bluuebunny/crossref_metadata_2025_split huggingface dataset:
Human Leukocyte Antigen-DQ8 Transgenic Mice: a Model To Examine the Toxicity of Aerosolized Staphylococcal Enterotoxin B
Authors: Roy Chad J. , Warfield Kelly L. , Welcher Brent C. , Gonzales Raoul F. , Larsen Tom , Hanson Julie , David Chella S. , Krakauer Theresa , Bavari Sina 
Published: March 2005

ABSTRACTStaphylococcal enterotoxins (SEs) belong to a large group of bacterial exotoxins that cause severe immunopathologies, especially when delivered as an aerosol. SEs elicit the release of lethal amounts of cytokines by binding to major histocompatibility complex (MHC) class II and cross-linking susceptible T-cell receptors. Efforts to develop effective therapeutic strategies to protect against SEs delivered as an aerosol have been hampered by the lack of small animal models that consistently emulate human responses to these toxins. Here, we report that human leukocyte antigen-DQ8 (HLA-DQ8) transgenic (Tg) mice, but not littermate controls, succumbed to lethal shock induced by SEB aerosols without potentiation. Substantial amounts of perivascular edema and inflammatory infiltrates were noted in the lungs of Tg mice, similar to the pathology observed in nonhuman primates exposed by aerosol to SEB. Furthermore, the observed pathologies and lethal shock correlated with an upsurge in proinflammatory cytokine mRNA gene expression in the lungs and spleens, as well as with marked increases in the levels of proinflammatory circulating cytokines in the Tg mice. Unlike the case for littermate controls, telemetric evaluation showed significant hypothermia in Tg mice exposed to lethal doses of SEB. Taken together, these results show that this murine model will allow for the examination of therapeutics and vaccines developed specifically against SEB aerosol exposure and possibly other bacterial superantigens in the context of human MHC class II receptors.
Q Fever Pneumonia: Virulence of
Coxiella burnetii
Pathovars in a Murine Model of Aerosol Infection
Authors: Stein Andreas , Louveau Céline , Lepidi Hubert , Ricci Fanny , Baylac Pascal , Davoust Bernard , Raoult Didier 
Published: March 2005

ABSTRACT

Q fever is a worldwide zoonosis caused by
Coxiella burnetii
, a strictly intracellular bacterium that is a potential bioweapon. Humans usually acquires Q fever after inhalation of dust infected by subclinical animals. We used an aerosol exposure apparatus to challenge immunocompetent (BALB/c) and severe combined immunodeficient (SCID) mice with two different strains (strain Nine Mile and strain Q 212) of
C. burnetii
at two different inocula. Pathological lesions and dissemination of the bacteria were related to the size of the inoculum. SCID mice showed major pulmonary lesions, whereas similarly infected BALB/c mice were more able to eliminate the bacteria. Pathological differences were found between the strains, with Nine Mile showing more severe histological lesions and quantified spread of bacteria. Our animal model could provide a new tool for the study of acute Q fever pneumonia, the development of Q fever in immunodeficient hosts, and the differentiation of pathogenicity among
C. burnetii
isolates.
Heterologous Immunity in the Absence of Variant-Specific Antibodies after Exposure to Subpatent Infection with Blood-Stage Malaria
Authors: Elliott Salenna R. , Kuns Rachel D. , Good Michael F. 
Published: March 2005

ABSTRACTWe examined immunity induced by subpatent blood-stage malaria (undetectable by microscopy) using the rodent malaria parasite,Plasmodium chabaudi chabaudi, postulating that limited infection may allow expansion of antigen-specific T cells that are normally deleted by apoptosis. After three infections drug cured at 48 h, mice were protected against high-dose challenge with homologous or heterologous parasites (different strain or variant). Immunity differed from that generated by three untreated, patent infections. Subpatently infected mice lacked immunoglobulin G (IgG) to variant surface antigens, despite producing similar titers of total malaria-specific IgG to those produced by patently infected mice, including antibodies specific for merozoite surface antigens conserved between heterologous strains. Antigen-specific proliferation of splenocytes harvested prechallenge was significantly higher in subpatently infected mice than in patently infected or naive mice. In subpatently infected mice, lymphoproliferation was similar in response to homologous and heterologous parasites, suggesting that antigenic targets of cell-mediated immunity were conserved. A Th1 cytokine response was evident during challenge. Apoptosis of CD4+and CD8+splenic lymphocytes occurred during patent but not subpatent infection, suggesting a reason for the relative prominence of cell-mediated immunity after subpatent infection. In conclusion, subpatent infection with blood stage malaria parasites induced protective immunity, which differed from that induced by patent infection and targeted conserved antigens. These findings suggest that alternative vaccine strategies based on delivery of multiple parasite antigens at low dose may induce effective immunity targeting conserved determinants.
Potential Role of the Chemokine Macrophage Inflammatory Protein 1α in Human and Experimental Schistosomiasis
Authors: Souza Adriano L. S. , Roffê Ester , Pinho Vanessa , Souza Danielle G. , Silva Adriana F. , Russo Remo C. , Guabiraba Rodrigo , Pereira Cíntia A. J. , Carvalho Flávia M. , Barsante Michele M. , Correa-Oliveira Rodrigo , Fraga Lúcia A. O. , Negrão-Correa Deborah , Teixeira Mauro M. 
Published: March 2005

