Computational prediction of neural progenitor cell fates

Understanding how stem and progenitor cells choose between alternative cell fates is a major challenge in developmental biology. Efforts to tackle this problem have been hampered by the scarcity of markers that can be used to predict cell division outcomes. Here we present a computational method, based on algorithmic information theory, to analyze dynamic features of living cells over time. Using this method, we asked whether rat retinal progenitor cells (RPCs) display characteristic phenotypes before undergoing mitosis that could foretell their fate. We predicted whether RPCs will undergo a self-renewing or terminal division with 99% accuracy, or whether they will produce two photoreceptors or another combination of offspring with 87% accuracy. Our implementation can segment, track and generate predictions for 40 cells simultaneously on a standard computer at 5 min per frame. This method could be used to isolate cell populations with specific developmental potential, enabling previously impossible investigations.

Design thinking and the precautionary principle : development of a theoretical model complementing preventive judgment for design for sustainability enriched through a study of architectural competitions adopting LEED

Cette thèse contribue à une théorie générale de la conception du projet. S’inscrivant dans une demande marquée par les enjeux du développement durable, l’objectif principal de cette recherche est la contribution d’un modèle théorique de la conception permettant de mieux situer l’utilisation des outils et des normes d’évaluation de la durabilité d’un projet. Les principes fondamentaux de ces instruments normatifs sont analysés selon quatre dimensions : ontologique, méthodologique, épistémologique et téléologique. Les indicateurs de certains effets contre-productifs reliés, en particulier, à la mise en compte de ces normes confirment la nécessité d’une théorie du jugement qualitatif. Notre hypothèse principale prend appui sur le cadre conceptuel offert par la notion de « principe de précaution » dont les premières formulations remontent du début des années 1970, et qui avaient précisément pour objectif de remédier aux défaillances des outils et méthodes d’évaluation scientifique traditionnelles. La thèse est divisée en cinq parties. Commençant par une revue historique des modèles classiques des théories de la conception (design thinking) elle se concentre sur l’évolution des modalités de prise en compte de la durabilité. Dans cette perspective, on constate que les théories de la « conception verte » (green design) datant du début des années 1960 ou encore, les théories de la « conception écologique » (ecological design) datant des années 1970 et 1980, ont finalement convergé avec les récentes théories de la «conception durable» (sustainable design) à partir du début des années 1990. Les différentes approches du « principe de précaution » sont ensuite examinées sous l’angle de la question de la durabilité du projet. Les standards d’évaluation des risques sont comparés aux approches utilisant le principe de précaution, révélant certaines limites lors de la conception d’un projet. Un premier modèle théorique de la conception intégrant les principales dimensions du principe de précaution est ainsi esquissé. Ce modèle propose une vision globale permettant de juger un projet intégrant des principes de développement durable et se présente comme une alternative aux approches traditionnelles d’évaluation des risques, à la fois déterministes et instrumentales. L’hypothèse du principe de précaution est dès lors proposée et examinée dans le contexte spécifique du projet architectural. Cette exploration débute par une présentation de la notion classique de «prudence» telle qu’elle fut historiquement utilisée pour guider le jugement architectural. Qu’en est-il par conséquent des défis présentés par le jugement des projets d’architecture dans la montée en puissance des méthodes d’évaluation standardisées (ex. Leadership Energy and Environmental Design; LEED) ? La thèse propose une réinterprétation de la théorie de la conception telle que proposée par Donald A. Schön comme une façon de prendre en compte les outils d’évaluation tels que LEED. Cet exercice révèle cependant un obstacle épistémologique qui devra être pris en compte dans une reformulation du modèle. En accord avec l’épistémologie constructiviste, un nouveau modèle théorique est alors confronté à l’étude et l’illustration de trois concours d'architecture canadienne contemporains ayant adopté la méthode d'évaluation de la durabilité normalisée par LEED. Une série préliminaire de «tensions» est identifiée dans le processus de la conception et du jugement des projets. Ces tensions sont ensuite catégorisées dans leurs homologues conceptuels, construits à l’intersection du principe de précaution et des théories de la conception. Ces tensions se divisent en quatre catégories : (1) conceptualisation - analogique/logique; (2) incertitude - épistémologique/méthodologique; (3) comparabilité - interprétation/analytique, et (4) proposition - universalité/ pertinence contextuelle. Ces tensions conceptuelles sont considérées comme autant de vecteurs entrant en corrélation avec le modèle théorique qu’elles contribuent à enrichir sans pour autant constituer des validations au sens positiviste du terme. Ces confrontations au réel permettent de mieux définir l’obstacle épistémologique identifié précédemment. Cette thèse met donc en évidence les impacts généralement sous-estimés, des normalisations environnementales sur le processus de conception et de jugement des projets. Elle prend pour exemple, de façon non restrictive, l’examen de concours d'architecture canadiens pour bâtiments publics. La conclusion souligne la nécessité d'une nouvelle forme de « prudence réflexive » ainsi qu’une utilisation plus critique des outils actuels d’évaluation de la durabilité. Elle appelle une instrumentalisation fondée sur l'intégration globale, plutôt que sur l'opposition des approches environnementales.

