient to accomplish release of plasmid-derived VLPs. This sequence lies on the plasma membrane-proximal side of the neuraminidase globular head. Most importantly, we demonstrate that the antiviral restriction factor tetherin plays a role in determining the strain-specific limitations of release competency. If tetherin is counteracted by small interfering RNA knockdown or expression of the HIV anti-tetherin factor vpu, budding and release capability is bestowed upon an otherwise budding-deficient neuraminidase. These data suggest that budding-competent neuraminidase proteins possess an as-yet-unidentified means of counteracting the antiviral restriction factor tetherin and identify a novel way in which the influenza virus neuraminidase can contribute to virus release.
Genetic Elements in the VP Region of Porcine Parvovirus Are Critical to Replication Efficiency in Cell Culture
Authors: Fernandes Sandra , Boisvert Maude , Tijssen Peter
Published: January 2011

Factors controlling porcine parvovirus (PPV) replication efficiency are poorly characterized. Two prototype strains of PPV, NADL-2 and Kresse, differ greatly in pathogenic capacity both
in vivo
and
in vitro
, yet their genomic sequence is nearly identical (13 single-nucleotide substitutions and a 127-nucleotide noncoding repeated sequence). We have created a series of chimeras of these strains to identify the genetic elements involved in replication efficiency in the host porcine cell line. While the capsid proteins ultimately determine viral replication fitness, interaction between the NS1 protein and the
VP
gene occurs and involves interaction with the noncoding repeated sequence.
Functional Genetic and Biophysical Analyses of Membrane Disruption by Human Adenovirus
Authors: Moyer Crystal L. , Wiethoff Christopher M. , Maier Oana , Smith Jason G. , Nemerow Glen R.
Published: January 2011

The identification of the adenovirus (AdV) protein that mediates endosome penetration during infection has remained elusive. Several lines of evidence from previous studies suggest that the membrane lytic factor of AdV is the internal capsid protein VI. While these earlier results imply a role for protein VI in endosome disruption, direct evidence during cell entry has not been demonstrated. To acquire more definitive proof, we engineered random mutations in a critical N-terminal amphipathic α-helix of VI in an attempt to generate AdV mutants that lack efficient membrane penetration and infection. Random mutagenesis within the context of the AdV genome was achieved via the development of a novel technique that incorporates both error-prone PCR and recombineering. Using this system, we identified a single mutation, L40Q, that significantly reduced infectivity and selectively impaired endosome penetration. Furthermore, we obtained biophysical data showing that the lack of efficient endosomalysis is associated with reduced insertion of the L40Q mutation in protein VI (VI-L40Q) into membranes. Our studies indicate that protein VI is the critical membrane lytic factor of AdV during cellular entry and reveal the biochemical basis for its membrane interactions.
Effects of Microtubule Modulators on HIV-1 Infection of Transformed and Resting CD4 T Cells
Authors: Yoder Alyson , Guo Jia , Yu Dongyang , Cui Zongqiang , Zhang Xian-En , Wu Yuntao
Published: January 2011

Previous studies have observed fluorescently labeled HIV particles tracking along microtubule networks for nuclear localization. To provide direct evidence for the involvement of microtubules in early steps of HIV infection of human CD4 T cells, we used multiple microtubule modulators such as paclitaxel (originally called taxol; 1 μM), vinblastine (1 and 10 μM), colchicine (10 and 100 μM), and nocodazole (10 and 100 μM) to disturb microtubule networks in transformed and resting CD4 T cells. Although these drugs disrupted microtubule integrity, almost no inhibition of HIV-1 infection was observed. Our results do not appear to support an essential role for microtubules in the initiation of HIV infection of CD4 T cells.
Titanocene and ansa-titanocene complexes bearing 2,6-bis(isopropyl)phenoxide ligand(s). Syntheses, characterization and use in catalytic dehydrocoupling polymerization of phenylsilane
Authors: Horáček Michal , Merna Jan , Gyepes Róbert , Sýkora Jan , Kubišta Jiří , Pinkas Jiří
Published: January 2011

