bluuebunny/crossref_metadata_2025_split huggingface dataset:
Bayesian modelling to estimate the test characteristics of coprology, coproantigen ELISA and a novel real‐time PCR for the diagnosis of taeniasis
Authors: Praet Nicolas , Verweij Jaco J. , Mwape Kabemba E. , Phiri Isaac K. , Muma John B. , Zulu Gideon , van Lieshout Lisette , Rodriguez‐Hidalgo Richar , Benitez‐Ortiz Washington , Dorny Pierre , Gabriël Sarah 
Published: March 2013

AbstractObjectiveTo estimate and compare the performances of coprology, copro‐Ag ELISA and real‐time polymerase chain reaction assay (copro‐PCR) for detection of Taenia solium tapeworm carriers.MethodsThe three diagnostic tests were applied on 817 stool samples collected in two Zambian communities where taeniasis is endemic. A Bayesian approach was used to allow estimation of the test characteristics. Two (0.2%; 95% Confidence Interval (CI): 0–0.8), 67 (8.2%; 95% CI: 6.4–10.3) and 10 (1.2%; 95% CI: 0.5–2.2) samples were positive using coprology, copro‐Ag ELISA and copro‐PCR, respectively.ResultsSpecificities of 99.9%, 92.0% and 99.0% were determined for coprology, copro‐Ag ELISA and copro‐PCR, respectively. Sensitivities of 52.5%, 84.5% and 82.7% were determined for coprology, copro‐Ag ELISA and copro‐PCR, respectively.ConclusionsWe urge for additional studies exploring possible cross‐reactions of the copro‐Ag ELISA and for the use of more sensitive tests, such as copro‐PCR, for the detection of tapeworm carriers, which is a key factor in controlling the parasite in endemic areas.
Reference values for the production of the aqueous fraction of the tear film measured by the standardized endodontic absorbent paper point test in different exotic and laboratory animal species
Authors: Lange Rogério R. , Lima Leandro , Przydzimirski Andreise C. , Montiani‐Ferreira Fabiano 
Published: March 2013

AbstractThe aqueous fraction of the tear film and the horizontal palpebral fissure length (HPFL) were measured in exotic and laboratory animals, specifically saffron finches (Sicalis flaveola), chestnut‐bellied seed‐finches (Sporophila angolensis), red‐eared sliders (Trachemys scripta elegans), rats (Rattus norvegicus) and mice (Mus musculus). These species possess small eyes making it difficult to perform the typical Schirmer tear test. Measurement of the aqueous fraction of the tear was performed using the standardized endodontic absorbent paper point tear test (PPTT), accomplished with manual restraint by a single operator. The following results were obtained: saffron finches (n = 42)—HPFL (4.46 ± 0.09 mm) and PPTT (5.10 ± 0.26 mm); chestnut‐bellied seed‐finches (n = 38)—HPFL (4.77 ± 0.05 mm) and PPTT (4.11 ± 0.34 mm); red‐eared sliders (n = 56)—HPFL (8.59 ± 0.08 mm) and PPTT (8.79 ± 0.38 mm); rats (n = 60)—HPFL (6.45 ± 0.09 mm) and PTT (6.18 ± 2.06 mm); and mice (n = 22)—HPFL (3.59 ± 0.27 mm) and PPTT (4.39 ± 1.45 mm).
The effects of mapping CT images to Monte Carlo materials on GEANT4 proton simulation accuracy
Authors: Barnes Samuel , McAuley Grant , Slater James , Wroe Andrew 
Published: March 2013

Purpose: Monte Carlo simulations of radiation therapy require conversion from Hounsfield units (HU) in CT images to an exact tissue composition and density. The number of discrete densities (or density bins) used in this mapping affects the simulation accuracy, execution time, and memory usage in GEANT4 and other Monte Carlo code. The relationship between the number of density bins and CT noise was examined in general for all simulations that use HU conversion to density. Additionally, the effect of this on simulation accuracy was examined for proton radiation.Methods: Relative uncertainty from CT noise was compared with uncertainty from density binning to determine an upper limit on the number of density bins required in the presence of CT noise. Error propagation analysis was also performed on continuously slowing down approximation range calculations to determine the proton range uncertainty caused by density binning. These results were verified with Monte Carlo simulations.Results: In the presence of even modest CT noise (5 HU or 0.5%) 450 density bins were found to only cause a 5% increase in the density uncertainty (i.e., 95% of density uncertainty from CT noise, 5% from binning). Larger numbers of density bins are not required as CT noise will prevent increased density accuracy; this applies across all types of Monte Carlo simulations. Examining uncertainty in proton range, only 127 density bins are required for a proton range error of <0.1 mm in most tissue and <0.5 mm in low density tissue (e.g., lung).Conclusions: By considering CT noise and actual range uncertainty, the number of required density bins can be restricted to a very modest 127 depending on the application. Reducing the number of density bins provides large memory and execution time savings in GEANT4 and other Monte Carlo packages.
Hepatitis C Virus (HCV)-Related Cryoglobulinemia: Cryoglobulin Type and Anti-HCV Profile
Authors: Minopetrou Martha , Hadziyannis Emilia , Deutsch Melanie , Tampaki Maria , Georgiadou Asimina , Dimopoulou Eleni , Vassilopoulos Dimitrios , Koskinas John 
Published: March 2013

