bluuebunny/crossref_metadata_2025_split huggingface dataset:
A Comparison of Real World and Virtual World Interior Environments
Authors: Lindsey Patricia F. , McLain–Kark Joan 
Published: October 2008

Objective The objective of the study was to investigate whether observation of virtual reality simulation (virtual world) of interior environments provides the same information about characteristics of that environment as observation of the existing (real world) interior environment. Research Design The participants observed a real world test environment, a virtual simulation of the environment, and a virtual simulation with some altered components. A questionnaire was developed to compare observations. The questions consisted of comparative rating scales, closed–ended questions, open–ended questions, and a semantic differential scale. Real, virtual, and altered virtual worlds were compared for differences in visual accessibility, reach accessibility, and perception of ability to converse. Analysis Wilcoxon's Signed Ranks Test and tests were used to test the hypotheses. Additionally, frequencies, percentages, and mean scores were used to analyze the data. Key Findings Comparisons among a real world environment, a virtual world environment, and an altered virtual world environment suggest that visibility of objects and obstacles, the ability to reach objects and specified points, and the ability to share or communicate with other persons within the environments are consistent among the three worlds. Conclusion The findings of the study suggest that a virtual simulation can be a viable method for planning, creating, and testing environments before they are constructed or for creating recognizable simulations of existing environments, furnishings, and architectural components. Virtual simulation may be used to assess planned environments and changes to existing environments.
Computer Animation: A Tool for Teaching Design Fundamentals to Elementary School Students
Authors: Clemons Stephanie 
Published: October 2008

Issue Teaching design fundamentals to elementary school students can help create in them awareness about interior design. Elementary school teachers may not have the time, budget, or knowledge to add this subject to their curriculum, yet they are teaching basic computer skills. Therefore, this project explored using the computer to teach design fundamentals related to interior design. Goal Exploration of design fundamentals during the elementary grades may create an awareness of their importance in everyday life. This awareness of design could generate interest in the interior design profession. Application This project explored the use of computer technology, specifically animation, to teach design fundamentals to students in 3rd through 6th grades. Description A computer animation workshop was developed and offered to elementary students during the summer months at a higher education institution. Selected design elements and principles were taught through a series of 2–dimensional, 3–dimensional, and animation exercises. Conclusion Students are successful in learning both design fundamentals and computer animation. Computer animation techniques appeal to elementary students and encourage them to discover more about design.
Immunogenicity of Proteome-DeterminedMycobacterium aviumsubsp.paratuberculosis-Specific Proteins in Sheep with Paratuberculosis
Authors: Hughes Valerie , Bannantine John P. , Denham Susan , Smith Stuart , Garcia-Sanchez Alfredo , Sales Jill , Paustian Michael L. , Mclean Kevin , Stevenson Karen 
Published: October 2008

ABSTRACTMycobacterium aviumsubsp.paratuberculosiscauses paratuberculosis, a chronic granulomatous enteritis. Detecting animals with paratuberculosis infections is difficult because the currently available tools have low sensitivity and lack specificity; these tools are prone to generating spurious positive test results caused by exposure to environmentalM. aviumcomplex organisms. To generate candidate antigens for incorporation into a specific test for paratuberculosis, subspecies-specific proteins were determined by proteomic comparison ofM. aviumsubsp.paratuberculosisandM. aviumsubsp.avium. Analysis was aimed at revealing proteins only expressed (or predominant) in the protein profile ofM. aviumsubspeciesparatuberculosis. Two-dimensional gel electrophoresis resolved approximately 1,000 protein spots from each subspecies. Proteome analysis identified protein spots whose expression profile appeared markedly increased inM. aviumsubsp.paratuberculosis, and 32 were identified by analysis of their tryptic peptide profile by matrix-assisted laser desorption ionization-time of flight analysis. Thirty of these proteins were cloned, and their recombinant proteins were expressed. Ovine paratuberculosis sera were used to assess their immunoreactivity by enzyme-linked immunosorbent assay (ELISA), Western blotting, and dot blot analysis. Seventeen proteins were detected in at least one of the immunoassays, and eleven proteins were detected by ELISA with an optical density in excess of the cutoff of 0.1 in four of six sera tested. The immunoreactivity of these proteins indicates their potential as unique diagnostic antigens for the development of a specific serological detection of paratuberculosis.
Performance Characteristics of the Platelia
Aspergillus
Enzyme Immunoassay for Detection of
Aspergillus
Galactomannan Antigen in Bronchoalveolar Lavage Fluid
Authors: Husain S. , Clancy C. J. , Nguyen M. H. , Swartzentruber S. , Leather H. , LeMonte A. M. , Durkin M. M. , Knox K. S. , Hage C. A. , Bentsen C. , Singh N. , Wingard J. R. , Wheat L. J. 
Published: October 2008

