Archiving Primary Data: Solutions for Long-Term Studies.

The recent trend for journals to require open access to primary data included in publications has been embraced by many biologists, but has caused apprehension amongst researchers engaged in long-term ecological and evolutionary studies. A worldwide survey of 73 principal investigators (Pls) with long-term studies revealed positive attitudes towards sharing data with the agreement or involvement of the PI, and 93% of PIs have historically shared data. Only 8% were in favor of uncontrolled, open access to primary data while 63% expressed serious concern. We present here their viewpoint on an issue that can have non-trivial scientific consequences. We discuss potential costs of public data archiving and provide possible solutions to meet the needs of journals and researchers.

The influence of oscillations on global existence for a class of semi-linear wave equations

The goal of this paper is to study the global existence of small data solutions to the Cauchy problem for the nonlinear wave equation u(tt) - a(t)(2) Delta u = u(t)(2) - a(t)(2)vertical bar del u vertical bar(2). In particular we are interested in statements for the 1D case. We will explain how the interplay between the increasing and oscillating behavior of the coefficient will influence global existence of small data solutions. Copyright c 2011 John Wiley & Sons, Ltd.

Master data quality management in a global enterprise

In a networked business environment the visibility requirements towards the supply operations and customer interface has become tighter. In order to meet those requirements the master data of case company is seen as an enabler. However the current state of master data and its quality are not seen good enough to meet those requirements. In this thesis the target of research was to develop a process for managing master data quality as a continuous process and find solutions to cleanse the current customer and supplier data to meet the quality requirements defined in that process. Based on the theory of Master Data Management and data cleansing, small amount of master data was analyzed and cleansed using one commercial data cleansing solution available on the market. This was conducted in cooperation with the vendor as a proof of concept. In the proof of concept the cleansing solution’s applicability to improve the quality of current master data was proved. Based on those findings and the theory of data management the recommendations and proposals for improving the quality of data were given. In the results was also discovered that the biggest reasons for poor data quality is the lack of data governance in the company, and the current master data solutions and its restrictions.

Analytical solutions of a minimal model of species migration in a bounded domain

A minimal model of species migration is presented which takes the form of a parabolic equation with boundary conditions and initial data. Solutions to the differential problem are obtained that can be used to describe the small- and large-time evolution of a species distribution within a bounded domain. These expressions are compared with the results of numerical simulations and are found to be satisfactory within appropriate temporal regimes. The solutions presented can be used to describe existing observations of nematode distributions, can be used as the basis for further work on nematode migration, and may also be interpreted more generally.

Analytical solutions of linear finite- and small-strain one-dimensional consolidation

Analytical solutions are presented for linear finite-strain one-dimensional consolidation of initially unconsolidated soil layers with surcharge loading for both one- and two-way drainage. These solutions complement earlier solutions for initially unconsolidated soil layers without surcharge and initially normally consolidated soil layers with surcharge. Small-strain solutions for the consolidation of initially unconsolidated soil layers with surcharge loading are also presented, and the relationship between the earlier solutions for initially unconsolidated soil without surcharge and the corresponding small-strain solutions, which was not addressed in the earlier work, is clarified. The new solutions for initially unconsolidated soil with surcharge loading can be applied to the analysis of low stress consolidation tests and to the partial validation of numerical solutions of non-linear finite-strain consolidation. They also clarify a formerly perplexing aspect of finite-strain solution charts first noted in numerical solutions. Copyright (C) 2004 John Wiley Sons, Ltd.

