bluuebunny/crossref_metadata_2025 huggingface dataset:
Constructal Design of Cavities Inserted Into a Cylindrical Solid Body
Authors: Lorenzini Giulio , Alberto Oliveira Rocha Luiz , Biserni Cesare , Domingues dos Santos Elizaldo , André Isoldi Liércio
Published: May 2012

This paper considers the numerical optimization of the shape of cavities that intrude into a cylindrical solid body. The objective is to minimize the global thermal resistance between the solid body and the cavities. Internal heat generating is distributed uniformly throughout the solid body. The cavities are isothermal, while the solid body has adiabatic conditions on the outer surface. The total volume is fixed. The cavities are rectangular, with fixed volume and variable aspect ratio. The number of cavities of the conducting body, N, is a design parameter. The optimized geometry and performance are reported graphically as functions of the ratio between the volume of the cavities and the total volume, φ0, and N. The paper shows an example of the application of optimal distribution of imperfections principle. The results indicate that the optimal distribution of the hot spots is affected not only by the complexity of the configuration (larger N) but also by the area of cavities fraction φ0.
Effects of showerhead hole structure on the deposition of hydrogenated microcrystalline silicon thin films by vhf PECVD
Authors: Wi Sung-Suk , Kim Yun-Gi , Lee Ho-Jun , Kim Daeil , Hwang Doosup , Chang Woo Sok
Published: May 2012

The authors present the characteristics of hydrogenated microcrystalline silicon (μc-Si:H) thin films deposited from an SiH4/H2 in 40 MHz plasma enhanced chemical vapor deposition system equipped with a multihole-array showerhead. The effects of a hole-array structure are analyzed in terms of deposition rate, crystallinity, and electrical conductivity of the μc-Si:H film. The effects of process parameters, such as SiH4 concentration, radio frequency power, and total gas flow rate are also investigated. The deposition rate of a multihole-array electrode is generally lower compared with that of the flat electrode. However, a higher deposition rate is found in the deep and dense hole region when the hole shape and density are varied on the electrode. The crystallinity and conductivity are almost not affected by hole dimension and density. It is demonstrated that the multihole-array electrode can be a useful tool for uniformity improvement in a large-sized very high frequency capacitively couple plasma μc-Si:H deposition system.
Effect of p-type doping on the oxidation of H–Si(111) studied by second-harmonic generation
Authors: Gokce Bilal , Dougherty Daniel B. , Gundogdu Kenan
Published: May 2012

Atomic force microscopy and second-harmonic generation data show that boron doping enhances the rate of oxidation of H-terminated silicon. Holes cause a greater increase in the reactivity of the Si–H up bonds than that of the Si–Si back bonds.
A statistically defined anthropomorphic software breast phantom
Authors: Lau Beverly A. , Reiser Ingrid , Nishikawa Robert M. , Bakic Predrag R.
Published: May 2012

Purpose:

Digital anthropomorphic breast phantoms have emerged in the past decade because of recent advances in 3D breast x‐ray imaging techniques. Computer phantoms in the literature have incorporated power‐law noise to represent glandular tissue and branching structures to represent linear components such as ducts. When power‐law noise is added to those phantoms in one piece, the simulated fibroglandular tissue is distributed randomly throughout the breast, resulting in dense tissue placement that may not be observed in a real breast. The authors describe a method for enhancing an existing digital anthropomorphic breast phantom by adding binarized power‐law noise to a limited area of the breast.

Methods:

Phantoms with (0.5 mm)3 voxel size were generated using software developed by Bakic et al. Between 0% and 40% of adipose compartments in each phantom were replaced with binarized power‐law noise (β = 3.0) ranging from 0.1 to 0.6 volumetric glandular fraction. The phantoms were compressed to 7.5 cm thickness, then blurred using a 3 × 3 boxcar kernel and up‐sampled to (0.1 mm)3 voxel size using trilinear interpolation. Following interpolation, the phantoms were adjusted for volumetric glandular fraction using global thresholding. Monoenergetic phantom projections were created, including quantum noise and simulated detector blur. Texture was quantified in the simulated projections using power‐spectrum analysis to estimate the power‐law exponent β from 25.6 × 25.6 mm2 regions of interest.

Results:

Phantoms were generated with total volumetric glandular fraction ranging from 3% to 24%. Values for β (averaged per projection view) were found to be between 2.67 and 3.73. Thus, the range of textures of the simulated breasts covers the textures observed in clinical images.

Conclusions:

Using these new techniques, digital anthropomorphic breast phantoms can be generated with a variety of glandular fractions and patterns. β values for this new phantom are comparable with published values for breast tissue in x‐ray projection modalities. The combination of conspicuous linear structures and binarized power‐law noise added to a limited area of the phantom qualitatively improves its realism.
Real-Time Imaging of Pt
3
Fe Nanorod Growth in Solution
Authors: Liao Hong-Gang , Cui Likun , Whitelam Stephen , Zheng Haimei
Published: May 2012

Growing in Liquid

The ability to control the growth of materials at the nanometer scale is key to nanotechnology. Materials grown in liquids, however, are difficult to track on a particle-by-particle basis during growth. Two studies used an in situ liquid cell to follow the formation of larger nanoparticles or nanorods grown in solvents using high-resolution transmission electron microscopes.

Liao
et al.

(p.
1011
) watched platinum iron nanorods form from kinked chains of connected nanoparticles that gradually reoriented and straightened to form rigid rods.

Li
et al.

