From gene expression to serum proteins: biomarker discovery in ankylosing spondylitis.

OBJECTIVES: Studying post-infliximab gene expression changes could provide insights into the pathogenesis of ankylosing spondylitis (AS). METHODS: Gene expression changes were screened by microarray on peripheral blood RNA of 16 AS patients at baseline and 2 weeks post-infliximab, and selected results were confirmed by quantitative real-time (qRT)-PCR. Corresponding serum-soluble LIGHT (sLIGHT) was estimated by ELISA and the fold change in sLIGHT was correlated to the fold change in erythrocyte sedimentation rate (ESR), C-reactive protein (CRP) and the Bath AS disease activity index. RESULTS: Post-infliximab, 69% of the patients (11/16) achieved an ASAS20 response. Six candidate genes were differentially expressed by microarray; four of which were validated by qRT-PCR. sLIGHT showed the most significant difference. There was good correlation of baseline sLIGHT with CRP (R = 0.60; p = 0.01) and ESR (R = 0.51; p = 0.04). The fold change in sLIGHT correlated with change in both CRP (R = 0.71, p = 0.002) and ESR (R = 0.77, p<0.001). CONCLUSION: LIGHT is significantly downregulated by infliximab. sLIGHT correlated well with changes in inflammatory markers.

Study of magnetic anisotropy and magnetization reversal using the quadratic magnetooptical effect in epitaxial Co(x)Mn(y)Ge(z)(111) films.

Magnetic anisotropy, magnetization reversal and the magnetooptic Kerr effect in Co(x)Mn(y)Ge(z) have been studied over a range of compositions between 0 and 50 at.% of Ge and between 1 and 3 in the Co to Mn atomic ratio, including the Heusler alloy Co(2)MnGe. A strong quadratic magnetooptic Kerr effect has been observed within a narrow region of composition centered around the Co to Mn atomic ratio of 2, which has been used to probe and quantify the magnetic anisotropy and magnetization reversal of the system. The anisotropy is sixfold with a weak uniaxial component, and it exhibits sensitive dependence on composition, especially on the atomic ratio between Co and Mn. The magnetization reversal process is consistent with the single-domain Stoner-Wohlfarth model.

Self-organization of carbide superlattice and nucleation of carbon nanotubes.

In metal-carbon systems with known stable compounds, carbide nanocrystals self-organize epitaxially on metal surfaces to form two-dimensional arrays during carbon deposition. The process is energetically driven by the competition between the strain and surface energies, and it appears to play an important role in the nucleation of single-walled carbon nanotubes. Interplay between energetics and kinetics controls carbon precipitation from the superlattice, such that the length scale of the carbide and superlattice appears to control the size and morphology of the precipitates. Furthermore, carbon precipitates appear to be "seedlings" of carbon nanotubes grown on top of the carbide nanocrystals. These findings reveal that the nucleation of carbon nanotubes is a nonequilibrium process and that a stable carbide superlattice can be used as an ordered template of carbon saturated "roots" for nucleating nanotube bundles with controlled diameter, spacing, and perhaps chirality.

Syndrome and outbreak detection using chief-complaint data--experience of the Real-Time Outbreak and Disease Surveillance project.

This paper summarizes the experience of the Real-Time Outbreak and Disease Surveillance (RODS) project in collecting and analyzing free-text emergency department (ED) chief complaints. The technical approach involves real-time transmission of chief-complaint data as Health Level 7 messages from hospitals to a regional data center, where a Bayesian text classifier assigns each chief complaint to one of eight syndrome categories. Time-series algorithms analyze the syndrome data and generate alerts. Authorized public health users review the syndrome data by using Internet interfaces with timelines and maps. Deployments in Pennsylvania, Utah, Atlantic City, and Ohio have demonstrated feasibility of real-time collection of chief complaints. Retrospective experiments that measured case-classification accuracy demonstrated that the Bayesian classifier can discriminate between different syndrome presentations. Retrospective experiments that measured outbreak-detection accuracy determined that the classifier's performance was adequate to support accurate and timely detection of seasonal disease outbreaks. Prospective evaluation revealed that a cluster of carbon monoxide exposures was detected by RODS within 4 hours of the presentation of the first case to an emergency department.

Removing a barrier to computer-based outbreak and disease surveillance--the RODS Open Source Project.