ABSTRACTIn human schistosomiasis, the concentrations of the chemokine macrophage inflammatory protein 1α (MIP-1α/CCL3) is greater in the plasma of patients with clinical hepatosplenic disease. The objective of the present study was to confirm the ability of CCL3 to detect severe disease in patients classified by ultrasonography (US) and to evaluate the potential role of CCL3 inSchistosoma mansoni-infected mice. CCL3 was measured by enzyme-linked immunosorbent assay in the plasma ofS. mansoni-infected patients. CCL3-deficient mice were infected with 25 cercariae, and various inflammatory and infectious indices were evaluated. The concentration of CCL3 was higher in the plasma ofS. mansoni-infected than noninfected patients. Moreover, CCL3 was greater in those with US-defined hepatosplenic than with the intestinal form of the disease. In CCL3-deficient mice, the size of the granuloma and the liver eosinophil peroxidase activity and collagen content were diminished compared to wild-type mice. In CCL3-deficient mice, the worm burden after 14 weeks of infection, but not after 9 weeks, was consistently smaller. The in vitro response of mesenteric lymph node cells to antigen stimulation was characterized by lower levels of interleukin-4 (IL-4) and IL-10. CCL3 is a marker of disease severity in infected humans, and experimental studies in mice suggest that CCL3 may be a causative factor in the development of severe schistosomiasis.
Antibody against the Carboxyl Terminus of Intimin α Reduces Enteropathogenic
Escherichia coli
Adherence to Tissue Culture Cells and Subsequent Induction of Actin Polymerization
Authors: Carvalho Humberto M. , Teel Louise D. , Kokai-Kun John F. , O'Brien Alison D. 
Published: March 2005

ABSTRACT

The C-terminal third of intimin binds to its translocated receptor (Tir) to promote attaching and effacing lesion formation during infection with enteropathogenic
Escherichia coli
(EPEC). We observed that the adherence of EPEC strains to HEp-2 cells was reduced and that actin polymerization was blocked by antibody raised against the C-terminal third of intimin α.
Linkage of the Horizontally AcquiredypmandpilGenes inYersinia pseudotuberculosis
Authors: Collyn François , Fukushima Hiroshi , Carnoy Christophe , Simonet Michel , Vincent Pascal 
Published: March 2005

ABSTRACTThe superantigen-encodingypmgene and thepilgene cluster governing type IV pilus biogenesis have been laterally acquired byYersinia pseudotuberculosis.PCR assays on 270 unrelated strains from various environmental and animal sources revealed a significant association ofypmandpilin isolates.
Restaurants, Inns and Taverns That Never Were: Some Reflections on Public Consumption in Medieval Cairo
Authors: Lewicka Paulina 
Published: March 2005

AbstractThe article shows that, contrary to a commonly accepted assumption, no public consumption facilities such as restaurants, taverns or inns existed in medieval Cairo. This was caused on the one hand by the Egyptians' faithfulness to their own ancient practices and their indifference to pre-Islamic influences of foreign origin, and on the other by the Cairenes' compliance with the ordinances of the legal sources of Islam. These two factors led to the results described in the article because they complemented each other, as Islam was rooted in the same ancient social and cultural tradition as Egypt. Dans cet article on a avancé une thèse que – malgré une opinion bien etendue – les établissements alimentaires, tels que les restaurants, les tavernes et les auberges, n'existaient pas au Caire médiéval. Les causes de cette situation on peut expliquer, d'une part, par l'attachement des Égyptiens à leur cultures indigènes et leur indifférence aux traditions culturelles étrangères, alimentaires inclues, provenant d'une époque preislamique; d'autre part, par le fait que le comportement des Cairots était très strictement lié aux ordonnances de la religion islamique, enracinées dans la même tradition sociale et religieuse que les traditions égyptiennes. Or, on peut conclure que les évènements décrits dans cet article pouvaient avoir lieu puisque la tradition musulmane concernante les questions presentées ici était très strictement liée à la culture indigène.
Jesus as Merkabah Mystic
Authors: Quarles Charles 
Published: March 2005

