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

The Case for Quantum Key Distribution

Quantum key distribution (QKD) promises secure key agreement by using quantum mechanical systems. We argue that QKD will be an important part of future cryptographic infrastructures. It can provide long-term confidentiality for encrypted information without reliance on computational assumptions. Although QKD still requires authentication to prevent man-in-the-middle attacks, it can make use of either information-theoretically secure symmetric key authentication or computationally secure public key authentication: even when using public key authentication, we argue that QKD still offers stronger security than classical key agreement.Comment: 12 pages, 1 figure; to appear in proceedings of QuantumComm 2009 Workshop on Quantum and Classical Information Security; version 2 minor content revision

The Social Climbing Game

The structure of a society depends, to some extent, on the incentives of the individuals they are composed of. We study a stylized model of this interplay, that suggests that the more individuals aim at climbing the social hierarchy, the more society's hierarchy gets strong. Such a dependence is sharp, in the sense that a persistent hierarchical order emerges abruptly when the preference for social status gets larger than a threshold. This phase transition has its origin in the fact that the presence of a well defined hierarchy allows agents to climb it, thus reinforcing it, whereas in a "disordered" society it is harder for agents to find out whom they should connect to in order to become more central. Interestingly, a social order emerges when agents strive harder to climb society and it results in a state of reduced social mobility, as a consequence of ergodicity breaking, where climbing is more difficult.Comment: 14 pages, 9 figure

Identification of Alkaloids from Hippeastrum aulicum (Ker Gawl.) Herb.(Amaryllidaceae) Using CGC-MS and Ambient Ionization Mass Spectrometry (PS-MS and LS-MS)

Amaryllidaceae alkaloids are well-known isoquinolines which have demonstrated a wide range of biological activities such as antiviral, anticancer, acetylcholinesterase inhibition, antimalarial, among others. Mass spectrometry (MS) studies based on capillary gas chromatography (CGC), paper spray (PS), and leaf spray (LS) ionization were carried out for alkaloid investigation of the native Brazilian species Hippeastrum aulicum, along with nuclear magnetic resonance (NMR) techniques. Thirty-one alkaloids were identified including the new compound haemanthamine N-oxide. The results from PS- and LS-MS techniques were consistent with those observed in CGC-MS analysis. To the best of our knowledge, it is the first study combining NMR, CGC-MS and the ambient ionization-mass spectrometry (PS- and LS-MS) on Amaryllidaceae plants

Fungos associados ao declínio da videira no Nordeste do Brasil.

Suplemento. Edição dos Resumos do 44 Congresso Brasileiro de Fitopatologia, Bento Gonçalves, ago. 2011

Rapid tests and urine sampling techniques for the diagnosis of urinary tract infection (UTI) in children under five years: a systematic review

Background: Urinary tract infection (UTI) is one of the most common sources of infection in children under five. Prompt diagnosis and treatment is important to reduce the risk of renal scarring. Rapid, cost-effective, methods of UTI diagnosis are required as an alternative to culture. Methods: We conducted a systematic review to determine the diagnostic accuracy of rapid tests for detecting UTI in children under five years of age. Results: The evidence supports the use of dipstick positive for both leukocyte esterase and nitrite (pooled LR+ = 28.2, 95% CI: 17.3, 46.0) or microscopy positive for both pyuria and bacteriuria (pooled LR+ = 37.0, 95% CI: 11.0, 125.9) to rule in UTI. Similarly dipstick negative for both LE and nitrite (Pooled LR- = 0.20, 95% CI: 0.16, 0.26) or microscopy negative for both pyuria and bacteriuria (Pooled LR- = 0.11, 95% CI: 0.05, 0.23) can be used to rule out UTI. A test for glucose showed promise in potty-trained children. However, all studies were over 30 years old. Further evaluation of this test may be useful. Conclusion: Dipstick negative for both LE and nitrite or microscopic analysis negative for both pyuria and bacteriuria of a clean voided urine, bag, or nappy/pad specimen may reasonably be used to rule out UTI. These patients can then reasonably be excluded from further investigation, without the need for confirmatory culture. Similarly, combinations of positive tests could be used to rule in UTI, and trigger further investigation

La vida en las lagunas, una propuesta de turismo científico

Fil: Berasain, Gustavo. Estación Hidrobiológica Chascomús. Dirección de Desarrollo Pesquero. Ministerio de Asuntos Agrarios y Producción; ArgentinaFil: Lavigne, Andrea S.. División Ficología. Facultad de Ciencias Naturales y Museo. Universidad Nacional de La Plata; ArgentinaFil: Marzoratti, Graciana. Liceo Víctor Mercante. Universidad Nacional de La Plata; ArgentinaFil: Sunesen, Inés. División Ficología. Facultad de Ciencias Naturales y Museo. Universidad Nacional de La Plata; ArgentinaFil: Cano, María Gabriela. División Ficología. Facultad de Ciencias Naturales y Museo. Universidad Nacional de La Plata; ArgentinaFil: Brentassi, María Eugenia. División Entomología. Facultad de Ciencias Naturales y Museo. Universidad Nacional de La Plata; ArgentinaFil: Velasco, Claudia. Estación Hidrobiológica Chascomús. Dirección de Desarrollo Pesquero. Ministerio de Asuntos Agrarios y Producción; ArgentinaFil: Dos Santos, Analía. División Ficología. Facultad de Ciencias Naturales y Museo. Universidad Nacional de La Plata; ArgentinaFil: Atencio, Adrián. División Ficología. Facultad de Ciencias Naturales y Museo. Universidad Nacional de La Plata; ArgentinaFil: Carbone, Alejandra. Instituto de Fisiología Vegetal. Departamento de Biología y Ecología. Facultad de Ciencias Agrarias y Forestales. Universidad Nacional de La PlataFil: López Armengol, María Fernanda. Secretaría de Extensión, Becas y Acción Social. Facultad de Ciencias Naturales y Museo. Universidad Nacional de La Plata; Argentin

