bluuebunny/crossref_metadata_2025_split huggingface dataset:
Comparison of Enzyme-Linked Immunosorbent Assay, Western Blotting, Microagglutination, Indirect Immunofluorescence Assay, and Flow Cytometry for Serological Diagnosis of Tularemia
Authors: Porsch-Özcürümez Mustafa , Kischel Nele , Priebe Heidi , Splettstösser Wolf , Finke Ernst-Jürgen , Grunow Roland 
Published: November 2004

ABSTRACT

The serodiagnostic efficiencies of five different approaches to detecting antibodies (immunoglobulins G, A, and M) developed in clinically proven infections with
Francisella tularensis
have been assessed. Fifty serum samples from patients suffering from tularemia during an outbreak in Sweden were compared with samples from 50 healthy blood donors (controls) by using an enzyme-linked immunosorbent assay (ELISA), microagglutination (MA), Western blotting (WB), an indirect immunofluorescence assay (IIFA), and flow cytometry (FC). ELISA, WB, and FC were based on the use of preparations of lipopolysaccharides (LPS) of the live vaccine strain of
Francisella tularensis
subsp.
holarctica
(ATCC 29684) as a capture antigen. Whole methanol-fixed bacteria were used for IIFA and MA. Optimized protocols yielded a diagnostic sensitivity and specificity of 100% for WB, MA, and FC, 98% for ELISA, and 93% for IIFA. A total of 6,632 serum samples from individuals between the ages of 18 and 79 years, representatively recruited from all regions of Germany, were screened to estimate and confirm the positive predictive value (PVpos) of the ELISA. Serum samples from 15 (0.226%) individuals tested positive for
F. tularensis
-specific antibodies by ELISA and confirmatory WB. The resulting prevalence-dependent PVpos of 10.2% and specificity of 98.1% were consistent with our findings for tularemia patients and controls. We conclude that the combined usage of a screening ELISA and a confirmatory WB based on LPS as a common antigen, as well as the MA, is a suitable serodiagnostic tool, while the quality of the IIFA is hampered by subjective variations of the results. FC is a promising new approach that might be improved further in terms of multiplex analyses or high-throughput applications.
Establishment of Diagnostic Cutoff Points for Levels of Serum Antibodies to Pertussis Toxin, Filamentous Hemagglutinin, and Fimbriae in Adolescents and Adults in the United States
Authors: Baughman Andrew L. , Bisgard Kristine M. , Edwards Kathryn M. , Guris Dalya , Decker Michael D. , Holland Kathy , Meade Bruce D. , Lynn Freyja 
Published: November 2004

ABSTRACT

Numerous reports have documented that serologic methods are much more sensitive than culture for the diagnosis of pertussis in adolescents and adults. However, a standardized serologic test for pertussis is not routinely available to most clinicians, and the serologic test levels or cutoff points correlated with diseases have not been determined. The goal of the present study was to examine the distribution of immunoglobulin G (IgG) levels against three
Bordetella pertussis
antigens (pertussis toxin [PT], filamentous hemagglutinin [FHA], and fimbria types 2 and 3 [FIM]) and to determine population-based antibody levels for the purpose of establishing such diagnostic cutoff points. Enzyme-linked immunosorbent assays (ELISAs) were performed with sera from >6,000 U.S. residents aged 6 to 49 years who participated in the Third National Health and Nutrition Examination Survey. Mixture models were developed to identify hypothesized exposure groups and establish diagnostic cutoffs. Quantifiable (>20 ELISA units/ml [EU]) anti-FHA and anti-FIM IgG antibodies were common (65 and 62% of individuals, respectively), but quantifiable anti-PT IgG antibodies were less frequent (16%). Given the distributions of antibody levels, an anti-PT IgG level of ≥94 EU was proposed as the diagnostic cutoff point. Application of this cutoff point to culture-confirmed illness in a prior study investigating cough illness yielded a high diagnostic sensitivity (80%) and specificity (93%). A standardized ELISA for anti-PT IgG with a single serum sample appears to be useful for the identification of recent
B. pertussis
infection in adolescents and adults with cough illness. The PT cutoff point will be further evaluated in prospective studies of confirmed
B. pertussis
infection.
Monoclonal Antibodies for Specific Detection of
Encephalitozoon cuniculi
Authors: Mo Lan , Drancourt Michel 
Published: November 2004

