bluuebunny/crossref_metadata_2025 huggingface dataset:
Fatigue Testing and Life Estimates of Welded Flat Head Pressure Vessel Joints
Authors: Hinnant Chris
Published: July 2008

Experimental results for the cyclic pressure fatigue of several pressure vessels with flat heads are reported and compared against various fatigue design methods. The geometry is based on a welded joint presented in a recent paper by Kalnins, Bergsten, and Rana (2005). Weld designs between the head and shell include full penetration welds completed from a single side and both sides of the shell. Unique characteristics of this test include thin plate design, a large D/t ratio, and a low membrane-to-bending ratio. These are aspects of flat head geometries which have not been widely reported in the literature. Allowable fatigue cycles for ASME Section VIII, Division 2, IIW, PD 5500, EN 13445, API 579, and the Master S-N method (proposed for the ASME Section VIII, Division 2 rewrite project) are presented. Results show that several of these design method produce non-conservative fatigue life predictions. In addition, the fatigue results demonstrate that size effects and plate thickness effects have diminishing influence for thin plates failing at less than 100,000 cycles. Finally, the fatigue strength of stainless steel is compared to carbon steel and the lack of a unified approach to stainless steel fatigue design is discussed.
Current Status of Developing RBI Guideline in Japan
Authors: Sakai Shinsuke
Published: July 2008

This paper describes the outline of RBM related activities in both nuclear and non-nuclear field in Japan. One of the key elements to promote RBM activities in Japan is to develop RBM related standard. For the maintenance code, the fitness for service (FFS) code is now available in many industries. The next step to improve the inspection process for the aged plants is considered to be a risk based inspection (RBI). This paper summarizes the activities for developing RBI guideline in two societies. Background and subjects to be solved are also shown.
Fatigue Design Check of Welded Regions: A Proposal for Combining EN 13445 and ASME Division VIII Section 2 Rewrite Concepts
Authors: Zeman Josef L.
Published: July 2008

For the cyclic fatigue design check the respective codes and standards working groups in ASME and CEN have developed new concepts, laid down in diverse ASME Section VIII Division 2 Rewrite Drafts and in EN 13445-3 Clauses 17 and 18, published May 2002. This paper discusses the (many) common elements, the deviations, and proposes ideas for convergence of the approaches by joining the more promising ideas in both.
Safe Operation and FFS Assessment for Pressure Equipment: Updated With Study for Local Metal Loss Assessment
Authors: Ohno Atsushi , Uno Yoshiaki , Tahara Takayasu
Published: July 2008

Recently, Codes and Standards for FFS assessment has been developed and applied in United States and other countries such as API RP579 as a series of maintenance procedures for pressure equipment. Activities developing FFS assessment procedures in conjunction with new safe inspection standards are also progressing in Japan. In order to prove applicability of the FFS procedure for assessment of damaged pressure equipment, it is also important to validate how much of inservice safe margin is derived from the FFS assessment procedures in compared with design margin of pressure equipment. Local metal loss assessment procedure specified by API RP579 is studied using finite element analysis and discussed how much of in-service safe margin will be sufficient as standardized FFS assessment procedure.
Analysis and Experimental Verification of SCC Characteristics of Typical Chinese Steels for Pressure Vessels Under Wet H2S Environment
Authors: Chen Xuedong , Jiang Jialing , Yang Tiecheng , Hu Jiushao , Ai Zhibin , Guan Weihe , Cheng Chuanqing
Published: July 2008

In this paper, the estimation expression of critical concentration for hydrogen-induced cracking and estimation expression of critical stress intensity factor KISCC for hydrogen-induced delayed brittle fracture of the three Chinese steels for pressure vessels — 16MnR, 15MnVR and 07MnCrMoVR in Chinese standard GB 6654 are derived first according to SCC mechanism and in combination with fracture mechanics techniques, and verified by comparison with test values. The estimation expressions of diffusion-dominated crack plateau growth rate da/dt of these three materials are derived using Gerberich model based on the analysis of dynamic control mechanism of hydrogen-induced crack propagation under wet H2S environment and the estimated values are verified with the test results for WOL specimens. And the effect of concentration limit and concentration of the medium at normal temperature on the dynamic control process of crack propagation is also discussed.
Fracture Assessment of Welded Joint With Geometrical Discontinuity Using the Weibull Stress
Authors: Igi Satoshi , Kubo Takahiro , Kurihara Masayoshi , Minami Fumiyoshi
Published: July 2008

Recently the Weibull stress is used as a fracture driving force parameter in fracture assessment. The Weibull stress is derived from a statistical analysis of local instability of micro cracks leading to brittle fracture initiation. The critical Weibull stress is expected to be a critical parameter independent of the geometrical condition of specimens. Fracture toughness test using 3-point bending and tensile tests of welded joint specimens with geometrical discontinuity were conducted in order to study the applicability of fracture assessment procedure based on Weibull stress criterion. Steel plates prepared for this study had tensile strength of 490 MPa for structural use. Two kinds of welded joint specimens, “one-bead welded joint” and “multi-pass welded joint” were prepared for fracture toughness test by using gas metal are welding. In tensile test specimen, corner flaws were introduced at the geometrical discontinuity part at where stress concentration is existed. Three dimensional elastoplastic finite element analyses were also carried out using the welded joint specimen models in order to calculate the Weibull stress. The critical loads for brittle fracture predicted by the Weibull stress criterion from CTOD test results of one-bead and multi-pass welded joint specimens show fairly good agreement with experimental results of welded joint specimens with geometrical discontinuity.
Studying Atomic Structures by Aberration-Corrected Transmission Electron Microscopy
Authors: Urban Knut W.
Published: July 2008

