AllerTOP v.2 - a server for in silico prediction of allergens

Allergy is an overreaction by the immune system to a previously encountered, ordinarily harmless substance - typically proteins - resulting in skin rash, swelling of mucous membranes, sneezing or wheezing, or other abnormal conditions. The use of modified proteins is increasingly widespread: their presence in food, commercial products, such as washing powder, and medical therapeutics and diagnostics, makes predicting and identifying potential allergens a crucial societal issue. The prediction of allergens has been explored widely using bioinformatics, with many tools being developed in the last decade; many of these are freely available online. Here, we report a set of novel models for allergen prediction utilizing amino acid E-descriptors, auto- and cross-covariance transformation, and several machine learning methods for classification, including logistic regression (LR), decision tree (DT), naïve Bayes (NB), random forest (RF), multilayer perceptron (MLP) and k nearest neighbours (kNN). The best performing method was kNN with 85.3% accuracy at 5-fold cross-validation. The resulting model has been implemented in a revised version of the AllerTOP server (http://www.ddg-pharmfac.net/AllerTOP). © Springer-Verlag 2014.

Importance and Benefits of OPEN SCIENCE for Ubiquitous Sharing, Dissemination and Impact

While openness is well applied to software development and exploitation (open sources), and successfully applied to new business models (open innovation), fundamental and applied research seems to lag behind. Even after decades of advocacy, in 2011 only 50% of the public-funded research was freely available and accessible (Archambault et al., 2013). The current research workflows, stemming from a pre-internet age, result in loss of opportunity not only for the researchers themselves (cf. extensive literature on topic at Open Access citation project, http://opcit.eprints.org/), but also slows down innovation and application of research results (Houghton & Swan, 2011). Recent studies continue to suggest that lack of awareness among researchers, rather than lack of e-infrastructure and methodology, is a key reason for this loss of opportunity (Graziotin 2014). The session will focus on why Open Science is ideally suited to achieving tenure-relevant researcher impact in a “Publish or Perish” reality. Open Science encapsulates tools and approaches for each step along the research cycle: from Open Notebook Science to Open Data, Open Access, all setting up researchers for capitalising on social media in order to promote and discuss, and establish unexpected collaborations. Incorporating these new approaches into a updated personal research workflow is of strategic beneficial for young researchers, and will prepare them for expected long term funder trends towards greater openness and demand for greater return on investment (ROI) for public funds.

Graphical Approach to Teaching Compound Interest in High School Math Classes

Report published in the Proceedings of the National Conference on "Education and Research in the Information Society", Plovdiv, May, 2015

Spatial ecological complexity measures in GRASS GIS

Good estimates of ecosystem complexity are essential for a number of ecological tasks: from biodiversity estimation, to forest structure variable retrieval, to feature extraction by edge detection and generation of multifractal surface as neutral models for e.g. feature change assessment. Hence, measuring ecological complexity over space becomes crucial in macroecology and geography. Many geospatial tools have been advocated in spatial ecology to estimate ecosystem complexity and its changes over space and time. Among these tools, free and open source options especially offer opportunities to guarantee the robustness of algorithms and reproducibility. In this paper we will summarize the most straightforward measures of spatial complexity available in the Free and Open Source Software GRASS GIS, relating them to key ecological patterns and processes.

Az online fogyasztói elégedettségmérés hatása a vállalatok versenyképességére (Effect of the online-customer satisfaction’s measurement to the corporate’s competitiveness)

