Multigrid algorithms for hp-version interior penalty discontinuous Galerkin methods on polygonal and polyhedral meshes

In this paper we analyze the convergence properties of two-level and W-cycle multigrid solvers for the numerical solution of the linear system of equations arising from hp-version symmetric interior penalty discontinuous Galerkin discretizations of second-order elliptic partial differential equations on polygonal/polyhedral meshes. We prove that the two-level method converges uniformly with respect to the granularity of the grid and the polynomial approximation degree p, provided that the number of smoothing steps, which depends on p, is chosen sufficiently large. An analogous result is obtained for the W-cycle multigrid algorithm, which is proved to be uniformly convergent with respect to the mesh size, the polynomial approximation degree, and the number of levels, provided the latter remains bounded and the number of smoothing steps is chosen sufficiently large. Numerical experiments are presented which underpin the theoretical predictions; moreover, the proposed multilevel solvers are shown to be convergent in practice, even when some of the theoretical assumptions are not fully satisfied

A Semantic Web Management Model for Integrative Biomedical Informatics

Data, data everywhere. The diversity and magnitude of the data generated in the Life Sciences defies automated articulation among complementary efforts. The additional need in this field for managing property and access permissions compounds the difficulty very significantly. This is particularly the case when the integration involves multiple domains and disciplines, even more so when it includes clinical and high throughput molecular data.The emergence of Semantic Web technologies brings the promise of meaningful interoperation between data and analysis resources. In this report we identify a core model for biomedical Knowledge Engineering applications and demonstrate how this new technology can be used to weave a management model where multiple intertwined data structures can be hosted and managed by multiple authorities in a distributed management infrastructure. Specifically, the demonstration is performed by linking data sources associated with the Lung Cancer SPORE awarded to The University of Texas MD Anderson Cancer Center at Houston and the Southwestern Medical Center at Dallas. A software prototype, available with open source at www.s3db.org, was developed and its proposed design has been made publicly available as an open source instrument for shared, distributed data management.The Semantic Web technologies have the potential to addresses the need for distributed and evolvable representations that are critical for systems Biology and translational biomedical research. As this technology is incorporated into application development we can expect that both general purpose productivity software and domain specific software installed on our personal computers will become increasingly integrated with the relevant remote resources. In this scenario, the acquisition of a new dataset should automatically trigger the delegation of its analysis

Current issues in medically assisted reproduction and genetics in Europe: research, clinical practice, ethics, legal issues and policy. European Society of Human Genetics and European Society of Human Reproduction and Embryology.

In March 2005, a group of experts from the European Society of Human Genetics and European Society of Human Reproduction and Embryology met to discuss the interface between genetics and assisted reproductive technology (ART), and published an extended background paper, recommendations and two Editorials. Seven years later, in March 2012, a follow-up interdisciplinary workshop was held, involving representatives of both professional societies, including experts from the European Union Eurogentest2 Coordination Action Project. The main goal of this meeting was to discuss developments at the interface between clinical genetics and ARTs. As more genetic causes of reproductive failure are now recognised and an increasing number of patients undergo testing of their genome before conception, either in regular health care or in the context of direct-to-consumer testing, the need for genetic counselling and preimplantation genetic diagnosis (PGD) may increase. Preimplantation genetic screening (PGS) thus far does not have evidence from randomised clinical trials to substantiate that the technique is both effective and efficient. Whole-genome sequencing may create greater challenges both in the technological and interpretational domains, and requires further reflection about the ethics of genetic testing in ART and PGD/PGS. Diagnostic laboratories should be reporting their results according to internationally accepted accreditation standards (International Standards Organisation - ISO 15189). Further studies are needed in order to address issues related to the impact of ART on epigenetic reprogramming of the early embryo. The legal landscape regarding assisted reproduction is evolving but still remains very heterogeneous and often contradictory. The lack of legal harmonisation and uneven access to infertility treatment and PGD/PGS fosters considerable cross-border reproductive care in Europe and beyond. The aim of this paper is to complement previous publications and provide an update of selected topics that have evolved since 2005

