bluuebunny/crossref_metadata_2025_split huggingface dataset:
Optimization of Culture of
Leptospira
from Humans with Leptospirosis
Authors: Wuthiekanun Vanaporn , Chierakul Wirongrong , Limmathurotsakul Direk , Smythe Lee D. , Symonds Meegan L. , Dohnt Michael F. , Slack Andrew T. , Limpaiboon Roongreung , Suputtamongkol Yupin , White Nicholas J. , Day Nicholas P. J. , Peacock Sharon J. 
Published: February 2007

ABSTRACT

A prospective study of 989 patients with acute febrile illness was performed in northeast Thailand to define the yield of
Leptospira
from four different types of blood sample. Based on a comparison of the yields from whole blood, surface plasma, deposit from spun plasma, and clotted blood samples from 80 patients with culture-proven leptospirosis, we suggest a sampling strategy in which culture is performed using whole blood and deposit from spun plasma.
Analysis of Multiple Differing Copies of the 16S rRNA Gene in Five Clinical Isolates and Three Type Strains of
Nocardia
Species and Implications for Species Assignment
Authors: Conville Patricia S. , Witebsky Frank G. 
Published: February 2007

ABSTRACT

Five clinical isolates of
Nocardia
that showed ambiguous bases within the variable region of the 16S rRNA gene sequence were evaluated for the presence of multiple copies of this gene. The type strains of three
Nocardia
species,
Nocardia concava
,
Nocardia ignorata
, and
Nocardia yamanashiensis
, which also showed ambiguous bases in the variable region, were also examined. Cloning experiments using an amplified region of the 16S rRNA that contains the variable region showed that each isolate possessed 16S rRNA genes with at least two different sequences. In addition, hybridization studies using a 16S rRNA gene-specific probe and extracted genomic DNA of the patient isolates and of the type strain of
N. ignorata
showed that each isolate possessed at least three copies of the gene. These multiple differing copies of the 16S rRNA gene and the results of DNA-DNA hybridization studies indicate problems of species definition and identification for such isolates. A broader species concept than that currently in vogue may be required to accommodate such organisms.
Human Rhinovirus Type 54 Infection via Heparan Sulfate Is Less Efficient and Strictly Dependent on Low Endosomal pH
Authors: Khan Abdul Ghafoor , Pichler Johannes , Rosemann Anke , Blaas Dieter 
Published: February 2007

ABSTRACT

K-type major-group human rhinoviruses (HRVs) (including HRV54) share a prominent lysine residue in the HI surface loop of VP1 with all minor-group HRVs. Despite the presence of this residue, they cannot use members of the low-density lipoprotein receptor family for productive infection. Reexamining all K-type viruses for receptor usage, we noticed that HRV54 is able to replicate in RD cells that lack the major-group receptor intercellular adhesion molecule 1 (ICAM-1). By using receptor blocking assays, inhibition of sulfation, enzymatic digestion, and proteoglycan-deficient cell lines, we show here that wild-type HRV54, without any adaptation, uses heparan sulfate (HS) proteoglycan as an alternate receptor. However, infection via HS is less efficient than infection via ICAM-1. Moreover, HRV54 has an acid lability profile similar to that of the minor-group virus HRV2. In ICAM-1-deficient cells its replication is completely blocked by the H
+
-ATPase inhibitor bafilomycin A1, whereas in ICAM-1-expressing cells it replicates in the presence of the drug. Thus, use of a “noncatalytic” receptor requires the virus to be highly unstable at low pH.
Production of Infectious Hepatitis C Virus of Various Genotypes in Cell Cultures
Authors: Kato Takanobu , Matsumura Takuya , Heller Theo , Saito Satoru , Sapp Ronda K. , Murthy Krishna , Wakita Takaji , Liang T. Jake 
Published: February 2007

