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1.  The Shape of the Proximal Femur Influences Acetabular Wear Patterns Over Time 
Femoroacetabular impingement has been proposed as a cause of early osteoarthritis, but it is not known how this develops over time or whether the shape of the proximal femur influences this risk.
(1) Which areas of the acetabulum are worn more frequently by individuals with a cam deformity of the proximal femur? (2) Do observed acetabular wear patterns differ based on the etiology of the cam deformity? (3) Do wear patterns of individuals with a cam deformity differ based on an individual’s age?
We examined 645 corresponding femora and acetabuli from the Hamann-Todd Osteological Collection and determined the offset and alpha angle using photographs; 370 specimens met inclusion criteria and were examined for signs of wear and the locations of wear were recorded. Specimens were separated into eight subgroups based on age either younger than 40 years or older than 60 years, alpha angle greater or less than 55°, and degree of anterior head-neck offset. We compared the prevalence of wear between groups in each location.
Individuals with abnormal geometry of the proximal femur demonstrated different wear patterns from individuals with normal geometry. There were few differences in wear patterns identified based on the etiology of the femoral deformity. Abnormal femoral geometry was associated with more frequent wear primarily at the anterosuperior acetabulum for individuals younger than 40 years of age and globally for individuals older than 60 years of age.
Femoral geometry appears to influence the pattern of acetabular wear occurring over time.
PMCID: PMC3549172  PMID: 23224910
2.  Automatic extraction of angiogenesis bioprocess from text 
Bioinformatics  2011;27(19):2730-2737.
Motivation: Understanding key biological processes (bioprocesses) and their relationships with constituent biological entities and pharmaceutical agents is crucial for drug design and discovery. One way to harvest such information is searching the literature. However, bioprocesses are difficult to capture because they may occur in text in a variety of textual expressions. Moreover, a bioprocess is often composed of a series of bioevents, where a bioevent denotes changes to one or a group of cells involved in the bioprocess. Such bioevents are often used to refer to bioprocesses in text, which current techniques, relying solely on specialized lexicons, struggle to find.
Results: This article presents a range of methods for finding bioprocess terms and events. To facilitate the study, we built a gold standard corpus in which terms and events related to angiogenesis, a key biological process of the growth of new blood vessels, were annotated. Statistics of the annotated corpus revealed that over 36% of the text expressions that referred to angiogenesis appeared as events. The proposed methods respectively employed domain-specific vocabularies, a manually annotated corpus and unstructured domain-specific documents. Evaluation results showed that, while a supervised machine-learning model yielded the best precision, recall and F1 scores, the other methods achieved reasonable performance and less cost to develop.
Availability: The angiogenesis vocabularies, gold standard corpus, annotation guidelines and software described in this article are available at
PMCID: PMC3179660  PMID: 21821664

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