bluuebunny/crossref_metadata_2025 huggingface dataset:
Supernova Shock Breakout from a Red Supergiant
Authors: Schawinski Kevin , Justham Stephen , Wolf Christian , Podsiadlowski Philipp , Sullivan Mark , Steenbrugge Katrien C. , Bell Tony , Röser Hermann-Josef , Walker Emma S. , Astier Pierre , Balam Dave , Balland Christophe , Carlberg Ray , Conley Alex , Fouchez Dominique , Guy Julien , Hardin Delphine , Hook Isobel , Howell D. Andrew , Pain Reynald , Perrett Kathy , Pritchet Chris , Regnault Nicolas , Yi Sukyoung K.
Published: June 2008

Massive stars undergo a violent death when the supply of nuclear fuel in their cores is exhausted, resulting in a catastrophic “core-collapse” supernova. Such events are usually only detected at least a few days after the star has exploded. Observations of the supernova SNLS-04D2dc with the Galaxy Evolution Explorer space telescope reveal a radiative precursor from the supernova shock before the shock reached the surface of the star and show the initial expansion of the star at the beginning of the explosion. Theoretical models of the ultraviolet light curve confirm that the progenitor was a red supergiant, as expected for this type of supernova. These observations provide a way to probe the physics of core-collapse supernovae and the internal structures of their progenitor stars.
Diagnosis of Bovine Paratuberculosis by a Novel Enzyme-Linked Immunosorbent Assay Based on Early Secreted Antigens of
Mycobacterium avium
subsp.
paratuberculosis
Authors: Shin Sung Jae , Cho Donghee , Collins Michael T.
Published: June 2008

We previously reported that protein antigens of serodiagnostic potential were more abundant in culture filtrates than cellular extracts from liquid cultures of
Mycobacterium avium
subsp.
paratuberculosis
(D. Cho and M. T. Collins, Clin. Vaccine Immunol. 13:1155-1161, 2006). Based on this observation, a novel enzyme-linked immunosorbent assay (ELISA) using antigens secreted by young (early- to mid-log-phase) cultures of
M. avium
subsp.
paratuberculosis
JTC303 (a low-passage isolate originating from the ileum of a Holstein bull) in mycobactin-supplemented Watson-Reid medium (pH 6.0) was developed and evaluated using a previously described panel of bovine sera (M. T. Collins et al., Clin. Diagn. Lab. Immunol. 12:685-692, 2005) that included 444 paratuberculosis cases and 412 controls. The new assay, called JTC-ELISA, had a significantly higher diagnostic sensitivity and an equivalent specificity compared to those of five commercial paratuberculosis ELISA kits. By receiver-operating characteristic analysis, the JTC-ELISA had the highest area under the curve of the six assays evaluated. The JTC-ELISA was particularly sensitive at detecting low-level fecal shedders of
Mavium
subsp.
paratuberculosis
(40%; the sensitivity of the commercial kits was 20%). The JTC-ELISA works effectively on both serum and milk samples for the detection of cattle with subclinical
M. avium
subsp.
paratuberculosis
infections, providing a cost-effective diagnostic tool to support paratuberculosis control programs in cattle herds.
Comparative Testing of Six Antigen-Based Malaria Vaccine Candidates Directed Toward Merozoite-StagePlasmodium falciparum
Authors: Arnot David E. , Cavanagh David R. , Remarque Edmond J. , Creasey Alison M. , Sowa Mercy P. K. , Morgan William D. , Holder Anthony A. , Longacre Shirley , Thomas Alan W.
Published: June 2008

Immunogenicity testing ofPlasmodium falciparumantigens being considered as malaria vaccine candidates was undertaken in rabbits. The antigens compared were recombinant baculovirus MSP-119and fivePichia pastoriscandidates, including two versions of MSP-119, AMA-1 (domains I and II), AMA-1+MSP-119, and fused AMA-1/MSP-119). Animals were immunized with equimolar amounts of each antigen, formulated in Montanide ISA720. The specificities and titers of antibodies were compared using immunofluorescence assays and enzyme-linked immunosorbent assay (ELISA). The antiparasite activity of immunoglobulin G (IgG) in in vitro cultures was determined by growth inhibition assay, flow cytometry, lactate dehydrogenase assay, and microscopy. Baculovirus MSP-119immunizations produced the highest parasite-specific antibody titers in immunofluorescence assays. In ELISAs, baculovirus-produced MSP-119induced more antibodies than any other single MSP-119immunogen and three times more MSP-119specific antibodies than the AMA-1/MSP-119fusion. Antibodies induced by baculovirus MSP-119gave the highest levels of growth inhibition in HB3 and 3D7 parasite cultures, followed by AMA-1+MSP-119and the AMA-1/MSP-119fusion. With the FCR3 isolate (homologous to the AMA-1 construct), antibodies to the three AMA-1-containing candidates gave the highest levels of growth inhibition at high IgG concentrations, but antibodies to baculovirus MSP-119inhibited as well or better at lower IgG concentrations. The twoP. pastoris-produced MSP-119-induced IgGs conferred the lowest growth inhibition. Comparative analysis of immunogenicity of vaccine antigens can be used to prioritize candidates before moving to expensive GMP production and clinical testing. The assays used have given discriminating readouts but it is not known whether any of them accurately reflect clinical protection.
Loop-Mediated Isothermal Amplification Assay for Rapid Detection of Common Strains ofEscherichia coli
Authors: Hill Joshua , Beriwal Shilpa , Chandra Ishwad , Paul Vinod K. , Kapil Aarti , Singh Tripti , Wadowsky Robert M. , Singh Vinita , Goyal Ankur , Jahnukainen Timo , Johnson James R. , Tarr Phillip I. , Vats Abhay
Published: June 2008

