bluuebunny/crossref_metadata_2025 huggingface dataset:
On the Steady Performance of Annular Hydrostatic Thrust Bearing: Rabinowitsch Fluid Model
Authors: Singh Udaya P. , Gupta Ram S. , Kapur Vijay K.
Published: August 2012

The present theoretical analysis investigates the simultaneous effect of lubricant inertia and non-Newtonian pseudoplastic lubricant (lubricant blended with viscosity index improver and viscosity thickener)–Rabinowitsch fluid model on the performance of externally pressurized annular hydrostatic thrust bearings. A close form solution is obtained for pressure distribution. The effect of centrifugal inertia on the pressure distribution in the recess region is considered by taking non-constant recess pressure under a hydrodynamic condition. The load capacity and flow rate have been numerically calculated for various values of viscosity index improver together with the centrifugal inertia effects. In the limiting case in which there is an absence of pseudoplasticity, the results are compared with the pre-established Newtonian lubricants and are found to be in good agreement.
Effects of the Nonlinear Elastic Behavior of Bicycle Chain on Transmission Efficiency
Authors: Spicer James B.
Published: August 2012

A model for nonfrictional power loss in derailleur-type, bicycle chain drives is developed to identify factors that influence transmission efficiency. Existing treatments of chain drive efficiency consider frictional losses but these do not explain the measured tension dependence of power losses and efficiencies for derailleur-type systems. Based on a nonlinear, spring-mass, mechanical transmission line, the model developed in this work shows that losses can be related to harmonic generation and dispersion in the chain. The nonlinear response leading to harmonic generation results from elastic contact at pin-bushing interfaces while dispersion is related to the periodic nature of the chain construction. Using this approach, the tension-dependence of power loss and efficiency are modeled and the influences of various chain-related characteristics on efficiency are assessed. If Hertzian contact descriptions are used, then the dependence of loss and efficiency on pin-bushing clearance, contact length and modulus can be estimated. Modeled results agree with experiment and show that power loss decreases with increasing chain tension and that efficiency varies nearly linearly with the reciprocal of the chain tension under operational conditions that are typical for bicycle chain drives. Significant increases to the power transmission efficiency of bicycle chain drives in derailleur-based systems could be achieved by altering the geometries and materials of current chain components.
Oxidation behavior of arc evaporated Al-Cr-Si-N thin films
Authors: Tritremmel Christian , Daniel Rostislav , Mitterer Christian , Mayrhofer Paul H. , Lechthaler Markus , Polcik Peter
Published: August 2012

The impact of Al and Si on the oxidation behavior of Al-Cr-(Si)-N thin films synthesized by arc evaporation of powder metallurgically prepared AlxCr1−x targets with x = Al/(Al + Cr) of 0.5, 0.6, and 0.7 and (Al0.5Cr0.5)1−zSiz targets with Si contents of z = 0.05, 0.1, and 0.2 in N2 atmosphere was studied in detail by means of differential scanning calorimetry, thermogravimetric analysis (TGA), x-ray diffraction, and Raman spectroscopy. Dynamical measurements in synthetic air (up to 1440 °C) revealed the highest onset temperature of pronounced oxidation for nitride coatings prepared from the Al0.4Cr0.4Si0.2 target. Isothermal TGA at 1100, 1200, 1250, and 1300 °C highlight the pronounced improvement of the oxidation resistance of AlxCr1−xN coatings by the addition of Si. The results show that Si promotes the formation of a dense coating morphology as well as a dense oxide scale when exposed to air.
Influence of imaging source and panel position uncertainties on the accuracy of 2D/3D image registration of cranial images
Authors: Warmerdam Guy , Steininger Philipp , Neuner Markus , Sharp Gregory , Winey Brian
Published: August 2012

Purpose:

To determine the effects of imager source and panel positioning uncertainties on the accuracy of dual intensity‐based 2D/3D image registration of cranial images.

Methods:

An open source 2D/3D image registration algorithm has been developed for registration of two orthogonal x‐rays to a 3D volumetric image. The initialization files of the algorithm allow for nine degrees of freedom system calibration includingx, y, z positions of the source and panel, and three rotational degrees of freedom of the panel about each of the three translational axes. A baseline system calibration was established and a baseline 2D/3D registration between two orthogonal x‐rays and the volumetric image was determined. The calibration file was manipulated to insert errors into each of the nine calibration variables of both imager geometries. Rigid six degrees of freedom registrations were iterated for each panel or source positional error over a range of predetermined calibration errors to determine the resulting error in the registration versus the baseline registration due to the manipulated error of the panel or source calibration.

Results:

Panel and source translational errors orthogonal to the imager/panel axis introduced the greatest errors in the registration accuracy (4.0 mm geometric error results in up to 2.7 mm registration error). Panel rotation about the imaging direction also resulted in errors of the registration (2.0° geometric error results in up to 1.7° registration error). Differences in magnification and panel tilt and roll, i.e., source and/or panel translation along the imaging direction and panel rotations about the orthogonal axes had minimal effects on the registration accuracy (below 0.3 mm and 0.2° registration error).

