A graph theoretic approach to testing associations between disparate sources of functional genomic data

The last few years have seen the advent of high-throughput technologies to analyze various properties of the transcriptome and proteome of several organisms. The congruency of these different data sources, or lack thereof, can shed light on the mechanisms that govern cellular function. A central challenge for bioinformatics research is to develop a unified framework for combining the multiple sources of functional genomics information and testing associations between them, thus obtaining a robust and integrated view of the underlying biology. We present a graph theoretic approach to test the significance of the association between multiple disparate sources of functional genomics data by proposing two statistical tests, namely edge permutation and node label permutation tests. We demonstrate the use of the proposed tests by finding significant association between a Gene Ontology-derived "predictome" and data obtained from mRNA expression and phenotypic experiments for Saccharomyces cerevisiae. Moreover, we employ the graph theoretic framework to recast a surprising discrepancy presented in Giaever et al. (2002) between gene expression and knockout phenotype, using expression data from a different set of experiments.

Design and implementation of a 3D computer game controller using inertial MEMS sensors

Though 3D computer graphics has seen tremendous advancement in the past two decades, most available mechanisms for computer interaction in 3D are high cost and targeted for industry and virtual reality applications. Recent advances in Micro-Electro-Mechanical-System (MEMS) devices have brought forth a variety of new low-cost, low-power, miniature sensors with high accuracy, which are well suited for hand-held devices. In this work a novel design for a 3D computer game controller using inertial sensors is proposed, and a prototype device based on this design is implemented. The design incorporates MEMS accelerometers and gyroscopes from Analog Devices to measure the three components of the acceleration and angular velocity. From these sensor readings, the position and orientation of the hand-held compartment can be calculated using numerical methods. The implemented prototype is utilizes a USB 2.0 compliant interface for power and communication with the host system. A Microchip dsPIC microcontroller is used in the design. This microcontroller integrates the analog to digital converters, the program memory flash, as well as the core processor, on a single integrated circuit. A PC running Microsoft Windows operating system is used as the host machine. Prototype firmware for the microcontroller is developed and tested to establish the communication between the design and the host, and perform the data acquisition and initial filtering of the sensor data. A PC front-end application with a graphical interface is developed to communicate with the device, and allow real-time visualization of the acquired data.

Electronic medical record systems, data quality and loss to follow-up: survey of antiretroviral therapy programmes in resource-limited settings

OBJECTIVE: To describe the electronic medical databases used in antiretroviral therapy (ART) programmes in lower-income countries and assess the measures such programmes employ to maintain and improve data quality and reduce the loss of patients to follow-up. METHODS: In 15 countries of Africa, South America and Asia, a survey was conducted from December 2006 to February 2007 on the use of electronic medical record systems in ART programmes. Patients enrolled in the sites at the time of the survey but not seen during the previous 12 months were considered lost to follow-up. The quality of the data was assessed by computing the percentage of missing key variables (age, sex, clinical stage of HIV infection, CD4+ lymphocyte count and year of ART initiation). Associations between site characteristics (such as number of staff members dedicated to data management), measures to reduce loss to follow-up (such as the presence of staff dedicated to tracing patients) and data quality and loss to follow-up were analysed using multivariate logit models. FINDINGS: Twenty-one sites that together provided ART to 50 060 patients were included (median number of patients per site: 1000; interquartile range, IQR: 72-19 320). Eighteen sites (86%) used an electronic database for medical record-keeping; 15 (83%) such sites relied on software intended for personal or small business use. The median percentage of missing data for key variables per site was 10.9% (IQR: 2.0-18.9%) and declined with training in data management (odds ratio, OR: 0.58; 95% confidence interval, CI: 0.37-0.90) and weekly hours spent by a clerk on the database per 100 patients on ART (OR: 0.95; 95% CI: 0.90-0.99). About 10 weekly hours per 100 patients on ART were required to reduce missing data for key variables to below 10%. The median percentage of patients lost to follow-up 1 year after starting ART was 8.5% (IQR: 4.2-19.7%). Strategies to reduce loss to follow-up included outreach teams, community-based organizations and checking death registry data. Implementation of all three strategies substantially reduced losses to follow-up (OR: 0.17; 95% CI: 0.15-0.20). CONCLUSION: The quality of the data collected and the retention of patients in ART treatment programmes are unsatisfactory for many sites involved in the scale-up of ART in resource-limited settings, mainly because of insufficient staff trained to manage data and trace patients lost to follow-up.