ABSTRACTCryoglobulin characteristics in chronic hepatitis C (CHC) might be of importance for knowing more about the pathogenesis and treatment of the disease. We aimed to investigate the relationship between cryoglobulin types and their specificity against hepatitis C virus (HCV) antigenic epitopes in CHC patients. We analyzed samples from 43 patients with HCV-associated cryoglobulinemia, of whom 4 had concomitant lymphoma. Cryoglobulins were measured, purified, typed by immunofixation electrophoresis, and tested for IgG and IgM anti-HCV antibodies by immunoblot analysis and an enzyme-linked immunosorbent assay (ELISA). Clinical and other laboratory data were recorded. The median cryocrit level of the tested samples was 6%. Type I cryoglobulins were detected in 9.3% (4/43) of the cryoprecipitates, and type II cryoglobulins were detected in 48.8% (21/43) of the cryoprecipitates. IgM monoclonal protein, mainly IgM(κ), was found in 92% (23/25) of type I and II cryoprecipitates. Type III cryoglobulins were identified in 41.9% (18/43) of the patients and were associated with high blood serum IgG levels. In 81.3% (13/16) of type II and 92.3% (12/13) of type III cryoglobulins, there was IgG reactivity against the viral core region. Ninety-two percent and 32% of IgG anti-HCV core-positive cryoprecipitates had additional specificities against the NS3 and NS4 regions, respectively. Also, IgM anti-HCV antibodies were detected in 31% of the cryoprecipitates. In conclusion, all types of cryoglobulins were found in patients with HCV-associated cryoglobulinemia, with type II being the most frequently identified. Type III cryoglobulins were common and were associated with high serum IgG levels. HCV-related cryoglobulins demonstrated IgM, and particularly IgG, anti-HCV specificities, mainly against the core and NS3 epitopes.
Development of Immunochromatography-Based Methods for Detection of Leptospiral Lipopolysaccharide Antigen in Urine
Authors: Widiyanti Dian , Koizumi Nobuo , Fukui Takashi , Muslich Lisa T. , Segawa Takaya , Villanueva Sharon Y. A. M. , Saito Mitsumasa , Masuzawa Toshiyuki , Gloriani Nina G. , Yoshida Shin-ichi 
Published: March 2013

ABSTRACTLeptospirosis is an infectious disease caused by the spirochete bacteriaLeptospiraspp. and is commonly found throughout the world. Diagnosis of leptospirosis performed by culture and microscopic agglutination tests is laborious and time-consuming. Therefore, we aimed to develop a novel immunochromatography (ICG)-based method for detectingLeptospiraantigen in the urine of patients and animals. We used the 1H6 monoclonal antibody (MAb), which is specific to the lipopolysaccharide (LPS) that is common amongLeptospiraspp. The MAb was coupled to 40-nm-diameter colloidal gold, and the amounts of labeled antibody and immobilized antibody were 23 μg and 2 μg per test, respectively. Several strains ofLeptospiraand other bacterial species were used to evaluate the sensitivities and specificities of the assays we developed. The detection limit of the assays was 106cells/ml when disrupted whole bacterial cells were used. The assays wereLeptospiraspecific since they did not cross-react with non-Leptospirabacteria used in the study. Application of diagnostic assays was done on the urine samples of 46Leptospira-infected hamsters, 44 patients with suspected leptospirosis, and 14 healthy individuals. Pretreatment of the urine samples by boiling and centrifugation (for ultrafiltration and concentration) eliminated nonspecific reactions that occurred in the assay. The sensitivity and specificity of the ICG-based lateral flow assay (LFA) were 89% and 87%, respectively, which were higher than those of the dipstick assay, which were 80% and 74%, respectively. In summary, this ICG-based LFA can be used as an alternative diagnostic assay for leptospirosis. Further development is still necessary to improve the assay.
Development and Evaluation of a Trivalent Riemerella anatipestifer-Inactivated Vaccine
Authors: Liu Haiwen , Wang Xiaolan , Ding Chan , Han Xiangan , Cheng Anchun , Wang Shaohui , Yu Shengqing 
Published: March 2013