Conclusions:

While five of the nine imaging system variables were found to have a considerable effect on 2D/3D registration accuracy of cranial images, the other four variables showed minimal effects. Vendors typically provide simplified calibration procedures which aim to remove encountered geometric uncertainties by accounting for two panel translations. This study shows that at least the five relevant positional variables should be separately calibrated, if accurate alignment is required for 2D/3D registration.
Changes Coming to the International System of Units
Authors: Aubrecht Gordon J.
Published: August 2012

The International System of Units (SI) is a coherent system based originally on measurements of properties of material objects. In more recent times, the adopted definitions depend on setting values of universal constants wherever possible. The last remaining humanmade material object on which a standard is based is a platinum-iridium kilogram located in Sèvres, France. The International Bureau of Weights and Measures is considering replacing this physical object as the standard and tying all base units to physical constants that are fixed. The reasons will be explicated in this paper.
Luminous Supernovae
Authors: Gal-Yam Avishay
Published: August 2012

Stellar Explosions

Stars that are born with masses greater than eight times that of the Sun end their lives in luminous explosions known as supernovae. Over the past decade, access to improved sky surveys has revealed rare types of supernovae that are much more luminous than any of those that were known before.
Gal-Yam
(p.
927
) reviews these superluminous events and groups them into three classes that share common observational and physical characteristics. Gamma-ray bursts are another type of extreme explosive events related to the death of massive stars, which occur once per day somewhere in the universe and produce short-lived bursts of gamma-ray light.
Gehrels and Mészáros
(p.
932
) review what has been learned about these events since the launch of NASA's Swift (2004) and Fermi (2008) satellites. The current interpretation is that gamma-ray bursts are related to the formation of black holes. Type Ia supernovae are used as cosmological distance indicators. They are thought to be the result of the thermonuclear explosion of white dwarf stars in binary systems, but the nature of the stellar companion to the white dwarf is still debated.

Dilday
et al.

(p.
942
) report high-resolution spectroscopy of the supernova PTF 11kx, which was detected on 26 January 2011 by the Palomar Transient Factory survey. The data suggest a red giant star companion whose material got transferred to the white dwarf.
PTF 11kx: A Type Ia Supernova with a Symbiotic Nova Progenitor
Authors: Dilday B. , Howell D. A. , Cenko S. B. , Silverman J. M. , Nugent P. E. , Sullivan M. , Ben-Ami S. , Bildsten L. , Bolte M. , Endl M. , Filippenko A. V. , Gnat O. , Horesh A. , Hsiao E. , Kasliwal M. M. , Kirkman D. , Maguire K. , Marcy G. W. , Moore K. , Pan Y. , Parrent J. T. , Podsiadlowski P. , Quimby R. M. , Sternberg A. , Suzuki N. , Tytler D. R. , Xu D. , Bloom J. S. , Gal-Yam A. , Hook I. M. , Kulkarni S. R. , Law N. M. , Ofek E. O. , Polishook D. , Poznanski D.
Published: August 2012

Stellar Explosions

Stars that are born with masses greater than eight times that of the Sun end their lives in luminous explosions known as supernovae. Over the past decade, access to improved sky surveys has revealed rare types of supernovae that are much more luminous than any of those that were known before.
Gal-Yam
(p.
927
) reviews these superluminous events and groups them into three classes that share common observational and physical characteristics. Gamma-ray bursts are another type of extreme explosive events related to the death of massive stars, which occur once per day somewhere in the universe and produce short-lived bursts of gamma-ray light.
Gehrels and Mészáros
(p.
932
) review what has been learned about these events since the launch of NASA's Swift (2004) and Fermi (2008) satellites. The current interpretation is that gamma-ray bursts are related to the formation of black holes. Type Ia supernovae are used as cosmological distance indicators. They are thought to be the result of the thermonuclear explosion of white dwarf stars in binary systems, but the nature of the stellar companion to the white dwarf is still debated.

Dilday
et al.

(p.
942
) report high-resolution spectroscopy of the supernova PTF 11kx, which was detected on 26 January 2011 by the Palomar Transient Factory survey. The data suggest a red giant star companion whose material got transferred to the white dwarf.
Phosphofructokinase 1 Glycosylation Regulates Cell Growth and Metabolism
Authors: Yi Wen , Clark Peter M. , Mason Daniel E. , Keenan Marie C. , Hill Collin , Goddard William A. , Peters Eric C. , Driggers Edward M. , Hsieh-Wilson Linda C.
Published: August 2012

Metabolic Sensor

The enzyme O-GlcNAc transferase (OGT) catalyzes the transfer of
N
-acetylglucosamine from uridine diphospho-
N
-acetylglucosamine (UDP-GlcNAc) to serine or threonine residues of intracellular proteins and responds to the metabolic status of the cell.

Yi
et al.

(p.
975
; see the Perspective by

Mattaini and Vander Heiden

) show that O-GlcNAcylation of phosphofructokinase 1 (PFK1) reduces its activity, thus influencing rates of glycolysis within cells. O-GlcNAcylation of PFK1 was increased in cells exposed to hypoxia, and was increased in several cell lines derived from human tumors. Thus, metabolic changes mediated by O-GlcNAcylation may benefit anabolism and growth of cancer cells. However, glycosylation of PFK1 was not detected in rapidly proliferating normal cells.
Cis
-
Acting Transcriptional Repression Establishes a Sharp Boundary in Chordate Embryos
Authors: Imai Kaoru S. , Daido Yutaka , Kusakabe Takehiro G. , Satou Yutaka
Published: August 2012

BMP Signaling and Transcription

Bone morphogenetic protein signaling (BMP) is widely used for dorsoventral axis determination in animal embryos, which involves specific interactions between BMPs and their antagonists. In the genomes of many animals, the gene
Pinhead
is encoded as a neighbor of one of the BMP ligand genes,
Admp
(antidorsalizing morphogenetic protein). Working in ascidian tailbud-stage embryos,

Imai
et al.

