1,745 research outputs found
Hierarchy and assortativity as new tools for affinity investigation: the case of the TBA aptamer-ligand complex
Aptamers are single stranded DNA, RNA or peptide sequences having the ability
to bind a variety of specific targets (proteins, molecules as well as ions).
Therefore, aptamer production and selection for therapeutic and diagnostic
applications is very challenging. Usually they are in vitro generated, but,
recently, computational approaches have been developed for the in silico
selection, with a higher affinity for the specific target. Anyway, the
mechanism of aptamer-ligand formation is not completely clear, and not obvious
to predict. This paper aims to develop a computational model able to describe
aptamer-ligand affinity performance by using the topological structure of the
corresponding graphs, assessed by means of numerical tools such as the
conventional degree distribution, but also the rank-degree distribution
(hierarchy) and the node assortativity. Calculations are applied to the
thrombin binding aptamer (TBA), and the TBA-thrombin complex, produced in the
presence of Na+ or K+. The topological analysis reveals different affinity
performances between the macromolecules in the presence of the two cations, as
expected by previous investigations in literature. These results nominate the
graph topological analysis as a novel theoretical tool for testing affinity.
Otherwise, starting from the graphs, an electrical network can be obtained by
using the specific electrical properties of amino acids and nucleobases.
Therefore, a further analysis concerns with the electrical response, which
reveals that the resistance sensitively depends on the presence of sodium or
potassium thus posing resistance as a crucial physical parameter for testing
affinity.Comment: 12 pages, 5 figure
A pH-based bio-rheostat: A proof-of-concept
Biological matter is attracting increasing attention because it shows innovative features that have found several applications in technology, from highly sensitive sensors for medical treatments to devices for energy harvesting. Furthermore, most of its phenomenology remains unclear thus giving hints for speculative investigations. In this letter, we explore the possibility to use a well-known photosensitive protein, the Reaction Center of Rhodobacter Sphaeroides, to build up an electrical pH sensor, i.e., a device able to change its resistance depending on the pH of the solution in which it crystalizes. By using a microscopic model previously tested on analogue proteins, we investigate the electrical response of the Reaction Center single protein under different conditions of applied bias, showing the feasibility of the bio-rheostat hypothesis. As a matter of facts, the calculated resistance of this protein grows of about 100% when going from a pH = 10 to a pH = 6.5. Moreover, calculations of the current voltage characteristics well agree with available experiments performed with a current atomic force microscopy under neutral conditions. All findings are in qualitative agreement with the known role of pH in biochemical activities of Reaction Center and similar proteins, therefore supporting a proof-of-concept for the development of innovative electron devices based on biomaterials
Searching for gas giant planets on Solar System scales - A NACO/APP L'-band survey of A- and F-type Main Sequence stars
We report the results of a direct imaging survey of A- and F-type main
sequence stars searching for giant planets. A/F stars are often the targets of
surveys, as they are thought to have more massive giant planets relative to
solar-type stars. However, most imaging is only sensitive to orbital
separations 30 AU, where it has been demonstrated that giant planets are
rare. In this survey, we take advantage of the high-contrast capabilities of
the Apodizing Phase Plate coronagraph on NACO at the Very Large Telescope.
