EMMA 2--a MAGE-compliant system for the collaborative analysis and integration of microarray data

Background: Understanding transcriptional regulation by genome-wide microarray studies can contribute to unravel complex relationships between genes. Attempts to standardize the annotation of microarray data include the Minimum Information About a Microarray Experiment (MIAME) recommendations, the MAGE-ML format for data interchange, and the use of controlled vocabularies or ontologies. The existing software systems for microarray data analysis implement the mentioned standards only partially and are often hard to use and extend. Integration of genomic annotation data and other sources of external knowledge using open standards is therefore a key requirement for future integrated analysis systems. Results: The EMMA 2 software has been designed to resolve shortcomings with respect to full MAGE-ML and ontology support and makes use of modern data integration techniques. We present a software system that features comprehensive data analysis functions for spotted arrays, and for the most common synthesized oligo arrays such as Agilent, Affymetrix and NimbleGen. The system is based on the full MAGE object model. Analysis functionality is based on R and Bioconductor packages and can make use of a compute cluster for distributed services. Conclusion: Our model-driven approach for automatically implementing a full MAGE object model provides high flexibility and compatibility. Data integration via SOAP-based web-services is advantageous in a distributed client-server environment as the collaborative analysis of microarray data is gaining more and more relevance in international research consortia. The adequacy of the EMMA 2 software design and implementation has been proven by its application in many distributed functional genomics projects. Its scalability makes the current architecture suited for extensions towards future transcriptomics methods based on high-throughput sequencing approaches which have much higher computational requirements than microarrays.

Computational approaches to emotional decision making

Findings on the role that emotion plays in human behavior have transformed Artificial Intelligence computations. Modern research explores how to simulate more intelligent and flexible systems. Several studies focus on the role that emotion has in order to establish values for alternative decision and decision outcomes. For instance, Busemeyer et al. (2007) argued that emotional state affects the subjectivity value of alternative choice. However, emotional concepts in these theories are generally not defined formally and it is difficult to describe in systematic detail how processes work. In this sense, structures and processes cannot be explicitly implemented. Some attempts have been incorporated into larger computational systems that try to model how emotion affects human mental processes and behavior (Becker-Asano & Wachsmuth, 2008; Marinier, Laird & Lewis, 2009; Marsella & Gratch, 2009; Parkinson, 2009; Sander, Grandjean & Scherer, 2005). As we will see, some tutoring systems have explored this potential to inform user models. Likewise, dialogue systems, mixed-initiative planning systems, or systems that learn from observation could also benefit from such an approach (Dickinson, Brew & Meurers, 2013; Jurafsky & Martin, 2009). That is, considering emotion as interaction can be relevant in order to explain the dynamic role it plays in action and cognition (see Boehner et al., 2007).

Espionage against Poland in the Documents and Analyses of the Polish Special Services (1944 - 1989) - as Illustrated by the Intelligence Activities of the USA

