Using Machine Learning and Natural Language Processing to Review and Classify the Medical Literature on Cancer Susceptibility Genes

PURPOSE: The medical literature relevant to germline genetics is growing exponentially. Clinicians need tools monitoring and prioritizing the literature to understand the clinical implications of the pathogenic genetic variants. We developed and evaluated two machine learning models to classify abstracts as relevant to the penetrance (risk of cancer for germline mutation carriers) or prevalence of germline genetic mutations. METHODS: We conducted literature searches in PubMed and retrieved paper titles and abstracts to create an annotated dataset for training and evaluating the two machine learning classification models. Our first model is a support vector machine (SVM) which learns a linear decision rule based on the bag-of-ngrams representation of each title and abstract. Our second model is a convolutional neural network (CNN) which learns a complex nonlinear decision rule based on the raw title and abstract. We evaluated the performance of the two models on the classification of papers as relevant to penetrance or prevalence. RESULTS: For penetrance classification, we annotated 3740 paper titles and abstracts and used 60% for training the model, 20% for tuning the model, and 20% for evaluating the model. The SVM model achieves 89.53% accuracy (percentage of papers that were correctly classified) while the CNN model achieves 88.95 % accuracy. For prevalence classification, we annotated 3753 paper titles and abstracts. The SVM model achieves 89.14% accuracy while the CNN model achieves 89.13 % accuracy. CONCLUSION: Our models achieve high accuracy in classifying abstracts as relevant to penetrance or prevalence. By facilitating literature review, this tool could help clinicians and researchers keep abreast of the burgeoning knowledge of gene-cancer associations and keep the knowledge bases for clinical decision support tools up to date

Looking-ahead in backtracking algorithms for abstract argumentation

We refine implemented backtracking algorithms for a number of problems related to Dung's argumentation frameworks. Under admissible, preferred, complete, stable, semi stable, and ideal semantics we add enhancements, what are so-called global looking-ahead pruning strategies, to the-state-of-the-art implementations of two problems. First, we tackle the extension enumeration problem: constructing some/all set(s) of acceptable arguments of a given argumentation framework. Second, we address the acceptance decision problem: deciding whether an argument is in some/all set(s) of accepted arguments of a given argumentation framework. The experiments that we report show that the speedup gain of the new enhancements is quite significant

HEPATOPROTECTIVE AND HEPATOTHERAPUTIC EFFECTS OF PROPOLIS AGAINST D-GALACTOSAMINE/LIPOPOLYSACCHARIDE-INDUCED LIVER DAMAGE IN RATS

Objective: The aim of the present study was to investigate the potential hepatoprotective and hepatotherapeutic activities of propolis against D-galactosamine and lipopolysaccharide (D-GaIN/LPS)-induced hepatotoxicity in rats.Methods: Hepatotoxicity was induced in rats by intra peritoneal injection of GalN (300 mg/kg) and LPS (30 μg/kg). In the hepatoprotection experiment, propolis was administered orally for 10 days before induction of hepatoxicity. In another experiment (hepatotherapy), propolis was dosed immediately after GalN/LPS injection.Results: Injection of GalN/LPS to rats induced hepatic damage that was manifested by a significant increase in the activities of aminotransferases, alkaline phosphatase, lactate dehydrogenase and levels of tumor necrosis factor-alpha (TNF-α) and total bilirubin in serum. Liver homogenate of intoxicated animals had the lower content of reduced glutathione with increased levels of the hepatic malondialdehyde and caspase-3 enzyme. Histological data presented marked damage in liver sections of intoxicated rats. Oral dosing of propolis before or once immediately after intoxication reversed these altered parameters near to normal values.Conclusion: Liver apoptotic events such as DNA fragmentation and increased caspase-3 activity observed during intoxication were prevented by pre and post- propolis treatment. These results suggest that propolis could afford significant protection and therapy in alleviation of hepatotoxicity.Â

Evaluation of the safety and antioxidant activities of Crocus sativus and Propolis ethanolic extracts