Seventy-five years after its invention, transmission electron microscopy has taken a great step forward with the introduction of aberration-corrected electron optics. An entirely new generation of instruments enables studies in condensed-matter physics and materials science to be performed at atomic-scale resolution. These new possibilities are meeting the growing demand of nanosciences and nanotechnology for the atomic-scale characterization of materials, nanosynthesized products and devices, and the validation of expected functions. Equipped with electron-energy filters and electron-energy–loss spectrometers, the new instruments allow studies not only of structure but also of elemental composition and chemical bonding. The energy resolution is about 100 milli–electron volts, and the accuracy of spatial measurements has reached a few picometers. However, understanding the results is generally not straightforward and only possible with extensive quantum-mechanical computer calculations.
Did Cooling Oceans Trigger Ordovician Biodiversification? Evidence from Conodont Thermometry
Authors: Trotter Julie A. , Williams Ian S. , Barnes Christopher R. , Lécuyer Christophe , Nicoll Robert S.
Published: July 2008

The Ordovician Period, long considered a supergreenhouse state, saw one of the greatest radiations of life in Earth's history. Previous temperature estimates of up to ∼70°C have spawned controversial speculation that the oxygen isotopic composition of seawater must have evolved over geological time. We present a very different global climate record determined by ion microprobe oxygen isotope analyses of Early Ordovician–Silurian conodonts. This record shows a steady cooling trend through the Early Ordovician reaching modern equatorial temperatures that were sustained throughout the Middle and Late Ordovician. This favorable climate regime implies not only that the oxygen isotopic composition of Ordovician seawater was similar to that of today, but also that climate played an overarching role in promoting the unprecedented increases in biodiversity that characterized this period.
BSKs Mediate Signal Transduction from the Receptor Kinase BRI1 in
Arabidopsis
Authors: Tang Wenqiang , Kim Tae-Wuk , Oses-Prieto Juan A. , Sun Yu , Deng Zhiping , Zhu Shengwei , Wang Ruiju , Burlingame Alma L. , Wang Zhi-Yong
Published: July 2008

Brassinosteroids (BRs) bind to the extracellular domain of the receptor kinase BRI1 to activate a signal transduction cascade that regulates nuclear gene expression and plant development. Many components of the BR signaling pathway have been identified and studied in detail. However, the substrate of BRI1 kinase that transduces the signal to downstream components remains unknown. Proteomic studies of plasma membrane proteins lead to the identification of three homologous BR-signaling kinases (BSK1, BSK2, and BSK3). The BSKs are phosphorylated by BRI1 in vitro and interact with BRI1 in vivo. Genetic and transgenic studies demonstrate that the BSKs represent a small family of kinases that activate BR signaling downstream of BRI1. These results demonstrate that BSKs are the substrates of BRI1 kinase that activate downstream BR signal transduction.
Response to Comment on "Major Australian-Antarctic Plate Reorganization at Hawaiian-Emperor Bend Time"
Authors: Whittaker J. M. , Müller R. D. , Leitchenkov G. , Stagg H. , Sdrolias M. , Gaina C. , Goncharov A.
Published: July 2008

Accurately locating boundaries between continental and oceanic crust is topical in view of locating offshore boundaries relevant to margin formation models, plate kinematics, and frontier resource exploration. Although we disagree with Tikku and Direen's interpretations, the associated controversies reflect an absence of agreed-upon geophysical criteria for distinguishing stretched continental from oceanic crust, and a lack of samples from nonvolcanic margins.
An Argonaute Transports siRNAs from the Cytoplasm to the Nucleus
Authors: Guang Shouhong , Bochner Aaron F. , Pavelec Derek M. , Burkhart Kirk B. , Harding Sandra , Lachowiec Jennifer , Kennedy Scott
Published: July 2008

Ribonucleoprotein complexes consisting of Argonaute-like proteins and small regulatory RNAs function in a wide range of biological processes. Many of these small regulatory RNAs are predicted to act, at least in part, within the nucleus. We conducted a genetic screen to identify factors essential for RNA interference (RNAi) in nuclei of
Caenorhabditis elegans
and identified the Argonaute protein NRDE-3. In the absence of small interfering RNAs (siRNAs), NRDE-3 resides in the cytoplasm. NRDE-3 binds siRNAs generated by RNA-dependent RNA polymerases acting on messenger RNA templates in the cytoplasm and redistributes to the nucleus. Nuclear redistribution of NRDE-3 requires a functional nuclear localization signal, is required for nuclear RNAi, and results in NRDE-3 association with nuclear-localized nascent transcripts. Thus, specific Argonaute proteins can transport specific classes of small regulatory RNAs to distinct cellular compartments to regulate gene expression.
Eco1-Dependent Cohesin Acetylation During Establishment of Sister Chromatid Cohesion
Authors: Ben-Shahar Tom Rolef , Heeger Sebastian , Lehane Chris , East Philip , Flynn Helen , Skehel Mark , Uhlmann Frank
Published: July 2008

Replicated chromosomes are held together by the chromosomal cohesin complex from the time of their synthesis in S phase onward. This requires the replication fork–associated acetyl transferase Eco1, but Eco1's mechanism of action is not known. We identified spontaneous suppressors of the thermosensitive eco1-1 allele in budding yeast. An acetylation-mimicking mutation of a conserved lysine in cohesin's Smc3 subunit makes Eco1 dispensable for cell growth, and we show that Smc3 is acetylated in an Eco1-dependent manner during DNA replication to promote sister chromatid cohesion. A second set of eco1-1 suppressors inactivate the budding yeast ortholog of the cohesin destabilizer Wapl. Our results indicate that Eco1 modifies cohesin to stabilize sister chromatid cohesion in parallel with a cohesion establishment reaction that is in principle Eco1-independent.
A Molecular Determinant for the Establishment of Sister Chromatid Cohesion
Authors: Ünal Elçin , Heidinger-Pauli Jill M. , Kim Woong , Guacci Vincent , Onn Itay , Gygi Steven P. , Koshland Douglas E.
Published: July 2008

