bluuebunny/crossref_metadata_2025_split huggingface dataset:
Rapid Detection of H5N1 Subtype Influenza Viruses by Antigen Capture Enzyme-Linked Immunosorbent Assay Using H5- and N1-Specific Monoclonal Antibodies
Authors: Ho Hui-Ting , Qian Hong-Liang , He Fang , Meng Tao , Szyporta Milene , Prabhu Nayana , Prabakaran Mookkan , Chan Kwai-Peng , Kwang Jimmy 
Published: March 2009

ABSTRACT
Highly pathogenic avian influenza (HPAI) virus of the H5N1 subtype has caused devastating damage to poultry flocks and sporadic human H5N1 infections. There is concern that this virus subtype may gain transmissibility and become pandemic. Rapid diagnosis and surveillance for H5N1 subtype viruses are critical for the control of H5N1 infection. In this study, we report a robust antigen-capture enzyme-linked immunosorbent assay (AC-ELISA) based on H5- and N1-specific monoclonal antibodies (MAbs) for the rapid detection of H5N1 subtype viruses. The H5 hemagglutinin (HA)-specific MAb (2D9) targets a conformational epitope which recognized multiple clades of H5N1 viruses, including clades 0, 1, 2.1, 2.2, 2.3, 4, 7, and 8. The N1 neuraminidase (NA)-specific MAb (8H12) recognized a linear epitope comprising the sequence AELPF. This epitope was 99% conserved in the NA of 708 analyzed H5N1 viruses, while the epitope was absent in NAs of subtypes N2 through N9. The specificity of the AC-ELISA was examined by using 41 H5N1 HPAI strains from multiple clades, 36 non-H5N1 viruses, and 4 influenza B viruses. No cross-reactivity was observed for any of the non-H5N1 viruses tested. The estimated detection limit was 1 to 2 HA titers. It is concluded that this H5N1 AC-ELISA can simultaneously detect H5 and N1 subtype antigens, eliminating the need for secondary testing for the NA subtype. Implementation of this assay in ELISA-like formats suitable for field use, such as dot ELISA, immunofiltration, or electrochemical biosensor technologies, would provide dual on-site detection of H5 and N1 in clinical or environmental specimens.
Laboratory Diagnosis of Amoebic Keratitis: Comparison of Four Diagnostic Methods for Different Types of Clinical Specimens
Authors: Boggild Andrea K. , Martin Donald S. , Lee Theresa YuLing , Yu Billy , Low Donald E. 
Published: March 2009

ABSTRACT

Amoebic keratitis causes significant ocular morbidity in contact lens wearers. Current diagnostic methods for amoebic keratitis are insensitive and labor-intensive and have poor turnaround time. We evaluated four laboratory methods for detection of acanthamoebae in clinical specimens. Deidentified, delinked consecutive specimens from patients with suspected amoebic keratitis were assayed for acanthamoebae by direct smear analysis, culture, and PCR using two different primer sets specific for
Acanthamoeba
ribosomal DNA. The consensus reference standard was considered fulfilled when the results for any two of the four tests were positive, and the outcome measures were sensitivity and specificity. Of 107 specimens assayed over an 18-month period, 20 were positive for acanthamoebae. The sensitivity and specificity of each assay were as follows, respectively: for smear analysis, 55% (95% confidence interval [CI], 33.2 to 76.8%) and 100%; for culture, 73.7% (95% CI, 54.4 to 93.0%) and 100%; for PCR using Nelson primers, 90% (95% CI, 76.9 to 100%) and 90.8% (95% CI, 84.7 to 96.9%); and for PCR using JDP primers, 65% (95% CI, 44.1 to 85.9%) and 100%. Nelson primer PCR demonstrated a single-organism level of analytic sensitivity. The performance characteristics of the assays varied by specimen type, with contact lenses and casings showing the highest rates of detectable acanthamoebae and the highest diagnostic sensitivities for direct smear analysis, culture, and JDP primer PCR, though these results are based on small numbers and should be interpreted cautiously. These findings have important implications for clinicians collecting diagnostic specimens and for diagnostic laboratories, especially in outbreak situations.
Influenza Antiviral Resistance Testing in New York and Wisconsin, 2006 to 2008: Methodology and Surveillance Data
Authors: Laplante Jennifer M. , Marshall Steven A. , Shudt Matthew , Van Tam T. , Reisdorf Erik S. , Mingle Lisa A. , Shult Peter A. , St. George Kirsten 
Published: March 2009