Approaches in biotechnological applications of natural polymers

Natural polymers, such as gums and mucilage, are biocompatible, cheap, easily available and non-toxic materials of native origin. These polymers are increasingly preferred over synthetic materials for industrial applications due to their intrinsic properties, as well as they are considered alternative sources of raw materials since they present characteristics of sustainability, biodegradability and biosafety. As definition, gums and mucilages are polysaccharides or complex carbohydrates consisting of one or more monosaccharides or their derivatives linked in bewildering variety of linkages and structures. Natural gums are considered polysaccharides naturally occurring in varieties of plant seeds and exudates, tree or shrub exudates, seaweed extracts, fungi, bacteria, and animal sources. Water-soluble gums, also known as hydrocolloids, are considered exudates and are pathological products; therefore, they do not form a part of cell wall. On the other hand, mucilages are part of cell and physiological products. It is important to highlight that gums represent the largest amounts of polymer materials derived from plants. Gums have enormously large and broad applications in both food and non-food industries, being commonly used as thickening, binding, emulsifying, suspending, stabilizing agents and matrices for drug release in pharmaceutical and cosmetic industries. In the food industry, their gelling properties and the ability to mold edible films and coatings are extensively studied. The use of gums depends on the intrinsic properties that they provide, often at costs below those of synthetic polymers. For upgrading the value of gums, they are being processed into various forms, including the most recent nanomaterials, for various biotechnological applications. Thus, the main natural polymers including galactomannans, cellulose, chitin, agar, carrageenan, alginate, cashew gum, pectin and starch, in addition to the current researches about them are reviewed in this article.. }To the Conselho Nacional de Desenvolvimento Cientfíico e Tecnológico (CNPq) for fellowships (LCBBC and MGCC) and the Coordenação de Aperfeiçoamento de Pessoal de Nvíel Superior (CAPES) (PBSA). This study was supported by the Portuguese Foundation for Science and Technology (FCT) under the scope of the strategic funding of UID/BIO/04469/2013 unit, the Project RECI/BBB-EBI/0179/2012 (FCOMP-01-0124-FEDER-027462) and COMPETE 2020 (POCI-01-0145-FEDER-006684) (JAT)

Large expert-curated database for benchmarking document similarity detection in biomedical literature search

Document recommendation systems for locating relevant literature have mostly relied on methods developed a decade ago. This is largely due to the lack of a large offline gold-standard benchmark of relevant documents that cover a variety of research fields such that newly developed literature search techniques can be compared, improved and translated into practice. To overcome this bottleneck, we have established the RElevant LIterature SearcH consortium consisting of more than 1500 scientists from 84 countries, who have collectively annotated the relevance of over 180 000 PubMed-listed articles with regard to their respective seed (input) article/s. The majority of annotations were contributed by highly experienced, original authors of the seed articles. The collected data cover 76% of all unique PubMed Medical Subject Headings descriptors. No systematic biases were observed across different experience levels, research fields or time spent on annotations. More importantly, annotations of the same document pairs contributed by different scientists were highly concordant. We further show that the three representative baseline methods used to generate recommended articles for evaluation (Okapi Best Matching 25, Term Frequency–Inverse Document Frequency and PubMed Related Articles) had similar overall performances. Additionally, we found that these methods each tend to produce distinct collections of recommended articles, suggesting that a hybrid method may be required to completely capture all relevant articles. The established database server located at https://relishdb.ict.griffith.edu.au is freely available for the downloading of annotation data and the blind testing of new methods. We expect that this benchmark will be useful for stimulating the development of new powerful techniques for title and title/abstract-based search engines for relevant articles in biomedical research

Major Factors Affecting Incidence of Childhood Thyroid Cancer in Belarus after the Chernobyl Accident: Do Nitrates in Drinking Water Play a Role?