(p.
1014
) observed the coalescence of iron oxyhydroxide nanoparticles through an oriented attachment mechanism, whereby two similar particles rotated until their corresponding crystal lattices aligned.
Pushing Your Back into Place
Authors: Bowerman Bruce , O'Rourke Sean M.
Published: May 2012

Establishment of the dorsal-ventral body axis during fly oogenesis depends on pushing forces provided by polymerizing microtubules.
Guided Tour to the Heart of RISC
Authors: Kaya Emine , Doudna Jennifer A.
Published: May 2012

The crystal structures of human and yeast Argonaute proteins reveal the intricacies of the multidomain enzyme at the hub of the RNA interference machinery.
An Avian Magnetometer
Authors: Winklhofer Michael
Published: May 2012

Neurons in the pigeon brain encode information on Earth's magnetic field for orientation and navigation.
Dams Along Sudanese Nile Threaten Ancient Sites
Authors: Lawler Andrew
Published: May 2012

Sudanese officials said last week that their government intends to move ahead with three massive dams along the Nile River and its tributaries, threatening hundreds of largely unexplored ancient sites.
NSF's ‘Big Pitch’ Tests Anonymized Grant Reviews
Authors: Bhattacharjee Yudhijit
Published: May 2012

An experiment being conducted at the U.S. National Science Foundation indicates that NSF may be turning down deserving research proposals because of potential biases in the grant-review process.
Lack of Interference with Immunogenicity of a Chimeric Alphavirus Replicon Particle-Based Influenza Vaccine by Preexisting Antivector Immunity
Authors: Uematsu Yasushi , Vajdy Michael , Lian Ying , Perri Silvia , Greer Catherine E. , Legg Harold S. , Galli Grazia , Saletti Giulietta , Otten Gillis R. , Rappuoli Rino , Barnett Susan W. , Polo John M.
Published: May 2012

Antivector immunity has been recognized as a potential caveat of using virus-based vaccines. In the present study, an alphavirus-based replicon particle vaccine platform, which has demonstrated robust immunogenicity in animal models, was tested for effects of antivector immunity on immunogenicity against hemagglutinin of influenza virus as a target antigen and efficacy for protection against lethal challenge with the virus. Chimeric alphavirus-based replicon particles, comprising Venezuelan equine encephalitis virus nonstructural and Sindbis virus structural components, induced efficient protective antibody responses, which were not adversely influenced after multiple immunizations with the same vector expressing various antigens.
Rectal Screening for Klebsiella pneumoniae Carbapenemases: Comparison of Real-Time PCR and Culture Using Two Selective Screening Agar Plates
Authors: Singh Kamaljit , Mangold Kathy A. , Wyant Kody , Schora Donna M. , Voss Barbara , Kaul Karen L. , Hayden Mary K. , Chundi Vishnu , Peterson Lance R.
Published: May 2012

Klebsiella pneumoniae
carbapenemases (KPCs) have recently been described in Chicago, IL, especially among residents of long-term acute care hospitals (LTACHs). These patients are frequently transferred to local Chicago hospitals for higher acuity of medical care, and rapid detection and isolation of KPC-colonized LTACH residents may interrupt the introduction of KPCs into acute care hospitals. We evaluated the performance of a real-time PCR for
bla
KPC
from enrichment broth versus direct plating of rectal surveillance swabs on two selective culture media, CHROMagar extended-spectrum-β-lactamase (ESBL) and vancomycin, amphotericin B, ceftazidime, and clindamycin (VACC) plates. Rectal surveillance swabs were collected as part of a point prevalence study of KPC carriage rates among 95 residents of two Chicago area LTACHs. Discrepant results between PCR and culture were resolved by subculturing the enrichment broth. Overall, 66 of 95 patients (69.5%) were colonized with KPCs, using the cumulative results of culture as a reference standard. Real-time PCR from enrichment broth was positive in 64 of 66 (97%) colonized patients, including nine surveillance swabs that were missed by both selective culture media. PCR demonstrated higher sensitivity, 97.0%, than culture using either CHROMagar or VACC plates (both with sensitivity of 77.3%). In addition, turnaround time was significantly shorter for the PCR-based method than for culture, with a mean of 24 h versus 64 to 72 h for CHROMagar and VACC plates (
P
< 0.0001). Overall, PCR for
bla
KPC
represents the best screening test for KPCs with significantly higher sensitivity and with less hands-on time, resulting in a shorter time to results.
Invasive Apophysomyces variabilis Infection in a Burn Patient
Authors: dela Cruz Wilfred P. , Calvano Tatjana P. , Griffith Matthew E. , White Christopher E. , Kim Seung H. , Sutton Deanna A. , Thompson Elizabeth H. , Fu Jianmin , Wickes Brian L. , Guarro Josep , Hospenthal Duane R.
Published: May 2012

Apophysomyces variabilis
is an emerging fungal pathogen that can cause significant infections in immunocompetent patients. We report a case of
A. variabilis
invasive wound infection in a 21-year-old male after a self-inflicted burn injury.
Characterization of a Viral Phosphoprotein Binding Site on the Surface of the Respiratory Syncytial Nucleoprotein
Authors: Galloux Marie , Tarus Bogdan , Blazevic Ilfad , Fix Jenna , Duquerroy Stéphane , Eléouët Jean-François
Published: May 2012