We developed a highly sensitive and specific LAMP assay forEscherichia coli. It does not require DNA extraction and can detect as few as 10 copies. It detected all 36 of 36E. coliisolates and all 22 urine samples (out of 89 samples tested) that hadE. coli. This assay is rapid, low in cost, and simple to perform.
Discriminating between Varicella-Zoster Virus Vaccine and Wild-Type Strains by Loop-Mediated Isothermal Amplification
Authors: Higashimoto Yuki , Ihira Masaru , Ohta Akane , Inoue Shigeki , Usui Chie , Asano Yoshizo , Yoshikawa Tetsushi
Published: June 2008

The loop-mediated isothermal amplification (LAMP) method was developed to distinguish between the varicella-zoster virus (VZV) vaccine (vOka) strain and wild-type strains. Two single nucleotide polymorphisms (SNPs) (nucleotide [nt] 105705 for VR-1 VZV LAMP and nt 106262 for VR-2 VZV LAMP) located in the open reading frame 62 gene were selected as LAMP targets. Amplified vOka DNA demonstrated a typical ladder pattern; however, no LAMP product was detected in reactions performed with DNAs from other human herpesviruses by either VR-1 VZV LAMP or VR-2 VZV LAMP. This result was confirmed by a turbidity assay. The sensitivities of both VR-1 and VR-2 VZV LAMP determined by either the turbidity assay or agarose gel electrophoresis were 100 copies per reaction. To discriminate the vOka strain from wild-type strains, VR-1 and VR-2 VZV LAMP products were digested with the appropriate restriction enzymes (SacII for VR-1 LAMP and SmaΙ for VR-2 LAMP). The digested products were clearly different in the vOka strain and wild-type strains. To evaluate the utility of the LAMP methods for rapid differentiation, viral DNA (without DNA extraction) in swab samples was directly tested. Wild-type VZV DNA was detected in 20 swab samples by either VR-1 VZV LAMP or VR-2 VZV LAMP. Sequence analysis confirmed the expected SNPs in the LAMP products amplified from the vOka strain and the five wild-type strains.
Assessment of Cryptodiag for Diagnosis of Cryptosporidiosis and Genotyping
Cryptosporidium
Species
Authors: Savin C. , Sarfati C. , Menotti J. , Jaouhari J. , Wurtzer S. , Garin Y. J. F. , Derouin F.
Published: June 2008

The performance of a new commercial PCR-enzyme-linked immunosorbent assay (ELISA) (Cryptodiag; Bio Advance, France) for the diagnosis of cryptosporidiosis and the identification of
Cryptosporidium hominis
and
C. parvum
from stool samples was examined. This test is based on PCR amplification of
Cryptosporidium
DNA extracted from stools, followed by an ELISA based on hybridization with
Cryptosporidium
sp.-,
C. hominis
-, or
C. parvum
-specific probes. In spiking experiments, approximately five oocysts were detected either in water or in stool suspensions while assessing for the efficient removal of stool PCR inhibitors. No cross-reactivity was observed in the detection of
C. parvum
and
C. homin
is using the respective specific probes. Thirty-three fecal samples from patients with microscopically proven cryptosporidiosis and 118 from patients with or without other digestive protozoan infections were tested by Cryptodiag, blinded to the results of microscopy. Compared to microscopy, the sensitivity of Cryptodiag was 97.0% (32/33) and 100% (33/33), including the gray zone, and specificity was 98.3% (116/118) and 96.6% (114/118), including the gray zone. Among 34 positive results, Cryptodiag identified 19 due to
C. hominis
, 8 due to
C. parvum
, and 7 due to
Cryptosporidium
spp. Genotyping by Cryptodiag agreed with reference typing methods in 85% of cases of
C. parvum
or
C. hominis
infections. Cryptodiag proved to be reliable and sensitive for the diagnosis of cryptosporidiosis. The use of specific probes allowed the identification of
C. hominis
and
C. parvum
, i.e., the two main species responsible for human cryptosporidiosis, and rapidly provided information on the possible source of infection.
Multicenter Comparison of PCR Assays for Detection of Human Herpesvirus 6 DNA in Serum
Authors: Flamand Louis , Gravel Annie , Boutolleau David , Alvarez-Lafuente Roberto , Jacobson Steve , Malnati Mauro S. , Kohn Debra , Tang Yi-Wei , Yoshikawa Tetsushi , Ablashi Dharam
Published: June 2008

Human herpesvirus 6 (HHV-6) is a ubiquitous virus with which infections have been associated with pathologies ranging from delayed bone marrow engraftment to a variety of neurological diseases. The lack of a standardized assay that can be used to detect and estimate HHV-6 DNA contents in various clinical specimens can lead and has led to discordant results among investigators and on the potential association of HHV-6 to diseases. To identify the most reliable and sensitive assays, an identical set of 11 coded serum samples spiked with various quantities of the HHV-6A variant (range, 4 to 400,000 genome copies/ml) was sent to eight independent laboratories around the world. Each laboratory was asked to estimate the HHV-6 DNA content by use of its own protocols and assays. Among the various assays, three TaqMan-based real-time PCR assays yielded quantities that were closest to the quantity of HHV-6 that had been spiked. To provide better homogeneity between the results from the different laboratories working on HHV-6, we propose that investigators interested in quantifying HHV-6 in clinical samples adopt one of these assays.
Extended-Spectrum-Beta-Lactamase Production in a
Salmonella enterica
Serotype Typhi Strain from the Philippines
Authors: Al Naiemi Nashwan , Zwart Bastiaan , Rijnsburger Martine C. , Roosendaal Robert , Debets-Ossenkopp Yvette J. , Mulder Janet A. , Fijen Cees A. , Maten Willemina , Vandenbroucke-Grauls Christina M. , Savelkoul Paul H.
Published: June 2008