(p.
964
) now show that
Pinhead
is an antagonist of ADMP and is important for the establishment of the sharp boundary of the ventral epidermis. Transcription of
Pinhead
disturbs transcription of
Admp
by a
cis
-acting mechanism, which may explain the mutually exclusive expression of these two functionally opposed genes.
Retaining the Nano in Nanocrystalline Alloys
Authors: Weertman Julia R.
Published: August 2012

Judicious alloying can prevent grain growth in nanocrystalline metals, preserving their useful properties at high temperatures.
Probing Black Hole Gravity
Authors: McKinney Jonathan C.
Published: August 2012

Oscillations in x-ray emission from near an accreting black hole may provide a route to probe Einstein's general relativity theory beyond our local universe.
Walking on Solid Ground
Authors: Dickey B. F.
Published: August 2012

A gel-on-brush model for the mucosal surfaces in the human airways helps to explain how common airway diseases arise.
The Unusual Case of Porcupine
Authors: Lum Lawrence , Clevers Hans
Published: August 2012

A compound that targets the Wnt signaling pathway in cancer moves into therapeutic trials, 30 years after Wnt was discovered.
Calling All Baby Boomers: Get Your Hepatitis C Test
Authors: Cohen Jon
Published: August 2012

A report issued by the U.S. Centers for Disease Control and Prevention last week recommended that all Americans born between 1945 and 1965 be tested for the hepatitis C virus.
Phase I Safety and Immunogenicity Evaluations of an Alphavirus Replicon HIV-1 Subtype CgagVaccine in Healthy HIV-1-Uninfected Adults
Authors: Wecker M. , Gilbert P. , Russell N. , Hural J. , Allen M. , Pensiero M. , Chulay J. , Chiu Ya-Lin , Abdool Karim S. S. , Burke D. S.
Published: August 2012

On the basis of positive preclinical data, we evaluated the safety and immunogenicity of an alphavirus replicon HIV-1 subtype Cgagvaccine (AVX101), expressing a nonmyristoylated form of Gag, in two double-blind, randomized, placebo-controlled clinical trials in healthy HIV-1-uninfected adults. Escalating doses of AVX101 or placebo were administered subcutaneously to participants in the United States and Southern Africa. Because of vaccine stability issues, the first trial was halted prior to completion of all dose levels and a second trial was implemented. The second trial was also stopped prematurely due to documentation issues with the contract manufacturer. Safety and immunogenicity were evaluated through assessments of reactogenicity, reports of adverse events, and assessment of replication-competent and Venezuelan equine encephalitis (VEE) viremia. Immunogenicity was measured using the following assays: enzyme-linked immunosorbent assay (ELISA), chromium 51 (51Cr)-release cytotoxic T lymphocyte (CTL), gamma interferon (IFN-γ) ELISpot, intracellular cytokine staining (ICS), and lymphoproliferation assay (LPA). Anti-vector antibodies were also measured. AVX101 was well tolerated and exhibited only modest local reactogenicity. There were 5 serious adverse events reported during the trials; none were considered related to the study vaccine. In contrast to the preclinical data, immune responses in humans were limited. Only low levels of binding antibodies and T-cell responses were seen at the highest doses. This trial also highlighted the difficulties in developing a novel vector for HIV.
Reduced Frequency of Memory T Cells and Increased Th17 Responses in Patients with Active Tuberculosis
Authors: Marín Nancy D. , París Sara C. , Rojas Mauricio , García Luis F.
Published: August 2012

Phenotypic and functional alterations inMycobacterium tuberculosisT cell subsets have been reported in patients with active tuberculosis. A better understanding of these alterations will increase the knowledge about immunopathogenesis and also may contribute to the development of new diagnostics and prophylactic strategies. Here, theex vivophenotype of CD4+and CD8+T cells and the frequency and phenotype of gamma interferon (IFN-γ)- and interleukin 17 (IL-17)-producing cells elicited in short-term and long-term cultures following CFP-10 and purified protein derivative (PPD) stimulation were determined in noninfected persons (non-TBi), latently infected persons (LTBi), and patients with active tuberculosis (ATB). Phenotypic characterization of T cells was done based on the expression of CD45RO and CD27. Results show that ATB had a reduced frequency of circulating CD4+CD45RO+CD27+T cells and an increased frequency of CD4+CD45RO−CD27+T cells. ATB also had a higher frequency of circulating IL-17-producing CD4+T cells than did LTBi after PPD stimulation, whereas LTBi had more IFN-γ-producing CD4+T cells than did non-TBi. The phenotype of IFN-γ-producing cells at 24 h differs from the phenotype of IL-17-producing cells with no differences between LTBi and ATB. At 144 h, IFN-γ- and IL-17-producing cells were mainly CD45RO+CD27+T cells and they were more frequent in ATB. These results suggest thatM. tuberculosisinfection induces alterations in T cells which interfere with an adequate specific immune response.
Comparative Whole-Genome Mapping To Determine Staphylococcus aureus Genome Size, Virulence Motifs, and Clonality
Authors: Shukla Sanjay K. , Pantrang Madhulatha , Stahl Buffy , Briska Adam M. , Stemper Mary E. , Wagner Trevor K. , Zentz Emily B. , Callister Steven M. , Lovrich Steven D. , Henkhaus John K. , Dykes Colin W.
Published: August 2012

Despite being a clonal pathogen,
Staphylococcus aureus
continues to acquire virulence and antibiotic-resistant genes located on mobile genetic elements such as genomic islands, prophages, pathogenicity islands, and the staphylococcal chromosomal cassette
mec
(SCC
mec
) by horizontal gene transfer from other staphylococci. The potential virulence of a
S. aureus
strain is often determined by comparing its pulsed-field gel electrophoresis (PFGE) or multilocus sequence typing profiles to that of known epidemic or virulent clones and by PCR of the toxin genes. Whole-genome mapping (formerly optical mapping), which is a high-resolution ordered restriction mapping of a bacterial genome, is a relatively new genomic tool that allows comparative analysis across entire bacterial genomes to identify regions of genomic similarities and dissimilarities, including small and large insertions and deletions. We explored whether whole-genome maps (WGMs) of methicillin-resistant
S. aureus
(MRSA) could be used to predict the presence of methicillin resistance, SCC
mec
type, and Panton-Valentine leukocidin (PVL)-producing genes on an
S. aureus
genome. We determined the WGMs of 47 diverse clinical isolates of
S. aureus
, including well-characterized reference MRSA strains, and annotated the signature restriction pattern in SCC
mec
types, arginine catabolic mobile element (ACME), and PVL-carrying prophage, PhiSa2 or PhiSa2-like regions on the genome. WGMs of these isolates accurately characterized them as MRSA or methicillin-sensitive
S. aureus
based on the presence or absence of the SCC
mec
motif, ACME and the unique signature pattern for the prophage insertion that harbored the PVL genes. Susceptibility to methicillin resistance and the presence of
mecA
, SCC
mec
types, and PVL genes were confirmed by PCR. A WGM clustering approach was further able to discriminate isolates within the same PFGE clonal group. These results showed that WGMs could be used not only to genotype
S. aureus
but also to identify genetic motifs in MRSA that may predict virulence.
Clinical and Microbiological Differences between Mycobacterium abscessus and Mycobacterium massiliense Lung Diseases
Authors: Harada Toshiyuki , Akiyama Yasushi , Kurashima Atsuyuki , Nagai Hideaki , Tsuyuguchi Kazunari , Fujii Takashi , Yano Syuichi , Shigeto Eriko , Kuraoka Toshihiko , Kajiki Akira , Kobashi Yoshihiro , Kokubu Fumio , Sato Atsuo , Yoshida Shiomi , Iwamoto Tomotada , Saito Hajime
Published: August 2012

