Search results for "computational"
showing 10 items of 5884 documents
gNOMO: a multi-omics pipeline for integrated host and microbiome analysis of non-model organisms
2020
The study of bacterial symbioses has grown exponentially in the recent past. However, existing bioinformatic workflows of microbiome data analysis do commonly not integrate multiple meta-omics levels and are mainly geared toward human microbiomes. Microbiota are better understood when analyzed in their biological context; that is together with their host or environment. Nevertheless, this is a limitation when studying non-model organisms mainly due to the lack of well-annotated sequence references. Here, we present gNOMO, a bioinformatic pipeline that is specifically designed to process and analyze non-model organism samples of up to three meta-omics levels: metagenomics, metatranscriptomic…
Between Interactions and Aggregates: The PolyQ Balance
2021
Abstract Polyglutamine regions (polyQ) are highly abundant consecutive runs of glutamine residues. They have been generally studied in relation to the so-called polyQ-associated diseases, characterized by protein aggregation caused by the expansion of the polyglutamine tract via a CAG-slippage mechanism. However, more than 4800 human proteins contain a polyQ, and only 9 of these regions are known to be associated with disease. Computational sequence studies and experimental structure determinations are completing a more interesting picture in which polyQ emerge as a motif for modulation of protein-protein interactions. But long polyQ regions may lead to an excess of interactions, and produc…
Characterization and Tuning of Ultra High Gradient Permanent Magnet Quadrupoles
2009
The application of quadrupole devices with high field gradients and small apertures requires precise control over higher order multipole field components. We present a new scheme for performance control and tuning, which allows the illumination of most of the quadrupole device aperture because of the reduction of higher order field components. Consequently, the size of the aperture can be minimized to match the beam size achieving field gradients of up to $500\text{ }\text{ }\mathrm{T}\text{ }{\mathrm{m}}^{\ensuremath{-}1}$ at good imaging quality. The characterization method based on a Hall probe measurement and a Fourier analysis was confirmed using the high quality electron beam at the M…
Acetogenins from Annonaceae: Recent Progress in Isolation, Synthesis and Mechanisms of Action
2005
Covering: the literature from 1998 to 2004 The aim of the present review is to summarise the knowledge about newly isolated acetogenins (ACGs) in the last six years. It will also report the total syntheses that have allowed either the confirmation or the revision of some structures, together with the biological activities and mechanism of action of such interesting natural products. In fact, of the 417 isolated compounds reviewed, over 176 have been added during the period from 1998 to 2004.
A SYMMETRIC AND POSITIVE DEFINITE BEM FOR 2-D FORCED VIBRATIONS
1997
A BEM formulation for 2D elastodynamics in the time domain has been presented. The formulation gives a resolving system that involves boundary displacements only. The stiffness and mass matrices of the boundary discretized body are frequency independent, symmetric and positive definite
Incorporation of Li dopant into Cu2ZnSnSe4 photovoltaic absorber: hybrid-functional calculations
2015
We have studied the formation of Li extrinsic defects in CuZnSnSe by first-principles hybrid functional calculations. Li atoms in the Cu site (Li) and Li atoms in the Se site (Li) are the most and the least stable point defect, respectively. The formation energies of two Li interstitial defects with different numbers of nearest neighbors are the same. These interstitial point defects act as a donor but do not create gap states. Formation of the acceptor point defects (Li and Li) is less likely in p-type CuZnSnSe compared with n-type CuZnSnSe. In contrast to Li which does not create gap states, the formation of Li creates two charge transition levels in the middle of the bandgap which might …
A series expansion of the extended Debye-H�ckel equation and application to linear prediction of stability constants
1996
The Debye-Hückel semiempirical extended equation is frequently used to calculate activity coefficients of chemical species and equilibrium constants at ionic strengths different from those used in their experimental evaluation. A series expansion of the extended Debye-Hückel equation is proposed here and checked with experimental data taken from the literature. The expansion is linear in the ionic parameters and yields a geometrical series which converges rapidly and that enables the accurate calculation of interpolated and extrapolated activity coefficients and equilibrium constants by simple and multiple linear regression without previous knowledge of the ionic parameters.
A fuzzy ranking strategy for portfolio selection applied to the Spanish stock market
2007
In this paper we present a fuzzy ranking procedure for the portfolio selection problem. The uncertainty on the returns of each portfolio is approximated by means of a trapezoidal fuzzy number. The expected return and risk of the portfolio are then characteristics of that fuzzy number. A rank index that accounts for both expected return and risk is defined, allowing the decision-maker to compare different portfolios. The paper ends with an application of that fuzzy ranking strategy to the Spanish stock market.
A quantum mechanics/molecular mechanics study of the acylation reaction of TEM1 β-lactamase and penicillanate
2000
The acylation step in β-lactamase catalyzed hydrolysis of β-lactams has been explored by means of a quantum mechanics/molecular mechanics approach (AM1/CHARMM). The TEM1 enzyme, a class A β-lactamase, and the penicillanate constitute the system employed in our study. The entire molecular system is divided into a quantum and a classical region: the quantum part is composed by the substrate, the serine Ser70 and the essential moieties of key active site residues, Lys73, Ser130 and Glu166, as well as a water molecule present in the active site region, while the classical part is formed by the remaining residues and structural waters of the enzyme. In particular, the sequence of steps proposed …
Customised next-generation sequencing multigene panel to screen a large cohort of individuals with chromatin-related disorder
2020
BackgroundThe regulation of the chromatin state by epigenetic mechanisms plays a central role in gene expression, cell function, and maintenance of cell identity. Hereditary disorders of chromatin regulation are a group of conditions caused by abnormalities of the various components of the epigenetic machinery, namely writers, erasers, readers, and chromatin remodelers. Although neurological dysfunction is almost ubiquitous in these disorders, the constellation of additional features characterizing many of these genes and the emerging clinical overlap among them indicate the existence of a community of syndromes. The introduction of high-throughput next generation sequencing (NGS) methods f…