COUGER-co-factors associated with uniquely-bound genomic regions

Most transcription factors (TFs) belong to protein families that share a common DNA binding domain and have very similar DNA binding preferences. However, many paralogous TFs (i.e. members of the same TF family) perform different regulatory functions and interact with different genomic regions in the cell. A potential mechanism for achieving this differential in vivo specificity is through interactions with protein co-factors. Computational tools for studying the genomic binding profiles of paralogous TFs and identifying their putative co-factors are currently lacking. Here, we present an interactive web implementation of COUGER, a classification-based framework for identifying protein co-factors that might provide specificity to paralogous TFs. COUGER takes as input two sets of genomic regions bound by paralogous TFs, and it identifies a small set of putative co-factors that best distinguish the two sets of sequences. To achieve this task, COUGER uses a classification approach, with features that reflect the DNA-binding specificities of the putative co-factors. The identified co-factors are presented in a user-friendly output page, together with information that allows the user to understand and to explore the contributions of individual co-factor features. COUGER can be run as a stand-alone tool or through a web interface: http://couger.oit.duke.edu

Obtendo información útil para a mellora dunha materia a partir dos resultados dos exames de resposta múltiple

[Resumo] Os procesos de avaliación, deben aplicarse ós docentes e mesmo á materia en si, non só ós alumnos. Con esta finalidade formúlase unha análise dos resultados acadados polo alumnado durante a proba de avaliación empregada na materia de Marcos de Desenvolvemento (Grao en Enxeñaría Informática – Facultade de Informática). O exame é de resposta múltiple (4 opcións por pregunta, só unha válida e restando puntos as respostas erróneas). Os exames analízanse en dúas ramas: por unha banda, estúdanse as taxas de acerto/fallo/en branco de cada unha das preguntas; por outra, a porcentaxe de opcións (a,b,c,d, branco) en cada pregunta. Este sinxelo estudo, automatizado mediante o emprego dunha folla de cálculo, permite, non obstante, obter interesantes conclusións: • Detecta ambigüidades ou erros na formulación das preguntas que, polo xeral, se derivan nunha elevada porcentaxe de respostas en branco. • Detecta lagoas de coñecemento nalgunha das áreas da materia, que orixinan preguntas cunha elevada taxa de erros. Cada pregunta está asociada a un bloque teórico, polo que se podes establecer en qué aspectos os alumnos presentan máis ou menos coñecementos. Ambos aspectos poden ser empregados para detectar erros na formulación da materia e/ou exame e facer posible así a definición de plans de mellora de cara ós vindeiros cursos académicos

Mejora continua de la calidad de la docencia a partir del análisis de los resultados de evaluación

[Resumen] El objetivo de cualquier docente debería ser la mejora continua en sus materias. En este trabajo se muestra una aproximación para adecuar las enseñanzas a aquellos aspectos más necesarios dentro de una materia. Para ello es necesario tomar nota de las debilidades mostradas por el alumnado. Por lo tanto, se plantea un análisis exhaustivo del rendimiento, más allá de una simple evaluación numérica, con el objetivo de dirigir los esfuerzos docentes a las áreas en las que se detecta una mayor necesidad. Así, para valorar los conocimientos teóricos se mostrará un análisis estadístico a partir de los resultados de la prueba teórica realizada (de tipo respuesta múltiple) analizando no sólo la cantidad de fallos sino analizando dónde y en qué porcentaje se producen éstos. En relación a la práctica, se desarrolla una rúbrica que permite una corrección exhaustiva de los trabajos, dejando además abierta la posibilidad a apuntar las observaciones necesarias en todos los puntos de interés. Se contextualiza la propuesta realizada en una materia concreta (Marcos de Desarrollo), puesto que es la materia que se empleó para su puesta en marcha. Sin embargo, el método propuesto es totalmente genérico y puede ser trasladado sin apenas cambio a cualquier otra materia.[Abstract] The objective of any teaching should be the continuous improvement of the subjects. This paper shows an approach to adapt the teachings to those aspects most necessary within a subject. For this, it is necessary to take note of the weaknesses shown by the students. Therefore, an exhaustive analysis of the performance is proposed, beyond a simple numerical evaluation, with the aim of directing the teaching efforts to the areas in which a greater need is detected. Thus, to assess theoretical knowledge, statistical analysis will be shown based on the results of the theoretical test carried out (multiple response type) analyzing not only the number of failures but analyzing where and in what percentage these occur. In relation to the practice, a rubric is developed that allows an exhaustive correction of the works, leaving also open the possibility to record the necessary observations in all the points of interest. The proposal made in a specific subject (Development Frameworks) is contextualized, since it is the material used for its implementation. However, the proposed method is totally generic and can be transferred with little change to any other subject

