Integrated Data Repository Toolkit (IDRT). A Suite of Programs to Facilitate Health Analytics on Heterogeneous Medical Data.

BACKGROUND: In recent years, research data warehouses moved increasingly into the focus of interest of medical research. Nevertheless, there are only a few center-independent infrastructure solutions available. They aim to provide a consolidated view on medical data from various sources such as clinical trials, electronic health records, epidemiological registries or longitudinal cohorts. The i2b2 framework is a well-established solution for such repositories, but it lacks support for importing and integrating clinical data and metadata. OBJECTIVES: The goal of this project was to develop a platform for easy integration and administration of data from heterogeneous sources, to provide capabilities for linking them to medical terminologies and to allow for transforming and mapping of data streams for user-specific views. METHODS: A suite of three tools has been developed: the i2b2 Wizard for simplifying administration of i2b2, the IDRT Import and Mapping Tool for loading clinical data from various formats like CSV, SQL, CDISC ODM or biobanks and the IDRT i2b2 Web Client Plugin for advanced export options. The Import and Mapping Tool also includes an ontology editor for rearranging and mapping patient data and structures as well as annotating clinical data with medical terminologies, primarily those used in Germany (ICD-10-GM, OPS, ICD-O, etc.). RESULTS: With the three tools functional, new i2b2-based research projects can be created, populated and customized to researcher's needs in a few hours. Amalgamating data and metadata from different databases can be managed easily. With regards to data privacy a pseudonymization service can be plugged in. Using common ontologies and reference terminologies rather than project-specific ones leads to a consistent understanding of the data semantics. CONCLUSIONS: i2b2's promise is to enable clinical researchers to devise and test new hypothesis even without a deep knowledge in statistical programing. The approach presented here has been tested in a number of scenarios with millions of observations and tens of thousands of patients. Initially mostly observant, trained researchers were able to construct new analyses on their own. Early feedback indicates that timely and extensive access to their "own" data is appreciated most, but it is also lowering the barrier for other tasks, for instance checking data quality and completeness (missing data, wrong coding).

Secure Secondary Use of Clinical Data with Cloud-based NLP Services. Towards a Highly Scalable Research Infrastructure.

OBJECTIVES: The secondary use of clinical data provides large opportunities for clinical and translational research as well as quality assurance projects. For such purposes, it is necessary to provide a flexible and scalable infrastructure that is compliant with privacy requirements. The major goals of the cloud4health project are to define such an architecture, to implement a technical prototype that fulfills these requirements and to evaluate it with three use cases. METHODS: The architecture provides components for multiple data provider sites such as hospitals to extract free text as well as structured data from local sources and de-identify such data for further anonymous or pseudonymous processing. Free text documentation is analyzed and transformed into structured information by text-mining services, which are provided within a cloud-computing environment. Thus, newly gained annotations can be integrated along with the already available structured data items and the resulting data sets can be uploaded to a central study portal for further analysis. RESULTS: Based on the architecture design, a prototype has been implemented and is under evaluation in three clinical use cases. Data from several hundred patients provided by a University Hospital and a private hospital chain have already been processed. CONCLUSIONS: Cloud4health has shown how existing components for secondary use of structured data can be complemented with text-mining in a privacy compliant manner. The cloud-computing paradigm allows a flexible and dynamically adaptable service provision that facilitates the adoption of services by data providers without own investments in respective hardware resources and software tools.

An outbreak of pertussis among young Israeli soldiers.

In winter 2001, an outbreak of pertussis involving an estimated 75 people occurred among soldiers serving in an infantry regiment of the Israeli Defense Forces (IDF). Nasopharyngeal swabs were obtained from patients and contacts for culture and PCR. Serum samples were obtained and assayed by ELISA for the presence of IgA, IgM and IgG antibodies to a lysate antigen of Bordetella pertussis. The calculated attack rate was 21% based on clinical signs alone (cough lasting 30 days or longer) and 9.5% based on clinical signs with laboratory confirmation (by PCR, IgA or IgM). A high carriage rate was observed; 20% of the asymptomatic and previously symptomatic subjects were PCR-positive for B. pertussis. These findings emphasize the importance of B. pertussis as a causative agent of epidemic respiratory infections in young adults and reveal the occurrence of a significant proportion of pertussis transient carriers during an outbreak of the disease.