Aryloxychloro and bis(aryloxy) titanocenes of general formula L2TiCl2–x(OAr′)x where L = η5-C5H5 (x = 1 (1) and 2 (2)), L2 = SiMe2(η5-C5H4)2 (x = 1 (3) and 2 (4)), and Ar′ = 2,6-(CHMe2)2C6H3 were prepared by the reaction of corresponding titanocene dichloride with LiOAr′ and characterized by spectroscopic methods and compound 3 by single crystal X-ray diffraction analysis. The bulky aryloxy ligand in 1 and 3 exerts a hindered rotation around the Ti–O bond on the 1H NMR time scale, resulting in its dynamic behavior in CDCl3 solution. Variable temperature NMR measurements proved the rotation barrier in 3 (ΔG‡298 = 13.9 ± 0.3 kcal/mol) to be lower than that in 1 (ΔG‡298 = 14.7 ± 0.2 kcal/mol) as a consequence of the more open titanocene shell in the ansa-structure of 3. The catalytic behavior of complexes 1–4, [(η5-C5H5)2TiCl2] and [{SiMe2(η5-C5H4)2}TiCl2], was examined in dehydrocoupling polymerization of phenylsilane under comparable conditions, showing a remarkable higher activity for the titanocene complexes with regards to the ansa-titanocene ones. The order of catalytic activities 2 ~ 1 > [(η5-C5H5)2TiCl2] >> [{SiMe2(η5-C5H4)2}TiCl2] ~ 3 ~ 4 reveals the aryloxy ligands to have an enhancing effect on activity in the titanocene series.
HUMANOID LOW-LEVEL CONTROLLER DEVELOPMENT BASED ON A REALISTIC SIMULATION
Authors: LIMA JOSÉ L. , GONÇALVES JOSÉ C. , COSTA PAULO G. , MOREIRA A. PAULO
Published: January 2011

This article describes a joint trajectory optimized controller developed in a humanoid robot simulator following the real robot characteristics. As simulation is a powerful tool for speeding up the control software development, the proposed accurate simulator allows to fulfill this goal. The simulator, based on the Open Dynamics Engine and GLScene graphics library, provides instant visual feedback. The proposed simulator, with realistic dynamics, allows to design and test behaviors and control strategies without access to the real hardware in order to carry out research on robot control without damaging the real robot. The low-level joints controller techniques, such as acceleration, speed, and energy consumption minimization, are discussed and experimental results are presented in order to validate the proposed simulator.
ON THE REDEFINITION OF FAN OUT METRIC FOR HUMAN ROBOT INTERACTIONS WITH HUMANOID SOCCER ROBOTS
Authors: ELARA MOHAN RAJESH , CALDERON CARLOS ANTONIO ACOSTA , ZHOU CHANGJIU , WIJESOMA WIJERUPAGE SARDHA
Published: January 2011

Fan out (FO) is adopted as a general index among human robot interaction researchers in predicting the maximum number of robots a single operator can handle simultaneously while maintaining performance at acceptable levels. Neglect tolerance model forms the basis for FO metric that assumes ideal conditions wherein the operator switches control between robots sequentially based on acceptable performance ignoring any false alarms due to erroneous interactions. In this article, we redefine the FO metric to account for any additional demands due to the occurrence of false alarms, as these additional demands could lead to task failure. Experiments with our virtual and real humanoid soccer robots across tele-operation and semi-autonomous modes of autonomy showed significant drop in FO predictions with inclusion of demands due to false alarms for all experimental cases.
VISUAL DETECTION OF LEGGED ROBOTS AND ITS APPLICATION TO ROBOT SOCCER PLAYING AND REFEREEING
Authors: RUIZ-DEL-SOLAR JAVIER , ARENAS MATIAS , VERSCHAE RODRIGO , LONCOMILLA PATRICIO
Published: January 2011

The visual detection of robots is a difficult but relevant problem in several robotic applications. In this article, a framework for the robust and fast visual detection of legged robots is proposed. This framework uses cascades of nested classifiers, the Adaboost boosting algorithm, and domain-partitioning-based weak classifiers. Using the proposed framework, frontal, profile, and back detectors for AIBO robots (model ERS7), as well as detectors for humanoid robots, are built. The detection rate (DR) of the obtained systems is quite high: 90% with an average of 0.1 false positives (FPs) per image, when the final detections are filtered out using context information (horizon line). In addition, a robot referee that uses these detectors to track players during a soccer game is described. Experiment results showed that the referee achieves very high robot DRs (98.7% DR with ~ 1 false detection every 16 images) and fast processing speed.
STABILITY ANALYSIS AND ROBUST CONTROL OF A PLANAR UNDERACTUATED BIPED ROBOT
Authors: DEHGHANI REZA , FATTAH ABBAS
Published: January 2011

