Optical modeling of Fresnel zoneplate microscopes

Defect free masks remain one of the most significant challenges facing the commercialization of extreme ultraviolet (EUV) lithography. Progress on this front requires high-performance wavelength-specific metrology of EUV masks, including high-resolution and aerial-image microscopy performed near the 13.5?nm wavelength. Arguably the most cost-effective and rapid path to proliferating this capability is through the development of Fresnel zoneplate-based microscopes. Given the relative obscurity of such systems, however, modeling tools are not necessarily optimized to deal with them and their imaging properties are poorly understood. Here we present a modeling methodology to analyze zoneplate microscopes based on commercially available optical modeling software and use the technique to investigate the imaging performance of an off-axis EUV microscope design. The modeling predicts that superior performance can be achieved by tilting the zoneplate, making it perpendicular to the chief ray at the center of the field, while designing the zoneplate to explicitly work in that tilted plane. Although the examples presented here are in the realm of EUV mask inspection, the methods described and analysis results are broadly applicable to zoneplate microscopes in general, including full-field soft-x-ray microscopes routinely used in the synchrotron community.     

A systematic literature review of Linked Data‐based recommender systems

Recommender systems (RS) are software tools that use analytic technologies to suggest different items of interest to an end user. Linked Data is a set of best practices for publishing and connecting structured data on the Web. This paper presents a systematic literature review to summarize the state of the art in RS that use structured data published as Linked Data for providing recommendations of items from diverse domains. It considers the most relevant research problems addressed and classifies RS according to how Linked Data have been used to provide recommendations. Furthermore, it analyzes contributions, limitations, application domains, evaluation techniques, and directions proposed for future research. We found that there are still many open challenges with regard to RS based on Linked Data in order to be efficient for real applications. The main ones are personalization of recommendations, use of more datasets considering the heterogeneity introduced, creation of new hybrid RS for adding information, definition of more advanced similarity measures that take into account the large amount of data in Linked Data datasets, and implementation of testbeds to study evaluation techniques and to assess the accuracy scalability and computational complexity of RS. Copyright © 2015 John Wiley & Sons, Ltd.     

Crossing Bacterial Genomic Features and Methylation Patterns with MeStudio: An Epigenomic Analysis Tool

DNA methylation is one of the most observed epigenetic modifications. It is present in eukaryotes and prokaryotes and is related to several biological phenomena, including gene flow and adaptation to environmental conditions. The widespread use of third-generation sequencing technologies allows direct and easy detection of genome-wide methylation profiles, offering increasing opportunities to understand and exploit the epigenomic landscape of individuals and populations. Here, we present a pipeline named MeStudio, with the aim of analyzing and combining genome-wide methylation profiles with genomic features. Outputs report the presence of DNA methylation in coding sequences (CDSs) and noncoding sequences, including both intergenic sequences and sequences upstream of the CDS. We apply this novel tool, showing the usage and performance of MeStudio, on a set of single-molecule real-time sequencing outputs from strains of the bacterial species Sinorhizobium meliloti.