ABSTRACT

Seven species-specific monoclonal antibodies (MAbs) were produced against
Encephalitozoon cuniculi
and characterized. The MAbs were immunoglobulin G, and when used for indirect microimmunofluorescence microscopy and Western immunoblot assays, they detected
E. cuniculi
originating from clinical samples. They did not cross-react with other
Encephalitozoon
species (
E. intestinalis
and
E. hellem
) or with a collection of gram-negative bacteria, yeast, and other parasites. The MAbs reacted primarily with 121-, 56-, 45-, 43-, and 41-kDa protein epitopes of
E. cuniculi.
These epitopes were demonstrated to be
E. cuniculi
species specific by sodium dodecyl sulfate-polyacrylamide gel electrophoresis. We developed MAbs to strains of
E. cuniculi
that can be used successfully to distinguish
E. cuniculi
from other microsporidial species in cultures established from clinical specimens. These MAbs may provide a specific, simple, rapid, and low-cost tool for the identification and diagnosis of infections due to microsporidia.
Association of CD4+CD25+T Cells with Prevention of Severe Destructive Arthritis inBorrelia burgdorferi-Vaccinated and Challenged Gamma Interferon-Deficient Mice Treated with Anti-Interleukin-17 Antibody
Authors: Nardelli Dean T. , Burchill Matthew A. , England Douglas M. , Torrealba Jose , Callister Steven M. , Schell Ronald F. 
Published: November 2004

ABSTRACTCD4+CD25+T cells are a population of regulatory T cells responsible for active suppression of autoimmunity. Specifically, CD4+CD25+T cells have been shown to prevent insulin-dependent diabetes mellitus, inflammatory bowel disease, and pancreatitis. Here, we present evidence that CD4+CD25+T cells also play a major role in controlling the severity of arthritis detected inBorrelia burgdorferi-vaccinated gamma interferon-deficient (IFN-γ°) C57BL/6 mice challenged with the Lyme spirochete. WhenB. burgdorferi-vaccinated and challenged IFN-γ° mice were treated with anti-interleukin-17 (IL-17) antibody, the number of CD4+CD25+T cells increased in the local lymph nodes. Furthermore, histopathologic examination showed the mice to be free of destructive arthritis. When these anti-IL-17-treatedB. burgdorferi-vaccinated and challenged mice were also administered anti-CD25 antibody, the number of CD4+CD25+T cells in the local lymph nodes decreased. More importantly, severe destructive arthropathy was induced. In addition, delayed administration of anti-CD25 antibody decreased the severity of the arthritis. These results suggest that CD4+CD25+T cells are involved in regulation of a severe destructive arthritis induced with an experimental model of vaccination and challenge withB. burgdorferi.
RecombinantHelicobacter bilisProtein P167 for Mouse Serodiagnosis in a Multiplex Microbead Assay
Authors: Feng Sunlian , Kendall Lon V. , Hodzic Emir , Wong Scott , Lorenzana Edward , Freet Kimberly , Ku Karin S. , Luciw Paul A. , Barthold Stephen W. , Khan Imran H. 
Published: November 2004

ABSTRACTInfection of mice withHelicobacter bilisis widespread in research and commercial mouse colonies. Therefore, sensitive, specific, and high-throughput assays are needed for rapid and accurate testing of mice in large numbers. This report describes a novel multiplex assay, based on fluorescent microbeads, for serodetection ofH. bilisinfection. The assay requires only a few microliters of serum to perform and is amenable to a high-throughput format. Individual microbead sets were conjugated to purified,H. bilis-specific, recombinant proteins P167C and P167D and bacterial membrane extracts fromH. bilisandHelicobacter hepaticus. For detectingH. bilisinfection in the microbead multiplex assay, P167C and P167D provided significantly higher sensitivities (94 and 100%, respectively) and specificities (100 and 95%, respectively) than membrane extract (78% sensitivity and 65% specificity). Microbead multiplex assay results were validated by enzyme-linked immunosorbent assay. Purified recombinant proteins showed low batch-to-batch variation; this feature allows for ease of quality control, assay robustness, and affordability. Thus, recombinant antigens are highly suitable in the multiplex microbead assay format for serodetection ofH. bilisinfection.
Regulation of Fungal Infection by a Combination of Amphotericin B and Peptide 2, a Lactoferrin Peptide That Activates Neutrophils
Authors: Okamoto Tetsuro , Tanida Toyohiro , Wei Benjuan , Ueta Eisaku , Yamamoto Tetsuya , Osaki Tokio 
Published: November 2004

