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

Pacific climate influences on ocean conditions and extreme shell growth events in the Northwestern Atlantic (Gulf of Maine)

The Gulf of Maine is undergoing rapid environmental and ecological changes, yet our spatial and temporal understanding of the climatic and hydrographic variability in this region, including extreme events, is limited and biased to recent decades. In this study, we utilize a highly replicated, multi-century master shell growth chronology derived from the annual increments formed in the shells of the long-lived bivalve Arctica islandica collected in 38 m from the central coastal region in the Gulf of Maine. Our results indicate that shell growth is highly synchronous and inversely related to local seawater temperatures. Using composite analyses of extreme shell growth events from CE 1900 to 2013, we extend our understanding of the factors driving oceanic variability and shell growth in the Northwestern Atlantic back to CE 1761. We suggest that extreme shell growth events are primarily controlled by Gulf of Maine sea surface temperature (SST) and stratification conditions, which in turn appear to be largely influenced by SST patterns in the Pacific Ocean through their influence on mid-latitude atmospheric circulation patterns and the location of the eddy-driven jet. The large-scale jet dynamics during these extreme years manifest as precipitation and moisture transport anomalies and regional SST conditions in the Gulf of Maine that either enhance or inhibit shell growth. Pacific climate variability is thus an important, yet understudied, influence on Gulf of Maine ocean conditions

Predictors of tuberculosis (TB) and antiretroviral (ARV) medication non-adherence in public primary care patients in South Africa: A cross sectional study

Background: Despite the downward trend in the absolute number of tuberculosis (TB) cases since 2006 and the fall in the incidence rates since 2001, the burden of disease caused by TB remains a global health challenge. The co-infection between TB and HIV adds to this disease burden. TB is completely curable through the intake of a strict anti-TB drug treatment regimen which requires an extremely high and consistent level of adherence.The aim of this study was to investigate factors associated with adherence to anti-TB and HIV treatment drugs. Methods: A cross-sectional survey method was used. Three study districts (14 primary health care facilities in each) were selected on the basis of the highest TB caseload per clinic. All new TB and new TB retreatment patients were consecutively screened within one month of anti-tuberculosis treatment. The sample comprised of 3107 TB patients who had been on treatment for at least three weeks and a sub-sample of the total sample were on both anti-TB treatment and anti-retro-viral therapy(ART) (N = 757). Data collection tools included: a Socio-Demographic Questionnaire; a Post-Traumatic-Stress-Disorder (PTSD) Screen; a Psychological Distress Scale; the Alcohol Use Disorder Identification Test (AUDIT); and self-report measures of tobacco use, perceived health status and adherence to anti-TB drugs and ART. Results: The majority of the participants (N = 3107) were new TB cases with a 55.9% HIV co-infection rate in this adult male and female sample 18 years and older. Significant predictors of non-adherence common to both anti-TB drugs and to dual therapy (ART and anti-TB drugs) included poverty, having one or more co-morbid health condition, being a high risk for alcohol mis-use and a partner who is HIV positive. An additional predictor for non-adherence to anti-TB drugs was tobacco use. Conclusions: A comprehensive treatment programme addressing poverty, alcohol mis-use, tobacco use and psycho-social counseling is indicated for TB patients (with and without HIV). The treatment care package needs to involve not only the health sector but other relevant government sectors, such as social development.IS

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

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