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

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

Determination of the aldosterone/plasma renin activity ratio for the screening of primary hyperaldosteronism in essential hypertension: a multicentric study

El hiperaldosteronismo primario (HAP) es una afección caracterizada por la producción inapropiadamente elevada y una relativa autonomía del sistema renina-angiotensina. Estimaciones previas, basadas sólo en la evaluación de hipertensos con hipokalemia, consideraban al HAP como una causa poco frecuente de hipertensión (1%). Sin embargo, estudios actuales fundamentados en el cálculo de la relación aldosterona/ actividad de renina plasmática (RAA) arrojan una incidencia mayor (5-10%), siendo la hipertensión arterial (HTA) normokalémica la presentación más frecuente. Dada la amplitud de los valores de corte de la RAA, el Departamento de Suprarrenal de SAEM diseñó un estudio multicéntrico prospectivo en una población de Argentina con el objetivo de establecer nuestro propio valor y determinar así la prevalencia de HAP. Fueron estudiados 353 individuos de ambos sexos, 104 controles normotensos, sin antecedentes familiares de HTA y 249 pacientes hipertensos. Se indicó dieta normosódica y la suspensión de antihipertensivos que interfieran con el eje mineralocorticoideo. Las determinaciones de la actividad de renina plasmática (ARP), DIA-SorinRIA, y de aldosterona, RIA-DPC, fueron realizadas en un único laboratorio. Se realizó ionograma y se evaluaron parámetros clínicos y bioquímicos de síndrome metabólico. La RAA calculada según el percentilo 95 en los controles, fue establecida en la cifra de 36 como valor de corte para sospechar HAP en los hipertensos, requiriéndose una concentración de aldosterona >15 ng/ml. Con una RAA≥36, se realizaron pruebas confirmatorias de sobrecarga salina o de fludrocortisona. La RAA fue ≥36 en 31/249 pacientes, confirmándose HAP en 8 (7 adenomas y 1 hiperplasia), con una prevalencia del 3.2%. Los restantes no completaron estudios confirmatorios. La presencia de síndrome metabólico fue similar en los hipertensos con y sin HAP. En conclusión, este primer estudio multicéntrico argentino determinó nuestro valor de corte de la RAA en 36. Su aplicación permitió establecer una prevalencia de HAP del 3,2% que, aunque podría estar subestimada, resulta significativamente mayor que la previa histórica y concuerda con la incidencia referida en la bibliografía.Primary hyperaldosteronism (PHA) or Conn's disease was classically suspected in the presence of hypertension (H) and hypokalemia. It was previously considered as a rare cause of H, being reported in only 1% of hypertensive patients. It can be caused by an adrenal adenoma (the former usual presentation) or by adrenal hyperplasia. But since the use of the aldosterone/plasma renin activity ratio (AAR) as the screening method in the last years, it is currently considered as almost the most frequent cause of secondary H., accounting for 5-10% of essential H. Plasma rennin activity (PRA) determination is a laborious procedure with low reproducibility and it directly affects the AAR; thus each laboratory must assess its own cut-off value. Therefore, in the Adrenal Department of the Argentine Society of Endocrinology and Metabolism (SAEM), we performed this multicentric prospective study of a population of Argentina with the aim of assessing our own AAR cut-off level in normotensive controls in order to apply it for PHA screening in essential hypertensive patients. We studied 353 adult subjects: 104 controls, aged 45,18 ± 13,78 years-old ( X±SD), with no history of arterial hypertension in their first-degree relatives and with two separate day-registry of blood pressure≤ 139/85 mmHg and 249 hypertensive patients, aged 51± 13,6 years-old ( X ± SD), with arterial blood pressure≥ 140/90 mmHg in the sitting position. Subjects with cardiac, renal, hepatic and neurological diseases were excluded as well as those with Cushing´s syndrome, hyperthyroidism, untreated hypothyroidism, diabetes mellitus and patients under glucocorticoids, oral contraceptive pills or estrogen therapy. A normal sodium diet was indicated and potassium was supplemented when needed. Blood was withdrawn between 8 and 10:00 a.m. with the subjects in the upright position. Aldosterone (A) was determined by DPC radioimmunoassay (RIA) and PRA, by DIA-Sorin RIA. The A normal levels are 4-30 ng/dl for ambulatory individuals on a normal sodium diet and the PRA normal values are < 3,3 ng/ml/h. In order to avoid false positive results in the hypertensive group, AAR was calculated when A was above 15 ng/dl. We measured the waist circumference and we determined the body mass index. Blood sodium, potassium, calcium, urea, creatinine, cholesterol, HDL-C, LDL-C, triglyceride and liver function tests were performed. Statistical Analysis and Results Since the AAR variable showed a non-normal distribution, the cut-off value was considered as the 95th percentile in the control group, which was calculated as 36. This is also in accordance to the function of the empirical distribution of Collings and Hamilton. In our 249 hypertensive patients, 31 had an AAR ≥ 36. PHA was confirmed in 8: seven has an adrenal adenoma and one had hyperplasia. The prevalence of PHA in our population was 3,2 %, with a 95th confidence interval ranging from 1,4 to 6,2 %. In the remaining 23 patients, confirmatory tests could not be completed. There was no correlation between the severity of the hypertension and the AAR value, with no statistical significant differences between those with or without PHA. Likewise, we found no correlation between PRA and advancing age. In hypertensive patients, metabolic syndrome was more prevalent than in controls, but it was present to the same extent in those with or without PHA. Conclusions To our knowledge, this is the first multicentric study performed in Argentina to determine the aldosterone/ plasma renin activity ratio in our normotensive control population. Our AAR value of 36 agrees with the levels reported in the international literature: thus an AAR ≥ 36 along with an aldosterone ≥ 15 ng/ml in hypertensive patients lead us to suspect PHA and to perform confirmatory tests. Applying these criteria, we found a prevalence of 3,2% of PHA in essential HTA. It is possible that this value may be underestimated due to the fact that confirmatory tests could not be completed in all the hypertensive subjects with an AAR≥ 36. In spite of this, our prevalence is significantly greater than the historical one and it lies in the range reported in the literature.Fil: Pardes, E.. Gobierno de la Ciudad de Buenos Aires. Hospital General de Agudos "Ramos Mejía"; ArgentinaFil: Belli, S.. Hospital Dr. C. Durand; ArgentinaFil: Cornaló, D.. Hospital Rivadavia; ArgentinaFil: Contreras, Liliana Noemi. Universidad de Buenos Aires. Facultad de Medicina. Instituto de Investigaciones Médicas; Argentina. Consejo Nacional de Investigaciones Cientificas y Tecnicas. Oficina de Coordinacion Administrativa Houssay. Instituto de Investigaciones Medicas; ArgentinaFil: Costa, L.. Hospital Dr. A. Posadas; ArgentinaFil: Chervin. R.. Universidad de Buenos Aires. Facultad de Medicina. Hospital de Clínicas General San Martín; ArgentinaFil: Damilano, S.. Laboratorio de Bioanalítica; ArgentinaFil: Fenili, C.. Laboratorio de Bioanalítica; ArgentinaFil: Gómez, R. M.. Universidad de Buenos Aires. Facultad de Medicina. Hospital de Clínicas General San Martín; ArgentinaFil: Leal Reyna, M.. Complejo Médico Policial "Churruca"; ArgentinaFil: Lupi, S.. Gobierno de la Ciudad de Buenos Aires. Hospital General de Agudos "Ramos Mejía"; ArgentinaFil: Martínez, M.. Hospital Francés; ArgentinaFil: Nofal, M.. Clínica Bazterrica; ArgentinaFil: Ruibal, G.. Gobierno de la Ciudad de Buenos Aires. Hospital General de Agudos "Dr. Teodoro Álvarez"; Argentin

