Search results for "20(60)"

SpaceScanner: COPASI wrapper for automated management of global stochastic optimization experiments

2017

Abstract Motivation Due to their universal applicability, global stochastic optimization methods are popular for designing improvements of biochemical networks. The drawbacks of global stochastic optimization methods are: (i) no guarantee of finding global optima, (ii) no clear optimization run termination criteria and (iii) no criteria to detect stagnation of an optimization run. The impact of these drawbacks can be partly compensated by manual work that becomes inefficient when the solution space is large due to combinatorial explosion of adjustable parameters or for other reasons. Results SpaceScanner uses parallel optimization runs for automatic termination of optimization tasks in case…

Fractional hereditariness of lipid membranes: Instabilities and linearized evolution

2016

In this work lipid ordering phase changes arising in planar membrane bilayers is investigated both accounting for elas- ticity alone and for effective viscoelastic response of such assemblies. The mechanical response of such membranes is studied by minimizing the Gibbs free energy which penalizes perturbations of the changes of areal stretch and their gradients only [1]. As material instabilities arise whenever areal stretches characterizing homogeneous configurations lie inside the spinoidal zone of the free energy density, bifurcations from such configurations are shown to occur as oscillatory perturbations of the in-plane displacement. Experimental observations [2] show a power-law in-pl…

Automated detection of protein unfolding events in atomic force microscopy force curves

2016

Atomic force microscopy is not only a high-resolution imaging device but also a mechanical machine, which can be used either to indent or stretch (soft) biomaterials. Due to the statistical nature of such materials (i.e., hydrogels or polymers) hundreds of force-distance curves are required to describe their mechanical properties. In this manuscript, we present an automated system for polymer unfolding detection based on continuous wavelet analysis. We have tested the automated program on elastin, which is an important protein that provides elasticity to tissues and organs. Our results show that elastin changes its mechanical behavior in the presence of electrolytes. In particular, we show …

How to deal with Haplotype data: An Extension to the Conceptual Schema of the Human Genome

2016

[EN] The goal of this work is to describe the advantages of the application of Conceptual Modeling (CM) in complex domains, such as genomics. Nowadays, the study and comprehension of the human genome is a major challenge due to its high level of complexity. The constant evolution in the genomic domain contributes to the generation of ever larger amounts of new data, which means that if we do not manage it correctly data quality could be compromised (i.e., problems related with heterogeneity and inconsistent data). In this paper, we propose the use of a Conceptual Schema of the Human Genome (CSHG), designed to understand and improve our ontological commitment to the domain and also extend (e…

In Vivo Articular Cartilage Regeneration Using Human Dental Pulp Stem Cells Cultured in an Alginate Scaffold: A Preliminary Study

2017

Osteoarthritis is an inflammatory disease in which all joint-related elements, articular cartilage in particular, are affected. The poor regeneration capacity of this tissue together with the lack of pharmacological treatment has led to the development of regenerative medicine methodologies including microfracture and autologous chondrocyte implantation (ACI). The effectiveness of ACI has been shown in vitro and in vivo, but the use of other cell types, including bone marrow and adipose-derived mesenchymal stem cells, is necessary because of the poor proliferation rate of isolated articular chondrocytes. In this investigation, we assessed the chondrogenic ability of human dental pulp stem c…

Paving the way for synthetic biology-based bioremediation in Europe

2009

Synthetic biology (SB) has a dual definition. It is both the design and construction of new biological parts, devices and systems, and also the re‐design of existing, natural systems for useful purposes. The latter field is maybe one of the major challenges within this discipline, since the promising prospect that biological systems may be used as biomachines will certainly be exploited in the near future. Synthetic biology has challenging conceptual possibilities (Moya et al., 2009a) and impressive progress has already been made in biotechnology following SB approaches (de Lorenzo and Danchin, 2008). Much more is expected in the near future from current efforts aiming to make synthetic gen…

Primary Mucosal Epithelial Cell Cultivation: A Reliable and Accelerated Isolation

2019

We illustrate a reliable and accelerated isolation routine for mucosal epithelial cells, which thereupon can be used for soft tissue engineering. This is highly important in the field of soft tissue engineering because mucosal equivalents are frequently usable in several surgical fields like gynecology, urology, otorhinolaryngology, ophthalmology, maxillofacial surgery, and many others. In this context the isolation of mucosal epithelial cells suitable for tissue engineering is mandatory. The reliable cultivation of mucosal or skin epithelial cells is challenging and there is currently no reproducible method. We demonstrate a solution for this problem by developing an accelerated and nevert…

MAGA: A Supervised Method to Detect Motifs From Annotated Groups in Alignments

2020

Multiple sequence alignments are usually phylogenetically driven. They are studied in the framework of evolution. But sometimes, it is interesting to study residue conservation at positions unconstrained by evolutionary rules. We present a supervised method to access a layer of information difficult to appreciate visually when many protein sequences are aligned. This new tool (MAGA; http://cbdm-01.zdv.uni-mainz.de/~munoz/maga/ ) locates positions in multiple sequence alignments differentially conserved in manually defined groups of sequences.

Deep Neural Network Frontend for Continuous EMG-Based Speech Recognition

2016

Anilato-based multifunctional molecular materials

2018

En esta Tesis presentamos varias series de compuestos moleculares basados en el ligando anilato (anilato = C6O4X22- = 2,5-disustituida-3,6-dihidroxi-1,4-benzoquinona) y diferentes átomos metálicos incluyendo metales de los bloques s, p, d y f. En el capítulo uno presentamos la síntesis y caracterización de nuevas sales precursoras, basadas en el ligando anilato, con fórmula general A3[M(C6O4X2)3]; (MIII = Fe, Cr y Ga; X = Cl, Br and NO2). Hemos usado diferentes cationes A+ (A = K+, [PPh3Et]+, [PPh3Pr]+, [PBu4]+, [NBu4]+, [NHep4]+, [PPh4]+ y K+, compuestos 1-20) para estudiar el papel que juega la forma y el tamaño del catión en la estructura y simetría de las correspondientes sales. Este es…