ABSTRACTRiemerella anatipestiferinfections cause major economic losses in the duck industry. In this study, a trivalent inactivated vaccine ofR. anatipestifer, including strains CH3 (serotype 1), NJ3 (serotype 2), and HXb2 (serotype 10), was developed. Animal experiments showed that the ducks that received two immunizations with the vaccine were 100% protected from challenge with strains from any of the three serotypes (1, 2, or 10). No death or clinical signs of diarrhea, tremors, or limb swelling were shown in the protected ducks. Also, noR. anatipestiferbacteria were isolated from the livers or brains of the protected ducks. Furthermore, no histopathological changes were observed in the liver, spleen, or brain samples from the protected ducks during histological examination. The ducks that received two immunizations with the vaccine generated high antibody titers of 1:3,200 to 1:6,400 against the three serotypes of strains. The vaccine significantly enhanced the production of gamma interferon (IFN-γ) and interleukin 2 (IL-2) after one immunization and enhanced the production of IL-4 and IL-10 after two immunizations. In addition, real-time PCR indicated that the expression of major histocompatibility complex I (MHC-I), as well as that of CD40 and CD154 molecules, was significantly increased after one immunization, and the expressions of both MHC-I and MHC-II molecules were increased after two immunizations. Our study indicates that the vaccine can induce both humoral and cellular immunities in ducks and offer effective protection againstR. anatipestiferinfection.
Rothia mucilaginosa Prosthetic Device Infections: a Case of Prosthetic Valve Endocarditis
Authors: Bruminhent Jackrapong , Tokarczyk Mindy J. , Jungkind Donald , DeSimone Joseph A. 
Published: March 2013

ABSTRACT

Rothia mucilaginosa
is increasingly recognized as an emerging opportunistic pathogen associated with prosthetic device infections. Infective endocarditis is one of the most common clinical presentations. We report a case of
R. mucilaginosa
prosthetic valve endocarditis and review the literature of prosthetic device infections caused by this organism.
A Protein (ORF2) Encoded by the Latency-Related Gene of Bovine Herpesvirus 1 Interacts with DNA
Authors: Pittayakhajonwut Daraporn , Sinani Devis , Jones Clinton 
Published: March 2013

ABSTRACTBovine herpesvirus 1 (BHV-1), like other members of theAlphaherpesvirinaesubfamily, establishes latency in sensory neurons. The virally encoded latency-related RNA (LR-RNA) is expressed abundantly in latently infected sensory neurons and encodes several proteins, including ORF2. An LR mutant virus with stop codons at the amino terminus of ORF2 does not reactivate from latency after treatment with the synthetic corticosteroid dexamethasone, in part because it induces higher levels of apoptosis during the establishment of latency. ORF2 inhibits apoptosis, interacts with three cellular transcription factors (Notch1, Notch3, and C/EBP-α), and interferes with Notch-mediated signaling. Consequently, we predict that ORF2 expression is crucial for the latency reactivation cycle in cattle. In this study, we tested whether ORF2 interacts with nucleic acids, because it contains 18% basic amino acids and localizes to the nucleus. A subset of ORF2 proteins was associated with chromatin and preferentially associated with single-stranded DNA in transfected neuroblastoma cells (Neuro-2A). Alanine substitution of serine, threonine, and tyrosine residues in ORF2 increased the steady-state protein levels in Neuro-2A cells, and this protein preferentially interacted with double-stranded DNA. Certain in-frame transposon insertion mutants did not interact with DNA as efficiently as wild-type (wt) ORF2 did. ORF2 purified from bacteria under denaturing conditions preferentially interacted with double-stranded DNA, suggesting that the interaction between ORF2 and DNA was direct. In contrast, ORF2 purified under native conditions preferentially interacted with single-stranded DNA. We suggest that interactions between ORF2 and DNA mediate certain aspects of the latency reactivation cycle.
Conformational Epitope Consisting of the V3 and V4 Loops as a Target for Potent and Broad Neutralization of Simian Immunodeficiency Viruses
Authors: Kuwata Takeo , Takaki Kaori , Yoshimura Kazuhisa , Enomoto Ikumi , Wu Fan , Ourmanov Ilnour , Hirsch Vanessa M. , Yokoyama Masaru , Sato Hironori , Matsushita Shuzo 
Published: March 2013