A design and a prototype for a mobile information service for tourists

Tourism is one of the biggest industry branches with billions of tourists traveling every year around the world. Therefore, solutions providing tourist information have to be up to date with both changes in the industry and the world’s technological progress. The aim of this thesis is to present a design and a prototype of a tourist mobile service which is individual-oriented, cost-free for the end user, and secure. On the information providers’ side, the solution is implemented as a Webbased database. The end users access the information through a Bluetooth application on their mobile devices. The Bluetooth-based solution allows to avoid any costs for the end users, that is tourists. The study shows that, even with small data transfers, the tourists could save significantly when compared to possible roaming charges for data transfer. Also, the proposed mobile service is not intrusive, as it is provided through an application installed by tourists voluntarily on their mobile devices. Through design and implementation this work shows that it is possible to build a system which can be used to provide information services to tourists through mobile phones. The work achieved a successful ongoing synchronization between the client and the server databases. Implementation and usage were limited to smart phones only, as they provide better technological support for the solution having features like maps, GPS, Wi-Fi, Bluetooth and Databases. Moreover, the design of this system shows how Bluetooth technology can be used effectively as a means of communication while minimizing its shortcomings and risks, such as security, by bypassing Bluetooth server service discovery protocol (SDP) and connecting directly to the device. Apart from showing the design and implementation of the end-user costfree mobile information service, the results of this work also highlight the possible business opportunities to the provider of the service.

Managing groups of files in a rule oriented data management system (iRODS)

The iRODS system, created by the San Diego Supercomputing Centre, is a rule oriented data management system that allows the user to create sets of rules to define how the data is to be managed. Each rule corresponds to a particular action or operation (such as checksumming a file) and the system is flexible enough to allow the user to create new rules for new types of operations. The iRODS system can interface to any storage system (provided an iRODS driver is built for that system) and relies on its’ metadata catalogue to provide a virtual file-system that can handle files of any size and type. However, some storage systems (such as tape systems) do not handle small files efficiently and prefer small files to be packaged up (or “bundled”) into larger units. We have developed a system that can bundle small data files of any type into larger units - mounted collections. The system can create collection families and contains its’ own extensible metadata, including metadata on which family the collection belongs to. The mounted collection system can work standalone and is being incorporated into the iRODS system to enhance the systems flexibility to handle small files. In this paper we describe the motivation for creating a mounted collection system, its’ architecture and how it has been incorporated into the iRODS system. We describe different technologies used to create the mounted collection system and provide some performance numbers.

Orphan nuclear receptor NGFI-B forms dimers with nonclassical interface

The orphan receptor nerve growth factor-induced B (NGFI-B) is a member of the nuclear receptor's subfamily 4A (Nr4a). NGFI-B was shown to be capable of binding both as a monomer to an extended half-site containing a single AAAGGTCA motif and also as a homodimer to a widely separated everted repeat, as opposed to a large number of nuclear receptors that recognize and bind specific DNA sequences predominantly as homo- and/or heterodimers. To unveil the structural organization of NGFI-B in solution, we determined the quaternary structure of the NGFI-B LBD by a combination of ab initio procedures from small-angle X-ray scattering (SAXS) data and hydrogen-deuterium exchange followed by mass spectrometry. Here we report that the protein forms dimers in solution with a radius of gyration of 2.9 nm and maximum dimension of 9.0 nm. We also show that the NGFI-B LBD dimer is V-shaped, with the opening angle significantly larger than that of classical dimer's exemplified by estrogen receptor (ER) or retinoid X receptor (RXR). Surprisingly, NGFI-B dimers formation does not occur via the classical nuclear receptor dimerization interface exemplified by ER and RXR, but instead, involves an extended surface area composed of the loop between helices 3 and 4 and C-terminal fraction of the helix 3. Remarkably, the NGFI-B dimer interface is similar to the dimerization interface earlier revealed for glucocorticoid nuclear receptor (GR), which might be relevant to the recognition of cognate DNA response elements by NGFI-B and to antagonism of NGFI-B-dependent transcription exercised by GR in cells. Published by Cold Spring Harbor Laboratory Press. Copyright © 2007 The Protein Society.

