Boundary quantum critical phenomena with entanglement renormalization

We extend the formalism of entanglement renormalization to the study of boundary critical phenomena. The multi-scale entanglement renormalization ansatz (MERA), in its scale invariant version, offers a very compact approximation to quantum critical ground states. Here we show that, by adding a boundary to the scale invariant MERA, an accurate approximation to the critical ground state of an infinite chain with a boundary is obtained, from which one can extract boundary scaling operators and their scaling dimensions. Our construction, valid for arbitrary critical systems, produces an effective chain with explicit separation of energy scales that relates to Wilson's RG formulation of the Kondo problem. We test the approach by studying the quantum critical Ising model with free and fixed boundary conditions.Comment: 8 pages, 12 figures, for a related work see arXiv:0912.289

WikiPathways: building research communities on biological pathways.

Here, we describe the development of WikiPathways (http://www.wikipathways.org), a public wiki for pathway curation, since it was first published in 2008. New features are discussed, as well as developments in the community of contributors. New features include a zoomable pathway viewer, support for pathway ontology annotations, the ability to mark pathways as private for a limited time and the availability of stable hyperlinks to pathways and the elements therein. WikiPathways content is freely available in a variety of formats such as the BioPAX standard, and the content is increasingly adopted by external databases and tools, including Wikipedia. A recent development is the use of WikiPathways as a staging ground for centrally curated databases such as Reactome. WikiPathways is seeing steady growth in the number of users, page views and edits for each pathway. To assess whether the community curation experiment can be considered successful, here we analyze the relation between use and contribution, which gives results in line with other wiki projects. The novel use of pathway pages as supplementary material to publications, as well as the addition of tailored content for research domains, is expected to stimulate growth further

BridgeDb: standardized access to gene, protein and metabolite identifier mapping services

Many interesting problems in bioinformatics require integration of data from various sources. For example when combining microarray data with a pathway database, or merging co-citation networks with protein-protein interaction networks. Invariably this leads to an identifier mapping problem, where different datasets are annotated with identifiers that are related, but originate from different databases.

Solutions for the identifier mapping problem exist, such as Biomart, Synergizer, Cronos, PICR, HMS and many more. This creates an opportunity for bioinformatics tool developers. Tools can be made to flexibly support multiple mapping services or mapping services could be combined to get broader coverage. This approach requires an interface layer between tools and mapping services. BridgeDb provides such an interface layer, in the form of both a Java and REST API.

Because of the standardized interface layer, BridgeDb is not tied to a specific source of mapping information. You can switch easily between flat files, relational databases and several different web services. Mapping services can be combined to support multi-omics experiments or to integrate custom microarray annotations. BridgeDb isn't just yet another mapping service: it tries to build further on existing work, and integrate multiple partial solutions. The framework is intended for customization and adaptation to any identifier mapping service. 

BridgeDb makes it easy to add an important capability to existing tools. BridgeDb has already been integrated into several popular bioinformatics applications, such as Cytoscape, WikiPathways, PathVisio, Vanted and Taverna. To encourage tool developers to start using BridgeDb, we've created code examples, online documentation, and a mailinglist to ask questions. 

We believe that, to meet the challenges that are encountered in bioinformatics today, the software development process should follow a few essential principles: user friendliness, code reuse, modularity and open source. BridgeDb adheres to these principles, and can serve as a useful model for others to follow. BridgeDb can function to increase user-friendliness of graphical applications. It re-uses work from other projects such as BioMart and MIRIAM. BridgeDb consists of several small modules, integrated through a common interface (API). Components of BridgeDb can be left out or replaced, for maximum flexibility. BridgeDb was open source from the very beginning of the project. The philosophy of open source is closely aligned to academic values, of building on top of the work of giants. 

Many interesting problems in bioinformatics require integration of data from various sources. For example when combining microarray data with a pathway database, or merging co-citation networks with protein-protein interaction networks. Invariably this leads to an identifier mapping problem, where different datasets are annotated with identifiers that are related, but originate from different databases.

Solutions for the identifier mapping problem exist, such as Biomart, Synergizer, Cronos, PICR, HMS and many more. This creates an opportunity for bioinformatics tool developers. Tools can be made to flexibly support multiple mapping services or mapping services could be combined to get broader coverage. This approach requires an interface layer between tools and mapping services. BridgeDb provides such an interface layer, in the form of both a Java and REST API.