The human respiratory syncytial virus (HRSV) genome is composed of a negative-sense single-stranded RNA that is tightly associated with the nucleoprotein (N). This ribonucleoprotein (RNP) complex is the template for replication and transcription by the viral RNA-dependent RNA polymerase. RNP recognition by the viral polymerase involves a specific interaction between the C-terminal domain of the phosphoprotein (P) (P
CTD
) and N. However, the P binding region on N remains to be identified. In this study, glutathione
S
-transferase (GST) pulldown assays were used to identify the N-terminal core domain of HRSV N (N
NTD
) as a P binding domain. A biochemical characterization of the P
CTD
and molecular modeling of the N
NTD
allowed us to define four potential candidate pockets on N (pocket I [PI] to PIV) as hydrophobic sites surrounded by positively charged regions, which could constitute sites complementary to the P
CTD
interaction domain. The role of selected amino acids in the recognition of the N-RNA complex by P was first screened for by site-directed mutagenesis using a polymerase activity assay, based on an HRSV minigenome containing a luciferase reporter gene. When changed to Ala, most of the residues of PI were found to be critical for viral RNA synthesis, with the R132A mutant having the strongest effect. These mutations also reduced or abolished
in vitro
and
in vivo
P-N interactions, as determined by GST pulldown and immunoprecipitation experiments. The pocket formed by these residues is critical for P binding to the N-RNA complex, is specific for pneumovirus N proteins, and is clearly distinct from the P binding sites identified so far for other nonsegmented negative-strand viruses.
Orthobunyavirus Entry into Neurons and Other Mammalian Cells Occurs via Clathrin-Mediated Endocytosis and Requires Trafficking into Early Endosomes
Authors: Hollidge Bradley S. , Nedelsky Natalia B. , Salzano Mary-Virginia , Fraser Jonathan W. , González-Scarano Francisco , Soldan Samantha S.
Published: May 2012

La Crosse virus (LACV) is a leading cause of pediatric encephalitis and aseptic meningitis in the midwestern and southern United States, where it is considered an emerging human pathogen. No specific therapies or vaccines are available for LACV or any other orthobunyaviruses. Inhibition of LACV entry into cells is a potential target for therapeutic intervention, but this approach is limited by our current knowledge of the entry process. Here, we determined that clathrin-mediated endocytosis is the primary mechanism of orthobunyavirus entry and identified key cellular factors in this process. First, we demonstrated that LACV colocalized with clathrin shortly after infection in HeLa cells; we then confirmed the functional requirement of dynamin- and clathrin-mediated endocytosis for orthobunyavirus entry using several independent assays and, importantly, extended these findings to primary neuronal cultures. We also determined that macropinocytosis and caveolar endocytosis, both established routes of virus entry, are not critical for cellular entry of LACV. Moreover, we demonstrated that LACV infection is dependent on Rab5, which plays an important regulatory role in early endosomes, but not on Rab7, which is associated with late endosomes. These findings provide the first description of bunyavirus entry into cells of the central nervous system, where infection can cause severe neurological disease, and will aid in the design and development of antivirals and therapeutics that may be useful in the treatment of LACV and, more broadly, arboviral infections of the central nervous system.
Human Respiratory Syncytial Virus Nucleoprotein and Inclusion Bodies Antagonize the Innate Immune Response Mediated by MDA5 and MAVS
Authors: Lifland Aaron W. , Jung Jeenah , Alonas Eric , Zurla Chiara , Crowe James E. , Santangelo Philip J.
Published: May 2012

Currently, the spatial distribution of human respiratory syncytial virus (hRSV) proteins and RNAs in infected cells is still under investigation, with many unanswered questions regarding the interaction of virus-induced structures and the innate immune system. Very few studies of hRSV have used subcellular imaging as a means to explore the changes in localization of retinoic-acid-inducible gene-I (RIG-I)-like receptors or the mitochondrial antiviral signaling (MAVS) protein, in response to the infection and formation of viral structures. In this investigation, we found that both RIG-I and melanoma differentiation-associated gene 5 (MDA5) colocalized with viral genomic RNA and the nucleoprotein (N) as early as 6 h postinfection (hpi). By 12 hpi, MDA5 and MAVS were observed within large viral inclusion bodies (IB). We used a proximity ligation assay (PLA) and determined that the N protein was in close proximity to MDA5 and MAVS in IBs throughout the course of the infection. Similar results were found with the transient coexpression of N and the phosphoprotein (P). Additionally, we demonstrated that the localization of MDA5 and MAVS in IBs inhibited the expression of interferon β mRNA 27-fold following Newcastle disease virus infection. From these data, we concluded that the N likely interacts with MDA5, is in close proximity to MAVS, and localizes these molecules within IBs in order to attenuate the interferon response. To our knowledge, this is the first report of a specific function for hRSV IBs and of the hRSV N protein as a modulator of the innate immune response.
Shutoff of BZLF1 Gene Expression Is Necessary for Immortalization of Primary B Cells by Epstein-Barr Virus
Authors: Yu Xianming , McCarthy Patrick J. , Wang Zhenxun , Gorlen Daniel A. , Mertz Janet E.
Published: May 2012

The
BZLF1
gene controls the switch between latent and lytic infection by Epstein-Barr virus (EBV). We previously reported that both the ZV and ZIIR elements within the
BZLF1
promoter, Zp, are potent transcription silencers within the context of an intact EBV genome. We report here identification of another sequence element, ZV′, which synergized with ZV in repressing Zp via binding ZEB1 or ZEB2. We then determined the phenotype of a variant of EBV strain B95.8 in which the ZV, ZV′, and ZIIR elements were concurrently mutated. HEK293 cell lines infected with this triple mutant (tmt) virus spontaneously synthesized 6- to 10-fold more viral
BZLF1
,
BRLF1
,
BMRF1
, and
BLLF1
RNAs, 3- to 6-fold more viral Zta, Rta, and EAD proteins, 3- to 5-fold more viral DNA, and 7- to 9-fold more infectious virus than did 293 cell lines latently infected with either the ZV ZV′ double mutant (dmt) or ZIIR mutant (mt) virus. While ZV ZV′ ZIIR tmt EBV efficiently infected human primary blood B cells
in vitro
, it was highly defective in immortalizing them. Instead of the nearly complete silencing of
BZLF1
gene expression that occurs within 4 days after primary infection with wild-type EBV, the ZV ZV′ ZIIR tmt-infected cells continued to synthesize
BZLF1
RNA, with 90% of them dying within 9 days postinfection. BL41 cells infected with this “superlytic” virus also exhibited increased synthesis of
BZLF1
and
BMRF1
RNAs. Thus, we conclude that the ZV, ZV′, and ZIIR silencing elements act synergistically to repress transcription from Zp, thereby tightly controlling
BZLF1
gene expression, which is crucial for establishing and maintaining EBV latency.
Epstein-Barr Virus BPLF1 Deubiquitinates PCNA and Attenuates Polymerase η Recruitment to DNA Damage Sites
Authors: Whitehurst Christopher B. , Vaziri Cyrus , Shackelford Julia , Pagano Joseph S.
Published: May 2012

