"Self" and "nonself" manipulation of interferon defense during persistent infection: bovine viral diarrhea virus resists alpha/beta interferon without blocking antiviral activity against unrelated viruses replicating in its host cells

Bovine viral diarrhea virus (BVDV), together with Classical swine fever virus (CSFV) and Border disease virus (BDV) of sheep, belongs to the genus Pestivirus of the Flaviviridae. BVDV is either cytopathic (cp) or noncytopathic (ncp), as defined by its effect on cultured cells. Infection of pregnant animals with the ncp biotype may lead to the birth of persistently infected calves that are immunotolerant to the infecting viral strain. In addition to evading the adaptive immune system, BVDV evades key mechanisms of innate immunity. Previously, we showed that ncp BVDV inhibits the induction of apoptosis and alpha/beta interferon (IFN-alpha/beta) synthesis by double-stranded RNA (dsRNA). Here, we report that (i) both ncp and cp BVDV block the induction by dsRNA of the Mx protein (which can also be induced in the absence of IFN signaling); (ii) neither biotype blocks the activity of IFN; and (iii) once infection is established, BVDV is largely resistant to the activity of IFN-alpha/beta but (iv) does not interfere with the establishment of an antiviral state induced by IFN-alpha/beta against unrelated viruses. The results of our study suggest that, in persistent infection, BVDV is able to evade a central element of innate immunity directed against itself without generally compromising its activity against unrelated viruses ("nonself") that may replicate in cells infected with ncp BVDV. This highly selective "self" and "nonself" model of evasion of the interferon defense system may be a key element in the success of persistent infection in addition to immunotolerance initiated by the early time point of fetal infection.

Object-Oriented Legacy System Trace-based Logic Testing

When reengineering legacy systems, it is crucial to assess if the legacy behavior has been preserved or how it changed due to the reengineering effort. Ideally if a legacy system is covered by tests, running the tests on the new version can identify potential differences or discrepancies. However, writing tests for an unknown and large system is difficult due to the lack of internal knowledge. It is especially difficult to bring the system to an appropriate state. Our solution is based on the acknowledgment that one of the few trustable piece of information available when approaching a legacy system is the running system itself. Our approach reifies the execution traces and uses logic programming to express tests on them. Thereby it eliminates the need to programatically bring the system in a particular state, and handles the test-writer a high-level abstraction mechanism to query the trace. The resulting system, called TESTLOG, was used on several real-world case studies to validate our claims.

Genetic and pharmacologic manipulation of oxidative stress after neonatal hypoxia-ischemia

Oxidative stress is a critical component of the injury response to hypoxia-ischemia (HI) in the neonatal brain, and this response is unique and at times paradoxical to that seen in the mature brain. Previously, we showed that copper-zinc superoxide-dismutase (SOD1) over-expression is not beneficial to the neonatal mouse brain with HI injury, unlike the adult brain with ischemic injury. However, glutathione peroxidase 1 (GPx1) over-expression is protective to the neonatal mouse brain with HI injury. To further test the hypothesis that an adequate supply of GPx is critical to protection from HI injury, we crossed SOD1 over-expressing mice (hSOD-tg) with GPx1 over-expressing mice (hGPx-tg). Resulting litters contained wild-type (wt), hGPx-tg, hSOD-tg and hybrid hGPx-tg/hSOD-tg pups, which were subjected to HI at P7. Confirming previous results, the hGPx-tg mice had reduced injury compared to both Wt and hSOD-tg littermates. Neonatal mice over-expressing both GPx1 and SOD1 also had less injury compared to wt or hSOD-tg alone. A result of oxidative stress after neonatal HI is a decrease in the concentration of reduced (i.e. antioxidant-active) glutathione (GSH). In this study, we tested the effect of systemic administration of alpha-lipoic acid on levels of GSH in the cortex after HI. Although GSH levels were restored by 24h after HI, injury was not reduced compared to vehicle-treated mice. We also tested two other pharmacological approaches to reducing oxidative stress in hSOD-tg and wild-type littermates. Both the specific inhibitor of neuronal nitric oxide synthase, 7-nitroindazole (7NI), and the spin-trapping agent alpha-phenyl-tert-butyl-nitrone (PBN) did not reduce HI injury, however. Taken together, these results imply that H2O2 is a critical component of neonatal HI injury, and GPx1 plays an important role in the defense against this H2O2 and is thereby neuroprotective.