Combined with optimized principal component analysis post-processing, we are
sensitive to planetary-mass companions (2 to 12 ) at Solar System
scales (30 AU). We obtained data on 13 stars in L'-band and detected one
new companion as part of this survey: an M dwarf companion around HD
984. We re-detect low-mass companions around HD 12894 and HD 20385, both
reported shortly after the completion of this survey. We use Monte Carlo
simulations to determine new constraints on the low-mass (80 )
companion frequency, as a function of mass and separation. Assuming solar-type
planet mass and separation distributions, normalized to the planet frequency
appropriate for A-stars, and the observed companion mass-ratio distribution for
stellar companions extrapolated to planetary masses, we derive a truncation
radius for the planetary mass companion surface density of 135 AU at 95%
confidence.Comment: Accepted for publication in MNRAS, 8 pages, 4 figure
Special issue
Mobility as a key feature of a modern society takes place at all geographic scales. The past decades have witnessed an enormous and unprecedented increase in the volume of intercontinental transport (e.g., between Europe and North-America, and between Asia and North-America) (Black and Nijkamp, 2002). Interestingly enough, a similar development is also present at a local level, where not only the activity radius is increasing, but also the frequency of trips. Geographically, our world is becoming less distant (resembling a ‘small world network’; see, e.g., Barabasi, 2002 and Watts, 1999) and more local and close-by, the so-called ‘global village’ (Poot, 2004)
Special issue
Mobility as a key feature of a modern society takes place at all geographic scales. The past decades have witnessed an enormous and unprecedented increase in the volume of intercontinental transport (e.g., between Europe and North-America, and between Asia and North-America) (Black and Nijkamp, 2002). Interestingly enough, a similar development is also present at a local level, where not only the activity radius is increasing, but also the frequency of trips. Geographically, our world is becoming less distant (resembling a 'small world network'; see, e.g., Barabasi, 2002 and Watts, 1999) and more local and close-by, the so-called 'global village' (Poot, 2004)
Neural networks for cross-sectional employment forecasts: A comparison of model specifications for Germany
In this paper, we present a review of various computational experiments – and consequent results – concerning Neural Network (NN) models developed for regional employment forecasting. NNs are widely used in several fields because of their flexible specification structure. Their utilization in studying/predicting economic variables, such as employment or migration, is justified by the ability of NNs of learning from data, in other words, of finding functional relationships – by means of data – among the economic variables under analysis. A series of NN experiments is presented in the paper. Using two data sets on German NUTS 3 districts (326 and 113 labour market districts in the former West and East Germany, respectively), the results emerging from the implementation of various NN models – in order to forecast variations in full-time employment – are provided and discussed In our approach, single forecasts are computed by the models for each district. Different specifications of the NN models are first tested in terms of: (a) explanatory variables; and (b) NN structures. The average statistical results of simulated out-of-sample forecasts on different periods are summarized and commented on. In addition to variable and structure specification, the choice of NN learning parameters and internal functions is also critical to the success of NNs. Comprehensive testing of these parameters is, however, limited in the literature. A sensitivity analysis is therefore carried out and discussed, in order to evaluate different combinations of NN parameters. The paper concludes with methodological and empirical remarks, as well as with suggestions for future research
Iron-rich Metal-poor Stars and the Astrophysics of Thermonuclear Events Observationally Classified as Type Ia Supernovae. I. Establishing the Connection
The progenitor systems and explosion mechanisms responsible for the
thermonuclear events observationally classified as Type Ia supernovae are
uncertain and difficult to uniquely constrain using traditional observations of
Type Ia supernova host galaxies, progenitors, light curves, and remnants. For
the subset of thermonuclear events that are prolific producers of iron, we use
published theoretical nucleosynthetic yields to identify a set of elemental
abundance ratios infrequently observed in metal-poor stars but shared across a
range of progenitor systems and explosion mechanisms: [Na,Mg,Co/Fe]<0. We label
stars with this abundance signature ``iron-rich metal-poor'' or IRMP stars. We
suggest that IRMP stars formed in environments dominated by thermonuclear
nucleosynthesis and consequently that their elemental abundances can be used to
constrain both the progenitor systems and explosion mechanisms responsible for
thermonuclear explosions. We identify three IRMP in the literature and
homogeneously infer their elemental abundances. We find that the elemental
abundances of BD+80 245, HE 0533--5340, and SMSS J034249.53--284216.0 are best
explained by the (double) detonations of sub-Chandrasekhar mass CO white
dwarfs. If our interpretation of IRMP stars is accurate, then they should be
very rare in globular clusters and more common in the Magellanic Clouds and
dwarf spheroidal galaxies than in the Milky Way's halo. We propose that future
studies of IRMP stars will quantify the relative occurrences of different
thermonuclear event progenitor systems and explosion mechanisms.Comment: Accepted for publication at A
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Tbr1 instructs laminar patterning of retinal ganglion cell dendrites.
Visual information is delivered to the brain by >40 types of retinal ganglion cells (RGCs). Diversity in this representation arises within the inner plexiform layer (IPL), where dendrites of each RGC type are restricted to specific sublaminae, limiting the interneuronal types that can innervate them. How such dendritic restriction arises is unclear. We show that the transcription factor Tbr1 is expressed by four mouse RGC types with dendrites in the outer IPL and is required for their laminar specification. Loss of Tbr1 results in elaboration of dendrites within the inner IPL, while misexpression in other cells retargets their neurites to the outer IPL. Two transmembrane molecules, Sorcs3 and Cdh8, act as effectors of the Tbr1-controlled lamination program. However, they are expressed in just one Tbr1+ RGC type, supporting a model in which a single transcription factor implements similar laminar choices in distinct cell types by recruiting partially non-overlapping effectors
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