PCNA is monoubiquitinated in response to DNA damage and fork stalling and then initiates recruitment of specialized polymerases in the DNA damage tolerance pathway, translesion synthesis (TLS). Since PCNA is reported to associate with Epstein-Barr virus (EBV) DNA during its replication, we investigated whether the EBV deubiquitinating (DUB) enzyme encoded by BPLF1 targets ubiquitinated PCNA and disrupts TLS. An N-terminal BPLF1 fragment (a BPLF1 construct containing the first 246 amino acids [BPLF1 1-246]) associated with PCNA and attenuated its ubiquitination in response to fork-stalling agents UV and hydroxyurea in cultured cells. Moreover, monoubiquitinated PCNA was deubiquitinated after incubation with purified BPLF1 1-246
in vitro
. BPLF1 1-246 dysregulated TLS by reducing recruitment of the specialized repair polymerase polymerase η (Polη) to the detergent-resistant chromatin compartment and virtually abolished localization of Polη to nuclear repair foci, both hallmarks of TLS. Expression of BPLF1 1-246 decreased viability of UV-treated cells and led to cell death, presumably through deubiquitination of PCNA and the inability to repair damaged DNA. Importantly, deubiquitination of PCNA could be detected endogenously in EBV-infected cells in comparison with samples expressing short hairpin RNA (shRNA) against BPLF1. Further, the specificity of the interaction between BPLF1 and PCNA was dependent upon a PCNA-interacting peptide (PIP) domain within the N-terminal region of BPLF1. Both DUB activity and PIP sequence are conserved in the members of the family
Herpesviridae
. Thus, deubiquitination of PCNA, normally deubiquitinated by cellular USP1, by the viral DUB can disrupt repair of DNA damage by compromising recruitment of TLS polymerase to stalled replication forks. PCNA is the first cellular target identified for BPLF1 and its deubiquitinating activity.
Cofilin 1-Mediated Biphasic F-Actin Dynamics of Neuronal Cells Affect Herpes Simplex Virus 1 Infection and Replication
Authors: Xiang Yangfei , Zheng Kai , Ju Huaiqiang , Wang Shaoxiang , Pei Ying , Ding Weichao , Chen Zhenping , Wang Qiaoli , Qiu Xianxiu , Zhong Meigong , Zeng Fanli , Ren Zhe , Qian Chuiwen , Liu Ge , Kitazato Kaio , Wang Yifei
Published: May 2012

Herpes simplex virus 1 (HSV-1) invades the nervous system and causes pathological changes. In this study, we defined the remodeling of F-actin and its possible mechanisms during HSV-1 infection of neuronal cells. HSV-1 infection enhanced the formation of F-actin-based structures in the early stage of infection, which was followed by a continuous decrease in F-actin during the later stages of infection. The disruption of F-actin dynamics by chemical inhibitors significantly reduced the efficiency of viral infection and intracellular HSV-1 replication. The active form of the actin-depolymerizing factor cofilin 1 was found to increase at an early stage of infection and then to continuously decrease in a manner that corresponded to the remodeling pattern of F-actin, suggesting that cofilin 1 may be involved in the biphasic F-actin dynamics induced by HSV-1 infection. Knockdown of cofilin 1 impaired HSV-1-induced F-actin assembly during early infection and inhibited viral entry; however, overexpression of cofilin 1 did not affect F-actin assembly or viral entry during early infection but decreased intracellular viral reproduction efficiently. Our results, for the first time, demonstrated the biphasic F-actin dynamics in HSV-1 neuronal infection and confirmed the association of F-actin with the changes in the expression and activity of cofilin 1. These results may provide insight into the mechanism by which HSV-1 productively infects neuronal cells and causes pathogenesis.
Complete Genome Sequence of a Novel Porcine Enterovirus Strain in China
Authors: Zhang Wen , Yang Shixing , Shen Quan , Ren Liping , Shan Tongling , Wei Jianzhong , Cui Li , Hua Xiuguo
Published: May 2012

The porcine enteroviruses (PEVs) belong to the family
Picornaviridae
. We report a complete genome sequence of a novel PEV strain that is widely prevalent in pigs at least in central and eastern China. The complete genome consists of 7,390 nucleotides, excluding the 3′ poly(A) tail, and has an open reading frame that maps between nucleotide positions 812 and 7318 and encodes a 2,168-amino-acid polyprotein. Phylogenetic analysis based on the 3CD and VP1 regions reveals that this PEV strain belongs to a species of PEV9 but may represent a novel sero-/genotype in CPE group III. We also report the major findings from bootscan analysis based on the whole genomes of PEVs in the present study and those available in GenBank.
Human T-Cell Leukemia Virus Type 2 Antisense Viral Protein 2 Is Dispensable for
In Vitro
Immortalization but Functions To Repress Early Virus Replication
In Vivo
Authors: Yin Han , Kannian Priya , Dissinger Nathan , Haines Robyn , Niewiesk Stefan , Green Patrick L.
Published: May 2012