In recent years, many novel nontuberculous mycobacterial species have been discovered through genetic analysis.
Mycobacterium massiliense
and
M. bolletii
have recently been identified as species separate from
M. abscessus
. However, little is known regarding their clinical and microbiological differences in Japan. We performed a molecular identification of stored
M. abscessus
clinical isolates for further identification. We compared clinical characteristics, radiological findings, microbiological findings, and treatment outcomes among patients with
M. abscessus
and
M. massiliense
lung diseases. An analysis of 102 previous isolates of
M. abscessus
identified 72 (71%)
M. abscessus
, 27 (26%)
M. massiliense
, and 3 (3%)
M. bolletii
isolates. Clinical and radiological findings were indistinguishable between the
M. abscessus
and
M. massiliense
groups. Forty-two (58%) patients with
M. abscessus
and 20 (74%) patients with
M. massiliense
infections received antimicrobial treatment. Both the
M. abscessus
and
M. massiliense
groups showed a high level of resistance to all antimicrobials, except for clarithromycin, kanamycin, and amikacin. However, resistance to clarithromycin was more frequently observed in the
M. abscessus
than in the
M. massiliense
group (16% and 4%, respectively;
P
= 0.145). Moreover, the level of resistance to imipenem was significantly lower in
M. abscessus
isolates than in
M. massiliense
isolates (19% and 48%, respectively;
P
= 0.007). The proportions of radiological improvement, sputum smear conversion to negativity, and negative culture conversion during the follow-up period were higher in patients with
M. massiliense
infections than in those with
M. abscessus
infections. Patients with
M. massiliense
infections responded more favorably to antimicrobial therapy than those with
M. abscessus
infections.
Direct Blood PCR in Combination with Nucleic Acid Lateral Flow Immunoassay for Detection of Plasmodium Species in Settings Where Malaria Is Endemic
Authors: Mens P. F. , de Bes H. M. , Sondo P. , Laochan N. , Keereecharoen L. , van Amerongen A. , Flint J. , Sak J. R. S. , Proux S. , Tinto H. , Schallig H. D. F. H.
Published: August 2012

Declining malaria transmission and known difficulties with current diagnostic tools for malaria, such as microscopy and rapid diagnostic tests (RDTs) in particular at low parasite densities, still warrant the search for sensitive diagnostic tests. Molecular tests need substantial simplification before implementation in clinical settings in countries where malaria is endemic. Direct blood PCR (db-PCR), circumventing DNA extraction, to detectPlasmodiumwas developed and adapted to be visualized by nucleic acid lateral flow immunoassay (NALFIA). The assay was evaluated in the laboratory against samples from confirmed Sudanese patients (n= 51), returning travelers (n= 214), samples from the Dutch Blood Bank (n= 100), and in the field in Burkina Faso (n= 283) and Thailand (n= 381) on suspected malaria cases and compared to RDT and microscopy. The sensitivity and specificity of db-PCR-NALFIA compared to the initial diagnosis in the laboratory were 94.4% (95% confidence interval [CI] = 0.909 to 0.969) and 97.4% (95% CI = 0.909 to 0.969), respectively. In Burkina Faso, the sensitivity was 94.8% (95% CI = 0.88.7 to 97.9%), and the specificity was 82.4% (95% CI = 75.4 to 87.7%) compared to microscopy and 93.3% (95% CI = 87.4 to 96.7%) and 91.4% (95% CI = 85.2 to 95.3%) compared to RDT. In Thailand, the sensitivity and specificity were 93.4% (CI = 86.4 to 97.1%) and 90.9 (95% CI = 86.7 to 93.9%), respectively, compared to microscopy and 95.6% (95% CI = 88.5 to 98.6%) and 87.1% (95% CI = 82.5 to 90.6) compared to RDT. db-PCR-NALFIA is highly sensitive and specific for easy and rapid detection ofPlasmodiumparasites and can be easily used in countries where malaria is endemic. The inability of the device to discriminatePlasmodiumspecies requires further investigation.
Association of Campylobacter upsaliensis with Persistent Bloody Diarrhea
Authors: Couturier Brianne A. , Hale DeVon C. , Couturier Marc Roger
Published: August 2012

Campylobacter upsaliensisis a zoonotic, emerging pathogen that is not readily recovered in traditional stool culture. This case represents the first report of persistent bloody diarrhea withC. upsaliensisthat was confirmed by filtration culture, PCR, and sequencing.
Localization of a Region in the Fusion Protein of Avian Metapneumovirus That Modulates Cell-Cell Fusion
Authors: Wei Yongwei , Feng Kurtis , Yao Xiangjie , Cai Hui , Li Junan , Mirza Anne M. , Iorio Ronald M. , Li Jianrong
Published: August 2012