Chromosome segregation, transcriptional regulation, and repair of DNA double-strand breaks require the cohesin protein complex. Cohesin holds the replicated chromosomes (sister chromatids) together to mediate sister chromatid cohesion. The mechanism of how cohesion is established is unknown. We found that in budding yeast, the head domain of the Smc3p subunit of cohesin is acetylated by the Eco1p acetyltransferase at two evolutionarily conserved residues, promoting the chromatin-bound cohesin to tether sister chromatids. Smc3p acetylation is induced in S phase after the chromatin loading of cohesin and is suppressed in G
1
and G
2
/M. Smc3 head acetylation and its cell cycle regulation provide important insights into the biology and mechanism of cohesion establishment.
Phase Transitions of Dirac Electrons in Bismuth
Authors: Li Lu , Checkelsky J. G. , Hor Y. S. , Uher C. , Hebard A. F. , Cava R. J. , Ong N. P.
Published: July 2008

The Dirac Hamiltonian, which successfully describes relativistic fermions, applies equally well to electrons in solids with linear energy dispersion, for example, in bismuth and graphene. A characteristic of these materials is that a magnetic field less than 10 tesla suffices to force the Dirac electrons into the lowest Landau level, with resultant strong enhancement of the Coulomb interaction energy. Moreover, the Dirac electrons usually come with multiple flavors or valley degeneracy. These ingredients favor transitions to a collective state with novel quantum properties in large field. By using torque magnetometry, we have investigated the magnetization of bismuth to fields of 31 tesla. We report the observation of sharp field-induced phase transitions into a state with striking magnetic anisotropy, consistent with the breaking of the threefold valley degeneracy.
Entangling the Spatial Properties of Laser Beams
Authors: Wagner Katherine , Janousek Jiri , Delaubert Vincent , Zou Hongxin , Harb Charles , Treps Nicolas , Morizur Jean François , Lam Ping Koy , Bachor Hans A.
Published: July 2008

Position and momentum were the first pair of conjugate observables explicitly used to illustrate the intricacy of quantum mechanics. We have extended position and momentum entanglement to bright optical beams. Applications in optical metrology and interferometry require the continuous measurement of laser beams, with the accuracy fundamentally limited by the uncertainty principle. Techniques based on spatial entanglement of the beams could overcome this limit, and high-quality entanglement is required. We report a value of 0.51 for inseparability and 0.62 for the Einstein-Podolsky-Rosen criterion, both normalized to a classical limit of 1. These results are a conclusive optical demonstration of macroscopic position and momentum quantum entanglement and also confirm that the resources for spatial multimode protocols are available.
Thoughts on Humane Genetics
Authors: Pollack Robert
Published: July 2008

Davenport's Dream
. 21st Century Reflections on Heredity and Eugenics.
By Jan A. Witkowski and John R. Inglis, Eds.
. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY, 2008. 520 pp. $55. ISBN 9780879697563.

This volume combines a reprint of Charles Davenport's 1911 Heredity in Relation to Eugenics with discussions of its themes---including human genetic variation, mental illness, nature versus nurture, and human evolution---in a contemporary context.
Whither or Wither Microbicides?
Authors: Grant Robert M. , Hamer Dean , Hope Thomas , Johnston Rowena , Lange Joep , Lederman Michael M. , Lieberman Judy , Miller Christopher J , Moore John P. , Mosier Donald E. , Richman Douglas D. , Schooley Robert T. , Springer Marty S. , Veazey Ronald S. , Wainberg Mark A.
Published: July 2008

After disappointing results from all efficacy trials conducted to date, the field of microbicides research now faces substantial challenges. Poor coordination among interested parties and the choice of nonvalidated scientific targets for phase III studies have hampered progress and created mistrust about the use of microbicides as a method to prevent HIV-1 sexual transmission. Although new promising strategies are available, there will need to be serious reappraisals of how decisions are made to advance the next generations of candidates into clinical trials, and the use of appropriate animal models in this process will be critical.
HIV Vaccine Research: The Way Forward
Authors: Fauci Anthony S. , Johnston Margaret I. , Dieffenbach Carl W. , Burton Dennis R. , Hammer Scott M. , Hoxie James A. , Martin Malcolm , Overbaugh Julie , Watkins David I. , Mahmoud Adel , Greene Warner C.
Published: July 2008

The need to broaden research directed at answering fundamental questions in HIV vaccine discovery through laboratory, nonhuman primate (NHP), and clinical research has recently been emphasized. In addition, the importance of attracting and retaining young researchers, developing better NHP models, and more closely linking NHP and clinical research is being stressed. In an era of a level budget for biomedical research at the U.S. National Institutes of Health (NIH), HIV/AIDS vaccine research efforts will need to be carefully prioritized such that resources to energize HIV vaccine discovery can be identified. This article summarizes progress and challenges in HIV vaccine research, the priorities arising from a recent summit at NIAID, and the actions needed, some already under way, to address those priorities.
Characterization of an Outer Membrane Protein ofSalmonella entericaSerovar Typhimurium That Confers Protection against Typhoid
Authors: Hamid Nowsheen , Jain S. K.
Published: July 2008