AbstractThis article examines and critiques the portrayal of Jesus as a merkabah mystic in Bruce Chilton’s Rabbi Jesus. After providing a brief summary of Chilton’s presentation of Jesus’ spirituality, the article explores the origin of merkabah mysticism and questions whether available sources confirm the existence of a developed mysticism that included the practice of the ascent during Jesus’ lifetime. The article also examines the New Testament texts to which Chilton appeals as evidence of Jesus’ mysticism. The article concludes that Chilton’s fascinating theory has only meager support in the canonical Gospels since a careful comparison of the words and activities of Jesus of Nazareth and the descenders of chariot in Tannaitic and hekhaloth literature discovers more differences than similarities.
Jesus: Glutton and Drunkard?
Authors: Marshall Mary 
Published: March 2005

AbstractThe basic premise is that Jesus had a reputation for arriving at meals uninvited, thus provoking the accusations cited in Lk. 7.34 and Mt. 11.19. His table fellowship with toll collectors and sinners is viewed in light of ancient hospitality traditions, and with reference to Lk. 15.1-2; Mk 2.14-17; Lk. 19.1-10; and Lk. 6.27-36. It is argued that true hospitality involves welcoming outsiders, and that the toll collectors’ hospitality to Jesus demonstrates their reformation, and is salvific. In contrast, the so-called ‘sinners’ accompanying Jesus gain entry to earthly meals, and the heavenly banquet, ‘in Jesus’ name’. Attention is drawn to the centrality of hospitality, commensality, and humility in the gospel, and the importance of Abraham as a role model.
The Failure of Functional Theologies of Ministry and the Promise of a Relational Alternative
Authors: Buxton Graham 
Published: March 2005

AbstractThe author critiques inductive approaches to pastoral theology that rely on the empirical methodology of the social and human sciences, and presents an alternative Christocentric praxis model of pastoral ministry. The result is an attempt to integrate pastoral theory and practice that shifts the perspective away from functionally-determined theologies of ministry to a relationally oriented and hermeneutically coherent model of orthopraxis in which theory and practice interact in a way that is intended to both deepen faith and transform lives. Some of the key themes that inform the discussion are the importance of theological method, the role of the community as the context for care, the relationship between practical ministry and systematic theology, and the notion of praxis in articulating the nature and scope of practical theology today.
BMP4 and Madh5 regulate the erythroid response to acute anemia
Authors: Lenox Laurie E. , Perry John M. , Paulson Robert F. 
Published: March 2005

AbstractAcute anemia initiates a systemic response that results in the rapid mobilization and differentiation of erythroid progenitors in the adult spleen. The flexed-tail (f) mutant mice exhibit normal steady-state erythropoiesis but are unable to rapidly respond to acute erythropoietic stress. Here, we show that f/f mutant mice have a mutation in Madh5. Our analysis shows that BMP4/Madh5-dependent signaling, regulated by hypoxia, initiates the differentiation and expansion of erythroid progenitors in the spleen. These findings suggest a new model where stress erythroid progenitors, resident in the spleen, are poised to respond to changes in the microenvironment induced by acute anemia.
Identification of human chronic myelogenous leukemia progenitor cells with hemangioblastic characteristics
Authors: Fang Baijun , Zheng Chunmei , Liao Lianming , Han Qin , Sun Zhao , Jiang Xueying , Zhao Robert C. H. 
Published: March 2005

