SciTech News Volume 71, No. 2 (2017)

Columns and Reports From the Editor 3 Division News Science-Technology Division 5 Chemistry Division 8 Engineering Division 9 Aerospace Section of the Engineering Division 12 Architecture, Building Engineering, Construction and Design Section of the Engineering Division 14 Reviews Sci-Tech Book News Reviews 16 Advertisements IEEE

Using Isabelle/HOL to verify first-order relativity theory

Logicians at the Rényi Mathematical Institute in Budapest have spent several years developing versions of relativity theory (special, general, and other variants) based wholly on first-order logic, and have argued in favour of the physical decidability, via exploitation of cosmological phenomena, of formally unsolvable questions such as the Halting Problem and the consistency of set theory. As part of a joint project, researchers at Sheffield have recently started generating rigorous machine-verified versions of the Hungarian proofs, so as to demonstrate the soundness of their work. In this paper, we explain the background to the project and demonstrate a first-order proof in Isabelle/HOL of the theorem “no inertial observer can travel faster than light”. This approach to physical theories and physical computability has several pay-offs, because the precision with which physical theories need to be formalised within automated proof systems forces us to recognise subtly hidden assumptions

Membrane Computing as a Modeling Framework. Cellular Systems Case Studies

Membrane computing is a branch of natural computing aiming to abstract computing models from the structure and functioning of the living cell, and from the way cells cooperate in tissues, organs, or other populations of cells. This research area developed very fast, both at the theoretical level and in what concerns the applications. After a very short description of the domain, we mention here the main areas where membrane computing was used as a framework for devising models (biology and bio-medicine, linguistics, economics, computer science, etc.), then we discuss in a certain detail the possibility of using membrane computing as a high level computational modeling framework for addressing structural and dynamical aspects of cellular systems. We close with a comprehensive bibliography of membrane computing applications

SYNTHESIS AND EVALUATION OF ANTIMICROBIAL ACTIVITY OF PHENYL AND FURAN-2-YL[1,2,4] TRIAZOLO[4,3-a]QUINOXALIN-4(5H)-ONE AND THEIR HYDRAZONE PRECURSORS

A variety of 1-(s-phenyl)-[1,2,4]triazolo[4,3-a]quinoxalin-4(5H)-one (3a-3h) and 1-(s-furan-2-yl)-[1,2,4]triazolo[4,3- a]quinoxalin-4(5H)-one (5a-d) were synthesized from thermal annelation of corresponding hydrazones (2a-h) and (4a-d) respectively in the presence of ethylene glycol which is a high boiling solvent. The structures of the compounds prepared were confirmed by analytical and spectral data. Also, the newly synthesized compounds were evaluated for possible antimicrobial activity. 3-(2-(4-hydroxylbenzylidene)hydrazinyl)quinoxalin-2(1H)-one (2e) was the most active antibacterial agent while 1-(5-Chlorofuran-2-yl)-[1,2,4]triazolo[4,3-a]quinoxalin-4(5H)-one (5c) stood out as the most potent antifungal agent

Stepping Beyond the Newtonian Paradigm in Biology. Towards an Integrable Model of Life: Accelerating Discovery in the Biological Foundations of Science

