Stepwise approach for combining many sources of evidence for site-recognition in genomic sequences

Background: Recognizing the different functional parts of genes, such as promoters, translation initiation sites, donors, acceptors and stop codons, is a fundamental task of many current studies in Bioinformatics. Currently, the most successful methods use powerful classifiers, such as support vector machines with various string kernels. However, with the rapid evolution of our ability to collect genomic information, it has been shown that combining many sources of evidence is fundamental to the success of any recognition task. With the advent of next-generation sequencing, the number of available genomes is increasing very rapidly. Thus, methods for making use of such large amounts of information are needed. Results: In this paper, we present a methodology for combining tens or even hundreds of different classifiers for an improved performance. Our approach can include almost a limitless number of sources of evidence. We can use the evidence for the prediction of sites in a certain species, such as human, or other species as needed. This approach can be used for any of the functional recognition tasks cited above. However, to provide the necessary focus, we have tested our approach in two functional recognition tasks: translation initiation site and stop codon recognition. We have used the entire human genome as a target and another 20 species as sources of evidence and tested our method on five different human chromosomes. The proposed method achieves better accuracy than the best state-of-the-art method both in terms of the geometric mean of the specificity and sensitivity and the area under the receiver operating characteristic and precision recall curves. Furthermore, our approach shows a more principled way for selecting the best genomes to be combined for a given recognition task. Conclusions: Our approach has proven to be a powerful tool for improving the performance of functional site recognition, and it is a useful method for combining many sources of evidence for any recognition task in Bioinformatics. The results also show that the common approach of heuristically choosing the species to be used as source of evidence can be improved because the best combinations of genomes for recognition were those not usually selected. Although the experiments were performed for translation initiation site and stop codon recognition, any other recognition task may benefit from our methodology

Organización : Diferentes estructura organizacional en la empresas

El término organización presenta dos referencias básicas. Por un lado, la palabra organización se utiliza para referirse a la acción u efecto de organizar u organizarse y la organización como la condición necesaria en cualquier actividad. Esta última es la que se hace referencia en el proceso administrativo como el eje fundamental que asegura el desarrollo correcto de las demás funciones. Para ello la presente investigación está centrada en el tema de la organización como parte del proceso administrativo y específicamente desarrolla el tema de las formas estructurales de organización, cuyo objetivo general es analizar el funcionamiento, la aplicación, implementación y adaptación de las diferentes formas estructurales de organización. La base teórica que sustenta la investigación está ajustada a las diferentes teorías de la administración, temas relacionados a la organización en las empresas, como el diseño y la preparación de organigramas así también como la generación y aplicación de las estructuras de trabajos o modelos de trabajos y el diseño mismo de organización, dicha información está contemplada a partir de los diferentes autores y pensadores del ramo de la administración cuya autoría es meramente aceptada en todos los campos. La metodología empleada es una serie documental-investigativa que extrae la información a partir de los métodos de lecturas, por otra parte la investigación contempla la aplicación de las rubricas sugeridas por el programa de seminario de graduación de la UNAN-Managua, y las normas APAs sexta edición. La información está contenida en cinco capítulos o escenarios que proporcionan una mejor apreciación de la información sustraída

Environmental sustainability assessment of municipal solid waste management through carbon footprint

One of the most challenging issues for building sustainable cities is the improvement of municipal solid waste management (MSWM), which requires a substantial effort to reduce its production and improve its different stages: collection (or pre-collection/containerization), transport and treatment. Each of these stages has environmental impacts stemming from the use of bags to hold the waste generated by residents in their homes, from the containers placed in public roads for drop-off, from the use of lorries or systems to transport waste to the processing plants, and from the construction and operation of plants to treat each waste fraction. In Europe, the Waste Framework Directive specifies Life Cycle Assessment (LCA) as a necessary policy-making tool, ensuring that impacts are assessed from cradle to grave, and avoiding ?hiding? impacts by moving them to other countries or stages of production/consumption. One of the environmental impacts evaluated is climate change (CC), in which greenhouse gas (GHG) emissions from the whole life cycle are calculated: carbon footprint (CF). This poster shows a methodology, based on LCA standards (ISO 14040 / 14044 / 14067), to calculate CF of MSWM. This methodology was applied to Madrid City

