Cross-Species Application of Illumina iScan Microarrays for Cost-Effective, High-Throughput SNP Discovery

Microarrays can be a cost-effective alternative to high-throughput sequencing for discovering novel single-nucleotide polymorphisms (SNPs). Illumina’s iScan platform dominates the market, but their commercial microarray products are designed for model organisms. Further, the platform outputs data in a proprietary format. This cannot be easily converted to human-readable genotypes or be merged with pre-existing data. To address this, we present and validate a novel pipeline to facilitate data analysis from cross-species application of Illumina microarrays. This facilitates the generation of a compatible VCF from iScan data and the merging of this with a second VCF comprising genotypes derived from other samples and sources. Our pipeline includes a custom script, iScanVCFMerge (presented as a Python package), which we validate using iScan data from three great ape genera. We conclude that cross-species application of microarrays can be a rapid, cost-effective approach for SNP discovery in non-model organisms. Our pipeline surmounts the common challenges of integrating iScan genotypes with pre-existing data.

Evaluating Manual Mappings of Russian Proprietary Formats and Terminologies to FHIR

Background Evaluating potential data losses from mapping proprietary medical data formats to standards is essential for decision making. The article implements a method to evaluate the preliminary content overlap of proprietary medical formats, including national terminologies and Fast Healthcare Interoperability Resources (FHIR)—international medical standard. Methods Three types of mappings were evaluated in the article: proprietary format matched to FHIR, national terminologies matched to the FHIR mappings, and concepts from national terminologies matched to Systematized Nomenclature of Medicine–Clinical Terms (SNOMED CT). We matched attributes of the formats with FHIR definitions and calculated content overlap. Results The article reports the results of a manual mapping between a proprietary medical format and the FHIR standard. The following results were obtained: 81% of content overlap for the proprietary format to FHIR mapping, 88% of content overlap for the national terminologies to FHIR mapping, and 98.6% of concepts matching can be reached from national terminologies to SNOMED CT mapping. Twenty tables from the proprietary format and 20 dictionaries were matched with FHIR resources; nine dictionaries were matched with SNOMED CT concepts. Conclusion Mapping medical formats is a challenge. The obtained overlaps are promising in comparison with the investigated results. The study showed that standardization of data exchange between proprietary formats and FHIR is possible in Russia, and national terminologies can be used in FHIR-based information systems.

Testing of the MTConnect–OPC UA Companion Specification

Smart Manufacturing (SM) is the future of the manufacturing industry. Seamless, accurate, and fast connection and communications among devices are critical for SM. By leveraging information technologies, devices can dynamically communicate with each other to increase factory production, while decreasing engineering costs. MTConnect and Open Platform Communications - Unified Architecture (OPC-UA) standards facilitate such communication. MTConnect is a manufacturing interoperability standard that provides a semantic vocabulary for manufacturing equipment to provide structured contextualized data with no proprietary format. The OPC-UA is a platform-independent standard through which various systems and devices can communicate by sending messages between clients and servers over various networks. OPC-UA enables syntactic interoperability between clients and servers. The MTConnect - OPC-UA Companion Specification integrates the two standards to provide manufacturers more efficient and powerful interoperability capabilities. In this paper, we report the test of version 1.02 of this companion specification. This specification sets a standard means of communication between MTConnect devices and OPC-UA Clients/Servers based on Extensible Markup Language (XML) structures. To test the standard, the following components have been developed: an OPC-UA Server, an OPC-UA Client, a probe that translates data structures in MTConnect XML format to MTConnect OPC-UA Companion XML format that can be recognized by the server, a MTConnect XML data parser, and a MTConnect device simulator. The activities of the standard testing include passing varying data structures and objects through the server and confirming the information is received accurately by the client. The findings of the standard testing will be provided to the standard developing organizations for improving the future versions of the standard.