Processing and characterization of PbSnTe-based thermoelectric materials made by mechanical alloying

The research reported in this dissertation investigates the processes required to mechanically alloy Pb1-xSnxTe and AgSbTe2 and a method of combining these two end compounds to result in (y)(AgSbTe2)–(1 - y)(Pb1-xSnxTe) thermoelectric materials for power generation applications. In general, traditional melt processing of these alloys has employed high purity materials that are subjected to time and energy intensive processes that result in highly functional material that is not easily reproducible. This research reports the development of mechanical alloying processes using commercially available 99.9% pure elemental powders in order to provide a basis for the economical production of highly functional thermoelectric materials. Though there have been reports of high and low ZT materials fabricated by both melt alloying and mechanical alloying, the processing-structure-properties-performance relationship connecting how the material is made to its resulting functionality is poorly understood. This is particularly true for mechanically alloyed material, motivating an effort to investigate bulk material within the (y)(AgSbTe2)–(1 - y)(Pb1-xSnx- Te) system using the mechanical alloying method. This research adds to the body of knowledge concerning the way in which mechanical alloying can be used to efficiently produce high ZT thermoelectric materials. The processes required to mechanically alloy elemental powders to form Pb1-xSnxTe and AgSbTe2 and to subsequently consolidate the alloyed powder is described. The composition, phases present in the alloy, volume percent, size and spacing of the phases are reported. The room temperature electronic transport properties of electrical conductivity, carrier concentration and carrier mobility are reported for each alloy and the effect of the presence of any secondary phase on the electronic transport properties is described. An mechanical mixing approach for incorporating the end compounds to result in (y)(AgSbTe2)–(1-y)(Pb1-xSnxTe) is described and when 5 vol.% AgSbTe2 was incorporated was found to form a solid solution with the Pb1-xSnxTe phase. An initial attempt to change the carrier concentration of the Pb1-xSnxTe phase was made by adding excess Te and found that the carrier density of the alloys in this work are not sensitive to excess Te. It has been demonstrated using the processing techniques reported in this research that this material system, when appropriately doped, has the potential to perform as highly functional thermoelectric material.

Growth curves for cardio-metabolic risk factors in children and adolescents

OBJECTIVE: This study developed percentile curves for anthropometric (waist circumference) and cardiovascular (lipid profile) risk factors for US children and adolescents. STUDY DESIGN: A representative sample of US children and adolescents from the National Health and Nutrition Examination Survey from 1988 to 1994 (NHANES III) and the current national series (NHANES 1999-2006) were combined. Percentile curves were constructed, nationally weighted, and smoothed using the Lambda, Mu, and Sigma method. The percentile curves included age- and sex-specific percentile values that correspond with and transition into the adult abnormal cut-off values for each of these anthropometric and cardiovascular components. To increase the sample size, a second series of percentile curves was also created from the combination of the 2 NHANES databases, along with cross-sectional data from the Bogalusa Heart Study, the Muscatine Study, the Fels Longitudinal Study and the Princeton Lipid Research Clinics Study. RESULTS: These analyses resulted in a series of growth curves for waist circumference, total cholesterol, LDL cholesterol, triglycerides, and HDL cholesterol from a combination of pediatric data sets. The cut-off for abnormal waist circumference in adult males (102 cm) was equivalent to the 94(th) percentile line in 18-year-olds, and the cut-off in adult females (88 cm) was equivalent to the 84(th) percentile line in 18-year-olds. Triglycerides were found to have a bimodal pattern among females, with an initial peak at age 11 and a second at age 20; the curve for males increased steadily with age. The HDL curve for females was relatively flat, but the male curve declined starting at age 9 years. Similar curves for total and LDL cholesterol were constructed for both males and females. When data from the additional child studies were added to the national data, there was little difference in their patterns or rates of change from year to year. CONCLUSIONS: These curves represent waist and lipid percentiles for US children and adolescents, with identification of values that transition to adult abnormalities. They could be used conditionally for both epidemiological and possibly clinical applications, although they need to be validated against longitudinal data.