The genus
Metapneumovirus
within the subfamily
Pneumovirinae
of the family
Paramyxoviridae
includes two members, human metapneumovirus (hMPV) and avian metapneumovirus (aMPV), causing respiratory tract infections in humans and birds, respectively. Paramyxoviruses enter host cells by fusing the viral envelope with a host cell membrane. Membrane fusion of hMPV appears to be unique, in that fusion of some hMPV strains requires low pH. Here, we show that the fusion (F) proteins of aMPV promote fusion in the absence of the attachment protein and low pH is not required. Furthermore, there are notable differences in cell-cell fusion among aMPV subtypes. Trypsin was required for cell-cell fusion induced by subtype B but not subtypes A and C. The F protein of aMPV subtype A was highly fusogenic, whereas those from subtypes B and C were not. By construction and evaluation of chimeric F proteins composed of domains from the F proteins of subtypes A and B, we localized a region composed of amino acid residues 170 to 338 in the F protein that is responsible for the hyperfusogenic phenotype of the F from subtype A. Further mutagenesis analysis revealed that residues R295, G297, and K323 in this region collectively contributed to the hyperfusogenicity. Taken together, we have identified a region in the aMPV F protein that modulates the extent of membrane fusion. A model for fusion consistent with these data is presented.
High-Resolution Functional Profiling of the Norovirus Genome
Authors: Thorne Lucy , Bailey Dalan , Goodfellow Ian
Published: August 2012

Human noroviruses (HuNoV) are a major cause of nonbacterial gastroenteritis worldwide, yet details of the life cycle and replication of HuNoV are relatively unknown due to the lack of an efficient cell culture system. Studies with murine norovirus (MNV), which can be propagated in permissive cells, have begun to probe different aspects of the norovirus life cycle; however, our understanding of the specific functions of the viral proteins lags far behind that of other RNA viruses. Genome-wide functional profiling by insertional mutagenesis can reveal protein domains essential for replication and can lead to generation of tagged viruses, which has not yet been achieved for noroviruses. Here, transposon-mediated insertional mutagenesis was used to create 5 libraries of mutagenized MNV infectious clones, each containing a 15-nucleotide sequence randomly inserted within a defined region of the genome. Infectious virus was recovered from each library and was subsequently passaged in cell culture to determine the effect of each insertion by insertion-specific fluorescent PCR profiling. Genome-wide profiling of over 2,000 insertions revealed essential protein domains and confirmed known functional motifs. As validation, several insertion sites were introduced into a wild-type clone, successfully allowing the recovery of infectious virus. Screening of a number of reporter proteins and epitope tags led to the generation of the first infectious epitope-tagged noroviruses carrying the FLAG epitope tag in either NS4 or VP2. Subsequent work confirmed that epitope-tagged fully infectious noroviruses may be of use in the dissection of the molecular interactions that occur within the viral replication complex.
Flavivirus Replication Complex Assembly Revealed by DNAJC14 Functional Mapping
Authors: Yi Zhigang , Yuan Zhenghong , Rice Charles M. , MacDonald Margaret R.
Published: August 2012

DNAJC14 is an Hsp40 family member that broadly modulates flavivirus replication. The mechanism by which DNAJC14 stoichiometrically participates in flavivirus replication complex (RC) formation is unknown; both reduced and elevated levels result in replication inhibition. Using yellow fever virus (YFV), we demonstrate that DNAJC14 redistributes and clusters with YFV nonstructural proteins via a transmembrane domain and a newly identified membrane-binding domain (MBD), which both mediate targeting to detergent-resistant membranes. Furthermore, the RC and DNAJC14 reside as part of a protein interaction network that remains after 1% Triton solubilization. Mutagenesis studies demonstrate that entry into this protein interaction network requires the DNAJC14 C-terminal self-interaction domain. Fusion of the DNAJC14 MBD and self-interaction domain with another Hsp40 family protein is sufficient to confer YFV-inhibitory activity. Our findings support a novel model of DNAJC14 action that includes specific membrane targeting of both DNAJC14 and YFV replication proteins, the formation of protein interactions, and a microdomain-specific chaperone event leading to RC formation. This process alters the properties of the RC membrane and results in the formation of a protein scaffold that maintains the RC.
Glycan-Dependent Immunogenicity of Recombinant Soluble Trimeric Hemagglutinin
Authors: de Vries Robert P. , Smit Cornelis H. , de Bruin Erwin , Rigter Alan , de Vries Erik , Cornelissen Lisette A. H. M. , Eggink Dirk , Chung Nancy P. Y. , Moore John P. , Sanders Rogier W. , Hokke Cornelis H. , Koopmans Marion , Rottier Peter J. M. , de Haan Cornelis A. M.
Published: August 2012

Recombinant soluble trimeric influenza A virus (IAV) hemagglutinin (sHA
3
) has proven an effective vaccine antigen against IAV. Here, we investigate to what extent the glycosylation status of the sHA
3
glycoprotein affects its immunogenicity. Different glycosylation forms of subtype H5 trimeric HA protein (sH5
3
) were produced by expression in insect cells and different mammalian cells in the absence and presence of inhibitors of N-glycan-modifying enzymes or by enzymatic removal of the oligosaccharides. The following sH5
3
preparations were evaluated: (i) HA proteins carrying complex glycans produced in HEK293T cells; (ii) HA proteins carrying Man
9
GlcNAc
2
moieties, expressed in HEK293T cells treated with kifunensine; (iii) HA proteins containing Man
5
GlcNAc
2
moieties derived from HEK293S GnTI(−) cells; (iv) insect cell-produced HA proteins carrying paucimannosidic N-glycans; and (v) HEK293S GnTI(−) cell-produced HA proteins treated with endoglycosidase H, thus carrying side chains composed of only a single
N
-acetylglucosamine each. The different HA glycosylation states were confirmed by comparative electrophoretic analysis and by mass spectrometric analysis of released glycans. The immunogenicity of the HA preparations was studied in chickens and mice. The results demonstrate that HA proteins carrying terminal mannose moieties induce significantly lower hemagglutination inhibition antibody titers than HA proteins carrying complex glycans or single
N
-acetylglucosamine side chains. However, the glycosylation state of the HA proteins did not affect the breadth of the antibody response as measured by an HA1 antigen microarray. We conclude that the glycosylation state of recombinant antigens is a factor of significant importance when developing glycoprotein-based vaccines, such as recombinant HA proteins.
Seoul Virus-Infected Rat Lung Endothelial Cells and Alveolar Macrophages Differ in Their Ability To Support Virus Replication and Induce Regulatory T Cell Phenotypes
Authors: Li Wei , Klein Sabra L.
Published: August 2012