ABSTRACT
The need for effective influenza antiviral susceptibility surveillance methods has increased due to the emergence of near-universal adamantane resistance in influenza A/H3N2 viruses during the 2005-2006 season and the appearance of oseltamivir resistance in the influenza A/H1N1 virus subtype during the 2007-2008 season. The two classes of influenza antivirals, the neuraminidase inhibitors (NAIs) and the adamantanes, are well characterized, as are many mutations that can confer resistance to these drugs. Adamantane resistance is imparted mainly by a S31N mutation in the matrix gene, while NAI resistance can result from a number of mutations in the neuraminidase gene. During the 2007-2008 season, a neuraminidase mutation (H274Y) conferring resistance to the NAI oseltamivir emerged worldwide in the A/H1N1 virus subtype. Surveillance methodology and data from New York (NY) and Wisconsin (WI) for the 2006-2007 and 2007-2008 influenza seasons are presented. We used an existing pyrosequencing method (R. A. Bright et al., Lancet 366:1175-1181, 2005) and a modified version of this method for detection of adamantane resistance mutations. For NAI resistance mutation detection, we used a mutation-specific pyrosequencing technique and developed a neuraminidase gene dideoxy sequencing method. Adamantane resistance in the A/H3N2 virus samples was 100% for 2007-2008, similar to the 99.8% resistance nationwide as reported by the CDC. Adamantane resistance was found in only 1.2% of NY and WI A/H1N1 virus samples, compared to that found in 10.8% of samples tested nationwide as reported by the CDC. Influenza A/H1N1 virus H274Y mutants were found in 11.1% of NY samples for 2007-2008, a level comparable to the 10.9% nationwide level reported by the CDC; in contrast, mutants were found in 17.4% of WI samples. These results indicate the need for regional influenza antiviral surveillance.
Molecular Identification and Susceptibility ofTrichosporonSpecies Isolated from Clinical Specimens in Qatar: Isolation ofTrichosporon dohaenseTaj-Aldeen, Meis & Boekhout sp. nov
Authors: Taj-Aldeen Saad J. , Al-Ansari Nasser , El Shafei Sittana , Meis Jacques F. , Curfs-Breuker Ilse , Theelen Bart , Boekhout Teun 
Published: March 2009