INTRODUCTION: Computer-based outbreak and disease surveillance requires high-quality software that is well-supported and affordable. Developing software in an open-source framework, which entails free distribution and use of software and continuous, community-based software development, can produce software with such characteristics, and can do so rapidly. OBJECTIVES: The objective of the Real-Time Outbreak and Disease Surveillance (RODS) Open Source Project is to accelerate the deployment of computer-based outbreak and disease surveillance systems by writing software and catalyzing the formation of a community of users, developers, consultants, and scientists who support its use. METHODS: The University of Pittsburgh seeded the Open Source Project by releasing the RODS software under the GNU General Public License. An infrastructure was created, consisting of a website, mailing lists for developers and users, designated software developers, and shared code-development tools. These resources are intended to encourage growth of the Open Source Project community. Progress is measured by assessing website usage, number of software downloads, number of inquiries, number of system deployments, and number of new features or modules added to the code base. RESULTS: During September--November 2003, users generated 5,370 page views of the project website, 59 software downloads, 20 inquiries, one new deployment, and addition of four features. CONCLUSIONS: Thus far, health departments and companies have been more interested in using the software as is than in customizing or developing new features. The RODS laboratory anticipates that after initial installation has been completed, health departments and companies will begin to customize the software and contribute their enhancements to the public code base.

National Retail Data Monitor for public health surveillance.

The National Retail Data Monitor (NRDM) is a public health surveillance tool that collects and analyzes daily sales data for over-the-counter (OTC) health-care products. NRDM collects sales data for selected OTC health-care products in near real time from >15,000 retail stores and makes them available to public health officials. NRDM is one of the first examples of a national data utility for public health surveillance that collects, redistributes, and analyzes daily sales-volume data of selected health-care products, thereby reducing the effort for both data providers and health departments.

Novel germanium-based magnetic semiconductors.

Epitaxial synthesis and properties of novel Co and Mn-doped Ge magnetic semiconductors were studied. Epitaxial growth of high quality films with high doping concentrations has been stabilized by the use of two dopants. The magnetic and transport properties of the system exhibit high T(C) and large magnetoresistance effects that can be controlled systematically by the doping concentration. The maximum T(C) achieved in the semiconducting materials is approximately 270 K at a composition of Co0.12Mn0.03Ge0.85.

Self-organization of carbide superlattice and nucleation of carbon nanotubes.

In metal-carbon systems with known stable compounds, carbide nanocrystals self-organize epitaxially on metal surfaces to form two-dimensional arrays during carbon deposition. The process is energetically driven by the competition between the strain and surface energies, and it appears to play an important role in the nucleation of single-walled carbon nanotubes. Interplay between energetics and kinetics controls carbon precipitation from the superlattice, such that the length scale of the carbide and superlattice appears to control the size and morphology of the precipitates. Furthermore, carbon precipitates appear to be "seedlings" of carbon nanotubes grown on top of the carbide nanocrystals. These findings reveal that the nucleation of carbon nanotubes is a nonequilibrium process and that a stable carbide superlattice can be used as an ordered template of carbon saturated "roots" for nucleating nanotube bundles with controlled diameter, spacing, and perhaps chirality.

Self-organization of a carbide superlattice during deposition of carbon on Mo.

Formation and evolution of a carbide superlattice (SL) during C deposition on Mo have been studied using molecular beam epitaxy techniques. The ordering of the SL is energetically driven, such that the interplay between strain and surface energies determines the length scale of the SL. Surface precipitation of C occurs within a narrow range of SL spacing that appears to control the size and spacing of the precipitates leading to a possible mechanism for nucleation of single-walled carbon nanotubes.

The emerging science of very early detection of disease outbreaks.

A surge of development of new public health surveillance systems designed to provide more timely detection of outbreaks suggests that public health has a new requirement: extreme timeliness of detection. The authors review previous work relevant to measuring timeliness and to defining timeliness requirements. Using signal detection theory and decision theory, the authors identify strategies to improve timeliness of detection and position ongoing system development within that framework.

Environmentally sensitive, SA-dependent defense responses in the cpr22 mutant of Arabidopsis.

