Comparisons between analogue and numerical models of thrust wedge development

Analogue and finite element numerical models with frictional and viscous properties are used to model thrust wedge development. Comparison between model types yields valuable information about analogue model evolution, scaling laws and the relative strengths and limitations of the techniques. Both model types show a marked contrast in structural style between ‘frictional-viscous domains’ underlain by a thin viscous layer and purely ‘frictional domains’. Closely spaced thrusts form a narrow and highly asymmetric fold-and-thrust belt in the frictional domain, characterized by in-sequence propagation of forward thrusts. In contrast, the frictional-viscous domain shows a wide and low taper wedge and a thrust belt with a more symmetrical vergence, with both forward and back thrusts. The frictional-viscous domain numerical models show that the viscous layer initially simple shears as deformation propagates along it, while localized deformation resulting in the formation of a pop-up structure occurs in the overlying frictional layers. In both domains, thrust shear zones in the numerical model are generally steeper than the equivalent faults in the analogue model, because the finite element code uses a non-associated plasticity flow law. Nevertheless, the qualitative agreement between analogue and numerical models is encouraging. It shows that the continuum approximation used in numerical models can be used to model frictional materials, such as sand, provided caution is taken to properly scale the experiments, and some of the limitations are taken into account.

Automatic Labeling of Software Components and their Evolution using Log-Likelihood Ratio of Word Frequencies in Source Code

As more and more open-source software components become available on the internet we need automatic ways to label and compare them. For example, a developer who searches for reusable software must be able to quickly gain an understanding of retrieved components. This understanding cannot be gained at the level of source code due to the semantic gap between source code and the domain model. In this paper we present a lexical approach that uses the log-likelihood ratios of word frequencies to automatically provide labels for software components. We present a prototype implementation of our labeling/comparison algorithm and provide examples of its application. In particular, we apply the approach to detect trends in the evolution of a software system.

A Trustability Metric for Code Search based on Developer Karma

The promise of search-driven development is that developers will save time and resources by reusing external code in their local projects. To efficiently integrate this code, users must be able to trust it, thus trustability of code search results is just as important as their relevance. In this paper, we introduce a trustability metric to help users assess the quality of code search results and therefore ease the cost-benefit analysis they undertake trying to find suitable integration candidates. The proposed trustability metric incorporates both user votes and cross-project activity of developers to calculate a "karma" value for each developer. Through the karma value of all its developers a project is ranked on a trustability scale. We present JBENDER, a proof-of-concept code search engine which implements our trustability metric and we discuss preliminary results from an evaluation of the prototype.

Evaluating Code Duplication to Identify Rich Business Objects from Data Transfer Objects

Java Enterprise Applications (JEAs) are complex software systems written using multiple technologies. Moreover they are usually distributed systems and use a database to deal with persistence. A particular problem that appears in the design of these systems is the lack of a rich business model. In this paper we propose a technique to support the recovery of such rich business objects starting from anemic Data Transfer Objects (DTOs). Exposing the code duplications in the application's elements using the DTOs we suggest which business logic can be moved into the DTOs from the other classes.

Spy: A Flexible Code Profiling Framework

Code profiling is an essential activity to increase software quality. It is commonly employed in a wide variety of tasks, such as supporting program comprehension, determining execution bottlenecks, and assessing code coverage by unit tests. Spy is an innovative framework to easily build profilers and visualize profiling information. The profiling information is obtained by inserting dedicated code before or after method execution. The gathered profiling information is structured in line with the application structure in terms of packages, classes, and methods. Spy has been instantiated on four occasions so far. We created profilers dedicated to test coverage, time execution, type feedback, and profiling evolution across version. We also integrated Spy in the Pharo IDE. Spy has been implemented in the Pharo Smalltalk programming language and is available under the MIT license.

Uses and misuses of the STROBE statement: bibliographic study

Objectives Appropriate reporting is central to the application of findings from research to clinical practice. The Strengthening the Reporting of Observational Studies in Epidemiology (STROBE) recommendations consist of a checklist of 22 items that provide guidance on the reporting of cohort, case-control and cross-sectional studies, in order to facilitate critical appraisal and interpretation of results. STROBE was published in October 2007 in several journals including The Lancet, BMJ, Annals of Internal Medicine and PLoS Medicine. Within the framework of the revision of the STROBE recommendations, the authors examined the context and circumstances in which the STROBE statement was used in the past. Design The authors searched the Web of Science database in August 2010 for articles which cited STROBE and examined a random sample of 100 articles using a standardised, piloted data extraction form. The use of STROBE in observational studies and systematic reviews (including meta-analyses) was classified as appropriate or inappropriate. The use of STROBE to guide the reporting of observational studies was considered appropriate. Inappropriate uses included the use of STROBE as a tool to assess the methodological quality of studies or as a guideline on how to design and conduct studies. Results The authors identified 640 articles that cited STROBE. In the random sample of 100 articles, about half were observational studies (32%) or systematic reviews (19%). Comments, editorials and letters accounted for 15%, methodological articles for 8%, and recommendations and narrative reviews for 26% of articles. Of the 32 observational studies, 26 (81%) made appropriate use of STROBE, and three uses (10%) were considered inappropriate. Among 19 systematic reviews, 10 (53%) used STROBE inappropriately as a tool to assess study quality. Conclusions The STROBE reporting recommendations are frequently used inappropriately in systematic reviews and meta-analyses as an instrument to assess the methodological quality of observational studies.

High-resolution electrophoretic simulations: performance characteristics of one-dimensional simulators

Three comprehensive one-dimensional simulators were used on the same PC to simulate the dynamics of different electrophoretic configurations, including two migrating hybrid boundaries, an isotachophoretic boundary and the zone electrophoretic separation of ten monovalent anions. Two simulators, SIMUL5 and GENTRANS, use a uniform grid, while SPRESSO uses a dynamic adaptive grid. The simulators differ in the way components are handled. SIMUL5 and SPRESSO feature one equation for all components, whereas GENTRANS is based on the use of separate modules for the different types of monovalent components, a module for multivalent components and a module for proteins. The code for multivalent components is executed more slowly compared to those for monovalent components. Furthermore, with SIMUL5, the computational time interval becomes smaller when it is operated with a reduced calculation space that features moving borders, whereas GENTRANS offers the possibility of using data smoothing (removal of negative concentrations), which can avoid numerical oscillations and speed up a simulation. SPRESSO with its adaptive grid could be employed to simulate the same configurations with smaller numbers of grid points and thus is faster in certain but not all cases. The data reveal that simulations featuring a large number of monovalent components distributed such that a high mesh is required throughout a large proportion of the column are fastest executed with GENTRANS.

Alternative DNA base-pairs: from efforts to expand the genetic code to potential material applications

The complementary Watson-Crick base-pairs, A:T and G:C, have long been recognized as pivotal to both the stability of the DNA double helix and replication/transcription. Recently, the replacement of the Watson-Crick base-pairs with other molecular entities has received considerable attention. In this tutorial review we highlight different approaches used to replace natural base-pairs and equip them with novel function. We also discuss the advantages that non-natural base-pairs convey with respect to practical applications.