Semi-supervised clinical text classification with Laplacian SVMs: An application to cancer case management

AbstractObjectiveTo compare linear and Laplacian SVMs on a clinical text classification task; to evaluate the effect of unlabeled training data on Laplacian SVM performance.BackgroundThe development of machine-learning based clinical text classifiers requires the creation of labeled training data, obtained via manual review by clinicians. Due to the effort and expense involved in labeling data, training data sets in the clinical domain are of limited size. In contrast, electronic medical record (EMR) systems contain hundreds of thousands of unlabeled notes that are not used by supervised machine learning approaches. Semi-supervised learning algorithms use both labeled and unlabeled data to train classifiers, and can outperform their supervised counterparts.MethodsWe trained support vector machines (SVMs) and Laplacian SVMs on a training reference standard of 820 abdominal CT, MRI, and ultrasound reports labeled for the presence of potentially malignant liver lesions that require follow up (positive class prevalence 77%). The Laplacian SVM used 19,845 randomly sampled unlabeled notes in addition to the training reference standard. We evaluated SVMs and Laplacian SVMs on a test set of 520 labeled reports.ResultsThe Laplacian SVM trained on labeled and unlabeled radiology reports significantly outperformed supervised SVMs (Macro-F1 0.773 vs. 0.741, Sensitivity 0.943 vs. 0.911, Positive Predictive value 0.877 vs. 0.883). Performance improved with the number of labeled and unlabeled notes used to train the Laplacian SVM (pearson’s ρ=0.529 for correlation between number of unlabeled notes and macro-F1 score). These results suggest that practical semi-supervised methods such as the Laplacian SVM can leverage the large, unlabeled corpora that reside within EMRs to improve clinical text classification

A case of congenital unilateral absence of the vas deferens

Background Congenital unilateral absence of the vas deferens occurs in 0.5%–1.0% of males. It has been associated with various genitourinary abnormalities, including renal agenesis. We report a case of congenital unilateral absence of the vas deferens found incidentally during vasectomy in a patient with known unilateral renal agenesis. Case presentation A 24-year-old male presented to our urology clinic requesting vasectomy. His past history was significant for left renal agenesis. Following successful right vasectomy, several attempts to locate the left vas deferens were unsuccessful. We diagnosed congenital unilateral absence of the vas deferens. Follow-up semen analysis showed azoospermia. Conclusion As vasectomies are increasingly performed in outpatient settings, it is imperative that physicians be aware of this condition, which can be recognized by a simple physical exam. Recognition could prevent unnecessary surgery and prompt providers to investigate for associated abnormalities

Systemic mastocytosis: a rare cause of osteoporosis

A 61-year old female patient who was referred to the endocrine clinic for evaluation of an elevated alkaline phosphatase. She was originally referred to gastroenterology (GI), however no GI causes of elevated alkaline phosphatase was found. Upon fractionation, it was noted that she had elevation in bone specific alkaline phosphatase. Past history was significant for hypertension, atrial fibrillation and menopause 6 years ago. She was also noted to have multiple drug allergies manifesting as urticaria and flushing. Review of the past records revealed a persistently elevated alkaline phosphatase over the last two years. She had no history of falls or fractures. Computed tomography (CT) abdomen done to rule out biliary pathology, revealed osteosclerotic and osteolytic lesion in the pelvis concerning neoplastic disease. Bone marrow biopsy however, was negative for cancer but consistent with systemic mastocytosis (SM). Dual Energy X-ray absorbimetery (DEXA) scan revealed osteoporosis Serum tryptase levels were elevated; further genetic analysis showed a positive CKIT D816 mutation. She was started on bisphosphonates (initially alendronate and then ibandronate). Upon follow up at two years she had not experienced any fractures and her bone mineral density also had improved significantly

GEMS: Goals, Expectations, Measurements and Strategies for Critical Thinking and Decision-Making

GEMS are sparkling stones that are very attractive and precious. Its attractiveness and spackles are derived from the meticulous precision of the way the stones were cut. It takes a perfect design, planning and execution to achieve such results. GEMS is also an acronym that represents leadership excellence. GEMS stands for Goals, Expectations, Measurements, and Strategies. The team concluded that a leadership handbook for the 21st century must be simple but forward looking in addressing the issues of today and the immediate future. The handbook is broken down into sections that are easy to follow. It is design for leaders to think critically in all aspects of the business. Effective leaders must know and understand clearly the goals or mission of the company. The handbook provides a detailed but simple way on how to formulate company’s goals. Shared goals are more effective than top down goals as it gives all employees or participants of the company ownership which translates to empowerment and accountability. Expectations are standards developed by each company and are designed to maintain its competitive advantage. Critical thinking is an expectation that organizations look for from the employees. This handbook laid out the techniques leaders need to know to achieve such goals. As goals and expectations are clearly defined and preached to the leader’s constituency another important element of GEMS is Measurement. Once goals are set and agreed with by all stakeholders the next important step is the development of a measuring tool. The company’s success is dependent upon the effective execution of each processes or tasks of each and every employees in the organization. The handbook covered the key role that Human Resources played in ensuring its success. Finally, the last element of GEMS is strategy. It outlined in detail how a global leader can be consistently successful in this dynamic business environment. The important topics discussed were goal setting, resources required, timeline, and actual execution of the strategy. A successful implementation of a leadership handbook will only be achieved if the organizational leadership accepts and understands the necessity of thinking outside the box. This handbook is intentionally design to force global leaders to think beyond the norm of doing business. It forces all employees and senior leadership to be self-critical and accept changes as the new normal in doing business. We all hope that you enjoy the fruits of this excellent leadership handbook