The INBIOSA project brings together a group of experts across many disciplines who believe that science requires a revolutionary transformative step in order to address many of the vexing challenges presented by the world. It is INBIOSA’s purpose to enable the focused collaboration of an interdisciplinary community of original thinkers. This paper sets out the case for support for this effort. The focus of the transformative research program proposal is biology-centric. We admit that biology to date has been more fact-oriented and less theoretical than physics. However, the key leverageable idea is that careful extension of the science of living systems can be more effectively applied to some of our most vexing modern problems than the prevailing scheme, derived from abstractions in physics. While these have some universal application and demonstrate computational advantages, they are not theoretically mandated for the living. A new set of mathematical abstractions derived from biology can now be similarly extended. This is made possible by leveraging new formal tools to understand abstraction and enable computability. [The latter has a much expanded meaning in our context from the one known and used in computer science and biology today, that is "by rote algorithmic means", since it is not known if a living system is computable in this sense (Mossio et al., 2009).] Two major challenges constitute the effort. The first challenge is to design an original general system of abstractions within the biological domain. The initial issue is descriptive leading to the explanatory. There has not yet been a serious formal examination of the abstractions of the biological domain. What is used today is an amalgam; much is inherited from physics (via the bridging abstractions of chemistry) and there are many new abstractions from advances in mathematics (incentivized by the need for more capable computational analyses). Interspersed are abstractions, concepts and underlying assumptions “native” to biology and distinct from the mechanical language of physics and computation as we know them. A pressing agenda should be to single out the most concrete and at the same time the most fundamental process-units in biology and to recruit them into the descriptive domain. Therefore, the first challenge is to build a coherent formal system of abstractions and operations that is truly native to living systems. Nothing will be thrown away, but many common methods will be philosophically recast, just as in physics relativity subsumed and reinterpreted Newtonian mechanics. This step is required because we need a comprehensible, formal system to apply in many domains. Emphasis should be placed on the distinction between multi-perspective analysis and synthesis and on what could be the basic terms or tools needed. The second challenge is relatively simple: the actual application of this set of biology-centric ways and means to cross-disciplinary problems. In its early stages, this will seem to be a “new science”. This White Paper sets out the case of continuing support of Information and Communication Technology (ICT) for transformative research in biology and information processing centered on paradigm changes in the epistemological, ontological, mathematical and computational bases of the science of living systems. Today, curiously, living systems cannot be said to be anything more than dissipative structures organized internally by genetic information. There is not anything substantially different from abiotic systems other than the empirical nature of their robustness. We believe that there are other new and unique properties and patterns comprehensible at this bio-logical level. The report lays out a fundamental set of approaches to articulate these properties and patterns, and is composed as follows. Sections 1 through 4 (preamble, introduction, motivation and major biomathematical problems) are incipient. Section 5 describes the issues affecting Integral Biomathics and Section 6 -- the aspects of the Grand Challenge we face with this project. Section 7 contemplates the effort to formalize a General Theory of Living Systems (GTLS) from what we have today. The goal is to have a formal system, equivalent to that which exists in the physics community. Here we define how to perceive the role of time in biology. Section 8 describes the initial efforts to apply this general theory of living systems in many domains, with special emphasis on crossdisciplinary problems and multiple domains spanning both “hard” and “soft” sciences. The expected result is a coherent collection of integrated mathematical techniques. Section 9 discusses the first two test cases, project proposals, of our approach. They are designed to demonstrate the ability of our approach to address “wicked problems” which span across physics, chemistry, biology, societies and societal dynamics. The solutions require integrated measurable results at multiple levels known as “grand challenges” to existing methods. Finally, Section 10 adheres to an appeal for action, advocating the necessity for further long-term support of the INBIOSA program. The report is concluded with preliminary non-exclusive list of challenging research themes to address, as well as required administrative actions. The efforts described in the ten sections of this White Paper will proceed concurrently. Collectively, they describe a program that can be managed and measured as it progresses

31th International Conference on Information Modelling and Knowledge Bases

Information modelling is becoming more and more important topic for researchers, designers, and users of information systems.The amount and complexity of information itself, the number of abstractionlevels of information, and the size of databases and knowledge bases arecontinuously growing. Conceptual modelling is one of the sub-areas ofinformation modelling. The aim of this conference is to bring together experts from different areas of computer science and other disciplines, who have a common interest in understanding and solving problems on information modelling and knowledge bases, as well as applying the results of research to practice. We also aim to recognize and study new areas on modelling and knowledge bases to which more attention should be paid. Therefore philosophy and logic, cognitive science, knowledge management, linguistics and management science are relevant areas, too. In the conference, there will be three categories of presentations, i.e. full papers, short papers and position papers

Turku Centre for Computer Science – Annual Report 2013

Due to a major reform of organization and responsibilities of TUCS, its role, activities, and even structures have been under reconsideration in 2013. The traditional pillar of collaboration at TUCS, doctoral training, was reorganized due to changes at both universities according to the renewed national system for doctoral education. Computer Science and Engineering and Information Systems Science are now accompanied by Mathematics and Statistics in newly established doctoral programs at both University of Turku and &Aring;bo Akademi University. Moreover, both universities granted sufficient resources to their respective programmes for doctoral training in these fields, so that joint activities at TUCS can continue. The outcome of this reorganization has the potential of proving out to be a success in terms of scientific profile as well as the quality and quantity of scientific and educational results.&nbsp; International activities that have been characteristic to TUCS since its inception continue strong. TUCS&rsquo; participation in European collaboration through EIT ICT Labs Master&rsquo;s and Doctoral School is now more active than ever. The new double degree programs at MSc and PhD level between University of Turku and Fudan University in Shaghai, P.R.China were succesfully set up and are&nbsp; now running for their first year. The joint students will add to the already international athmosphere of the ICT House.&nbsp; The four new thematic reseach programmes set up acccording to the decision by the TUCS Board have now established themselves, and a number of events and other activities saw the light in 2013. The TUCS Distinguished Lecture Series managed to gather a large audience with its several prominent speakers. The development of these and other research centre activities continue, and&nbsp; new practices and structures will be initiated to support the tradition of close academic collaboration.&nbsp; The TUCS&rsquo; slogan Where Academic Tradition Meets the Exciting Future has proven true throughout these changes. Despite of the dark clouds on the national and European economic sky, science and higher education in the field have managed to retain all the key ingredients for success. Indeed, the future of ICT and Mathematics in Turku seems exciting.</p