A versenyképes működés elengedhetetlen feltétele a fogyasztói elégedettség, melynek egyik meghatározó eleme az észlelt és elvárt minőség közti kapcsolat. A minőségi elvárások az internettel, mint napjaink egyik meghatározó csatornájával kapcsolatban is megfogalmazódtak már, így kapott jelentős szerepet az online szolgáltatás minőségének meghatározása, illetve ezzel összekapcsolódva az online fogyasztói elégedettségmérés. Jelen tanulmány első része szakirodalmi áttekintést nyújt az online szolgáltatás minőségének fogyasztói érzékelésével, értékelésével kapcsolatos elméletekről, melyek az online fogyasztók elégedettségmérésének alapját képezik. Ezután kerül sor a különböző mérési módszerek bemutatására, kiemelt szerepet szánva a szakirodalomban sokat tárgyalt E-S-QUAL és E-RecS-QUAL skálának. Az áttekintés középpontjában azok az elméletek állnak, melyek az online vásárlást is nyújtó honlapokra vonatkoznak. A cikk további része két empirikus kutatást tartalmaz. Az első az elégedettségmérés hazai helyzetét tárgyalja, a másik pedig a szakirodalomból ismert E-S-QUAL és E-RecS-QUAL skálákat felhasználva részletesen elemzi az elektronikus szolgáltatásminőség dimenziói és a fogyasztói elégedettség közötti fontosabb összefüggéseket, emellett röviden vizsgálja az alkalmazott skálák megbízhatóságát és érvényességét. A kutatás fő célja a gyakorlati szakemberek számára is releváns kapcsolatok feltárása és bemutatása. _______ A company’s competitiveness significantly depends on the satisfaction of its consumers, which is influenced by the relationship between the expected and perceived quality. As over the last decade internet has become a significant channel, in parallel its customers have built some expectation about the quality of different websites and online services. Therefore the marketing literature should focus on the dimensions of e-service quality (e-sq) and online-customer satisfaction. This study first resumes with different concepts of e-sq, which are the principles of the online-customer satisfaction’s measurement. Than the different e-sq measurement methods are reviewed and the dimensions of E-S-QUAL and ERecS- QUAL scales are deeply explained. The study is focusing on concepts relating to web shops. The next part of the article includes two empirical studies. The first is about the situation of satisfaction measurement at Hungarian companies. The other one analyzes the most relevant relationships between the dimension of e-sq and customer satisfaction based on the E-S-QUAL and E-RecS-QUAL scales for measuring e-sq and briefly outlines the reliability and validity of these scales. The main purpose of this empirical research is to summarise the managerial and practical implications.

Fifty shades of innovation – from open toward user, and open collaborative forms of innovation – an overview

Starting from the Schumpeterian producer-driven understanding of innovation, followed by user-generated solutions and understanding of collaborative forms of co-creation, scholars investigated the drivers and the nature of interactions underpinning success in various ways. Innovation literature has gone a long way, where open innovation has attracted researchers to investigate problems like compatibilities of external resources, networks of innovation, or open source collaboration. Openness itself has gained various shades in the different strands of literature. In this paper the author provides with an overview and a draft evaluation of the different models of open innovation, illustrated with some empirical findings from various fields drawn from the literature. She points to the relevance of transaction costs affecting viable forms of (open) innovation strategies of firms, and the importance to define the locus of innovation for further analyses of different firm and interaction level formations.

The effects of intellectual property rights on knowledge spillovers and innovation: An empirical investigation

FDI is believed to be a conduit of new technologies between countries. The first chapter of this dissertation studies the advantages of outward FDI for the home country of multinationals conducting research and development abroad. We use patent citations as a proxy for technology spillovers and we bring empirical evidence that supports the hypothesis that a U.S. subsidiary conducting research and development overseas facilitates the flow of knowledge between its host and home countries.^ The second chapter examines the impact of intellectual property rights (IPR) reforms on the technology flows between the U.S. and host countries of U.S. affiliates. We again use patent citations to examine whether the diffusion of new technology between the host countries and the U.S. is accelerated by the reforms. Our results suggest that the reforms favor innovative efforts of domestic firms in the reforming countries rather than U.S. affiliates efforts. In other words, reforms mediate the technology flows from the U.S. to the reforming countries.^ The third chapter deals with another form of IPR, open source (OS) licenses. These differ in the conditions under which licensors and OS contributors are allowed to modify and redistribute the source code. We measure OS project quality by the speed with which programming bugs are fixed and test whether the license chosen by project leaders influences bug resolution rates. In initial regressions, we find a strong correlation between the hazard of bug resolution and the use of highly restrictive licenses. However, license choices are likely to be endogenous. We instrument license choice using (i) the human language in which contributors operate and (ii) the license choice of the project leaders for a previous project. We then find weak evidence that restrictive licenses adversely affect project success.^

Electrocardiogram breathing: A study of electrocardiogram derived respiration plus multiresolution wavelet analysis of heartbeat interval variability in sleep study patients

This dissertation presents a unique research opportunity by using recordings which provide electrocardiogram (ECG) plus a reference breathing signal (RBS). ECG derived breathing (EDR) is measured and correlated against RBS. Standard deviations of multiresolution wavelet analysis coefficients (SDMW) are obtained from heart rate and classified using RBS. Prior works by others used select patients for sleep apnea scoring with EDR but no RBS. Another prior work classified select heart disease patients with SDMW but no RBS. This study used randomly chosen sleep disorder patient recordings; central and obstructive apneas, with and without heart disease.^ Implementation required creating an application because existing systems were limited in power and scope. A review survey was created to choose a development environment. The survey is presented as a learning tool and teaching resource. Development objectives were rapid development using limited resources (manpower and money). Open Source resources were used exclusively for implementation. ^ Results show: (1) Three groups of patients exist in the study. Grouping RBS correlations shows a response with either ECG interval or amplitude variation. A third group exists where neither ECG intervals nor amplitude variation correlate with breathing. (2) Previous work done by other groups analyzed SDMW. Similar results were found in this study but some subjects had higher SDMW, attributed to a large number of apneas, arousals and/or disconnects. SDMW does not need RBS to show apneic conditions exist within ECG recordings. (3) Results in this study support the assertion that autonomic nervous system variation was measured with SDMW. Measurements using RBS are not corrupted due to breathing even though respiration overlaps the same frequency band.^ Overall, this work becomes an Open Source resource which can be reused, modified and/or expanded. It might fast track additional research. In the future the system could also be used for public domain data. Prerecorded data exist in similar formats in public databases which could provide additional research opportunities. ^