Typhoid caused bySalmonella entericaserovar Typhi remains a major health concern worldwide. The emergence of multidrug-resistant strains ofSalmonellawith increased virulence, communicability, and survivability leading to increased morbidity and mortality has further complicated its management. Currently available vaccines for typhoid have less-than-desired efficacy and certain unacceptable side effects, making it pertinent to search for new immunogens suitable for vaccine formulation. The outer membrane proteins (OMPs) ofSalmonellahave been considered possible candidates for conferring protection against typhoid. OMPs interface the cell with the environment, thus representing important virulence factors with a significant role in the pathobiology of gram-negative bacteria and bacterial adaptation. An OMP ofSalmonella entericaserovar Typhimurium with an apparent molecular mass of 49 kDa that is highly immunogenic, evokes humoral and cell-mediated immune responses, and confers 100% protection to immunized rats against challenge with very high doses (up to 100 times the 50% lethal dose) ofSalmonella entericaserovar Typhimurium has been identified. Further, very efficient clearance of bacteria from the reticuloendothelial systems of immunized animals was seen. This protein is recognized by the antibodies present in serum of typhoid patients. When sodium dodecyl sulfate-polyacrylamide gel electrophoresis gel-eluted protein was further analyzed by high-performance liquid chromatography (HPLC) and two-dimensional electrophoresis, two polypeptides with the same molecular weight were resolved. These have different isoelectric points and gave two peaks with different retention times in reverse-phase HPLC. However, only one of the two bands interacted with patient serum. The immunogenicity studies (enzyme-linked immunosorbent assay and delayed-type hypersensitivity [DTH]) indicated that the immunoreactive protein evoked a strong immune response in rats. The N-terminal sequencing and analysis of the homology of this protein with sequences in the protein database ofSalmonellaresulted in a match with the N-terminal sequences of a protein inSalmonella entericaserovar Typhi (CT18 and Ty2 strains). The homology search further revealed it to be a hypothetical protein, whose gene had unidentified open reading frames inSalmonellaserovar Typhi encoding 447 amino acid residues, corresponding to a molecular mass of 49 kDa. The nucleotide sequence of the encoding gene was deduced, and the gene was amplified by PCR using appropriate primers. An amplified 1.3-kb band was purified and sequenced to confirm its identity. These OMPs provide promising targets for the development of a candidate vaccine against typhoid.
Molecular Method for Discrimination between
Francisella tularensis
and
Francisella
-Like Endosymbionts
Authors: Escudero Raquel , Toledo A. , Gil Horacio , Kovácsová Katarina , Rodríguez-Vargas Manuela , Jado Isabel , García-Amil Cristina , Lobo Bruno , Bhide Mangesh , Anda Pedro
Published: July 2008

Environmental studies on the distribution of
Francisella
spp. are hampered by the frequency of
Francisella
-like endosymbionts that can produce a misleading positive result. A new, efficient molecular method for detection of
Francisella tularensis
and its discrimination from
Francisella
-like endosymbionts, as well as two variants associated with human disease (unusual
F. tularensis
strain FnSp1 and
F. tularensis
subsp.
novicida
-like strain 3523), is described. The method is highly specific and sensitive, detecting up to one plasmid copy or 10 genome equivalents.
Analysis of Integrated Virological and Epidemiological Reports of Norovirus Outbreaks Collected within the Foodborne Viruses in Europe Network from 1 July 2001 to 30 June 2006
Authors: Kroneman A. , Verhoef L. , Harris J. , Vennema H. , Duizer E. , van Duynhoven Y. , Gray J. , Iturriza M. , Böttiger B. , Falkenhorst G. , Johnsen C. , von Bonsdorff C.-H. , Maunula L. , Kuusi M. , Pothier P. , Gallay A. , Schreier E. , Höhne M. , Koch J. , Szücs G. , Reuter G. , Krisztalovics K. , Lynch M. , McKeown P. , Foley B. , Coughlan S. , Ruggeri F. M. , Di Bartolo I. , Vainio K. , Isakbaeva E. , Poljsak-Prijatelj M. , Grom A. Hocevar , Mijovski J. Zimsek , Bosch A. , Buesa J. , Fauquier A. Sanchez , Hernandéz-Pezzi G. , Hedlund K.-O. , Koopmans M.
Published: July 2008

The Foodborne Viruses in Europe network has developed integrated epidemiological and virological outbreak reporting with aggregation and sharing of data through a joint database. We analyzed data from reported outbreaks of norovirus (NoV)-caused gastroenteritis from 13 European countries (July 2001 to July 2006) for trends in time and indications of different epidemiology of genotypes and variants. Of the 13 countries participating in this surveillance network, 11 were capable of collecting integrated epidemiological and virological surveillance data and 10 countries reported outbreaks throughout the entire period. Large differences in the numbers and rates of reported outbreaks per country were observed, reflecting the differences in the focus and coverage of national surveillance systems. GII.4 strains predominated throughout the 5-year surveillance period, but the proportion of outbreaks associated with GII.4 rose remarkably during years in which NoV activity was particularly high. Spring and summer peaks indicated the emergence of genetically distinct variants within GII.4 across Europe and were followed by increased NoV activity during the 2002-2003 and 2004-2005 winter seasons. GII.4 viruses predominated in health care settings and in person-to-person transmission. The consecutive emergence of new GII.4 variants is highly indicative of immune-driven selection. Their predominance in health care settings suggests properties that facilitate transmission in settings with a high concentration of people such as higher virus loads in excreta or a higher incidence of vomiting. Understanding the mechanisms driving the changes in epidemiology and clinical impact of these rapidly evolving RNA viruses is essential to design effective intervention and prevention measures.
Detection of 11 Common Viral and Bacterial Pathogens Causing Community-Acquired Pneumonia or Sepsis in Asymptomatic Patients by Using a Multiplex Reverse Transcription-PCR Assay with Manual (Enzyme Hybridization) or Automated (Electronic Microarray) Detection
Authors: Kumar Swati , Wang Lihua , Fan Jiang , Kraft Andrea , Bose Michael E. , Tiwari Sagarika , Van Dyke Meredith , Haigis Robert , Luo Tingquo , Ghosh Madhushree , Tang Huong , Haghnia Marjan , Mather Elizabeth L. , Weisburg William G. , Henrickson Kelly J.
Published: July 2008

