bluuebunny/crossref_metadata_2025_split huggingface dataset:
Cytological grading of canine cutaneous mast cell tumours
Authors: Scarpa Filippo , Sabattini Silvia , Bettini Giuliano 
Published: April 2014

AbstractA cytological grading for mast cell tumours (MCTs) would be highly desirable, allowing to select the most appropriate therapeutic intervention prior to surgery. This study evaluates the applicability on fine‐needle aspirations (FNAs) of the novel Kiupel grading system, based on number of mitoses, multinucleated cells, bizarre nuclei and presence of karyomegaly. Fifty consecutive cases with pre‐operative cytological diagnosis were included. In cytological specimens, approximately 1000 cells were evaluated, and the histological grade was assessed on the corresponding resected specimens. On cytology, the above parameters were significantly different between histologically low‐grade and high‐grade tumours (P < 0.001). The cytograding correctly predicted the histological grade in 47 cases (accuracy, 94%; sensitivity, 84.6%; specificity, 97.3%). Two high‐grade MCTs (4%) were not detected on cytology. The cytograding can provide helpful insights to assist clinical decisions in most cases. However, the risk of underestimation in a minority of patients represents a limit to the overall utility of the technique.
Evaluation of Anticoagulants for Serologic Assays of Cholera Vaccination
Authors: Yang Jae Seung , Kang Seok-Seong , Yun Cheol-Heui , Han Seung Hyun 
Published: April 2014

ABSTRACT

Blood collected with an anticoagulant is beneficial for simultaneous evaluation of immune cells and humoral components such as antibodies. However, it is critical that the anticoagulant does not affect quantitative and qualitative analyses of antibodies. In the present study, we examined the potential interference of the widely used anticoagulants heparin, EDTA, and acid citrate dextrose (ACD) on vibriocidal antibody activities and
Vibrio cholerae
lipopolysaccharide (LPS)-specific IgG, IgM, and IgA levels in the plasma and sera obtained from cholera patients or vaccinees. Serum vibriocidal antibody titer was inhibited in the presence of EDTA or ACD but not in the presence of heparin. Moreover, 100% (8/8) of the vibriocidal antibody titers of plasma samples obtained from the vaccinees in tubes containing heparin were identical to the titers of matched sera when compared with 37.5% (3/8) and 50% (4/8) of the plasma samples prepared with EDTA and ACD, respectively. Among LPS-specific Igs, the Pearson correlation coefficient (
r
) for IgA in serum and plasma was low (
r
= 0.716), and the coefficients for IgG and IgM were relatively high (
r
= 0.997 and
r
= 0.945, respectively) in heparinized plasma samples compared with the coefficient for IgG and IgM of EDTA- and ACD-treated plasma. Our results suggest that heparin is an appropriate anticoagulant for the collection of blood when measuring vibriocidal activities and antibody levels in plasma samples.
Prevalence of Isolates of Streptococcus pneumoniae Putative Serotype 6E in South Korea
Authors: Baek Jin Yang , Park In Ho , Song Jae-Hoon , Ko Kwan Soo 
Published: April 2014

ABSTRACT

The prevalence of serogroup 6 among 1,206
Streptococcus pneumoniae
clinical isolates collected from Korean hospitals over three periods (1996 to 2001, 2004 to 2006, and 2008 to 2009) was investigated. The number of serogroup 6 isolates increased from 9.7 to 17.5% over the three periods. While the proportion of serotype 6A and 6D isolates increased significantly, that of serotype 6B isolates decreased. Twenty-four isolates (2.0%) were typed as the recently identified putative serotype 6E or genetic variants of serotype 6B. The results suggest that the lack of change in frequency of serotype 6B, in spite of the introduction of the PCV7 vaccine as seen in previous studies in South Korea, might be due mainly to the improper inclusion of putative serotype 6E in serotype 6B. All but three serotype 6E isolates belonged to CC90, indicating their clonal expansion.
Improving Oral Human Papillomavirus Detection Using Toothbrush Sampling in HIV-Positive Men Who Have Sex with Men
Authors: Ong Jason J. , Read Tim , Chen Marcus , Walker Sandra , Law Matthew , Bradshaw Catriona , Garland Suzanne M. , Tabrizi Sepehr N. , Cornall Alyssa , Grulich Andrew , Hocking Jane , Fairley Christopher K. 
Published: April 2014