Four new additions to the marine flora of Fernando de Noronha Archipelago, tropical western South Atlantic Ocean

Non

Apolar Compounds in Seaweeds from Fernando de Noronha Archipelago (Northeastern Coast of Brazil)

Hyphenated techniques of gas chromatography coupled to mass spectrometer were used to determine fatty acids in eleven species of seaweeds from Fernando de Noronha archipelago. The main compounds detected in all studied species were the alcohol phytol and the fatty acids 14 : 0; 15 : 0; 16 : 0; 18 : 0; 18 : 1 n9; 18 : 2 Δ9,12; 20 : 4; 20 : 5. These fatty acids are commonly found in seaweeds present in warm regions. Thus, we found no specificity in the presence of a particular set of fatty acids and the studied species indicating that they are not useful as taxonomic indicators. However, they could be used in a comparative study with algae found in polluted area because many of the studied seaweeds are widespread and Fernando de Noronha has low human influence

Genetic divergence analysis in groundnut (Arachis Hypogaea l.) Under calcareous soil of northen Karnataka

Groundnut (Arachis hypogaea L.) is an important annual oilseed legume crop, valued as a rich source of proteins, minerals and vitamins. It is an unpredictable crop due to its underground pods development. For improvement of yield in groundnut direct selection is often misleading. The knowledge of existing variability is essential for developing high yielding genotypes in groundnut. An experiment was conducted with 43 gronudnut genotypes at college of agriculture, Vijayapura, UAS Dharwad, during kharif, 2013-14 to study the genetic diversity for IDC resistance related traits, yield and its component characters. The estimates of GCV and PCV were high for net plot yield (22.722 and 47.915) and low heritability with moderate GA as % mean was observed for net plot yield (22.5 and 22.197). The genotypes were highly diverse for IDC resistance and classified into 18 clusters. The diversity among the genotypes measured by intra-cluster & inter cluster distance in the present investigation was adequate for improvement of groundnut genotypes for IDC resistance by hybridization and selection. Seventeen clusters found to be solitary these can be used as promising parents for hybridization programme for obtaining high heterotic response for IDC resistance and thus better sergeants in groundnut

Genetic Connectivity of a Coral Reef Ecosystem Predator: The Population Genetic Structure and Evolutionary History of the Caribbean Reef Shark (Carcharhinus perezi)

Aim The Caribbean reef shark (Carcharhinus perezi) is one of few extant reef sharks inhabiting the Atlantic Ocean. Its variability in movements across habitat types suggests the possibility of a complex genetic population structure. Here, we use mitochondrial and nuclear DNA to investigate the genetic connectivity of the Caribbean reef shark across contemporary and evolutionary time-scales and relate our findings to the ecology of this understudied species. Location Tropical western Atlantic and Caribbean. Methods Samples were obtained from 216 individuals from six western Atlantic and Caribbean locations. Individuals were genotyped at seven nuclear microsatellite DNA loci and sequenced at two mitochondrial (control region [CR]; NADH dehydrogenase subunit 4 [ND4]) and one nuclear locus (lactate dehydrogenase [LDH]). Analyses to resolve the population genetic structure and evolutionary history of this species were adopted. Results Sequencing of the CR (1,068 bp, n = 216), ND4 (741 bp, n = 213) and LDH (258 bp, n = 165) loci, resolved 11, 8 and 13 unique haplotypes (or alleles), respectively. Overall, Caribbean reef sharks showed low levels of genetic diversity and most marker sets identified strong genetic differences (FSTand ΦST) between sharks sampled in Brazil versus all other locations (msat FST \u3e 0.017; CR-ND4 ΦST \u3e 0.013). Mitochondrial DNA showed evidence of increased genetic partitioning among western North Atlantic sampling sites, although widespread haplotype sharing (~85%–92%) and a shallow population history were found. Main Conclusions Findings of genetic differentiation are concordant with previous movement studies showing residency and/or site-fidelity to specific locations by individuals. However, similar to other reef shark studies, we found that the level of genetic connectivity among populations was context dependent—i.e., sharks occupying isolated habitats showed greater genetic differentiation compared with those sharks occupying semi-isolated or continuous reef habitats. Furthermore, low genetic diversity and a shallow mitochondrial population history were found, suggesting historical demographic fluctuations, including population collapse and more recent expansions