Community-acquired pneumonia (CAP) and sepsis are important causes of morbidity and mortality. We describe the development of two molecular assays for the detection of 11 common viral and bacterial agents of CAP and sepsis: influenza virus A, influenza virus B, respiratory syncytial virus A (RSV A), RSV B,
Mycoplasma pneumoniae, Chlamydophila pneumoniae, Legionella pneumophila, Legionella micdadei, Bordetella pertussis, Staphylococcus aureus
, and
Streptococcus pneumoniae
. Further, we report the prevalence of carriage of these pathogens in respiratory, skin, and serum specimens from 243 asymptomatic children and adults. The detection of pathogens was done using both a manual enzyme hybridization assay and an automated electronic microarray following reverse transcription and PCR amplification. The analytical sensitivities ranged between 0.01 and 100 50% tissue culture infective doses, cells, or CFU per ml for both detection methods. Analytical specificity testing demonstrated no significant cross-reactivity among 19 other common respiratory organisms. One hundred spiked “surrogate” clinical specimens were all correctly identified with 100% specificity (95% confidence interval, 100%). Overall, 28 (21.7%) of 129 nasopharyngeal specimens, 11 of 100 skin specimens, and 2 of 100 serum specimens from asymptomatic subjects tested positive for one or more pathogens, with
S. pneumoniae
and
S. aureus
giving 89% of the positive results. Our data suggest that asymptomatic carriage makes the use of molecular assays problematic for the detection of
S. pneumoniae
or
S. aureus
in upper respiratory tract secretions; however, the specimens tested showed virtually no carriage of the other nine viral and bacterial pathogens, and the detection of these pathogens should not be a significant diagnostic problem. In addition, slightly less sensitive molecular assays may have better correlation with clinical disease in the case of CAP.
Molecular Epidemiology of Human Enterovirus 71 in the United Kingdom from 1998 to 2006
Authors: Bible Jon M. , Iturriza-Gomara Miren , Megson Brian , Brown David , Pantelidis Panagiotis , Earl Pam , Bendig Justin , Tong C. Y. William
Published: July 2008

The last decade witnessed a significant increase in epidemic activity of human enterovirus 71 (EV71) in the Western Pacific Region (WPR). In most European countries, this risk is unrecognized despite occasional cases of severe disease and two severe outbreaks in Eastern Europe 30 years ago. In this study we report the first examination of the molecular epidemiology of EV71 in the United Kingdom from 1998 to 2006. Genomic regions encoding the 1D coat protein (VP1) and 3D polymerase (Pol) from 32 EV71 isolates associated with neurological or cutaneous manifestations were sequenced. Phylogenetic analyses of VP1 and 3D Pol sequences identified genotype C as the dominant strain. Several United Kingdom isolates had genetic linkages with predated C1 or C2 strains from Europe and the WPR. Recombination events were not detected between United Kingdom strains. However, a previously published Taiwanese strain was identified as an intergenotypic recombinant. EV71 genotype C appears to have continuous circulation in the United Kingdom from 1998 to 2006 with repeated introductions of new strains replacing previous strains. It is necessary to continuously monitor the molecular evolution and recombination events of EV71.
Identities of
Arthrobacter
spp. and
Arthrobacter
-Like Bacteria Encountered in Human Clinical Specimens
Authors: Mages Irene S. , Frodl Reinhard , Bernard Kathryn A. , Funke Guido
Published: July 2008

After the initial description of
Arthrobacter
spp. isolated from clinical specimens in the mid-1990s, very few further reports on
Arthrobacter
spp. have appeared in the clinical microbiology literature. The aim of the present study was to elucidate the distribution of
Arthrobacter
spp. and
Arthrobacter
-like bacteria encountered in clinical specimens by studying 50 consecutively isolated or received strains of large-colony-forming, whiteish-grayish, non-cheese-like-smelling, nonfermentative gram-positive rods by applying phenotypic methods as well as 16S rRNA gene sequencing. We observed a very heterogenous distribution, with the 50 strains belonging to 20 different taxa and each of 13 strains as a single representative of its particular taxon. Thirty-eight strains represented true
Arthrobacter
strains, 7 strains belonged to the genus
Brevibacterium
, 2 were
Microbacterium
species, and each of 3 single strains was a member of the rarely encountered genera
Pseudoclavibacter, Leucobacter
, and
Brachybacterium
, respectively.
A. cumminsii
(
n
= 14) and
A. oxydans
(
n
= 11) were the most frequently found species. The present report describes the first three
A. aurescens
strains isolated from human clinical specimens. Comprehensive antimicrobial susceptibility data are given for the 38
Arthrobacter
isolates.
Fatal-Stroke Syndrome Revealing Fungal Cerebral Vasculitis Due to
Arthrographis kalrae
in an Immunocompetent Patient
Authors: Pichon N. , Ajzenberg D. , Desnos-Ollivier M. , Clavel M. , Gantier J. C. , Labrousse F.
Published: July 2008

