TU Dortmund University

When small RNA is sequenced on current sequencing machines, the resulting reads are usually longer than the RNA and therefore contain parts of the 3' adapter. That adapter must be found and removed error-tolerantly from each read before read mapping. Previous solutions are either hard to use or do not offer required features, in particular support for color space data. As an easy to use alternative, we developed the command-line tool cutadapt, which supports 454, Illumina and SOLiD (color space) data, offers two adapter trimming algorithms, and has other useful features. Cutadapt, including its MIT-licensed source code, is available for download at http://code.google.com/p/cutadapt/

Resolving the molecular details of proteome variation in the different tissues and organs of the human body will greatly increase our knowledge of human biology and disease. Here, we present a map of the human tissue proteome based on an integrated omics approach that involves quantitative transcriptomics at the tissue and organ level, combined with tissue microarray-based immunohistochemistry, to achieve spatial localization of proteins down to the single-cell level. Our tissue-based analysis detected more than 90% of the putative protein-coding genes. We used this approach to explore the human secretome, the membrane proteome, the druggable proteome, the cancer proteome, and the metabolic functions in 32 different tissues and organs. All the data are integrated in an interactive Web-based database that allows exploration of individual proteins, as well as navigation of global expression patterns, in all major tissues and organs in the human body.

Abstract The Astropy Project supports and fosters the development of open-source and openly developed Python packages that provide commonly needed functionality to the astronomical community. A key element of the Astropy Project is the core package astropy , which serves as the foundation for more specialized projects and packages. In this article, we provide an overview of the organization of the Astropy project and summarize key features in the core package, as of the recent major release, version 2.0. We then describe the project infrastructure designed to facilitate and support development for a broader ecosystem of interoperable packages. We conclude with a future outlook of planned new features and directions for the broader Astropy Project.

Full list of authors: Price-Whelan, Adrian M.; Lim, Pey Lian; Earl, Nicholas; Starkman, Nathaniel; Bradley, Larry; Shupe, David L.; Patil, Aarya A.; Corrales, Lia; Brasseur, C. E.; Noethe, Maximilian; Donath, Axel; Tollerud, Erik; Morris, Brett M.; Ginsburg, Adam; Vaher, Eero; Weaver, Benjamin A.; Tocknell, James; Jamieson, William; van Kerkwijk, Marten H.; Robitaille, Thomas P.; Merry, Bruce; Bachetti, Matteo; Gunther, H. Moritz; Aldcroft, Thomas L.; Alvarado-Montes, Jaime A.; Archibald, Anne M.; Bodi, Attila; Bapat, Shreyas; Barentsen, Geert; Bazan, Juanjo; Biswas, Manish; Boquien, Mederic; Burke, D. J.; Cara, Daria; Cara, Mihai; Conroy, Kyle E.; Conseil, Simon; Craig, Matthew W.; Cross, Robert M.; Cruz, Kelle L.; D'Eugenio, Francesco; Dencheva, Nadia; Devillepoix, Hadrien A. R.; Dietrich, Jorg P.; Eigenbrot, Arthur Davis; Erben, Thomas; Ferreira, Leonardo; Foreman-Mackey, Daniel; Fox, Ryan; Freij, Nabil; Garg, Suyog; Geda, Robel; Glattly, Lauren; Gondhalekar, Yash; Gordon, Karl D.; Grant, David; Greenfield, Perry; Groener, Austen M.; Guest, Steve; Gurovich, Sebastian; Handberg, Rasmus; Hart, Akeem; Hatfield-Dodds, Zac; Homeier, Derek; Hosseinzadeh, Griffin; Jenness, Tim; Jones, Craig K.; Joseph, Prajwel; Kalmbach, J. Bryce; Karamehmetoglu, Emir; Kaluszynski, Mikolaj; Kelley, Michael S. P.; Kern, Nicholas; Kerzendorf, Wolfgang E.; Koch, Eric W.; Kulumani, Shankar; Lee, Antony; Ly, Chun; Ma, Zhiyuan; MacBride, Conor; Maljaars, Jakob M.; Muna, Demitri; Murphy, N. A.; Norman, Henrik; O'Steen, Richard; Oman, Kyle A.; Pacifici, Camilla; Pascual, Sergio; Pascual-Granado, J.; Patil, Rohit R.; Perren, Gabriel, I; Pickering, Timothy E.; Rastogi, Tanuj; Roulston, Benjamin R.; Ryan, Daniel F.; Rykoff, Eli S.; Sabater, Jose; Sakurikar, Parikshit; Salgado, Jesus; Sanghi, Aniket; Saunders, Nicholas; Savchenko, Volodymyr; Schwardt, Ludwig; Seifert-Eckert, Michael; Shih, Albert Y.; Jain, Anany Shrey; Shukla, Gyanendra; Sick, Jonathan; Simpson, Chris; Singanamalla, Sudheesh; Singer, Leo P.; Singhal, Jaladh; Sinha, Manodeep; Sipocz, Brigitta M.; Spitler, Lee R.; Stansby, David; Streicher, Ole; Sumak, Jani; Swinbank, John D.; Taranu, Dan S.; Tewary, Nikita; Tremblay, Grant R.; De Val-Borro, Miguel; Vasovic, Zlatan; Van Kooten, Samuel J.; Verma, Shresth; Cardoso, Jose Vinicius de Miranda; Williams, Peter K. G.; Wilson, Tom J.; Winkel, Benjamin; Wood-Vasey, W. M.; Xue, Rui; Yoachim, Peter; Zhang, Chen; Zonca, Andrea; Astropy Project Contributors; TARDIS Collaboration; Astropy Coordination Comm.--This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited.