The fiscal and macroeconomic effects of government wages and employment reform

Este artículo examina el impacto macroeconómico de la implementación de reformas en el ámbito de los salarios y el empleo público, en particular en momentos de consolidación fiscal. La reforma de la masa salarial de las Administraciones Públicas (AAPP) ha formado parte de las estrategias de respuesta a las consecuencias de la crisis de deuda soberana en numerosos países de la Unión Europea. Dichas reformas implicaron, en algunos casos, la introducción de medidas de ahorro, como parte de paquetes de ajuste fiscal que habitualmente han pesado más sobre el uso de otros instrumentos presupuestarios, en particular, la inversión pública. En general, las medidas de ajuste fiscal, de acuerdo con los modelos y estimaciones de multiplicadores fiscales disponibles, habrían tenido efectos adversos sobre el crecimiento económico en el corto plazo. No obstante, en el caso concreto de las orientadas a contener la masa salarial de las AAPP, dado que su impacto incide de manera directa en la dinámica del mercado de trabajo, parte de estos efectos de corto plazo se podrían compensar, de acuerdo con la evidencia disponible, a través de las potenciales ganancias de competitividad y eficiencia que pudieran producirse. En este artículo se proporciona evidencia de estos efectos de medio y largo plazo, sobre la base de información macro y microeconómica para el área del euro y la Unión Europea en su conjunto. Se concluye que, para que estos efectos mitigadores aparezcan, las políticas de reforma de la masa salarial de las AAPP deben diseñarse con una orientación de medio plazo (reformas estructurales). Asimismo, se discute el modo en que dichos efectos dependen de circunstancias idiosincrásicas de los países (tales como el marco institucional)This paper examines the overall macroeconomic impact arising from reform in government wages and employment, at times of fiscal consolidation. Reform of these two components of the government wage bill appeared necessary for containing the deterioration of the public finances in several EU countries, as a consequence of the financial crisis. Such reforms entailed in some instances, but not always, the implementation of cost cutting measures affecting the government wage bill, as part of broader consolidation packages that typically hinged more heavily on other fiscal instruments, like public investment. While such measures have adverse short-term macroeconomic effects, public wage bill restraining policy changes present the idiosyncrasy that they can yield medium- to longer-term benefits due to possible competitiveness and efficiency gains through their impact on labour market dynamics. This paper provides some evidence of such medium- to long-run effects, based on a wealth of micro and macro data in the euro area and the EU. It concludes that appropriately designed government wage bill moderation could indeed produce positive dividends to the economy, which depend on certain country-specific conditions. These gains can be reinforced by relevant fiscal-structural reform

OligoIS: Scalable Instance Selection for Class-Imbalanced Data Sets

In current research, an enormous amount of information is constantly being produced, which poses a challenge for data mining algorithms. Many of the problems in extremely active research areas, such as bioinformatics, security and intrusion detection, or text mining, share the following two features: large data sets and class-imbalanced distribution of samples. Although many methods have been proposed for dealing with class-imbalanced data sets, most of these methods are not scalable to the very large data sets common to those research fields. In this paper, we propose a new approach to dealing with the class-imbalance problem that is scalable to data sets with many millions of instances and hundreds of features. This proposal is based on the divide-and-conquer principle combined with application of the selection process to balanced subsets of the whole data set. This divide-and-conquer principle allows the execution of the algorithm in linear time. Furthermore, the proposed method is easy to implement using a parallel environment and can work without loading the whole data set into memory. Using 40 class-imbalanced medium-sized data sets, we will demonstrate our method's ability to improve the results of state-of-the-art instance selection methods for class-imbalanced data sets. Using three very large data sets, we will show the scalability of our proposal to millions of instances and hundreds of features

Improving translation initiation site and stop codon recognition by using more than two classes