ABSTRACT
Pre- and postabrasion oral rinse samples (ORS) and a toothbrush sample detected human papillomavirus (HPV) DNA in at least one sample among 45 (26%) of 173 HIV-positive men who have sex with men. There was moderate agreement for HPV genotype detection between the preabrasion and postabrasion ORS (κ = 0.49; 95% confidence interval [CI], 0.37 to 0.61). There was good agreement between postabrasion ORS and toothbrushes (κ = 0.70; 95% CI, 0.60 to 0.80). The sensitivities for HPV genotypes detected were 80% (95% CI, 69 to 88) for preabrasion ORS, 65% (95% CI, 54 to 76) for postabrasion ORS, and 75% (95% CI, 63 to 84) for toothbrushes.
Clinical Performance of Roche Cobas 4800 HPV Test
Authors: Cui Miao , Chan Nicholas , Liu Momo , Thai Khanh , Malaczynska Joanna , Singh Ila , Zhang David , Ye Fei 
Published: April 2014

ABSTRACT
Evaluation of the Cobas 4800 test demonstrated that Cobas had a low rate of cross-reactivity with low-risk human papillomavirus (lrHPV), a 3.74% disconcordance rate between prealiquots and postaliquots, and failure rates of 4.57% and 1.16%, respectively, after vortexing and swirling. This study demonstrated that the Cobas test has good sensitivity, accuracy, and reproducibility for detecting 14 high-risk HPV (hrHPV) genotypes.
Comparison of Commercial Antimicrobial Susceptibility Test Methods for Testing of Staphylococcus aureus and Enterococci against Vancomycin, Daptomycin, and Linezolid
Authors: Riedel Stefan , Neoh Kar Mun , Eisinger Stephen W. , Dam Lisa M. , Tekle Tsigereda , Carroll Karen C. 
Published: April 2014

ABSTRACT

Three commercial antimicrobial susceptibility testing (AST) methods were compared to broth microdilution for testing of
Staphylococcus aureus
and enterococci against vancomycin, daptomycin, and linezolid. Despite high levels of categorical agreement and essential agreement, vancomycin MICs determined by MicroScan were often 1 log
2
concentration higher and MICs determined by Phoenix 1 log
2
concentration lower. Daptomycin MICs were 1 to 2 log
2
concentrations higher by all AST methods, except Etest, potentially impacting definitive antimicrobial therapy for bloodstream infections due to these organisms.
Streptococcus suis-Related Prosthetic Joint Infection and Streptococcal Toxic Shock-Like Syndrome in a Pig Farmer in the United States
Authors: Gomez Eric , Kennedy Cassie C. , Gottschalk Marcelo , Cunningham Scott A. , Patel Robin , Virk Abinash 
Published: April 2014

ABSTRACT

Streptococcus suis
is an emerging swine-associated zoonotic agent that can cause meningitis and septicemia in humans. We present, to our knowledge, the first case of
S. suis
arthroplasty infection and streptococcal toxic shock-like syndrome due to an nonencapsulated serotype 5 strain in North America.
Alternative Recognition of the Conserved Stem Epitope in Influenza A Virus Hemagglutinin by a V
H
3-30-Encoded Heterosubtypic Antibody
Authors: Wyrzucki Arkadiusz , Dreyfus Cyrille , Kohler Ines , Steck Marco , Wilson Ian A. , Hangartner Lars 
Published: April 2014