ABSTRACTTrichosporonspecies have been reported as emerging pathogens and usually occur in severely immunocompromised patients. In the present work, 27 clinical isolates ofTrichosporonspecies were recovered from 27 patients. The patients were not immunocompromised, except for one with acute myeloid leukemia. Sequence analysis revealed the isolation ofTrichosporon dohaenseTaj-Aldeen, Meis & Boekhout sp. nov., with CBS 10761Tas the holotype strain, belonging to the Ovoides clade. In the D1-D2 large-subunit rRNA gene analysis,T. dohaenseis a sister species toT. coremiiforme, and in the internal transcribed spacer analysis, the species is basal to the other species of this clade. Molecular identification of the strains yielded 17T. asahii, 3T. inkin, 2T. japonicum, 2T. faecale, and 3T. dohaenseisolates. The former four species exhibited low MICs for five antifungal azoles but showed high MICs for amphotericin B.T. dohaensedemonstrated the lowest amphotericin B MIC (1 mg/liter). For the majority ofT. asahiiisolates, amphotericin B MICs were high (MIC at which 90% of isolates were inhibited [MIC90], ≥16 mg/liter), and except for fluconazole (MIC90, 8 mg/liter), the azole MICs were low: MIC90s were 0.5 mg/liter for itraconazole, 0.25 mg/liter for voriconazole, 0.25 mg/liter for posaconazole, and 0.125 mg/liter for isavuconazole. The echinocandins, caspofungin and anidulafungin, demonstrated no activity againstTrichosporonspecies.
Characterization of Methicillin-Resistant
Staphylococcus aureus
Isolates Collected in 2005 and 2006 from Patients with Invasive Disease: a Population-Based Analysis
Authors: Limbago Brandi , Fosheim Gregory E. , Schoonover Valerie , Crane Christina E. , Nadle Joelle , Petit Susan , Heltzel David , Ray Susan M. , Harrison Lee H. , Lynfield Ruth , Dumyati Ghinwa , Townes John M. , Schaffner William , Mu Yi , Fridkin Scott K. 
Published: March 2009

ABSTRACT

This study characterizes 1,984 methicillin-resistant
Staphylococcus aureus
(MRSA) isolates collected in 2005 and 2006 from normally sterile sites in patients with invasive MRSA infection. These isolates represent a convenience sample of all invasive MRSA cases reported as part of the Active Bacterial Core surveillance system in eight states in the United States. The majority of isolates were from blood (83.8%), joints (4.1%), and bone (4.2%). Isolates were characterized by pulsed-field gel electrophoresis (PFGE); SCC
mec
typing; susceptibility to 15 antimicrobial agents; and PCR analysis of staphylococcal enterotoxin A (SEA) to SEH, toxic shock syndrome toxin 1, and Panton-Valentine leukocidin. Thirteen established PFGE types were recognized among these isolates, although USA100 and USA300 predominated, accounting for 53.2% and 31.4% of the isolates, respectively. As expected, isolates from hospital onset cases were predominantly USA100, whereas those from community-associated cases were predominantly USA300. USA100 isolates were diverse (Simpson's discriminatory index [DI] = 0.924); generally positive only for enterotoxin D (74.5%); and resistant to clindamycin (98.6%), erythromycin (99.0%), and levofloxacin (99.6%), in addition to β-lactam agents. USA300 isolates were less diverse (DI = 0.566), positive for Panton-Valentine leukocidin (96.3%), and resistant to erythromycin (94.1%) and, less commonly, levofloxacin (54.6%), in addition to β-lactam agents. This collection provides a reference collection of MRSA isolates associated with invasive disease, collected in 2005 and 2006 in the United States, for future comparison and ongoing studies.
Less-FrequentFusariumSpecies of Clinical Interest: Correlation between Morphological and Molecular Identification and Antifungal Susceptibility
Authors: Azor Mónica , Gené Josepa , Cano Josep , Manikandan Palanisamy , Venkatapathy Narendran , Guarro Josep 
Published: March 2009

ABSTRACTForty-eightFusariumisolates morphologically identified as belonging to seven species of clinical interest (i.e.,Fusarium chlamydosporum,Fusarium dimerum,Fusarium incarnatum,Fusarium napiforme,Fusarium nygamai,Fusarium proliferatum, andFusarium sacchari) were characterized molecularly by the analysis of the sequences of the TUB region of the β-tubulin gene.F. chlamydosporumandF. dimerumwere the most genetically heterogeneous species. A high degree of correlation between the morphological and molecular identification was shown among the isolates studied. A table with the key morphological features for the identification of theseFusariumspecies is provided. The antifungal susceptibilities of theFusariumisolates to 11 antifungal drugs were tested; terbinafine was the most active drug against all the species tested with the exception ofF. incarnatum, for which amphotericin B was the most active.
Utility of the Pneumoslide Test in Identification of
Streptococcus pneumoniae
in Blood Cultures and Its Relation to Capsular Serotype
Authors: Chan Wilson W. , Lovgren Marguerite , Tyrrell Gregory J. 
Published: March 2009

