The LAILAPS Search Engine: A Feature Model for Relevance Ranking in Life Science Databases

Efficient and effective information retrieval in life sciences is one of the most pressing challenge in bioinformatics. The incredible growth of life science databases to a vast network of interconnected information systems is to the same extent a big challenge and a great chance for life science research. The knowledge found in the Web, in particular in life-science databases, are a valuable major resource. In order to bring it to the scientist desktop, it is essential to have well performing search engines. Thereby, not the response time nor the number of results is important. The most crucial factor for millions of query results is the relevance ranking. In this paper, we present a feature model for relevance ranking in life science databases and its implementation in the LAILAPS search engine. Motivated by the observation of user behavior during their inspection of search engine result, we condensed a set of 9 relevance discriminating features. These features are intuitively used by scientists, who briefly screen database entries for potential relevance. The features are both sufficient to estimate the potential relevance, and efficiently quantifiable. The derivation of a relevance prediction function that computes the relevance from this features constitutes a regression problem. To solve this problem, we used artificial neural networks that have been trained with a reference set of relevant database entries for 19 protein queries. Supporting a flexible text index and a simple data import format, this concepts are implemented in the LAILAPS search engine. It can easily be used both as search engine for comprehensive integrated life science databases and for small in-house project databases. LAILAPS is publicly available for SWISSPROT data at http://lailaps.ipk-gatersleben.d

The Treatment of Primary Arthritis of the Finger and Thumb Joint

Background: Primary finger and thumb joint arthritis is common, with a markedly rising prevalence from age 50 onward. As the population as a whole ages, the need for effective, stage-appropriate treatment of this condition is increasing. Methods: This review is based on pertinent publications retrieved by a selective search in the PubMed and Cochrane Library databases. Results: Pain on movement and morning stiffness are commonly reported symptoms. Thorough physical examination and plain x-rays are mandatory. In the early stages of primary finger and thumb joint arthritis, a conservative, multimodal treatment approach involving the use of splints, physiotherapy, and non-steroidal anti-inflammatory drugs can be helpful. The intra-articular injection of hyaluronic acid or cortisone seems to relieve pain in the short term, but its long-term efficacy in primary finger and thumb joint arthritis is questionable. Arthrodesis (joint fusion) is a reliable surgical treatment option for arthritis of the metacarpophalangeal and interphalangeal joints of the thumb. For mobility-preserving surgery of the metacarpophalangeal joints of the second through fifth fingers, silicone implant arthroplasty remains the gold standard. Symptomatic, advanced arthritis of the distal interphalangeal joint is most effectively treated with arthrodesis. Conclusion: The efficacy of conservative treatment has been documented in high-quality clinical trials, while that of surgical treatment has not. The various surgical methods have yielded benefits in routine clinical use, but these remain to be assessed in randomized and controlled trials

The LAILAPS Search Engine: A Feature Model for Relevance Ranking in Life Science Databases

Efficient and effective information retrieval in life sciences is one of the most pressing challenge in bioinformatics. The incredible growth of life science databases to a vast network of interconnected information systems is to the same extent a big challenge and a great chance for life science research. The knowledge found in the Web, in particular in life-science databases, are a valuable major resource. In order to bring it to the scientist desktop, it is essential to have well performing search engines. Thereby, not the response time nor the number of results is important. The most crucial factor for millions of query results is the relevance ranking

Analysis of the accuracy of fit of five anatomically precontoured clavicle plate systems

A common method in surgical treatment of midshaft clavicular fractures is the clavicle plating system. In addition to traditional osteosynthetic devices, anatomically preformed plate systems also exist. Advantages are described in greater accuracy of fit and less irritation of surrounding soft tissues. The purpose of this study was to compare the anatomical fit of five different precontoured clavicle plating systems. The anatomical fit of five different types of anatomical precontoured clavicle plates, 3 times VariaxSystemA (R) (Stryker, Kalamazoo, MI), MevesA (R) Plate (Ulrich medical Ulm, Germany) and LCP clavicle plate (Synthes, Bettlach, Switzerland) were investigated in 20 embalmed human cadaveric clavicles. An imprint of the space between the well-positioned plate and the clavicle was obtained using a silicone mass and the silicone imprint was digitally measured. Additionally, the anatomical fit was evaluated by three investigators following a standardized protocol (+2 to -2 points at lateral, midshaft and medial clavicle portions). The first three ranks went to the Stryker Variax-plates. They showed the least distance (Stryker 628027: 7aEurohole 1.44 mm, low curvature 0.93 mm-2.36 mm, 2. Stryker 628028: 8aEurohole low curvature 1.68 mm, 1.03 mm-2.4 mm and 3. Stryker 628128: 8aEurohole high curvature 1.87 mm, range 1.09 mm-3.1 mm) The evaluation of the anatomical fit by the investigators was in agreement with the measurement results. Although there was no complete congruency between the plates and the clavicle, all clavicle plates investigated in this study presented a reasonable anatomical shape. The 7aEurohole VariAx Stryker plate with slight curvature showed the best anatomical fit. A low profile and optimized anatomical precontouring can minimize irritation of the surrounding soft tissues and should be considered in plate design and implant choice

Short-term radiological results after spheroid-based autologous chondrocyte implantation in the knee are independent of defect localisation