RuleML-based mechanism of building information models verification

The issues of automated verification of design results based on information models have been raised recently by scientists and specialists from different countries, including the Russian Federation. Interoperability of expertise based on information models of objects should be provided using open formats for the presentation and exchange of the data. Each software that performs the functions of information modeling, as a rule, stores the results of the work in files of its proprietary format. IFC allows exchanging information about the geometry, attributes and relationships between the elements of information models of capital construction, that is, provides the transfer of all types of information stored by the information model. The MVD (Model View Definition) format is used to specify the subset of data volume that is used to solve a particular problem. RuleML is a system of families of modeling languages web of rules designed for the purpose of uniform presentation and exchange of the main types of web rules and logic between different platforms. BCF (BIM Collaboration Format) is an open standard maintained and distributed by buildingSMART that allows for various information modeling applications sharing information about issues related to IFC models that were previously shared by project participants.

Abstract 428: Lipoprotein(a) Targeting With RNAi Delivery Platforms in Transgenic Mice and Cynomolgus Monkeys

Background: Meta-analyses of clinical studies have demonstrated that high levels of lipoprotein(a), known as Lp(a), correlate with residual risk of cardiovascular disease (CVD) while Mendelian genetic studies indicate that Lp(a) is an independent cause of CVD. Lp(a) is a complex lipoprotein particle similar in structure to LDL (consisting of cholesterol, triglycerides, phospholipids and apoB-100), but contains the genetically variable liver-expressed protein apo(a). Lp(a) may contribute to atherosclerosis by targeting oxidized phospholipids to vascular injury sites, promoting both inflammation and accumulation of lipids. Methods: RNA interference (RNAi) based approaches for reducing liver apo(a) expression were developed using both a targeted intravenous platform called Dynamic Polyconjugates (DPC) TM and a subcutaneous (SQ) format. The DPC platform comprises an RNAi trigger conjugated to cholesterol, and a hepatocyte-targeted, membrane active peptide to promote endosomal release of the RNAi trigger. The SQ platform is an RNAi trigger targeted to liver by N-acetyl galactosamine in a proprietary format. RNAi activity was assessed in two different humanized transgenic mice and cynomolgus monkeys. Results: In Lp(a) transgenic mice expressing human apo(a) and apoB-100 genes, treatment with a single DPC dose reduced serum Lp(a) by >98% at nadir and >90% for >5 weeks. A single DPC injection in cynomolgus monkeys resulted in >95% reduction in endogenous Lp(a) particles at 5 weeks post injection, without significant changes in toxicity biomarkers. Treatment with a SQ RNAi trigger reduced serum apo(a) in transgenic mice by >90% at nadir, while that in monkeys reached 64% reduction of Lp(a). Additional modifications to the RNAi trigger improved both depth and duration of knockdown in transgenic mice. Conclusion: Long-duration reductions in circulating apo(a) and Lp(a) have been shown with hepatocyte-directed delivery of apo(a)-specific RNAi triggers in mice and monkeys. This represents an intriguing mechanism to evaluate in humans for reducing residual risk of CVD in LDL-controlled individuals with elevated Lp(a).

Increasing the accessibility of acoustic data through global access and imagery

The National Oceanographic and Atmospheric Administration (NOAA) uses water column sonar data to assess physical and biological characteristics from the ocean surface to the seabed. Acoustic surveys produce large volumes of data that can deliver valuable information beyond their original collection purpose if the data are properly managed, discoverable, and accessible to the public. NOAA's National Centers for Environmental Information, in partnership with NOAA's National Marine Fisheries Service and the University of Colorado, have created a national archive for water column sonar data to help achieve these goals. Through these efforts, over 21 TB of sonar data are now publicly available. Raw sonar files are difficult to interpret due to their size, complexity, and proprietary format. In order for users to understand the quality and composition of large volumes of archived data more easily, several visualization products were explored. Three processing methods were applied to multifrequency single-beam data (Simrad EK60) collected off the US northwest coast between 2007 and 2013. One method illustrates these complex data in a single image using a novel colour scale [multifrequency single-beam imaging (MFSBI)], another examines the nautical area scattering coefficients between two frequencies (ΔNASC), and the third indices the data into acoustic classifications [multifrequency indicator (MFI)]. The ability to apply the algorithms efficiently to multiyear datasets was explored. MFSBI proved effective at conveying the composition of the data and was easily adaptable to automated processing. ΔNASC, which required manual seabed corrections, illustrated a generalized pattern for changes in the water column across the shelf. MFI provided an empirically based statistical approach but will require more effort in the near term to evaluate and assess the accuracy and precision of each classification. Overall, spatio-temporal patterns of the acoustic backscatter identified large interannual variations in composition with the continental shelf break often playing a key role in attracting biological assemblages.