ABSTRACTTo establish a novel strategy for the control of fungal infection, we examined the antifungal and neutrophil-activating activities of antimicrobial peptides. The duration of survival of 50% of mice injected with a lethal dose ofCandida albicans(5 × 108cells) orAspergillus fumigatus(1 × 108cells) was prolonged 3 to 5 days by the injection of 10 μg of peptide 2 (a lactoferrin peptide) and 10 μg of α-defensin 1 for five consecutive days and was prolonged 5 to 13 days by the injection of 0.1 μg of granulocyte-monocyte colony-stimulating factor (GM-CSF) and 0.5 μg of amphotericin B. When mice received a combined injection of peptide 2 (10 μg/day) with amphotericin B (0.5 μg/day) for 5 days after the lethal fungal inoculation, their survival was greatly prolonged and some mice continued to live for more than 5 weeks, although the effective doses of peptide 2 for 50 and 100% suppression ofCandidaorAspergilluscolony formation were about one-third and one-half those of amphotericin B, respectively. In vitro, peptide 2 as well as GM-CSF increased theCandidaandAspergilluskilling activities of neutrophils, but peptides such as α-defensin 1, β-defensin 2, and histatin 5 did not upregulate the killing activity. GM-CSF together with peptide 2 but not other peptides enhanced the production of superoxide (O2−) by neutrophils. The upregulation by peptide 2 was confirmed by the activation of the O2−-generating pathway, i.e., activation of large-molecule guanine binding protein, phosphatidyl-inositol 3-kinase, protein kinase C, and p47phoxas well as p67phox. In conclusion, different from natural antimicrobial peptides, peptide 2 has a potent neutrophil-activating effect which could be advantageous for its clinical use in combination with antifungal drugs.
Specific Immunoglobulin G Antibody Detected in Umbilical Blood and Amniotic Fluid from a Pregnant Woman Infected by the Coronavirus Associated with Severe Acute Respiratory Syndrome
Authors: Jiang Xiugao , Gao Xing , Zheng Han , Yan Meiying , Liang Weili , Shao Zhujun , Li Wei , Zhang Enmin , Hu Yuan , Hai Rong , Yu Dongzheng , Kan Biao , Xu Jianguo 
Published: November 2004

ABSTRACTSpecific immunoglobulin G antibody for severe acute respiratory syndrome (SARS) coronavirus was detected in maternal blood, umbilical blood, and amniotic fluid from a pregnant SARS patient. Potential protection of fetus from infection was suggested.
Biased Immunoglobulin G (IgG) Subclass Production in a Case of Hyper-IgM Syndrome
Authors: McLean G. R. , Miller K. K. , Schrader J. W. , Junker A. K. 
Published: November 2004

ABSTRACT
Hyper-immunoglobulin M (IgM) syndrome (HIGM) is a rare heterogeneous primary immune deficiency. We describe a patient with HIGM characterized by skewed production of serum IgG subclasses and normal somatic hypermutation. This case may represent a subgroup of HIGM type 4 that is characterized by a biased switching to the V-region proximal constant regions.
A Decision Support Framework for Sustainable Waste Management
Authors: Kijak Robert , Moy David 
Published: November 2004