ABSTRACT

The performance of the Pneumoslide test for rapid identification of
Streptococcus pneumoniae
was evaluated when used directly on positive blood culture specimens. The sensitivity was 75.3%, and the specificity was 98.6%. Pneumoslide test performance accuracy varied depending on the pneumococcal serotype.
Mutations in Hepatitis C Virus E2 Located outside the CD81 Binding Sites Lead to Escape from Broadly Neutralizing Antibodies but Compromise Virus Infectivity
Authors: Keck Zhen-yong , Li Sophia H. , Xia Jinming , von Hahn Thomas , Balfe Peter , McKeating Jane A. , Witteveldt Jeroen , Patel Arvind H. , Alter Harvey , Rice Charles M. , Foung Steven K. H. 
Published: March 2009

ABSTRACT
Broadly neutralizing antibodies are commonly present in the sera of patients with chronic hepatitis C virus (HCV) infection. To elucidate possible mechanisms of virus escape from these antibodies, retrovirus particles pseudotyped with HCV glycoproteins (HCVpp) isolated from sequential samples collected over a 26-year period from a chronically infected patient, H, were used to characterize the neutralization potential and binding affinity of a panel of anti-HCV E2 human monoclonal antibodies (HMAbs). Moreover, AP33, a neutralizing murine monoclonal antibody (MAb) to a linear epitope in E2, was also tested against selected variants. The HMAbs used were previously shown to broadly neutralize HCV and to recognize a cluster of highly immunogenic overlapping epitopes, designated domain B, containing residues that are also critical for binding of viral E2 glycoprotein to CD81, a receptor essential for virus entry. Escape variants were observed at different time points with some of the HMAbs. Other HMAbs neutralized all variants except for the isolate 02.E10, obtained in 2002, which was also resistant to MAb AP33. The 02.E10 HCVpp that have reduced binding affinities for all antibodies and for CD81 also showed reduced infectivity. Comparison of the 02.E10 nucleotide sequence with that of the strain H-derived consensus variant, H77c, revealed the former to have two mutations in E2, S501N and V506A, located outside the known CD81 binding sites. Substitution A506V in 02.E10 HCVpp restored binding to CD81, but its antibody neutralization sensitivity was only partially restored. Double substitutions comprising N501S and A506V synergistically restored 02.E10 HCVpp infectivity. Other mutations that are not part of the antibody binding epitope in the context of N501S and A506V were able to completely restore neutralization sensitivity. These findings showed that some nonlinear overlapping epitopes are more essential than others for viral fitness and consequently are more invariant during earlier years of chronic infection. Further, the ability of the 02.E10 consensus variant to escape neutralization by the tested antibodies could be a new mechanism of virus escape from immune containment. Mutations that are outside receptor binding sites resulted in structural changes leading to complete escape from domain B neutralizing antibodies, while simultaneously compromising viral fitness by reducing binding to CD81.
Comparison of Human and Rhesus Macaque T-Cell Responses Elicited by Boosting with NYVAC Encoding Human Immunodeficiency Virus Type 1 Clade C Immunogens
Authors: Mooij Petra , Balla-Jhagjhoorsingh Sunita S. , Beenhakker Niels , van Haaften Patricia , Baak Ilona , Nieuwenhuis Ivonne G. , Heidari Shirin , Wolf Hans , Frachette Marie-Joelle , Bieler Kurt , Sheppard Neil , Harari Alexandre , Bart Pierre-Alexandre , Liljeström Peter , Wagner Ralf , Pantaleo Giuseppe , Heeney Jonathan L. 
Published: March 2009