Hantaviruses cause a persistent infection in reservoir hosts that is attributed to the upregulation of regulatory responses and downregulation of proinflammatory responses. To determine whether rat alveolar macrophages (AMs) and lung microvascular endothelial cells (LMVECs) support Seoul virus (SEOV) replication and contribute to the induction of an environment that polarizes CD4
+
T cell differentiation toward a regulatory T (Treg) cell phenotype, cultured primary rat AMs and LMVECs were mock infected or infected with SEOV and analyzed for viral replication, cytokine and chemokine responses, and expression of cell surface markers that are related to T cell activation. Allogeneic CD4
+
T cells were cocultured with SEOV-infected or mock-infected AMs or LMVECs and analyzed for helper T cell (i.e., Treg, Th17, Th1, and Th2) marker expression and Treg cell frequency. SEOV RNA and infectious particles in culture media were detected in both cell types, but at higher levels in LMVECs than in AMs postinfection. Expression of
Ifn
β,
Ccl5
, and
Cxcl10
and surface major histocompatibility complex class II (MHC-II) and MHC-I was not altered by SEOV infection in either cell type. SEOV infection significantly increased
Tgf
β mRNA in AMs and the amount of programmed cell death 1 ligand 1 (PD-L1) in LMVECs. SEOV-infected LMVECs, but not AMs, induced a significant increase in
Foxp3
expression and Treg cell frequency in allogeneic CD4
+
T cells, which was virus replication and cell contact dependent. These data suggest that in addition to supporting viral replication, AMs and LMVECs play distinct roles in hantavirus persistence by creating a regulatory environment through increased
Tgf
β, PD-L1, and Treg cell activity.
A Safe Foot-and-Mouth Disease Vaccine Platform with Two Negative Markers for Differentiating Infected from Vaccinated Animals
Authors: Uddowla Sabena , Hollister Jason , Pacheco Juan M. , Rodriguez Luis L. , Rieder Elizabeth
Published: August 2012

Vaccination of domestic animals with chemically inactivated foot-and-mouth disease virus (FMDV) is widely practiced to control FMD. Currently, FMD vaccine manufacturing requires the growth of large volumes of virulent FMDV in biocontainment-level facilities. Here, two marker FMDV vaccine candidates (A24LL3DYRand A24LL3BPVKV3DYR) featuring the deletion of the leader coding region (Lpro) and one of the 3B proteins were constructed and evaluated. These vaccine candidates also contain either one or two sets of mutations to create negative antigenic markers in the 3D polymerase (3Dpol) and 3B nonstructural proteins. Two mutations in 3Dpol, H27Y and N31R, as well as RQKP9-12→PVKV substitutions, in 3B2abolish reactivity with monoclonal antibodies targeting the respective sequences in 3Dpoland 3B. Infectious cDNA clones encoding the marker viruses also contain unique restriction endonuclease sites flanking the capsid-coding region that allow for easy derivation of custom designed vaccine candidates. In contrast to the parental A24WT virus, single A24LL3DYRand double A24LL3BPVKV3DYRmutant viruses were markedly attenuated upon inoculation of cattle using the natural aerosol or direct tongue inoculation. Likewise, pigs inoculated with live A24LL3DYRvirus in the heel bulbs showed no clinical signs of disease, no fever, and no FMD transmission to in-contact animals. Immunization of cattle with chemically inactivated A24LL3DYRand A24LL3BPVKV3DYRvaccines provided 100% protection from challenge with parental wild-type virus. These attenuated, antigenically marked viruses provide a safe alternative to virulent strains for FMD vaccine manufacturing. In addition, a competitive enzyme-linked immunosorbent assay targeted to the negative markers provides a suitable companion test for differentiating infected from vaccinated animals.
Intranasal Treatment with Poly(I·C) Protects Aged Mice from Lethal Respiratory Virus Infections
Authors: Zhao Jincun , Wohlford-Lenane Christine , Zhao Jingxian , Fleming Erica , Lane Thomas E. , McCray Paul B. , Perlman Stanley
Published: August 2012

In the 2002-2003 severe acute respiratory syndrome coronavirus (SARS-CoV) epidemic, no patients under 24 years of age died, while mortality was greater than 50% in those over 65 years. Greater than 90% of all deaths from influenza A virus (IAV) occur in the elderly (>65 years of age). To address this age-related susceptibility to SARS-CoV and IAV, we infected C57BL/6 (B6) mice with mouse-adapted SARS-CoV (MA15) or IAV (PR8), both of which cause severe disease in aged mice. Intranasal pretreatment of aged mice with poly(I·C) (a TLR3 agonist) and, to a lesser extent, CpG, R848, or lipopolysaccharide (TLR9, TLR7/8, or TLR4 agonists), provided a high level of protection [90% to 100% survival rate after poly(I·C) treatment] against lethal MA15 or IAV challenge and reduced pathological changes and virus loads in the lungs at early times after infection. Poly(I·C) pretreatment upregulated beta interferon (IFN-β), IFN-γ, IL-1β, and tumor necrosis factor (TNF) gene expression in the lungs. Intranasal pretreatment with IFN-β or IFN-γ but not IL-1β or TNF also protected aged mice, consistent with the notion that poly(I·C) pretreatment functioned, at least in part, by inducing IFN-β and IFN-γ. We also identified a potential cellular target for poly(I·C) by showing that treatment inhibited virus replication in primary human airway epithelial cells. These results suggest that intranasal poly(I·C) should be evaluated as a prophylactic agent in aged individuals at high risk for contracting SARS-CoV or IAV infections.
Complete Genome Analysis of Porcine Enterovirus B Isolated in Korea
Authors: Moon Hyoung-Joon , Song DaeSub , Seon Bo Hyeon , Kim Hye-Kwon , Park Seong-Jun , An Dong-Jun , Kim Jong-Man , Kang Bo-Kyu , Park Bong-Kyun
Published: August 2012