Human T-cell leukemia virus type 1 (HTLV-1) and HTLV-2 are closely related but pathogenically distinct human retroviruses. The antisense strand of the HTLV-1 genome encodes HTLV-1 basic leucine zipper (b-ZIP) protein (HBZ), a protein that inhibits Tax-mediated viral transcription, enhances T-cell proliferation, and promotes viral persistence. Recently, an HTLV-2 antisense viral protein (APH-2) was identified. Despite its lack of a typical b-ZIP domain, APH-2, like HBZ, interacts with cyclic AMP response element binding protein (CREB) and downregulates Tax-mediated viral transcription. Here, we provide evidence that the APH-2 C-terminal LXXLL motif is important for CREB binding and Tax repression. In order to investigate the functional role of APH-2 in the HTLV-2-mediated immortalization of primary T lymphocytes
in vitro
and in HTLV-2 infection
in vivo
, we generated APH-2 mutant viruses. In cell cultures, the immortalization capacities of APH-2 mutant viruses were indistinguishable from that of wild-type HTLV-2 (wtHTLV-2), indicating that, like HBZ, APH-2 is dispensable for viral infection and cellular transformation.
In vivo
, rabbits inoculated with either wtHTLV-2 or APH-2 mutant viruses established a persistent infection. However, the APH-2 knockout virus displayed an increased replication rate, as measured by an increased viral antibody response and a higher proviral load. In contrast to HTLV-1 HBZ, we show that APH-2 is dispensable for the establishment of an efficient infection and persistence in a rabbit animal model. Therefore, antisense proteins of HTLV-1 and HTLV-2 have evolved different functions
in vivo
, and further comparative studies will provide fundamental insights into the distinct pathobiologies of these two viruses.
Complete Genome Sequence of Porcine Kobuvirus Strain WUH1
Authors: Lin Yuchen , Xiao Shaobo , Zeng Yuqing , Song Tao , Zeng Songlin , Chen Huanchun , Fang Liurong
Published: May 2012

Porcine kobuvirus, an emerging virus, was first identified in Hungary in 2007. We report here the complete genome sequence of porcine kobuvirus strain WUH1 isolated from piglets with severe diarrhea, which will help toward understanding the molecular and evolutionary characteristics of the porcine kobuvirus.
Complete Genome Sequence of a New-Genotype Porcine Norovirus Isolated from Piglets with Diarrhea
Authors: Shen Quan , Zhang Wen , Yang Shixing , Cui Li , Hua Xiuguo
Published: May 2012

Noroviruses (NoVs) are members of the family
Caliciviridae
and are emerging enteric pathogens of humans and animals. So far, porcine NoVs have been detected exclusively in fecal samples from adult swine without clinical signs. Here we report the genome sequence of a NoV strain isolated from piglets with diarrhea. Experimental infection of miniature pigs with this porcine NoV-positive fecal sample confirmed that this strain can cause diarrhea in piglets. A phylogenetic tree based on the predicted amino acid sequence of the complete capsid region showed that this strain is separate from known porcine GII strains (GII-11, GII-18, and GII-19), constituting the sole member of a new branch.
A Novel Porcine Circovirus Type 2a Strain, 10JS-2, with Eleven-Nucleotide Insertions in the Origin of Genome Replication
Authors: Cai Lin , Han Xue , Hu Dongmei , Li Xiaoxia , Wang Baoyue , Ni Jianqiang , Zhou Zhi , Yu Xiuling , Zhai Xinyan , Tian Kegong
Published: May 2012

Here, we report a novel porcine circovirus type 2a (PCV2a) strain with 11 nucleotides (nt) inserted in the origin of genome replication (Ori). This is the first report of a PCV2a strain with nucleotide insertion in Ori. Our study will help further epidemiological studies and extend our knowledge of evolutionary characteristics of PCV2.
Complete Genome Sequence of Avian Bornavirus Genotype 1 from a Macaw with Proventricular Dilatation Disease
Authors: Mirhosseini Negin , Gray Patricia L. , Tizard Ian , Payne Susan
Published: May 2012

Avian bornaviruses (ABV) were first detected and described in 2008. They are the etiologic agents of proventricular dilatation disease (PDD), a frequently fatal neurologic disease of captive parrots. Seven ABV genogroups have been identified worldwide from a variety of sources, and that number may increase as surveillance for novel bornaviruses continues. Here, we report the first complete sequence of a genogroup 1 avian bornavirus (ABV1).
Organization of the Ambisense Genome of the Helicoverpa armigera Densovirus
Authors: El-Far Mohamed , Szelei Jozsef , Yu Qian , Fédière Gilles , Bergoin Max , Tijssen Peter
Published: May 2012

A natural densovirus (DNV) of a serious phytophagous pest,
Helicoverpa armigera
, was isolated. The genome of HaDNV contained 6,039 nucleotides (nt) and included inverted terminal repeats (ITRs) of 545 nt with terminal Y-shaped hairpins of 126 nt. Its DNA sequence and ambisense organization with four typical open reading frames (ORFs) demonstrated that it belonged to the genus
Densovirus
in the subfamily
Densovirinae
of the family
Parvoviridae
.
Characterization of
Magnaporthe oryzae
Chrysovirus 1 Structural Proteins and Their Expression in
Saccharomyces cerevisiae
Authors: Urayama Syunichi , Ohta Tomoko , Onozuka Nobuya , Sakoda Hirofumi , Fukuhara Toshiyuki , Arie Tsutomu , Teraoka Tohru , Moriyama Hiromitsu
Published: May 2012