The text analyses the intelligence activity against Poland in the period 1944-1989. The paper also contains a case study, i.e. an analysis of the American intelligence service activity held against Poland. While examining the research thesis, the author used the documents and analyses prepared by the Ministry of Internal Affairs. In order to best illustrate the point, the author presented a number of cases of persons who spied for the USA, which was possible thanks to the analysis of the training materials of the Ministry of Internal Affairs directed to the officers of the Security Service and the Citizens’ Militia. The text tackles the following issues: (1) to what extent did the character of the socio-political system influence the number of persons convicted for espionage against Poland in the period under examination?, (2) what was the level of interest of the foreign intelligence services in Poland before the year 1990?, (3) is it possible to indicate the specificity of the U.S. intelligence activity against Poland? 1) The analysis of data indicates that the period 1946-1956 witnessed a great number of convictions for espionage, which is often associated with the peculiar political situation in Poland of that time. Up to 1953, the countries of the Eastern bloc had reproduced the Stalin’s system, which only ceased due to the death of Stalin himself. Since then, the communist systems gradually transformed into the system of nomenklatura. Irrespective of these changes, Poland still witnessed a wave of repressions, which resulted from the threats continuously looming over the communist authorities – combating the anti-communist underground movement, fighting with the Ukrainian Insurgent Army, the Polish government-in-exile, possible revisionism of borders, social discontent related to the socio-political reforms. Hence, a great number of convictions for espionage at that time could be ascribed to purely political sentences. Moreover, equally significant was the fact that the then judicial practice was preoccupied assessing negatively any contacts and relations with foreigners. This excessive number of convictions could ensue from other criminal-law provisions, which applied with respect to the crimes against the State, including espionage. What is also important is the fact that in the Stalin’s period the judiciary personnel acquired their skills and qualifications through intensive courses in law with the predominant spirit of the theory of evidence and law by Andrey Vyshinsky. Additionally, by the decree of 1944 the Penal Code of the Polish Armed Forces was introduced; the code envisaged the increase in the number of offences classified as penalised with death penalty, whereas the high treason was subject to the military jurisdiction (the civilians were prosecuted in military courts till 1955; the espionage, however, still stood under the military jurisdiction). In 1946, there was introduced the Decree on particularly dangerous crimes in the period of the State’s recovery, which was later called a Small Penal Code. 2) The interest that foreign intelligence services expressed in relation to Poland was similar to the one they had in all countries of Eastern and Central Europe. In the case of Poland, it should be noted that foreign intelligence services recruited Polish citizens who had previously stayed abroad and after WWII returned to their home country. The services also gathered information from Poles staying in immigrant camps (e.g. in FRG). The activity of the American intelligence service on the territory of FRG and West Berlin played a key role. The documents of the Ministry of Internal Affairs pointed to the global range of this activity, e.g. through the recruitment of Polish sailors in the ports of the Netherlands, Japan, etc. In line with the development in the 1970s, espionage, which had so far concentrated on the defence and strategic sectors, became focused on science and technology of the People’s Republic of Poland. The acquisition of collaborators in academic circles was much easier, as PRL opened to academic exchange. Due to the system of visas, the process of candidate selection for intelligence services (e.g. the American) began in embassies. In the 1980s, the activity of the foreign intelligence services concentrated on the specific political situation in Poland, i.e. the growing significance of the “Solidarity” social movement. 3) The specificity of the American intelligence activity against Poland was related to the composition of the residency staff, which was the largest in comparison to other Western countries. The wide range of these activities can be proved by the quantitative data of convictions for espionage in the years 1944-1984 (however, one has to bear in mind the factors mentioned earlier in the text, which led to the misinterpretation of these data). Analysing the data and the documents prepared by the Ministry of Internal Affairs, one should treat them with caution, as, frequently, the Polish counter-intelligence service used to classify the ordinary diplomatic practice and any contacts with foreigners as espionage threats. It is clearly visible in the language of the training materials concerned with “secret service methods of the intelligence activity” as well as in the documents on operational activities of the Security Service in relation to foreigners. The level of interest the USA had in Poland was mirrored in the classification of diplomatic posts, according to which Warsaw occupied the second place (the so-called Group “B”) on the three-point scale. The CIA experienced spectacular defeats during their activity in Poland: supporting the Polish underground anti-communist organisation Freedom and Independence and the so-called Munich-Berg episode (both cases took place in the 1950s). The text focuses only on selected issues related to the espionage activities against Poland. Similarly, the analysis of the problem has been based on selected sources, which has limited the research scope - however, it was not the aim of the author to present the espionage activity against Poland in a comprehensive way. In order to assess the real threat posed by the espionage activity, one should analyse the case of persons convicted for espionage in the period 1944-1989, as the available quantitative data, mentioned in the text, cannot constitute an explicit benchmark for the scale of espionage activity. The inaccuracies in the interpretation of data and variables, which can affect the evaluation of this phenomenon, have been pointed out in the text.

