Nanostructured Fe-N-C as bifunctional catalysts for oxygen reduction and hydrogen evolution

The development of electrocatalysts for energy conversion and storage devices is of paramount importance to promote sustainable development. Among the different families of materials, catalysts based on transition metals supported on a nitrogen-containing carbon matrix have been found to be effective catalysts toward oxygen reduction reaction (ORR) and hydrogen evolution reaction (HER) with high potential to replace conventional precious metal-based catalysts. In this work, we developed a facile synthesis strategy to obtain a Fe-N-C bifunctional ORR/HER catalysts, involving wet impregnation and pyrolysis steps. Iron (II) acetate and imidazole were used as iron and nitrogen sources, respectively, and functionalized carbon black pearls were used as conductive support. The bifunctional performance of the Fe-N-C catalyst toward ORR and HER was investigated by cyclic voltammetry, rotating ring disk electrode experiments, and electrochemical impedance spectroscopy in alkaline environment. ORR onset potential and half-wave potential were 0.95 V and 0.86 V, respectively, indicating a competitive performance in comparison with the commercial platinum-based catalyst. In addition, Fe-N-C had also a good HER activity, with an overpotential of 478 mV @10 mAcm(-2) and Tafel slope of 133 mVdec(-1), demonstrating its activity as bifunctional catalyst in energy conversion and storage devices, such as alkaline microbial fuel cell and microbial electrolysis cells

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

Subgingival microbiota in health compared to periodon tis and the influence of smoking

PI11/01383 from Carlos III Institute of Health (General Division of Evaluation and Research Promotion, Madrid, Spain), which is integrated in National Plan of Research, Development and Innovation (PN I+D+I 2008–2011). This project was co-financed by European Regional Development Fund (ERDF 2007–2013)

Peri-implantitis, systemic inflammation, and dyslipidemia: a cross-sectional biochemical study

Purpose: The aim of this study was to compare the inflammatory and lipid profile of patients with and without peri-implantitis. / Methods: A cross-sectional biochemical study was carried out in which blood samples were collected from 16 patients with peri-implantitis and from 31 subjects with healthy implants. Clinical peri-implant parameters were obtained from all subjects. Levels of tumor necrosis factor-alpha and interleukin-10 (IL-10) were measured in serum. Lipid fractions, glucose and creatinine levels, and complete blood count were also assessed. / Results: After controlling for a history of periodontitis, statistically significant differences between peri-implantitis patients and controls were found for total cholesterol (estimated adjusted mean difference, 76.4 mg/dL; 95% confidence interval [CI], 39.6, 113.2 mg/dL; P<0.001), low-density lipoprotein (LDL) cholesterol (estimated adjusted mean difference, 57.7 mg/dL; 95% CI, 23.8, 91.6 mg/dL; P<0.001), white blood cells (WBC) (estimated adjusted mean difference, 2.8×103/μL; 95% CI, 1.6, 4.0×103/μL; P<0.001) and IL-10 (estimated adjusted mean difference, −10.4 pg/mL; 95% CI, −15.8, −5.0 pg/mL; P<0.001). The peri- implant probing pocket depth (PPD) was modestly positively correlated with total cholesterol (r=0.512; P<0.001), LDL cholesterol (r=0.463; P=0.001), and WBC (r=0.519; P<0.001). A moderate negative correlation was observed between IL-10 and PPD (r=0.609; P<0.001). / Cardiovascular diseases; Dyslipidemias; Peri-implantitis; Inflammation; Leukocytes Conclusions: Otherwise healthy individuals with peri-implantitis showed increased low- grade systemic inflammation and dyslipidemia

On the Use of Finite-Size Scaling to Measure Spin-Glass Exponents

Finite-size scaling (FSS) is a standard technique for measuring scaling exponents in spin glasses. Here we present a critique of this approach, emphasizing the need for all length scales to be large compared to microscopic scales. In particular we show that the replacement, in FSS analyses, of the correlation length by its asymptotic scaling form can lead to apparently good scaling collapses with the wrong values of the scaling exponents.Comment: RevTeX, 5 page

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

Transcriptome analysis in blood cells from children reveals potential early biomarkers of metabolic alterations

OBJECTIVES: The development of effective strategies to prevent childhood obesity and its comorbidities requires new, reliable early biomarkers. Here, we aimed to identify in peripheral blood cells potential transcript-based biomarkers of unhealthy metabolic profile associated to overweight/obesity in children. METHODS: We performed a whole-genome microarray analysis in blood cells to identify genes differentially expressed between overweight and normal weight children to obtain novel transcript-based biomarkers predictive of metabolic complications. RESULTS: The most significant enriched pathway of differentially expressed genes was related to oxidative phosphorylation, for which most of genes were downregulated in overweight versus normal weight children. Other genes were involved in carbohydrate metabolism/glucose homoeostasis or in lipid metabolism (for example, TCF7L2, ADRB3, LIPE, GIPR), revealing plausible mechanisms according to existing biological knowledge. A set of differentially expressed genes was identified to discriminate in overweight children those with high or low triglyceride levels. CONCLUSIONS: Functional microarray analysis has revealed a set of potential blood-cell transcript-based biomarkers that may be a useful approach for early identification of children with higher predisposition to obesity-related metabolic alterations

Blood cells as a source of transcriptional biomarkers of childhood obesity and its related metabolic alterations: results of the IDEFICS Study

Background: IDEFICS (Identification and Prevention of Dietary-and Lifestyle-Induced Health Effects in Children and Infants Project) is a European multicenter study on childhood obesity. One of its goals is to define early biomarkers of risk associated with obesity and its comorbid conditions. Objective: We considered blood cells as a new potential source of transcriptional biomarkers for these metabolic disorders and examined whether blood cell mRNA levels of some selected genes (LEPR, INSR, CPT1A, SLC27A2, UCP2, FASN, and PPAR alpha) were altered in overweight children and whether their expression levels could be defined as markers of the insulin-resistant or dyslipidemic state associated with overweight. Design: Blood samples were obtained from 306 normal-weight and overweight children, aged 2-9 yr, from eight different European countries. Whole-blood mRNA levels were assessed by quantitative RT-PCR. Results: LEPR, INSR, and CPT1A mRNA levels were higher in overweight compared with normal-weight children (the two latter only in males), whereas SLC27A2 mRNA levels were lower in overweight children. Significant associations were also found between expression levels of LEPR, INSR, CPT1A, SLC27A2, FASN, PPAR alpha, and different parameters, including body mass index, homeostasis model assessment index, and plasma triglycerides and cholesterol levels. These associations showed that high expression levels of CPT1A, SLC27A2, INSR, FASN, or PPAR alpha may be indicative of a lower risk for the insulin-resistant or dyslipidemic state associated with obesity, whereas low LEPR mRNA levels appear as a marker of high low-density lipoprotein cholesterol, independently of body mass index. Conclusions: These findings point toward the possibility of using the expression levels of these genes in blood cells as markers of metabolic status and can potentially provide an early warning of a future disorder

Autonomy, Good Humor and Support Networks, Potential of Community Resilience Intervention in People Victims of the Earthquake in the Calderón Parish

Resilience is a concept widely used in recent years, especially when it comes to evaluating the level of recovery of communities that are hit by natural phenomena. It can be stated that conceptually resilience constitutes the ability to react effectively and quickly to the effects of disasters, being a complex phenomenon to evaluate and define. And although the level of resilience does not necessarily imply greater control of vulnerability, it can be affirmed that the reduction of vulnerable conditions can strengthen and consolidate the resilient capacity of individuals and communities, in the face of the effects of natural disasters