A One Step Optimal Homotopy Analysis Method for Propagation of Harmonic Waves in Nonlinear Generalized Magnetothermoelasticity with Two Relaxation Times under Influence of Rotation

The aim of this paper is to apply OHAM to solve numerically the problem of harmonic wave propagation in a nonlinear thermoelasticity under influence of rotation, thermal relaxation times, and magnetic field. The problem is solved in one-dimensional elastic half-space model subjected initially to a prescribed harmonic displacement and the temperature of the medium. The HAM contains a certain auxiliary parameter which provides us with a simple way to adjust and control the convergence region and rate of convergence of the series solution. This optimal approach has a general meaning and can be used to get fast convergent series solutions of the different type of nonlinear fractional differential equation. The displacement and temperature are calculated for the models with the variations of the magnetic field, relaxation times, and rotation. The results obtained are displayed graphically to show the influences of the new parameters.</jats:p

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

Rab27a and Rab27b control different steps of the exosome secretion pathway

Exosomes are secreted membrane vesicles that share structural and biochemical characteristics with intraluminal vesicles of multivesicular endosomes (MVEs). Exosomes could be involved in intercellular communication and in the pathogenesis of infectious and degenerative diseases. The molecular mechanisms of exosome biogenesis and secretion are, however, poorly understood. Using an RNA interference (RNAi) screen, we identified five Rab GTPases that promote exosome secretion in HeLa cells. Among these, Rab27a and Rab27b were found to function in MVE docking at the plasma membrane. The size of MVEs was strongly increased by Rab27a silencing, whereas MVEs were redistributed towards the perinuclear region upon Rab27b silencing. Thus, the two Rab27 isoforms have different roles in the exosomal pathway. In addition, silencing two known Rab27 effectors, Slp4 (also known as SYTL4, synaptotagmin-like 4) and Slac2b (also known as EXPH5, exophilin 5), inhibited exosome secretion and phenocopied silencing of Rab27a and Rab27b, respectively. Our results therefore strengthen the link between MVEs and exosomes, and introduce ways of manipulating exosome secretion in vivo

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

Lipid Metabolites Enhance Secretion Acting on SNARE Microdomains and Altering the Extent and Kinetics of Single Release Events in Bovine Adrenal Chromaffin Cells

Lipid molecules such as arachidonic acid (AA) and sphingolipid metabolites have been implicated in modulation of neuronal and endocrine secretion. Here we compare the effects of these lipids on secretion from cultured bovine chromaffin cells. First, we demonstrate that exogenous sphingosine and AA interact with the secretory apparatus as confirmed by FRET experiments. Examination of plasma membrane SNARE microdomains and chromaffin granule dynamics using total internal reflection fluorescent microscopy (TIRFM) suggests that sphingosine production promotes granule tethering while arachidonic acid promotes full docking. Our analysis of single granule release kinetics by amperometry demonstrated that both sphingomyelinase and AA treatments enhanced drastically the amount of catecholamines released per individual event by either altering the onset phase of or by prolonging the off phase of single granule catecholamine release kinetics. Together these results demonstrate that the kinetics and extent of the exocytotic fusion pore formation can be modulated by specific signalling lipids through related functional mechanisms

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