Methods and Applications in Interactive Broadcasting

Interactive TV technology has been addressed in many previous works, but there is sparse research on the topic of interactive content broadcasting and how to support the production process. In this article, the interactive broadcasting process is broadly defined to include studio technology and digital TV applications at consumer set-top boxes. In particular, augmented reality studio technology employs smart-projectors as light sources and blends real scenes with interactive computer graphics that are controlled at end-user terminals. Moreover, TV producer-friendly multimedia authoring tools empower the development of novel TV formats. Finally, the support for user-contributed content raises the potential to revolutionize the hierarchical TV production process, by introducing the viewer as part of content delivery chain.

Increasing Realism and Supporting Content Planning for Dynamic Scenes in a Mixed Reality System incorporating a Time-of-Flight Camera

For broadcasting purposes MIXED REALITY, the combination of real and virtual scene content, has become ubiquitous nowadays. Mixed Reality recording still requires expensive studio setups and is often limited to simple color keying. We present a system for Mixed Reality applications which uses depth keying and provides threedimensional mixing of real and artificial content. It features enhanced realism through automatic shadow computation which we consider a core issue to obtain realism and a convincing visual perception, besides the correct alignment of the two modalities and correct occlusion handling. Furthermore we present a possibility to support placement of virtual content in the scene. Core feature of our system is the incorporation of a TIME-OF-FLIGHT (TOF)-camera device. This device delivers real-time depth images of the environment at a reasonable resolution and quality. This camera is used to build a static environment model and it also allows correct handling of mutual occlusions between real and virtual content, shadow computation and enhanced content planning. The presented system is inexpensive, compact, mobile, flexible and provides convenient calibration procedures. Chroma-keying is replaced by depth-keying which is efficiently performed on the GRAPHICS PROCESSING UNIT (GPU) by the usage of an environment model and the current ToF-camera image. Automatic extraction and tracking of dynamic scene content is herewith performed and this information is used for planning and alignment of virtual content. An additional sustainable feature is that depth maps of the mixed content are available in real-time, which makes the approach suitable for future 3DTV productions. The presented paper gives an overview of the whole system approach including camera calibration, environment model generation, real-time keying and mixing of virtual and real content, shadowing for virtual content and dynamic object tracking for content planning.

Cloud Computing in the EU Policy Sphere Interoperability, Vertical Integration and the Internal Market

Cloud computing is a new development that is based on the premise that data and applications are stored centrally and can be accessed through the Internet. Thisarticle sets up a broad analysis of how the emergence of clouds relates to European competition law, network regulation and electronic commerce regulation, which we relate to challenges for the further development of cloud services in Europe: interoperability and data portability between clouds; issues relating to vertical integration between clouds and Internet Service Providers; and potential problems for clouds to operate on the European Internal Market. We find that these issues are not adequately addressed across the legal frameworks that we analyse, and argue for further research into how to better facilitate innovative convergent services such as cloud computing through European policy – especially in light of the ambitious digital agenda that the European Commission has set out.

