FTDD973: A multimedia knowledge-based system and methodology for operator training and diagnostics

FTDD973 (973 Fabricator Training, Documentation, and Diagnostics) is an interactive multimedia knowledge based system and methodology for computer-aided training and certification of operators, as well as tool and process diagnostics in IBM's CMOS SGP fabrication line (building 973). FTDD973 is an example of what can be achieved with modern multimedia workstations. Knowledge-based systems, hypertext, hypergraphics, high resolution images, audio, motion video, and animation are technologies that in synergy can be far more useful than each by itself. FTDD973's modular and object-oriented architecture is also an example of how improvements in software engineering are finally making it possible to combine many software modules into one application. FTDD973 is developed in ExperMedia/2; and OS/2 multimedia expert system shell for domain experts

Machine learning based detection of Kepler objects of interest

The authors would like to thank CNPq-Brazil and the University of St Andrews for their kind supportPostprintPeer reviewe

Stress Response SCF Ubiquitin Ligase F box Protein Fbx15 Controls Nuclear Co repressor Localization and Virulence of the Opportunistic Human Fungal Pathogen Aspergillus fumigatus

Aspergillus fumigatus ist die häufigste Ursache für Lungeninfektionen in immunsuppri-mierten Patienten. Virulenzfaktoren sind häufig an Kontrollmechanismen für Entwick-lung gekoppelt, welche im verwandten Modellorganismus Aspergillus nidulans entdeckt wurden. Diese Arbeit präsentiert die Charakterisierung des F-box Proteins Fbx15 in A. fumigatus, welches einen starken Einfluss auf die Entwicklung in A. nidulans hat. Die Deletion von fbx15 resultierte in starken Wachstumsdefekten unter vielen Stress induzie-renden Bedingungen, welche klassische Virulenz Faktoren beinhalten, wie erhöhte Tem-peratur, oxidativer Stress und Aminosäuremangel, während das Wachstum unter Stan-dardbedingungen nicht beeinflusst war. Oxidativer Stress induziert eine transiente Erhöhung der fbx15 Expression, welche nach 40 Minuten zu einer dreifach erhöhten Pro-teinmenge führte. Fbx15 ist ein stabiles F-box Protein mit einer Halbwertszeit von 90 Minuten. Generell funktionieren F-box Proteine als Substratadapter für SCF-E3-Ubiquitin-Ligasen. Fbx15 liegt unter normalen Bedingungen phosphoryliert vor und in-teragiert mit der Skp1/A Untereinheit des SCF-Komplexes, vorzugsweise in kleineren Subpopulationen im Zytoplasma. Phosphoryliertes Fbx15 wird bevorzugt in SCF-Komplexe eingebaut. Oxidativer Stress führt zu einer schnellen Dephosphorylierung von Fbx15. Fbx15 Varianten, welche nicht phosphoryliert werden können, interagieren mit Skp1/A primär im Kern. Fbx15 rekrutiert drei Untereinheiten des COP9-Signalosoms und Proteine welche in Transkription, Translation, Signalübertragung, Morphologie oder Stoffwechsel involviert sind. Fbx15 bindet die Ssn6/F Untereinheit des konservierten Ssn6/SsnF-Tup1/RcoA Co-Repressors und wird für dessen Kernlokalisation benötigt. Dephosphoryliertes Fbx15 interagiert mit Ssn6/F im Kern und eine Fbx15-Ssn6/F be-dingte Genrepression wird für die Reduzierung der Gliotoxin-Biosynthese benötigt. fbx15 Deletionsstämme sind nicht in der Lage immunsupprimierte Mäuse in einem Model für invasive Aspergillose zu infizieren, was eine essentielle Funktion von Fbx15 für die Viru-lenz bestätigt. Diese Arbeit zeigt, dass Fbx15 nicht nur Teil von SCF-E3-Ubiquitin-Ligasen sein kann, sondern eine zweite neue molekulare Funktion aufweist, welche die physische Interaktion mit der Co-Repressor Untereinheit Ssn6/F und dessen Lokalisa-tionskontrolle beinhaltet. Diese duale Funktion resultiert in einer essentiellen Funktion von Fbx15 für die Kontrolle der oxidativen Stressantwort, des Sekundärmetabolismus und der Virulenz im opportunistischen Humanpathogen A. fumigatus

Cation-Responsive and Photocleavable Hydrogels from Noncanonical Amphiphilic DNA Nanostructures.

