Transparency tools in gene patenting for informing policy and practice

In the recent decision Association for Molecular Pathology v. Myriad Genetics1, the US Supreme Court held that naturally occurring sequences from human genomic DNA are not patentable subject matter. Only certain complementary DNAs (cDNA), modified sequences and methods to use sequences are potentially patentable. It is likely that this distinction will hold for all DNA sequences, whether animal, plant or microbial2. However, it is not clear whether this means that other naturally occurring informational molecules, such as polypeptides (proteins) or polysaccharides, will also be excluded from patents. The decision underscores a pressing need for precise analysis of patents that disclose and reference genetic sequences, especially in the claims. Similarly, data sets, standards compliance and analytical tools must be improved—in particular, data sets and analytical tools must be made openly accessible—in order to provide a basis for effective decision making and policy setting to support biological innovation. Here, we present a web-based platform that allows such data aggregation, analysis and visualization in an open, shareable facility. To demonstrate the potential for the extension of this platform to global patent jurisdictions, we discuss the results of a global survey of patent offices that shows that much progress is still needed in making these data freely available for aggregation in the first place.

False-colour spectrograms of long duration acoustic recordings

Acoustic recordings of the environment are an important aid to ecologists monitoring biodiversity and environmental health. However, rapid advances in recording technology, storage and computing make it possible to accumulate thousands of hours of recordings, of which, ecologists can only listen to a small fraction. The big-data challenge is to visualize the content of long-duration audio recordings on multiple scales, from hours, days, months to years. The visualization should facilitate navigation and yield ecologically meaningful information. Our approach is to extract (at one minute resolution) acoustic indices which reflect content of ecological interest. An acoustic index is a statistic that summarizes some aspect of the distribution of acoustic energy in a recording. We combine indices to produce false-colour images that reveal acoustic content and facilitate navigation through recordings that are months or even years in duration.

Overview of INEX 2013

INEX investigates focused retrieval from structured documents by providing large test collections of structured documents, uniform evaluation measures, and a forum for organizations to compare their results. This paper reports on the INEX 2013 evaluation campaign, which consisted of four activities addressing three themes: searching professional and user generated data (Social Book Search track); searching structured or semantic data (Linked Data track); and focused retrieval (Snippet Retrieval and Tweet Contextualization tracks). INEX 2013 was an exciting year for INEX in which we consolidated the collaboration with (other activities in) CLEF and for the second time ran our workshop as part of the CLEF labs in order to facilitate knowledge transfer between the evaluation forums. This paper gives an overview of all the INEX 2013 tracks, their aims and task, the built test-collections, and gives an initial analysis of the results

The α5 subunit regulates the expression and function of α4*-containing neuronal nicotinic acetylcholine receptors in the ventral-tegmental area

Human genetic association studies have shown gene variants in the α5 subunit of the neuronal nicotinic receptor (nAChR) influence both ethanol and nicotine dependence. The α5 subunit is an accessory subunit that facilitates α4* nAChRs assembly in vitro. However, it is unknown whether this occurs in the brain, as there are few research tools to adequately address this question. As the α4*-containing nAChRs are highly expressed in the ventral tegmental area (VTA) we assessed the molecular, functional and pharmacological roles of α5 in α4*-containing nAChRs in the VTA. We utilized transgenic mice α5+/+(α4YFP) and α5-/-(α4YFP) that allow the direct visualization and measurement of α4-YFP expression and the effect of the presence (α5+/+) and absence of α5 (-/-) subunit, as the antibodies for detecting the α4* subunits of the nAChR are not specific. We performed voltage clamp electrophysiological experiments to study baseline nicotinic currents in VTA dopaminergic neurons. We show that in the presence of the α5 subunit, the overall expression of α4 subunit is increased significantly by 60% in the VTA. Furthermore, the α5 subunit strengthens baseline nAChR currents, suggesting the increased expression of α4* nAChRs to be likely on the cell surface. While the presence of the α5 subunit blunts the desensitization of nAChRs following nicotine exposure, it does not alter the amount of ethanol potentiation of VTA dopaminergic neurons. Our data demonstrates a major regulatory role for the α5 subunit in both the maintenance of α4*-containing nAChRs expression and in modulating nicotinic currents in VTA dopaminergic neurons. Additionally, the α5α4* nAChR in VTA dopaminergic neurons regulates the effect of nicotine but not ethanol on currents. Together, the data suggest that the α5 subunit is critical for controlling the expression and functional role of a population of α4*-containing nAChRs in the VTA.