ABSTRACT

A human monoclonal heterosubtypic antibody, MAb 3.1, with its heavy chain encoded by V
H
3-30, was isolated using phage display with immobilized hemagglutinin (HA) from influenza virus A/Japan/305/1957(H2N2) as the target. Antibody 3.1 potently neutralizes influenza viruses from the H1a clade (i.e., H1, H2, H5, H6) but has little neutralizing activity against the H1b clade. Its crystal structure in complex with HA from a pandemic H1N1 influenza virus, A/South Carolina/1/1918(H1N1), revealed that like other heterosubtypic anti-influenza virus antibodies, MAb 3.1 contacts a hydrophobic groove in the HA stem, primarily using its heavy chain. However, in contrast to the closely related monoclonal antibody (Mab) FI6 that relies heavily on HCDR3 for binding, MAb 3.1 utilizes residues from HCDR1, HCDR3, and framework region 3 (FR3). Interestingly, HCDR1 of MAb 3.1 adopts an α-helical conformation and engages in hydrophobic interactions with the HA very similar to those of the
de novo in silico
-designed and affinity-matured synthetic protein HB36.3. These findings improve our understanding of the molecular requirements for binding to the conserved epitope in the stem of the HA protein and, therefore, aid the development of more universal influenza vaccines targeting these epitopes.

IMPORTANCE
Influenza viruses rapidly evade preexisting immunity by constantly altering the immunodominant neutralizing antibody epitopes (antigenic drift) or by acquiring new envelope serotypes (antigenic shift). As a consequence, the majority of antibodies elicited by immunization or infection protect only against the immunizing or closely related strains. Here, we describe a novel monoclonal antibody that recognizes the conserved heterosubtypic epitope in the stem of influenza A virus hemagglutinin. This antibody, referred to as MAb 3.1, recognizes its epitope in a manner that resembles recognition of a similar epitope by the
de novo in silico
-designed and affinity-matured synthetic protein HB36.3. Thus, besides providing novel insights into the molecular interactions between heterosubtypic antibodies and influenza virus hemagglutinin, MAb 3.1 demonstrates that
de novo in silico
-designed and affinity-matured synthetic proteins can foretell naturally selected antibody binding. This knowledge will aid development of a pan-influenza virus vaccine.
Enhanced Immunogenicity of an HIV-1 DNA Vaccine Delivered with Electroporation via Combined Intramuscular and Intradermal Routes
Authors: Mann Jamie F. S. , McKay Paul F. , Fiserova Anezka , Klein Katja , Cope Alethea , Rogers Paul , Swales Julie , Seaman Michael S. , Combadiere Behazine , Shattock Robin J. 
Published: April 2014

ABSTRACT
It is accepted that an effective prophylactic HIV-1 vaccine is likely to have the greatest impact on viral transmission rates. As previous reports have implicated DNA-priming, protein boost regimens to be efficient activators of humoral responses, we sought to optimize this regimen to further augment vaccine immunogenicity. Here we evaluated single versus concurrent intradermal (i.d.) and intramuscular (i.m.) vaccinations as a DNA-priming strategy for their abilities to elicit humoral and cellular responses against a model HIV-1 vaccine antigen, CN54-gp140. To further augment vaccine-elicited T and B cell responses, we enhanced cellular transfection with electroporation and then boosted the DNA-primed responses with homologous protein delivered subcutaneously (s.c.), intranasally (i.n.), i.m., or transcutaneously (t.c.). In mice, the concurrent priming regimen resulted in significantly elevated gamma interferon T cell responses and high-avidity antigen-specific IgG B cell responses, a hallmark of B cell maturation. Protein boosting of the concurrent DNA strategy further enhanced IgG concentrations but had little impact on T cell reactivity. Interestingly protein boosting by the subcutaneous route increased antibody avidity to a greater extent than protein boosting by either the i.m., i.n., or t.c. route, suggesting that this route may be preferential for driving B cell maturation. Using an alternative and larger animal model, the rabbit, we found the concurrent DNA-priming strategy followed by s.c. protein boosting to again be capable of eliciting high-avidity humoral responses and to also be able to neutralize HIV-1 pseudoviruses from diverse clades (clades A, B, and C). Taken together, we show that concurrent multiple-route DNA vaccinations induce strong cellular immunity, in addition to potent and high-avidity humoral immune responses.