An immune inspired Network Intrusion Detection System utilising correlation

Network Intrusion Detection Systems (NIDS) are computer systems which monitor a network with the aim of discerning malicious from benign activity on that network. While a wide range of approaches have met varying levels of success, most IDSs rely on having access to a database of known attack signatures which are written by security experts. Nowadays, in order to solve problems with false positive alerts, correlation algorithms are used to add additional structure to sequences of IDS alerts. However, such techniques are of no help in discovering novel attacks or variations of known attacks, something the human immune system (HIS) is capable of doing in its own specialised domain. This paper presents a novel immune algorithm for application to the IDS problem. The goal is to discover packets containing novel variations of attacks covered by an existing signature base.

Computational analysis and physico-chemical characterization of an inclusion compound between praziquantel and methyl-beta-cyclodextrin for use as an alternative in the treatment of schistosomiasis

Schistosomiasis is still an endemic disease in many regions, with 250 million people infected with Schistosoma and about 500,000 deaths per year. Praziquantel (PZQ) is the drug of choice for schistosomiasis treatment, however it is classified as Class II in the Biopharmaceutics Classification System, as its low solubility hinders its performance in biological systems. The use of cyclodextrins is a useful tool to increase the solubility and bioavailability of drugs. The aim of this work was to prepare an inclusion compound of PZQ and methyl-beta-cyclodextrin (MeCD), perform its physico-chemical characterization, and explore its in vitro cytotoxicity. SEM showed a change of the morphological characteristics of PZQ:MeCD crystals, and IR data supported this finding, with changes after interaction with MeCD including effects on the C-H of the aromatic ring, observed at 758 cm(-1). Differential scanning calorimetry measurements revealed that complexation occurred in a 1:1 molar ratio, as evidenced by the lack of a PZQ transition temperature after inclusion into the MeCD cavity. In solution, the PZQ UV spectrum profile in the presence of MeCD was comparable to the PZQ spectrum in a hydrophobic solvent. Phase solubility diagrams showed that there was a 5.5-fold increase in PZQ solubility, and were indicative of a type A(L) isotherm, that was used to determine an association constant (K(a)) of 140.8 M(-1). No cytotoxicity of the PZQ:MeCD inclusion compound was observed in tests using 3T3 cells. The results suggest that the association of PZQ with MeCD could be a good alternative for the treatment of schistosomiasis.

An AAL Collaborative System: The AAL4ALL and a Mobile Assistant Case Study

Part 20: Health and Care Networks

Double Hybrid Functionals and the Π-System Bond Length Alternation Challenge: Rivaling Accuracy of Post-HF Methods

Predicting accurate bond length alternations (BLAs) in long conjugated oligomers has been a significant challenge for electronic-structure methods for many decades, made particularly important by the close relationships between BLA and the rich optoelectronic properties of π-delocalized systems. Here, we test the accuracy of recently developed, and increasingly popular, double hybrid (DH) functionals, positioned at the top of Jacobs Ladder of DFT methods of increasing sophistication, computational cost, and accuracy, due to incorporation of MP2 correlation energy. Our test systems comprise oligomeric series of polyacetylene, polymethineimine, and polysilaacetylene up to six units long. MP2 calculations reveal a pronounced shift in BLAs between the 6-31G(d) basis set used in many studies of BLA to date and the larger cc-pVTZ basis set, but only modest shifts between cc-pVTZ and aug-cc-pVQZ results. We hence perform new reference CCSD(T)/cc-pVTZ calculations for all three series of oligomers against which we assess the performance of several families of DH functionals based on BLYP, PBE, and TPSS, along with lower-rung relatives including global- and range-separated hybrids. Our results show that DH functionals systematically improve the accuracy of BLAs relative to single hybrid functionals. xDH-PBE0 (N4 scaling using SOS-MP2) emerges as a DH functional rivaling the BLA accuracy of SCS-MP2 (N5 scaling), which was found to offer the best compromise between computational cost and accuracy the last time the BLA accuracy of DFT- and wave function-based methods was systematically investigated. Interestingly, xDH-PBE0 (XYG3), which differs to other DHs in that its MP2 term uses PBE0 (B3LYP) orbitals that are not self-consistent with the DH functional, is an outlier of trends of decreasing average BLA errors with increasing fractions of MP2 correlation and HF exchange.