A
Salmonella enterica
serotype Typhi strain was cultured from blood and fecal samples from a 54-year-old man with fever and diarrhea. He had returned from travel to the Philippines a few days earlier. Phenotypic and genotypic analysis confirmed the production of the SHV-12 extended-spectrum beta-lactamase.
Association between 16S-23S Internal Transcribed Spacer Sequence Groups of
Mycobacterium avium
Complex and Pulmonary Disease
Authors: Stout Jason E. , Hopkins Gregory W. , McDonald Jay R. , Quinn Anita , Hamilton Carol D. , Reller L. Barth , Frothingham Richard
Published: June 2008

Organisms within the
Mycobacterium avium
complex (MAC) may have differential virulence. We compared 33 subjects with MAC pulmonary disease to 75 subjects with a single positive culture without disease.
M. avium
isolates were significantly more likely to be associated with MAC pulmonary disease (odds ratio = 5.14, 95% confidence interval = 1.25 to 22.73) than
M. intracellulare
.
Gram Stain-Specific-Probe-Based Real-Time PCR for Diagnosis and Discrimination of Bacterial Neonatal Sepsis
Authors: Wu Yi-Dong , Chen Li-Hua , Wu Xiu-Jing , Shang Shi-Qiang , Lou Jin-Tu , Du Li-Zhong , Zhao Zheng-Yan
Published: June 2008

Sepsis is a serious disease with high mortality in newborns. It is very important to have a convenient and accurate method for pathogenic diagnosis of neonatal sepsis. We developed a method of simultaneous detection and Gram classification of clinically relevant bacterial pathogens causing sepsis directly from blood samples with Gram stain-specific-probe-based real-time PCR (GSPBRT-PCR). With GSPBRT-PCR, 53 clinically important strains representing 25 gram-positive and 28 gram-negative bacterial species were identified correctly with the corresponding Gram probe. The limits of the GSPBRT-PCR assay in serial dilutions of the bacteria revealed that
Staphylococcus aureus
could be detected at concentrations of 3 CFU per PCR and
Escherichia coli
at concentrations as low as 1 CFU per PCR. The GSPBRT-PCR assay was further evaluated on 600 blood specimens from patients with suspicioon of neonatal sepsis and compared to the results obtained from blood cultures. The positive rate of the GSPBRT-PCR array was 50/600 (8.33%), significantly higher than that of blood culture (34/600; 5.67%) (
P
= 0.00003). When blood culture was used as a control, the sensitivity of GSPBRT-PCR was 100%, the specificity was 97.17%, and the index of accurate diagnosis was 0.972. This study suggests that GSPBRT-PCR is very useful for the rapid and accurate diagnosis of bacterial infection and that it can have an important impact on the current inappropriate and unnecessary use of antibiotics in the treatment of newborns.
Effective Chemokine Secretion by Dendritic Cells and Expansion of Cross-Presenting CD4−/CD8+Dendritic Cells Define a Protective Phenotype in the Mouse Model of Coxsackievirus Myocarditis
Authors: Weinzierl Andreas Oliver , Szalay Gudrun , Wolburg Hartwig , Sauter Martina , Rammensee Hans-Georg , Kandolf Reinhard , Stevanović Stefan , Klingel Karin
Published: June 2008

Enteroviruses such as coxsackievirus B3 (CVB3) are able to induce lethal acute and chronic myocarditis. In resistant C57BL/6 mice, CVB3 myocarditis is abrogated by T-cell-dependent mechanisms, whereas major histocompatibility complex (MHC)-matched permissive A.BY/SnJ mice develop chronic myocarditis based on virus persistence. To define the role of T-cell-priming dendritic cells (DCs) in the outcome of CVB3 myocarditis, DCs were analyzed in this animal model in the course of CVB3 infection. In both mouse strains, DCs were found to be infectible with CVB3; however, formation of infectious virions was impaired. In DCs derived from C57BL/6 mice, significantly higher quantities of interleukin-10 (IL-10) and the proinflammatory cytokines IL-6 and tumor necrosis factor alpha were measured compared to those from A.BY/SnJ mice. Additionally, the chemokines interferon-inducible protein 10 (IP-10) and RANTES were secreted by DCs from resistant C57BL/6 mice earlier in infection and at significantly higher levels. The protective role of IP-10 in CVB3 myocarditis was confirmed in IP-10−/−mice, which had increased myocardial injury compared to the immunocompetent control animals. Also, major differences in resistant and permissive mice were found in DC subsets, with C57BL/6 mice harboring more cross-priming CD4−CD8+DCs. As CD4−CD8+DCs are known to express 10 times more Toll-like receptor 3 (TLR3) than other DC subsets, we followed the course of CVB3 infection in TLR3−/−mice. These mice developed a fulminant acute myocarditis and secreted sustained low amounts of type I interferons; secretion of IP-10 and RANTES was nearly abrogated in DCs. We conclude that MHC-independent genetic factors involving DC-related IP-10 secretion and TLR3 expression are beneficial in the prevention of chronic coxsackievirus myocarditis.
Sf29
Gene of
Spodoptera frugiperda
Multiple Nucleopolyhedrovirus Is a Viral Factor That Determines the Number of Virions in Occlusion Bodies
Authors: Simón Oihane , Williams Trevor , Asensio Aaron C. , Ros Sarhay , Gaya Andrea , Caballero Primitivo , Possee Robert D.
Published: June 2008