IMPORTANCE
The route of vaccination has profound effects on prevailing immune responses. Due to the insufficient immunogenicity and protection of current DNA delivery strategies, we evaluated concurrent DNA delivery via simultaneous administration of plasmid DNA by the i.m. and i.d. routes. The rationale behind this study was to provide clear evidence of the utility of concurrent vaccinations for an upcoming human clinical trial. Furthermore, this work will guide future preclinical studies by evaluating the use of model antigens and plasmids for prime-boost strategies. This paper will be of interest not only to virologists and vaccinologists working in the HIV field but also to researchers working in other viral vaccine settings and, critically, to the wider field of vaccine delivery.
Cullin4A and Cullin4B Are Interchangeable for HIV Vpr and Vpx Action through the CRL4 Ubiquitin Ligase Complex
Authors: Sharifi Hamayun John , Furuya Andrea K. M. , Jellinger Robert M. , Nekorchuk Michael D. , de Noronha Carlos M. C. 
Published: April 2014

ABSTRACT

Human immunodeficiency virus (HIV) seizes control of cellular cullin-RING E3 ubiquitin ligases (CRLs) to promote viral replication. HIV-1 Vpr and HIV-2/simian immunodeficiency virus (SIV) Vpr and Vpx engage the cullin4 (CUL4)-containing ubiquitin ligase complex (CRL4) to cause polyubiquitination and proteasomal degradation of host proteins, including ones that block infection. HIV-1 Vpr engages CRL4 to trigger the degradation of uracil-
N
-glycosylase 2 (UNG2). Both HIV-1 Vpr and HIV-2/SIV Vpr tap CRL4 to initiate G
2
cell cycle arrest. HIV-2/SIV Vpx secures CRL4 to degrade the antiviral protein SAMHD1. CRL4 includes either cullin4A (CUL4A) or cullin4B (CUL4B) among its components. Whether Vpr or Vpx relies on CUL4A, CUL4B, or both to act through CRL4 is not known. Reported structural, phenotypic, and intracellular distribution differences between the two CUL4 types led us to hypothesize that Vpr and Vpx employ these in a function-specific manner. Here we determined CUL4 requirements for HIV-1 and HIV-2/SIV Vpr-mediated G
2
cell cycle arrest, HIV-1 Vpr-mediated UNG2 degradation, and HIV-2 Vpx-mediated SAMHD1 degradation. Surprisingly, CUL4A and CUL4B are exchangeable for CRL4-dependent Vpr and Vpx action, except in primary macrophages, where Vpx relies on both CUL4A and CUL4B for maximal SAMHD1 depletion. This work highlights the need to consider both CUL4 types for Vpr and Vpx functions and also shows that the intracellular distribution of CUL4A and CUL4B can vary by cell type.

IMPORTANCE
The work presented here shows for the first time that HIV Vpr and Vpx do not rely exclusively on CUL4A to cause ubiquitination through the CRL4 ubiquitin ligase complex. Furthermore, our finding that intracellular CUL4 and SAMHD1 distributions can vary with cell type provides the basis for reconciling previous disparate findings regarding the site of SAMHD1 depletion. Finally, our observations with primary immune cells provide insight into the cell biology of CUL4A and CUL4B that will help differentiate the functions of these similar proteins.
HIV-1 Protease-Substrate Coevolution in Nelfinavir Resistance
Authors: Kolli Madhavi , Özen Ayşegül , Kurt-Yilmaz Nese , Schiffer Celia A. 
Published: April 2014