We report an uncommon clinical presentation of a unique case of fatal invasive fungal cerebral vasculitis due to
Arthrographis kalrae
in a nonimmunocompromised host. The identity of the fungus was determined by morphological characteristics and by analysis of internal transcribed spacer 1 sequences and was confirmed by postmortem examination of the brain tissues. Establishing rapidly the link between the clinical syndromes and the fungal infection of the central nervous system is essential to improve the outcome. As our case has shown, it is more challenging to make a diagnosis of fungal infection when there are no risk factors of immunodeficiency and when the clinical presentation seems uncommon.
Phylogenetic Analysis of Viridans Group Streptococci Causing Endocarditis
Authors: Simmon Keith E. , Hall Lori , Woods Christopher W. , Marco Francesc , Miro Jose M. , Cabell Christopher , Hoen Bruno , Marin Mercedes , Utili Riccardo , Giannitsioti Efthymia , Doco-Lecompte Thanh , Bradley Suzanne , Mirrett Stanley , Tambic Arjana , Ryan Suzanne , Gordon David , Jones Phillip , Korman Tony , Wray Dannah , Reller L. Barth , Tripodi Marie-Francoise , Plesiat Patrick , Morris Arthur J. , Lang Selwyn , Murdoch David R. , Petti Cathy A.
Published: July 2008

Identification of viridans group streptococci (VGS) to the species level is difficult because VGS exchange genetic material. We performed multilocus DNA target sequencing to assess phylogenetic concordance of VGS for a well-defined clinical syndrome. The hierarchy of sequence data was often discordant, underscoring the importance of establishing biological relevance for finer phylogenetic distinctions.
Poliovirus
cis
-Acting Replication Element-Dependent VPg Uridylylation Lowers the

K
m

of the Initiating Nucleoside Triphosphate for Viral RNA Replication
Authors: Steil Benjamin P. , Barton David J.
Published: July 2008

Initiation of RNA synthesis by RNA-dependent RNA polymerases occurs when a phosphodiester bond is formed between the first two nucleotides in the 5′ terminus of product RNA. The concentration of initiating nucleoside triphosphates (NTPi) required for RNA synthesis is typically greater than the concentration of NTPs required for elongation. VPg, a small viral protein, is covalently attached to the 5′ end of picornavirus negative- and positive-strand RNAs. A
cis
-acting replication element (CRE) within picornavirus RNAs serves as a template for the uridylylation of VPg, resulting in the synthesis of VPgpUpU
OH
. Mutations within the CRE RNA structure prevent VPg uridylylation. While the tyrosine hydroxyl of VPg can prime negative-strand RNA synthesis in a CRE- and VPgpUpU
OH
-independent manner, CRE-dependent VPgpUpU
OH
synthesis is absolutely required for positive-strand RNA synthesis. As reported herein, low concentrations of UTP did not support negative-strand RNA synthesis when CRE-disrupting mutations prevented VPg uridylylation, whereas correspondingly low concentrations of CTP or GTP had no negative effects on the magnitude of CRE-independent negative-strand RNA synthesis. The experimental data indicate that CRE-dependent VPg uridylylation lowers the

K
m

of UTP required for viral RNA replication and that CRE-dependent VPgpUpU
OH
synthesis was required for efficient negative-strand RNA synthesis, especially when UTP concentrations were limiting. By lowering the concentration of UTP needed for the initiation of RNA replication, CRE-dependent VPg uridylylation provides a mechanism for a more robust initiation of RNA replication.
Control of Cytoplasmic Maturation Events by Cytomegalovirus Tegument Protein pp150
Authors: Tandon Ritesh , Mocarski Edward S.
Published: July 2008

Cytomegalovirus replication depends upon a betaherpesvirus-conserved 150-kDa tegument phosphoprotein (pp150; encoded by UL32) that supports the final steps in virion maturation at cytoplasmic assembly compartments. Amino acid substitutions were introduced into conserved region 1 (CR1) and CR2 of pp150, affecting a region that may interact with nucleocapsids. Two independent CR2 point mutants (N201A and G207A) failed to support viral replication in evaluations by a transient complementation assay or after reconstruction into recombinant viruses. An assembly compartment-like cytoplasmic inclusion developed in UL32 mutant virus-infected cells that was similar to that of wild-type virus-infected cells. The cellular localization of the
trans
-Golgi marker Golgin-97 suggested differences in the organization of the assembly compartment compared to that of wild-type virus-infected cells. Replication-defective CR2 point mutants exhibited the same phenotype as that of a virus carrying a complete deletion of the UL32 open reading frame in these assays. Electron micrographs of fibroblasts at 3 or 5 days postinfection with a deletion mutant (ΔUL32) grown on UL32-complementing cells showed a similar number and morphology of capsids in the nucleus, but the cytoplasmic region associated with virion assembly appeared highly vesiculated and contained few recognizable nucleocapsids or complete virus particles. These data demonstrate that the principle role of pp150 is to retain nucleocapsid organization through secondary envelopment at the assembly compartment.
Inhibition of Human Immunodeficiency Virus Type 1 Assembly and Release by the Cholesterol-Binding Compound Amphotericin B Methyl Ester: Evidence for Vpu Dependence
Authors: Waheed Abdul A. , Ablan Sherimay D. , Soheilian Ferri , Nagashima Kunio , Ono Akira , Schaffner Carl P. , Freed Eric O.
Published: July 2008