AbstractThe possible toxicological effects and in vitro antioxidant activity of the ethanolic extracts of Crocus sativus and Propolis were investigated. Both extracts did not cause any mortalities or signs of toxicity in mice when administered orally at doses up to 5g/kgb.wt. In the sub-chronic study; the tested extracts did not produce any significant change in liver and kidney functions of rats, following oral administration for 8 successive weeks at doses of 500mg/kgb.wt. of each. Propolis showed remarkable in vitro antioxidant activity at concentrations of (40–100mg/ml). In contrast, the ethanolic extract of C. sativus ethanolic extract showed weak antioxidant activity in concentrations of (1–10mg/ml) while at concentrations of (20–100mg/ml) failed to exhibit any antioxidant activity. It was concluded that: both extracts were non-toxic, as they did not cause any mortalities or signs of toxicity in mice when administered orally at doses up to 5g/kgb.wt. Daily oral administration of C. sativus, Propolis ethanolic extracts alone or in combination for 8 successive weeks to rats was quiet safe and didn't cause any toxic changes in liver and kidney. Antioxidant study showed that Propolis ethanolic extract was a more potent antioxidant than C. sativus extract

Encoding argument graphs in logic

International audienceArgument graphs are a common way to model argumentative reasoning. For reasoning or computational purposes, such graphs may have to be encoded in a given logic. This paper aims at providing a systematic approach for this encoding. This approach relies upon a general, principle-based characterization of argumentation semantics

Resistance of barley landraces and wild barley populations to powdery mildew in Jordan

Eleven barley (Hordeum vulgare L.) landraces and 12 wild barley (H. spontaneum) populations, collected from diverse eco-geographical regions of Jordan, were screened for resistance to powdery mildew. The average powdery mildew disease score (based on a 0 to 4 severity scale) wa

Herpes Simplex Virus Type 2 Seroprevalence among Different National Populations of Middle East and North African Men

© 2018 The Author(s). Published by Wolters Kluwer Health, Inc. on behalf of the American Sexually Transmitted Diseases Association. Background There are limited data on herpes simplex virus type 2 (HSV-2) seroprevalence in the Middle East and North Africa (MENA). We examined country- and age-specific HSV-2 seroprevalence among select MENA populations residing in Qatar. Methods Sera were collected from male blood donors attending Hamad Medical Corporation between June 2013 and June 2016. Specimens were screened for anti-HSV-2 IgG antibodies following a 2-test algorithm: HerpeSelect 2 ELISA was used to identify HSV-2-positive specimens, and Euroline-WB was used to confirm positive and equivocal specimens for final HSV-2 status. Trends and associations with HSV-2 seropositivity were assessed. Results Of the 2077 tested sera, 61 were found and confirmed positive. The proportion of those confirmed positive increased steadily with HerpeSelect 2 ELISA index value, ranging from 16.3% for index values of 1.101 to 1.999 to 92.9% for index values of 4 or greater. Nationality-specific seroprevalence was 6.0% (95% confidence interval [CI], 4.1%-8.8%) in Qataris, 5.3% (95% CI, 2.5%-11.1%) in Iranians, 4.2% (95% CI, 1.8%-9.5%) in Lebanese, 3.1% (95% CI, 1.2%-7.7%) in Sudanese, 3.0% (95% CI, 1.4%-6.4%) in Palestinians, 2.2% (95% CI, 1.1%-4.3%) in Egyptians, 2.0% (95% CI, 1.0%-5.0%) in Syrians, 1.0% (95% CI, 0.3%-3.6%) in Jordanians, 0.7% (95% CI, 0.1%-3.7%) in Yemenis, and 0.5% (95% CI, 0.1%-2.8%) in Pakistanis. There was evidence for higher seroprevalence in older age groups. Conclusions The seroprevalence of HSV-2 was in the range of few percentage points. There were no major differences in seroprevalence by nationality. These findings add to our understanding of HSV-2 epidemiology in MENA and indicate unmet needs for sexual health and control of sexually transmitted infections.Funding text #1 From the *Infectious Disease Epidemiology Group, Weill Cornell Medicine—Qatar, Cornell University, Qatar Foundation—Education City; †Department of Biomedical Science, College of Health Sciences, and ‡BioMedical Research Center, Qatar University, Doha, Qatar; and §Department of Healthcare Policy and Research, Weill Cornell Medi-cine, Cornell University, Ithaca, NY Acknowledgments: The authors gratefully acknowledge the administrative support of Ms Adona Canlas. They are also grateful to Dr Asmaa Al-Marwani, Ms Maria Samatti, and Ms Sana Abohasera for their work on blood specimen collection. The authors are further grateful for sup-port provided by the Biostatistics, Epidemiology, and Biomathematics Research Core at Weill Cornell Medicine—Qatar. Funding text #2 Funding: Testing kits were provided through pilot funding by the Biomedical Research Program at Weill Cornell Medicine—Qatar. Funding text #3 G.K.N. acknowledges support by Qatar University internal grant No. QUST-CHS-SPR-15/16-7. L.J.A. and S.R.D. acknowledge study conception and design support through NPRP grant number 9-040-3-008 from the Qatar National Research Fund (a member of Qatar Foundation), and G.K.N. acknowledges support from the Qatar National Research Fund UREP grant number UREP18-001-3-001. The findings achieved herein are solely the responsibility of the authors