Manipulation of antioxidant pathways in neonatal murine brain

To assess the role of brain antioxidant capacity in the pathogenesis of neonatal hypoxic-ischemic brain injury, we measured the activity of glutathione peroxidase (GPX) in both human-superoxide dismutase-1 (hSOD1) and human-GPX1 overexpressing transgenic (Tg) mice after neonatal hypoxia-ischemia (HI). We have previously shown that mice that overexpress the hSOD1 gene are more injured than their wild-type (WT) littermates after HI, and that H(2)O(2) accumulates in HI hSOD1-Tg hippocampus. We hypothesized that lower GPX activity is responsible for the accumulation of H(2)O(2). Therefore, increasing the activity of this enzyme through gene manipulation should be protective. We show that brains of hGPX1-Tg mice, in contrast to those of hSOD-Tg, have less injury after HI than WT littermates: hGPX1-Tg, median injury score = 8 (range, 0-24) versus WT, median injury score = 17 (range, 2-24), p < 0.01. GPX activity in hSOD1-Tg mice, 2 h and 24 h after HI, showed a delayed and bilateral decline in the cortex 24 h after HI (36.0 +/- 1.2 U/mg in naive hSOD1-Tg versus 29.1 +/- 1.7 U/mg in HI cortex and 29.2 +/- 2.0 for hypoxic cortex, p < 0.006). On the other hand, GPX activity in hGPX1-Tg after HI showed a significant increase by 24 h in the cortex ipsilateral to the injury (48.5 +/- 5.2 U/mg, compared with 37.2 +/- 1.5 U/mg in naive hGPX1-Tg cortex, p < 0.008). These findings support the hypothesis that the immature brain has limited GPX activity and is more susceptible to oxidative damage and may explain the paradoxical effect seen in ischemic neonatal brain when SOD1 is overexpressed.

Hip2Norm: an object-oriented cross-platform program for 3D analysis of hip joint morphology using 2D pelvic radiographs

We developed an object-oriented cross-platform program to perform three-dimensional (3D) analysis of hip joint morphology using two-dimensional (2D) anteroposterior (AP) pelvic radiographs. Landmarks extracted from 2D AP pelvic radiographs and optionally an additional lateral pelvic X-ray were combined with a cone beam projection model to reconstruct 3D hip joints. Since individual pelvic orientation can vary considerably, a method for standardizing pelvic orientation was implemented to determine the absolute tilt/rotation. The evaluation of anatomically morphologic differences was achieved by reconstructing the projected acetabular rim and the measured hip parameters as if obtained in a standardized neutral orientation. The program had been successfully used to interactively objectify acetabular version in hips with femoro-acetabular impingement or developmental dysplasia. Hip(2)Norm is written in object-oriented programming language C++ using cross-platform software Qt (TrollTech, Oslo, Norway) for graphical user interface (GUI) and is transportable to any platform.

Simple virtual reality display of fetal volume ultrasound

Three-dimensional (3D) ultrasound volume acquisition, analysis and display of fetal structures have enhanced their visualization and greatly improved the general understanding of their anatomy and pathology. The dynamic display of volume data generally depends on proprietary software, usually supplied with the ultrasound system, and on the operator's ability to maneuver the dataset digitally. We have used relatively simple tools and an established storage, display and manipulation format to generate non-linear virtual reality object movies of prenatal images (including moving sequences and 3D-rendered views) that can be navigated easily and interactively on any current computer. This approach permits a viewing or learning experience that is superior to watching a linear movie passively.

Manipulation of energy transfer processes in nanochannels

The realisation of molecular assemblies featuring specific macroscopic properties is a prime example for the versatility of supramolecular organisation. Microporous materials such as zeolite L are well suited for the preparation of host-guest composites containing dyes, complexes, or clusters. This short tutorial focuses on the possibilities offered by zeolite L to study and influence Förster resonance energy transfer inside of its nanochannels. The highly organised host-guest materials can in turn be structured on a larger scale to form macroscopic patterns, making it possible to create large-scale structures from small, highly organised building blocks for novel optical applications.

A comparison of pixel and object-based land cover classification. A case study of the Asmara region, Eritrea

In this paper we compare the performance of two image classification paradigms (object- and pixel-based) for creating a land cover map of Asmara, the capital of Eritrea and its surrounding areas using a Landsat ETM+ imagery acquired in January 2000. The image classification methods used were maximum likelihood for the pixel-based approach and Bhattacharyya distance for the object-oriented approach available in, respectively, ArcGIS and SPRING software packages. Advantages and limitations of both approaches are presented and discussed. Classifications outputs were assessed using overall accuracy and Kappa indices. Pixel- and object-based classification methods result in an overall accuracy of 78% and 85%, respectively. The Kappa coefficient for pixel- and object-based approaches was 0.74 and 0.82, respectively. Although pixel-based approach is the most commonly used method, assessment and visual interpretation of the results clearly reveal that the object-oriented approach has advantages for this specific case-study.