Funder: Imperial College LondonThanks to its biocompatibility, versatility, and programmable interactions, DNA has been proposed as a building block for functional, stimuli-responsive frameworks with applications in biosensing, tissue engineering, and drug delivery. Of particular importance for in vivo applications is the possibility of making such nanomaterials responsive to physiological stimuli. Here, we demonstrate how combining noncanonical DNA G-quadruplex (G4) structures with amphiphilic DNA constructs yields nanostructures, which we termed "Quad-Stars", capable of assembling into responsive hydrogel particles via a straightforward, enzyme-free, one-pot reaction. The embedded G4 structures allow one to trigger and control the assembly/disassembly in a reversible fashion by adding or removing K+ ions. Furthermore, the hydrogel aggregates can be photo-disassembled upon near-UV irradiation in the presence of a porphyrin photosensitizer. The combined reversibility of assembly, responsiveness, and cargo-loading capabilities of the hydrophobic moieties make Quad-Stars a promising candidate for biosensors and responsive drug delivery carriers

Genome-scale bacterial transcriptional regulatory networks: reconstruction and integrated analysis with metabolic models

Advances in sequencing technology are resulting in the rapid emergence of large numbers of complete genome sequences. High throughput annotation and metabolic modeling of these genomes is now a reality. The high throughput reconstruction and analysis of genome-scale transcriptional regulatory networks represents the next frontier in microbial bioinformatics. The fruition of this next frontier will depend upon the integration of numerous data sources relating to mechanisms, components, and behavior of the transcriptional regulatory machinery, as well as the integration of the regulatory machinery into genome-scale cellular models. Here we review existing repositories for different types of transcriptional regulatory data, including expression data, transcription factor data, and binding site locations, and we explore how these data are being used for the reconstruction of new regulatory networks. From template network based methods to de novo reverse engineering from expression data, we discuss how regulatory networks can be reconstructed and integrated with metabolic models to improve model predictions and performance. Finally, we explore the impact these integrated models can have in simulating phenotypes, optimizing the production of compounds of interest or paving the way to a whole-cell model.J.P.F. acknowledges funding from [SFRH/BD/70824/2010] of the FCT (Portuguese Foundation for Science and Technology) PhD program. The work was supported in part by the ERDF—European Regional Development Fund through the COMPETE Programme (operational programme for competitiveness), National Funds through the FCT within projects [FCOMP-01-0124-FEDER015079] (ToMEGIM—Computational Tools for Metabolic Engineering using Genome-scale Integrated Models) and FCOMP-01-0124-FEDER009707 (HeliSysBio—molecular Systems Biology in Helicobacter pylori), the U.S. Department of Energy under contract [DE-ACO2-06CH11357] and the National Science Foundation under [0850546]

Evaluation of a fuzzy-expert system for fault diagnosis in power systems

A major problem with alarm processing and fault diagnosis in power systems is the reliance on the circuit alarm status. If there is too much information available and the time of arrival of the information is random due to weather conditions etc., the alarm activity is not easily interpreted by system operators. In respect of these problems, this thesis sets out the work that has been carried out to design and evaluate a diagnostic tool which assists power system operators during a heavy period of alarm activity in condition monitoring. The aim of employing this diagnostic tool is to monitor and raise uncertain alarm information for the system operators, which serves a proposed solution for restoring such faults. The diagnostic system uses elements of AI namely expert systems, and fuzzy logic that incorporate abductive reasoning. The objective of employing abductive reasoning is to optimise an interpretation of Supervisory Control and Data Acquisition (SCADA) based uncertain messages when the SCADA based messages are not satisfied with simple logic alone. The method consists of object-oriented programming, which demonstrates reusability, polymorphism, and readability. The principle behind employing objectoriented techniques is to provide better insights and solutions compared to conventional artificial intelligence (Al) programming languages. The characteristics of this work involve the development and evaluation of a fuzzy-expert system which tries to optimise the uncertainty in the 16-lines 12-bus sample power system. The performance of employing this diagnostic tool is assessed based on consistent data acquisition, readability, adaptability, and maintainability on a PC. This diagnostic tool enables operators to control and present more appropriate interpretations effectively rather than a mathematical based precise fault identification when the mathematical modelling fails and the period of alarm activity is high. This research contributes to the field of power system control, in particular Scottish Hydro-Electric PLC has shown interest and supplied all the necessary information and data. The AI based power system is presented as a sample application of Scottish Hydro-Electric and KEPCO (Korea Electric Power Corporation)

Understanding The Structure-Function Relationships In The Mechanosensitive Channel Of Small Conductance (MscS) And Bacterial Cyclic Nucleotide Gated (bCNG) Ion Channels