We investigated the mechanism by which the cholesterol-binding compound amphotericin B methyl ester (AME) inhibits human immunodeficiency virus type 1 (HIV-1) particle production. We observed no significant effect of AME on Gag binding to the plasma membrane, Gag association with lipid rafts, or Gag multimerization, indicating that the mechanism of inhibition by AME is distinct from that by cholesterol depletion. Electron microscopy analysis indicated that AME significantly disrupts virion morphology. Interestingly, we found that AME does not inhibit the release of Vpu-defective HIV-1 or Vpu
−
retroviruses such as murine leukemia virus and simian immunodeficiency virus. We demonstrated that the ability of Vpu to counter the activity of CD317/BST-2/tetherin is markedly reduced by AME. These results indicate that AME interferes with the anti-CD317/BST-2/tetherin function of Vpu.
Dynamic Histone H3 Acetylation and Methylation at Human Cytomegalovirus Promoters during Replication in Fibroblasts
Authors: Cuevas-Bennett Christian , Shenk Thomas
Published: July 2008

Human cytomegalovirus DNA is packaged in virions without histones but associates with histones upon reaching the nucleus of an infected cell. Since transcription is modulated by the interplay of histone modifications, we used chromatin immunoprecipitation to detect acetylation and methylation of histone H3 at viral promoters at different times during the viral replication cycle. Histone H3 at immediate-early promoters is acetylated at the start of infection, while it is initially methylated at early and late promoters. Acetylation at immediate-early promoters is dynamic, with a high level of activating modifications at 3 and 6 h postinfection (hpi), followed by a marked reduction at 12 hpi. All viral promoters, as well as nonpromoter regions, are modified with activating acetylations at 24 to 72 hpi. The transient reduction in histone H3 acetylation at the major immediate-early promoter depends on the
cis
-repressive sequence to which the UL122-coded IE2 protein binds. A mutant virus lacking this element exhibited decreased IE2 binding at the major immediate-early promoter and failed to show reduced acetylation of histone H3 residing at this promoter at 12 hpi. Our results demonstrate that cytomegalovirus chromatin undergoes dynamic, promoter-specific histone modifications early in the infectious cycle, after which the entire chromosome becomes highly acetylated.
Gag-Specific CD4+T-Cell Frequency Is Inversely Correlated with Proviral Load and Directly Correlated with Immune Activation in Infection with Human Immunodeficiency Virus Type 2 (HIV-2) but Not HIV-1
Authors: Foxall Russell B. , Cortesão Catarina S. , Albuquerque Adriana S. , Soares Rui S. , Victorino Rui M. M. , Sousa Ana E.
Published: July 2008

Human immunodeficiency virus type 2 (HIV-2) infection, unlike HIV-1 infection, is normally characterized by low rates of CD4 depletion and low-to-undetectable viremia. We found that the frequency of Gag-specific CD4+T cells featured positive correlations with the expression of markers of CD4 activation and a negative correlation with peripheral blood mononuclear cell-associated proviral load in infection with HIV-2, in contrast with HIV-1. Moreover, HIV-2-infected individuals exhibited a greater ability to respond to HIV-1 Gag peptides (heterologous responses). Our data suggest a potential link between HIV-2-specific CD4 responses, immune activation, and viral control, which may in turn relate to the better prognosis associated with HIV-2 infection.
Acid Hydrolysis of Olive-Pruning Debris for D-Xylose Production
Authors: García Juan F. , Sánchez Sebastián , Bravo Vicente , Rigal Luc , Cuevas Manuel
Published: July 2008

Selective hydrolysis of the hemicellulose fraction of olive-pruning debris was attempted in order to achieve a maximum yield of fermentable D-xylose without degrading the cellulose fraction. To this end, hydrolysis with a dilute acid was conducted in a heterogeneous stirred tank reactor at mild temperature (70-90 °C) and sulfuric acid concentration (0.0-0.5 mol l-1) for 300 min. Temperature was the determining factor in sugar formation and fiber conversion. The highest hemicellulose and cellulose conversion at 90 °C were 92.9 and 16.0%, respectively. From 100 g of the raw material, 35.8 g of sugars were recovered. At this temperature, using 0.5 M H2SO4 for 4.5 h, D-glucose and D-xylose yields of 13.1 and 10.4%, respectively, were obtained.
Cytostatic and Antiviral 6-Arylpurine Ribonucleosides IX. Synthesis and Evaluation of 6-Substituted 3-Deazapurine Ribonucleosides
Authors: Nauš Petr , Kuchař Martin , Hocek Michal
Published: July 2008

A series of 3-deazapurine ribonucleosides5a-5lbearing diverseC-substituents (alkyl, aryl and heteroaryl) in the position 6 were prepared by Pd-catalyzed cross-coupling reactions of either free 6-chloro-3-deazapurine ribonucleoside4or its acetyl protected congener3followed by deprotection. An improved synthesis of the starting 4-chloro-1-(2,3,5-tri-O-acetyl-β-D-ribofuranosyl)-1H-imidazo[4,5-c]pyridine (3) was developed by the application of Vorbrüggen glycosylation of silylated nucleobase with 1,2,3,5-tetra-O-acetyl-β-D-ribofuranose (2). None of compounds5a-5lshowed any considerable cytostatic or antiviral activity.
Stereoselective Preparation of 2,3-Dideoxy-3-C-[(α-D-galactopyranosyl)methyl]-D-arabino-hexopyranose and 2,3-Dideoxy-3-C-[(α-D-galactopyranosyl)methyl]-L-arabino-hexopyranose
Authors: Parkan Kamil , Vích Ondřej , Dvořáková Hana , Kniežo Ladislav
Published: July 2008