One of the major health consequences of the Chernobyl Nuclear Power Plant accident in 1986 was a dramatic increase in incidence of thyroid cancer among those who were aged less than 18 years at the time of the accident. This increase has been directly linked in several analytic epidemiological studies to iodine-131 (131I) thyroid doses received from the accident. However, there remains limited understanding of factors that modify the 131Irelated risk. Focusing on post-Chernobyl pediatric thyroid cancer in Belarus, we reviewed evidence of the effects of radiation, thyroid screening, and iodine deficiency on regional differences in incidence rates of thyroid cancer. We also reviewed current evidence on content of nitrate in groundwater and thyroid cancer risk drawing attention to high levels of nitrates in open well water in several contaminated regions of Belarus, i.e. Gomel and Brest, related to the usage of nitrogen fertilizers. In this hypothesis generating study, based on ecological data and biological plausibility, we suggest that nitrate pollution may modify the radiationrelated risk of thyroid cancer contributing to regional differences in rates of pediatric thyroid cancer in Belarus. Analytic epidemiological studies designed to evaluate joint effect of nitrate content in groundwater and radiation present a promising avenue of research and may provide useful insights into etiology of thyroid cancer

A vivência de mães de bebês com malformação La vivencia de madres de bebés con mala formación The experience of mothers of babies with malformation

O objetivo do estudo foi conhecer e compreender a vivência de mães diante do diagnóstico e nascimento de bebês com malformação. Trata-se de uma pesquisa descritivo-exploratória, de natureza qualitativa, desenvolvida em Maringá- PR, com sete mães. Os dados foram coletados em abril de 2009, por meio de entrevista semiestruturada, e analisados mediante a análise de conteúdo. Os dados mostraram que os diferentes momentos do ciclo gravídico-puerperal apresentam fatos e emoções distintos, mas completamente interligados, destacando-se momentos como a constatação da malformação, geralmente durante a gravidez, a sua confirmação ao nascimento e a vivência com o bebê após o nascimento. Conclui-se que a descoberta e confirmação da malformação produz crise e negação das expectativas na mãe e em todos os membros da família, desencadeando mudanças em seu modo de viver; porém, aos poucos, a mãe demonstra superação e aprende maneiras para enfrentar o problema e os preconceitos ligados à malformação.<br>El presente estudio tuvo como objetivo conocer y comprender la vivencia de madres delante del diagnóstico y nacimiento de bebés con mala formación. Se trata de una investigación descriptiva y exploratoria, de naturaleza cualitativa, desarrollada en Maringá (PR), con siete madres. Los datos fueron recogidos en abril de 2009, por medio de entrevista seme estructurada y analizados mediante el análisis de contenido. Los datos mostraron que los diferentes momentos del ciclo, del embarazo al nacimiento, presentan hechos y emociones distintos, pero, completamente interconectados, destacándose momentos como la constatación de la mala formación, generalmente durante el embarazo, su confirmación al nacimiento y la vivencia con el bebé después del nacimiento. Se concluye que la descubierta y confirmación de la mala formación produce crisis y negación de las expectativas en la madre y en todos los miembros de la familia, desencadenando cambios en su modo de vivir, pero a los pocos la madre demuestra superación y aprende maneras para enfrentar el problema y los prejuicios relacionados a la mala formación.<br>The objective of the present study was to discover and understand the experience of mothers faced with the diagnosis and birth of babies with malformation. It was a descriptive-exploratory qualitative research study, performed with seven mothers in Maringá-PR, Brazil. Data were collected in April 2009 through previously scheduled semi-structured interviews, and analyzed using content analysis. The data showed that the different moments of the pregnancy-puerperium cycle involve various facts and emotions, which are nevertheless interconnected, including confirmation of malformation (usually during pregnancy), confirmed diagnosis at birth, and life with the baby after birth. It is concluded that the discovery and confirmation of malformation leads to crisis and denial of expectations in the mother and all family members, resulting in changes in their way of life. However, the mother gradually overcomes and learns ways to cope with the problem and prejudices associated with malformation