TMAX – a Database System Integrating Tissue Biomarker & Genomic Data

Background: Popular approaches in human tissue-based biomarker discovery include tissue microarrays (TMAs) and DNA Microarrays (DMAs) for protein and gene expression profiling respectively. The data generated by these analytic platforms, together with associated image, clinical and pathological data currently reside on widely different information platforms, making searching and cross-platform analysis difficult. Consequently, there is a strong need to develop a single coherent database capable of correlating all available data types.

Method: This study presents TMAX, a database system to facilitate biomarker discovery tasks. TMAX organises a variety of biomarker discovery-related data into the database. Both TMA and DMA experimental data are integrated in TMAX and connected through common DNA/protein biomarkers. Patient clinical data (including tissue pathological data), computer assisted tissue image and associated analytic data are also included in TMAX to enable the truly high throughput processing of ultra-large digital slides for both TMAs and whole slide tissue digital slides. A comprehensive web front-end was built with embedded XML parser software and predefined SQL queries to enable rapid data exchange in the form of standard XML files.

Results & Conclusion: TMAX represents one of the first attempts to integrate TMA data with public gene expression experiment data. Experiments suggest that TMAX is robust in managing large quantities of data from different sources (clinical, TMA, DMA and image analysis). Its web front-end is user friendly, easy to use, and most importantly allows the rapid and easy data exchange of biomarker discovery related data. In conclusion, TMAX is a robust biomarker discovery data repository and research tool, which opens up the opportunities for biomarker discovery and further integromics research.

SurfaceSlide: A Multitouch Digital Pathology Platform

Background: Digital pathology provides a digital environment for the management and interpretation of pathological images and associated data. It is becoming increasing popular to use modern computer based tools and applications in pathological education, tissue based research and clinical diagnosis. Uptake of this new technology is stymied by its single user orientation and its prerequisite and cumbersome combination of mouse and keyboard for navigation and annotation.

Methodology: In this study we developed SurfaceSlide, a dedicated viewing platform which enables the navigation and annotation of gigapixel digitised pathological images using fingertip touch. SurfaceSlide was developed using the Microsoft Surface, a 30 inch multitouch tabletop computing platform. SurfaceSlide users can perform direct panning and zooming operations on digitised slide images. These images are downloaded onto the Microsoft Surface platform from a remote server on-demand. Users can also draw annotations and key in texts using an on-screen virtual keyboard. We also developed a smart caching protocol which caches the surrounding regions of a field of view in multi-resolutions thus providing a smooth and vivid user experience and reducing the delay for image downloading from the internet. We compared the usability of SurfaceSlide against Aperio ImageScope and PathXL online viewer.

Conclusion: SurfaceSlide is intuitive, fast and easy to use. SurfaceSlide represents the most direct, effective and intimate human–digital slide interaction experience. It is expected that SurfaceSlide will significantly enhance digital pathology tools and applications in education and clinical practice.

A systematic review evaluating the impact of online or blended learning vs. face-to-face learning of clinical skills in undergraduate nurse education.

Aim: To determine whether the use of an online or blended learning paradigm has the potential to enhance the teaching of clinical skills in undergraduate nursing.

Background: The need to adequately support and develop students in clinical skills is now arguably more important than previously considered due to reductions in practice opportunities. Online and blended teaching methods are being developed to try and meet this requirement, but knowledge about their effectiveness in teaching clinical skills is limited.

Design: Mixed methods systematic review, which follows the Joanna Briggs Institute User guide version 5.

Data Sources: Computerized searches of five databases were undertaken for the period 1995-August 2013.

Review Methods: Critical appraisal and data extraction were undertaken using Joanna Briggs Institute tools for experimental/observational studies and interpretative and critical research. A narrative synthesis was used to report results.

Results: Nineteen published papers were identified. Seventeen papers reported on online approaches and only two papers reported on a blended approach. The synthesis of findings focused on the following four areas: performance/clinical skill, knowledge, self-efficacy/clinical confidence and user experience/satisfaction. The e-learning interventions used varied throughout all the studies.

Conclusion: The available evidence suggests that online learning for teaching clinical skills is no less effective than traditional means. Highlighted by this review is the lack of available evidence on the implementation of a blended learning approach to teaching clinical skills in undergraduate nurse education. Further research is required to assess the effectiveness of this teaching methodology.

Extracting Query Interfaces Based on Form Structures and Semantic Similarity

Web databases are now pervasive. Such a database can be accessed via its query interface (usually HTML query form) only. Extracting Web query interfaces is a critical step in data integration across multiple Web databases, which creates a formal representation of a query form by extracting a set of query conditions in it. This paper presents a novel approach to extracting Web query interfaces. In this approach, a generic set of query condition rules are created to define query conditions that are semantically equivalent to SQL search conditions. Query condition rules represent the semantic roles that labels and form elements play in query conditions, and how they are hierarchically grouped into constructs of query conditions. To group labels and form elements in a query form, we explore both their structural proximity in the hierarchy of structures in the query form, which is captured by a tree of nested tags in the HTML codes of the form, and their semantic similarity, which is captured by various short texts used in labels, form elements and their properties. We have implemented the proposed approach and our experimental results show that the approach is highly effective.