To investigate the signaling pathways through which defense responses are activated following pathogen infection, we have isolated and characterized the cpr22 mutant. This plant carries a semidominant, conditional lethal mutation that confers constitutive expression of the pathogenesis-related (PR) genes PR-1, PR-2, PR-5 and the defensin gene PDF1.2. cpr22 plants also display spontaneous lesion formation, elevated levels of salicylic acid (SA) and heightened resistance to Peronospora parasitica Emco5. The cpr22 locus was mapped to chromosome 2, approximately 2 cM telomeric to the AthB102 marker. By analyzing the progeny of crosses between cpr22 plants and either NahG transgenic plants or npr1 mutants, all of the cpr22-associated phenotypes except PDF1.2 expression were found to be SA dependent. However, the SA signal transducer NPR1 was required only for constitutive PR-1 expression. A cross between cpr22 and ndr1-1 mutants revealed that enhanced resistance to P. parasitica is mediated by an NDR1-dependent pathway, while the other cpr22-induced defenses are not. Crosses between either coi1-1 or etr1-1 mutants further demonstrated that constitutive PDF1.2 expression is mediated by a JA- and ethylene-dependent pathway. Based on these results, the cpr22 mutation appears to induce its associated phenotypes by activating NPR1-dependent and NPR1-independent branches of the SA pathway, as well as an ethylene/JA signaling pathway. Interestingly, the SA-dependent phenotypes, but not the SA-independent phenotypes, are suppressed when cpr22 mutants are grown under high humidity.

Value of ICD-9 coded chief complaints for detection of epidemics.

To assess the value of ICD-9 coded chief complaints for early detection of epidemics, we measured sensitivity, positive predictive value, and timeliness of Influenza detection using a respiratory set (RS) of ICD-9 codes and an Influenza set (IS). We also measured inherent timeliness of these data using the cross-correlation function. We found that, for a one-year period, the detectors had sensitivity of 100% (1/1 epidemic) and positive predictive values of 50% (1/2) for RS and 25% (1/4) for IS. The timeliness of detection using ICD-9 coded chief complaints was one week earlier than the detection using Pneumonia and Influenza deaths (the gold standard). The inherent timeliness of ICD-9 data measured by the cross-correlation function was two weeks earlier than the gold standard.

A feasibility study of two methods for end-user configuration of a clinical event monitor.

We developed and evaluated a feature that allows users to control what types of clinical information are delivered to them. Using a paper or web-based configuration form, users turn individual alerts and sets of results on or off, and set how they are delivered. We used usage rates to evaluate this feature. Of 16 residents who had received clinical information from our clinical event monitor, 4 (25%) made at least one change (range 10-25). Of 41 interns, 5 (12.2%) made at least one change (range 5-91). The difference was borderline significant (p < 0.1). 5/7 web users changed preferences through a dial-up connection from home. More users used the web-based preference form than the paper form. This difference may be due to the better accessibility of the web-based form. A survey established that this feature was not as highly utilized as anticipated partly because the initial (default) preference setting was acceptable and partly because the users were too busy to customize their alert settings. We conclude that user configuration of a system that delivers information using a web-based preference form is feasible and may become important as the volume of information and number of available communication channels increase.

Design of a clinical notification system.

We describe the requirements and design of an enterprise-wide notification system. From published descriptions of notification schemes, our own experience, and use cases provided by diverse users in our institution, we developed a set of functional requirements. The resulting design supports multiple communication channels, third party mappings (algorithms) from message to recipient and/or channel of delivery, and escalation algorithms. A requirement for multiple message formats is addressed by a document specification. We implemented this system in Java as a CORBA object. This paper describes the design and current implementation of our notification system.

Murine SHP-1 splice variants with altered Src homology 2 (SH2) domains. Implications for the SH2-mediated intramolecular regulation of SHP-1.

SHP-1 is a protein-tyrosine phosphatase with two Src homology 2 (SH2) domains. These SH2 domains determine which proteins SHP-1 associates with, but they also autoregulate the activity of the catalytic domain. In this report, we find that the murine SHP-1 transcript is processed to yield a series of alternatively spliced in-frame transcripts, the majority of which exclude exons encoding one or the other SH2 domain. We have examined the corresponding protein isoforms in several ways. First, our measurements of V(max) and K(m) under different conditions indicate that the SH2 variants have elevated activity because of lessened autoregulation. Second, to ascertain whether regulation by the SH2 domains reflects intra- or intermolecular effects, we analyzed the state of SHP-1 by high performance liquid chromatography and sucrose density gradient centrifugation. Our results showed that SHP-1 is a monomer and, thus, is regulated in an intramolecular manner. Third, our analyses detected shape differences between SHP-1 and the active splice variant protein deleted of the amino-terminal SH2 domain; i.e. SHP-1 was globular and resistant to proteolytic digestion, while the splice variant protein was "rod-shaped" and more susceptible to proteolytic digestion.

