Decision support based on genomics:integration of data-and knowledge-driven reasoning

The breadth and depth of available clinico-genomic information, present an enormous opportunity for improving our ability to study disease mechanisms and meet the individualised medicine needs. A difficulty occurs when the results are to be transferred 'from bench to bedside'. Diversity of methods is one of the causes, but the most critical one relates to our inability to share and jointly exploit data and tools. This paper presents a perspective on current state-of-the-art in the analysis of clinico-genomic data and its relevance to medical decision support. It is an attempt to investigate the issues related to data and knowledge integration. Copyright © 2010 Inderscience Enterprises Ltd.

Exploring the integration of data mining and data visualization

Due to the rapid advances in computing and sensing technologies, enormous amounts of data are being generated everyday in various applications. The integration of data mining and data visualization has been widely used to analyze these massive and complex data sets to discover hidden patterns. For both data mining and visualization to be effective, it is important to include the visualization techniques in the mining process and to generate the discovered patterns for a more comprehensive visual view. In this dissertation, four related problems: dimensionality reduction for visualizing high dimensional datasets, visualization-based clustering evaluation, interactive document mining, and multiple clusterings exploration are studied to explore the integration of data mining and data visualization. In particular, we 1) propose an efficient feature selection method (reliefF + mRMR) for preprocessing high dimensional datasets; 2) present DClusterE to integrate cluster validation with user interaction and provide rich visualization tools for users to examine document clustering results from multiple perspectives; 3) design two interactive document summarization systems to involve users efforts and generate customized summaries from 2D sentence layouts; and 4) propose a new framework which organizes the different input clusterings into a hierarchical tree structure and allows for interactive exploration of multiple clustering solutions.

Data compilation on the biological response to ocean acidification: environmental and experimental context of data sets and related literature

The exponential growth of studies on the biological response to ocean acidification over the last few decades has generated a large amount of data. To facilitate data comparison, a data compilation hosted at the data publisher PANGAEA was initiated in 2008 and is updated on a regular basis (doi:10.1594/PANGAEA.149999). By January 2015, a total of 581 data sets (over 4 000 000 data points) from 539 papers had been archived. Here we present the developments of this data compilation five years since its first description by Nisumaa et al. (2010). Most of study sites from which data archived are still in the Northern Hemisphere and the number of archived data from studies from the Southern Hemisphere and polar oceans are still relatively low. Data from 60 studies that investigated the response of a mix of organisms or natural communities were all added after 2010, indicating a welcomed shift from the study of individual organisms to communities and ecosystems. The initial imbalance of considerably more data archived on calcification and primary production than on other processes has improved. There is also a clear tendency towards more data archived from multifactorial studies after 2010. For easier and more effective access to ocean acidification data, the ocean acidification community is strongly encouraged to contribute to the data archiving effort, and help develop standard vocabularies describing the variables and define best practices for archiving ocean acidification data.

Patient-reported quality-of-life analysis of radium-223 dichloride from the phase III ALSYMPCA study

BACKGROUND: Radium-223 dichloride (radium-223), a first-in-class α-emitting radiopharmaceutical, is recommended in both pre- and post-docetaxel settings in patients with castration-resistant prostate cancer (CRPC) and symptomatic bone metastases based on overall survival benefit demonstrated in the phase III ALSYMPCA study. ALSYMPCA included prospective measurements of health-related quality of life (QOL) using two validated instruments: the general EuroQoL 5D (EQ-5D) and the disease-specific Functional Assessment of Cancer Therapy-Prostate (FACT-P).

PATIENTS AND METHODS: Analyses were conducted to determine treatment effects of radium-223 plus standard of care (SOC) versus placebo plus SOC on QOL using FACT-P and EQ-5D. Outcomes assessed were percentage of patients experiencing improvement, percentage of patients experiencing worsening, and mean QOL scores during the study.