SummaryThis article describes a decision support framework for the evaluation of scenarios for the integrated management of municipal solid waste within a local government area (LGA).The work is initially focused on local government (i.e., municipal councils) in the state of Queensland, Australia; however, it is broadly applicable to LGAs anywhere. The goal is to achieve sustainable waste management practices by balancing global and regional environmental impacts, social impacts at the local community level, and economic impacts. The framework integrates life‐cycle assessment (LCA) with other environmental, social, and economic tools. For this study, social and economic impacts are assumed to be similar across developed countries of the world. LCA was streamlined at both the life‐cycle inventory and life‐cycle impact assessment stages.For this process, spatial resolution is introduced into the LCA process to account for impacts occurring at the local and regional levels. This has been done by considering social impacts on the local community and by use of a regional procedure for LCA data for emissions to the environment that may have impacts at the regional level.The integration follows the structured approach of the pressure‐state‐response (PSR) model suggested by the Organisation for Economic Cooperation and Development (OECD). This PSR model has been extended to encompass nonenvironmental issues and to guide the process of applying multiple tools.The framework primarily focuses on decision analysis and interpretation processes. Multiattribute utility theory (MAUT) is used to assist with the integration of qualitative and quantitative information. MAUT provides a well‐structured approach to information assessment and facilitates objective, transparent decisions. A commercially available decision analysis software package based on MAUT has been used as the platform for the framework developed in this study.
Long‐term Coordination of Timber Production and Consumption Using a Dynamic Material and Energy Flow Analysis
Authors: Müller Daniel B. , Bader Hans‐Peter , Baccini Peter 
Published: November 2004

SummaryA dynamic model for wood and energy flows is used to analyze regional timber management. The model combines a sitequality‐dependent forest‐growth module with modules for the timber industry, timber products use, waste management, and energy supply. The model is calibrated with data of a Swiss lowland region for the period of 1900–1997. Scenarios are developed for the period until 2100 in order to discuss possible future roles of domestic timber.Model simulations show that, with present strategies, timber overproduction will further increase in the twenty‐first century because of an increase in forest site quality in the second half of the twentieth century, among other reasons. The increase in building gross floor area of the region by a factor of 5 during the twentieth century coincides with a reduction of timber use in building construction by a factor of 4.5, from 90 kg/m2 to 20 kg/m2. Increasing timber density in buildings could address overproduction; however, a strategy of timber construction could not be accomplished with domestic timber alone. A balance of production and consumption on the present level could also be achieved in a scenario in which the present building stock is gradually exchanged during the twenty‐first century with buildings that exclusively use a combination of solar panels on roofs and domestic firewood and used wood as heat‐energy sources. These replacement buildings would have density typical of late twentieth‐century buildings, and they would need to perform on a low‐energy standard of not more than 130 MJ/m2/yr.
Three Strategies to Overcome the Limitations of Life‐Cycle Assessment
Authors: de Haes Helias A. Udo , Heijungs Reinout , Suh Sangwon , Huppes Gjalt 
Published: November 2004

SummaryMany research efforts aim at an extension of life‐cycle assessment (LCA) in order to increase its spatial or temporal detail or to enlarge its scope. This is an important contribution to industrial ecology as a scientific discipline, but from the application viewpoint other options are available to obtain more detailed information, or to obtain information over a broader range of impacts in a life‐cycle perspective. This article discusses three different strategies to reach these aims: (1) extension of LCA—one consistent model; (2) use of a toolbox—separate models used in combination; and (3) hybrid analysis—combination of models with data flows between them.Extension of LCA offers the most consistent solution. Developments in LCA are moving toward greater spatial detail and temporal resolution and the inclusion of social issues. Creating a supertool with too many data and resource requirements is, however, a risk. Moreover, a number of social issues are not easily modeled in relation to a functional unit.The development of a toolbox offers the most flexibility regarding spatial and temporal information and regarding the inclusion of other types of impacts. The rigid structure of LCA no longer sets limits; every aspect can be dealt with according to the logic of the relevant tool. The results lack consistency, however, preventing further formal integration.The third strategy, hybrid analysis, takes up an intermediate position between the other two. This strategy is more flexible than extension of LCA and more consistent than a toolbox. Hybrid analysis thus has the potential to combine the strong points of the other two strategies. It offers an interesting path for further discovery, broader than the already well‐known combination of process‐LCA and input‐output‐LCA. We present a number of examples of hybrid analysis to illustrate the potentials of this strategy.Developments in the field of a toolbox or of hybrid analysis may become fully consistent with LCA, and then in fact become part of the first solution, extension of LCA.
PhyME: A probabilistic algorithm for finding motifs in sets of orthologous sequences
Authors: Sinha Saurabh , Blanchette Mathieu , Tompa Martin 
Published: November 2004

Abstract
Background
This paper addresses the problem of discovering transcription factor binding sites in heterogeneous sequence data, which includes regulatory sequences of one or more genes, as well as their orthologs in other species.