ABSTRACT

We have evaluated the Platelia
Aspergillus
enzyme immunoassay for detection of galactomannan in bronchoalveolar lavage (BAL) specimens in solid organ transplant patients with aspergillosis. The precision and reproducibility in serum or BAL to which galactomannan was added were similar. Sensitivity was 81.8% in patients with aspergillosis, and specificity was 95.8% in lung transplant patients who underwent BAL for surveillance for infection or rejection. Among transplant controls, positive results were more common in patients (i) who underwent diagnostic BAL performed for evaluation of symptoms or chest computed tomographic abnormalities, (ii) who had undergone lung transplantation, or (iii) who were colonized with
Aspergillus
. Galactomannan testing in BAL is useful for diagnosis of aspergillosis in transplant patients. The significance of positive results in patients without confirmed aspergillosis requires further evaluation.
Evaluation of a Recombinant Hc of
Clostridium botulinum
Neurotoxin Serotype F as an Effective Subunit Vaccine
Authors: Yu Yun-Zhou , Li Na , Wang Rui-Lin , Zhu Heng-Qi , Wang Shuang , Yu Wei-Yuan , Sun Zhi-Wei 
Published: October 2008

ABSTRACT

A new gene encoding the Hc domain of
Clostridium botulinum
neurotoxin serotype F (FHc) was designed and completely synthesized with oligonucleotides. A soluble recombinant Hc of
C. botulinum
neurotoxin serotype F was highly expressed in
Escherichia coli
with this synthetic FHc gene. Subsequently, the purified FHc was used to vaccinate mice and evaluate their survival against challenge with active botulinum neurotoxin serotype F (BoNT/F). After the administration of FHc protein mixed with Freund adjuvant via the subcutaneous route, a strong protective immune response was elicited in the vaccinated mice. Mice that were given two or three vaccinations with a dosage of 1 or 10 μg of FHc were completely protected against an intraperitoneal administration of 20,000 50% lethal doses (LD
50
) of BoNT/F. The BoNT/F neutralization assay showed that the sera from these vaccinated mice contained high titers of protective antibodies. Furthermore, mice were vaccinated once, twice, or three times at four different dosages of FHc using Alhydrogel (Sigma) adjuvant via the intramuscular route and subsequently challenged with 20,000 LD
50
of neurotoxin serotype F. A dose response was observed in both the antibody titer and the protective efficacy with increasing dosage of FHc and number of vaccinations. Mice that received one injection of 5 μg or two injections of ≥0.04 μg of FHc were completely protected. These findings suggest that the recombinant FHc expressed in
E. coli
is efficacious in protecting mice against challenge with BoNT/F and that the recombinant FHc subunit vaccine may be useful in humans.
Comparison of Three Enzyme-Linked Immunosorbent Assays for Detection of Immunoglobulin G Antibodies to Tetanus Toxoid with Reference Standards and the Impact on Clinical Practice
Authors: van Hoeven Karen H. , Dale Connie , Foster Phil , Body Barbara 
Published: October 2008