Stability analysis is one of the main issues in the research area of biped robots with point feet. This article develops stability analysis and robust control of a planar biped robot with point feet with one degree of underactuation. A stability analysis is presented for the bipedal motion comprising single support and impact phases by using Poincaré map for nonlinear systems. Then, the stability conditions of periodic orbits are derived and stable gait pattern is determined using an optimization process. Thereafter, a robust sliding mode control with a time-invariant feedback is proposed to track stable gait in the presence of parameter uncertainties of the biped. Proposed approach is carried out for two types of bipeds, namely, a normal model and a balanced model in which the biped center of mass located at the hip using a novel model. Energy efficiency of biped is investigated for both models. Moreover, the stability of biped motion is studied in the presence of an unexpected stair. Simulation results show the biped motion quickly converges to cyclic motion during the first gait in both models.
UNDERACTUATED HAND DYNAMIC MODELING, ITS REAL-TIME SIMULATION, AND CONTROL
Authors: HUANG HAI , PANG YONG-JIE , LI JIANG , FAN SHAO-WEI , WANG XIN-QING , LIU HONG
Published: January 2011

The forward and inverse dynamic models of the underactuated 2-DOF finger have been established in this article based on virtual spring approach. This approach not only avoids the solution of differential-algebraic equations but also leads to a completely decoupled dynamic model that is ideal for directly inverse dynamic analysis, real-time dynamic simulation and control. To verify this approach, an underactuated 3-joint finger has been brought forward. Simulation results from Matlab/Simulink are consistent with those obtained from ADAMS grasp simulations. For the hand real-time dynamic control, the velocity observer has been established based on the dynamic model, the adaptive curve fitting with the observer has obtained precise velocity signals, made up the uncertain parameters such as torsion spring, inertial, damps, etc. and achieved ideal results. By applying dynamics model and observer, the force-based impedance control can realize more accurate and stable force control during grasp.
PLANNING OF SAGITTAL GAIT OF BIPED ROBOTS BASED ON MINIMUM MOTION ENERGY
Authors: TU KUO-YANG , LIU MI-SHIN
Published: January 2011

Traditional planning of biped robot walking patterns solves optimal trajectory for minimizing energy consumption. However, a diversity of biped robot walking functions lead to a variety of walking types. The walking patterns to implement a variety of biped robot objectives should have enough parameters to cope with their functions. In this article, walking patterns based on two 4-3-4 polynomials for the trajectories of biped robot waist and lower limb are proposed. The main advantage of the walking pattern is that 4-3-4 polynomials containing the parameters of acceleration and deceleration for biped walking make the implementation of a variety of walking types possible. In the study, the prototype mechanism of a biped robot is designed. After that, the direct and inverse kinematic equations of the biped robot are derived. For studying motion energy of biped robots, kinetic and potential energies are also defined. Based on these definitions, the parameters of the biped robot trajectories for minimum motion energy are solved. The solution is summarized by a development procedure. In addition, the study of zero moment point (ZMP) during the biped robot in walking is included.
AUTOMOTIVE PARTS' LOADING OPTIMIZATION BASED ON IMPROVED QUADRATIC PARTICLE SWARM OPTIMIZATION
Authors: LIU JIAN , WU CHUNYAN , WANG XIANGYIN , YU DEJIE
Published: January 2011

The present article designed a genetic quadratic particle swarm optimization (GQPSO). Aiming at the low particle diversity at the early searching stage of quadratic particle swarm optimization (QPSO), the method adopts mutation and exchanging and regenerating mechanisms from genetic algorithm so as to avoid premature convergence and improves optimization. Meanwhile, the present article gave a comprehensive consideration to decision elements such as cost, resources, and service in the process of automotive parts' logistics, transportation, and loading; a model of automotive parts' logistics, transportation, and loading optimization was set up. GQPSO was introduced for solutions. Simulation examples show that GQPSO improves the computational efficiency, significantly, and there is a higher probability of searching the global optimum. It provides optimization method for the automobile parts' logistics and transportation plans.
The nature and origin of the Barrovian metamorphism, Scotland:
40
Ar/
39
Ar apparent age patterns and the duration of metamorphism in the biotite zone
Authors: Viete Daniel R. , Forster Marnie A. , Lister Gordon S.
Published: January 2011