AbstractOverwhelming evidence from leukemia research has shown that the clonal population of neoplastic cells exhibits marked heterogeneity with respect to proliferation and differentiation. There are rare stem cells within the leukemic population that possess extensive proliferation and self-renewal capacity not found in the majority of the leukemic cells. These leukemic stem cells are necessary and sufficient to maintain the leukemia. Interestingly, the BCR/ABL fusion gene, which is present in chronic myelogenous leukemia (CML), was also detected in the endothelial cells of patients with CML, suggesting that CML might originate from hemangioblastic progenitor cells that can give rise to both blood cells and endothelial cells. Here we isolated fetal liver kinase-1–positive (Flk1+) cells carrying the BCR/ABL fusion gene from the bone marrow of 17 Philadelphia chromosome–positive (Ph+) patients with CML and found that these cells could differentiate into malignant blood cells and phenotypically defined endothelial cells at the single-cell level. These findings provide direct evidence for the first time that rearrangement of the BCR/ABL gene might happen at or even before the level of hemangioblastic progenitor cells, thus resulting in detection of the BCR/ABL fusion gene in both blood and endothelial cells.
Lower levels of surface B-cell-receptor expression in chronic lymphocytic leukemia are associated with glycosylation and folding defects of the μ and CD79a chains
Authors: Vuillier Françoise , Dumas Gérard , Magnac Christian , Prevost Marie-Christine , Lalanne Ana Inés , Oppezzo Pablo , Melanitou Evie , Dighiero Guillaume , Payelle-Brogard Béatrice 
Published: March 2005

AbstractLow levels of B-cell-receptor (BCR) expression are the hallmark of tumoral B lymphocytes in B-cell chronic lymphocytic leukemia (B-CLL). These cells also respond inadequately to stimulation through the BCR. This receptor consists of a surface immunoglobulin associated with a CD79a/CD79b heterodimer. We previously showed that the intracellular synthesis of BCR components, from transcription onward, is normal. Here, we investigated the glycosylation status and cellular localization of μ, CD79a, and CD79b chains in 10 CLL patients differing in surface immunoglobulin M (IgM) expression. We reported a severe impairment of the glycosylation and folding of μ and CD79a. These defects were associated with the retention of both chains in the endoplasmic reticulum and lower levels of surface IgM expression. In contrast, no clear impairment of glycosylation and folding was observed for CD79b. No sequence defects were identified for BCR components and for the chaperone proteins involved in BCR folding processes. These data show, for the first time, that lower levels of BCR surface expression observed in CLL are accounted for by an impaired glycosylation and folding of the μ and CD79a chains.
Distinct IL-4-induced gene expression, proliferation, and intracellular signaling in germinal center B-cell-like and activated B-cell-like diffuse large-cell lymphomas
Authors: Lu Xiaoqing , Nechushtan Hovav , Ding Feiying , Rosado Manuel F. , Singal Rakesh , Alizadeh Ash A. , Lossos Izidore S. 
Published: March 2005

AbstractDiffuse large B-cell lymphomas (DLBCLs) can be subclassified into germinal center B-cell (GCB)-like and activated B-cell (ABC)-like tumors characterized by long and short survival, respectively. In contrast to ABC-like DLBCL, GCB-like tumors exhibit high expression of components of the interleukin 4 (IL-4) signaling pathway and of IL-4 target genes such as BCL6 and HGAL, whose high expression independently predicts better survival. These observations suggest distinct activity of the IL-4 signaling pathway in DLBCL subtypes. Herein, we demonstrate similar IL-4 expression but qualitatively different IL-4 effects on GCB-like and ABC-like DLBCL. In GCB-like DLBCL, IL-4 induces expression of its target genes, activates signal transducers and activators of transcription 6 (STAT6) signaling, and increases cell proliferation. In contrast, in the ABC-like DLBCL, IL-4 activates AKT, decreases cell proliferation by cell cycle arrest, and does not induce gene expression due to aberrant Janus kinase (JAK)-STAT6 signaling attributed to STAT6 dephosphorylation. We found distinct expression profiles of tyrosine phosphatases in DLBCL subtypes and identified putative STAT6 tyrosine phosphatases—protein tyrosine phosphatase nonreceptor type 1 (PTPN1) and PTPN2, whose expression is significantly higher in ABC-like DLBCL. These differences in tyrosine phosphatase expression might underlie distinct expression profiles of some of the IL-4 target genes and could contribute to a different clinical outcome of patients with GCB-like and ABC-like DLBCLs.
Graphical representation of ribosomal RNA probe accessibility data using ARB software package
Authors: Kumar Yadhu , Westram Ralf , Behrens Sebastian , Fuchs Bernhard , Glöckner Frank Oliver , Amann Rudolf , Meier Harald , Ludwig Wolfgang 
Published: March 2005

Abstract
Background
Taxon specific hybridization probes in combination with a variety of commonly used hybridization formats nowadays are standard tools in microbial identification. A frequently applied technology, fluorescence in situ hybridization (FISH), besides single cell identification, allows the localization and functional studies of the microbial community composition. Careful in silico design and evaluation of potential oligonucleotide probe targets is therefore crucial for performing successful hybridization experiments.