Social Preferences, Skill Segregation and Wage Dynamics

We study the earning structure and the equilibrium asignment of workers to firms in a model in which workers have social preferences, and skills are perfectly substitutable in production. Firms offer long-term contracts, and we allow for frictions in the labour market in the form of mobility costs. The model delivers specific predictions about the nature of worker flows, about the characteristic of workplace skill segregation, and about wage dispersion both within and cross firms. We shows that long-term contracts in the resence of social preferences associate within-firm wage dispersion with novel "internal labour market" features such as gradual promotions, productivity-unrelated wage increases, and downward wage flexibility. These three dynamic features lead to productivity-unrelated wage volatily within firms.Publicad

Seasonal wetlands in the Pacific coast of Costa Rica and Nicaragua: environmental characterisation and conservation state.

Seasonal wetlands in the Pacific coast of Costa Rica and Nicaragua: environmental characterisation and conservation status On the Pacific coast of Nicaragua and Costa Rica, rainfall patterns and clay-rich soils allow the development of extensive wetlands. These environments constitute unique habitats for the maintenance of aquatic biodiversity and provide significant ecological services to the surrounding seasonal dry forest. Despite these benefits, wetlands have been severely reduced in the last four decades, and little information is available on their biology and current conservation status. Here, we describe the main limnological traits of 30 sites representing different types of wetlands from four distinct physiographic regions: Tempisque River Lower Basin; Tempisque River Middle Basin; Delta del Estero Real River; and the Oriental Region of Nicaragua. At each site, samples were taken at the beginning (infilling phase), middle (maximum flooded areas) and end (desiccation phase) of the 2010 hydrological cycle. We analysed a set of water parameters (depth, temperature, pH, conductivity, dissolved oxygen, major ions and nutrient concentrations) and biological parameters (shoreline vegetation, chlorophyll a, macrophyte cover) and assessed the conservation status of wetlands using the Index of the State of Conservation of Shallow Lentic Ecosystems (ECELS). In most sites, the water was relatively clear with near basic pH-values, low conductivity, and low levels of dissolved oxygen, nitrates, nitrites, phosphates and sulphates. Chlorophyll a and alkalinity varied through the season and among regions. Ion concentrations were generally low in most wetlands except for those close to estuarine and marine coastal areas. A total of 49 taxa of aquatic plants were found in the study sites, the most common being the emergent Typha domingensis and Thalia geniculata, and the floating Pistia stratiotes and Eichhornia crassipes. Wetlands within the same region exhibited We great similarity in their aquatic plant communities but not necessarily in their physicochemical attributes. According to the ECELS index, wetlands could be ranked from medium to good quality, although most of them are threatened by anthropogenic impacts, including those protected at Delta del Estero Real Nature Reserve (Nicaragua) and Palo Verde National Park (Costa Rica). On the Pacific coast of Nicaragua and Costa Rica, rainfall patterns and clay-rich soils allow the development of extensive wetlands. These environments constitute unique habitats for the maintenance of aquatic biodiversity and provide significant ecological services to the surrounding seasonal dry forest. Despite these benefits, wetlands have been severely reduced in the last four decades, and little information is available on their biology and current conservation status. Here, we describe the main limnological traits of 30 sites representing different types of wetlands from four distinct physiographic regions: Tempisque River Lower Basin; Tempisque RiverMiddle Basin; Delta del Estero Real River; and the Oriental Region of Nicaragua. At each site, samples were taken at the beginning (infilling phase), middle (maximum flooded areas) and end (desiccation phase) of the 2010 hydrological cycle. We analysed a set of water parameters (depth, temperature, pH, conductivity, dissolved oxygen, major ions and nutrient concentrations) and biological parameters (shoreline vegetation, chlorophyll a, macrophyte cover) and assessed the conservation status of wetlands using the Index of the State of Conservation of Shallow Lentic Ecosystems (ECELS). In most sites, the water was relatively clear with near basic pH-values, low conductivity, and low levels of dissolved oxygen, nitrates, nitrites, phosphates and sulphates. Chlorophyll a and alkalinity varied through the season and among regions. Ion concentrations were generally low in most wetlands except for those close to estuarine and marine coastal areas. A total of 49 taxa of aquatic plants were found in the study sites, the most common being the emergent Typha domingensis and Thalia geniculata, and the floating Pistia stratiotes and Eichhornia crassipes. Wetlands within the same region exhibited great similarity in their aquatic plant communities but not necessarily in their physicochemical attributes. According to the ECELS index, wetlands could be ranked from medium to good quality, although most of them are threatened by anthropogenic impacts, including those protected at Delta del Estero Real Nature Reserve (Nicaragua) and Palo Verde National Park (Costa Rica)

Some properties of the k-dimensional Lyness' map

This paper is devoted to study some properties of the k-dimensional Lyness' map. Our main result presentes a rational vector field that gives a Lie symmetry for F. This vector field is used, for k less or equal to 5 to give information about the nature of the invariant sets under F. When k is odd, we also present a new (as far as we know) first integral for F^2 which allows to deduce in a very simple way several properties of the dynamical system generated by F. In particular for this case we prove that, except on a given codimension one algebraic set, none of the positive initial conditions can be a periodic point of odd period.Comment: 22 pages; 3 figure