In this dissertation, we discuss the relationship between structure and function within the mechanosensitive channel of small conductance: MscS) superfamily. Specifically, we explore the function of the bacterial cyclic nucleotide gated: bCNG) ion channels and the lipid interactions of MscS in the closed and open state. Our main goal was to identify similarities between MscS and bCNG channels and to understand the differences between the two channel families. The bCNG channel family is a unique subset of the MscS superfamily. These channels are structurally composed of a channel domain homologous to MscS, a non-conserved linker domain, and a cyclic adenosine monophosphate: cAMP) binding domain. Several bCNG channels gate in response to cAMP alone, indicating that these channels function as ligand gated ion channels. bCNG channels are highly homologous to the pore lining helix and the upper vestibule domain of MscS suggesting that these channels should gate in response to mechanical tension. The majority of bCNG channels are unable to gate in response to mechanical tension however, upon the removal of the cAMP binding domain limited mechanosensation is restored to bCNG channels. Some bacterial genomes are predicted to encode for multiple bCNG homologues. RT-PCR analysis of several different bacterial strains shows that the mRNA for these bCNG homologues is detected at similar levels. When two bCNG channels are heterologously expressed in E. coli, they form heteromultimeric channels. These results suggest that bCNG channels are likely to form heteromultimers in vivo. E. coli MscS is a well studied mechanosensitive channel. Previous research has identified critical residues for channel function; these residues are located throughout the channel but are not predicted to interact with the lipid tails. As a mechanosensitive channel, we would expect that the amino acids in the transmembrane domains interact with the hydrophobic lipid tails to allow for gating in response to mechanical tension. To identify these residues, an all atom molecular dynamics simulation was conducted on a closed state model of MscS. The combination of this simulation and phenotypic data identified seven residues in the closed state that interact with the lipids and are essential for channel function. The identification of lipid interacting residues in the closed state of MscS suggests that similar interactions would be important for the open state. However, no lipid interacting residues were identified in the open state of MscS. The lack of lipid interactions suggests that the open state of MscS does not have essential lipid interactions. This has lead us to propose a new gating paradigm for MscS, the Jack-In-The-Box gating model. This study of the relationship between structure and function within the MscS superfamily has given us a greater understanding of the molecular interactions needed for channel function. We have learned that lipid interactions are essential for gating in response to mechanical tension and that the appendage of the C-terminal cAMP binding domain inhibits mechanical gating of bCNG channels

Semantic relations between sentences: from lexical to linguistically inspired semantic features and beyond

This thesis is concerned with the identification of semantic equivalence between pairs of natural language sentences, by studying and computing models to address Natural Language Processing tasks where some form of semantic equivalence is assessed. In such tasks, given two sentences, our models output either a class label, corresponding to the semantic relation between the sentences, based on a predefined set of semantic relations, or a continuous score, corresponding to their similarity on a predefined scale. The former setup corresponds to the tasks of Paraphrase Identification and Natural Language Inference, while the latter corresponds to the task of Semantic Textual Similarity. We present several models for English and Portuguese, where various types of features are considered, for instance based on distances between alternative representations of each sentence, following lexical and semantic frameworks, or embeddings from pre-trained Bidirectional Encoder Representations from Transformers models. For English, a new set of semantic features is proposed, from the formal semantic representation of Discourse Representation Structure. In Portuguese, suitable corpora are scarce and formal semantic representations are unavailable, hence an evaluation of currently available features and corpora is conducted, following the modelling setup employed for English. Competitive results are achieved on all tasks, for both English and Portuguese, particularly when considering that our models are based on generally available tools and technologies, and that all features and models are suitable for computation in most modern computers, except for those based on embeddings. In particular, for English, our semantic features from DRS are able to improve the performance of other models, when integrated in the feature set of such models, and state of the art results are achieved for Portuguese, with models based on fine tuning embeddings to a specific task; Sumário: Relações semânticas entre frases: de aspectos lexicais a aspectos semânticos inspirados em linguística e além destes Esta tese é dedicada à identificação de equivalência semântica entre frases em língua natural, através do estudo e computação de modelos destinados a tarefas de Processamento de Linguagem Natural relacionadas com alguma forma de equivalência semântica. Em tais tarefas, a partir de duas frases, os nossos modelos produzem uma etiqueta de classificação, que corresponde à relação semântica entre as frases, baseada num conjunto predefinido de possíveis relações semânticas, ou um valor contínuo, que corresponde à similaridade das frases numa escala predefinida. A primeira configuração mencionada corresponde às tarefas de Identificação de Paráfrases e de Inferência em Língua Natural, enquanto que a última configuração mencionada corresponde à tarefa de Similaridade Semântica em Texto. Apresentamos diversos modelos para Inglês e Português, onde vários tipos de aspectos são considerados, por exemplo baseados em distâncias entre representações alternativas para cada frase, seguindo formalismos semânticos e lexicais, ou vectores contextuais de modelos previamente treinados com Representações Codificadas Bidirecionalmente a partir de Transformadores. Para Inglês, propomos um novo conjunto de aspectos semânticos, a partir da representação formal de semântica em Estruturas de Representação de Discurso. Para Português, os conjuntos de dados apropriados são escassos e não estão disponíveis representações formais de semântica, então implementámos uma avaliação de aspectos actualmente disponíveis, seguindo a configuração de modelos aplicada para Inglês. Obtivemos resultados competitivos em todas as tarefas, em Inglês e Português, particularmente considerando que os nossos modelos são baseados em ferramentas e tecnologias disponíveis, e que todos os nossos aspectos e modelos são apropriados para computação na maioria dos computadores modernos, excepto os modelos baseados em vectores contextuais. Em particular, para Inglês, os nossos aspectos semânticos a partir de Estruturas de Representação de Discurso melhoram o desempenho de outros modelos, quando integrados no conjunto de aspectos de tais modelos, e obtivemos resultados estado da arte para Português, com modelos baseados em afinação de vectores contextuais para certa tarefa