Early thymocyte development is regulated by modulation of E2A protein activity.

The E2A gene encodes the E47 and E12 basic helix-loop-helix (bHLH) transcription factors. T cell development in E2A-deficient mice is partially arrested before lineage commitment. Here we demonstrate that E47 expression becomes uniformly high at the point at which thymocytes begin to commit towards the T cell lineage. E47 protein levels remain high until the double positive developmental stage, at which point they drop to relatively moderate levels, and are further downregulated upon transition to the single positive stage. However, stimuli that mimic pre-T cell receptor (TCR) signaling in committed T cell precursors inhibit E47 DNA-binding activity and induce the bHLH inhibitor Id3 through a mitogen-activated protein kinase kinase-dependent pathway. Consistent with these observations, a deficiency in E2A proteins completely abrogates the developmental block observed in mice with defects in TCR rearrangement. Thus E2A proteins are necessary for both initiating T cell differentiation and inhibiting development in the absence of pre-TCR expression. Mechanistically, these data link pre-TCR mediated signaling and E2A downstream target genes into a common pathway.

The function of E- and Id proteins in lymphocyte development.

Helix-loop-helix proteins are essential factors for lymphocyte development and function. In particular, E-proteins are crucial for commitment of lymphoid progenitors to the B- and T-cell lineages. E-proteins are negatively regulated by the Id class of helix-loop-helix proteins. The Id proteins function as dominant-negative inhibitors of E-proteins by inhibiting their ability to bind DNA. Here, we review the role of E-proteins and their Id protein antagonists in lymphocyte proliferation and developmental progression. In addition, we discuss how E-protein activity and Id gene expression are regulated by T-cell receptor (TCR) and pre-TCR-mediated signalling.

Human osteoblast-like cells phagocytose metal particles and express the macrophage marker CD68 in vitro.

Periprosthetic osteolysis is a major cause of aseptic loosening in artificial joint replacement. It is assumed to occur in conjunction with the activation of macrophages. We have shown in vitro that human osteoblast-like cells, isolated from bone specimens obtained from patients undergoing hip replacement, phagocytose fine particles of titanium alloy (TiAlV). The human osteoblast-like cells were identified immunocytochemically by the presence of bone-specific alkaline phosphatase (BAP). With increasing duration of culture, a variable number of the osteoblastic cells became positive for the macrophage marker CD68, independent of the phagocytosis of particles, with a fine granular cytoplasmic staining which was coexpressed with BAP as revealed by immunodoublestaining. The metal particles were not toxic to the osteoblastic cells since even in culture for up to four weeks massively laden cells were vital and had a characteristic morphology. Cells of the human osteosarcoma cell line (HOS 58) were also able to phagocytose metal particles but had only a low expression of the CD68 antigen. Fluorescence-activated cell scanning confirmed our immunocytochemical results. Additionally, the cells were found to be negative for the major histocompatibility complex-II (MHC-II) which is a marker for macrophages and other antigen-presenting cells. Negative results of histochemical tests for tartrate-resistant acid phosphatase excluded the contamination by osteoclasts or macrophages in culture. Our observations suggest that the osteoblast can either change to a phagocytosing cell or that the phagocytosis is an underestimated property of the osteoblast. The detection of the CD68 antigen is insufficient to prove the monocytic lineage. In order to discriminate between macrophages and osteoblasts additional markers should be used. To our knowledge, this is the first demonstration of cells of an osteoblastic origin which have acquired a mixed phenotype of both osteoblasts and macrophages.

Transcription factors in hematopoiesis.