The genome of
Spodoptera frugiperda
multiple nucleopolyhedrovirus (NPV) was inserted into a bacmid (Sfbac) and used to produce a mutant lacking open reading frame 29 (Sf29null). Sf29null bacmid DNA was able to generate an infection in
S. frugiperda
. Approximately six times less DNA was present in occlusion bodies (OBs) produced by the Sf29null bacmid in comparison to viruses containing this gene. This reduction in DNA content was consistent with fewer virus particles being packaged within Sf29null bacmid OBs, as determined by fractionation of dissolved polyhedra and comparison of occlusion-derived virus (ODV) infectivity in cell culture. DNA from Sfbac, Sf29null, or Sf29null-repair, in which the gene deletion had been repaired, were equally infectious when used to transfect
S. frugiperda
. All three viruses produced similar numbers of OBs, although those from Sf29null were 10-fold less infectious than viruses with the gene. Insects infected with Sf29null bacmid died ∼24 h later than positive controls, consistent with the reduced virus particle content of Sf29null OBs. Transcripts from
Sf29
were detected in infected insects 12 h prior to those from the polyhedrin gene. Homologs to
Sf29
were present in other group II NPVs, and similar sequences were present in entomopoxviruses. Analysis of the
Sf29
predicted protein sequence revealed signal peptide and transmembrane domains, but the presence of 12 potential N
-
glycosylation sites suggest that it is not an ODV envelope protein. Other motifs, including zinc-binding and threonine-rich regions, suggest degradation and adhesion functions. We conclude that
Sf29
is a viral factor that determines the number of ODVs occluded in each OB.
The Envelope of Intracellular African Swine Fever Virus Is Composed of a Single Lipid Bilayer
Authors: Hawes Philippa C. , Netherton Christopher L. , Wileman Thomas E. , Monaghan Paul
Published: June 2008

African swine fever virus (ASFV) is a member of a family of large nucleocytoplasmic DNA viruses that include poxviruses, iridoviruses, and phycodnaviruses. Previous ultrastructural studies of ASFV using chemical fixation and cryosectioning for electron microscopy (EM) have produced uncertainty over whether the inner viral envelope is composed of a single or double lipid bilayer. In this study we prepared ASFV-infected cells for EM using chemical fixation, cryosectioning, and high-pressure freezing. The appearance of the intracellular viral envelope was determined and compared to that of mitochondrial membranes in each sample. The best resolution of membrane structure was obtained with samples prepared by high-pressure freezing, and images suggested that the envelope of ASFV consisted of a single lipid membrane. It was less easy to interpret virus structure in chemically fixed or cryosectioned material, and in the latter case the virus envelope could be interpreted as having two membranes. Comparison of membrane widths in all three preparations indicated that the intracellular viral envelope of ASFV was not significantly different from the outer mitochondrial membrane (
P
< 0.05). The results support the hypothesis that the intracellular ASFV viral envelope is composed of a single lipid bilayer.
Phylogenetic and Genetic Analysis of Feline Immunodeficiency Virus
gag
,
pol
, and
env
Genes from Domestic Cats Undergoing Nucleoside Reverse Transcriptase Inhibitor Treatment or Treatment-Naïve Cats in Rio de Janeiro, Brazil
Authors: Martins Angelica N. , Medeiros Sheila O. , Simonetti Jose P. , Schatzmayr Hermann G. , Tanuri Amílcar , Brindeiro Rodrigo M.
Published: June 2008

Feline immunodeficiency virus (FIV) is the
Lentivirus
responsible for an immunodeficiency-like disease in domestic cats (
Felis catus
). FIV is divided into five phylogenetic subtypes (A, B, C, D, and E), based on genetic diversity. Knowledge of the geographical distribution of subtypes is relevant for understanding different disease progressions and for vaccine development. In this study, viral sequences of 26 infected cats from Rio de Janeiro, 8 undergoing treatment with zidovudine (AZT) for at least 5 years, were successfully amplified from blood specimens.
gag
capsid (CA),
pol
reverse transcriptase (RT), and
env
gp120 (V3-V4) regions were analyzed to determine subtypes and to evaluate potential mutations related to antiretroviral drug resistance among treated cats. Subtyping based on phylogenetic analysis was performed by the neighbor-joining and maximum likelihood methods. All of the sequences clustered with subtype B in the three regions, exhibiting low genetic variability. Additionally, we found evidence that the same virus is circulating in animals in close contact. The analysis of FIV RT sequences identified two new putative mutations related to drug resistance located in the RT “finger” domain, which has 60% identity to human immunodeficiency virus (HIV) sequence. Amino acid change K→R at codons 64 and 69 was found in 25% and 37.5% of the treated animals, respectively. These signatures were comparable to K65R and K70R thymidine-associated mutations found in the HIV-1 HXB2 counterpart. This finding strongly suggests a position correlation between the mutations found in FIV and the K65R and K70R substitutions from drug-resistant HIV-1 strains.
The Core Element of a CpG Island Protects Avian Sarcoma and Leukosis Virus-Derived Vectors from Transcriptional Silencing
Authors: Šenigl Filip , Plachý Jiří , Hejnar Jiří
Published: June 2008

Unmethylated CpG islands are known to keep adjacent promoters transcriptionally active. In the CpG island adjacent to the adenosine phosphoribosyltransferase gene, the protection against transcriptional silencing can be attributed to the short CpG-rich core element containing Sp1 binding sites. We report here the insertion of this CpG island core element, IE, into the long terminal repeat of a retroviral vector derived from Rous sarcoma virus, which normally suffers from progressive transcriptional silencing in mammalian cells. IE insertion into a specific position between enhancer and promoter sequences led to efficient protection of the integrated vector from silencing and gradual CpG methylation in rodent and human cells. Individual cell clones with IE-modified reporter vectors display high levels of reporter expression for a sustained period and without substantial variegation in the cell culture. The presence of Sp1 binding sites is important for the protective effect of IE, but at least some part of the entire antisilencing capacity is maintained in IE with mutated Sp1 sites. We suggest that this strategy of antisilencing protection by the CpG island core element may prove generally useful in retroviral vectors.
The Large Polymerase Protein Is Associated with the Virulence of Newcastle Disease Virus
Authors: Rout Subrat N. , Samal Siba K.
Published: June 2008