Author(s): Collaboration, The ATLAS; Aad, G; Abat, E; Abdallah, J; Abdelalim, AA; Abdesselam, A; Abdinov, O; Abi, BA; Abolins, M; Abramowicz, H; Acerbi, E; Acharya, BS; Achenbach, R; Ackers, M; Adams, DL; Adamyan, F; Addy, TN; Aderholz, M; Adorisio, C; Adragna, P; Aharrouche, M; Ahlen, SP; Ahles, F; Ahmad, A; Ahmed, H; Aielli, G; Åkesson, PF; Åkesson, TPA; Akimov, AV; Alam, SM; Albert, J; Albrand, S; Aleksa, M; Aleksandrov, IN; Aleppo, M; Alessandria, F; Alexa, C; Alexander, G; Alexopoulos, T; Alimonti, G; Aliyev, M; Allport, PP; Allwood-Spiers, SE; Aloisio, A; Alonso, J; Alves, R; Alviggi, MG; Amako, K; Amaral, P; Amaral, SP; Ambrosini, G; Ambrosio, G; Amelung, C; Ammosov, VV; Amorim, A; Amram, N; Anastopoulos, C; Anderson, B; Anderson, KJ; Anderssen, EC; Andreazza, A; Andrei, V; Andricek, L; Andrieux, M-L; Anduaga, XS; Anghinolfi, F; Antonaki, A; Antonelli, M; Antonelli, S; Apsimon, R; Arabidze, G; Aracena, I; Arai, Y; Arce, ATH; Archambault, JP; Arguin, J-F; Arik, E; Arik, M; Arms, KE; Armstrong, SR; Arnaud, M; Arnault, C; Artamonov, A; Asai, S; Ask, S

A modified SAFT equation of state is developed by applying the perturbation theory of Barker and Henderson to a hard-chain reference fluid. With conventional one-fluid mixing rules, the equation of state is applicable to mixtures of small spherical molecules such as gases, nonspherical solvents, and chainlike polymers. The three pure-component parameters required for nonassociating molecules were identified for 78 substances by correlating vapor pressures and liquid volumes. The equation of state gives good fits to these properties and agrees well with caloric properties. When applied to vapor−liquid equilibria of mixtures, the equation of state shows substantial predictive capabilities and good precision for correlating mixtures. Comparisons to the SAFT version of Huang and Radosz reveal a clear improvement of the proposed model. A brief comparison with the Peng−Robinson model is also given for vapor−liquid equilibria of binary systems, confirming the good performance of the suggested equation of state. The applicability of the proposed model to polymer systems was demonstrated for high-pressure liquid−liquid equilibria of a polyethylene mixture. The pure-component parameters of polyethylene were obtained by extrapolating pure-component parameters of the n-alkane series to high molecular weights.

The increasing integration of the Internet of Everything into the industrial value chain has built the foundation for the next industrial revolution called Industrie 4.0. Although Industrie 4.0 is currently a top priority for many companies, research centers, and universities, a generally accepted understanding of the term does not exist. As a result, discussing the topic on an academic level is difficult, and so is implementing Industrie 4.0 scenarios. Based on a quantitative text analysis and a qualitative literature review, the paper identifies design principles of Industrie 4.0. Taking into account these principles, academics may be enabled to further investigate on the topic, while practitioners may find assistance in identifying appropriate scenarios. A case study illustrates how the identified design principles support practitioners in identifying Industrie 4.0 scenarios.