ABSTRACT

Accurate determination of the concentrations of immunoglobulin G (IgG) antibody to tetanus toxoid is important in order to evaluate the immunogenicity of tetanus toxoid vaccines, determine immune competence in individual patients, and measure the prevalence of immunity in populations. The performance of three commercially available enzyme-linked immunosorbent assays (ELISAs) for IgG antibodies to tetanus toxoid were evaluated. Serially diluted NIBSC 76/589 and TE-3 human tetanus IgG immunoglobulin international reference standards were analyzed in quadruplicate using ELISAs manufactured by The Binding Site, Inc. (VaccZyme); Scimedx; and Euroimmun. In addition, IgG antibodies to tetanus toxoid were measured in 83 deidentified serum specimens using each manufacturer's ELISA. Each ELISA provided linear results when evaluated with the reference preparations. The Binding Site ELISA provided results that closely corresponded to the reference preparations (
y
= 1.09
x
− 0.08), whereas the Scimedx ELISA gave results that were consistently lower (
y
= 0.21
x
− 0.07) and the Euroimmun ELISA gave results that were consistently higher (
y
= 1.5
x
+ 0.30) than the reference preparation concentrations. Using the recommended cutoff for each ELISA (<0.10 IU/ml), the overall agreement of all of the ELISA methods was 78%. Three of eighty-three (3.6%) human serum samples demonstrated inadequate immunity with all three assays. The Binding Site ELISA yielded nonprotective antibody concentrations in only these 3 samples, whereas 19 samples (22.9%) according to the Scimedx ELISA and 6 samples (7.2%) according to the Euroimmun ELISA demonstrated nonprotective concentrations. The performance characteristics of ELISAs for tetanus immunoglobulin titers were manufacturer dependent, and the differences translated into important disparities in reported results.
Candidate Antigens for Q Fever Serodiagnosis Revealed by Immunoscreening of a
Coxiella burnetii
Protein Microarray
Authors: Beare Paul A. , Chen Chen , Bouman Timo , Pablo Jozelyn , Unal Berkay , Cockrell Diane C. , Brown Wendy C. , Barbian Kent D. , Porcella Stephen F. , Samuel James E. , Felgner Philip L. , Heinzen Robert A. 
Published: October 2008

ABSTRACT

Q fever is a widespread zoonosis caused by
Coxiella burnetii
. Diagnosis of Q fever is usually based on serological testing of patient serum. The diagnostic antigen of test kits is formalin-fixed phase I and phase II organisms of the Nine Mile reference strain. Deficiencies of this antigen include (i) potential for cross-reactivity with other pathogens; (ii) an inability to distinguish between
C. burnetii
strains; and (iii) a need to propagate and purify
C. burnetii
, a difficult and potentially hazardous process. Consequently, there is a need for sensitive and specific serodiagnostic tests utilizing defined antigens, such as recombinant
C. burnetii
protein(s). Here we describe the use of a
C. burnetii
protein microarray to comprehensively identify immunodominant antigens recognized by antibody in the context of human
C. burnetii
infection or vaccination. Transcriptionally active PCR products corresponding to 1,988
C. burnetii
open reading frames (ORFs) were generated. Full-length proteins were successfully synthesized from 75% of the ORFs by using an
Escherichia coli
-based in vitro transcription and translation system (IVTT). Nitrocellulose microarrays were spotted with crude IVTT lysates and probed with sera from acute Q fever patients and individuals vaccinated with Q-Vax. Immune sera strongly reacted with approximately 50
C. burnetii
proteins, including previously identified immunogens, an ankyrin repeat-domain containing protein, and multiple hypothetical proteins. Recombinant protein corresponding to selected array-reactive antigens was generated, and the immunoreactivity was confirmed by enzyme-linked immunosorbent assay. This sensitive and high-throughput method for identifying immunoreactive
C. burnetii
proteins will aid in the development of Q fever serodiagnostic tests based on recombinant antigen.
Reliability of Rapid Subtyping Tools Compared to That of Phylogenetic Analysis for Characterization of Human Immunodeficiency Virus Type 1 Non-B Subtypes and Recombinant Forms
Authors: Holguín África , López Marisa , Soriano Vincent 
Published: October 2008

