PCR-Based Analysis of Mitochondrial DNA Copy Number, Mitochondrial DNA Damage, and Nuclear DNA Damage.

Because of the role that DNA damage and depletion play in human disease, it is important to develop and improve tools to assess these endpoints. This unit describes PCR-based methods to measure nuclear and mitochondrial DNA damage and copy number. Long amplicon quantitative polymerase chain reaction (LA-QPCR) is used to detect DNA damage by measuring the number of polymerase-inhibiting lesions present based on the amount of PCR amplification; real-time PCR (RT-PCR) is used to calculate genome content. In this unit, we provide step-by-step instructions to perform these assays in Homo sapiens, Mus musculus, Rattus norvegicus, Caenorhabditis elegans, Drosophila melanogaster, Danio rerio, Oryzias latipes, Fundulus grandis, and Fundulus heteroclitus, and discuss the advantages and disadvantages of these assays.

Global Value Chain Analysis: A Primer, 2nd Edition

The first edition of Global Value Chain Analysis: A Primer was released five years ago (May 2011) in order to provide an overview of the key concepts and methodological tools used by Duke University’s Center on Globalization, Governance & Competitiveness (Duke CGGC) a university-based research center that focuses on innovative applications of the GVC framework, which was developed by Duke CGGC’s founding director, Gary Gereffi. The Second Edition of Global Value Chain Analysis: A Primer (July 2016) retains a simple, expository style and use of recent research examples in order to offer an entry point for those wishing to better understand and use the GVC framework as a tool to analyze how local actors (firms, communities, workers) are linked to and affected by major transformations in the global economy. The GVC framework focuses on structural shifts in global industries, anchored by the core concepts of governance and upgrading. This Second Edition highlights some of the refinements in these concepts, and introduces a number of new illustrations drawing from recent Duke CGGC research. The bibliography offers a sampling of the broad array of studies available on the Duke CGGC website and in related academic publications. We hope this work stimulates continued interest in and use of the GVC framework as a tool to promote more dynamic, inclusive and sustainable development outcomes for all economies and the local actors within them.

Introducing molaR: a New R Package for Quantitative Topographic Analysis of Teeth (and Other Topographic Surfaces)

© 2016 Springer Science+Business Media New YorkResearchers studying mammalian dentitions from functional and adaptive perspectives increasingly have moved towards using dental topography measures that can be estimated from 3D surface scans, which do not require identification of specific homologous landmarks. Here we present molaR, a new R package designed to assist researchers in calculating four commonly used topographic measures: Dirichlet Normal Energy (DNE), Relief Index (RFI), Orientation Patch Count (OPC), and Orientation Patch Count Rotated (OPCR) from surface scans of teeth, enabling a unified application of these informative new metrics. In addition to providing topographic measuring tools, molaR has complimentary plotting functions enabling highly customizable visualization of results. This article gives a detailed description of the DNE measure, walks researchers through installing, operating, and troubleshooting molaR and its functions, and gives an example of a simple comparison that measured teeth of the primates Alouatta and Pithecia in molaR and other available software packages. molaR is a free and open source software extension, which can be found at the doi:10.13140/RG.2.1.3563.4961(molaR v. 2.0) as well as on the Internet repository CRAN, which stores R packages.

Professional development programs in health promotion : tools and processes to favor new practices

Developing innovative interventions that are in sync with a health promotion paradigm often represents a challenge for professionals working in local public health organizations. Thus, it is critical to have both professional development programs that favor new practices and tools to examine these practices. In this case study, we analyze the health promotion approach used in a pilot intervention addressing children’s vulnerability that was developed and carried out by participants enrolled in a public health professional development program. More specifically, we use a modified version of Guichard and Ridde’s (Une grille d’analyse des actions pour lutter contre les inégalités sociales de santé. In Potvin, L., Moquet, M.-J. and Jones, C. M. (eds), Réduire les Inégalités Sociales en Santé. INPES, Saint-Denis Cedex, pp. 297– 312, 2010) analytical grid to assess deductively the program participants’ use of health promotion practices in the analysis and planning, implementation, evaluation, sustainability and empowerment phases of the pilot intervention. We also seek evidence of practices involving (empowerment, participation, equity, holism, an ecological approach, intersectorality and sustainability) in the intervention. The results are mixed: our findings reveal evidence of the application of several dimensions of health promotion (equity, holism, an ecological approach, intersectorality and sustainability), but also a lack of integration of two key dimensions; that is, empowerment and participation, during various phases of the pilot intervention. These results show that the professional development program is associated with the adoption of a pilot intervention integrating multiple but not all dimensions of health promotion. We make recommendations to facilitate a more complete integration. This research also shows that the Guichard and Ridde grid proves to be a thorough instrument to document the practices of participants.

Formal Modeling and Analysis Techniques for High Level Petri Nets

Petri Nets are a formal, graphical and executable modeling technique for the specification and analysis of concurrent and distributed systems and have been widely applied in computer science and many other engineering disciplines. Low level Petri nets are simple and useful for modeling control flows but not powerful enough to define data and system functionality. High level Petri nets (HLPNs) have been developed to support data and functionality definitions, such as using complex structured data as tokens and algebraic expressions as transition formulas. Compared to low level Petri nets, HLPNs result in compact system models that are easier to be understood. Therefore, HLPNs are more useful in modeling complex systems. There are two issues in using HLPNs - modeling and analysis. Modeling concerns the abstracting and representing the systems under consideration using HLPNs, and analysis deals with effective ways study the behaviors and properties of the resulting HLPN models. In this dissertation, several modeling and analysis techniques for HLPNs are studied, which are integrated into a framework that is supported by a tool. For modeling, this framework integrates two formal languages: a type of HLPNs called Predicate Transition Net (PrT Net) is used to model a system's behavior and a first-order linear time temporal logic (FOLTL) to specify the system's properties. The main contribution of this dissertation with regard to modeling is to develop a software tool to support the formal modeling capabilities in this framework. For analysis, this framework combines three complementary techniques, simulation, explicit state model checking and bounded model checking (BMC). Simulation is a straightforward and speedy method, but only covers some execution paths in a HLPN model. Explicit state model checking covers all the execution paths but suffers from the state explosion problem. BMC is a tradeoff as it provides a certain level of coverage while more efficient than explicit state model checking. The main contribution of this dissertation with regard to analysis is adapting BMC to analyze HLPN models and integrating the three complementary analysis techniques in a software tool to support the formal analysis capabilities in this framework. The SAMTools developed for this framework in this dissertation integrates three tools: PIPE+ for HLPNs behavioral modeling and simulation, SAMAT for hierarchical structural modeling and property specification, and PIPE+Verifier for behavioral verification.