Ad hoc radiometric calibration of a thermal-infrared camera

Many applications can benefit from the accurate surface temperature estimates that can be made using a passive thermal-infrared camera. However, the process of radiometric calibration which enables this can be both expensive and time consuming. An ad hoc approach for performing radiometric calibration is proposed which does not require specialized equipment and can be completed in a fraction of the time of the conventional method. The proposed approach utilizes the mechanical properties of the camera to estimate scene temperatures automatically, and uses these target temperatures to model the effect of sensor temperature on the digital output. A comparison with a conventional approach using a blackbody radiation source shows that the accuracy of the method is sufficient for many tasks requiring temperature estimation. Furthermore, a novel visualization method is proposed for displaying the radiometrically calibrated images to human operators. The representation employs an intuitive coloring scheme and allows the viewer to perceive a large variety of temperatures accurately.

HeatWave : a handheld 3D thermography system for energy auditing

Energy auditing is an effective but costly approach for reducing the long-term energy consumption of buildings. When well-executed, energy loss can be quickly identified in the building structure and its subsystems. This then presents opportunities for improving energy efficiency. We present a low-cost, portable technology called "HeatWave" which allows non-experts to generate detailed 3D surface temperature models for energy auditing. This handheld 3D thermography system consists of two commercially available imaging sensors and a set of software algorithms which can be run on a laptop. The 3D model can be visualized in real-time by the operator so that they can monitor their degree of coverage as the sensors are used to capture data. In addition, results can be analyzed offline using the proposed "Spectra" multispectral visualization toolbox. The presence of surface temperature data in the generated 3D model enables the operator to easily identify and measure thermal irregularities such as thermal bridges, insulation leaks, moisture build-up and HVAC faults. Moreover, 3D models generated from subsequent audits of the same environment can be automatically compared to detect temporal changes in conditions and energy use over time.

Contours in Motion

My practice-led research explores and maps workflows for generating experimental creative work involving inertia based motion capture technology. Motion capture has often been used as a way to bridge animation and dance resulting in abstracted visuals outcomes. In early works this process was largely done by rotoscoping, reference footage and mechanical forms of motion capture. With the evolution of technology, optical and inertial forms of motion capture are now more accessible and able to accurately capture a larger range of complex movements. The creative work titled “Contours in Motion” was the first in a series of studies on captured motion data used to generating experimental visual forms that reverberate in space and time. With the source or ‘seed’ comes from using an Xsens MVN - Inertial Motion Capture system to capture spontaneous dance movements, with the visual generation conducted through a customised dynamics simulation. The aim of the creative work was to diverge way from a standard practice of using particle system and/or a simple re-targeting of the motion data to drive a 3d character as a means to produce abstracted visual forms. To facilitate this divergence a virtual dynamic object was tether to a selection of data points from a captured performance. The proprieties of the dynamic object were then adjusted to balance the influences from the human movement data with the influence of computer based randomization. The resulting outcome was a visual form that surpassed simple data visualization to project the intent of the performer’s movements into a visual shape itself. The reported outcomes from this investigation have contributed to a larger study on the use of motion capture in the generative arts, furthering the understanding of and generating theories on practice.

Managing and analysing big audio data for environmental monitoring

Environmental monitoring is becoming critical as human activity and climate change place greater pressures on biodiversity, leading to an increasing need for data to make informed decisions. Acoustic sensors can help collect data across large areas for extended periods making them attractive in environmental monitoring. However, managing and analysing large volumes of environmental acoustic data is a great challenge and is consequently hindering the effective utilization of the big dataset collected. This paper presents an overview of our current techniques for collecting, storing and analysing large volumes of acoustic data efficiently, accurately, and cost-effectively.