A computational fluid dynamic study on the filtering mechanics in suspension feeding marine invertebrates

Les suspensivores ont la tâche importante de séparer les particules de l'eau. Bien qu'une grande gamme de morphologies existe pour les structures d'alimentation, elles sont pratiquement toutes constituées de rangées de cylindres qui interagissent avec leur environnement fluide. Le mécanisme de capture des particules utilisé dépend des contraintes morphologiques, des besoins énergétiques et des conditions d'écoulement. Comme nos objectifs étaient de comprendre ces relations, nous avons eu recours à des études de comparaison pour interpréter les tendances en nature et pour comprendre les conditions qui provoquent de nouveaux fonctionnements. Nous avons utilisé la dynamique des fluides numérique (computational fluid dynamics, CFD) pour créer des expériences contrôlées et pour simplifier les analyses. Notre première étude démontre que les coûts énergétiques associés au pompage dans les espaces petits sont élevés. De plus, le CFD suggère que les fentes branchiales des ptérobranches sont des structures rudimentaires, d'un ancêtre plus grande. Ce dernier point confirme l'hypothèse qu'un ver se nourrit par filtration tel que l'ancêtre des deuterostomes. Notre deuxième étude détermine la gamme du nombre de Reynolds number critique où la performance d'un filtre de balane change. Quand le Re est très bas, les différences morphologiques n'ont pas un grand effet sur le fonctionnement. Cependant, une pagaie devient une passoire lorsque le Re se trouve entre 1 et 3,5. Le CFD s’est dévoilé être un outil très utile qui a permis d’obtenir des détails sur les microfluides. Ces études montrent comment la morphologie et les dynamiques des fluides interagissent avec la mécanisme de capture ou de structures utilisées, ainsi que comment des petits changements de taille, de forme, ou de vitesse d'écoulement peuvent conduire à un nouveau fonctionnement.

Computational models for the prediction of severe thunderstorms over east indian region

Thunderstorm is one of the most spectacular weather phenomena in the atmosphere. Many parts over the Indian region experience thunderstorms at higher frequency during pre-monsoon months (March- May), when the atmosphere is highly unstable because of high temperatures prevailing at lower levels. Most dominant feature of the weather during the pre-monsoon season over the eastern Indo-Gangetic plain and northeast India is the outburst of severe local convective storms, commonly known as ‘Nor’wester’ or ‘Kalbaishakhi’. The severe thunderstorms associated with thunder, squall line, lightning and hail cause extensive losses in agriculture, damage to structure and also loss of life. The casualty due to lightning associated with thunderstorms in this region is the highest in the world. The highest numbers of aviation hazards are reported during occurrence of these thunderstorms. In India, 72% of tornadoes are associated with this thunderstorm.

Vibrational spectroscopic studies and computational study of quinoline-2-carbaldehyde benzoyl hydrazone

FT-IR spectrum of quinoline-2-carbaldehyde benzoyl hydrazone (HQb H2O) was recorded and analyzed. The synthesis and crystal structure data are also described. The vibrational wavenumbers were examined theoretically using the Gaussian03 package of programs using HF/6-31G(d) and B3LYP/6-31G(d) levels of theory. The data obtained from vibrational wavenumber calculations are used to assign vibrational bands obtained in infrared spectroscopy of the studied molecule. The first hyperpolarizability, infrared intensities and Raman activities are reported. The calculated first hyperpolarizability is comparable with the reported values of similar derivatives and is an attractive object for future studies of non-linear optics. The geometrical parameters of the title compound obtained from XRD studies are in agreement with the calculated values. The changes in the CAN bond lengths suggest an extended p-electron delocalization over quinoline and hydrazone moieties which is responsible for the non-linearity of the molecule

Reliability Estimation of Open Source Software based Computational Systems

Software systems are progressively being deployed in many facets of human life. The implication of the failure of such systems, has an assorted impact on its customers. The fundamental aspect that supports a software system, is focus on quality. Reliability describes the ability of the system to function under specified environment for a specified period of time and is used to objectively measure the quality. Evaluation of reliability of a computing system involves computation of hardware and software reliability. Most of the earlier works were given focus on software reliability with no consideration for hardware parts or vice versa. However, a complete estimation of reliability of a computing system requires these two elements to be considered together, and thus demands a combined approach. The present work focuses on this and presents a model for evaluating the reliability of a computing system. The method involves identifying the failure data for hardware components, software components and building a model based on it, to predict the reliability. To develop such a model, focus is given to the systems based on Open Source Software, since there is an increasing trend towards its use and only a few studies were reported on the modeling and measurement of the reliability of such products. The present work includes a thorough study on the role of Free and Open Source Software, evaluation of reliability growth models, and is trying to present an integrated model for the prediction of reliability of a computational system. The developed model has been compared with existing models and its usefulness of is being discussed.