Three main streams of evolutionary algorithms (EAs), probabilistic optimization algorithms based on the model of natural evolution, are compared in this article: evolution strategies (ESs), evolutionary programming (EP), and genetic algorithms (GAs). The comparison is performed with respect to certain characteristic components of EAs: the representation scheme of object variables, mutation, recombination, and the selection operator. Furthermore, each algorithm is formulated in a high-level notation as an instance of the general, unifying basic algorithm, and the fundamental theoretical results on the algorithms are presented. Finally, after presenting experimental results for three test functions representing a unimodal and a multimodal case as well as a step function with discontinuities, similarities and differences of the algorithms are elaborated, and some hints to open research questions are sketched.

The LHCb experiment is dedicated to precision measurements of CP violation and rare decays of B hadrons at the Large Hadron Collider (LHC) at CERN (Geneva). The initial configuration and expected performance of the detector and associated systems, as established by test beam measurements and simulation studies, is described.

The explanation of heterogeneity plays an important role in meta-analysis. The random effects meta-regression model allows the inclusion of trial-specific covariates which may explain a part of the heterogeneity. We examine the commonly used tests on the parameters in the random effects meta-regression with one covariate and propose some new test statistics based on an improved estimator of the variance of the parameter estimates. The approximation of the distribution of the newly proposed tests is based on some theoretical considerations. Moreover, the newly proposed tests can easily be extended to the case of more than one covariate. In a simulation study, we compare the tests with regard to their actual significance level and we consider the log relative risk as the parameter of interest. Our simulation study reflects the meta-analysis of the efficacy of a vaccine for the prevention of tuberculosis originally discussed in Berkey et al. The simulation study shows that the newly proposed tests are superior to the commonly used test in holding the nominal significance level.

In quantum-confined semiconductor nanostructures, electrons exhibit distinctive behavior compared with that in bulk solids. This enables the design of materials with tunable chemical, physical, electrical, and optical properties. Zero-dimensional semiconductor quantum dots (QDs) offer strong light absorption and bright narrowband emission across the visible and infrared wavelengths and have been engineered to exhibit optical gain and lasing. These properties are of interest for imaging, solar energy harvesting, displays, and communications. Here, we offer an overview of advances in the synthesis and understanding of QD nanomaterials, with a focus on colloidal QDs, and discuss their prospects in technologies such as displays and lighting, lasers, sensing, electronics, solar energy conversion, photocatalysis, and quantum information.

Meta-analyses are typically used to estimate the overall/mean of an outcome of interest. However, inference about between-study variability, which is typically modelled using a between-study variance parameter, is usually an additional aim. The DerSimonian and Laird method, currently widely used by default to estimate the between-study variance, has been long challenged. Our aim is to identify known methods for estimation of the between-study variance and its corresponding uncertainty, and to summarise the simulation and empirical evidence that compares them. We identified 16 estimators for the between-study variance, seven methods to calculate confidence intervals, and several comparative studies. Simulation studies suggest that for both dichotomous and continuous data the estimator proposed by Paule and Mandel and for continuous data the restricted maximum likelihood estimator are better alternatives to estimate the between-study variance. Based on the scenarios and results presented in the published studies, we recommend the Q-profile method and the alternative approach based on a 'generalised Cochran between-study variance statistic' to compute corresponding confidence intervals around the resulting estimates. Our recommendations are based on a qualitative evaluation of the existing literature and expert consensus. Evidence-based recommendations require an extensive simulation study where all methods would be compared under the same scenarios.

The R2WinBUGS package provides convenient functions to call WinBUGS from R. It automatically writes the data and scripts in a format readable by WinBUGS for processing in batch mode, which is possible since version 1.4. After the WinBUGS process has finished, it is possible either to read the resulting data into R by the package itself--which gives a compact graphical summary of inference and convergence diagnostics--or to use the facilities of the coda package for further analyses of the output. Examples are given to demonstrate the usage of this package.

Evolutionary computation has started to receive significant attention during the last decade, although the origins can be traced back to the late 1950's. This article surveys the history as well as the current state of this rapidly growing field. We describe the purpose, the general structure, and the working principles of different approaches, including genetic algorithms (GA) (with links to genetic programming (GP) and classifier systems (CS)), evolution strategies (ES), and evolutionary programming (EP) by analysis and comparison of their most important constituents (i.e. representations, variation operators, reproduction, and selection mechanism). Finally, we give a brief overview on the manifold of application domains, although this necessarily must remain incomplete.

