Empirical modelling of products

Modelling - the activity of creating a representation of a physical object - has a very important role in modern product design. Modelling has benefited greatly from the use of a computational environment to construct models. We present here the concepts of an approach known as Empirical Modelling (EM) that offers an environment with a high level of interaction with a computer-based model. This environment allows the construction of models with a richness of interaction, openness and flexibility. Two case studies, simulating real products, are used to show how the interesting principles of EM can be applied in the development of tools to support product modelling. The application of EM in an educational environment is also discussed

A machine learning based framework to identify and classify long terminal repeat retrotransposons

Transposable elements (TEs) are repetitive nucleotide sequences that make up a large portion of eukaryotic genomes. They can move and duplicate within a genome, increasing genome size and contributing to genetic diversity within and across species. Accurate identification and classification of TEs present in a genome is an important step towards understanding their effects on genes and their role in genome evolution. We introduce TE-LEARNER, a framework based on machine learning that automatically identifies TEs in a given genome and assigns a classification to them. We present an implementation of our framework towards LTR retrotransposons, a particular type of TEs characterized by having long terminal repeats (LTRs) at their boundaries. We evaluate the predictive performance of our framework on the well-annotated genomes of Drosophila melanogaster and Arabidopsis thaliana and we compare our results for three LTR retrotransposon superfamilies with the results of three widely used methods for TE identification or classification: REPEATMASKER, CENSOR and LTRDIGEST. In contrast to these methods, TE-LEARNER is the first to incorporate machine learning techniques, outperforming these methods in terms of predictive performance , while able to learn models and make predictions efficiently. Moreover, we show that our method was able to identify TEs that none of the above method could find, and we investigated TE-LEARNER'S predictions which did not correspond to an official annotation. It turns out that many of these predictions are in fact strongly homologous to a known TE

Antiferromagnetic Ising model in small-world networks

The antiferromagnetic Ising model in small-world networks generated from two-dimensional regular lattices has been studied. The disorder introduced by long-range connections causes frustration, which gives rise to a spin-glass phase at low temperature. Monte Carlo simulations have been carried out to study the paramagnetic to spin-glass transition, as a function of the rewiring probability p, which measures the disorder strength. The transition temperature Tc goes down for increasing disorder, and saturates to a value Tc ~ 1.7 J for p > 0.4, J being the antiferromagnetic coupling. For small p and at low temperature, the energy increases linearly with p. In the strong-disorder limit p=1, this model is equivalent to a short-range +-J spin glass in random networks.Comment: 8 pages, 8 figure

Analog gravity from field theory normal modes?

We demonstrate that the emergence of a curved spacetime ``effective Lorentzian geometry'' is a common and generic result of linearizing a field theory around some non-trivial background. This investigation is motivated by considering the large number of ``analog models'' of general relativity that have recently been developed based on condensed matter physics, and asking whether there is something more fundamental going on. Indeed, linearization of a classical field theory (a field theoretic ``normal mode analysis'') results in fluctuations whose propagation is governed by a Lorentzian-signature curved spacetime ``effective metric''. For a single scalar field, this procedure results in a unique effective metric, which is quite sufficient for simulating kinematic aspects of general relativity (up to and including Hawking radiation). Quantizing the linearized fluctuations, the one-loop effective action contains a term proportional to the Einstein--Hilbert action, suggesting that while classical physics is responsible for generating an ``effective geometry'', quantum physics can be argued to induce an ``effective dynamics''. The situation is strongly reminiscent of Sakharov's ``induced gravity'' scenario, and suggests that Einstein gravity is an emergent low-energy long-distance phenomenon that is insensitive to the details of the high-energy short-distance physics. (We mean this in the same sense that hydrodynamics is a long-distance emergent phenomenon, many of whose predictions are insensitive to the short-distance cutoff implicit in molecular dynamics.)Comment: Revtex 4 (beta 5); 12 pages in single-column forma

Ultrafast Structural Dynamics of BlsA, a Photoreceptor from the Pathogenic Bacterium Acinetobacter baumannii

Acinetobacter baumannii is an important human pathogen that can form biofilms and persist under harsh environmental conditions. Biofilm formation and virulence are modulated by blue light, which is thought to be regulated by a BLUF protein, BlsA. To understand the molecular mechanism of light sensing, we have used steady-state and ultrafast vibrational spectroscopy to compare the photoactivation mechanism of BlsA to the BLUF photosensor AppA from Rhodobacter sphaeroides. Although similar photocycles are observed, vibrational data together with homology modeling identify significant differences in the β5 strand in BlsA caused by photoactivation, which are proposed to be directly linked to downstream signaling