A NATURALISTIC COMPUTATIONAL MODEL OF HUMAN BEHAVIOR IN NAVIGATION AND SEARCH TASKS

Planning, navigation, and search are fundamental human cognitive abilities central to spatial problem solving in search and rescue, law enforcement, and military operations. Despite a wealth of literature concerning naturalistic spatial problem solving in animals, literature on naturalistic spatial problem solving in humans is comparatively lacking and generally conducted by separate camps among which there is little crosstalk. Addressing this deficiency will allow us to predict spatial decision making in operational environments, and understand the factors leading to those decisions. The present dissertation is comprised of two related efforts, (1) a set of empirical research studies intended to identify characteristics of planning, execution, and memory in naturalistic spatial problem solving tasks, and (2) a computational modeling effort to develop a model of naturalistic spatial problem solving. The results of the behavioral studies indicate that problem space hierarchical representations are linear in shape, and that human solutions are produced according to multiple optimization criteria. The Mixed Criteria Model presented in this dissertation accounts for global and local human performance in a traditional and naturalistic Traveling Salesman Problem. The results of the empirical and modeling efforts hold implications for basic and applied science in domains such as problem solving, operations research, human-computer interaction, and artificial intelligence.

Nuclear Magnetic Resonance Spectroscopic and Computational Investigations of Chloroperoxidase Catalyzed Regio- and Enantio-Selective Transformations

Chloroperoxidase (CPO) is the most versatile heme-containing enzyme that catalyzes a broad spectrum of reactions. The remarkable feature of this enzyme is the high regio- and enantio-selectivity exhibited in CPO-catalyzed oxidation reactions. The aim of this dissertation is to elucidate the structural basis for regio- and enantio-selective transformations and investigate the application of CPO in biodegradation of synthetic dyes. To unravel the mechanism of CPO-catalyzed regioselective oxidation of indole, the dissertation explored the structure of CPO-indole complex using paramagnetic relaxation and molecular modeling. The distances between the protons of indole and the heme iron revealed that the pyrrole ring of indole is oriented toward the heme with its 2-H pointing directly at the heme iron. This provides the first experimental and theoretical explanation for the "unexpected" regioselectivity of CPO-catalyzed indole oxidation. Furthermore, the residues including Leu 70, Phe 103, Ile 179, Val 182, Glu 183, and Phe 186 were found essential to the substrate binding to CPO. These results will serve as a lighthouse in guiding the design of CPO mutants with tailor-made activities for biotechnological applications. To understand the origin of the enantioselectivity of CPO-catalyzed oxidation reactions, the interactions of CPO with substrates such as 2-(methylthio)thiophene were investigated by nuclear magnetic resonance spectroscopy (NMR) and computational techniques. In particular, the enantioselectivity is partly explained by the binding orientation of substrates. In third facet of this dissertation, a green and efficient system for degradation of synthetic dyes was developed. Several commercial dyes such as orange G were tested in the CPO-H2O2-Cl- system, where degradation of these dyes was found very efficient. The presence of halide ions and acidic pH were found necessary to the decomposition of dyes. Significantly, the results revealed that this degradation of azo dyes involves a ferric hypochlorite intermediate of CPO (Fe-OCl), compound X.

A computational model of hydrogen production by steam reforming of dimethyl ether in a large scale CFB reactor. Part II:parametric analysis

This study presents a computational parametric analysis of DME steam reforming in a large scale Circulating Fluidized Bed (CFB) reactor. The Computational Fluid Dynamic (CFD) model used, which is based on Eulerian-Eulerian dispersed flow, has been developed and validated in Part I of this study [1]. The effect of the reactor inlet configuration, gas residence time, inlet temperature and steam to DME ratio on the overall reactor performance and products have all been investigated. The results have shown that the use of double sided solid feeding system remarkable improvement in the flow uniformity, but with limited effect on the reactions and products. The temperature has been found to play a dominant role in increasing the DME conversion and the hydrogen yield. According to the parametric analysis, it is recommended to run the CFB reactor at around 300 °C inlet temperature, 5.5 steam to DME molar ratio, 4 s gas residence time and 37,104 ml gcat -1 h-1 space velocity. At these conditions, the DME conversion and hydrogen molar concentration in the product gas were both found to be around 80%.

