Analysis of opposed jet hydrogen-air counter flow diffusion flame

A computational simulation of the opposed-jet diffusion flame is performed to study its structure and extinction limits. The present analysis concentrates on the nitrogen-diluted hydrogen-air diffusion flame, which provides the basic information for many vehicle designs such as the aerospace plane for which hydrogen is a candidate as the fuel. The computer program uses the time-marching technique to solve the energy and species equations coupled with the momentum equation solved by the collocation method. The procedure is implemented in two stages. In the first stage, a one-step forward overal chemical reaction is chosen with the gas phase chemical reaction rate determined by comparison with experimental data. In the second stage, a complete chemical reaction mechanism is introduced with detailed thermodynamic and transport property calculations. Comparison between experimental extinction data and theoretical predictions is discussed. The effects of thermal diffusion as well as Lewis number and Prandtl number variations on the diffusion flame are also presented

Neural Networks and Dynamic Complex Systems

We describe the use of neural networks for optimization and inference associated with a variety of complex systems. We show how a string formalism can be used for parallel computer decomposition, message routing and sequential optimizing compilers. We extend these ideas to a general treatment of spatial assessment and distributed artificial intelligence

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

Serotonin transporter polymorphisms and clinical response to sertraline across ethnicities

The aim of this pilot study was to examine the relationship between clinical response, adverse effects, sertraline (SERT) plasma concentrations and the genetic polymorphism of the serotonin transporter gene-linked polymorphic region (5HTTLPR) in 2 ethnic patient groups. The study involved 45 patients in a clinical trial who received a fixed dose regimen of 50 mg SERT for one week, then a variable-dose regimen for a further 6 weeks for major depressive disorder. At weeks 1 and 6, the following assessments were completed: Hamilton Depression Rating Scale (HDRS), Clinical Global Impression (CGI), drug adverse reaction scale and measurement of plasma SERT levels. Genomic analysis for the long and short allele variants of the 5HTTLPR polymorphism was also carried out. Caucasian subjects had a higher rate of l/l genotype while Chinese subjects had higher frequencies of l/s and s/s genotypes. Comparison of the subjects with the 5HTTLPR s/s genotype and those with the l/l and l/s genotypes found no significant differences in the HDRS scores, CGI scores, response rates, adverse effects and SERT plasma concentrations at week 6

HarvardX and MITx: The First Year of Open Online Courses, Fall 2012-Summer 2013

HarvardX and MITx are collaborative institutional efforts between Harvard University and MIT to enhance campus-based education, advance educational research, and increase access to online learning opportunities worldwide. Over the year from the fall of 2012 to the summer of 2013, HarvardX and MITx launched 17 courses on edX, a jointly founded platform for delivering massive open online courses (MOOCs). In that year, 43,196 registrants earned certificates of completion. Another 35,937 registrants explored half or more of course content without certification. An additional 469,702 registrants viewed less than half of the content. And 292,852 registrants never engaged with the online content. In total, there were 841,687 registrations from 597,692 unique users across the first year of HarvardX and MITx courses. This report is a joint effort by institutional units at Harvard and MIT to describe the registrant and course data provided by edX in the context of the diverse efforts and intentions of HarvardX and MITx instructor teams

HarvardX and MITx: The First Year of Open Online Courses, Fall 2012-Summer 2013

HarvardX and MITx are collaborative institutional efforts between Harvard University and MIT to enhance campus-based education, advance educational research, and increase access to online learning opportunities worldwide. Over the year from the fall of 2012 to the summer of 2013, HarvardX and MITx launched 17 courses on edX, a jointly founded platform for delivering massive open online courses (MOOCs). In that year, 43,196 registrants earned certificates of completion. Another 35,937 registrants explored half or more of course content without certification. An additional 469,702 registrants viewed less than half of the content. And 292,852 registrants never engaged with the online content. In total, there were 841,687 registrations from 597,692 unique users across the first year of HarvardX and MITx courses. This report is a joint effort by institutional units at Harvard and MIT to describe the registrant and course data provided by edX in the context of the diverse efforts and intentions of HarvardX and MITx instructor teams

Privacy, Anonymity, and Big Data in the Social Sciences

Quality social science research and the privacy of human subjects require trust

A comparative study of sertraline dosages, plasma concentrations, efficacy and adverse reactions in Chinese versus Caucasian patients

This prospective 6-week study examined the differences in dosage and steady state plasma concentrations of sertraline in Chinese versus Caucasian depressed patients. Two groups of Chinese patients from different geographical sites and a group of Caucasian patients were evaluated with clinical measures during an initial dose of 50 mg/day, with subsequent doses adjusted clinically. The results of 17 Australian Chinese (ACHI), 13 Malaysian Chinese (MCHI) and 15 Australian Caucasians (AC) were analysed. Despite controlling for weight, the AC subjects received a significantly higher dose than both the ACHI (P=0.002) and the MCHI groups (P=0.012). However, the mean sertraline concentration to dose ratios at weeks 1 and 6 were not significantly different between the three groups. Sertraline was effective and well tolerated in both ethnic groups with few adverse events. Although there was a lack of difference between groups in the pharmacokinetic results, Chinese depressed patients appeared to require lower dosages with consequently lower plasma concentrations of sertraline compared to Caucasian patients to achieve clinical efficacy. Further studies of the dosages, kinetics and adverse effects of selective serotonin reuptake inhibitors linked with genotyping are necessary

PH207x: Health in Numbers and PH278x: Human Health and Global Environmental Change: 2012-2013 Course Report

In the 2012-2013 academic year, the first two Harvard School of Public Health courses were offered through HarvardX on the edX platform: PH207x: Health in Numbers and PH278x: Human Health and Global Environmental Change. They were taught by Professors Earl Francis Cook and Marcello Pagano, and Aaron Bernstein and Jack Spengler, respectively. This report describes the structure of these two courses, the demographic characteristics of registrants, and the activity of students. This report was prepared by researchers external to the course teams and is based on examination of the courseware, analyses of the data collected by the edX platform, and interviews and consultations with the course faculty and team members

ER22x: JusticeX: Spring 2013 Course Report

ER22x was offered as a HarvardX course in Spring 2013 on edX, a platform for massive open online courses (MOOCs). It was taught by Professor Michael Sandel. The report was prepared by researchers external to the course team, based on an examination of the courseware, analyses of data collected by the edX platform, and interviews with the course faculty and team members