BACKGROUND: Lesions of articular cartilage represent a crucial risk factor for the early development of osteoarthritis. Autologous chondrocyte implantation (ACI) is a well-established procedure in therapy of those lesions in the knee. The aim of the presented study is to detect differences in short-term radiological outcome depending on defect localization (femoral condyle vs. retropatellar) after spheroid-based ACI. OBJECTIVE: This study aimed to demonstrate that radiological outcome after spheroid-based ACI in the knee is independent of defect localization. METHODS: MRI-scans after retropatellar ACI and ACI of the medial/lateral femoral condyle, with a preoperative Outerbridge grade of III or IV were evaluated regarding MOCART 2.0. RESULTS: The mean defect-size was 5.0 +/- 1.8 cm(2), with a minimum size of 2 cm(2) and a maximum size of 9 cm(2). Scans were performed 7.7 months (+/- 3.1 months) postoperatively. The mean MOCART 2.0 score was 78.5 +/- 15.6. No statistically significant influence neither of the localization (p = 0.159), the gender (p = 0.124) nor defect size ( 5 cm(2); p = 0.201) could be observed. CONCLUSIONS: The presented data demonstrate good to excellent radiological short-term results after spheroid-based ACI. Data indicates, that at least radiological results are independent of gender, defect-size and defect-localization

The Proximal Femoral Bone Geometry in Plain Radiographs

Background: Osteoporosis represents the most common bone disease and has to be respected in planning total hip replacement, especially against the background of increasing uncemented total hip replacement. In this context, the radiographic geometry of the proximal femur got into focus and is controversially discussed. The aim of the presented study was to find any difference regarding known indices for proximal femur bone geometry between patients with high-grade osteoarthritis and patients suffering from a femoral neck fracture caused by low impact trauma. Methods: Retrospective matched-paired analysis of 100 plane pelvic radiographs from 50 patients who suffered from high-grade hip osteoarthritis and 50 patients who suffered from femoral neck fracture was performed. Measurement of Canal-Bone Ratio (CBR), Canal-Calcar Ratio (CCR), Mineral Cortical Index (MCI) and Canal Flare Index (CFI) were performed. Results: CBR was significantly higher in the fracture-group (0.45 +/- 0.06 vs. 0.41 +1- 0.08) (P-value= 0.008). Moreover, the femoral thickness 10 cm below the trochanter minor [F] was significantly higher in the osteoarthritis-group (34.68 +/- 4.14 vs 32.11 +/- 3.43) (P-value 0.001). Conclusion: In conclusion, patients with a femoral neck fracture demonstrated a higher CBR, which indicates a poorer bone quality. In case of planning a THA, the CBR is an index which can easily be measured and can be seen as one decision criterion in THA regarding fixation technique

Midterm functional outcome after dorsal capsular imbrication for posttraumatic instability of the distal radioulnar joint

Introduction The dorsal capsular imbrication of the distal radioulnar joint (DRUJ) which was performed because of posttraumatic dorsal instability showed promising functional results after the first postoperative years. Therefore, we hypothesized that patients after capsular imbrication are characterized by good subjective and functional outcome measurements after a midterm period. Materials and methods Eleven patients (range 21-50 years of age; median 35 years of age) were examined after capsular imbrication of the DRUJ because of posttraumatic instability with a mean follow-up time of 72 months (range 46-114 months; median 66 months). Examination parameters included the determination of range of motion (ROM), grip strength, pain and functional outcome scores (modified Mayo wrist score (MMWS); Disabilities of the Arm, Shoulder and Hand questionnaire (DASH score)). Results A mean DASH score of 6.7 (range 0-22.5) and mean MMWS of 91.8 (range 75-100) were measured. Grip strength reached 96.7 % of the contralateral hand. Range of motion reached at least 93.1 % of the contralateral hand. Eight of 11 patients regarded functional outcome and pain reduction as excellent. Six of 11 patients did not recognize a diagnosed instability of DRUJ as such. Ulnar-sided wrist pain was the apparent symptom in these cases. Conclusions Capsular imbrication of the DRUJ is a reliable and sufficient treatment option in case of posttraumatic dorsal instability. Since DRUJ instability is seldom recognized by the patients as such, a standardised diagnostic algorithm is mandatory to guarantee reliability and efficacy for identifying DRUJ instability

Does increased femoral antetorsion predispose to cartilage lesions of the patellofemoral joint?

The purpose of this study was to investigate whether there was a relationship between femoral neck antetorsion and the presence and pattern of osteoarthritis of the patellofemoral joint. It was hypothesized that an increased femoral neck antetorsion (1) correlates with osteoarthritic changes of the lateral facet of the patellofemoral joint and (2) correlates with an increased lateral trochlear height and a decreased sulcus angle. Seventy-eight formalin-embedded cadaveric lower extremities from thirty-nine subjects with a median age of 74 years (range 60-88) were used. Surrounding soft tissues of the lower limb were removed. The femoral neck antetorsion was measured and referenced to the transepicondylar axis and the posterior condylar line. The height of the medial and lateral facet of the trochlea and the sulcus angle was measured. The location and the degree of patellofemoral cartilage degeneration were recorded. A Pearson's correlation analysis was performed to correlate the femoral neck antetorsion with the measured knee parameters. No significant correlation could be found between the femoral antetorsion and cartilage degeneration of the lateral patellofemoral joint (n.s.), the height of the lateral trochlea (n.s.) and the sulcus angle (n.s.). This study could not document that the femoral neck antetorsion and subsequent internal rotation of the distal femur correlated with the degree of degeneration of the lateral facet of the patellofemoral joint. Clinically, femoral internal rotation may play a minor role in the development of lateral patellofemoral joint degeneration