Naturally occurring Newcastle disease virus (NDV) strains vary greatly in virulence, ranging from no apparent infection to severe disease causing 100% mortality in chickens. The viral determinants of NDV virulence are not completely understood. Cleavage of the fusion protein is required for the initiation of infection, and it acts as a determinant of virulence. The attachment protein HN was found to play a minor role in virulence. In this study, we have evaluated the role of the internal proteins (N, P, and L) in NDV virulence by using a chimeric reverse-genetics approach. The N, P, and L genes were exchanged individually between an avirulent NDV strain, LaSota, and an intermediate virulent NDV strain, Beaudette C (BC), and the N and P genes were also exchanged together. The recovered chimeric viruses were evaluated for their pathogenicity in the natural host, chickens. Our results showed that the pathogenicities of N and P chimeric viruses were similar to those of their respective parental viruses, indicating that the N and P genes probably play minor roles in virulence. However, replacement of the L gene of BC with that of LaSota significantly increased the pathogenicity of the L-chimeric virus, suggesting that the L gene probably contributes to the virulence of NDV. The L-chimeric BC virus was found to replicate at a 100-fold-higher level than its parental virus in chicken brain, suggesting that the increase in pathogenicity may be due to the increased replication level of the chimeric virus. Our findings offer new insights into the pathogenesis of NDV infection.
The High Prevalence of Herpes Simplex Virus Type 1 DNA in Human Trigeminal Ganglia Is Not a Function of Age or Gender
Authors: Hill James M. , Ball Melvyn J. , Neumann Donna M. , Azcuy Ann M. , Bhattacharjee Partha S. , Bouhanik Saadallah , Clement Christian , Lukiw Walter J. , Foster Timothy P. , Kumar Manish , Kaufman Herbert E. , Thompson Hilary W.
Published: June 2008

The purpose of this study was to determine the presence and copy numbers of herpes simplex virus type 1 (HSV-1) DNA in human trigeminal ganglia (TG) with respect to age, gender, and postmortem interval (PMI). Human TG (
n
= 174, obtained from the Oregon Brain Bank, with data on age, gender, and PMI) were analyzed for HSV-1 DNA copies (HSV-1 DNA polymerase gene) by using real-time PCR. We found that 89.1% (131/147) of subjects and 90.1% (155/174) of TG contained HSV-1 DNA. The copy numbers of HSV-1 DNA in the positives ranged from very high (>10
6
) to very low (5). These data confirm and strengthen our previous findings that subjects were positive for HSV-1 DNA in tears (46/50; 92%) and saliva (47/50; 94%). These TG data and tear and saliva data demonstrated considerable variability in copy numbers of HSV-1 DNA per subject. Statistical analysis showed no significant relationship between gender and copy number, age and copy number, or PMI and copy number for each pair of variables. A factorial analysis of gender, age, and PMI with respect to copy number also showed no statistical significance. This is the first study that provides statistical analysis that documents that the prevalence of HSV-1 DNA in the human TG is not a function of either gender or age.
Amino Acid 226 in the Hemagglutinin of H4N6 Influenza Virus Determines Binding Affinity for α2,6-Linked Sialic Acid and Infectivity Levels in Primary Swine and Human Respiratory Epithelial Cells
Authors: Bateman Allen C. , Busch Marc G. , Karasin Alexander I. , Bovin Nicolai , Olsen Christopher W.
Published: June 2008

Avian lineage H4N6 influenza viruses previously isolated from pigs differ at hemagglutinin amino acids 226 and 228 from H4 subtype viruses isolated from birds. Using a parental H4N6 swine isolate and hemagglutinin mutant viruses (at residues 226 and/or 228), we determined that viruses which contain L226 had a higher affinity for sialic acid α2,6 galactose (SAα2,6Gal) and a higher infectivity level for primary swine and human respiratory epithelial cells, whereas viruses which contain Q226 had lower SAα2,6Gal affinity and lower infectivity levels for both types of cells. Using specific neuraminidases, we found that irrespective of their relative binding preferences, all of the influenza viruses examined utilized SAα2,6Gal to infect swine and human cells.
Mouse Hepatitis Virus Type 2 Enters Cells through a Clathrin-Mediated Endocytic Pathway Independent of Eps15
Authors: Pu Yinghui , Zhang Xuming
Published: June 2008

It has recently been shown that cell entry of mouse hepatitis virus type 2 (MHV-2) is mediated through endocytosis (Z. Qiu et al., J. Virol.
80
:5768-5776, 2006). However, the molecular mechanism underlying MHV-2 entry is not known. Here we employed multiple chemical and molecular approaches to determine the molecular pathways for MHV-2 entry. Our results showed that MHV-2 gene expression and infectivity were significantly inhibited when cells were treated with chemical and physiologic blockers of the clathrin-mediated pathway, such as chlorpromazine and hypertonic sucrose medium. Furthermore, viral gene expression was significantly inhibited when cells were transfected with a small interfering RNA specific to the clathrin heavy chain. However, these treatments did not affect the infectivity and gene expression of MHV-A59, demonstrating the specificity of the inhibitions. In addition, overexpression of a dominant-negative mutant of caveolin 1 did not have any effect on MHV-2 infection, while it significantly blocked the caveolin-dependent uptake of cholera toxin subunit B. These results demonstrate that MHV-2 utilizes the clathrin- but not caveolin-mediated endocytic pathway for entry. Interestingly, when the cells transiently overexpressed a dominant-negative form (DIII) of Eps15, which is thought to be an essential component of the clathrin pathway, viral gene expression and infectivity were unaffected, although DIII expression blocked transferrin uptake and vesicular stomatitis virus infection, which are dependent on clathrin-mediated endocytosis. Thus, MHV-2 entry is mediated through clathrin-dependent but Eps15-independent endocytosis.
Novel Astroviruses in Insectivorous Bats
Authors: Chu D. K. W. , Poon L. L. M. , Guan Y. , Peiris J. S. M.
Published: June 2008