ABSTRACT
A unique hepatitis C virus (HCV) strain JFH-1 has been shown to replicate efficiently in cell culture with production of infectious HCV. We previously developed a DNA expression system containing HCV cDNA flanked by two self-cleaving ribozymes to generate HCV particles in cell culture. In this study, we produced HCV particles of various genotypes, including 1a (H77), 1b (CG1b), and 2a (J6 and JFH-1), in the HCV-ribozyme system. The constructs also contain the secreted alkaline phosphatase gene to control for transfection efficiency and the effects of culture conditions. After transfection into the Huh7-derived cell line Huh7.5.1, continuous HCV replication and secretion were confirmed by the detection of HCV RNA and core antigen in the culture medium. HCV replication levels of strains H77, CG1b, and J6 were comparable, whereas the JFH-1 strain replicates at a substantially higher level than the other strains. To evaluate the infectivity in vitro, the culture medium of JFH-1-transfected cells was inoculated into naive Huh7.5.1 cells. HCV proteins were detected by immunofluorescence 3 days after inoculation. To evaluate the infectivity in vivo, the culture medium from HCV genotype 1b-transfected cells was inoculated into a chimpanzee and caused a typical course of HCV infection. The HCV 1b propagated in vitro and in vivo had sequences identical to those of the HCV genomic cDNA used for cell culture transfection. The development of culture systems for production of various HCV genotypes provides a valuable tool not only to study the replication and pathogenesis of HCV but also to screen for antivirals.
Detection and Genetic Characterization of Group A Rotavirus Strains Circulating among Children with Acute Gastroenteritis in Japan
Authors: Phan Tung Gia , Khamrin Pattara , Quang Trinh Duy , Dey Shuvra Kanti , Takanashi Sayaka , Okitsu Shoko , Maneekarn Niwat , Ushijima Hiroshi 
Published: February 2007

ABSTRACT
A total of 603 fecal specimens collected from July 2005 to June 2006 from children with acute gastroenteritis, encompassing five different localities in Japan, were screened for group A rotavirus by reverse transcription-PCR. It was found that 117 fecal specimens (19.4%) were positive for group A rotavirus. Rotavirus infection was detected continuously from November to June, with the highest prevalence in April. The G (VP7 genotypes) and P (VP4 genotypes) types were further investigated. The predominant genotype was G1P[8] (70.1%), followed by G3P[8] (17.9%), G9P[8] (6.8%), and G2P[4] (2.6%). A number of unusual G1P[4] combinations were also detected during this study period. A novel nomenclature for G1 is proposed, in which worldwide rotavirus G1 strains are classified into 11 lineages with 17 sublineages. A wide range of amino acid substitutions (up to 34) in VP7 that are specific for G1 lineages and sublineages were identified. Interestingly, only short amino acid motifs located at positions 29 to 75 and 211 to 213 of VP7 defined correctly the phylogenetic G1 lineages and sublineages. Examination of the deduced sequences of antigenic regions of VP7 also revealed multiple particular amino acid substitutions that correlated with the phylogenetic G1 lineages and sublineages. Of note, at least three distinct clusters of rotavirus G1 isolates were cocirculating in the Japanese pediatric population studied.
Proteins Associated with
Culex nigripalpus
Nucleopolyhedrovirus Occluded Virions
Authors: Perera Omaththage , Green Terry B. , Stevens Stanley M. , White Susan , Becnel James J. 
Published: February 2007

ABSTRACT

Occlusion-derived virions (ODVs) of the nucleopolyhedrovirus of
Culex nigripalpus
(CuniNPV) were purified by Ludox density gradient ultracentrifugation, and the proteins were separated by one-dimensional sodium dodecyl sulfate-polyacrylamide gel electrophoresis. Proteins were identified by using Edman sequencing, matrix-assisted laser desorption ionization-time of flight mass spectrometry, nanoelectrospray quadrupole time-of-flight mass spectrometry, or a combination of these methods. Half of the 44 polypeptide sequences identified in this analysis were unique open reading frames (ORFs) encoded by the CuniNPV genome and did not show similarity to any other sequences present in protein databases. Of the 22 polypeptides that showed similarities to other baculovirus-encoded proteins, only 17 sequences have previously been identified as structural proteins. The newly identified CuniNPV structural proteins cun058, cun059, cun087, cun106, and cun109 are homologues of
Autographa californica
nucleopolyhedrovirus (AcMNPV) ORFs 68, 62, 98, 81, and 2, respectively. The products of four genes, namely, lef-1 (cun045), alkaline exonuclease (cun054), helicase (cun089), and DNA polymerase (cun091), were not detected in the CuniNPV ODV preparations. These four genes are conserved among all annotated baculovirus genomes, and their homologues have been detected in the ODV of AcMNPV.
tRNA Isoacceptor Preference prior to Retrovirus Gag-Pol Junction Links Primer Selection and Viral Translation
Authors: Palmer Matthew T. , Kirkman Richard , Kosloff Barry R. , Eipers Peter G. , Morrow Casey D. 
Published: February 2007