ABSTRACT

Rhesus macaques (
Macaca mulatta
) have played a valuable role in the development of human immunodeficiency virus (HIV) vaccine candidates prior to human clinical trials. However, changes and/or improvements in immunogen quality in the good manufacturing practice (GMP) process or changes in adjuvants, schedule, route, dose, or readouts have compromised the direct comparison of T-cell responses between species. Here we report a comparative study in which T-cell responses from humans and macaques to HIV type 1 antigens (Gag, Pol, Nef, and Env) were induced by the same vaccine batches prepared under GMP and administered according to the same schedules in the absence and presence of priming. Priming with DNA (humans and macaques) or alphavirus (macaques) and boosting with NYVAC induced robust and broad antigen-specific responses, with highly similar Env-specific gamma interferon (IFN-γ) enzyme-linked immunospot assay responses in rhesus monkeys and human volunteers. Persistent cytokine responses of antigen-specific CD4
+
and CD8
+
T cells of the central memory as well as the effector memory phenotype, capable of simultaneously eliciting multiple cytokines (IFN-γ, interleukin 2, and tumor necrosis factor alpha), were induced. Responses were highly similar in humans and primates, confirming earlier data indicating that priming is essential for inducing robust NYVAC-boosted IFN-γ T-cell responses. While significant similarities were observed in Env-specific responses in both species, differences were also observed with respect to responses to other HIV antigens. Future studies with other vaccines using identical lots, immunization schedules, and readouts will establish a broader data set of species similarities and differences with which increased confidence in predicting human responses may be achieved.
Major Histocompatibility Complex Haplotype Determines hsp70-Dependent Protection against Measles Virus Neurovirulence
Authors: Carsillo Thomas , Carsillo Mary , Traylor Zachary , Rajala-Schultz Päivi , Popovich Phillip , Niewiesk Stefan , Oglesbee Michael 
Published: March 2009

ABSTRACTIn vitro studies show that hsp70 promotes gene expression for multiple viral families, although there are few reports on the in vivo significance of virus-hsp70 interaction. Previously we showed that hsp70-dependent stimulation of Edmonston measles virus (Ed MeV) transcription caused an increased cytopathic effect and mortality in transgenic hsp70-overexpressing C57BL/6 mice (H-2b). The response to MeV infection is influenced by the major histocompatibility complex haplotype;H-2dmice are resistant to brain infection due to robust antiviral immune responses, whereasH-2bmice are susceptible due to deficiencies in this response. We therefore tested the hypothesis that the outcome of MeV-hsp70 interaction may be dependent upon the hostH-2haplotype. The impact of selective neuronal hsp70 overexpression on Ed MeV brain infection was tested with congenic C57BL/10H-2dneonatal mice. In this context, hsp70 overexpression conferred complete protection against virus-induced mortality, compared to >30% mortality in nontransgenic mice. Selective depletion of T-cell populations showed that transgenic mice exhibit a diminished reliance on T cells for protection. Brain transcript analysis indicated enhanced innate immune activation and signaling through Toll-like receptors 2 and 4 at early times postinfection for transgenic infected mice relative to those for nontransgenic infected mice. Collectively, results suggest that hsp70 can enhance innate antiviral immunity through Toll-like receptor signaling, supporting a protective role for physiological responses that enhance tissue levels of hsp70 (e.g., fever), and that theH-2haplotype determines the effectiveness of this response.
Composite intestinal-type adenocarcinoma and small cell carcinoma of sinonasal tract
Authors: Jain R , Gramigna V , Sanchez-Marull R , Perez-Ordoñez B 
Published: March 2009