ABSTRACT
Inducing neutralizing antibodies (NAb) is the key to developing a protective vaccine against human immunodeficiency virus type 1 (HIV-1). To clarify the neutralization mechanism of simian immunodeficiency virus (SIV), we analyzed NAb B404, which showed potent and broad neutralizing activity against various SIV strains. In 4 SIVsmH635FC-infected macaques, B404-like antibodies using the specific VH3 gene with a long complementarity-determining region 3 loop and λ light chain were the major NAbs in terms of the number and neutralizing potency. This biased NAb induction was observed in all 4 SIVsmH635FC-infected macaques but not in 2 macaques infected with a SIV mix, suggesting that induction of B404-like NAbs depended on the inoculated virus. Analysis using Env mutants revealed that the V3 and V4 loops were critical for B404 binding. The reactivity to the B404 epitope on trimeric, but not monomeric, Env was enhanced by CD4 ligation. The B404-resistant variant, which was induced by passages with increasing concentrations of B404, accumulated amino acid substitutions in the C2 region of gp120. Molecular dynamics simulations of the gp120 outer domains indicated that the C2 mutations could effectively alter the structural dynamics of the V3/V4 loops and their neighboring regions. These results suggest that a conformational epitope consisting of the V3 and V4 loops is the target for potent and broad neutralization of SIV. Identifying the new neutralizing epitope, as well as specifying the VH3 gene used for epitope recognition, will help to develop HIV-1 vaccines.
Ebola Virus Does Not Block Apoptotic Signaling Pathways
Authors: Olejnik Judith , Alonso Jesus , Schmidt Kristina M. , Yan Zhen , Wang Wei , Marzi Andrea , Ebihara Hideki , Yang Jinghua , Patterson Jean L. , Ryabchikova Elena , Mühlberger Elke 
Published: March 2013

ABSTRACT
Since viruses rely on functional cellular machinery for efficient propagation, apoptosis is an important mechanism to fight viral infections. In this study, we sought to determine the mechanism of cell death caused by Ebola virus (EBOV) infection by assaying for multiple stages of apoptosis and hallmarks of necrosis. Our data indicate that EBOV does not induce apoptosis in infected cells but rather leads to a nonapoptotic form of cell death. Ultrastructural analysis confirmed necrotic cell death of EBOV-infected cells. To investigate if EBOV blocks the induction of apoptosis, infected cells were treated with different apoptosis-inducing agents. Surprisingly, EBOV-infected cells remained sensitive to apoptosis induced by external stimuli. Neither receptor- nor mitochondrion-mediated apoptosis signaling was inhibited in EBOV infection. Although double-stranded RNA (dsRNA)-induced activation of protein kinase R (PKR) was blocked in EBOV-infected cells, induction of apoptosis mediated by dsRNA was not suppressed. When EBOV-infected cells were treated with dsRNA-dependent caspase recruiter (dsCARE), an antiviral protein that selectively induces apoptosis in cells containing dsRNA, virus titers were strongly reduced. These data show that the inability of EBOV to block apoptotic pathways may open up new strategies toward the development of antiviral therapeutics.
Identification of an HIV-1 Clade A Envelope That Exhibits Broad Antigenicity and Neutralization Sensitivity and Elicits Antibodies Targeting Three Distinct Epitopes
Authors: Hoffenberg Simon , Powell Rebecca , Carpov Alexei , Wagner Denise , Wilson Aaron , Kosakovsky Pond Sergei , Lindsay Ross , Arendt Heather , DeStefano Joanne , Phogat Sanjay , Poignard Pascal , Fling Steven P. , Simek Melissa , LaBranche Celia , Montefiori David , Wrin Terri , Phung Pham , Burton Dennis , Koff Wayne , King C. Richter , Parks Christopher L. , Caulfield Michael J. 
Published: March 2013

