Interpol: An R package for preprocessing of protein sequences

<p>Abstract</p> <p>Background</p> <p>Most machine learning techniques currently applied in the literature need a fixed dimensionality of input data. However, this requirement is frequently violated by real input data, such as DNA and protein sequences, that often differ in length due to insertions and deletions. It is also notable that performance in classification and regression is often improved by numerical encoding of amino acids, compared to the commonly used sparse encoding.</p> <p>Results</p> <p>The software "Interpol" encodes amino acid sequences as numerical descriptor vectors using a database of currently 532 descriptors (mainly from AAindex), and normalizes sequences to uniform length with one of five linear or non-linear interpolation algorithms. Interpol is distributed with open source as platform independent R-package. It is typically used for preprocessing of amino acid sequences for classification or regression.</p> <p>Conclusions</p> <p>The functionality of Interpol widens the spectrum of machine learning methods that can be applied to biological sequences, and it will in many cases improve their performance in classification and regression.</p

Suárez on Visual Perception

This paper surveys the main issues in Suárez’s theory of visual perception, which in its complexity and systematical ordering has not been explored yet. These questions, exposed in the first five questions of the seventh disputation De sensibus exterioribus in particulari of Suárez’s Commentaria una cum quaestionibus in libros Aristotelis and in the first two sections of the fifth disputation De potentiis cognoscitivis in communi, are the following: 1) the nature of light; 2) the nature of colour; 3) the formal (adequate) object of vision; 4) the necessity and the nature of the visual species; 5) the critique of the theory of extramission; and 6) the organ of visual power. The main emphasis is laid on the presentation of the systematical dimension of Suárez’s visual theory

Suárez on sound and hearing

The author analyses Suárez’s theory of sound and hearing as presented in the sixth, eighth and ninth questions of the seventh disputation of the Jesuit’s Commentary on Aristotle’s De anima. In the study, Suárez’s stances to the following issues are laid out: 1) the nature, cause and subject of sound; 2) the kinds of media of sound and the manner of its dilatation in medio; and 3) the organ of hearing

Perceptions and understanding of research situations as a function of consent form characteristics and experimenter instructions

Two studies examined how research methodology affected participant behaviors. Study 1 tested (a) consent form perspective (1st, 2nd, or 3rd person) and (b) information on participants’ right to sue upon perceptions of coercion, ability to recall consent information, and performance on experimental tasks. Unexpectedly, participants who received instructions without the right to sue information had significantly better recall of their research rights. Study 2 manipulated (a) consent form complexity (presence or absence of jargon) and (b) the detail of verbal instructions (simple, elaborate); participants who received a consent form with simpler language spent more time on a difficult task, and participants in the elaborate instruction condition recalled more details. Together, these studies suggest (a) explaining the right to sue may actually be counterproductive; (b) providing a more detailed explanation may help participants remember procedural details; and (c) using jargon may decrease task performance

Statistical relational learning with soft quantifiers

Quantification in statistical relational learning (SRL) is either existential or universal, however humans might be more inclined to express knowledge using soft quantifiers, such as ``most'' and ``a few''. In this paper, we define the syntax and semantics of PSL^Q, a new SRL framework that supports reasoning with soft quantifiers, and present its most probable explanation (MPE) inference algorithm. To the best of our knowledge, PSL^Q is the first SRL framework that combines soft quantifiers with first-order logic rules for modelling uncertain relational data. Our experimental results for link prediction in social trust networks demonstrate that the use of soft quantifiers not only allows for a natural and intuitive formulation of domain knowledge, but also improves the accuracy of inferred results

Sex Differences in Jealousy in Response to Actual Infidelity

The present studies address two criticisms of the theory of evolved sex differences in jealousy: (a) that the sex difference in jealousy emerges only in response to hypothetical infidelity scenarios, and (b) that the sex difference emerges only using forced-choice measures. In two separate studies, one a paper-and-pencil survey with a student sample and the other a web-based survey targeting a non-student sample, men and women showed significant sex differences in jealousy in response to actual infidelity experiences; men experienced more jealousy in response to the sexual aspects of an actual infidelity, whereas women experienced more jealousy in response to the emotional aspects of the infidelity. Sex differences emerged using both continuous measures of jealousy as well as the traditional forced-choice measure. Overall, our results demonstrate that sex differences in jealousy are not limited to responses to hypothetical infidelity scenarios; they also emerge in response to actual infidelity experiences

Kink far below the Fermi level reveals new electron-magnon scattering channel in Fe

Many properties of real materials can be modeled using ab initio methods within a single-particle picture. However, for an accurate theoretical treatment of excited states, it is necessary to describe electron-electron correlations including interactions with bosons: phonons, plasmons, or magnons. In this work, by comparing spin- and momentum-resolved photoemission spectroscopy measurements to many-body calculations carried out with a newly developed first-principles method, we show that a kink in the electronic band dispersion of a ferromagnetic material can occur at much deeper binding energies than expected (E_b=1.5 eV). We demonstrate that the observed spectral signature reflects the formation of a many-body state that includes a photohole bound to a coherent superposition of renormalized spin-flip excitations. The existence of such a many-body state sheds new light on the physics of the electron-magnon interaction which is essential in fields such as spintronics and Fe-based superconductivity.Comment: 6 pages, 2 figure

Signal modeling of high-purity Ge detectors with a small read-out electrode and application to neutrinoless double beta decay search in Ge-76

The GERDA experiment searches for the neutrinoless double beta decay of Ge-76 using high-purity germanium detectors enriched in Ge-76. The analysis of the signal time structure provides a powerful tool to identify neutrinoless double beta decay events and to discriminate them from gamma-ray induced backgrounds. Enhanced pulse shape discrimination capabilities of "Broad Energy Germanium" detectors with a small read-out electrode have been recently reported. This paper describes the full simulation of the response of such a detector, including the Monte Carlo modeling of radiation interaction and subsequent signal shape calculation. A pulse shape discrimination method based on the ratio between the maximum current signal amplitude and the event energy applied to the simulated data shows quantitative agreement with the experimental data acquired with calibration sources. The simulation has been used to study the survival probabilities of the decays which occur inside the detector volume and are difficult to assess experimentally. Such internal decay events are produced by the cosmogenic radio-isotopes Ge-68 and Co-60 and the neutrinoless double beta decay of Ge-76. Fixing the experimental acceptance of the double escape peak of the 2.614 MeV photon to 90%, the estimated survival probabilities at Qbb = 2.039 MeV are (86+-3)% for Ge-76 neutrinoless double beta decays, (4.5+-0.3)% for the Ge-68 daughter Ga-68, and (0.9+0.4-0.2)% for Co-60 decays.Comment: 27 pages, 17 figures. v2: fixed typos and references. Submitted to JINS