Análise de tensões integrada a sistema de engenharia reversa para projeto e confecção de próteses

This work consists of the conception, developing and implementation of a Computational Routine CAE which has algorithms suitable for the tension and deformation analysis. The system was integrated to an academic software named as OrtoCAD. The expansion algorithms for the interface CAE genereated by this work were developed in FORTRAN with the objective of increase the applications of two former works of PPGEM-UFRN: project and fabrication of a Electromechanincal reader and Software OrtoCAD. The software OrtoCAD is an interface that, orinally, includes the visualization of prothetic cartridges from the data obtained from a electromechanical reader (LEM). The LEM is basically a tridimensional scanner based on reverse engineering. First, the geometry of a residual limb (i.e., the remaining part of an amputee leg wherein the prothesis is fixed) is obtained from the data generated by LEM by the use of Reverse Engineering concepts. The proposed core FEA uses the Shell's Theory where a 2D surface is generated from a 3D piece form OrtoCAD. The shell's analysis program uses the well-known Finite Elements Method to describe the geometry and the behavior of the material. The program is based square-based Lagragean elements of nine nodes and displacement field of higher order to a better description of the tension field in the thickness. As a result, the new FEA routine provide excellent advantages by providing new features to OrtoCAD: independency of high cost commercial softwares; new routines were added to the OrtoCAD library for more realistic problems by using criteria of fault engineering of composites materials; enhanced the performance of the FEA analysis by using a specific grid element for a higher number of nodes; and finally, it has the advantage of open-source project and offering customized intrinsic versatility and wide possibilities of editing and/or optimization that may be necessary in the future

Analisi della piattaforma Nutch

Nell’ultima decade abbiamo assistito alla transizione di buona parte dei business da offline ad online. Istantaneamente grazie al nuovo rapporto tra azienda e cliente fornito dalla tecnologia, molti dei metodi di marketing potevano essere rivoluzionati. Il web ci ha abilitato all’analisi degli utenti e delle loro opinioni ad ampio spettro. Capire con assoluta precisione il tasso di conversione in acquisti degli utenti fornito dalle piattaforme pubblicitarie e seguirne il loro comportamento su larga scala sul web, operazione sempre stata estremamente difficile da fare nel mondo reale. Per svolgere queste operazioni sono disponibili diverse applicazioni commerciali, che comportano un costo che può essere notevole da sostenere per le aziende. Nel corso della seguente tesi si punta a fornire una analisi di una piattaforma open source per la raccolta dei dati dal web in un database strutturato

The state of the nations:current and future developments in technology enhanced learning

Right across Europe technology is playing a vital part in enhancing learning for an increasingly diverse population of learners. Learning is increasingly flexible, social and mobile and supported by high quality multi-media resources. Institutional VLEs are seeing a shift towards open source products and these core systems are supplemented by a range of social and collaborative learning tools based on web 2.0 technologies. Learners undertaking field studies and those in the workplace are coming to expect that these off-campus experiences will also be technology-rich whether supported by institutional or user-owned devices. As well as keeping European businesses competitive, learning is seen as a means of increasing social mobility and supporting an agenda of social justice. For a number of years the EUNIS E-Learning Task Force (ELTF) has conducted snapshot surveys of e-learning across member institutions, collected case studies of good practice in e-learning see (Hayes, et al., 2009) in references, supported a group looking at the future of e-learning, and showcased the best of innovation in its e-learning Award. Now for the first time the ELTF membership has come together to undertake an analysis of developments in the member states and to assess what this might mean for the future. The group applied the techniques of World Café conversation and Scenario Thinking to develop its thoughts. The analysis is unashamedly qualitative and draws on expertise from leading universities across eight of the EUNIS member states. What emerges is interesting in terms of the common trends in developments in all of the nations and similarities in hopes and concerns about the future development of learning.

An Empirically Based Stochastic Turbulence Simulator with Temporal Coherence for Wind Energy Applications

In this dissertation, we develop a novel methodology for characterizing and simulating nonstationary, full-field, stochastic turbulent wind fields.

