Beyond element-wise interactions: identifying complex interactions in biological processes

Background: Biological processes typically involve the interactions of a number of elements (genes, cells) acting on each others. Such processes are often modelled as networks whose nodes are the elements in question and edges pairwise relations between them (transcription, inhibition). But more often than not, elements actually work cooperatively or competitively to achieve a task. Or an element can act on the interaction between two others, as in the case of an enzyme controlling a reaction rate. We call “complex” these types of interaction and propose ways to identify them from time-series observations. Methodology: We use Granger Causality, a measure of the interaction between two signals, to characterize the influence of an enzyme on a reaction rate. We extend its traditional formulation to the case of multi-dimensional signals in order to capture group interactions, and not only element interactions. Our method is extensively tested on simulated data and applied to three biological datasets: microarray data of the Saccharomyces cerevisiae yeast, local field potential recordings of two brain areas and a metabolic reaction. Conclusions: Our results demonstrate that complex Granger causality can reveal new types of relation between signals and is particularly suited to biological data. Our approach raises some fundamental issues of the systems biology approach since finding all complex causalities (interactions) is an NP hard problem

Estimating Impact Forces of Tail Club Strikes by Ankylosaurid Dinosaurs

BACKGROUND: It has been assumed that the unusual tail club of ankylosaurid dinosaurs was used actively as a weapon, but the biological feasibility of this behaviour has not been examined in detail. Ankylosaurid tail clubs are composed of interlocking vertebrae, which form the handle, and large terminal osteoderms, which form the knob. METHODOLOGY/PRINCIPAL FINDINGS: Computed tomographic (CT) scans of several ankylosaurid tail clubs referred to Dyoplosaurus and Euoplocephalus, combined with measurements of free caudal vertebrae, provide information used to estimate the impact force of tail clubs of various sizes. Ankylosaurid tails are modeled as a series of segments for which mass, muscle cross-sectional area, torque, and angular acceleration are calculated. Free caudal vertebrae segments had limited vertical flexibility, but the tail could have swung through approximately 100 degrees laterally. Muscle scars on the pelvis record the presence of a large M. longissimus caudae, and ossified tendons alongside the handle represent M. spinalis. CT scans showed that knob osteoderms were predominantly cancellous, which would have lowered the rotational inertia of the tail club and made it easier to wield as a weapon. CONCLUSIONS/SIGNIFICANCE: Large knobs could generate sufficient force to break bone during impacts, but average and small knobs could not. Tail swinging behaviour is feasible in ankylosaurids, but it remains unknown whether the tail was used for interspecific defense, intraspecific combat, or both

Investigation of the effect of temper rolling on the texture evolution and mechanical behavior of IF steels using multiscale simulation

The main objective of this study is to simulate texture and deformation during the temper-rolling process. To this end, a rate-independent crystal plasticity model, based on the self-consistent scale-transition scheme, is adopted to predict texture evolution and deformation heterogeneity during temper-rolling process. For computational efficiency, a decoupled analysis is considered between the polycrystalline plasticity model and the finite element analysis for the temper rolling. The elasto-plastic finite element analysis is first carried out to determine the history of velocity gradient during the numerical simulation of temper rolling. The thus calculated velocity gradient history is subsequently applied to the polycrystalline plasticity model. By following some appropriately selected strain paths (i.e., streamlines) along the rolling process, one can predict the texture evolution of the material at the half thickness of the sheet metal as well as other parameters related to its microstructure. The numerical results obtained by the proposed strategy are compared with experimental data in the case of IF steels.French program “Investment in the future” operated by the National Research Agency (ANR)-11-LABX-0008-01, LabEx DAMAS (LST)

Methodology of calculation of construction and hydrodynamic parameters of a foam layer apparatus for mass-transfer processes

Промислова реалізація методу стабілізації газорідинного шару дозволяє значно розширити галузь застосування пінних апаратів і відкриває нові можливості інтенсифікації технологічних процесів з одночасним створенням маловідходних технологій. У статті встановлені основні параметри, що впливають на гідродинаміку пінних апаратів, розглянуті основні конструкції та режими роботи пінних апаратів. Виявлено зв'язок гідродинамічних параметрів. Розглянуто гідродинамічні закономірності пінного шару. Вказані фактори, що впливають на процес масообміну, як в газовій, так і в рідкій фазах. Проведений аналіз ряду досліджень показав, що перспективним напрямком інтенсифікації процесу масообміну є розробка апаратів з трифазним псевдозрідженим шаром зрошуваної насадки складних форм із сітчастих матеріалів. Отже, необхідне проведення спеціальних досліджень гідродинамічних режимів роботи апарату з сітчастою насадкою і визначенням параметрів, що впливають на швидкість переходу насадки з одного режиму в інший.Industrial implementation of the stabilization method of the gas-liquid layer can significantly expand the field of use of foaming apparatus and opens up new opportunities for intensifying technological processes with the simultaneous creation of low-waste technologies. The article establishes the basic parameters influencing the hydrodynamics of foam apparatus, considers the basic constructions and operating modes of foam apparatus. The connection of hydrodynamic parameters is revealed. The hydrodynamic laws of the foam layer are considered. The indicated factors affecting the process of mass transfer, both in the gas and in the liquid phases. The conducted analysis of a number of studies showed that the perspective direction of intensification of the mass transfer process is the development of apparatuses with a three-phase fluidized bed of an irrigated nozzle of complex forms with mesh materials

Justifying the methods of OR

Operational research practitioners use mathematical, statistical, scientific, and other methods to structure and analyse issues in order to advise and assist their clients. In doing so they apply values, follow rules and use methodologies. The paper examines the justification of these methods, values and methodologies. Starting with a conceptual model drawn from the philosophy of science, a justification framework is developed for operational research (OR). Making a distinction between OR academic research and OR practice helps to clarify the issues. OR research is similar to scientific, mathematical and social science research; OR practice, as technology, is closer to engineering. While OR academic researchers will seek justification in the academic discipline within which they choose to work, it is argued that the justification of OR practice lies in its usefulness. For academic OR, justification lies in the justification of mathematics, statistics, science and social science; for practice, it is practitioners who decide what usefulness means in their context. Journal of the Operational Research Society (2010) 61, 1694-1708. doi:10.1057/jors.2009.147 Published online 2 December 200

A.-T. Tymieniecka: A Phenomenologist in the United States. The Adventures of a Polish-Born American.

Of great philosophical import, albeit yet to be entirely enlarged upon, has been the encounter between European phenomenology and American thought that took place in A.-T. Tymieniecka's evolution of classical phenomenology into the phenomenology of life, her creation. When she arrived in the United States in the 1950\u2019s, Tymieniecka became convinced that it was necessary to move forward from the later thought of Husserl, in order to endow phenomenology with the more immediate pertinence and practical functionality that the American environment demanded of philosophical and scientific thought. In effect, the phenomenology of life that Tymieniecka developed in her over 40 years in America brought about a positive hybridisation of the American pragmatic attitude and Continental phenomenology, enhancing this last with regard to the methodological approach to knowledge and the relationship with science, and launching it into the search for new epistemic and ontological horizons, away from sterile speculativism. Her discovery of the ontopoietic logos of life as the propulsive and ordering force intrinsic in life, enabled her to break through the opposing prejudices of phenomenology and pragmatism, and to embark upon a theory in which the synergy between the phenomenological attitude and the practical attitude reached a high level of efficiency