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

Heavy Superheated Droplet Detectors as a Probe of Spin-independent WIMP Dark Matter Existence

At present, application of Superheated Droplet Detectors (SDDs) in WIMP dark matter searches has been limited to the spin-dependent sector, owing to the general use of fluorinated refrigerants which have high spin sensitivity. Given their recent demonstration of a significant constraint capability with relatively small exposures and the relative economy of the technique, we consider the potential impact of heavy versions of such devices on the spin-independent sector. Limits obtainable from a $\mathrm{CF_{3}I}$-loaded SDD are estimated on the basis of the radiopurity levels and backgrounds already achieved by the SIMPLE and PICASSO experiments. With 34 kgd exposure, equivalent to the current CDMS, such a device may already probe to below 10$^{-6}$ pb in the spin-independent cross section.Comment: 9 pages, 4 figures, accepted Phys. Rev.

Evaluation of Al-Thagher Wastewater Treatment Plant

This study aims to evaluate the performance of the sewage treatment plant in Al-Thagher city, in the north of Basrah governorate, the southern part of Iraq. The plant’s performance was estimated based on an analysis of influent and effluent wastewater quality data that represented the monthly averages from Feb. 2017 to Dec. 2018. The results show that the values of temperature (T), pH, ammonia (NH3–N), chemical oxygen demand (COD) and biological oxygen demand (BOD) in all collected samples from the effluent of the plant met the Iraqi water quality standard (IWQS), whereas the values of electrical conductivity (EC), total dissolved solids (TDS), total suspended solids (TSS), sulfate (SO4–2), chloride (Cl–1) and phosphate (PO4–P) met the Iraqi water quality standard (IWQS) in some months and did not meet the standard in other months. The average removal efficiencies were in the following order: COD (77.12%) &gt; BOD (77.03%) &gt; TSS (62.26%) &gt; NH3–N (59.99%) &gt; PO4–P (12.42%) &gt; Cl–1 (1.97%). The removal percentages for the remaining parameters had negative values. The Canadian Council of Ministers of the Environment water quality index (CCME WQI) value of the treated water was 51.80 and classified as “marginal.” The coefficients of determination between each parameter in influent or effluent were calculated. Finally, linear regression equations between these parameters were formulated so that the value of one parameter could be used to predict the value of a different parameter

Structural and electronic investigations into subnanometre metallic clusters

This thesis presents computational studies of the geometric and electronic structures and energetic properties of homo- and heterometallic subnanometre clusters (SNCs). The first two chapters give an introductory overview of nanoparticles and the basics of the sophisticated search algorithms, Genetic Algorithms (GAs), as applied to clusters, and outline a general introduction to the computational methodologies applied in this work, the coupling of the recently developed combination of GAs with Density Functional Theory (DFT) calculations. This is followed by four results chapters, in which these computational methods are adapted to several SNC systems to elucidate their applicability in catalysis. Six publications are documented in the results chapters. Gold-palladium SNCs, which are promising catalysts for a wide variety of chemical reactions, are studied extensively in chapters 3 and 4. Chapter 3 considers the evolution of structural motifs as a function of size and composition for neutral Au-Pd clusters in the gas-phase and supported on a MgO(100) surface. Quantum-regime effects are observed and energetics are further studied. In chapter 4, a rigorous approach is presented to explore structure and stability of mono-cationic Pd-doped Au clusters and their reactivity with CO gas. The Birmingham Parallel Genetic Algorithm BPGA-DFT approach is combined with experimental techniques, including mass spectrometry, and infra-red multiphoton dissociation spectroscopy. This study gives unique insights into Pd dopant effects on cluster stability, as measured by their photo-fragmentation properties, and on their CO adsorption properties. Computational investigations into AuCu SNCs, using the Mexican Enhanced Genetic Algorithm MEGA-DFT code to rationalize the efficient catalytic properties, are presented in chapter 5. Free clusters and those supported on a MgO(100) surface are compared in this approach. The interactions with the support are extensively probed in order to better understand their role in catalysis at the atomistic level. Chapter 6 is dedicated to the structural characterisation, which is vital first step in order to understanding catalytic activity, of Ru-Pt clusters, which are electrode catalysts in direct methanol fuel cells. Ru@Pt core-shell chemical ordering is predicted. Finally, overall conclusions and outlook are presented in chapter 7

Numerical Methods to Quantify the Model Risk of Basket Default Swaps

Abstract The valuation of basket default swaps depends crucially on the joint default probability of the underlying assets in the basket. It is known that this probability can be modeled by means of a copula function which links the marginal default probabilities to a joint probability. The valuation bears risk due to the uncertainty of the copula, the relation of the assets to each other and the marginal distributions which we call together the model risk. To value basket default swaps and to compute model risk parameters we present an efficient numerical approach based on importance sampling and applicable to different classes of copula models. Our numerical findings show that the choice of the underlying copula model influences strongly the risk profile of the basket and should be tailored advisedly

Magnetic hysteresis and rotational hysteresis properties of hydrothermally grown multidomain magnetite

Accepted versio

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

Interpreting and acting upon home blood pressure readings: A qualitative study

This article is made available through the Brunel Open Access Publishing Fund. Copyright @ 2013 Vasileiou et al.; licensee BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.Background: Recent guidelines recognize the importance of home blood pressure monitoring (HBPM) as an adjunct to clinical measurements. We explored how people who have purchased and use a home blood pressure (BP) monitor make sense of, and act upon, readings and how they communicate with their doctor about the practice of home monitoring. Methods: A qualitative study was designed and participants were purposively recruited from several areas in England, UK. Semi-structured in-depth interviews were conducted with 18 users of home BP monitors. The transcribed data were thematically analysed. Results: Interpretation of home BP readings is complex, and is often characterised by uncertainty. People seek to assess value normality using ‘rules of thumb’, and often aim to identify the potential causes of the readings. This is done by drawing on lay models of BP function and by contextualising the readings to personal circumstances. Based on the perceived causes of the problematic readings, actions are initiated, mostly relating to changes in daily routines. Contacting the doctor was more likely when the problematic readings persisted and could not be easily explained, or when participants did not succeed in regulating their BP through their other interventions. Most users had notified their doctor of the practice of home monitoring, but medical involvement varied, with some participants reporting disinterest or reservations by doctors. Conclusions: Involvement from doctors can help people overcome difficulties and resolve uncertainties around the interpretation of home readings, and ensure that the rules of thumb are appropriate. Home monitoring can be used to strengthen the patient-clinician relationship