In this new method, nonstationarity is characterized and modeled via temporal coherence, which is quantified in the discrete frequency domain by probability distributions of the differences in phase between adjacent Fourier components.

The empirical distributions of the phase differences can also be extracted from measured data, and the resulting temporal coherence parameters can quantify the occurrence of nonstationarity in empirical wind data.

This dissertation (1) implements temporal coherence in a desktop turbulence simulator, (2) calibrates empirical temporal coherence models for four wind datasets, and (3) quantifies the increase in lifetime wind turbine loads caused by temporal coherence.

The four wind datasets were intentionally chosen from locations around the world so that they had significantly different ambient atmospheric conditions.

The prevalence of temporal coherence and its relationship to other standard wind parameters was modeled through empirical joint distributions (EJDs), which involved fitting marginal distributions and calculating correlations.

EJDs have the added benefit of being able to generate samples of wind parameters that reflect the characteristics of a particular site.

Lastly, to characterize the effect of temporal coherence on design loads, we created four models in the open-source wind turbine simulator FAST based on the \windpact turbines, fit response surfaces to them, and used the response surfaces to calculate lifetime turbine responses to wind fields simulated with and without temporal coherence.

The training data for the response surfaces was generated from exhaustive FAST simulations that were run on the high-performance computing (HPC) facilities at the National Renewable Energy Laboratory.

This process was repeated for wind field parameters drawn from the empirical distributions and for wind samples drawn using the recommended procedure in the wind turbine design standard \iec.

The effect of temporal coherence was calculated as a percent increase in the lifetime load over the base value with no temporal coherence.

An Exploration of the challenges associated with software logging in large systems

Over the past few years, logging has evolved from from simple printf statements to more complex and widely used logging libraries. Today logging information is used to support various development activities such as fixing bugs, analyzing the results of load tests, monitoring performance and transferring knowledge. Recent research has examined how to improve logging practices by informing developers what to log and where to log. Furthermore, the strong dependence on logging has led to the development of logging libraries that have reduced the intricacies of logging, which has resulted in an abundance of log information. Two recent challenges have emerged as modern software systems start to treat logging as a core aspect of their software. In particular, 1) infrastructural challenges have emerged due to the plethora of logging libraries available today and 2) processing challenges have emerged due to the large number of log processing tools that ingest logs and produce useful information from them. In this thesis, we explore these two challenges. We first explore the infrastructural challenges that arise due to the plethora of logging libraries available today. As systems evolve, their logging infrastructure has to evolve (commonly this is done by migrating to new logging libraries). We explore logging library migrations within Apache Software Foundation (ASF) projects. We i find that close to 14% of the pro jects within the ASF migrate their logging libraries at least once. For processing challenges, we explore the different factors which can affect the likelihood of a logging statement changing in the future in four open source systems namely ActiveMQ, Camel, Cloudstack and Liferay. Such changes are likely to negatively impact the log processing tools that must be updated to accommodate such changes. We find that 20%-45% of the logging statements within the four systems are changed at least once. We construct random forest classifiers and Cox models to determine the likelihood of both just-introduced and long-lived logging statements changing in the future. We find that file ownership, developer experience, log density and SLOC are important factors in determining the stability of logging statements.

The LiDAR Compass: Extremely Lightweight Heading Estimation with Axis Maps

This paper introduces the LiDAR compass, a bounded and extremely lightweight heading estimation technique that combines a two-dimensional laser scanner and axis maps, which represent the orientations of flat surfaces in the environment. Although suitable for a variety of indoor and outdoor environments, the LiDAR compass is especially useful for embedded and real-time applications requiring low computational overhead. For example, when combined with a sensor that can measure translation (e.g., wheel encoders) the LiDAR compass can be used to yield accurate, lightweight, and very easily implementable localization that requires no prior mapping phase. The utility of using the LiDAR compass as part of a localization algorithm was tested on a widely-available open-source data set, an indoor environment, and a larger-scale outdoor environment. In all cases, it was shown that the growth in heading error was bounded, which significantly reduced the position error to less than 1% of the distance travelled.

Supporting the Model-Driven Development of Real-time Embedded Systems with Run-Time Monitoring and Animation via Highly Customizable Code Generation

This paper presents a vision that allows the combined use of model-driven engineering, run-time monitoring, and animation for the development and analysis of components in real-time embedded systems. Key building block in the tool environment supporting this vision is a highly-customizable code generation process. Customization is performed via a configuration specification which describes the ways in which input is provided to the component, the ways in which run-time execution information can be observed, and how these observations drive animation tools. The environment is envisioned to be suitable for different activities ranging from quality assurance to supporting certification, teaching, and outreach and will be built exclusively with open source tools to increase impact. A preliminary prototype implementation is described.