Entity Linking for Web Search Queries

We consider the problem of linking web search queries to entities from a knowledge base such as Wikipedia. Such linking enables converting a user’s web search session to a footprint in the knowledge base that could be used to enrich the user profile. Traditional methods for entity linking have been directed towards finding entity mentions in text documents such as news reports, each of which are possibly linked to multiple entities enabling the usage of measures like entity set coherence. Since web search queries are very small text fragments, such criteria that rely on existence of a multitude of mentions do not work too well on them. We propose a three-phase method for linking web search queries to wikipedia entities. The first phase does IR-style scoring of entities against the search query to narrow down to a subset of entities that are expanded using hyperlink information in the second phase to a larger set. Lastly, we use a graph traversal approach to identify the top entities to link the query to. Through an empirical evaluation on real-world web search queries, we illustrate that our methods significantly enhance the linking accuracy over state-of-the-art methods.

Reasoning about orchestrations of web services using partial correctness

A service is a remote computational facility which is made available for general use by means of a wide-area network. Several types of service arise in practice: stateless services, shared state services and services with states which are customised for individual users. A service-based orchestration is a multi-threaded computation which invokes remote services in order to deliver results back to a user (publication). In this paper a means of specifying services and reasoning about the correctness of orchestrations over stateless services is presented. As web services are potentially unreliable the termination of even finite orchestrations cannot be guaranteed. For this reason a partial-correctness powerdomain approach is proposed to capture the semantics of recursive orchestrations.

Web Data Extraction from Query Result Pages Based on Visual and Content Features

A rapidly increasing number of Web databases are now become accessible via
their HTML form-based query interfaces. Query result pages are dynamically generated
in response to user queries, which encode structured data and are displayed for human
use. Query result pages usually contain other types of information in addition to query
results, e.g., advertisements, navigation bar etc. The problem of extracting structured data
from query result pages is critical for web data integration applications, such as comparison
shopping, meta-search engines etc, and has been intensively studied. A number of approaches
have been proposed. As the structures of Web pages become more and more complex, the
existing approaches start to fail, and most of them do not remove irrelevant contents which
may a®ect the accuracy of data record extraction. We propose an automated approach for
Web data extraction. First, it makes use of visual features and query terms to identify data
sections and extracts data records in these sections. We also represent several content and
visual features of visual blocks in a data section, and use them to ¯lter out noisy blocks.
Second, it measures similarity between data items in di®erent data records based on their
visual and content features, and aligns them into di®erent groups so that the data in the
same group have the same semantics. The results of our experiments with a large set of
Web query result pages in di®erent domains show that our proposed approaches are highly
e®ective.

Stressed Web Environments as Strategic Games: Risk Profiles and Weltanschauung

We consider the behaviour of a set of services in a stressed web environment where performance patterns may be difficult to predict. In stressed environments the performances of some providers may degrade while the performances of others, with elastic resources, may improve. The allocation of web-based providers to users (brokering) is modelled by a strategic non-cooperative angel-daemon game with risk profiles. A risk profile specifies a bound on the number of unreliable service providers within an environment without identifying the names of these providers. Risk profiles offer a means of analysing the behaviour of broker agents which allocate service providers to users. A Nash equilibrium is a fixed point of such a game in which no user can locally improve their choice of provider – thus, a Nash equilibrium is a viable solution to the provider/user allocation problem. Angel daemon games provide a means of reasoning about stressed environments and offer the possibility of designing brokers using risk profiles and Nash equilibria.

Visually extracting data records from the deep web

Web sites that rely on databases for their content are now ubiquitous. Query result pages are dynamically generated from these databases in response to user-submitted queries. Automatically extracting structured data from query result pages is a challenging problem, as the structure of the data is not explicitly represented. While humans have shown good intuition in visually understanding data records on a query result page as displayed by a web browser, no existing approach to data record extraction has made full use of this intuition. We propose a novel approach, in which we make use of the common sources of evidence that humans use to understand data records on a displayed query result page. These include structural regularity, and visual and content similarity between data records displayed on a query result page. Based on these observations we propose new techniques that can identify each data record individually, while ignoring noise items, such as navigation bars and adverts. We have implemented these techniques in a software prototype, rExtractor, and tested it using two datasets. Our experimental results show that our approach achieves significantly higher accuracy than previous approaches. Furthermore, it establishes the case for use of vision-based algorithms in the context of data extraction from web sites.

Analysing Web-Orchestrations Under Stress Using Uncertainty Profiles

An orchestration is a multi-threaded computation that invokes a number of remote services. In practice, the responsiveness of a web-service fluctuates with demand; during surges in activity service responsiveness may be degraded, perhaps even to the point of failure. An uncertainty profile formalizes a user's perception of the effects of stress on an orchestration of web-services; it describes a strategic situation, modelled by a zero-sum angel–daemon game. Stressed web-service scenarios are analysed, using game theory, in a realistic way, lying between over-optimism (services are entirely reliable) and over-pessimism (all services are broken). The ‘resilience’ of an uncertainty profile can be assessed using the valuation of its associated zero-sum game. In order to demonstrate the validity of the approach, we consider two measures of resilience and a number of different stress models. It is shown how (i) uncertainty profiles can be ordered by risk (as measured by game valuations) and (ii) the structural properties of risk partial orders can be analysed.