COL11A1 in FAP polyps and in sporadic colorectal tumors

BACKGROUND: We previously reported that the α-1 chain of type 11 collagen (COL11A1), not normally expressed in the colon, was up-regulated in stromal fibroblasts in most sporadic colorectal carcinomas. Patients with germline mutations in the APC gene show, besides colonic polyposis, symptoms of stromal fibroblast involvement, which could be related to COL11A1 expression. Most colorectal carcinomas are suggested to be a result of an activated Wnt- pathway, most often involving an inactivation of the APC gene or activation of β-catenin. METHODS: We used normal and polyp tissue samples from one FAP patient and a set of 37 sporadic colorectal carcinomas to find out if the up-regulation of COL11A1 was associated with an active APC/β-catenin pathway. RESULTS: In this study we found a statistically significant difference in COL11A1 expression between normal tissue and adenomas from one FAP patient, and all adenomas gave evidence for an active APC/β-catenin pathway. An active Wnt pathway has been suggested to involve stromal expression of WISP-1. We found a strong correlation between WISP-1 and COL11A1 expression in sporadic carcinomas. CONCLUSIONS: Our results suggest that expression of COL11A1 in colorectal tumors could be associated with the APC/β-catenin pathway in FAP and sporadic colorectal cancer

La teledetección como herramienta para la prevención, seguimiento y evaluación de incendios e inundaciones

Los incendios y las inundaciones son dos de los disturbios que más frecuentemente afectan a la población humana y a los recursos naturales. La teledetección, a través de sensores remotos activos y pasivos, constituye una herramienta muy útil para el desarrollo de sistemas de prevención, seguimiento y evaluación a diferentes escalas espaciales y temporales. En este trabajo se reseñan algunos de los principales avances logrados en el campo de la teledetección de áreas quemadas e inundadas, y en el análisis de sus condiciones predisponentes y de su dinámica posterior a la perturbación. Se ha dado especial énfasis en describir los alcances y las limitaciones de algunos productos derivados de la teledetección que ya están disponibles para los usuarios en general.Fires and floods are among the most frequent perturbations that negatively affect human societies and natural resources. The availability of prevention, monitoring and evaluation systems is therefore crucial to diminish their consequences. Active and passive remote sensing instruments are a valuable tool to achieve these goals because they provide information on different spatial and temporal scales. In this article we review the progress experienced in the field of remote sensing of burnt or flooded areas, its predisposing conditions and its post perturbation dynamics. Special emphasis is given to the description of the strengths and weaknesses of some of currently available remote sensing products.Fil: Di Bella, Carlos Marcelo. Instituto Nacional de Tecnología Agropecuaria (INTA). Instituto de Clima y Agua; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina.Fil: Posse Beaulieu, Gabriela. Instituto Nacional de Tecnología Agropecuaria (INTA). Instituto de Clima y Agua; ArgentinaFil: Beget, Maria Eugenia. Instituto Nacional de Tecnología Agropecuaria (INTA). Instituto de Clima y Agua; Argentina.Fil: Fisher, María de los Angeles. Instituto Nacional de Tecnología Agropecuaria (INTA). Instituto de Clima y Agua; ArgentinaFil: Mari, Nicolás Alejandro. Instituto Nacional de Tecnología Agropecuaria (INTA). Instituto de Clima y Agua, Hurlingham, ArgentinaFil: Verón, S. Instituto Nacional de Tecnología Agropecuaria (INTA). Instituto de Clima y Agua; Argentin

Somatostatin subtype-2 receptor-targeted metal-based anticancer complexes

Conjugates of a dicarba analogue of octreotide, a potent somatostatin agonist whose receptors are overexpressed on tumor cells, with [PtCl 2(dap)] (dap = 1-(carboxylic acid)-1,2-diaminoethane) (3), [(η 6-bip)Os(4-CO 2-pico)Cl] (bip = biphenyl, pico = picolinate) (4), [(η 6-p-cym)RuCl(dap)] + (p-cym = p-cymene) (5), and [(η 6-p-cym)RuCl(imidazole-CO 2H)(PPh 3)] + (6), were synthesized by using a solid-phase approach. Conjugates 3-5 readily underwent hydrolysis and DNA binding, whereas conjugate 6 was inert to ligand substitution. NMR spectroscopy and molecular dynamics calculations showed that conjugate formation does not perturb the overall peptide structure. Only 6 exhibited antiproliferative activity in human tumor cells (IC 50 = 63 ± 2 μ in MCF-7 cells and IC 50 = 26 ± 3 μ in DU-145 cells) with active participation of somatostatin receptors in cellular uptake. Similar cytotoxic activity was found in a normal cell line (IC 50 = 45 ± 2.6 μ in CHO cells), which can be attributed to a similar level of expression of somatostatin subtype-2 receptor. These studies provide new insights into the effect of receptor-binding peptide conjugation on the activity of metal-based anticancer drugs, and demonstrate the potential of such hybrid compounds to target tumor cells specifically. © 2012 American Chemical Society

Search for direct production of charginos and neutralinos in events with three leptons and missing transverse momentum in √s = 7 TeV pp collisions with the ATLAS detector

A search for the direct production of charginos and neutralinos in final states with three electrons or muons and missing transverse momentum is presented. The analysis is based on 4.7 fb−1 of proton–proton collision data delivered by the Large Hadron Collider and recorded with the ATLAS detector. Observations are consistent with Standard Model expectations in three signal regions that are either depleted or enriched in Z-boson decays. Upper limits at 95% confidence level are set in R-parity conserving phenomenological minimal supersymmetric models and in simplified models, significantly extending previous results