ABSTRACT

An essential step in the replication of all retroviruses is the capture of a cellular tRNA that is used as the primer for reverse transcription. The 3′-terminal 18 nucleotides of the tRNA are complementary to the primer binding site (PBS). Moloney murine leukemia virus (MuLV) preferentially captures tRNA
Pro
. To investigate the specificity of primer selection, the PBS of MuLV was altered to be complementary to different tRNAs. Analysis of the infectivity of the virus and stability of the PBS following in vitro replication revealed that MuLV prefers to select tRNA
Pro
, tRNA
Gly
, or tRNA
Arg
. Previous studies from our laboratory have suggested that tRNA primer capture is coordinated with translation. Coincidentally, a cluster of proline, arginine, and glycine precedes the Gag-Pol junction of MuLV. Human immunodeficiency virus type 1 (HIV-1), which prefers

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as the primer, can be forced to utilize tRNA
Met
,

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, tRNA
His
, or tRNA
Glu
, although these viruses replicate poorly. Codons for methionine, lysine, histidine, or glutamic acid are found prior to the Gag-Pol frameshift site. HIV-1 was mutated so that the 5 lysine codons prior to the Gag-Pol frameshift region were specific for

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. HIV-1 forced to use

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as the primer, with the mutation of codons specific for

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prior to the Gag-Pol junction, had enhanced infectivity and replicated similarly to the wild-type virus. The results demonstrate that codon preference prior to the Gag-Pol junction influences primer selection and suggest a coordination of Gag-Pol synthesis and acquisition of the tRNA primer required for retrovirus replication.
The Nasal Cavity Is a Route for Prion Infection in Hamsters
Authors: Kincaid Anthony E. , Bartz Jason C. 
Published: February 2007

ABSTRACT

Animals that naturally acquire the prion diseases have a well-developed olfactory sense that they utilize for a variety of basic behaviors. To assess the potential for the nasal cavity to serve as a point of entry for prion diseases, a small amount of prion-infected brain homogenate was placed inferior to the nostrils of hamsters, where it was immediately sniffed into the nasal cavity. Hamsters extranasally inoculated with the HY strain of transmissible mink encephalopathy (TME) agent had an incubation period that was not significantly different from per os inoculation of the same dose of the HY TME agent. However, the efficiency of the nasal route of inoculation was determined to be 10 to 100 times greater based on endpoint dilution analysis. Immunohistochemistry on tissues from hamsters killed at 2-week intervals after inoculation was used to identify the disease-associated form of the prion protein (PrP
d
) to determine the route of prion neuroinvasion. Nasal mucosa-associated lymphoid tissue and submandibular lymph nodes initially accumulated PrP
d
as early as 4 weeks postinfection. PrP
d
was first identified in cervical lymph nodes at 8 weeks, in the mesenteric lymph nodes, spleen, and Peyer's patches at 14 weeks, and in the tongue 20 weeks after inoculation. Surprisingly, there was no evidence of PrP
d
in olfactory epithelium or olfactory nerve fascicles at any time after inoculation. Therefore, the HY TME agent did not enter the central nervous system via the olfactory nerve; instead, PrP
d
accumulated in elements of the cranial lymphoreticular system prior to neuroinvasion.
Role for Actin in the Polarized Release of Rotavirus
Authors: Gardet Agnès , Breton Michelyne , Trugnan Germain , Chwetzoff Serge 
Published: February 2007