Bats are increasingly recognized to harbor a wide range of viruses, and in most instances these viruses appear to establish long-term persistence in these animals. They are the reservoir of a number of human zoonotic diseases including Nipah, Ebola, and severe acute respiratory syndrome. We report the identification of novel groups of astroviruses in apparently healthy insectivorous bats found in Hong Kong, in particular, bats belonging to the genera
Miniopterus
and
Myotis
. Astroviruses are important causes of diarrhea in many animal species, including humans. Many of the bat astroviruses form distinct phylogenetic clusters in the genus
Mamastrovirus
within the family
Astroviridae
. Virus detection rates of 36% to 100% and 50% to 70% were found in
Miniopterus magnater
and
Miniopterus pusillus
bats, respectively, captured within a single bat habitat during four consecutive visits spanning 1 year. There was high genetic diversity of viruses in bats found within this single habitat. Some bat astroviruses may be phylogenetically related to human astroviruses, and further studies with a wider range of bat species in different geographic locations are warranted. These findings are likely to provide new insights into the ecology and evolution of astroviruses and reinforce the role of bats as a reservoir of viruses with potential to pose a zoonotic threat to human health.
Human Parvovirus B19 NS1 Protein Modulates Inflammatory Signaling by Activation of STAT3/PIAS3 in Human Endothelial Cells
Authors: Duechting Anja , Tschöpe Carsten , Kaiser Heike , Lamkemeyer Tobias , Tanaka Nobuyuki , Aberle Susanne , Lang Florian , Torresi Joseph , Kandolf Reinhard , Bock C.-Thomas
Published: June 2008

The pathogenic mechanism by which parvovirus B19 may induce inflammatory cardiomyopathy (iCMP) is complex but is known to involve inflammatory processes, possibly including activation of JAK/STAT signaling. The nonstructural B19 protein NS1 acts as a transactivator triggering signaling cascades that eventually lead to activation of interleukin 6 (IL-6). We examined the impact of NS1 on modulation of STAT signaling in human endothelial cells (HMEC-1). The NS1 sequences were identified from B19 DNA isolated from the myocardia of patients with fatal iCMP. B19 infection as well as NS1 overexpression in HMEC-1 cells produced a significant upregulation in the phosphorylation of both tyrosine705and serine727STAT3 (P< 0.05). The increased STAT3 phosphorylation was accompanied by dimerization, nuclear translocation, and DNA binding of pSTAT3. In contrast, NS1 expression did not result in increased STAT1 activation. Notably, the expression levels of the negative regulators of STAT activation, SOCS1 and SOCS3, were not altered by NS1. However, the level of PIAS3 was upregulated in NS1-expressing HMEC-1 cells. Analysis of the transcriptional activation of target genes revealed that NS1-induced STAT3 signaling was associated with upregulation of genes involved in immune response (e.g., the IFNAR1 and IL-2 genes) and downregulation of genes associated with viral defense (e.g., the OAS1 and TYK2 genes). Our results demonstrate that B19 NS1 modulates the STAT/PIAS pathway. The NS1-induced upregulation of STAT3/PIAS3 in the absence of STAT1 phosphorylation and the lack of SOCS1/SOCS3 activation may contribute to the mechanisms by which B19 evades the immune response and establishes persistent infection in human endothelial cells. Thus, NS1 may play a critical role in the mechanism of viral pathogenesis in B19-associated iCMP.
A Novel Cellular Protein, VPEF, Facilitates Vaccinia Virus Penetration into HeLa Cells through Fluid Phase Endocytosis
Authors: Huang Cheng-Yen , Lu Tsai-Yi , Bair Chi-Horng , Chang Yuan-Shau , Jwo Jeng-Kuan , Chang Wen
Published: June 2008

Vaccinia virus is a large DNA virus that infects many cell cultures in vitro and animal species in vivo. Although it has been used widely as a vaccine, its cell entry pathway remains unclear. In this study, we showed that vaccinia virus intracellular mature virions bound to the filopodia of HeLa cells and moved toward the cell body and entered the cell through an endocytic route that required a dynamin-mediated pathway but not a clathrin- or caveola-mediated pathway. Moreover, virus penetration required a novel cellular protein, vaccinia virus penetration factor (VPEF). VPEF was detected on cell surface lipid rafts and on vesicle-like structures in the cytoplasm. Both vaccinia virus and dextran transiently colocalized with VPEF, and, importantly, knockdown of VPEF expression blocked vaccinia virus penetration as well as intracellular transport of dextran, suggesting that VPEF mediates vaccinia virus entry through a fluid uptake endocytosis process in HeLa cells. Intracellular VPEF-containing vesicles did not colocalize with Rab5a or caveolin but partially colocalized with Rab11, supporting the idea that VPEF plays a role in vesicle trafficking and recycling in HeLa cells. In summary, this study characterized the mechanism by which vaccinia virus enters HeLa cells and identified a cellular factor, VPEF, that is exploited by vaccinia virus for cell entry through fluid phase endocytosis.
Liver-Specific MicroRNA miR-122 Enhances the Replication of Hepatitis C Virus in Nonhepatic Cells
Authors: Chang Jinhong , Guo Ju-Tao , Jiang Dong , Guo Haitao , Taylor John M. , Block Timothy M.
Published: June 2008