RESULTS: Analyses were carried out on the intent-to-treat population of patients randomized to receive radium-223 (n = 614) or placebo (n = 307). The mean baseline EQ-5D utility and FACT-P total scores were similar between treatment groups. A significantly higher percentage of patients receiving radium-223 experienced meaningful improvement in EQ-5D utility score on treatment versus placebo {29.2% versus 18.5%, respectively; P = 0.004; odds ratio (OR) = 1.82 [95% confidence interval (CI) 1.21-2.74]}. Findings were similar for FACT-P total score [24.6% versus 16.1%, respectively; P = 0.020; OR = 1.70 (95% CI 1.08-2.65)]. A lower percentage of patients receiving radium-223 experienced meaningful worsening versus placebo measured by EQ-5D utility score and FACT-P total score. Prior docetaxel use and current bisphosphonate use did not affect these findings. Treatment was a significant predictor of EQ-5D utility score, with radium-223 associated with higher scores versus placebo (0.56 versus 0.50, respectively; P = 0.002). Findings were similar for FACT-P total score (99.08 versus 95.22, respectively; P = 0.004).

CONCLUSIONS: QOL data from ALSYMPCA demonstrated that improved survival with radium-223 is accompanied by significant QOL benefits, including a higher percentage of patients with meaningful QOL improvement and a slower decline in QOL over time in patients with CRPC.

Multiphase flow in porous media: meta-modeling techniques for sensitivity analysis and risk assessment

One of the biggest challenges that contaminant hydrogeology is facing, is how to adequately address the uncertainty associated with model predictions. Uncertainty arise from multiple sources, such as: interpretative error, calibration accuracy, parameter sensitivity and variability. This critical issue needs to be properly addressed in order to support environmental decision-making processes. In this study, we perform Global Sensitivity Analysis (GSA) on a contaminant transport model for the assessment of hydrocarbon concentration in groundwater. We provide a quantification of the environmental impact and, given the incomplete knowledge of hydrogeological parameters, we evaluate which are the most influential, requiring greater accuracy in the calibration process. Parameters are treated as random variables and a variance-based GSA is performed in a optimized numerical Monte Carlo framework. The Sobol indices are adopted as sensitivity measures and they are computed by employing meta-models to characterize the migration process, while reducing the computational cost of the analysis. The proposed methodology allows us to: extend the number of Monte Carlo iterations, identify the influence of uncertain parameters and lead to considerable saving computational time obtaining an acceptable accuracy.

Iowa Statewide Highway Transportation Study: Trip Data Analysis, Vol. 1-D, 1974

The object of this report is to present the data and conclusions drawn from the analysis of the origin and destination information. Comments on the advisability and correctness of the approach used by Iowa are encouraged.

Institutional entrepreneurship and techniques of inclusiveness in the creation of the Intergovernmental Platform on Biodiversity and Ecosystem Services

This article contributes to understanding the conditions of social-ecological change by focusing on the agency of individuals in the pathways to institutionalization. Drawing on the case of the Intergovernmental Platform on Biodiversity and Ecosystem Services (IPBES), it addresses institutional entrepreneurship in an emerging environmental science-policy institution (ESPI) at a global scale. Drawing on ethnographic observations, semistructured interviews, and document analysis, we propose a detailed chronology of the genesis of the IPBES before focusing on the final phase of the negotiations toward the creation of the institution. We analyze the techniques and skills deployed by the chairman during the conference to handle the tensions at play both to prevent participants from deserting the negotiations arena and to prevent a lack of inclusiveness from discrediting the future institution. We stress that creating a new global environmental institution requires the situated exercise of an art of “having everybody on board” through techniques of inclusiveness that we characterize. Our results emphazise the major challenge of handling the fragmentation and plasticity of the groups of interest involved in the institutionalization process, thus adding to the theory of transformative agency of institutional entrepreneurs. Although inclusiveness might remain partly unattainable, such techniques of inclusiveness appear to be a major condition of the legitimacy and success of the institutionalization of a new global ESPI. Our results also add to the literature on boundary making within ESPIs by emphasizing the multiplicity and plasticity of the groups actually at stake.