ABSTRACT
Broadly neutralizing antibodies (bNAbs) PG9 and PG16 were isolated from an International AIDS Vaccine Initiative (IAVI) Protocol G subject infected with human immunodeficiency virus type 1 (HIV-1) clade A. Both antibodies are highly potent and neutralize greater than 70% of viruses tested. We sought to begin immunogen design based on viral sequences from this patient; however, pseudoviruses prepared with 19 envelope sequences from this subject were resistant to neutralization by PG9 and PG16. Therefore, we used a bioinformatics approach to identify closely related viruses that were potentially sensitive to PG9 and PG16. A most-recent common ancestor (MRCA) sequence for the viral envelope (Env) was determined and aligned with 99 subtype A gp160 sequences from the Los Alamos HIV database. Virus BG505.W6M.ENV.C2 (BG505) was found to have the highest degree of homology (73%) to the MRCA sequence. Pseudoviruses prepared with this Env were sensitive to neutralization with a broad panel of bNAbs, including PG9 and PG16. When expressed by 293T cells as soluble gp120, the BG505 monomer bound well to both PG9 and PG16. We further showed that a point mutation (L111A) enabled more efficient production of a stable gp120 monomer that preserves the major neutralization epitopes. Finally, we showed that an adjuvanted formulation of this gp120 protein elicited neutralizing antibodies in rabbits (following a gp120 DNA vaccine prime) and that the antisera competed with bNAbs from 3 classes of nonoverlapping epitopes. Thus, the BG505 Env protein warrants further investigation as an HIV vaccine candidate, as a stand-alone protein, or as a component of a vaccine vector.
The Source of the PB1 Gene in Influenza Vaccine Reassortants Selectively Alters the Hemagglutinin Content of the Resulting Seed Virus
Authors: Cobbin Joanna C. A. , Verity Erin E. , Gilbertson Brad P. , Rockman Steven P. , Brown Lorena E. 
Published: March 2013

ABSTRACT
The yields of egg-grown influenza vaccines are maximized by the production of a seed strain using a reassortment of the seasonal influenza virus isolate with a highly egg-adapted strain. The seed virus is selected based on high yields of viral hemagglutinin (HA) and expression of the surface antigens from the seasonal isolate. The remaining proteins are usually derived from the high-growth parent. However, a retrospective analysis of vaccine seeds revealed that the seasonal PB1 gene was selected in more than 50% of reassortment events. Using the model seasonal H3N2 virus A/Udorn/307/72 (Udorn) virus and the high-growth A/Puerto Rico/8/34 (PR8) virus, we assessed the influence of the source of the PB1 gene on virus growth and vaccine yield. Classical reassortment of these two strains led to the selection of viruses that predominantly had the Udorn PB1 gene. The presence of Udorn PB1 in the seed virus, however, did not result in higher yields of virus or HA compared to the yields in the corresponding seed virus with PR8 PB1. The 8-fold-fewer virions produced with the seed virus containing the Udorn PB1 were somewhat compensated for by a 4-fold increase in HA per virion. A higher HA/nucleoprotein (NP) ratio was found in past vaccine preparations when the seasonal PB1 was present, also indicative of a higher HA density in these vaccine viruses. As the HA viral RNA (vRNA) and mRNA levels in infected cells were similar, we propose that PB1 selectively alters the translation of viral mRNA. This study helps to explain the variability of vaccine seeds with respect to HA yield.
Effects of Postchallenge Administration of ST-246 on Dissemination of IHD-J-Luc Vaccinia Virus in Normal Mice and in Immune-Deficient Mice Reconstituted with T Cells
Authors: Zaitseva Marina , Shotwell Elisabeth , Scott John , Cruz Stephanie , King Lisa R. , Manischewitz Jody , Diaz Claudia G. , Jordan Robert A. , Grosenbach Douglas W. , Golding Hana 
Published: March 2013

ABSTRACT

Whole-body bioimaging was used to study dissemination of vaccinia virus (VACV) in normal and in immune deficient (
nu
−
/nu
−
) mice protected from lethality by postchallenge administration of ST-246. Total fluxes were recorded in the liver, spleen, lungs, and nasal cavities of live mice after intranasal infection with a recombinant IHD-J-Luc VACV expressing luciferase. Areas under the flux curve were calculated for individual mice to assess viral loads. Treatment for 2 to 5 days of normal BALB/c mice with ST-246 at 100 mg/kg starting 24 h postchallenge conferred 100% protection and reduced viral loads in four organs compared to control mice. Mice also survived after 5 days of treatment with ST-246 at 30 mg/kg, and yet the viral loads and poxes were higher in these mice compared to 100-mg/kg treatment group. Nude mice were not protected by ST-246 alone or by 10 million adoptively transferred T cells. In contrast, nude mice that received T cells and 7-day treatment with ST-246 survived infection and exhibited reduced viral loads compared to nonreconstituted and ST-246-treated mice after ST-246 was stopped. Similar protection of nude mice was achieved using adoptively transferred 1.0 and 0.1 million, but not 0.01 million, purified T cells or CD4
+
or CD8
+
T cells in conjunction with ST-246 treatment. These data suggest that ST-246 protects immunocompetent mice from lethality and reduces viral dissemination in internal organs and poxvirus lesions. Furthermore, immune-deficient animals with partial T cell reconstitution can control virus replication after a course of ST-246 and survive lethal vaccinia virus challenge.