Magnaporthe oryzae chrysovirus
1 (MoCV1), which is associated with an impaired growth phenotype of its host fungus, harbors four major proteins: P130 (130 kDa), P70 (70 kDa), P65 (65 kDa), and P58 (58 kDa). N-terminal sequence analysis of each protein revealed that P130 was encoded by double-stranded RNA1 (dsRNA1) (open reading frame 1 [ORF1] 1,127 amino acids [aa]), P70 by dsRNA4 (ORF4; 812 aa), and P58 by dsRNA3 (ORF3; 799 aa), although the molecular masses of P58 and P70 were significantly smaller than those deduced for ORF3 and ORF4, respectively. P65 was a degraded form of P70. Full-size proteins of ORF3 (84 kDa) and ORF4 (85 kDa) were produced in
Escherichia coli
. Antisera against these recombinant proteins detected full-size proteins encoded by ORF3 and ORF4 in mycelia cultured for 9, 15, and 28 days, and the antisera also detected smaller degraded proteins, namely, P58, P70, and P65, in mycelia cultured for 28 days. These full-size proteins and P58 and P70 were also components of viral particles, indicating that MoCV1 particles might have at least two forms during vegetative growth of the host fungus. Expression of the ORF4 protein in
Saccharomyces cerevisiae
resulted in cytological changes, with a large central vacuole associated with these growth defects. MoCV1 has five dsRNA segments, as do two
Fusarium graminearum
viruses (FgV-ch9 and FgV2), and forms a separate clade with FgV-ch9, FgV2,
Aspergillus
mycovirus 1816 (AsV1816), and
Agaricus bisporus
virus 1 (AbV1) in the
Chrysoviridae
family on the basis of their RdRp protein sequences.
Equine Herpesvirus Type 4 UL56 and UL49.5 Proteins Downregulate Cell Surface Major Histocompatibility Complex Class I Expression Independently of Each Other
Authors: Said Abdelrahman , Azab Walid , Damiani Armando , Osterrieder Nikolaus
Published: May 2012

Major histocompatibility complex class I (MHC-I) molecules are critically important in the host defense against various pathogens through presentation of viral peptides to cytotoxic T lymphocytes (CTLs), a process resulting in the destruction of virus-infected cells. Herpesviruses interfere with CTL-mediated elimination of infected cells by various mechanisms, including inhibition of peptide transport and loading, perturbation of MHC-I trafficking, and rerouting and proteolysis of cell surface MHC-I. In this study, we show that equine herpesvirus type 4 (EHV-4) modulates MHC-I cell surface expression through two different mechanisms. First, EHV-4 can lead to a significant downregulation of MHC-I expression at the cell surface through the product of ORF1, a protein expressed with early kinetics from a gene that is homologous to herpes simplex virus 1 UL56. The EHV-4 UL56 protein reduces cell surface MHC-I as early as 4 h after infection. Second, EHV-4 can interfere with MHC-I antigen presentation, starting at 6 h after infection, by inhibition of the transporter associated with antigen processing (TAP) through its UL49.5 protein. Although pUL49.5 has no immediate effect on overall surface MHC-I levels in infected cells, it blocks the supply of antigenic peptides to the endoplasmic reticulum (ER) and transport of peptide-loaded MHC-I to the cell surface. Taken together, our results show that EHV-4 encodes at least two viral immune evasion proteins: pUL56 reduces MHC-I molecules on the cell surface at early times after infection, and pUL49.5 interferes with MHC-I antigen presentation by blocking peptide transport in the ER.
Challenges of making a diagnosis in the outpatient setting: a multi-site survey of primary care physicians
Authors: Sarkar Urmimala , Bonacum Doug , Strull William , Spitzmueller Christiane , Jin Nancy , López Andrea , Giardina Traber Davis , Meyer Ashley N D , Singh Hardeep
Published: May 2012

Background

Although misdiagnosis in the outpatient setting leads to significant patient harm and wasted resources, it is not well studied. The authors surveyed primary care physicians (PCPs) about barriers to timely diagnosis in the outpatient setting and assessed their perceptions of diagnostic difficulty.

Methods

Surveys of PCPs practicing in an integrated health system across 10 geographically dispersed states in 2005. The survey elicited information on key cognitive failures (including in clinical knowledge or judgement) for a specific case, and solicited strategies for reducing diagnostic delays. Content analysis was used to categorise cognitive failures and strategies for improvement. The authors examined the extent and predictors of diagnostic difficulty, defined as reporting >5% patients difficult to diagnose.

Results

Of 1817 physicians surveyed, 1054 (58%) responded; 848 (80%) respondents primarily practiced in outpatient settings and had an assigned patient panel (inclusion sample). Inadequate knowledge (19.9%) was the most commonly reported cognitive factor. Half reported >5% of their patients were difficult to diagnose; more experienced physicians reported less diagnostic difficulty. In adjusted analyses, problems with information processing (information availability and time to review it) and the referral process were associated with greater diagnostic difficulty. Strategies for improvement most commonly involved workload issues (panel size, non-visit tasks).

Conclusions

PCPs report a variety of reasons for diagnostic difficulties in primary care practice. In this study, knowledge gaps appear to be a prominent concern. Interventions that address these gaps as well as practice level issues such as time to process diagnostic information and better subspecialty input may reduce diagnostic difficulties in primary care.
Signal and noise: applying a laboratory trigger tool to identify adverse drug events among primary care patients
Authors: Brenner Stacey , Detz Alissa , López Andrea , Horton Claire , Sarkar Urmimala
Published: May 2012

Background

The extent of outpatient adverse drug events (ADEs) remains unclear. Trigger tools are used as a screening method to identify care episodes that may be ADEs, but their value in a population with high chronic-illness burden remains unclear.