Net-Net Auto Machine Learning (AutoML) Prediction of Complex Ecosystems

Biological Ecosystem Networks (BENs) are webs of biological species (nodes) establishing trophic relationships (links). Experimental confirmation of all possible links is difficult and generates a huge volume of information. Consequently, computational prediction becomes an important goal. Artificial Neural Networks (ANNs) are Machine Learning (ML) algorithms that may be used to predict BENs, using as input Shannon entropy information measures (Sh(k)) of known ecosystems to train them. However, it is difficult to select a priori which ANN topology will have a higher accuracy. Interestingly, Auto Machine Learning (AutoML) methods focus on the automatic selection of the more efficient ML algorithms for specific problems. In this work, a preliminary study of a new approach to AutoML selection of ANNs is proposed for the prediction of BENs. We call it the Net-Net AutoML approach, because it uses for the first time Shk values of both networks involving BENs (networks to be predicted) and ANN topologies (networks to be tested). Twelve types of classifiers have been tested for the Net-Net model including linear, Bayesian, trees-based methods, multilayer perceptrons and deep neuronal networks. The best Net-Net AutoML model for 338,050 outputs of 10 ANN topologies for links of 69 BENs was obtained with a deep fully connected neuronal network, characterized by a test accuracy of 0.866 and a test AUROC of 0.935. This work paves the way for the application of Net-Net AutoML to other systems or ML algorithms.The authors acknowledge Basque Government (Eusko Jaurlaritza) grant (IT1045-16) - 2016-2021 for consolidated research groups. This work was supported by the "Collaborative Project in Genomic Data Integration (CICLOGEN)" PI17/01826 funded by the Carlos III Health Institute, as part of the Spanish National plan for Scientific and Technical Research and Innovation 2013-2016 and the European Regional Development Funds (FEDER). This project was also supported by the General Directorate of Culture, Education and University Management of Xunta de Galicia ED431D 2017/16 and "Drug Discovery Galician Network" Ref. ED431G/01 and the "Galician Network for Colorectal Cancer Research" (Ref. ED431D 2017/23), and finally by the Spanish Ministry of Economy and Competitiveness for its support through the funding of the unique installation BIOCAI (UNLC08-1E-002, UNLC13-13-3503) and the European Regional Development Funds (FEDER) by the European Union. CR Munteanu acknowledges the support of NVIDIA Corporation with the donation of the Titan Xp GPU used for this research

The Carina dSph galaxy: where is the edge?

Recent cosmological N-body simulations suggest that current empirical estimates of tidal radii in dSphs might be underestimated by at least one order of magnitude. To constrain the plausibility of this theoretical framework, we undertook a multiband (U,B,V,I) survey of the Carina dSph. Deep B,V data of several fields located at radial distances from the Carina center ranging from 0.5 to 4.5 degrees show a sizable sample of faint blue objects with the same magnitudes and colors of old, Turn-Off stars detected across the center. We found that the (U-V,B-I) color-color plane is a robust diagnostic to split stars from background galaxies. Unfortunately, current U,I-band data are too shallow to firmly constrain the real extent of Carina.Comment: To be published on the proceedings of the XLIX meeting of the Italian Astronomical Society. Requires mem.cl

Sobre la ocurrencia del cretáceo superior marino en Coihaique , Provincia de Aisén