To salt or not to salt : three MALDI-TOF IMS protocols where (de)salting proved essential

Présentement, la désorption ionisation laser assistée par la matrice (MALDI) est la méthode d’ionisation préférentielle pour étudier les lipides par l’imagerie par spectrométrie de masse (IMS). Bien qu’il existe les matrices spécifiques aux lipides, tel que la 1,5-DAN pour les phospholipides et la 2,5-DHB pour les triacylglycérols, il est toujours nécessaire d’augmenter la sensibilité de cette technique pour les échantillons atypiques ou certaines classes de lipides. Dans la première étude, nous avons amélioré la sensitivité pour les phospholipides sur les tubes de Malpighi de mouches prélevés par microdissection dans un tampon physiologique à base de sodium et potassium. Un protocole de lavage à deux étapes a était trouvé favorable : un premier rinçage dans le glycérol suivi d’un second rinçage dans l’acétate d’ammonium. Ce protocole permet de réduire au maximum la présence de sels sans délocalisation notoire des phospholipides. La détection et l’imagerie des phospholipides en ionisation négative et positive ont suggéré une distribution uniforme sur toute la longueur des tubes. Ces résultats ont été comparés à ceux obtenus sur des sections tissulaires minces de mouche entière acquis avec les deux polarités. Néanmoins, la structure tridimensionnelle complexe des tubes rénaux suggère que la microdissection est l’approche la plus favorable pour en étudier leur lipidome. Dans la deuxième étude, nous avons déterminé que l’addition de formate d’ammonium (AF) peut améliorer la détection des gangliosides par IMS dans le cerveau. Curieusement, il est nécessaire de rincer l’échantillon dans une solution d’AF avant l’addition de ce même sel suivit d’une conservation de l’échantillon dans un congélateur pendant 24 heures après la déposition de la matrice afin d’obtenir la meilleure augmentation de sensibilité. En moyenne, cette approche a permis d’augmenter l’intensité d’un facteur dix avec trois fois plus d’espèces de gangliosides détectées. De plus, malgré l’étape de lavage, nous n’avons pas observé la délocalisation des gangliosides puisqu’il est toujours possible d’obtenir les résultats d’IMS de qualité avec une résolution spatiale de 20 µm. Finalement, nous avons établi que le nitrate d’argent permet l’analyse des oléfines par IMS, en particulier du cholestérol. En optimisant le protocole de déposition par nébulisation, il est possible de générer une couche mince et homogène de nitrate d’argent ce qui rend la possibilité d’effectuer l’IMS à haute résolution spatiale, jusqu’à 10 µm, sans perte de qualité comparativement aux autres approches publiées. L’ensemble de ce travail démontre l’effet du sel sur la sélectivité et la sensibilité pour cibler les familles de lipides désirées, ce qui nécessite les études ultérieures sur le rôle de ces sels lors du processus de la désorption-ionisation.Matrix-assisted laser desorption/ionization imaging mass spectrometry (MALDI IMS) is currently the ionization method of choice for elucidating the spatial distribution of lipids on thin tissue sections. Despite the discovery of lipid friendly matrices such as 1,5-DAN for phospholipids and 2,5-DHB for triacylglycerols, there is a continued need to improve sensitivity. In the first study, we improved the overall sensitivity for phospholipids of entire fly Malpighian tubules microdissected in PBS with a two-step wash in glycerol followed by ammonium acetate that removed the bulk of the salt with minimal species delocalization and tubule displacement. We were able to detect phospholipids in both positive and negative ion modes and revealed an even distribution of most phospholipids along the length of this organ. We compared the method to the results from whole body fly sections acquired in dual-polarity mode at the same spatial resolution and found it to be more suitable for studying the tubules because of the complex three-dimensional structure of this organ within the fly. In the second study, we observed a marked improvement in ganglioside signals on mouse brain tissue sections with ammonium salt addition. Specifically, when the sample was first desalted in a low concentration ammonium formate solution, spray-coated with the same salt, coated with matrix and finally left in the freezer overnight before data acquisition, we observed an average overall improvement in ganglioside signal intensity by ten-fold and the number of species detected by three-fold. This method also did not affect the spatial distribution of the gangliosides, as high spatial resolution IMS results acquired at 20 µm showed no species delocalization. Finally, we sought to determine if salts could be employed directly as matrices. In this work, we tested silver-based metal salts and discovered that spray depositing silver nitrate alone is a viable method for the IMS detection of olefins, particularly cholesterol. With the optimized dry spray parameter, the overall deposition is homogeneous and composed of microscopic salt crystals that allow for high spatial resolution IMS down to 10 µm while maintaining acceptable overall signal quality comparable to that of previously published protocols. Overall, this thesis demonstrates we can manipulate the local salt distribution to influence the sensitivity and selectivity to target specific lipid subfamilies, opening the door for future research to understanding the role salts play during the laser desorption/ionization process