SIGNATURE: A workbench for gene expression signature analysis

<p>Abstract</p> <p>Background</p> <p>The biological phenotype of a cell, such as a characteristic visual image or behavior, reflects activities derived from the expression of collections of genes. As such, an ability to measure the expression of these genes provides an opportunity to develop more precise and varied sets of phenotypes. However, to use this approach requires computational methods that are difficult to implement and apply, and thus there is a critical need for intelligent software tools that can reduce the technical burden of the analysis. Tools for gene expression analyses are unusually difficult to implement in a user-friendly way because their application requires a combination of biological data curation, statistical computational methods, and database expertise.</p> <p>Results</p> <p>We have developed SIGNATURE, a web-based resource that simplifies gene expression signature analysis by providing software, data, and protocols to perform the analysis successfully. This resource uses Bayesian methods for processing gene expression data coupled with a curated database of gene expression signatures, all carried out within a GenePattern web interface for easy use and access.</p> <p>Conclusions</p> <p>SIGNATURE is available for public use at <url>http://genepattern.genome.duke.edu/signature/</url>.</p

Biomechanical considerations in the pathogenesis of osteoarthritis of the knee

Osteoarthritis is the most common joint disease and a major cause of disability. The knee is the large joint most affected. While chronological age is the single most important risk factor of osteoarthritis, the pathogenesis of knee osteoarthritis in the young patient is predominantly related to an unfavorable biomechanical environment at the joint. This results in mechanical demand that exceeds the ability of a joint to repair and maintain itself, predisposing the articular cartilage to premature degeneration. This review examines the available basic science, preclinical and clinical evidence regarding several such unfavorable biomechanical conditions about the knee: malalignment, loss of meniscal tissue, cartilage defects and joint instability or laxity

Platelet concentrate vs. saline in a rat patellar tendon healing model.

To evaluate single centrifuge platelet concentrate as additive for improved tendon healing. Platelet-rich plasma has been reported to improve tendon healing. Single centrifuge platelet concentration may increase platelet concentration enough to positively affect tendon healing. A single centrifuge process will lead to a blood product with increased platelet concentrations which, when added to a surgically created tendon injury, will improve tendon healing when compared with a saline control.Lewis rats had a surgical transection of the patellar tendon that was subsequently stabilized with a cerclage suture. Prior to skin closure, the tendon was saturated with either a concentrated platelet solution or saline. At 14 days, all animals were killed, and the extensor mechanism was isolated for testing. Biomechanical testing outputs included ultimate tensile load, stiffness, and energy absorbed.Comparisons between the control group and the concentrated platelet group revealed no differences. A subgroup of the concentrated platelet group consisting of specimens in whom the concentration process was most successful showed significantly higher ultimate tensile load (P < 0.05) and energy absorbed to failure (P < 0.05) when compared to the control group.When successful, single centrifuge platelet concentration yields a solution that improves tendon healing when compared with a saline control. Single-spin platelet concentration may yield a biologically active additive that may improve tendon healing, but more studies must be undertaken to ensure that adequate platelet concentration is possible

A biomechanical comparison of 2 transosseous-equivalent double-row rotator cuff repair techniques using bioabsorbable anchors: cyclic loading and failure behavior.

PURPOSE: A novel double-row configuration was compared with a traditional double-row configuration for rotator cuff repair. METHODS: In 10 matched-pair sheep shoulders in vitro repair was performed with either a double-row technique with corkscrew suture anchors for the medial row and insertion anchors for the lateral row (group A) or a double-row technique with a new tape-like suture material with insertion anchors for both the medial and lateral rows (group B). Each specimen underwent cyclic loading from 10 to 150 N for 100 cycles, followed by unidirectional failure testing. Gap formation and strain within the repair area for the first and last cycles were analyzed with a video digitizing system, and stiffness and failure load were determined from the load-elongation curve. RESULTS: The results were similar for the 2 repair types. There was no significant difference between the ultimate failure loads of the 2 techniques (421 +/- 150 N in group A and 408 +/- 66 N in group B, P = .31) or the stiffness of the 2 techniques (84 +/- 26 N/mm in group A and 99 +/- 20 N/mm in group B, P = .07). In addition, gap formation was not different between the repair types. Strain over the repair area was also not different between the repair types. CONCLUSIONS: Both tested rotator cuff repair techniques had high failure loads, limited gap formation, and acceptable strain patterns. No significant difference was found between the novel and conventional double-row repair types. CLINICAL RELEVANCE: Two double-row techniques-one with corkscrew suture anchors for the medial row and insertion anchors for the lateral row and one with insertion anchors for both the medial and lateral rows-provided excellent biomechanical profiles at time 0 for double-row repairs in a sheep model. Although the sheep model may not directly correspond to in vivo conditions, all-insertion anchor double-row constructs are worthy of further investigation