Background and aims:Sinonasal intestinal-type adenocarcinomas (ITACs) are rare neoplasms resembling intestinal adenocarcinomas. Although several studies have documented neuroendocrine differentiation in ITACs, the combination of ITAC and small cell carcinoma has not been previously described in detail. The aim of this report is to detail the histopathological and immunohistochemical characteristics of two cases of composite ITAC with small cell carcinoma.Methods:Two cases of composite ITAC with small cell carcinoma were routinely processed, and representative sections were stained with CAM5.2, AE1:AE3, keratin 7, keratin 20, keratin 19, CDX-2, p63, villin, chromogranin, synaptophysin and CD56.Results:One tumour consisted of a mixed-type ITAC showing colonic-type and poorly differentiated adenocarcinoma with foci of “signet-ring” cells combined with small cell carcinoma. Both components stained positively with CAM5.2, AE1:AE3, CK7, CK20 and CK19, whereas only the small cell carcinoma expressed synaptophysin and CD56. Both components stained negatively with CDX-2, villin, CD99 and p63. The “signet-ring” cells stained positively with chromogranin and synaptophysin. The second tumour showed a papillary-type ITAC combined with a small cell carcinoma. The adenocarcinoma and small cell carcinoma stained positively with CAM5.2, AE1:AE3, CK7, CK19 and CK20. Only the adenocarcinoma was CDX-2 positive, whereas the small cell carcinoma expressed CD56 and synaptophysin.Conclusions:The two components of the combined ITACs and neuroendocrine small cell carcinoma show significant immunohistochemical overlap, supporting a common origin. The occurrence of a distinct neuroendocrine carcinoma combined with ITACs expands the histopathological spectrum of these tumours.
Fixed Points of Maps of a Nonaspherical Wedge
Authors: Kim Seung Won , Brown Robert F. , Ericksen Adam , Khamsemanan Nirattaya , Merrill Keith 
Published: March 2009

AbstractLet "Equation missing" be a finite polyhedron that has the homotopy type of the wedge of the projective plane and the circle. With the aid of techniques from combinatorial group theory, we obtain formulas for the Nielsen numbers of the selfmaps of "Equation missing".
Comparison of GPCP Monthly and Daily Precipitation Estimates with High-Latitude Gauge Observations
Authors: Bolvin David T. , Adler Robert F. , Huffman George J. , Nelkin Eric J. , Poutiainen Jani P. 
Published: March 2009

Abstract
Monthly and daily products of the Global Precipitation Climatology Project (GPCP) are evaluated through a comparison with Finnish Meteorological Institute (FMI) gauge observations for the period January 1995–December 2007 to assess the quality of the GPCP estimates at high latitudes. At the monthly scale both the final GPCP combination satellite–gauge (SG) product is evaluated, along with the satellite-only multisatellite (MS) product. The GPCP daily product is scaled to sum to the monthly product, so it implicitly contains monthly-scale gauge influence, although it contains no daily gauge information. As expected, the monthly SG product agrees well with the FMI observations because of the inclusion of limited gauge information. Over the entire analysis period the SG estimates are biased low by 6% when the same wind-loss adjustment is applied to the FMI gauges as is used in the SG analysis. The interannual anomaly correlation is about 0.9. The satellite-only MS product has a lesser, but still reasonably good, interannual correlation (∼0.6) while retaining a similar bias due to the use of a climatological bias adjustment. These results indicate the value of using even a few gauges in the analysis and provide an estimate of the correlation error to be expected in the SG analysis over ocean and remote land areas where gauges are absent. The daily GPCP precipitation estimates compare reasonably well at the 1° latitude × 2° longitude scale with the FMI gauge observations in the summer with a correlation of 0.55, but less so in the winter with a correlation of 0.45. Correlations increase somewhat when larger areas and multiday periods are analyzed. The day-to-day occurrence of precipitation is captured fairly well by the GPCP estimates, but the corresponding precipitation event amounts tend to show wide variability. The results of this study indicate that the GPCP monthly and daily fields are useful for meteorological and hydrological studies but that there is significant room for improvement of satellite retrievals and analysis techniques in this region. It is hoped that the research here provides a framework for future high-latitude assessment efforts such as those that will be necessary for the upcoming satellite-based Global Precipitation Measurement (GPM) mission.