Methods

The authors used six abnormal laboratory triggers for detecting ADEs among adults in outpatient care. Eligible patients were included if they were >18 years, sought primary or urgent care between November 2008 and November 2009 and were prescribed at least one medication. The authors then used the clinical / administrative database to identity patients with these triggers. Two physicians conducted in-depth chart review of any medical records with identified triggers.

Results

The authors reviewed 1342 triggers representing 622 unique episodes among 516 patients. The trigger tool identified 91 (15%) ADEs. Of the 91 ADEs included in the analysis, 49 (54%) occurred during medication monitoring, 41 (45%) during patient self-administration, and one could not be determined. 96% of abnormal international normalised ratio triggers were ADEs, followed by 12% of abnormal blood urea nitrogen triggers, 9% of abnormal alanine aminotransferase triggers, 8% of abnormal serum creatinine triggers and 3% of aspartate aminotransferase triggers.

Conclusions

The findings imply that other tools such as text triggers or more complex automated screening rules, which combine data hierarchically are needed to effectively screen for ADEs in chronically ill adults seen in primary care.
The impact of intense airway management training on paramedic knowledge and confidence measured before, immediately after and at 6 and 12 months after training
Authors: Walker Mark , Jensen Jan L , Leroux Yves , McVey Jennifer , Carter Alix E
Published: May 2012

Introduction

Airway management is a core component in the practice of advanced life support (ALS) paramedics.

Objective

To determine if an intense airway management course would improve ALS paramedic knowledge and confidence and if knowledge was retained over time.

Methods

An identical written survey (measuring demographics and confidence) and multiple-choice examination (measuring knowledge) was administered at the start and end of a 10 h airway course. At 6 and 12 months after the course, paramedics took the knowledge examination. Paired confidence and written knowledge examination scores before and immediately after the course were compared. Differences between knowledge examination scores at all four time points (before, immediately after and at 6 and 12 months) were tested using analysis of variance and Tukey's test.

Results

299 ALS paramedics were enrolled in the study. 209 (69%) reported 6 or more years of ALS experience. The mean pre-course confidence score was 2.74/4 and the mean post-course confidence score was 3.39/4; a difference of 0.7 points (95% CI 0.61 to 0.71). Post-course examination scores improved by 4.9 points (95% CI 4.58 to 5.20), from 7.7 to 12.6/20. At 6 months the mean score was 10.3/20, and at 12 months 10.2/20. Post-course scores were significantly better than pre-course scores. Scores at 6 and 12 months did not differ significantly and remained significantly improved from pre-course scores.

Conclusion

Significant improvement in confidence and knowledge was found after paramedics completed an intense airway management course. Knowledge at 6 and 12 months remained significantly better compared with pre-course.
Sexually transmitted diphtheria
Authors: Berger Anja , Lensing Carmen , Konrad Regina , Huber Ingrid , Hogardt Michael , Sing Andreas
Published: May 2012

Diphtheria is caused by diphtheria toxin-producingCorynebacteriumspecies. While classical respiratory diphtheria is transmitted by droplets, cutaneous diphtheria often results from minor trauma. This report concerns the first case of sexually transmitted diphtheria in a patient with non-gonococcal urethritis after orogenital contact.
O17 Sexual behaviour in younger MSM and self-perceived sexual risk using a local HIV Risk Assessment Tool (HIVRAT)
Authors: Alagaratnam J , Black A , Smith A
Published: May 2012

Background

HIV infection continues to disproportionately affect MSM in the UK. The 2011 HPA report “Sexually Transmitted Infections in MSM in the UK” highlights the need for one-to-one behavioural interventions. Thus, identifying those at highest risk is essential.

Aims

To profile the sexual behaviour of younger MSM attending a dedicated clinic. To establish how MSM perceive their sexual risk and explore the use of a simple HIV Risk Assessment Tool (HIVRAT).

Methods

MSM attending a weekly clinic offering HIV testing self-complete a 6 question HIVRAT in addition to standard history. The HIVRAT records number of male partners in previous 12 months, and number of unprotected anal intercourse (UPAI) partners (previous 3 and 12 months). It also contains a Likert scale of perceived sexual risk. Data was collected over 6 months from June 2011. Statistical analysis was performed in Excel and correlated using Spearman's Rank methodology.

Results

138 men completed the HIVRAT (aged 18–35). Median number of sexual partners in preceding 12 months = 8 (range 1–250, 42% reported >10 partners). Median number of UPAI partners in preceding 3 months =0 (range 0–5) and 12 months =1 (range 0–8). Perceived risk was scored as 1= Very low (20.4%), 2 (44.5%), 3 (28.5%), 4 (4.4%) and 5= Very high (2.2%). There was poor correlation between sexual behaviour and perceived risk. For MSM who had UPAI with one or more partners in the previous 3 and 12 months, there was a moderately positive correlation between actual risk and perceived risk (SRCC 0.517 and 0.544 respectively).

Conclusions

Only 6.6% of MSM judged their personal HIV risk as high in a cohort where 36% reported UPAI with two or more partners in 12 months. Tools like HIVRAT provide valuable information which is not routinely collected. Asking about UPAI during the 12-month period prior to testing showed the strongest correlation between actual and perceived risk, and could help identify MSM who would benefit most from behavioural intervention.
O6 Seniority improves specificity: differences in PID diagnosis between different grades of clinician
Authors: Morris G C , Stewart C M W , Wilson J D
Published: May 2012

Background

Pelvic inflammatory disease is difficult to diagnose; dependent on interpretation of clinical symptoms and signs that lack sensitivity and specificity. Differences in the rates of PID diagnoses have been noted among senior sexual health physicians. Given the potential severe consequences of untreated PID, we hypothesised that clinicians with less training and experience may tend to err on the side of caution and be more likely to diagnose PID than more senior colleagues.