Interactive Design and Gamification of eBooks for Mobile and Contextual Learning

Given the global spread of mobile platforms, such as iOS and Android, it is relevant to consider the potential of these devices in teaching and learning. Our exploratory research was designed to evaluate the possibility of using common ebook formats to create gamebooks (gamified books) that are effective in teaching and learning. After analyzing the features available in many free or open tools, we decided to use iBooks Author to build a model of a dynamic book that may function as an educational game for "Environmental Studies", aimed at children in the 4th grade, mostly 9-10 years old, in Portuguese schools. This paper presents the design and features of this interactive book titled "Adventures in the Guadiana River", developed using the Apple iBook format, and especially set for the iPad retina. Because this is a proprietary format we also built a prototype following the EPUB3 standard and developed new ways to interact with content within this universal format. Preliminary tests with our prototypes revealed very good usability and promising pedagogical potential in the proposed models.

illuminaio: An open source IDAT parsing tool for Illumina microarrays

The IDAT file format is used to store BeadArray data from the myriad of genomewide profiling platforms on offer from Illumina Inc. This proprietary format is output directly from the scanner and stores summary intensities for each probe-type on an array in a compact manner. A lack of open source tools to process IDAT files has hampered their uptake by the research community beyond the standard step of using the vendor’s software to extract the data they contain in a human readable text format. To fill this void, we have developed the illuminaio package that parses IDAT files from any BeadArray platform, including the decryption of files from Illumina’s gene expression arrays. illuminaio provides the first open-source package for this task, and will promote wider uptake of the IDAT format as a standard for sharing Illumina BeadArray data in public databases, in the same way that the CEL file serves as the standard for the Affymetrix platform.

SS-MIX: A Ministry Project to Promote Standardized Healthcare Information Exchange

Summary Objectives: To promote healthcare information exchange between providers and to allow hospital information systems (HIS) export information in standardized format (HL7 and DICOM) in an environment of widespread legacy systems, which only can export data in proprietary format. Methods: Through the Shizuoka prefecture EMR project in 2004–2005, followed by the ministry’s SS-MIX project, many software products have been provided, which consist of 1) a standardized storage to receive HL7 v2.5 mes sages of patient demographics, prescription orders, laboratory results, and diagnostic disease in ICD-10, 2) a referral letter creation system, 3) a formatted document creation system, 4) a progress note/nursing record system, and 5) an archive/viewer to incorporate incoming healthcare data CD and allow users to view on HIS terminal. Meanwhile, other useful applications have been produced, such as adverse event reporting and clinical information retrieval. To achieve the above-mentioned objectives, these software products were created and propagated, because users can use these software products, provided that their HIS can export the above information to the standardized storage in HL7 v2.5 format. Results: In 20 hospitals of Japan, the standardized storage has been installed and some applications have been used. As major HIS vendors are shipping HIS with HL7 export function since 2007, HIS of 594 hospitals in Japan became capable of exporting data in HL7 v2.5 format (as of March 2010). Conclusions: In high CPOE installation rate (85% in 400+ bed hospitals), though most of them only capable of exporting data in proprietary format, prefecture and ministry projects were effective to promote healthcare information exchange between providers. The standardized storage became an infrastructure for many useful applications, and many hospitals started using them. Ministry designation of proposed healthcare standards was effective so as to allow vendors to conform their products, and users to install them.