The advent of gene targeting in the mouse has led to rapid advances in the identification of factors controlling gene expression that are essential for normal hematopoietic development. Recent work has also uncovered roles for some of these factors in leukemogenesis and in the global regulation of chromatin structure.

Development of the osteoblast phenotype in primary human osteoblasts in culture: comparison with rat calvarial cells in osteoblast differentiation.

In rat osteoblast-like cells, a time-dependent sequence of growth and differentiation-dependent genes has been identified and a model of osteoblast differentiation in culture suggested. We investigated the expression of the bone matrix-associated proteins osteonectin and procollagen I and of the bone cell phenotype-related proteins alkaline phosphatase and osteocalcin during cell culture in primary human osteoblast like cells. Primary human explant cultures from nine young healthy donors were established under highly standardized conditions. Cells in the second passage were analyzed on different days from day 1 to 32, comparing cells growing under the influence of ascorbate with controls. Gene expression was determined by Northern blot analysis or polymerase chain reaction. Osteocalcin expression was also investigated after 1,25-(OH)(2)D(3) stimulation. On the protein level, newly synthesized collagen I, alkaline phosphatase activity, and secretion of osteocalcin were analyzed at all time points. On comparing our findings to the pattern of gene expression suggested for the rat calvarial osteoblast system, we found a similar developmental sequence for the so-called "proliferation" as well as a similar, but lengthened, sequence for the "matrix maturation stage." During "matrix maturation," we found an ongoing proliferation despite increased alkaline phosphatase and decreased procollagen I gene expression. Our study, therefore, shows that in pHOB the gene expression profile proceeded to the "matrix maturation stage," as defined by Owen and colleagues, independent of ongoing proliferation. We were unable to observe the mineralization period as demonstrated by the missing increase of osteocalcin expression and lack of nodule formation in our human osteoblast model. In contrast to the rat system, we found a proliferation stimulating influence of ascorbate, suggesting species-specific differences in response to differentiation factors. From these data, we conclude that general considerations on physiology and pathophysiology of bone cell differentiation have to be confirmed in the human osteoblastic cell system.

Ectopic expression of E47 or E12 promotes the death of E2A-deficient lymphomas.

Mice with null mutations in the E2A gene are highly susceptible to the spontaneous development of thymic lymphomas. To understand better how E2A deficiency may contribute to lymphomagenesis, we have observed the consequences of enforced expression of the E2A gene products E12 and E47 in cell lines derived from lymphomas that arose spontaneously in E2A-deficient mice. E2A-expressing cells are steadily eliminated from lymphoma cultures into which E47 or E12 was introduced. The mechanism underlying the loss of E2A-expressing cells does not involve an arrest in cell-cycle progression. Rather, the E2A proteins activate a programmed cell death pathway in these lymphomas. This E2A-mediated cell death appears to be preceded by a loss of mitochondrial transmembrane potential. These data provide direct evidence that E2A gene products can act as tumor suppressors.

Analysis of human primary bone cells by fluorescence activated cell scanning: methodological problems and preliminary results.

We describe the development of flowcytometrical methods to analyse human primary osteoblast-like cultures obtained from trabecular bone explants in comparison to the human osteosarcoma cell line HOS 58. Two antigens typical of osteoblasts were studied: bone alkaline phosphatase and collagen/procollagen I; the non-specific attachment protein fibronectin served as control. The morphology of all different antigens is shown by immunocytochemistry before flowcytometrical analysis. The establishment of flowcytometry is described in detail. While all antigens tested were nearly 100% positive in the HOS 58 cells in immunocytochemistry and flowcytometry, in primary osteoblast-like cells results varied widely between both methods. Cell permeabilisation before flowcytometry improved the homogeneity of results, probably by increasing the accessibility of the specific antibody to intracellular compartments. Though up to 80% of cells were lost during preparation the ratio of positive versus negative cells in specific experiment was not dependent on the cell recovery. Therefore, the cells finally analysed seemed to be representative of the total population.

E2A deficiency leads to abnormalities in alphabeta T-cell development and to rapid development of T-cell lymphomas.