ABSTRACT
Rotaviruses are characterized by polarized release from the apical side of infected enterocytes, and the rotavirus VP4 spike protein specifically binds to the actin network at the apical pole of differentiated enterocytic cells. To determine the functional consequences of this VP4-actin interaction, fluorescence recovery after photobleaching experiments were carried out to measure the diffusional mobility of VP4 associated with the microfilaments. Results show that VP4 binds to barbed ends of microfilaments by using actin treadmilling. Actin treadmilling inhibition results in the loss of rotavirus apical preferential release, suggesting a major role for actin in polarized rotavirus release.
Adenovirus-Platelet Interaction in Blood Causes Virus Sequestration to the Reticuloendothelial System of the Liver
Authors: Stone Daniel , Liu Ying , Shayakhmetov Dmitry , Li Zong-Yi , Ni Shaoheng , Lieber André 
Published: February 2007

ABSTRACT
Intravenous (i.v.) delivery of recombinant adenovirus serotype 5 (Ad5) vectors for gene therapy is hindered by safety and efficacy problems. We have discovered a new pathway involved in unspecific Ad5 sequestration and degradation. After i.v. administration, Ad5 rapidly binds to circulating platelets, which causes their activation/aggregation and subsequent entrapment in liver sinusoids. Virus-platelet aggregates are taken up by Kupffer cells and degraded. Ad sequestration in organs can be reduced by platelet depletion prior to vector injection. Identification of this new sequestration mechanism and construction of vectors that avoid it could improve levels of target cell transduction at lower vector doses.
η AND η′ MESONS PRODUCTION AT COSY-11
Authors:   COSY-11 COLLABORATION., Moskal P. , Adam H.-H. , Budzanowski A. , Czerwiński E. , Czyżykiewicz R. , Gil D. , Grzonka D. , Janusz M. , Jarczyk L. , Kamys B. , Khoukaz A. , Klaja P. , Majewski J. , Oelert W. , Piskor-Ignatowicz C. , Przerwa J. , Ritman J. , Rejdych B. , Rożek T. , Sefzick T. , Siemaszko M. , Smyrski J. , Täschner A. , Winter P. , Wolke M. , Wüstner P. , Zipper W. 
Published: February 2007

The low emittance and small momentum spread of the proton and deuteron beams of the Cooler Synchrotron COSY combined with the high mass resolution of the COSY-11 detection system permit to study the creation of mesons in the nucleon-nucleon interaction down to the fraction of MeV with respect to the kinematical threshold. At such small excess energies, the ejectiles possess low relative momenta and are predominantly produced with the relative angular momentum equal to zero. Taking advantage of these conditions we have performed investigations aiming to determine the mechanism of the production of η and η′ mesons in the collision of hadrons as well as the hadronic interaction of these mesons with nucleons and nuclei. In this proceedings we address the ongoing studies of the spin and isospin dependence for the production of the η and η′ mesons in free and quasi-free nucleon-nucleon collisions. New results on the spin observables for the [Formula: see text] reaction, combined with the previously determined total cross section isospin dependence, reveal a statistically significant indication that the excitation of the nucleon to the S11(1535) resonance, the process which intermediates the production of the η meson in the nucleon-nuleon interactions, is predominantly due to the exchange of the π meson between the colliding nucleons.
The Effect of Lower Stratospheric Shear on Baroclinic Instability
Authors: Wittman Matthew A. H. , Charlton Andrew J. , Polvani Lorenzo M. 
Published: February 2007

Abstract
Using a hierarchy of models, and observations, the effect of vertical shear in the lower stratosphere on baroclinic instability in the tropospheric midlatitude jet is examined. It is found that increasing stratospheric shear increases the phase speed of growing baroclinic waves, increases the growth rate of modes with low synoptic wavenumbers, and decreases the growth rate of modes with higher wavenumbers. The meridional structure of the linear modes, and their acceleration of the zonal mean jet, changes with increasing stratospheric shear, but in a way that apparently contradicts the observed stratosphere–troposphere northern annular mode (NAM) connection. This contradiction is resolved at finite amplitude. In nonlinear life cycle experiments it is found that increasing stratospheric shear, without changing the jet structure in the troposphere, produces a transition from anticyclonic (LC1) to cyclonic (LC2) behavior at wavenumber 7. All life cycles with wavenumbers lower than 7 are LC1, and all with wavenumber greater than 7 are LC2. For the LC1 life cycles, the effect of increasing stratospheric shear is to increase the poleward displacement of the zonal mean jet by the eddies, which is consistent with the observed stratosphere–troposphere NAM connection. Finally, it is found that the connection between high stratospheric shear and high-tropospheric NAM is present by NCEP–NCAR reanalysis data.
A Simple Model of the Millimeter-Wave Scattering Parameters of Randomly Oriented Aggregates of Finite Cylindrical Ice Hydrometeors
Authors: Weinman J. A. , Kim M-J. 
Published: February 2007

