Probabilistic reasoning with an enzyme-driven DNA device

We present a biomolecular probabilistic model driven by the action of a DNA toolbox made of a set of DNA templates and enzymes that is able to perform Bayesian inference. The model will take single-stranded DNA as input data, representing the presence or absence of a specific molecular signal (the evidence). The program logic uses different DNA templates and their relative concentration ratios to encode the prior probability of a disease and the conditional probability of a signal given the disease. When the input and program molecules interact, an enzyme-driven cascade of reactions (DNA polymerase extension, nicking and degradation) is triggered, producing a different pair of single-stranded DNA species. Once the system reaches equilibrium, the ratio between the output species will represent the application of Bayes? law: the conditional probability of the disease given the signal. In other words, a qualitative diagnosis plus a quantitative degree of belief in that diagno- sis. Thanks to the inherent amplification capability of this DNA toolbox, the resulting system will be able to to scale up (with longer cascades and thus more input signals) a Bayesian biosensor that we designed previously.

Automated end user-centred adaptation of web components through automated description logic-based reasoning

Context: This paper addresses one of the major end-user development (EUD) challenges, namely, how to pack today?s EUD support tools with composable elements. This would give end users better access to more components which they can use to build a solution tailored to their own needs. The success of later end-user software engineering (EUSE) activities largely depends on how many components each tool has and how adaptable components are to multiple problem domains. Objective: A system for automatically adapting heterogeneous components to a common development environment would offer a sizeable saving of time and resources within the EUD support tool construction process. This paper presents an automated adaptation system for transforming EUD components to a standard format. Method: This system is based on the use of description logic. Based on a generic UML2 data model, this description logic is able to check whether an end-user component can be transformed to this modeling language through subsumption or as an instance of the UML2 model. Besides it automatically finds a consistent, non-ambiguous and finite set of XSLT mappings to automatically prepare data in order to leverage the component as part of a tool that conforms to the target UML2 component model. Results: The proposed system has been successfully applied to components from four prominent EUD tools. These components were automatically converted to a standard format. In order to validate the proposed system, rich internet applications (RIA) used as an operational support system for operators at a large services company were developed using automatically adapted standard format components. These RIAs would be impossible to develop using each EUD tool separately. Conclusion: The positive results of applying our system for automatically adapting components from current tool catalogues are indicative of the system?s effectiveness. Use of this system could foster the growth of web EUD component catalogues, leveraging a vast ecosystem of user-centred SaaS to further current EUSE trends.

Aproximaciones y Procedimientos Creativos en los Procesos de Aprendizaje-Des_aprendizaje Proyectual

Se aborda como objetivo una reflexión operativa sobre los actos creativos en el proyecto de arquitectura investigando los procedimientos que intervienen recurrentemente en los procesos del aprendizaje y proyectación. Aprendizaje entendido como actitud ininterrumpida en el discurso del creador, estado inacabado, en constante evolución, continuo, no suscrito al momento particular, como situación connatural al hecho creativo. El marco epistemológico de la Creatividad y sus técnicas asociadas en constante aplicación en otras disciplinas se desvela como un sustrato gnoseológico referencial para el entendimiento de los procesos de génesis y producción del proyecto y su aprendizaje. Se inscribe la investigación de la tesis en una doble línea de pensamiento lógico-racional y lógico-intuitivo, mediante inferencias de naturaleza deductiva, inductiva y abductiva. Se busca suscitar un interés por la creatividad que contribuya a extender el campo de investigación sobre cómo se genera y se produce la arquitectura y su aplicación al aprendizaje. Proponemos la elaboración de una cartografía taxonómica de procedimientos creativos en el proyectar, de tal manera que nos conduzca hacia la enunciación de una Metaheurística de la Creatividad. Metaheurística que contenga el mapa operativo de Procedimientos y de sus Metaprincipios de aplicación a distintos entornos y problemas, con capacidad de respuesta adaptativa en todos los estados divergentes del proceso. Cartografía, en definitiva, de relaciones más que de sistematizaciones. Este mapa creativo estará formado por 9 Procedimientos resultado de 9 aproximaciones que constituyen 9 Lógicas de acción y razonamiento, en unas condiciones de campo hologramáticas. Enfocadas hacia una nueva actitud creativa, desprejuiciada, atenta a los flujos transdisciplinares, regida indistintamente por el azar y el rigor, expansiva y condensadora, múltiple y poliédrica, abierta e inconclusa, lúdica y frívola, automática e impredecible. Actitud creativa que actúa con lógicas procedimentales relacionales, siempre en constante redefinición, alejadas de toda teorización, sin constituir un meta-relato, más como gestión de información que como dispositivo disciplinar: abductiva, analógica, sinéctica, metafórica, difusa, azarosa, suspendida, divergente y des_aprendida. ABSTRACT Abstract: An operative reflection is approached as aim on the creative acts in the project of architecture, investigating the procedures involved recursively in the processes of learning and project. Learning understood as uninterrupted attitude in the speech of the creator, in unfinished condition, in constant evolution, continuous, not signed to the particular moment, as inherent to the creative fact. The epistemological framework of the Creativity and its techniques associated in constant application in other disciplines is revealed as a referential gnoseologic substratum for the understanding of the processes of genesis and production of the project and his learning. The investigation of the thesis registers in a double line of logical - rational and logical - intuitive thought, by means of inferences of deductive, inductive and abductive nature. One seeks to arouse an interest in the creativity that will help to extend the field of investigation on how it is generated and produces the architecture and its application to the learning. We propose the elaboration of a taxonomic mapping creative procedures in the project, in such a way to lead us towards the enunciation of a Metaheuristic of creativity. Metaheuristic that contains containing the operative map of Procedures and their Metaprinciples of application to different environments and problems, with capacity of adaptive response in all the divergent conditions of the process. Cartography, definitively, of relationships rather than of systematizings. The map of procedures will be formed by 9 procedures as result of 9 approaches that constitute 9 logics of action and reasoning, in hologramatics conditions of field. Focused on a new creative attitude, ideologically unbiased, attentive to transdisciplinary flows, governed either by random and rigor, expansive and condenser, multiple and multifaceted, open and unfinished, playful and frivolous, automatic and unpredictable. Creative attitude that acts with procedural relational logics, always in constant redefinition, away from all theorizing, without being a meta-relate, more like information that discipline as device management: abductive, analogical, synectical, metaphorical, diffuse, randomness, suspended, divergent and mis_learnt.