The E2A gene products, E12 and E47, are critical for proper early B-cell development and commitment to the B-cell lineage. Here we reveal a new role for E2A in T-lymphocyte development. Loss of E2A activity results in a partial block at the earliest stage of T-lineage development. This early T-cell phenotype precedes the development of a T-cell lymphoma which occurs between 3 and 9 months of age. The thymomas are monoclonal and highly malignant and display a cell surface phenotype similar to that of immature thymocytes. In addition, the thymomas generally express high levels of c-myc. As assayed by comparative genomic hybridization, each of the tumor populations analyzed showed a nonrandom gain of chromosome 15, which contains the c-myc gene. Taken together, the data suggest that the E2A gene products play a role early in thymocyte development that is similar to their function in B-lineage determination. Furthermore, the lack of E2A results in development of T-cell malignancies, and we propose that E2A inactivation is a common feature of a wide variety of human T-cell proliferative disorders, including those involving the E2A heterodimeric partners tal-1 and lyl-1.

Binary and ternary complexes between T-cell receptor, class II MHC and superantigen in vitro.

Superantigens are proteins that in association with class II major histocompatibility complex (MHC)-bearing cells can stimulate virtually all T cells that express particular classes of the variable beta-domains of the T-cell receptor (TCR). This mechanism of T-cell activation circumvents the usual requirement for peptide-specific MHC recognition. Staphylococcus aureus enterotoxin B (SEB) is a bacterial superantigen that causes food poisoning and shock. We have characterized the tertiary complex of SEB, a soluble T-cell receptor, and a soluble class II MHC molecule DR1, and the three binary complexes TCR-SEB, SEB-DR1, and the peptide-specific complex DR1-TCR. We report here that in each case the specificity of the interaction among the soluble molecules is the same as observed in biological assays. Native gel electrophoresis and plasmon resonance affinity measurements indicate that SEB-TCR complex can form in the absence of class II MHC and that SEB-TCR interaction increases the binding of DR1. The observation that a superantigen can form complexes with TCR in both the absence and presence of class II MHC may provide a mechanism for its ability to induce anergy in some circumstances and activation in others (reviewed in ref. 8).

A method for producing monoclonal antibodies to human T-cell-receptor beta-chain variable regions.

Study of the T-cell repertoire in humans has been hampered by the lack of monoclonal antibodies (mAbs) to the T-cell receptor (TCR) variable region (V) gene products. We describe a method for producing mAbs to the human TCR beta-chain V (V beta) gene products in which mice were immunized with a rat basophil cell line (RBL-2H3) transfected with the extracellular domain of the TCR heterodimer fused to the lambda chain of CD3. These cells acted as excellent immunogens for raising anti-TCR mAb and also formed the basis of a rapid screening assay. We generated mAbs against V beta protein of the TCR, showed that these mAbs stained approximately 1% of peripheral blood T cells, and further showed that the mAbs could stimulate proliferation of these T cells. We then characterized the mAbs by amplifying TCR cDNA derived from mAb-stimulated cells and sequencing the beta chain. All clones sequenced used the V beta 7.1 chain, proving conclusively that the mAbs generated were specific for V beta 7.1 subfamily. This method generates mAbs to human TCR V beta proteins efficiently and might allow production of a complete panel of mAbs directed against human TCR V beta proteins.

High-efficiency expression and solubilization of functional T cell antigen receptor heterodimers.

The T cell receptor (TCR) zeta chain was attached to the TCR alpha and beta extracellular domains to induce efficient expression of alpha beta heterodimers that can recognize complexes of antigen with major histocompatibility complex (MHC) molecules. Chimeric constructs expressed in RBL-2H3 cells were efficiently transported to the cell surface uniquely as disulfide-linked heterodimers. Transfectants were activated by specific antigen-MHC complexes, which demonstrated that the expressed alpha beta was functional and that CD3 was not required for antigen-MHC binding. Constructs with thrombin cleavage sites were efficiently cleaved to soluble disulfide-linked heterodimers. Thus, attachment of TCR zeta domains and protease cleavage sites to TCR alpha and beta induces expression of demonstrably functional heterodimers that can be solubilized.