Results
We propose an algorithm that integrates two important aspects of a motif's significance – overrepresentation and cross-species conservation – into one probabilistic score. The algorithm allows the input orthologous sequences to be related by any user-specified phylogenetic tree. It is based on the Expectation-Maximization technique, and scales well with the number of species and the length of input sequences. We evaluate the algorithm on synthetic data, and also present results for data sets from yeast, fly, and human.

Conclusions
The results demonstrate that the new approach improves motif discovery by exploiting multiple species information.
Adaptive evolution of transcription factor binding sites
Authors: Berg Johannes , Willmann Stana , Lässig Michael 
Published: November 2004

Abstract
Background
The regulation of a gene depends on the binding of transcription factors to specific sites located in the regulatory region of the gene. The generation of these binding sites and of cooperativity between them are essential building blocks in the evolution of complex regulatory networks. We study a theoretical model for the sequence evolution of binding sites by point mutations. The approach is based on biophysical models for the binding of transcription factors to DNA. Hence we derive empirically grounded fitness landscapes, which enter a population genetics model including mutations, genetic drift, and selection.

Results
We show that the selection for factor binding generically leads to specific correlations between nucleotide frequencies at different positions of a binding site. We demonstrate the possibility of rapid adaptive evolution generating a new binding site for a given transcription factor by point mutations. The evolutionary time required is estimated in terms of the neutral (background) mutation rate, the selection coefficient, and the effective population size.

Conclusions
The efficiency of binding site formation is seen to depend on two joint conditions: the binding site motif must be short enough and the promoter region must be long enough. These constraints on promoter architecture are indeed seen in eukaryotic systems. Furthermore, we analyse the adaptive evolution of genetic switches and of signal integration through binding cooperativity between different sites. Experimental tests of this picture involving the statistics of polymorphisms and phylogenies of sites are discussed.
Genomic structure and cloning of two transcript isoforms of human Sp8
Authors: Milona Maria-athina , Gough Julie E , Edgar Alasdair J 
Published: November 2004

Abstract
Background
The Specificity proteins (Sp) are a family of transcription factors that have three highly conserved zinc-fingers located towards the carboxy-terminal that bind GC-boxes and assist in the initiation of gene transcription. Human Sp1-7 genes have been characterized. Recently, the phenotype of Sp8 null mice has been described, being tailless and having severe truncation of both fore and hind limbs. They also have malformed brains with defective closure of the anterior and posterior neuropore during brain development.

Results
The human Sp8 gene is a three-exon gene that maps to 7p21.3, close to the related Sp4 gene. From an osteosarcoma cell line we cloned two transcript variants that use two different first exons and have a common second exon. One clone encodes a 508-residue protein, Sp8L (isoform 1) and the other a shorter 490-residue protein, Sp8S (isoform 2). These two isoforms are conserved being found also in mice and zebrafish. Analysis of the Sp8L protein sequence reveals an amino-terminal hydrophobic Sp-motif that is disrupted in Sp8S, a buttonhead box and three C2H2 zinc-fingers. Sp8 mRNA expression was detected in a wide range of tissues at a low level, with the highest levels being found in brain. Treatment of the murine pluripotent cell line C3H10T1/2 with 100 ng/mL BMP-2 induced Sp8 mRNA after 24 hours.

Conclusions
There is conservation of the two Sp8 protein isoforms between primates, rodents and fish, suggesting that the isoforms have differing roles in gene regulation. Sp8 may play a role in chondrogenic/osteoblastic differentiation in addition to its role in brain and limb development.