ABSTRACT
Resistance to various human immunodeficiency virus type 1 (HIV-1) protease inhibitors (PIs) challenges the effectiveness of therapies in treating HIV-1-infected individuals and AIDS patients. The virus accumulates mutations within the protease (PR) that render the PIs less potent. Occasionally, Gag sequences also coevolve with mutations at PR cleavage sites contributing to drug resistance. In this study, we investigated the structural basis of coevolution of the p1-p6 cleavage site with the nelfinavir (NFV) resistance D30N/N88D protease mutations by determining crystal structures of wild-type and NFV-resistant HIV-1 protease in complex with p1-p6 substrate peptide variants with L449F and/or S451N. Alterations of residue 30's interaction with the substrate are compensated by the coevolving L449F and S451N cleavage site mutations. This interdependency in the PR–p1-p6 interactions enhances intermolecular contacts and reinforces the overall fit of the substrate within the substrate envelope, likely enabling coevolution to sustain substrate recognition and cleavage in the presence of PR resistance mutations.

IMPORTANCE
Resistance to human immunodeficiency virus type 1 (HIV-1) protease inhibitors challenges the effectiveness of therapies in treating HIV-1-infected individuals and AIDS patients. Mutations in HIV-1 protease selected under the pressure of protease inhibitors render the inhibitors less potent. Occasionally, Gag sequences also mutate and coevolve with protease, contributing to maintenance of viral fitness and to drug resistance. In this study, we investigated the structural basis of coevolution at the Gag p1-p6 cleavage site with the nelfinavir (NFV) resistance D30N/N88D protease mutations. Our structural analysis reveals the interdependency of protease-substrate interactions and how coevolution may restore substrate recognition and cleavage in the presence of protease drug resistance mutations.
Potential Role for CA-SP in Nucleating Retroviral Capsid Maturation
Authors: England Matthew R. , Purdy John G. , Ropson Ira J. , Dalessio Paula M. , Craven Rebecca C. 
Published: April 2014

ABSTRACT
During virion maturation, the Rous sarcoma virus (RSV) capsid protein is cleaved from the Gag protein as the proteolytic intermediate CA-SP. Further trimming at two C-terminal sites removes the spacer peptide (SP), producing the mature capsid proteins CA and CA-S. Abundant genetic and structural evidence shows that the SP plays a critical role in stabilizing hexameric Gag interactions that form immature particles. Freeing of CA-SP from Gag breaks immature interfaces and initiates the formation of mature capsids. The transient persistence of CA-SP in maturing virions and the identification of second-site mutations in SP that restore infectivity to maturation-defective mutant viruses led us to hypothesize that SP may play an important role in promoting the assembly of mature capsids. This study presents a biophysical and biochemical characterization of CA-SP and its assembly behavior. Our results confirm cryo-electron microscopy (cryo-EM) structures reported previously by Keller et al. (J. Virol. 87:13655–13664, 2013, doi:10.1128/JVI.01408-13) showing that monomeric CA-SP is fully capable of assembling into capsid-like structures identical to those formed by CA. Furthermore, SP confers aggressive assembly kinetics, which is suggestive of higher-affinity CA-SP interactions than observed with either of the mature capsid proteins. This aggressive assembly is largely independent of the SP amino acid sequence, but the formation of well-ordered particles is sensitive to the presence of the N-terminal β-hairpin. Additionally, CA-SP can nucleate the assembly of CA and CA-S. These results suggest a model in which CA-SP, once separated from the Gag lattice, can actively promote the interactions that form mature capsids and provide a nucleation point for mature capsid assembly.

IMPORTANCE
The spacer peptide is a documented target for antiretroviral therapy. This study examines the biochemical and biophysical properties of CA-SP, an intermediate form of the retrovirus capsid protein. The results demonstrate a previously unrecognized activity of SP in promoting capsid assembly during maturation.
A Conformation-Dependent Neutralizing Monoclonal Antibody Specifically Targeting Receptor-Binding Domain in Middle East Respiratory Syndrome Coronavirus Spike Protein
Authors: Du Lanying , Zhao Guangyu , Yang Yang , Qiu Hongjie , Wang Lili , Kou Zhihua , Tao Xinrong , Yu Hong , Sun Shihui , Tseng Chien-Te K. , Jiang Shibo , Li Fang , Zhou Yusen 
Published: April 2014