Objectives

To ascertain whether the rates of PID diagnoses differ by grade of clinician.

Methods

Women attending our service as new or rebook patients between March 2009 and January 2010 were seen by eight different grades of clinician. Of these, all but Band five nurses saw symptomatic patients. Data were analysed by grade of staff conducting the consultation.

Results

Chlamydia (CT) prevalence was broadly similar across all staff groups. The rates of PID diagnoses were also similar. However, the proportion of PID patients with CT differed significantly between staff groups. In the cases of PID diagnosed by more experienced staff, CT was found in 24% to 32% of patients. This is broadly consistent with the current understanding of PID aetiology. PID diagnosed by nurses and more junior doctors was less likely to have a confirmed STI aetiology. The rate ratio of diagnosis of CT positive to CT negative PID by consultants vs Band six nurses is 5.43 (95% CI 0.77 to 38.01) p=0.089 The rate ratio of diagnosis of CT positive to CT negative PID by experienced doctors (GP, SAS, Registrar, Consultant) vs nurses, FY1 and ST2 doctors is 3.09 (95% CI 1.01 to 9.43) p=0.048 (see abstract O6 table 1).

Abstract O6 Table 1

Rates of chlamydia and gonorrhoea infections in relation to practitioner group

Grade of staffBand six nursesFY1ST2GPSASRegistrarConsultantWhole cohortNo of staff764219641No of consultations4421402072524869969303453No of PID diagnoses178914215047166% Of cohort diagnosed with PID3.85.74.35.64.355.14.8Chlamydia prevalence (%)10.19.36.312.38.610.911.410.4Gonorrhoea prevalence (%)20.71.43.61.62.73.12.5% Of PID patients chlamydia positive5.912.511.128.523.82431.923.5% Of PID patients gonorrhoea positive5.90028.50126.48.4% Chlamydia positive patients diagnosed with PID2.27.77.712.911.91114.210.9

Conclusions

Significant differences were found in the proportion of patients with chlamydia positive PID between experienced doctors and other clinicians. The broader experience of senior doctors may help them in differentiating PID from other causes of lower abdominal pain thus improving the specificity of their diagnosis.
C1 Pharyngeal lymphogranuloma venereum: four cases in men who have sex with men
Authors: Dosekun O , Edmonds S , Stockwell S , French P , White J A
Published: May 2012

Background

Lymphogranuloma venereum (LGV) is an established cause of proctitis in men who have sex with men (MSM). In the UK, testing for pharyngealChlamydia trachomatis(CT) is not routine, and LGV typing is seldom performed.

Objective

To describe clinical features of four cases of pharyngeal LGV seen across three different urban GUM/HIV clinics, all of who had LGV-specific DNA detected at this site.

Case reports

All four cases occurred in MSM; their past STI histories included HIV (2), syphilis (3) and hepatitis C (2; one diagnosed after LGV infection). Two cases had no oropharyngeal symptoms or local lymphadenopathy (LN) but had symptomatic LGV proctitis. One case had severe odynophagia, a tongue ulcer and cervical LN, and the final case reported severe pharyngitis with large unilateral cervical LN 10 days prior. Three of the four had concurrent rectal LGV infection. The infections responded to doxycycline: 21 days was given in two cases, and the other two received 7 and 14 days treatment, respectively. Test of cure swabs performed at 6 weeks to 5 months following treatment were negative in all cases. Three MSM had new STIs diagnosed at the time of their Test of cure.

Conclusion/Learning points

We describe a variety of clinical presentations of pharyngeal LGV infection in MSM. The oropharynx may act as reservoir for CT, and possibly LGV, and routine screening should be considered at this site for all MSM. The absence of localised symptoms does not exclude pharyngeal LGV infection. Symptomatic oropharyngeal LGV infection is probably rare but should be considered in the differential diagnosis of MSM with unusual or severe symptoms/signs at this site. There are no guidelines for treating pharyngeal CT or LGV infection, but treatment with 1- to 3-week regimens of doxycycline was effective. Ongoing high-risk sexual behaviour in this population makes outbreak containment difficult.
P10 Vitamin D levels in a sample of HIV+ patients
Authors: Brook G , Alagaratnam J , Barai K
Published: May 2012

Background

In the last few years it has been highlighted that vitamin D deficiency is common in the general population however, the extent of the problem in different HIV+ cohorts is less clear.

Aims

In a cohort of HIV+ patients in North West London we looked at the vitamin D levels to see what the prevalence of deficiency was and see if there were any correlates with ethnicity or season.

Methods

All HIV+ patients at this centre and who had a recorded vitamin D test result in the last 2 years were identified. The first result while not on treatment was recorded. The patients' electronic case records were examined to identify any correlates with the results. Vitamin D was classified as deficient, insufficient or adequate with total 25-hydroxy vitamin D blood levels of <12.5, 12.5–50 and >50 nmols/l respectively.

Results

143 patients had a least one vitamin D level measured. Of these 7 (5%) had vitamin D deficiency, 83 (58%) insufficient levels and 53 (37%) had adequate levels. Comparing patients who had levels tested in the winter months with those tested in the summer, they were more likely to show deficient or insufficient levels than adequate levels (44/90 (49%) vs 6/53 (11%) p<0.0001). All patients who showed gross deficiency were black or Asian but there wasn't a correlation between ethnicity and insufficient/deficient levels. Three (42%) of the patients with deficient levels had a raised serum alkaline phosphotase and/or a low serum phosphate.

Conclusions

High rates of vitamin D deficiency and insufficiency were found in this cohort, only part of which is explained by doing the test in the winter months. Some evidence of metabolic effects of deficiency on bone was found