Using the CCSD­(T) model, we evaluated the intermolecular potential energy surfaces of the He–, Ne–, and Ar–phosgene complexes. We considered a representative number of intermolecular geometries for which we calculated the corresponding interaction energies with the augmented (He complex) and double augmented (Ne and Ar complexes) correlation-consistent polarized valence triple-ζ basis sets extended with a set of 3s3p2d1f1g midbond functions. These basis sets were selected after systematic basis set studies carried out at geometries close to those of the surface minima. The He–, Ne–, and Ar–phosgene surfaces were found to have absolute minima of −72.1, −140.4, and −326.6 cm^–1 at distances between the rare-gas atom and the phosgene center of mass of 3.184, 3.254, and 3.516 Å, respectively. The potentials were further used in the evaluation of rovibrational states and the rotational constants of the complexes, providing valuable results for future experimental investigations. Comparing our results to those previously available for other phosgene complexes, we suggest that the results for Cl₂–phosgene should be revised

Automatic Seizure Detection Based on Star Graph Topological Indices

[Abstract] The recognition of seizures is very important for the diagnosis of patients with epilepsy. The seizure is a process of rhythmic discharge in brain and occurs rarely and unpredictably. This behavior generates a need of an automatic detection of seizures by using the signals of long-term electroencephalography (EEG) recordings. Due to the non-stationary character of EEG signals, the conventional methods of frequency analysis are not the best alternative to obtain good results in diagnostic purpose. The present work proposes a method of EEG signal analysis based on star graph topological indices (SGTIs) for the first time. The signal information, such as amplitude and time occurrence, is codified into invariant SGTIs which are the basis for the classification models that can discriminate the epileptic EEG records from the non-epileptic ones. The method with SGTIs and the simplest linear discriminant methods provide similar results to those previously published, which are based on the time-frequency analysis and artificial neural networks. Thus, this work proposes a simpler and faster alternative for automatic detection of seizures from the EEG recordings.Xunta de Galicia; 2007/127Xunta de Galicia; 2007/144Instituto de Salud Carlos III; PIO52048Instituto de Salud Carlos III; RD07/0067/0005Ministerio de Ciencia e Innovación; TIN2009—07707

Radiographic correlates of hallux valgus severity in older people

<p>Abstract</p> <p>Background</p> <p>The severity of hallux valgus is easily appreciated by its clinical appearance, however x-ray measurements are also frequently used to evaluate the condition, particularly if surgery is being considered. There have been few large studies that have assessed the validity of these x-ray observations across a wide spectrum of the deformity. In addition, no studies have specifically focused on older people where the progression of the disorder has largely ceased. Therefore, this study aimed to explore relationships between relevant x-ray observations with respect to hallux valgus severity in older people.</p> <p>Methods</p> <p>This study utilised 402 x-rays of 201 participants (74 men and 127 women) aged 65 to 94 years. All participants were graded using the Manchester Scale - a simple, validated system to grade the severity of hallux valgus - prior to radiographic assessment. A total of 19 hallux valgus-related x-ray observations were performed on each set of x-rays. These measurements were then correlated with the Manchester Scale scores.</p> <p>Results</p> <p>Strong, positive correlations were identified between the severity of hallux valgus and the hallux abductus angle, the proximal articular set angle, the sesamoid position and congruency of the first metatarsophalangeal joint. As hallux valgus severity increased, so did the frequency of radiographic osteoarthritis of the first metatarsophalangeal joint and a round first metatarsal head. A strong linear relationship between increased relative length of the first metatarsal and increased severity of hallux valgus was also observed.</p> <p>Conclusions</p> <p>Strong associations are evident between the clinical appearance of hallux valgus and a number of hallux valgus-related x-ray observations indicative of structural deformity and joint degeneration. As it is unlikely that metatarsal length increases as a result of hallux valgus deformity, increased length of the first metatarsal relative to the second metatarsal may be a contributing factor to the development and/or progression of hallux valgus.</p