AFL-1: A Programming Language for Massively Concurrent Computers

Computational models are arising is which programs are constructed by specifying large networks of very simple computational devices. Although such models can potentially make use of a massive amount of concurrency, their usefulness as a programming model for the design of complex systems will ultimately be decided by the ease in which such networks can be programmed (constructed). This thesis outlines a language for specifying computational networks. The language (AFL-1) consists of a set of primitives, ad a mechanism to group these elements into higher level structures. An implementation of this language runs on the Thinking Machines Corporation, Connection machine. Two significant examples were programmed in the language, an expert system (CIS), and a planning system (AFPLAN). These systems are explained and analyzed in terms of how they compare with similar systems written in conventional languages.

A Computational Model for Observation in Quantum Mechanics

A computational model of observation in quantum mechanics is presented. The model provides a clean and simple computational paradigm which can be used to illustrate and possibly explain some of the unintuitive and unexpected behavior of some quantum mechanical systems. As examples, the model is used to simulate three seminal quantum mechanical experiments. The results obtained agree with the predictions of quantum mechanics (and physical measurements), yet the model is perfectly deterministic and maintains a notion of locality.

Computational Structure of Human Language

The central thesis of this report is that human language is NP-complete. That is, the process of comprehending and producing utterances is bounded above by the class NP, and below by NP-hardness. This constructive complexity thesis has two empirical consequences. The first is to predict that a linguistic theory outside NP is unnaturally powerful. The second is to predict that a linguistic theory easier than NP-hard is descriptively inadequate. To prove the lower bound, I show that the following three subproblems of language comprehension are all NP-hard: decide whether a given sound is possible sound of a given language; disambiguate a sequence of words; and compute the antecedents of pronouns. The proofs are based directly on the empirical facts of the language user's knowledge, under an appropriate idealization. Therefore, they are invariant across linguistic theories. (For this reason, no knowledge of linguistic theory is needed to understand the proofs, only knowledge of English.) To illustrate the usefulness of the upper bound, I show that two widely-accepted analyses of the language user's knowledge (of syntactic ellipsis and phonological dependencies) lead to complexity outside of NP (PSPACE-hard and Undecidable, respectively). Next, guided by the complexity proofs, I construct alternate linguisitic analyses that are strictly superior on descriptive grounds, as well as being less complex computationally (in NP). The report also presents a new framework for linguistic theorizing, that resolves important puzzles in generative linguistics, and guides the mathematical investigation of human language.

Computational Models of Object Recognition in Cortex: A Review

Understanding how biological visual systems perform object recognition is one of the ultimate goals in computational neuroscience. Among the biological models of recognition the main distinctions are between feedforward and feedback and between object-centered and view-centered. From a computational viewpoint the different recognition tasks - for instance categorization and identification - are very similar, representing different trade-offs between specificity and invariance. Thus the different tasks do not strictly require different classes of models. The focus of the review is on feedforward, view-based models that are supported by psychophysical and physiological data.

Public and student awareness science: recreational science as a catalyst

When discussing the traditional and new missions of higher education (1996 Report to UNESCO of the International Commission on Education for the 21st Century) Jacques Delors stated that "Excessive attraction to social sciences has broken equilibrium of available graduates for workforce, thus causing doubts of graduates and employers on the quality of knowledge provided by higher education". Likewise, when discussing the progress of science and technology, the 1998 UNESCO World Conference on Higher Education concluded that "Another challenge concerts the latest advancements of Science, the sine qua non of sustainable development"; and that “with Information Technology, the unavoidable invasion of virtual reality has increased the distance between industrial and developing countries". Recreational Science has a long tradition all over the Educational World; it aims to show the basic aspects of Science, aims to entertain, and aims to induce thinking. Until a few years ago, this field of knowledge consisted of a few books, a few kits and other classical (yet innovative) ways to popularize the knowledge of Nature and the laws governing it. In Spain, the interest for recreational science has increased in the last years. First, new recreational books are being published and found in bookstores. Second the number of Science-related museums and exhibits is increasing. And third, new television shows are produced and new short science-based, superficial sketches are found in variety programs. However, actual programs in Spanish television dealing seriously with Science are scarce. Recreational Science, especially that related to physical phenomena like light or motion, is generally found at Science Museums because special equipment is required. On the contrary, Science related mathematics, quizzes and puzzles use to gather into books, e.g. the extensive collections by Martin Gardner. However, lately Science podcasts have entered the field of science communication. Not only traditional science journals and television channels are providing audio and video podcasts, but new websites deal exclusively with science podcasts, in particular on Recreational Science. In this communication we discuss the above mentioned trends and show our experience in the last two years in participating at Science Fairs and university-sponsored events to attract students to science and technology careers. We show a combination of real examples (e.g., mathemagic), imagination, use of information technology, and use of social networks. We present as well an experience on designing a computational, interactive tool to promote chemistry among high school, prospective students using computers ("Dancing with Bionanomolecules"). Like the concepts related to Web 2.0, it has been already proposed that a new framework for communication of science is emerging, i.e., Science Communication 2.0, where people and institutions develop new innovative ways to explain science topics to diverse publics – and where Recreational Science is likely to play a leading role

Critical thinking as a self-regulatory process component in teaching and learning

Resumen tomado de la publicaci??n