ABSTRACT

Human immunodeficiency virus type 1 (HIV-1) subtyping is often estimated on the basis of
pol
sequences by using online websites instead of phylogenetic analysis (phy). We evaluated the reliability of distinct rapid subtyping tools versus phy with a large panel of HIV-1 non-B subtypes and circulating recombinant forms (CRF).
pol
sequences (277 protease [PR] and 171 reverse transcriptase [RT] sequences) previously assigned by phy to eight distinct HIV-1 non-B subtypes were obtained from 277 HIV-infected patients. Phy was run again to identify CRF. Subtyping was then performed using three rapid tools (the Stanford, NCBI, and REGA online tools). Thirty-three additional clade B sequences were tested as controls. New phylogenetic analyses reclassified two-thirds of
pol
sequences previously assigned to HIV-1 non-B clades as CRF. CRF02_AG variants were correctly assigned by the Stanford and NCBI tools for 92 to 97% and 96 to 99% of PR-RT sequences, respectively, while they were correctly assigned by the REGA tool for only 18 to 32% of PR-RT sequences. The Stanford, NCBI, and REGA tools failed to assign pure non-B clades correctly for 24 to 33%, 35%, and 57 to 64% of PR-RT sequences, respectively. For PR-RT sequences from CRF other than CRF02_AG, discrepancies occurred in 98 to 100%, 18 to 43%, and 80 to 87% of sequences, respectively. The concordance between those tools and phy was almost complete for subtype B assignment. Rapid subtyping tools show relatively low agreement with phy in identifying HIV-1 non-B clades and CRF other than CRF02_AG. The Stanford tool shows the best concordance with phy for the assignment of pure non-B clades, while the NCBI tool performs better at identifying CRF. Before entering routine clinical use, rapid subtyping tools should be optimized and updated periodically. Larger numbers of different non-B subtypes and CRF sequences should be included.
Detection of a Molecular Biomarker for Zygomycetes by Quantitative PCR Assays of Plasma, Bronchoalveolar Lavage, and Lung Tissue in a Rabbit Model of Experimental Pulmonary Zygomycosis
Authors: Kasai Miki , Harrington Susan M. , Francesconi Andrea , Petraitis Vidmantas , Petraitiene Ruta , Beveridge Mara G. , Knudsen Tena , Milanovich Jeffery , Cotton Margaret P. , Hughes Johanna , Schaufele Robert L. , Sein Tin , Bacher John , Murray Patrick R. , Kontoyiannis Dimitrios P. , Walsh Thomas J. 
Published: October 2008

ABSTRACT

We developed two real-time quantitative PCR (qPCR) assays, targeting the 28S rRNA gene, for the diagnosis of zygomycosis caused by the most common, clinically significant Zygomycetes. The amplicons of the first qPCR assay (qPCR-1) from
Rhizopus, Mucor
, and
Rhizomucor
species were distinguished through melt curve analysis. The second qPCR assay (qPCR-2) detected
Cunninghamella
species using a different primer/probe set. For both assays, the analytic sensitivity for the detection of hyphal elements from germinating sporangiospores in bronchoalveolar lavage (BAL) fluid and lung tissue homogenates from rabbits was 1 to 10 sporangiospores/ml. Four unique and clinically applicable models of invasive pulmonary zygomycosis served as surrogates of human infections, facilitating the validation of these assays for potential diagnostic utility. For qPCR-1, 5 of 98 infarcted lung specimens were positive by qPCR and negative by quantitative culture (qCx). None were qCx positive only. Among 23 BAL fluid samples, all were positive by qPCR, while 22 were positive by qCx. qPCR-1 detected
Rhizopus
and
Mucor
DNA in 20 (39%) of 51 serial plasma samples as early as day 1 postinoculation. Similar properties were observed for qPCR-2, which showed greater sensitivity than qCx for BAL fluid (100% versus 67%;
P
= 0.04;
n
= 15). The assay detected
Cunninghamella
DNA in 18 (58%) of 31 serial plasma samples as early as day 1 postinoculation. These qPCR assays are sensitive and specific for the detection of
Rhizopus, Mucor, Rhizomucor
, and
Cunninghamella
species and can be used for the study and detection of infections caused by these life-threatening pathogens.
High Genetic Diversity of Nontypeable
Haemophilus influenzae
Isolates from Two Children Attending a Day Care Center
Authors: LaCross Nathan C. , Marrs Carl F. , Patel Mayuri , Sandstedt Sara A. , Gilsdorf Janet R. 
Published: October 2008

ABSTRACT

Twenty-one nontypeable
Haemophilus influenzae
(NTHi) isolates from the throats of two healthy children were genotyped by multilocus sequence typing. Nine unique sequence types (STs) were identified. These STs were scattered throughout the phylogenetic tree of reported NTHi STs, demonstrating the high level of NTHi diversity found in colonized children.
Three-Class-Resistant Human Immunodeficiency Virus Type 1 Variant in a Drug-Naive Heterosexual Couple
Authors: Razzolini Francesca , Saladini Francesco , Malincarne Lisa , Vicenti Ilaria , Palladino Nicola , Romano Laura , Francisci Daniela , Zazzi Maurizio 
Published: October 2008