Thermal Radiation and MHD Effects on Free Convective Flow of a Polar Fluid through a Porous Medium in the Presence of Internal Heat Generation and Chemical Reaction

An analysis is presented to study the MHD free convection with thermal radiation and mass transfer of polar fluid through a porous medium occupying a semi-infinite region of the space bounded by an infinite vertical porous plate with constant suction velocity in the presence of chemical reaction, internal heat source, viscous and Darcy's dissipation. The highly nonlinear coupled differential equations governing the boundary layer flow, heat, and mass transfer are solved by using a two-term perturbation method with Eckert number as a perturbation parameter. The results are obtained for velocity, angular velocity, temperature, concentration, skin friction, Nusselt number, and Sherwood number. The effect of various material parameters on flow, heat, and mass transfer variables is discussed and illustrated graphically

Performance evaluation of four type-specific commercial assays for detection of herpes simplex virus type 1 antibodies in a Middle East and North Africa population.

The number of diagnostic assays for the detection of herpes simplex virus type 1 (HSV-1) antibodies has increased over the years. However, their performance characteristics could vary among global populations. To investigate performance of two commercial ELISA kits, HerpeSelect1 ELISA and Euroimmun Anti-HSV-1 (gC1) ELISA (IgG); and two commercial immunoblot (IB)/Western blot (WB) assays, HerpeSelect1 and 2 Immunoblot IgG, and Euroimmun Anti-HSV-1/HSV-2 gG2 Euroline-WB (IgG/IgM); in detecting HSV-1 antibodies in a Middle East and North Africa (MENA) population. Blood specimens were collected from blood donors in Doha, Qatar, June 2013-2016. Twenty specimens were randomly selected from 10 MENA nationalities (Egypt, Iran, Jordan, Lebanon, Pakistan, Palestine, Qatar, Sudan, Syria, and Yemen; total = 200), and tested for HSV-1 antibodies. Across all six comparisons between assays, positive percent agreement ranged between 95.7% (95% CI: 91.4-98.3%) and 100.0% (95% CI: 97.8-100.0%). Negative percent agreement ranged between 86.2% (95% CI: 68.3-96.1%) and 96.2% (95% CI: 80.4-99.9%). Overall percent agreement ranged between 95.7% (95% CI: 91.7-97.8%) and 99.4% (95% CI: 96.7-99.9%). Cohen's kappa statistic ranged between 0.84 (95% CI: 0.73-0.95) and 0.98 (95% CI: 0.93-1.00). Compared against IB/WB, HerpeSelectand Euroimmun had sensitivities and specificities >96% and >86%, respectively. Positive and negative predictive values were >97% and >83%, respectively. The assays showed excellent concordance with one another, and with a high kappa statistic. The ELISA kits demonstrated robust diagnostic performance compared to the IB/WB assays. These findings support the assays' utility in clinical diagnosis and research in MENA populations

Trauma and Emergency Anesthesia Checklists

This study aimed at investigating the anesthesiologist critical role in stabilizing the patient and maintaining safe conditions during this dynamic period and frequently will find it necessary to shift management strategies as the case evolves. Ant to analyze the followed checklist upon the arrival of trauma patients and the using of the emergency anesthesia procedures. Besides the attempt to justify the use of medical checklists, and following up the checklists’ protocols, especially in the field of emergency anesthesia procedures for trauma patients by analyzing the most used checklists worldwide, and demonstrates the importance of adherence to regulations in the checklists for trauma patients. The study concluded that trauma and emergency anesthesia checklist can improve communication in the care of critically ill patients requiring an anesthetic