Parental values, reinforcement, and young children's prosocial behavior: a longitudinal study.

In this study, the authors assessed the relation of parental reinforcement and parental values to young children's prosocial behaviors. Parents' dyadic interactions with their 1- to 2-year-old children were videotaped in the home on two occasions approximately 6 months apart. The children also were videotaped playing with a peer at 3 1/2 to 4 1/2 years of age. Parental reinforcement of the children's prosocial behaviors was coded, as were the children's prosocial behaviors with the peer. The frequency of girls' spontaneous prosocial behaviors decreased in the early years; modest consistency was observed for boys (but not girls) across the two parental sessions. No relation existed between the frequency of children's prosocial behaviors with their parents and their behaviors with peers. Both maternal and paternal valuing of compliance were negatively related to the mothers' use of reinforcement for children's spontaneous prosocial behaviors. Parental reinforcement of compliant prosocial behaviors was negatively related to children's compliance with a peer's request for prosocial behavior and positively related to defensive behavior with the peer. Fathers' valuing of prosocial behavior was associated with children's compliance with the peer's requests for prosocial action. Parents who valued compliance had children who exhibited low levels of compliant prosocial behaviors with the peer, possibly because of the depressed level of peer interaction.

Structure and specificity of the T cell antigen receptor.

The antigen receptor on T lymphocytes is a multi-chain complex of which two chains determine its specificity for antigen. Although these receptor chains possess genetic and structural similarities with membrane-bound immunoglobulin, the B cell antigen receptor, they endow T cells with a distinct specificity. Unlike B cells, T cells recognize foreign antigenic properties only in the form of proteolytic fragments bound to molecules encoded by the major histocompatibility complex. In addition, one stage of the development of T cells in the thymus is dependent upon an antigen receptor-mediated event. Utilizing the response to a well defined antigen as a model system, we discuss the relationship between receptor structure and the specificity of these recognition events.

Structure/function analysis of the invariant subunits of the T cell antigen receptor.

The T cell antigen receptor (TCR) is a multimeric surface receptor on T cells responsible for recognizing MHC-restricted antigens and initiating the cellular immune response. The clonotypic nature of the TCR resides in the antigen binding TCR-alpha beta or TCR-gamma delta heterodimer. The CD3 complex of gamma, delta and epsilon and the zeta-family disulfide dimer comprise the invariant TCR chains. Assembly of the mature TCR complex requires specific subunit interactions, the detailed nature of which is becoming more evident. Surface targetting of the TCR appears dependent on a region of the zeta chain near its transmembrane domain. A functional role attributable to zeta residing in the cytoplasmic tail is the capacity to couple antigen stimulation to IL-2 secretion, likely through activation of a tyrosine kinase. Assignment of functional roles for the remaining CD3 chains is not as clear; the removal of the cytoplasmic tail of CD3-delta does not affect TCR-mediated IL-2 signalling. Mounting evidence indicates that the structural complexity of the TCR is further enhanced by the various zeta family disulfide dimer pairs that can associate with the other TCR chains. This subunit diversification may offer the possibility of multiple coupling pathways available to the TCR as it responds to foreign antigens in various contexts.

Site-directed mutations in the VDJ junctional region of a T cell receptor beta chain cause changes in antigenic peptide recognition.

In order to assess the importance of a conserved amino acid in the VDJ junctional region of the beta chain of T cell receptors (TCRs) specific for pigeon cytochrome c, we generated T cell transfectant clones that express either a TCR identical to that of the cytochrome c-specific clone D6 or a mutated form of the D6 TCR, in which the conserved residue was replaced by one of two other amino acids. We have found that one substitution alters antigen fine specificity, while the other substitution abolishes all detectable cytochrome c response. On the basis of these findings, we propose that this conserved amino acid is a key residue in determining the antigen specificity of the D6 TCR.