Because of the standardized interface layer, BridgeDb is not tied to a specific source of mapping information. You can switch easily between flat files, relational databases and several different web services. Mapping services can be combined to support multi-omics experiments or to integrate custom microarray annotations. BridgeDb isn't just yet another mapping service: it tries to build further on existing work, and integrate multiple partial solutions. The framework is intended for customization and adaptation to any identifier mapping service. 

BridgeDb makes it easy to add an important capability to existing tools. BridgeDb has already been integrated into several popular bioinformatics applications, such as Cytoscape, WikiPathways, PathVisio, Vanted and Taverna. To encourage tool developers to start using BridgeDb, we've created code examples, online documentation, and a mailinglist to ask questions. 

We believe that, to meet the challenges that are encountered in bioinformatics today, the software development process should follow a few essential principles: user friendliness, code reuse, modularity and open source. BridgeDb adheres to these principles, and can serve as a useful model for others to follow. BridgeDb can function to increase user-friendliness of graphical applications. It re-uses work from other projects such as BioMart and MIRIAM. BridgeDb consists of several small modules, integrated through a common interface (API). Components of BridgeDb can be left out or replaced, for maximum flexibility. BridgeDb was open source from the very beginning of the project. The philosophy of open source is closely aligned to academic values, of building on top of the work of giants. 

The BridgeDb library is available at "http://www.bridgedb.org":http://www.bridgedb.org.
A paper about BridgeDb was published in BMC _Bioinformatics_, 2010 Jan 4;11(1):5.

BridgeDb blog: "http://www.helixsoft.nl/blog/?tag=bridgedb":http://www.helixsoft.nl/blog/?tag=bridged

Tools and collaborative environments for bioinformatics research

Advanced research requires intensive interaction among a multitude of actors, often possessing different expertise and usually working at a distance from each other. The field of collaborative research aims to establish suitable models and technologies to properly support these interactions. In this article, we first present the reasons for an interest of Bioinformatics in this context by also suggesting some research domains that could benefit from collaborative research. We then review the principles and some of the most relevant applications of social networking, with a special attention to networks supporting scientific collaboration, by also highlighting some critical issues, such as identification of users and standardization of formats. We then introduce some systems for collaborative document creation, including wiki systems and tools for ontology development, and review some of the most interesting biological wikis. We also review the principles of Collaborative Development Environments for software and show some examples in Bioinformatics. Finally, we present the principles and some examples of Learning Management Systems. In conclusion, we try to devise some of the goals to be achieved in the short term for the exploitation of these technologies

Colheita de Tecidos em Dador em Coração Parado. Contribuição para a Autossuficiência Nacional?