The liver-specific microRNA miR-122 has been shown to be required for the replication of hepatitis C virus (HCV) in the hepatoma cell line Huh7. The aim of this study was to test if HCV replication can be modulated by exogenously expressed miR-122 in human embryonic kidney epithelial cells (HEK-293). Our results demonstrate that miR-122 enhances the colony formation efficiency of the HCV replicon and increases the steady-state level of HCV RNA in HEK-293 cells. Therefore, we conclude that although miR-122 is not absolutely required, it greatly enhances HCV replication in nonhepatic cells.
Cellular La Protein Shields Nonsegmented Negative-Strand RNA Viral Leader RNA from RIG-I and Enhances Virus Growth by Diverse Mechanisms
Authors: Bitko Vira , Musiyenko Alla , Bayfield Mark A. , Maraia Richard J. , Barik Sailen
Published: June 2008

The La antigen (SS-B) associates with a wide variety of cellular and viral RNAs to affect gene expression in multiple systems. We show that La is the major cellular protein found to be associated with the abundant 44-nucleotide viral leader RNA (leRNA) early after infection with respiratory syncytial virus (RSV), a nonsegmented negative-strand RNA virus. Consistent with this, La redistributes from the nucleus to the cytoplasm in RSV-infected cells. Upon RNA interference knockdown of La, leRNA is redirected to associate with the RNA-binding protein RIG-I, a known activator of interferon (IFN) gene expression, and this is accompanied by the early induction of IFN mRNA. These results suggest that La shields leRNA from RIG-I, abrogating the early viral activation of type I IFN. We mapped the leRNA binding function to RNA recognition motif 1 of La and showed that while wild-type La greatly enhanced RSV growth, a La mutant defective in RSV leRNA binding also did not support RSV growth. Comparative studies of RSV and Sendai virus and the use of IFN-negative Vero cells indicated that La supports the growth of nonsegmented negative-strand RNA viruses by both IFN suppression and a potentially novel IFN-independent mechanism.
UNIFORM ERGODIC THEOREMS ON APERIODIC LINEARLY REPETITIVE TILINGS AND APPLICATIONS
Authors: BESBES ADNENE
Published: June 2008

The paper is concerned with aperiodic linearly repetitive tilings. For such tilings, we establish a weak form of self-similarity that allows us to prove general (sub)additive ergodic theorems. Finally, we provide applications to the study of lattice gas models.
COMBINATORIAL BETHE ANSATZ AND GENERALIZED PERIODIC BOX-BALL SYSTEM
Authors: KUNIBA ATSUO , SAKAMOTO REIHO
Published: June 2008

We reformulate the Kerov–Kirillov–Reshetikhin (KKR) map in the combinatorial Bethe ansatz from paths to rigged configurations by introducing local energy distribution in crystal base theory. Combined with an earlier result on the inverse map, it completes the crystal interpretation of the KKR bijection for [Formula: see text]. As an application, we solve an integrable cellular automaton, a higher spin generalization of the periodic box-ball system, by an inverse scattering method and obtain the solution of the initial value problem in terms of the ultradiscrete Riemann theta function.
COMPLEMENTARY REGIONS FOR MAPS OF SURFACES
Authors: NOWIK TAHL
Published: June 2008

Let F be a closed connected surface, M a closed connected 3-manifold with H1(M,ℤ/2) = 0, and i: F → M a generic map. Then M - i(F) is a union of connected regions, which may be colored black and white by a checkerboard coloring. This coloring induces a color black or white to each cross-cap of i, namely, the color of the majority of the three local regions in its neighborhood. For k ≥ 0, let akand bkrespectively, be the number of black and white components U, with χ(U) = 1 - k. Let Ca, Cbrespectively be the number of black and white cross-caps of i. Two more integers attached to i are the number N of triple points of i, and χ = χ(F). In this work, we determine what sets of data ({ak}, {bk}, χ, N, Ca, Cb) may appear in this way.
FINITE ELEMENT METHODS FOR NONLINEAR ACOUSTICS IN FLUIDS
Authors: WALSH TIMOTHY , TORRES MONICA
Published: June 2008

In this paper, weak formulations and finite element discretizations of the governing partial differential equations of three-dimensional nonlinear acoustics in absorbing fluids are presented. The fluid equations are considered in an Eulerian framework, rather than a displacement framework, since in the latter case the corresponding finite element formulations suffer from spurious modes and numerical instabilities. When taken with the governing partial differential equations of a solid body and the continuity conditions, a coupled formulation is derived. The change in solid/fluid interface conditions when going from a linear acoustic fluid to a nonlinear acoustic fluid is demonstrated. Finite element discretizations of the coupled problem are then derived, and verification examples are presented that demonstrate the correctness of the implementations. We demonstrate that the time step size necessary to resolve the wave decreases as steepening occurs. Finally, simulation results are presented on a resonating acoustic cavity, and a coupled elastic/acoustic system consisting of a fluid-filled spherical tank.
ANALYZING DOMESTIC AND INTERNATIONAL CORPORATE INNOVATION USING THE DATA SURFACE MINING TECHNIQUE
Authors: BERG DANIEL , EINSPRUCH NORMAN G.
Published: June 2008