Action Research and Learning Analytics in Higher Education

Teaching is a dynamic activity. It can be very effective, if its impact is constantly monitored and adjusted to the demands of changing social contexts and needs of learners. This implies that teachers need to be aware about teaching and learning processes. Moreover, they should constantly question their didactical methods and the learning resources, which they provide to their students. They should reflect if their actions are suitable, and they should regulate their teaching, e.g., by updating learning materials based on new knowledge about learners, or by motivating learners to engage in further learning activities. In the last years, a rising interest in ‘learning analytics’ is observable. This interest is motivated by the availability of massive amounts of educational data. Also, the continuously increasing processing power, and a strong motivation for discovering new information from these pools of educational data, is pushing further developments within the learning analytics research field. Learning analytics could be a method for reflective teaching practice that enables and guides teachers to investigate and evaluate their work in future learning scenarios. However, this potentially positive impact has not yet been sufficiently verified by learning analytics research. Another method that pursues these goals is ‘action research’. Learning analytics promises to initiate action research processes because it facilitates awareness, reflection and regulation of teaching activities analogous to action research. Therefore, this thesis joins both concepts, in order to improve the design of learning analytics tools. Central research question of this thesis are: What are the dimensions of learning analytics in relation to action research, which need to be considered when designing a learning analytics tool? How does a learning analytics dashboard impact the teachers of technology-enhanced university lectures regarding ‘awareness’, ‘reflection’ and ‘action’? Does it initiate action research? Which are central requirements for a learning analytics tool, which pursues such effects? This project followed design-based research principles, in order to answer these research questions. The main contributions are: a theoretical reference model that connects action research and learning analytics, the conceptualization and implementation of a learning analytics tool, a requirements catalogue for useful and usable learning analytics design based on evaluations, a tested procedure for impact analysis, and guidelines for the introduction of learning analytics into higher education.

Learning in Virtual Worlds: Research and Applications

Three-dimensional (3D) immersive virtual worlds have been touted as being capable of facilitating highly interactive, engaging, multimodal learning experiences. Much of the evidence gathered to support these claims has been anecdotal but the potential that these environments hold to solve traditional problems in online and technology-mediated education—primarily learner isolation and student disengagement—has resulted in considerable investments in virtual world platforms like Second Life, OpenSimulator, and Open Wonderland by both professors and institutions. To justify this ongoing and sustained investment, institutions and proponents of simulated learning environments must assemble a robust body of evidence that illustrates the most effective use of this powerful learning tool. In this authoritative collection, a team of international experts outline the emerging trends and developments in the use of 3D virtual worlds for teaching and learning. They explore aspects of learner interaction with virtual worlds, such as user wayfinding in Second Life, communication modes and perceived presence, and accessibility issues for elderly or disabled learners. They also examine advanced technologies that hold potential for the enhancement of learner immersion and discuss best practices in the design and implementation of virtual world-based learning interventions and tasks. By evaluating and documenting different methods, approaches, and strategies, the contributors to Learning in Virtual Worlds offer important information and insight to both scholars and practitioners in the field. AU Press is an open access publisher and the book is available for free in PDF format as well as for purchase on our website: http://bit.ly/1W4yTRA

Investigating the consistency between proxy-based reconstructions and climate models using data assimilation: a mid-Holocene case study

The mid-Holocene (6 kyr BP; thousand years before present) is a key period to study the consistency between model results and proxy-based reconstruction data as it corresponds to a standard test for models and a reasonable number of proxy-based records is available. Taking advantage of this relatively large amount of information, we have compared a compilation of 50 air and sea surface temperature reconstructions with the results of three simulations performed with general circulation models and one carried out with LOVECLIM, a model of intermediate complexity. The conclusions derived from this analysis confirm that models and data agree on the large-scale spatial pattern but the models underestimate the magnitude of some observed changes and that large discrepancies are observed at the local scale. To further investigate the origin of those inconsistencies, we have constrained LOVECLIM to follow the signal recorded by the proxies selected in the compilation using a data-assimilation method based on a particle filter. In one simulation, all the 50 proxy-based records are used while in the other two only the continental or oceanic proxy-based records constrain the model results. As expected, data assimilation leads to improving the consistency between model results and the reconstructions. In particular, this is achieved in a robust way in all the experiments through a strengthening of the westerlies at midlatitude that warms up northern Europe. Furthermore, the comparison of the LOVECLIM simulations with and without data assimilation has also objectively identified 16 proxy-based paleoclimate records whose reconstructed signal is either incompatible with the signal recorded by some other proxy-based records or with model physics.