Overview of the ShARe/CLEF eHealth Evaluation Lab 2013

Discharge summaries and other free-text reports in healthcare transfer information between working shifts and geographic locations. Patients are likely to have difficulties in understanding their content, because of their medical jargon, non-standard abbreviations,and ward-specific idioms. This paper reports on an evaluation lab with an aim to support the continuum of care by developing methods and resources that make clinical reports in English easier to understand for patients, and which helps them in finding information related to their condition.

Damage evaluation based on a wave energy flow map using multiple PZT sensors

A new wave energy flow (WEF) map concept was proposed in this work. Based on it, an improved technique incorporating the laser scanning method and Betti’s reciprocal theorem was developed to evaluate the shape and size of damage as well as to realize visualization of wave propagation. In this technique, a simple signal processing algorithm was proposed to construct the WEF map when waves propagate through an inspection region, and multiple lead zirconate titanate (PZT) sensors were employed to improve inspection reliability. Various damages in aluminum and carbon fiber reinforced plastic laminated plates were experimentally and numerically evaluated to validate this technique. The results show that it can effectively evaluate the shape and size of damage from wave field variations around the damage in the WEF map.

Pulsed wall jet simulation of a stationary thunderstorm downburst, Part A: Physical structure and flow field characterization

A pulsed wall jet has been used to simulate the gust front of a thunderstorm downburst. Flow visualization, wind speed and surface pressure measurements were obtained. The characteristics of the hypothesized ring vortex of a full-scale downburst were reproduced at a scale estimated to be 1:3000.

Non-formal techniques for early assessment of design ideas for services

Designing systems for multiple stakeholders requires frequent collaboration with multiple stakeholders from the start. In many cases at least some stakeholders lack a professional habit of formal modeling. We report observations from student design teams as well as two case studies, respectively of a prototype for supporting creative communication to design objects, and of stakeholder-involvement in early design. In all observations and case studies we found that non-formal techniques supported strong collaboration resulting in deep understanding of early design ideas, of their value and of the feasibility of solutions.

A brief guide to synchrotron radiation-based microtomography in (structural) geology and rock mechanics

This contribution outlines Synchrotron-based X-ray micro-tomography and its potential use in structural geology and rock mechanics. The paper complements several recent reviews of X-ray microtomography. We summarize the general approach to data acquisition, post-processing as well as analysis and thereby aim to provide an entry point for the interested reader. The paper includes tables listing relevant beamlines, a list of all available imaging techniques, and available free and commercial software packages for data visualization and quantification. We highlight potential applications in a review of relevant literature including time-resolved experiments and digital rock physics. The paper concludes with a report on ongoing developments and upgrades at synchrotron facilities to frame the future possibilities for imaging sub-second processes in centimetre-sized samples.

Feeling the life : a look into the visual culture of life scientists

In order to deal with human biological problems, life scientists have started investigating artificial ways of generating tissues and growing cells ? leading to the evolution of tissue engineering. In this paper we explore visualization practices of life scientists working within the domain of tissue engineering. We carried out a small scale ethnographic exploration with 8 scientists and explored that the real value of scientists' experiments (and simulations), reasoning and collaborative processes go beyond their end results. We observed that these scientists' three-dimensional reasoning, corporeal knowledge and intimacy with biological objects and tools play a vital role in overall success.

Decision strategies for automated visual collision avoidance

This paper provides a preliminary analysis of an autonomous uncooperative collision avoidance strategy for unmanned aircraft using image-based visual control. Assuming target detection, the approach consists of three parts. First, a novel decision strategy is used to determine appropriate reference image features to track for safe avoidance. This is achieved by considering the current rules of the air (regulations), the properties of spiral motion and the expected visual tracking errors. Second, a spherical visual predictive control (VPC) scheme is used to guide the aircraft along a safe spiral-like trajectory about the object. Lastly, a stopping decision based on thresholding a cost function is used to determine when to stop the avoidance behaviour. The approach does not require estimation of range or time to collision, and instead relies on tuning two mutually exclusive decision thresholds to ensure satisfactory performance.