Motivation: The recognition of translation initiation sites and stop codons is a fundamental part of any gene recognition program. Currently, the most successful methods use powerful classifiers, such as support vector machines with various string kernels. These methods all use two classes, one of positive instances and another one of negative instances that are constructed using sequences from the whole genome. However, the features of the negative sequences differ depending on the position of the negative samples in the gene. There are differences depending on whether they are from exons, introns, intergenic regions or any other functional part of the genome. Thus, the positive class is fairly homogeneous, as all its sequences come from the same part of the gene, but the negative class is composed of different instances. The classifier suffers from this problem. In this article, we propose the training of different classifiers with different negative, more homogeneous, classes and the combination of these classifiers for improved accuracy. Results: The proposed method achieves better accuracy than the best state-of-the-art method, both in terms of the geometric mean of the specificity and sensitivity and the area under the receiver operating characteristic and precision recall curves. The method is tested on the whole human genome. The results for recognizing both translation initiation sites and stop codons indicated improvements in the rates of both false-negative results (FN) and false-positive results (FP). On an average, for translation initiation site recognition, the false-negative ratio was reduced by 30.2% and the FP ratio decreased by 10.9%. For stop codon prediction, FP were reduced by 41.4% and FN by 31.7%. Availability and implementation: The source code is licensed under the General Public License and is thus freely available. The datasets and source code can be obtained from http://cib.uco.es/site-recognition. Contact: [email protected]

Fiscal data revisions in Europe

Al igual que la mayoría de los datos macroeconómicos, las cifras de déficit público están sujetas a revisiones. Sin embargo, en el caso de Europa, estas podrían ser especialmente preocupantes dado el papel que desempeñan los datos fiscales en el funcionamiento de las reglas de supervisión multilateral a nivel europeo. El grado de cumplimiento de dichas reglas se juzga sobre la base de las publicaciones iniciales de datos de déficit público en el marco de las notificaciones del Procedimiento de Déficit Excesivo (PDE) europeo. Asimismo, la falta de fiabilidad de los datos fiscales puede menoscabar la credibilidad de los planes de consolidación. Este artículo muestra las propiedades empíricas de las revisiones de las cifras anuales de déficit en Europa a partir de la información ofrecida por un panel que contiene las diferentes notificaciones en tiempo real para 15 países de la UE a lo largo del período comprendido entre 1995 y 200

Counting Synapses Using FIB/SEM Microscopy: A True Revolution for Ultrastructural Volume Reconstruction

The advent of transmission electron microscopy (TEM) in the 1950s represented a fundamental step in the study of neuronal circuits. The application of this technique soon led to the realization that the number of synapses changes during the course of normal life, as well as under certain pathological or experimental circumstances. Since then, one of the main goals in neurosciences has been to define simple and accurate methods to estimate the magnitude of these changes. Contrary to analysing single sections, TEM reconstructions are extremely time-consuming and difficult. Therefore, most quantitative studies use stereological methods to define the three-dimensional characteristics of synaptic junctions that are studied in two dimensions. Here, to count the exact number of synapses per unit of volume we have applied a new three-dimensional reconstruction method that involves the combination of focused ion beam milling and scanning electron microscopy (FIB/SEM). We show that the images obtained with FIB/SEM are similar to those obtained with TEM, but with the advantage that FIB/SEM permits serial reconstructions of large volumes of tissue to be generated rapidly and automatically. Furthermore, we compared the estimates of the number of synapses obtained with stereological methods with the values obtained by FIB/SEM reconstructions. We concluded that FIB/SEM not only provides the actual number of synapses per volume but it is also much easier and faster to use than other currently available TEM methods. More importantly, it also avoids most of the errors introduced by stereological methods and overcomes the difficulties associated with these techniques

Challenges A ecting Access to Health and Social Care Resources and Time Management among Parents of Children with Rett Syndrome: A Qualitative Case Study.

Rare diseases face serious sustainability challenges regarding the distribution of resources geared at health and social needs. Our aim was to describe the barriers experienced by parents of children with Rett Syndrome for accessing care resources. A qualitative case study was conducted among 31 parents of children with Rett syndrome. Data were collected through in-depth interviews, focus groups, researchers’ field notes and parents’ personal documents. A thematic analysis was performed and the Standards for Reporting Qualitative Research (SRQR) guidelines were followed. Three main themes emerged from the data: (a) essential health resources; (b) bureaucracy and social care; and (c) time management constraints. Parents have difficulties accessing appropriate health services for their children. Administrative obstacles exist for accessing public health services, forcing parents to bear the financial cost of specialized care. Time is an essential factor, which conditions the organization of activities for the entire family. Qualitative research offers insight into how parents of children with Rett syndrome experience access to resources and may help improve understanding of how Rett syndrome impacts the lives of both the children and their parentspost-print353 K