Corporate innovation continues to be the subject of a stream of articles in the business press as well as the focus of international conferences. Several recent articles in FORTUNE and BusinessWeek have identified innovative companies on a national and international basis. Using a technique labeled "Data Surface Mining" (DSM), previously published data on corporate innovation were further analyzed to characterize the similarities and differences between the Goods and Service Sectors; the results of these analysis are presented herein. In addition, the issues of technology management especially relevant to the Service Sector are presented. These issues are of critical importance in light of the fact that the Service Sector represents 80% (GDP and/or employment) of the United States economy and are of increasing importance in the global economy. It is also important to note that technology management in the Service Sector has not to date been given proportionate attention in the academic literature.
INTELLECTUAL PROPERTY RIGHTS AND SMEs IN SOUTH-EAST ASIA: INNOVATION POLICY AND INNOVATION PRACTICE
Authors: MACDONALD STUART , TURPIN TIM
Published: June 2008

The paper is derived from a study carried out among the Association of South-East Asian Nations (ASEAN), comprising of Indonesia, Malaysia, the Philippines, Singapore, Thailand, Brunei Darussalam, Vietnam, Lao PDR , Myanmar and Cambodia [Macdonald, Turpin and Ancog (2006)]. The study focused on the relationship between the region's intellectual property rights (IPR) system and the innovation of its SMEs. IPR administrators and policymakers appear convinced that SMEs need IPR to be competitive. They are confirmed in this opinion by pressure to comply with the Trade Related Aspects of Intellectual Property Rights Agreement (TRIPS). Despite an extensive survey and many interviews in SMEs and relevant agencies in the ASEAN countries, the authors could find little evidence to support this belief. The business strategy of SMEs relies more on copying and deft, niche-focused marketing rather than on the prevailing IPR system.
Towards a Classification of 6 × 6 Complex Hadamard Matrices
Authors: Matolcsi Máté , Szöllősi Ferenc
Published: June 2008

Complex Hadamard matrices have received considerable attention in the past few years due to their application in quantum information theory. While a complete characterization currently available [5] is only up to order 5, several new constructions of higher order matrices have appeared recently [4, 12, 2, 7, 11]. In particular, the classification of self-adjoint complex Hadamard matrices of order 6 was completed by Beuachamp and Nicoara in [2], providing a previously unknown non-affine one-parameter orbit. In this paper we classify all dephased, symmetric complex Hadamard matrices with real diagonal of order 6. Furthermore, relaxing the condition on the diagonal entries we obtain a new non-affine one-parameter orbit connecting the Fourier matrix F6 and Diţă's matrix D6. This answers a recent question of Bengtsson et al. [3].
Density Matrices and Their Time Evolution
Authors: Brüning E. , Petruccione F.
Published: June 2008

Already in the case of finite dimensional Hilbert spaces [Formula: see text] the general form of density matrices ρ is not known. The main reason for this lack of knowledge is the nonlinear constraint for these matrices. We propose a representation of density matrices on finite dimensional Hilbert spaces in terms of finitely many independent parameters. For dimensions 2, 3, and 4 we write down this representation explicitly. As a further application of this representation we study the time dependence of density matrices ρ(t) which in our case is implemented through time dependence of the independent parameters. Under obvious differentiability assumptions the explicit form of [Formula: see text] is determined. As a special case we recover, for instance, the Lindblad form.
Rigorous Estimation of Computational Complexity for OMV SAT Algorithm
Authors: Iriyama Satoshi , Ohya Masanori
Published: June 2008

For SAT problem, which is known to be NP-complete, Ohya and Masuda found a quantum algorithm calculating a given boolean function for all truth assignments. They showed that we can decide whether this boolean function is satisfiable or not in polynomial time if a certain superposed state can be detected physically, which turns out to be related to an amplification process. Then Ohya and Volovich realized this amplification by means of chaos dynamics [4, 5]. In this paper, we study the complexity of the SAT algorithm by rigorously counting the steps of OMV algorithm discussed previously in [1, 2, 4, 5].
Cytoplasmic cAMP concentrations in intact cardiac myocytes
Authors: Iancu Radu V. , Ramamurthy Gopalakrishnan , Warrier Sunita , Nikolaev Viacheslav O. , Lohse Martin J. , Jones Stephen W. , Harvey Robert D.
Published: June 2008

In cardiac myocytes there is evidence that activation of some receptors can regulate protein kinase A (PKA)-dependent responses by stimulating cAMP production that is limited to discrete intracellular domains. We previously developed a computational model of compartmentalized cAMP signaling to investigate the feasibility of this idea. The model was able to reproduce experimental results demonstrating that both β1-adrenergic and M2 muscarinic receptor-mediated cAMP changes occur in microdomains associated with PKA signaling. However, the model also suggested that the cAMP concentration throughout most of the cell could be significantly higher than that found in PKA-signaling domains. In the present study we tested this counterintuitive hypothesis using a freely diffusible fluorescence resonance energy transfer-based biosensor constructed from the type 2 exchange protein activated by cAMP (Epac2-camps). It was determined that in adult ventricular myocytes the basal cAMP concentration detected by the probe is ∼1.2 μM, which is high enough to maximally activate PKA. Furthermore, the probe detected responses produced by both β1 and M2 receptor activation. Modeling suggests that responses detected by Epac2-camps mainly reflect what is happening in a bulk cytosolic compartment with little contribution from microdomains where PKA signaling occurs. These results support the conclusion that even though β1 and M2 receptor activation can produce global changes in cAMP, compartmentation plays an important role by maintaining microdomains where cAMP levels are significantly below that found throughout most of the cell. This allows receptor stimulation to regulate cAMP activity over concentration ranges appropriate for modulating both higher (e.g., PKA) and lower affinity (e.g., Epac) effectors.