Results
The PROBE Design tools of the ARB software package take into consideration several criteria such as number, position and quality of diagnostic sequence differences while designing oligonucleotide probes. Additionally, new visualization tools were developed to enable the user to easily examine further sequence associated criteria such as higher order structure, conservation, G+C content, transition-transversion profiles and in situ target accessibility patterns. The different types of sequence associated information (SAI) can be visualized by user defined background colors within the ARB primary and secondary structure editors as well as in the PROBE Match tool.

Conclusion
Using this tool, in silico probe design and evaluation can be performed with respect to in situ probe accessibility data. The evaluation of proposed probe targets with respect to higher-order rRNA structure is of importance for successful design and performance of in situ hybridization experiments. The entire ARB software package along with the probe accessibility data is available from the ARB home page http://www.arb-home.de.
A standard curve based method for relative real time PCR data processing
Authors: Larionov Alexey , Krause Andreas , Miller William 
Published: March 2005

Abstract
Background
Currently real time PCR is the most precise method by which to measure gene expression. The method generates a large amount of raw numerical data and processing may notably influence final results. The data processing is based either on standard curves or on PCR efficiency assessment. At the moment, the PCR efficiency approach is preferred in relative PCR whilst the standard curve is often used for absolute PCR. However, there are no barriers to employ standard curves for relative PCR. This article provides an implementation of the standard curve method and discusses its advantages and limitations in relative real time PCR.

Results
We designed a procedure for data processing in relative real time PCR. The procedure completely avoids PCR efficiency assessment, minimizes operator involvement and provides a statistical assessment of intra-assay variation.
The procedure includes the following steps. (I) Noise is filtered from raw fluorescence readings by smoothing, baseline subtraction and amplitude normalization. (II) The optimal threshold is selected automatically from regression parameters of the standard curve. (III) Crossing points (CPs) are derived directly from coordinates of points where the threshold line crosses fluorescence plots obtained after the noise filtering. (IV) The means and their variances are calculated for CPs in PCR replicas. (V) The final results are derived from the CPs' means. The CPs' variances are traced to results by the law of error propagation.
A detailed description and analysis of this data processing is provided. The limitations associated with the use of parametric statistical methods and amplitude normalization are specifically analyzed and found fit to the routine laboratory practice. Different options are discussed for aggregation of data obtained from multiple reference genes.

Conclusion
A standard curve based procedure for PCR data processing has been compiled and validated. It illustrates that standard curve design remains a reliable and simple alternative to the PCR-efficiency based calculations in relative real time PCR.
Evolutionary models for insertions and deletions in a probabilistic modeling framework
Authors: Rivas Elena 
Published: March 2005

Abstract
Background
Probabilistic models for sequence comparison (such as hidden Markov models and pair hidden Markov models for proteins and mRNAs, or their context-free grammar counterparts for structural RNAs) often assume a fixed degree of divergence. Ideally we would like these models to be conditional on evolutionary divergence time.
Probabilistic models of substitution events are well established, but there has not been a completely satisfactory theoretical framework for modeling insertion and deletion events.

Results
I have developed a method for extending standard Markov substitution models to include gap characters, and another method for the evolution of state transition probabilities in a probabilistic model. These methods use instantaneous rate matrices in a way that is more general than those used for substitution processes, and are sufficient to provide time-dependent models for standard linear and affine gap penalties, respectively.
Given a probabilistic model, we can make all of its emission probabilities (including gap characters) and all its transition probabilities conditional on a chosen divergence time. To do this, we only need to know the parameters of the model at one particular divergence time instance, as well as the parameters of the model at the two extremes of zero and infinite divergence.
I have implemented these methods in a new generation of the RNA genefinder QRNA (eQRNA).

Conclusion
These methods can be applied to incorporate evolutionary models of insertions and deletions into any hidden Markov model or stochastic context-free grammar, in a pair or profile form, for sequence modeling.