Development strategies for the information and communications technology sector in the Caribbean: A global perspective

This occasional paper examines the experiences of three leading global centres of the ICT industry – India, Silicon Valley, and Estonia – to reflect on how the lessons of these models can be applied to the context of countries in the Caribbean region.Several sectors of the technology industry are considered in relation to the suitability for their establishment in the Caribbean. Animation is an area that is showing encouraging signs of development in several countries, and which offers some promise to provide a significant source of employment in the region. However, the global market for animation production is likely to become increasingly competitive, as improved technology has reduced barriers to entry into the industry not only in the Caribbean, but around the world. The region’s animation industry will need to move swiftly up the value chain if it is to avoid the downsides of being caught in an increasingly commoditized market. Mobile applications development has also been widely a heralded industry for the Caribbean. However, the market for consumer-oriented smartphone applications has matured very quickly, and is now a very difficult sector in which to compete. Caribbean mobile developers would be better served to focus on creating applications to suit the needs of regional industries and governments, rather than attempting to gain notice in over-saturated consumer marketplaces such as the iTunes App Store and Google Play. Another sector considered for the Caribbean is “big data” analysis. This area holds significant potential for growth in coming years, but the Caribbean, which is generally considered to be a datapoor region, currently lacks a sufficient base of local customers to form a competitive foundation for such an industry. While a Caribbean big data industry could plausibly be oriented toward outsourcing, that orientation would limit positive externalities from the sector, and benefits from its establishment would largely accrue only to a relatively small number of direct participants in the industry. Instead, development in the big data sector should be twinned with the development of products to build a regional customer base for the industry. The region has pressing needs in areas such as disaster risk reduction, water resource management, and support for agricultural production. Development of big data solutions – and other technology products – to address areas such as these could help to establish niche industries that both support the needs of local populations, and provide viable opportunities for the export of higher-value products and services to regions of the world with similar needs.

Trees as Tools in Environmental Improvement; An Analysis of the Contribution of Vegetation to Energy and Water Conservation in the Front Range of Colorado

The Denver metropolitan area is facing rapid population growth that increases the stress on already limited resources. Research and advanced computer modeling show that trees, especially those in urban areas, have significant environmental benefits. These benefits include air quality improvements, energy savings, greenhouse gas reduction, and possible water conservation. This Capstone Project applies statistical methods to analyze a small data set of residential homes and their energy and water consumption, as a function of their individual landscape. Results indicate that tree shade can influence water conservation, and that irrigation methods can be an influential factor as well. The Capstone is a preliminary analysis for future study to be performed by the Institute for Environmental Solutions in 2007.

Advanced computing for systems biology

Systems biology is based on computational modelling and simulation of large networks of interacting components. Models may be intended to capture processes, mechanisms, components and interactions at different levels of fidelity. Input data are often large and geographically disperse, and may require the computation to be moved to the data, not vice versa. In addition, complex system-level problems require collaboration across institutions and disciplines. Grid computing can offer robust, scaleable solutions for distributed data, compute and expertise. We illustrate some of the range of computational and data requirements in systems biology with three case studies: one requiring large computation but small data (orthologue mapping in comparative genomics), a second involving complex terabyte data (the Visible Cell project) and a third that is both computationally and data-intensive (simulations at multiple temporal and spatial scales). Authentication, authorisation and audit systems are currently not well scalable and may present bottlenecks for distributed collaboration particularly where outcomes may be commercialised. Challenges remain in providing lightweight standards to facilitate the penetration of robust, scalable grid-type computing into diverse user communities to meet the evolving demands of systems biology.

Dissecting query performance in logical data models: Parsimony vs. greater ontological clarity

Even when data repositories exhibit near perfect data quality, users may formulate queries that do not correspond to the information requested. Users’ poor information retrieval performance may arise from either problems understanding of the data models that represent the real world systems, or their query skills. This research focuses on users’ understanding of the data structures, i.e., their ability to map the information request and the data model. The Bunge-Wand-Weber ontology was used to formulate three sets of hypotheses. Two laboratory experiments (one using a small data model and one using a larger data model) tested the effect of ontological clarity on users’ performance when undertaking component, record, and aggregate level tasks. The results indicate for the hypotheses associated with different representations but equivalent semantics that parsimonious data model participants performed better for component level tasks but that ontologically clearer data model participants performed better for record and aggregate level tasks.

Efficient use of training data in the n-tuple recognition method

A simple technique is presented for improving the robustness of the n-tuple recognition method against inauspicious choices of architectural parameters, guarding against the saturation problem, and improving the utilisation of small data sets. Experiments are reported which confirm that the method significantly improves performance and reduces saturation in character recognition problems.