Chest Breadths to Predict Individuals' Age - A Case Based View

It is well known that rib cage dimensions depend on the gender and vary with the age of the individual. Under this setting it is therefore possible to assume that a computational approach to the problem may be thought out and, consequently, this work will focus on the development of an Artificial Intelligence grounded decision support system to predict individual’s age, based on such measurements. On the one hand, using some basic image processing techniques it were extracted such descriptions from chest X-rays (i.e., its maximum width and height). On the other hand, the computational framework was built on top of a Logic Programming Case Base approach to knowledge representation and reasoning, which caters for the handling of incomplete, unknown, or even contradictory information. Furthermore, clustering methods based on similarity analysis among cases were used to distinguish and aggregate collections of historical data in order to reduce the search space, therefore enhancing the cases retrieval and the overall computational process. The accuracy of the proposed model is satisfactory, close to 90%.

An Assessment of Pharmacological Properties of Schinus Essential Oils: A Soft Computing Approach

Plants of genus Schinus are native South America and introduced in Mediterranean countries, a long time ago. Some Schinus species have been used in folk medicine, and Essential Oils of Schinus spp. (EOs) have been reported as having antimicrobial, anti-tumoural and anti-inflammatory properties. Such assets are related with the EOs chemical composition that depends largely on the species, the geographic and climatic region, and on the part of the plants used. Considering the difficulty to infer the pharmacological properties of EOs of Schinus species without a hard experimental setting, this work will focus on the development of an Artificial Intelligence grounded Decision Support System to predict pharmacological properties of Schinus EOs. The computational framework was built on top of a Logic Programming Case Base approach to knowledge representation and reasoning, which caters to the handling of incomplete, unknown, or even self-contradictory information. New clustering methods centered on an analysis of attribute’s similarities were used to distinguish and aggregate historical data according to the context under which it was added to the Case Base, therefore enhancing the prediction process.

Business intelligence em sistemas de apoio à gestão de frotas: Análise de Tecnologias e metodologias

O objecto de estudo desta tese de mestrado surgiu da necessidade de dar resposta a uma proposta para uma solução de business intelligence a pedido de um cliente da empresa onde até à data me encontro a desempenhar funções de analista programador júnior. O projecto consistiu na realização de um sistema de monitorização de eventos e análise de operações, portanto um sistema integrado de gestão de frotas com módulo de business intelligence. Durante o decurso deste projecto foi necessário analisar metodologias de desenvolvimento, aprender novas linguagens, ferramentas, como C#, JasperReport, visual studio, Microsoft SQL Server entre outros. ABSTRACT: Business Intelligence applied to fleet management systems - Technologies and Methodologies Analysis. The object of study of this master's thesis was the necessity of responding to a proposal for a business intelligence solution at the request of a client company where so far I find the duties of junior programmer. The project consisted of a system event monitoring and analysis of operations, so an integrated fleet management with integrated business intelligence. During the course of this project was necessary to analyze development methodologies, learn new languages, tools such as C #, JasperReports, visual studio, Microsoft Sql Server and others.

Computational Models Development and Demand Response Application for Smart Grids

This paper focuses on computational models development and its applications on demand response, within smart grid scope. A prosumer model is presented and the corresponding economic dispatch problem solution is analyzed. The prosumer solar radiation production and energy consumption are forecasted by artificial neural networks. The existing demand response models are studied and a computational tool based on fuzzy clustering algorithm is developed and the results discussed. Consumer energy management applications within the InovGrid pilot project are presented. Computation systems are developed for the acquisition, monitoring, control and supervision of consumption data provided by smart meters, allowing the incorporation of consumer actions on their electrical energy management. An energy management system with integration of smart meters for energy consumers in a smart grid is developed.