Normative Practical Reasoning via Argumentation and Dialogue

Postprint

Case-based reasoning to support decision making for managing drinking water quality events in distribution systems

Peer reviewed

GlycoSuiteDB: a new curated relational database of glycoprotein glycan structures and their biological sources

GlycoSuiteDB is a relational database that curates information from the scientific literature on glyco­protein derived glycan structures, their biological sources, the references in which the glycan was described and the methods used to determine the glycan structure. To date, the database includes most published O-linked oligosaccharides from the last 50 years and most N-linked oligosaccharides that were published in the 1990s. For each structure, information is available concerning the glycan type, linkage and anomeric configuration, mass and composition. Detailed information is also provided on native and recombinant sources, including tissue and/or cell type, cell line, strain and disease state. Where known, the proteins to which the glycan structures are attached are reported, and cross-references to the SWISS-PROT/TrEMBL protein sequence databases are given if applicable. The GlycoSuiteDB annotations include literature references which are linked to PubMed, and detailed information on the methods used to determine each glycan structure are noted to help the user assess the quality of the structural assignment. GlycoSuiteDB has a user-friendly web interface which allows the researcher to query the database using mono­isotopic or average mass, monosaccharide composition, glycosylation linkages (e.g. N- or O-linked), reducing terminal sugar, attached protein, taxonomy, tissue or cell type and GlycoSuiteDB accession number. Advanced queries using combinations of these parameters are also possible. GlycoSuiteDB can be accessed on the web at http://www.glycosuite.com.

Development of prospective mathematics teachers’ professional noticing in a specific domain: proportional reasoning

The aim of this research is to identify aspects that support the development of prospective mathematics teachers’ professional noticing in a b-learning context. The study presented here investigates the extent to which prospective secondary mathematics teachers attend and interpret secondary school students’ proportional reasoning and decide how to respond. Results show that interactions in an on-line discussion improve prospective mathematics teachers’ ability to identify and interpret important aspects of secondary school students’ mathematical thinking.

Interpersonal relations and nurses' job satisfaction through knowledge and usage of relational skills

Background/rationale: Many interpersonal labor disputes stem from the lack of communication skills and the relational problems in the interactions between health professionals. Aims/methods: A qualitative study was conducted in a Spanish hospital in order to get to know how the communicative interaction between hospital nurses is like in relation to the nurses' interpersonal interaction and communication skills developed in their working relationships. Twenty-one hospital nurses between 29 and 55 years old, working in different wards, were interviewed. Open-ended interview discourses were transcribed verbatim and analyzed using qualitative content analysis. Results: The following four key themes were analyzed: communication and sender; communication and awareness of who has the problem; non-verbal communication; communication and recipient. Conclusion: The results of this study highlight the need to broaden nurses' relational–communication skills in order to increase job satisfaction.

Co-design: setting relational domains for deep sustainability

This paper draws mainly on the work of Elizabeth Sanders who has being practising, thinking and mapping participatory design research for over 25 years, connecting it to insights from Maturana (1984), Capra (2002), Jovchelovitch (1995, 2000, 2007) and Preece (2011), to propose that the process of design per se is a relational domain of cocreativity that is essential to construct a way toward deeper sustainability.