Abstract
Spaceborne millimeter-wave radiometric measurements offer the potential to observe snowfall at high latitudes. A spaceborne W-band cloud radar on CloudSat has been able to observe snow. There is thus a need for a relatively simple representation of millimeter-wave scattering parameters of snow that can be incorporated into algorithms to retrieve snowfall from remotely sensed millimeter-wave brightness temperature measurements and for computing the millimeter-wave backscatter phase function of randomly oriented aggregates of ice prisms or columns.
The extinction coefficients, asymmetry factors, and backscatter phase functions describing scattering by randomly oriented aggregates of elongated cylinders were computed from the discrete dipole approximation. These parameters were also computed by means of a T-matrix model applied to single blunt cylinders by employing a phase delay that only depended on the frequency and the ratio of the volume to the projected area of the cylindrical aggregates. These scattering parameters were fitted by empirical analytical functions that only depended on that phase delay. This permitted consideration of numerous aggregate shapes with far less computational effort than that required by the discrete dipole approximation.
The results of this analysis were applied to measurements of millimeter-wave extinction, radar reflectivity, and snow size distributions obtained during the SNOW-TWO field experiment conducted by the U.S. Army in 1984. Although the simultaneity of the various measurements was not well documented, the theoretical results fell within the range of measurement uncertainty. Model results of the extinction coefficient and asymmetry factor needed to compute 183-GHz brightness temperatures measured by the NOAA Advanced Microwave Sounding Unit-B (AMSU-B) radiometers are presented in the appendix.
On the Definition of the Cloud Water Content Fluctuations and Its Effects on the Computation of a Second-Order Liquid Water Correlation
Authors: Bouzereau E. , Musson-Genon L. , Carissimo B. 
Published: February 2007

Abstract
In subgrid-scale condensation schemes of cloud models, the majority of previous authors have relied on results presented in a paper by Bougeault. In the present paper, second-order liquid water correlations are restated that differ from the former paper but are coherent with the corrigendum of Mellor. These differences are explained here through two different underlying definitions of cloud water content fluctuations; they can be summarized by whether or not unsaturated air within a grid box contributes to the eddy flux of the cloud water content. Taking into account the issue mentioned above, the “buoyancy flux” is also derived. Although the full impact of these changes has not been evaluated here, it may become important for future global cloud-resolving climate models.
On Boundary Layer Separation in the Lee of Mesoscale Topography
Authors: Jiang Qingfang , Doyle James D. , Wang Shouping , Smith Ronald B. 
Published: February 2007

AbstractThe onset of boundary layer separation (BLS) forced by gravity waves in the lee of mesoscale topography is investigated based on a series of numerical simulations and analytical formulations. It is demonstrated that BLS forced by trapped waves is governed by a normalized ratio of the vertical velocity maximum to the surface wind speed; other factors such as the mountain height, mountain slope, or the leeside speedup factor are less relevant. The onset of BLS is sensitive to the surface sensible heat flux—a positive heat flux tends to increase the surface wind speed through enhancing the vertical momentum mixing and accordingly inhibits the occurrence of BLS, and a negative heat flux does the opposite. The wave forcing required to cause BLS decreases with an increase of the aerodynamical roughness zo; a larger zo generates larger surface stress and weaker surface winds and therefore promotes BLS. In addition, BLS shows some sensitivity to the terrain geometry, which modulates the wave characteristics. For a wider ridge, a higher mountain is required to generate trapped waves with a wave amplitude comparable to that generated by a lower but narrower ridge. The stronger hydrostatic waves associated with the wider and higher ridge play only a minor role in the onset of BLS.It has been demonstrated that although hydrostatic waves generally do not directly induce BLS, undular bores may form associated with wave breaking in the lower troposphere, which in turn induce BLS. In addition, BLS could occur underneath undular jump heads or associate with trapped waves downstream of a jump head in the presence of a low-level inversion.