The diastereomeric substituted 2H-dihydropyran derivatives 2b and 3b were obtained by the stereoselective cycloaddition of (E)-4-(tetra-O-benzyl-α-D-galactopyranosyl)-1-(thiazol-2-yl)but-2-en-1-one (1) with either of the enantiomeric chiral vinyl ethers (R)-4 or (S)-4. Reduction of the ester group, transformation of the thiazole ring into an aldehyde group and reaction with an excess of borane afforded the final C-(1→3)-disaccharide structures. The obtained C-(1→3)-disaccharides, containing an L- or D-deoxy-arabino-hexopyranose moiety at the reducing end, were characterized as peracetylated methyl glycosides 9a, 9b and 12a, 12b.
Preparation of α-5-Aza-2'-deoxy-[6-3H]cytidine
Authors: Elbert Tomáš , Černý Bohuslav
Published: July 2008

α-5-Aza-2'-deoxy cytidine was labeled by tritium on the C-6 of the heterocyclic triazine ring. The structure of the α-5-aza-2'-deoxy-[6-3H]cytidine and the position of the label was proved by 3H and 1H NMR. The specific activity was 0.71 TBq mmol-1 (19.2 Ci mmol-1) and radiochemical purity was >99%. The long term stability of the product during the storage at -21 and -72 °C was followed by radio-HPLC.
A DNA barcode examination of the red algal family Dumontiaceae in Canadian waters reveals substantial cryptic species diversity. 1. The foliose Dilsea–Neodilsea complex and WeeksiaThis paper is one of a selection of papers published in the Special Issue on Systematics Research.
Authors: Saunders Gary W.
Published: July 2008

The field of DNA barcoding is working towards generating a genetic system for the quick and accurate identification of eukaryotic species. For the more systematic minded, however, DNA barcoding offers a new approach towards screening and uniting large numbers of biological specimens in genetic groups as a first step towards assigning them to species and genera in an approach best termed “molecular-assisted alpha taxonomy”. This approach is particularly amenable in organisms with simple morphologies, a propensity for convergence, extensive phenotypic plasticity, and life histories with an alternation of heteromorphic generations. It is hard to imagine a group of organisms better defined by all of these traits than the marine macroalgae. In an effort to assess the utility of the DNA barcode (COI-5′) for testing the current concepts of biodiversity of marine macroalgae in Canada, a study to assess species diversity in the red algal family, Dumontiaceae, was initiated. Through this work I confirm the presence in Canadian waters of Dilsea californica (J. Agardh) Kuntze, Dilsea integra (Kjellman) Rosenvinge, and Neodilsea borealis (I.A. Abbott) Lindstrom of the Dilsea–Neodilsea complex, and Weeksia coccinea (Harvey) Lindstrom for the genus Weeksia . However, our work has uncovered two additional species of the former complex, Dilsea lindstromiae Saunders sp. nov. and Dilsea pygmaea (Setchell) Setchell, and an additional species of the latter, Weeksia reticulata Setchell, effectively doubling representation of these foliose dumontiacean genera in Canadian waters.
Species delimitation, phylogenetic relationships, and two new species in the Cuscuta gracillima complex (Convolvulaceae)This paper is one of a selection of papers published in the Special Issue on Systematics Research.
Authors: Costea Mihai , Aiston Fiona , Stefanović Saša
Published: July 2008

Basic morphology, scanning electron microscopy, and DNA sequence data from the plastid trnL–F region and the nuclear internal transcribed spacer (ITS) regions were used to delimit the species of a recently circumscribed clade of Cuscuta (Convolvulaceae) and to investigate their phylogenetic relationships. This clade comprises the Cuscuta gracillima complex from Mexico, Central and northern South America, a group which is characterized by inflorescences that appear to emerge directly from the host stem. Eight lineages are recognized, with two of them described here as new species: Cuscuta punana Costea & Stefanović, sp. nov. from Ecuador and Cuscuta vandevenderi Costea & Stefanović, sp. nov. from Mexico. Cuscuta colombiana Yunck is redefined to include Cuscuta aristeguietae Yunck., and Cuscuta deltoidea Yunck. is broadened to encompass Cuscuta serruloba Yunck. A taxonomic treatment with an identification key, descriptions, and illustrations is provided; the biogeography and conservation status of the eight species are also discussed.
Morphological, biological, and molecular characteristics of the diatomPseudo-nitzschia delicatissimafrom the Canadian MaritimesThis paper is one of a selection of papers published in the Special Issue on Systematics Research.
Authors: Kaczmarska Irena , Reid Charlotte , Martin Jennifer L. , Moniz Mónica B.J.
Published: July 2008

Forty-six monoclonal cultures of the diatom Pseudo-nitzschia delicatissima (Cleve) Heiden were isolated from coastal waters of Eastern Canada. Of these, 12 clones were successfully sexualized. The range of their morphological and genetic divergence was used as a reference for clones whose sexual identity remains unknown. All characters that were examined, including valve morphology, the nuclear internal transcribed spacer (ITS) region, and mitochondrial cytochrome c oxidase (cox1) sequences, showed a high degree of similarity within and between mating and nonsexualized clones. Within the 638 bp long aligned fragment in the ITS region, only five variable sites were found and just two were found within the 576 bp fragment of cox1 near the 5′ terminus of the gene. Our own data and those retrieved from GenBank suggest that the northern North Atlantic is populated by a single metapopulation of genetically very similar P. delicatissima, as determined using the ITS sequence of the epitype of the species. The ITS region of our clones was distinct from ITS-types present in isolates that we will refer to as P. delicatissima-like diatoms from the Mediterranean Sea and other low latitude Atlantic sites, thereby providing a means to discriminate between otherwise morphologically indistinguishable (cryptic) species. Such a distribution pattern suggests different physiological and environmental requirements for mating optima. This work furthers our understanding of the relationship between biological, molecular, and morphological species boundaries in diatoms and their ecology, and contributes to evaluation of the utility of ITS and cox1 sequences in DNA barcoding of diatoms.