[Forensic disputation on reasoning], undated

Folio-sized leaf containing a handwritten disputation on reasoning. The disputation begins with the question: "Whether the Faculty of reasoning is improved by a Knowledge of Syllogym?"

National Minorities, Nationalizing States, and External National Homelands in the New Europe. Notes toward a Relational Analysis. Institute of Advanced Studies Political Science Series, 11 December 1993

Nationalism remains central to politics in and among the new nation-states. Far from »solving« the region's national question, the most recent reconfiguration of political space – the replacement of the Soviet Union, Yugoslavia, and Czechoslovakia by some twenty would-be nation-states – only recast it in a new form. It is this new phase and form of the national question that I explore in this paper. I begin by outlining a particular relational configuration – the triadic relational nexus between national minorities, nationalizing states, and external national homelands – that is central to the national question in post-Soviet Eurasia. In the second, and most substantial, section of the paper, I argue that each of the »elements« in this relational nexus – minority, nationalizing state, and homeland – should itself be understood in dynamic and relational terms, not as a fixed, given, or analytically irreducible entity but as a field of differentiated positions and an arena of struggles among competing »stances.« In a brief concluding section, I return to the relational nexus as a whole, underscoring the dynamically interactive quality of the triadic interplay.

Reasons withheld and insufficient reasoning as due process violations: two cases before the ECHR

Two very different cases decided by the European Court of Human Rights illustrate how the non-availability of sufficient reasons, for pre-trial judicial decisions in one case, and for a decision in a civil and administrative matter in the other, can lead to due process violations in terms of Articles 5 or 6 of the Convention of Human Rights and Fundamental Freedoms.

Relational Memory Is Evident in Eye Movement Behavior despite the Use of Subliminal Testing Methods

While it is generally agreed that perception can occur without awareness, there continues to be debate about the type of representational content that is accessible when awareness is minimized or eliminated. Most investigations that have addressed this issue evaluate access to well-learned representations. Far fewer studies have evaluated whether or not associations encountered just once prior to testing might also be accessed and influence behavior. Here, eye movements were used to examine whether or not memory for studied relationships is evident following the presentation of subliminal cues. Participants (assigned to experimental or control groups) studied scene-face pairs and test trials evaluated implicit and explicit memory for these pairs. Each test trial began with a subliminal scene cue, followed by three visible studied faces. For experimental group participants, one face was the studied associate of the scene (implicit test); for controls none were a match. Subsequently, the Display containing a match was presented to both groups, but now it was preceded by a visible scene cue (explicit test). Eye movements were recorded and recognition Memory responses were made. Participants in the experimental group looked disproportionately at matching faces on implicit test trials and participants from both groups looked disproportionately at matching faces on explicit test trials, even when that face had not been successfully identified as the associate. Critically, implicit memory-based viewing effects seemed not to depend on residual awareness of subliminal scenes cues, as subjective and objective measures indicated that scenes were successfully masked from view. The reported outcomes indicate that memory for studied relationships can be expressed in eye movement behavior without awareness.

Intracranial EEG correlates of implicit relational inference within the hippocampus

Drawing inferences from past experiences enables adaptive behavior in future situations. Inference has been shown to depend on hippocampal processes. Usually, inference is considered a deliberate and effortful mental act which happens during retrieval, and requires the focus of our awareness. Recent fMRI studies hint at the possibility that some forms of hippocampus-dependent inference can also occur during encoding and possibly also outside of awareness. Here, we sought to further explore the feasibility of hippocampal implicit inference, and specifically address the temporal evolution of implicit inference using intracranial EEG. Presurgical epilepsy patients with hippocampal depth electrodes viewed a sequence of word pairs, and judged the semantic fit between two words in each pair. Some of the word pairs entailed a common word (e.g.,‘winter - red’, ‘red - cat’) such that an indirect relation was established in following word pairs (e.g, ‘winter - cat’). The behavioral results suggested that drawing inference implicitly from past experience is feasible because indirect relations seemed to foster ‘fit’ judgments while the absence of indirect relations fostered 'do not fit' judgments, even though the participants were unaware of the indirect relations. A event-related potential (ERP) difference emerging 400 ms post-stimulus was evident in the hippocampus during encoding, suggesting that indirect relations were already established automatically during encoding of the overlapping word pairs. Further ERP differences emerged later post-stimulus (1500 ms), were modulated by the participants' responses and were evident during encoding and test. Furthermore, response-locked ERP effects were evident at test. These ERP effects could hence be a correlate of the interaction of implicit memory with decision-making. Together, the data map out a time-course in which the hippocampus automatically integrates memories from discrete but related episodes to implicitly influence future decision making.