ABSTRACT
Combination antiretroviral treatment was initiated in a heterosexual couple newly diagnosed with human immunodeficiency virus type 1 infection. Multiple genotypic drug resistance testing following early rebound of viral load revealed that the same three-class-resistant human immunodeficiency virus type 1 strain had been present in both patients since before initiation of treatment.
Self-Assembly of the Recombinant Capsid Protein of a Swine Norovirus into Virus-Like Particles and Evaluation of Monoclonal Antibodies Cross-Reactive with a Human Strain from Genogroup II
Authors: Almanza Horacio , Cubillos Carolina , Angulo Iván , Mateos Francisco , Castón José R. , van der Poel Wim H. M. , Vinje Jan , Bárcena Juan , Mena Ignacio 
Published: October 2008

ABSTRACT
Noroviruses (NoVs) are responsible for the majority of gastroenteritis outbreaks in humans. Recently, NoV strains which are genetically closely related to human genogroup II (GII) NoVs have been detected in fecal specimens from swine. These findings have raised concern about the possible role of pigs as reservoirs for NoVs that could infect humans. To better understand the epidemiology of swine NoVs in both the swine and the human populations, rapid immunoassays are needed. In this study, baculovirus recombinants were generated to express the capsid gene of a swine NoV GII genotype 11 (GII.11) strain which self-assembled into virus-like particles (VLPs). Subsequently, the purified VLPs were used to evoke monoclonal antibodies (MAbs) in mice. A panel of eight promising MAbs was obtained and evaluated for their ability to bind to heterologous VLPs, denaturated antigens, and truncated capsid proteins. The MAbs could be classified into two groups: two MAbs that recognized linear epitopes located at the amino-terminal half (shell domain) of the swine NoV GII.11 VLPs and that cross-reacted with human GII.4 NoV VLPs. The other six MAbs bound to conformational epitopes and did not cross-react with the human GII.4 VLPs. To our knowledge, this is the first report on the characterization of MAbs against swine NoVs. The swine NoV VLPs and the MAbs described here may be further used for the design of diagnostic reagents that could help increase our knowledge of the prevalence of NoV infections in pigs and the possible role of pigs as reservoirs for NoVs.
Cross-Sectional Study of Nasopharyngeal Carriage of
Streptococcus pneumoniae
in Human Immunodeficiency Virus-Infected Adults in the Conjugate Vaccine Era
Authors: Onwubiko Chinwendu , Swiatlo Edwin , McDaniel Larry S. 
Published: October 2008

ABSTRACT

Human immunodeficiency virus (HIV)-infected patients have an increased rate of pneumococcal infections. Within the HIV-infected population, patients with low CD4
+
cell counts have a higher rate of pneumococcal infection. The purpose of our study was to determine pneumococcal carriage and to examine the serotypes carried by HIV-infected patients after the introduction of the conjugate vaccine. Nasopharyngeal swabs were obtained from patients during routine clinic visits. Samples were cultured on blood agar plates with gentamicin and screened for alpha-hemolysis, optochin sensitivity, and bile solubility. Capsular serotypes were determined by multiplex PCR, multibead assay, or latex agglutination. Antibiotic susceptibility was determined by the Etest method. Multilocus sequence typing was also performed. Of the 175 patients enrolled, 120 patients had absolute CD4
+
cell counts above 200/mm
3
and 55 had counts below 200/mm
3
. A total of six (3.4%) patients carried pneumococci. All but one of these patients had received the 23-valent pneumococcal vaccine within the previous 5 years. Five of the isolates were serotypes that are not included in the 7-valent conjugate vaccine. Immunization with the pneumococcal polysaccharide vaccine does not prevent colonization in HIV-infected patients; however, the observation of carriage of serotypes not included in the conjugate vaccine may be due to herd immunity and serotype replacement effects in the general population.
Emergence of Amantadine-Resistant H3N2 Avian Influenza A Virus in South Korea
Authors: Lee Jiyeon , Song Young Jun , Park Jeung Hyun , Lee Jun-Han , Baek Yun Hee , Song Min-Suk , Oh Taek-Kyu , Han Heon-Seok , Pascua Philippe Noriel Q. , Choi Young-Ki 
Published: October 2008

ABSTRACTWe found a relatively high frequency of unique amantadine-resistant H3N2 and H9N2 avian influenza viruses (Val27Ile on M2 protein) isolated from live poultry markets in South Korea and confirmed that a Val27Ile single substitution in the M2 protein is enough to acquire the amantadine resistance phenotype by using reverse-genetically created human-avian reassortant viruses.