The complete genome sequence of porcine enterovirus B (PEV-B) from a Korean isolate was analyzed. The genome size was 7,393 bp. Previously, full genome sequences of PEV-B had been reported from the United Kingdom, Hungary, and China. The Korean PEV-B isolate presented polyprotein gene nucleotide sequence similarities of 77.9, 73.7, 78.9, and 80.3%, respectively, to PEV-B UKG/410/73, LP54, PEV15, and Chinese strains (Ch-ah-f1).
Entire Genomic Sequence of Novel Canine Papillomavirus Type 13
Authors: Lange Christian E. , Ackermann Mathias , Favrot Claude , Tobler Kurt
Published: August 2012

Papillomaviruses are associated with benign and malignant neoplasias of the skin and mucous membranes. The sequence of a novel canine papillomavirus was determined from DNA detected in the oral cavity of a dog. The sequence of the novel virus canine papillomavirus type 13 (CPV13) shares the highest levels of similarity with the Tau papillomaviruses CPV2 and CPV7.
Genome Sequence of an Unusual Human G10P[8] Rotavirus Detected in Vietnam
Authors: Matsushima Yuki , Nakajima Etsuko , Nguyen Tuan Anh , Shimizu Hideaki , Kano Atsuko , Ishimaru Yoko , Phan Tung Gia , Ushijima Hiroshi
Published: August 2012

A rare human G10P[8] rotavirus with a reassortment between bovine and human viruses was detected from a patient with acute gastroenteritis in Vietnam. Genetic analysis using complete coding sequences of all segments showed a genomic constellation of this virus of G10-P[8]-I1-R1-C1-M1-A1-N1-T1-E1-H1. Its VP7 region was genetically related to that of a bovine rotavirus derived from Australia (strain VICG10.01), whereas all other genes were identical to those of a human rotavirus derived from Australia (strain Victoria/CK00047). These results indicate a possibility that the reassortment of the rotavirus was caused by immune escape in Australia and the rotavirus was carried to Vietnam. Additionally, this finding will help further understanding the evolution of rotaviruses circulating in Vietnam.
Complete Genome of the Human Norovirus GIV.1 Strain Lake Macquarie Virus
Authors: Eden John-Sebastian , Lim Kun Lee , White Peter A.
Published: August 2012

Norovirus is an important human pathogen that is now recognized as the leading cause of acute gastroenteritis globally. Six viral genogroups have been described, although only genogroups GI, GII, and GIV are known to infect humans, with the GII viruses most commonly identified in both outbreak and sporadic settings. In contrast, infections by GIV viruses are rarely reported, and their overall prevalence in the community is unknown. Here, we report the complete genome sequence of the human GIV.1 strain Lake Macquarie virus, which caused two linked outbreaks of acute gastroenteritis in aged-care facilities in the Hunter region of New South Wales, Australia. The Lake Macquarie virus genome was 7,527 nucleotides (nt) in length and shared highest identity (70%) with the recently completed feline GIV.2 virus genome.
Genome Sequence of the Broad-Host-Range Pseudomonas Phage Φ-S1
Authors: Sillankorva Sanna , Kropinski Andrew M. , Azeredo Joana
Published: August 2012

The broad-host-range lytic
Pseudomonas
phage Φ-S1 possess a 40,192 bp double-stranded DNA (dsDNA) genome of 47 open reading frames (ORFs) and belongs to the family
Podoviridae
, subfamily
Autographivirinae
, genus
T7likevirus
.
Complete Genome Sequence of a Novel H9N2 Subtype Influenza Virus FJG9 Strain in China Reveals a Natural Reassortant Event
Authors: Xie Qingmei , Yan Zhuanqiang , Ji Jun , Zhang Huanmin , Liu Jun , Sun Yue , Li Guangwei , Chen Feng , Xue Chunyi , Ma Jingyun , Bee Yingzuo
Published: August 2012

A/chicken/FJ/G9/09 (FJ/G9) is an H9N2 subtype avian influenza virus (H9N2 AIV) strain causing high morbidity that was isolated from broilers in Fujian Province of China in 2009. FJ/G9 has been used as the vaccine strain against H9N2 AIV infection in Fujian Province of China. Here, we report the complete genome sequence of FJ/G9 with natural six-way reassortment, which is the most complex genotype strain in China and even in the world so far. The present findings will aid in understanding the complexity and diversity of H9N2 subtype avian influenza virus.
Complete Genome of Pseudomonas aeruginosa Phage PA26
Authors: Kim Min Soo , Cha Kyung Eun , Myung Heejoon
Published: August 2012

PA26, a novel lytic bacteriophage infecting
Pseudomonas aeruginosa
, was isolated, and the whole genome was sequenced. It was found to belong to the myoviridae by an electron microscopic observation. It had a linear double-stranded DNA genome of 72,321 bp. Genomic analysis showed that it resembled another
Pseudomonas
phage, LIT1.
Escherichia coli O157:H7 Typing Phage V7 Is a T4-Like Virus
Authors: Kropinski Andrew M. , Lingohr Erika J. , Moyles Dianne M. , Chibeu Andrew , Mazzocco Amanda , Franklin Kristyn , Villegas Andre , Ahmed Rafiq , She Yi-Min , Johnson Roger P.
Published: August 2012