New morpho-bathymetric and tectono-stratigraphic data on Naples and Salerno gulfs (southern tyrrhenian sea, Italy) derived from bathymetric and seismic data analysis and integrated geological interpretation

New morpho-bathymetric and tectono-stratigraphic data on Naples and Salerno Gulfs, derived from bathymetric and seismic data analysis and integrated geologic interpretation are here presented. The CUBE(Combined Uncertainty Bathymetric Estimator) method has been applied to complex morphologies, such as the Capri continental slope and the related geological structures occurring in the Salerno Gulf.The bathymetric data analysis has been carried out for marine geological maps of the whole Campania continental margin at scales ranging from 1:25.000 to 1:10.000, including focused examples in Naples and Salerno Gulfs, Naples harbour, Capri and Ischia Islands and Salerno Valley. Seismic data analysis has allowed for the correlation of main morpho-structural lineaments recognized at a regional scale through multichannel profiles with morphological features cropping out at the sea bottom, evident from bathymetry.Main fault systems in the area have been represented on a tectonic sketch map, including the master fault located northwards to the Salerno Valley half graben. Some normal faults parallel to the master fault have been interpreted from the slope map derived from bathymetric data. A complex system of antithetic faults bound two morpho-structural highs located 20km to the south of the Capri Island. Some hints of compressional reactivation of normal faults in an extensional setting involving the whole Campania continental margin have been shown from seismic interpretation.

An assessment of data leakage in Firefox under different conditions.

Data leakage is a serious issue and can result in the loss of sensitive data, compromising user accounts and details, potentially affecting millions of internet users. This paper contributes to research in online security and reducing personal footprint by evaluating the levels of privacy provided by the Firefox browser. The aim of identifying conditions that would minimize data leakage and maximize data privacy is addressed by assessing and comparing data leakage in the four possible browsing modes: normal and private modes using a browser installed on the host PC or using a portable browser from a connected USB device respectively. To provide a firm foundation for analysis, a series of carefully designed, pre-planned browsing sessions were repeated in each of the various modes of Firefox. This included low RAM environments to determine any effects low RAM may have on browser data leakage. The results show that considerable data leakage may occur within Firefox. In normal mode, all of the browsing information is stored within the Mozilla profile folder in Firefox-specific SQLite databases and sessionstore.js. While passwords were not stored as plain text, other confidential information such as credit card numbers could be recovered from the Form history under certain conditions. There is no difference when using a portable browser in normal mode, except that the Mozilla profile folder is located on the USB device rather than the host's hard disk. By comparison, private browsing reduces data leakage. Our findings confirm that no information is written to the Firefox-related locations on the hard disk or USB device during private browsing, implying that no deletion would be necessary and no remnants of data would be forensically recoverable from unallocated space. However, two aspects of data leakage occurred equally in all four browsing modes. Firstly, all of the browsing history was stored in the live RAM and was therefore accessible while the browser remained open. Secondly, in low RAM situations, the operating system caches out RAM to pagefile.sys on the host's hard disk. Irrespective of the browsing mode used, this may include Firefox history elements which can then remain forensically recoverable for considerable time.

Wind Waves in the Arctic Seas: Envisat and AltiKa Data Analysis

Wind-generated waves in the Kara, Laptev, and East-Siberian Seas are investigated using altimeter data from Envisat RA-2 and SARAL-AltiKa. Only isolated ice-free zones had been selected for analysis. Wind seas can be treated as pure wind-generated waves without any contamination by ambient swell. Such zones were identified using ice concentration data from microwave radiometers. Altimeter data, both significant wave height (SWH) and wind speed, for these areas were further obtained for the period 2002-2012 using Envisat RA-2 measurements, and for 2013 using SARAL-AltiKa. Dependencies of dimensionless SWH and wavelength on dimensionless wave generation spatial scale are compared to known empirical dependencies for fetch-limited wind wave development. We further check sensitivity of Ka- and Ku-band and discuss new possibilities that AltiKa's higher resolution can open.

Catalogue of data and platforms at Network GDAC level, including the example of Copernicus In Situ TAC

This document presents catalogue techniques used at network GDAC level to facilitate the discovery of platforms and data files. Some AtlantOS networks are organized as DAC-GDACs that continuously update a catalogue of metadata on observation datasets and platforms: • A DAC is a Data Assembly Centre operating at national or regional scale. It manages data and metadata for its area with a direct link to Scientifics and Operators. The DAC pushes observations to the network GDAC. • A GDAC is a Global Data Assembly Centre. It is designed for a global observation network such as Argo, OceanSITES, DBCP, EGO, Gosud, etc… The GDAC aggregates data and metadata of an observation network, in real-time and delayed mode, provided by DACs.