A geochronological traverse across the Barrovian metamorphic series, Scotland, shows
40
Ar/
39
Ar apparent age spectra that reflect the influence of progressive metamorphism during the Grampian orogenic episode. The lowest-grade units of the Barrovian metamorphic series retain pre-Grampian detrital ages as components of their white mica
40
Ar/
39
Ar apparent age spectra. These relict ages are progressively obliterated in the direction of increasing metamorphic grade, with a Grampian-age
40
Ar/
39
Ar step-heating plateau first occurring in the biotite zone. The microstructure at this point shows only limited recrystallization, suggesting loss of argon mainly by diffusion. Forward modelling of argon diffusion from white mica grains was therefore carried out, for various thermal histories and grain sizes, to match
40
Ar/
39
Ar step-heating apparent age spectra patterns preserved within the biotite zone of the Barrovian metamorphic series. The results imply a thermal duration of between 1 and 10 Ma for Barrovian metamorphism in the biotite zone. Such short time scales for metamorphism place a limit on length scales for the heat sources responsible. Mid-crustal extensional ductile shear zones that crop out in the NE of the Grampian Terrane once focused narrow, Grampian-age heat sources (e.g. magmas, hot fluids, shear heating) that drove a brief thermal episode, resulting in the Barrovian metamorphism.

Supplementary material:

40
Ar/
39
Ar data tables and plots, including (1) data from analyses on flux monitors and plots used for
J
-factor determination, and (2) data from analyses on unknowns and
40
Ar/
39
Ar step-heating spectra and inverse isochron plots for each unknown, are available at
http://www.geolsoc.org.uk/SUP18442
.
Early Cenozoic saucer-shaped sills of the Faroe Islands: an example of intrusive styles in basaltic lava piles
Authors: Hansen J. , Jerram D.A. , McCaffrey K. , Passey S.R.
Published: January 2011

The Early Cenozoic igneous activity of the North Atlantic Igneous Province that generated widespread sill complexes in sedimentary basins at the NW European margins also generated various intrusive systems in the contemporaneous basaltic lava pile of the Faroe Islands. The Faroe Island Basalt Group comprises seven formations with a total thickness of about 6.5 km, of which four major formations are built up of tholeiitic lava flows, each being several hundred metres thick, and three thinner formations are mostly built up of volcaniclastic lithologies, each being a few metres to a few tens of metres thick. The largest sills are exposed as partly saucer-shaped bodies in the three uppermost formations, where inner gently dipping basal sill sections gradually give way to more steeply inclined discordant outer rims that commonly cut several hundred metres into overlying lava flows. Numerous subvertical and moderately inclined dykes ranging in thickness from
c
. 0.5 to
c
. 4.0 m intersect the areas affected by sill intrusion, but only inclined dykes or sheets have been positively identified as sill feeders. Locally controlled rotations of least principal stress axes σ
3
during initial sill intrusion or propagation may have been an important contributing factor in determining the overall geometry of the investigated intrusions.
Timing of regional deformation and development of the Moine Thrust Zone in the Scottish Caledonides: constraints from the U–Pb geochronology of alkaline intrusions
Authors: Goodenough K.M. , Millar I. , Strachan R.A. , Krabbendam M. , Evans J.A.
Published: January 2011

The Moine Thrust Zone in the Scottish Highlands developed during the Scandian Event of the Caledonian Orogeny, and now forms the boundary between the Caledonian orogenic belt and the undeformed foreland. The Scandian Event, and the formation of the Moine Thrust Zone, have previously been dated by a range of isotopic methods, and relatively imprecise ages on a suite of alkaline intrusions localized along the thrust zone have provided the best age constraints for deformation. Recent British Geological Survey mapping has improved our understanding of the structural relationships of some of these intrusions, and this work is combined with new U–Pb dates in this paper to provide significantly improved ages for the Moine Thrust Zone. Our work shows that a single early intrusion (the Glen Dessarry Pluton) was emplaced within the orogenic belt to the east of the Moine Thrust Zone at 447.9 ± 2.9 Ma. A more significant pulse of magmatism centred in the Assynt area, which temporally overlapped movement in the thrust zone, occurred at 430.7 ± 0.5 Ma. Movement in the thrust zone had largely ceased by the time of emplacement of the youngest intrusions, the late suite of the Loch Borralan Pluton, at 429.2 ± 0.5 Ma, and the Loch Loyal Syenite Complex.