ABSTRACT
Prophylactic and therapeutic strategies are urgently needed to combat infections caused by the newly emerged Middle East respiratory syndrome coronavirus (MERS-CoV). Here, we have developed a neutralizing monoclonal antibody (MAb), designated Mersmab1, which potently blocks MERS-CoV entry into human cells. Biochemical assays reveal that Mersmab1 specifically binds to the receptor-binding domain (RBD) of the MERS-CoV spike protein and thereby competitively blocks the binding of the RBD to its cellular receptor, dipeptidyl peptidase 4 (DPP4). Furthermore, alanine scanning of the RBD has identified several residues at the DPP4-binding surface that serve as neutralizing epitopes for Mersmab1. These results suggest that if humanized, Mersmab1 could potentially function as a therapeutic antibody for treating and preventing MERS-CoV infections. Additionally, Mersmab1 may facilitate studies of the conformation and antigenicity of MERS-CoV RBD and thus will guide rational design of MERS-CoV subunit vaccines.

IMPORTANCE
MERS-CoV is spreading in the human population and causing severe respiratory diseases with over 40% fatality. No vaccine is currently available to prevent MERS-CoV infections. Here, we have produced a neutralizing monoclonal antibody with the capacity to effectively block MERS-CoV entry into permissive human cells. If humanized, this antibody may be used as a prophylactic and therapeutic agent against MERS-CoV infections. Specifically, when given to a person (e.g., a patient's family member or a health care worker) either before or after exposure to MERS-CoV, the humanized antibody may prevent or inhibit MERS-CoV infection, thereby stopping the spread of MERS-CoV in humans. This antibody can also serve as a useful tool to guide the design of effective MERS-CoV vaccines.
Mixed Triple: Allied Viruses in Unique Recent Isolates of Highly Virulent Type 2 Bovine Viral Diarrhea Virus Detected by Deep Sequencing
Authors: Jenckel Maria , Höper Dirk , Schirrmeier Horst , Reimann Ilona , Goller Katja V. , Hoffmann Bernd , Beer Martin 
Published: April 2014

ABSTRACT

In February 2013, very severe acute clinical symptoms were observed in calves, heifers, and dairy cattle in several farms in North Rhine Westphalia and Lower Saxony, Germany. Deep sequencing revealed the coexistence of three distinct genome variants within recent highly virulent bovine viral diarrhea virus type 2 (BVDV-2) isolates. While the major portion (ca. 95%) of the population harbored a duplication of a 222-nucleotide (nt) segment within the p7-NS2-encoding region, the minority reflected the standard structure of a BVDV-2 genome. Additionally, unusual mutations were found in both variants, within the highly conserved p7 protein and close to the p7-NS2 cleavage site. Using a reverse genetic system with a BVDV-2a strain harboring a similar duplication, it could be demonstrated that during replication, genomes without duplication are generated
de novo
from genomes with duplication. The major variant with duplication is compulsorily escorted by the minor variant without duplication. RNA secondary structure prediction allowed the analysis of the unique but stable mixture of three BVDV variants and also provided the explanation for their generation. Finally, our results suggest that the variant with duplication plays the major role in the highly virulent phenotype.

IMPORTANCE
This study emphasizes the importance of full-genome deep sequencing in combination with manual in-depth data analysis for the investigation of viruses in basic research and diagnostics. Here we investigated recent highly virulent bovine viral diarrhea virus isolates from a 2013 series of outbreaks. We discovered a unique special feature of the viral genome, an unstable duplication of 222 nucleotides which is eventually deleted by viral polymerase activity, leading to an unexpectedly mixed population of viral genomes for all investigated isolates. Our study is of high importance to the field because we demonstrate that these insertion/deletion events allow another level of genome plasticity of plus-strand RNA viruses, in addition to the well-known polymerase-induced single nucleotide variations which are generally considered the main basis for viral adaptation and evolution.