An Economic Comparison of Rotational Grazing Systems to Eight Crop Alternatives and the CRP Option for Highly Erodible Land in Southwest Iowa

Economic comparisons of income on highly erodible land (HEL) in Adams County were made utilizing five years of grazing data collected from a 13- paddock intensive-rotational grazing system and a four-paddock rotational-grazing system and four years of data collected from an 18-paddock intensive-rotational grazing system, all at the Adams County CRP Research and Demonstration Farm near Corning. Net income from the average grazing weight-gain of Angus-sired calves nursing crossbred cows was compared to the net income from grazing yearling steers, to the net income of eight NRCS-recommended crop rotations, and to the Conservation Reserve Program (CRP) option. Results of these comparisons show the 13-paddock intensive rotational grazing system with cow-calf pairs to be the most profitable alternative, with a net return of $19.86 per acre per year. The second most profitable alternative is the CRP option, with a net return of $13.09 per acre, and the third most profitable option is the fourpaddock rotation with cows and calves with a net return of $12.53 per acre. An 18-paddock system returned a net income of $2.47 per acre per year with cows and calves in 1993, but lost an average of $107.69 per acre each year in 1994 and 1995 with yearling steers. Each year, the steers were purchased high and sold low, contributing to the large loss per acre. The following recommended crop rotations all show net losses on these 9-14 % slope, Adair-Shelby Complex soils (ApD3): continuous corn; corn-soybean rotation; corn-soybean rotation with a farm program deficiency payment; corn-corn-corn-oats-meadow-meadow rotation with grass headlands; continuous corn to “T” with grass headlands and buffer strips; continuous corn to “T” with grass headlands, buffer strips, and a deficiency payment; corn-corn-oats-meadow rotation to “T”; and corn-soybeans-oats-meadow-meadow-meadow-meadow rotation to “T”. Per-acre yield assumptions of 90 bushels for corn, 30 bushels for soybeans, 45 bushels for oats, and four tons for alfalfa were used, with per-bushel prices of $2.40 on corn, $5.50 on soybeans, and $1.50 on oats. Alfalfa hay was priced at $40.00 per ton and grass hay at $33.33 per ton. The calf weight-gain in the cow/ calf systems was valued at $.90 per pound. All crop expenses except land costs were calculated from ISU publication Fm 1712, “Estimated Costs of Crop Production in Iowa - 1995.” Land costs were determined by using an opportunity cost and actual property tax figures for the land at the grazing site. In preparation for the end of the CRP beginning in 1996, further economic comparisons will be made after additional grazing seasons and data collection. This project is an interagency cooperative effort sponsored by the Southern Iowa Forage and Livestock Committee which has special permission from the USDA Farm Service Agency (FSA) to use CRP land for research and demonstration.

KrigInv: An efficient and user-friendly implementation of batch-sequential inversion strategies based on kriging

Several strategies relying on kriging have recently been proposed for adaptively estimating contour lines and excursion sets of functions under severely limited evaluation budget. The recently released R package KrigInv 3 is presented and offers a sound implementation of various sampling criteria for those kinds of inverse problems. KrigInv is based on the DiceKriging package, and thus benefits from a number of options concerning the underlying kriging models. Six implemented sampling criteria are detailed in a tutorial and illustrated with graphical examples. Different functionalities of KrigInv are gradually explained. Additionally, two recently proposed criteria for batch-sequential inversion are presented, enabling advanced users to distribute function evaluations in parallel on clusters or clouds of machines. Finally, auxiliary problems are discussed. These include the fine tuning of numerical integration and optimization procedures used within the computation and the optimization of the considered criteria.

Approximate decoding approaches for network coded correlated data

This paper considers a framework where data from correlated sources are transmitted with the help of network coding in ad hoc network topologies. The correlated data are encoded independently at sensors and network coding is employed in the intermediate nodes in order to improve the data delivery performance. In such settings, we focus on the problem of reconstructing the sources at decoder when perfect decoding is not possible due to losses or bandwidth variations. We show that the source data similarity can be used at decoder to permit decoding based on a novel and simple approximate decoding scheme. We analyze the influence of the network coding parameters and in particular the size of finite coding fields on the decoding performance. We further determine the optimal field size that maximizes the expected decoding performance as a trade-off between information loss incurred by limiting the resolution of the source data and the error probability in the reconstructed data. Moreover, we show that the performance of the approximate decoding improves when the accuracy of the source model increases even with simple approximate decoding techniques. We provide illustrative examples showing how the proposed algorithm can be deployed in sensor networks and distributed imaging applications.