Mouse NKR-P1B, a novel NK1.1 antigen with inhibitory function.

The mouse NK1.1 Ag originally defined as NK cell receptor (NKR)-P1C (CD161) mediates NK cell activation. Here, we show that another member of the mouse CD161 family, NKR-P1B, represents a novel NK1.1 Ag. In contrast to NKR-P1C, which functions as an activating receptor, NKR-P1B inhibits NK cell activation. Association of NKR-P1B with Src homology 2-containing protein tyrosine phosphatase-1 provides a molecular mechanism for this inhibition. The existence of these two NK1.1 Ags with opposite functions suggests a potential role for NKR-P1 molecules, such as those of the Ly-49 gene family, in regulating NK cell function.

Role of the intronic elements in the endogenous immunoglobulin heavy chain locus. Either the matrix attachment regions or the core enhancer is sufficient to maintain expression.

High level expression in mice of transgenes derived from the immunoglobulin heavy chain (IgH) locus requires both the core enhancer (Emu) and the matrix attachment regions (MARs) that flank Emu. The need for both elements implies that they each perform a different function in transcription. While it is generally assumed that expression of the endogenous IgH locus has similar requirements, it has been difficult to assess the role of these elements in expression of the endogenous heavy chain gene, because B cell development and IgH expression are strongly interdependent and also because the locus contains other redundant activating elements. We have previously described a gene-targeting approach in hybridoma cells that overcomes the redundancy problem to yield a stable cell line in which expression of the IgH locus depends strongly on elements in the MAR-Emu-MAR segment. Using this system, we have found that expression of the endogenous mu gene persists at substantially (approximately 50%) normal levels in recombinants which retain either the MARs or Emu. That is, despite the dissimilar biochemical activities of these two elements, either one is sufficient to maintain high level expression of the endogenous locus. These findings suggest new models for how the enhancer and MARs might collaborate in the initiation or maintenance of transcription.

SHP-1 variant proteins are absent in motheaten mice despite presence of splice variant transcripts with open reading frames.

Motheaten mice have a mutation that causes abnormal splicing of the SHP-1 gene producing transcripts that are out of frame. Thus, motheaten mice cannot produce normal SHP-1 protein. However, we have found that the SHP-1 locus in normal mice is expressed as multiple in-frame splice variant transcripts. We report here that the motheaten SHP-1 gene is likewise expressed in multiple spliced forms, two of which are in frame. One of these two variants, which is also present in normal mice, lacks the exon containing the motheaten mutation and is therefore expected to encode an active phosphatase with only one of the two SH2 domains of SHP-1. We showed that both of these variants produce phosphatases with a higher specific activity than SHP-1, suggesting that motheatein mice are not SHP-1 null. The possibility that motheaten mice produce disregulated phosphatases offered a simple explanation for the puzzling observation that substrates of SHP-1 are hypo-phosphorylated in motheaten mice. We tested this by measuring for SHP-1 protein and activity in motheaten macrophages. However, we did not detect specific activity, and found that one of these variant proteins was unstable. These findings likewise suggest that little or no SHP-1 variant proteins exist in normal cells.

Non-toxic concentrations of cadmium inhibit systemic movement of turnip vein clearing virus by a salicylic acid-independent mechanism.

Systemic movement of plant viruses is a central event in viral infection. To better understand this process, the heavy metal cadmium was used to inhibit systemic spread of turnip vein clearing virus (TVCV), a tobamovirus, in tobacco plants. Study of the mechanism by which cadmium exerts this inhibitory effect may provide insights into the essential steps of the TVCV systemic movement pathway. Our results demonstrated that cadmium treatment did not affect TVCV transport from the inoculated non-vascular tissue into the plant vasculature but blocked viral exit into uninoculated non-vascular tissues. Thus, TVCV virions may enter and exit the host plant vascular system by two different mechanisms. We also showed that cadmium-treated plants still supported systemic spread of an unrelated tobacco etch virus (TEV), suggesting multiple pathways for systemic infection. Finally, cadmium-induced arrest in TVCV systemic infection was shown to occur by a salicylic acid-independent mechanism.