The complete genome sequence of the
Escherichia coli
O157:H7 typing phage V7 was determined. Its double-stranded DNA genome is 166,452 bp long, encoding 273 proteins and including 11 tRNAs. This virus belongs to the genus T4-like viruses within the subfamily
Tevenvirinae
, family
Myoviridae
.
Complete Genome Sequence Analysis of a Reference Strain of Bluetongue Virus Serotype 16
Authors: Maan Sushila , Maan Narender S. , Singh Karam Pal , Belaganahalli Manjunatha N. , Guimera Marc , Pullinger Gillian , Nomikou Kyriaki , Mertens Peter P. C.
Published: August 2012

The entire genome of the reference strain of bluetongue virus (BTV) serotype 16 (strain RSArrrr/16) was sequenced (a total of 23,518 base pairs). The virus was obtained from the Orbivirus Reference Collection (ORC) at IAH, Pirbright, United Kingdom. The virus strain, which was previously provided by the Onderstepoort Veterinary Research Institute in South Africa, was originally isolated from the Indian subcontinent (Hazara, West Pakistan) in 1960. Previous phylogenetic comparisons show that BTV RNA sequences cluster according to the geographic origins of the virus isolate/lineage, identifying distinct BTV topotypes. Sequence comparisons of segments Seg-1 to Seg-10 show that RSArrrr/16 belongs to the major eastern topotype of BTV (BTV-16e) and can be regarded as a reference strain of BTV-16e for phylogenetic and molecular epidemiology studies. All 10 genome segments of RSArrrr/16 group closely with the vaccine strain of BTV-16 (RSAvvvv/16) that was derived from it, as well as those recently published for a Chinese isolate of BTV-16 (>99% nucleotide identity), suggesting a very recent common ancestry for all three viruses.
A Kaposi's Sarcoma-Associated Herpesvirus MicroRNA and Its Variants Target the Transforming Growth Factor β Pathway To Promote Cell Survival
Authors: Lei Xiufen , Zhu Ying , Jones Tiffany , Bai Zhiqiang , Huang Yufei , Gao Shou-Jiang
Published: August 2012

Transforming growth factor β (TGF-β) signaling regulates cell growth and survival. Dysregulation of the TGF-β pathway is common in viral infection and cancer. Latent infection by Kaposi's sarcoma-associated herpesvirus (KSHV) is required for the development of several AIDS-related malignancies, including Kaposi's sarcoma and primary effusion lymphoma (PEL). KSHV encodes more than two dozen microRNAs (miRs) derived from 12 pre-miRs with largely unknown functions. In this study, we show that miR variants processed from pre-miR-K10 are expressed in KSHV-infected PEL cells and endothelial cells, while cellular miR-142-3p and its variant miR-142-3p_-1_5, which share the same seed sequence with miR-K10a_ +1_5, are expressed only in PEL cells and not in uninfected and KSHV-infected TIME cells. KSHV miR-K10 variants inhibit TGF-β signaling by targeting TGF-β type II receptor (TβRII). Computational and reporter mutagenesis analyses identified three functional target sites in the TβRII 3′ untranslated region (3′UTR). Expression of miR-K10 variants is sufficient to inhibit TGF-β-induced cell apoptosis. A suppressor of the miRs sensitizes latent KSHV-infected PEL cells to TGF-β and induces apoptosis. These results indicate that miR-K10 variants manipulate the TGF-β pathway to confer cells with resistance to the growth-inhibitory effect of TGF-β. Thus, KSHV miRs might target the tumor-suppressive TGF-β pathway to promote viral latency and contribute to malignant cellular transformation.
Hypothyroid myopathy mimicking postpolio syndrome
Authors: Verma Rajesh , Lalla Rakesh , Sahu Ritesh
Published: August 2012

Hypothyroidism can have diverse neurological manifestations. Myopathy may rarely be the sole manifestation of autoimmune thyroiditis. We hereby report an atypical manifestation of severe hypothyroidism in a middle-aged woman with childhood onset of paralytic polio involving her right leg presenting with a recent onset of increased weakness in the right leg mimicking postpolio syndrome.
Purple glove syndrome: a dreadful complication of intravenous phenytoin administration: Figure 1
Authors: Lalla Rakesh , Malhotra Hardeep Singh , Garg Ravindra Kumar , Sahu Ritesh
Published: August 2012

Purple glove syndrome is an uncommon but dreaded complication of intravenous phenytoin administration characterised by pain, oedema and purple-blue discolouration of the limb distal to the site of injection. We describe a 37-year-old gentleman having the characteristic purple glove appearance after phenytoin loading, and discuss the salient features of this syndrome highlighting the pathophysiological and preventive aspects.
Gastrointestinal cancers accompanied by a dense lymphoid component: an overview with special reference to gastric and colonic medullary and lymphoepithelioma-like carcinomas
Authors: Chetty Runjan
Published: August 2012

This review highlights the difference between so-called medullary carcinoma and lymphoepithelioma-like carcinoma with reference to the gastrointestinal tract. The two terms have been applied synonymously in the gastrointestinal tract, with the majority of carcinomas associated with lymphocytes being termed medullary carcinomas. True medullary carcinomas are disposed in syncytial sheets and have well defined peripheral margins; the preponderance of inflammation is peri-tumoural. These tumours are also associated with microsatellite instability (MSI). Lymphoepithelioma-like carcinomas tend not to have continuous sheets of tumour but are instead made up of small clusters and aggregates of tumour that are broken up by large numbers of intra-tumoural lymphocytes. These tumours may be associated with Epstein–Barr virus (EBV). Occasional cases may be associated with epigenetic silencing of MLH-1. In conclusion, carcinomas associated with dense lymphoid stroma maybe associated with either MSI or EBV. There are some morphological features that favour either type and in the stomach MSI and EBV are mutually exclusive.