INTRODUÇÃO: O Gabinete Coordenador de Colheita e Transplantação (GCCT) do Hospital S. José – CHLC, EPE, criado através do Despacho nº 269/1993, de 17 de Novembro, tem como missão prestar um serviço de excelência na área da doação, colheita e transplantação de órgãos e tecidos, e propor soluções inovadoras com vista à otimização de processos e à melhoria contínua da qualidade dos serviços que presta. O programa de transplantação dos Hospitais Civis de Lisboa (HCL) remonta ao ano de 1961, com os primeiros transplantes de córnea no Hospital de Santo António dos Capuchos. Posteriormente entraram em funcionamento as unidades de transplantação cardíaca no Hospital de Sta Marta e unidade de transplantação renal no Hospital Curry Cabral em 1988. Em 1991, é realizado o primeiro transplante de coração pulmão no Hospital de Sta Marta, em 1992 iniciou-se o programa de transplante hepático no Hospital Curry Cabral e em 1997 tem inicio o programa de transplante de medula no Hospital de Stº António dos Capuchos. Nesta altura, o enxerto de pele era uma terapêutica vulgarizada nos Hospitais Civis de Lisboa. No ano de 2007, foi implementado o programa de colheita de membrana amniótica e até ao momento presente é o único GCCT que tem este programa ativo. Não obstante o esforço desenvolvido pelo GCCT, em estreita colaboração com o Banco de Tecidos do Instituto Português do Sangue e da Transplantação, IP (IPST, IP), entidade responsável pela análise, processamento, preservação, armazenamento e distribuição de tecidos de origem humana com a qual o GCCT estabeleceu protocolo de colaboração para todos os tecidos colhidos (à exceção das córneas), tem-se constatado que o país não é autossuficiente no que aos tecidos diz respeito sendo recorrente a importação de tecidos pelo referido Banco de forma a dar resposta às solicitações nacionais. METODOLOGIA E RESULTADOS: Para conhecer o potencial de doação de tecidos em dador em coração parado procuramos a nossa amostra em dois grupos diferentes: os dadores de córnea do CHLC, EPE em coração parado de 2013 (83 dadores) e os falecidos no CHLC, que em 2013 que cumpriam critérios para dadores de córneas e não foram referenciados. Para ambos os grupos foi definida a idade limite para doação de algum tipo de tecido (além das córneas), os 65 anos (idade limite para a doação de tecidos, de acordo com os critérios em vigor - 2010 - do Banco de Tecidos do IPST, IP com o qual o GCCT estabeleceu protocolo de colaboração). A nossa amostra é, então, composta por 29 dadores de córneas em 2013 com idade inferior a 65 anos e 26 falecidos não referenciados com idade inferior a 65 anos (consulta diária dos mapas dos falecidos permite identificar os falecidos não referenciados pelas unidades/serviços). Os resultados obtidos levam-nos a concluir que é decisiva a implementação de programas de colheita de tecidos em dador em coração parado de forma a alargar o número de dadores e, desta forma, contribuir para a autossuficiência nacional, em conjunto com a reorganização desta atividade nos dadores em morte cerebral bem como a revisão dos critérios de seleção de dadores de aloenxertos, de acordo com as várias recomendações internacionais

Pediatric Organ and Tissue Donation—A 10-Year Retrospective Study in Portugal

Organ and tissue donation can transform lives. One donor can ensure the survival of up to 8 people through their organs and improve the quality of life for dozens more through tissue donation. Portugal has an excellent transplantation rate, but deaths still occur while waiting for an organ. The study aimed to analyze pediatric organ and tissue donors nationally and evaluate brain deaths in a pediatric intensive care unit (PICU) over the past 10 years to identify any potential lost donors. We conducted a retrospective descriptive study of pediatric organ and tissue donors and diagnosed brain deaths from January 2011 to December 2021. Demographic and clinical data were analyzed, including those provided by the National Transplant Coordination. Over the past 10 years in Portugal, 121 pediatric donors (11.7 per million population) were collected, and 569 organs and tissues were collected. During the same period in the PICU, there were 125 deaths, including 20 brain deaths. Of this group, 4 were organ and tissue donors. In the non-donor group (n = 16), a potential lost donor case stands out. Pediatric specialists need to be more familiar with the donation process, which would enable the identification and optimization of all potential donors, thus minimizing the number of potentially lost organs.info:eu-repo/semantics/publishedVersio

Effect of surfactants during drop formation in a microfluidic channel: a combined experimental and computational fluid dynamics approach

The effect of surfactants on the flow characteristics during rapid drop formation in a microchannel is investigated using high-speed imaging, micro-particle image velocimetry and numerical simulations; the latter are performed using a three- dimensional multiphase solver that accounts for the transport of soluble surfactants in the bulk and at the interface. Drops are generated in a flow-focusing microchannel, using silicone oil ( 4.6 mPa s) as the continuous phase and a 52 % w/w glycerol solution as the dispersed phase. A non-ionic surfactant (Triton X-100) is dissolved in the dispersed phase at concentrations below and above the critical micelle concentration. Good agreement is found between experimental and numerical data for the drop size, drop formation time and circulation patterns. The results reveal strong circulation patterns in the forming drop in the absence of surfactants, whose intensity decreases with increasing surfactant concentration. The surfactant concentration profiles in the bulk and at the interface are shown for all stages of drop formation. The surfactant interfacial concentration is large at the front and the back of the forming drop, while the neck region is almost surfactant free. Marangoni stresses develop away from the neck, contributing to changes in the velocity profile inside the drop

WikiPathways: Pathway Editing for the People

WikiPathways provides a collaborative platform for creating, updating, and sharing pathway diagrams and serves as an example of content curation by the biology community