The task-switching paradigm offers enormous possibilities to study cognitive control as well as task interference. The current review provides an overview of recent research on both topics. First, we review different experimental approaches to task switching, such as comparing mixed-task blocks with single-task blocks, predictable task-switching and task-cuing paradigms, intermittent instructions, and voluntary task selection. In the 2nd part, we discuss findings on preparatory control mechanisms in task switching and theoretical accounts of task preparation. We consider preparation processes in two-stage models, consider preparation as an all-or-none process, address the question of whether preparation is switch-specific, reflect on preparation as interaction of cue encoding and memory retrieval, and discuss the impact of verbal mediation on preparation. In the 3rd part, we turn to interference phenomena in task switching. We consider proactive interference of tasks and inhibition of recently performed tasks indicated by asymmetrical switch costs and n-2 task-repetition costs. We discuss stimulus-based interference as a result of stimulus-based response activation and stimulus-based task activation, and response-based interference because of applying bivalent rather than univalent responses, response repetition effects, and carryover of response selection and execution. In the 4th and final part, we mention possible future research fields.

This paper analyzes the convergence properties of the canonical genetic algorithm (CGA) with mutation, crossover and proportional reproduction applied to static optimization problems. It is proved by means of homogeneous finite Markov chain analysis that a CGA will never converge to the global optimum regardless of the initialization, crossover, operator and objective function. But variants of CGA's that always maintain the best solution in the population, either before or after selection, are shown to converge to the global optimum due to the irreducibility property of the underlying original nonconvergent CGA. These results are discussed with respect to the schema theorem.

The wetting and the self-cleaning properties (the latter is often called the "Lotus-Effect") of three types of superhydrophobic surfaces have been investigated: silicon wafer specimens with different regular arrays of spikes hydrophobized by chemical treatment, replicates of water-repellent leaves of plants, and commercially available metal foils which were additionally hydrophobized by means of a fluorinated agent. Water droplets rolled off easily from those silicon samples which had a microstructure consisting of rather slender spikes with narrow pitches. Such samples could be cleaned almost completely from artificial particulate contaminations by a fog consisting of water droplets (diameter range, 8-20 microm). Some metal foils and some replicates had two levels of roughening. Because of this, a complete removal of all particles was not possible using artificial fog. However, water drops with some amount of kinetic impact energy were able to clean these surfaces perfectly. A substrate where pronounced structures in the range below 5 microm were lacking could not be cleaned by means of fog because this treatment resulted in a continuous water film on the samples.

A measurement of the Higgs boson mass is presented based on the combined data samples of the ATLAS and CMS experiments at the CERN LHC in the H→γγ and H→ZZ→4ℓ decay channels. The results are obtained from a simultaneous fit to the reconstructed invariant mass peaks in the two channels and for the two experiments. The measured masses from the individual channels and the two experiments are found to be consistent among themselves. The combined measured mass of the Higgs boson is m_{H}=125.09±0.21 (stat)±0.11 (syst) GeV.

In humans, glutathione-dependent conjugation of halomethanes is polymorphic, with 60% of the population classed as conjugators and 40% as non-conjugators. We report the characterization of the genetic polymorphism causing the phenotypic difference. We have isolated a cDNA that encodes a human class Theta GST (GSTT1) and which shares 82% sequence identity with rat class Theta GST5-5. From PCR and Southern blot analyses, it is shown that the GSTT1 gene is absent from 38% of the population. The presence or absence of the GSTT1 gene is coincident with the conjugator (GSST1+) and non-conjugator (GSTT1-) phenotypes respectively. The GSTT1+ phenotype can catalyse the glutathione conjugation of dichloromethane, a metabolic pathway which has been shown to be mutagenic in Salmonella typhimurium mutagenicity tester strains and is believed to be responsible for carcinogenicity of dichloromethane in the mouse. In humans, the enzyme is found in the erythrocyte and this may act as a detoxification sink. Characterization of the GSTT1 polymorphism will thus enable a more accurate assessment of human health risk from synthetic halomethanes and other industrial chemicals.

The perturbed-chain SAFT (PC−SAFT) equation of state is applied to pure associating components as well as to vapor−liquid and liquid−liquid equilibria of binary mixtures of associating substances. For these substances, the PC−SAFT equation of state requires five pure-component parameters, two of which characterize the association. The pure-component parameters were identified for 18 associating substances by correlating vapor pressure and liquid density data. A comparison to an earlier version of SAFT confirms the good results for pure substances. When only one associating compound is present in a mixture, the PC−SAFT equation of state does not require mixing rules for the association term. Using one binary interaction parameter kij for the dispersion term only, the model was applied to azeotropic and nonazeotropic vapor−liquid equilibria at low and at high pressures, as well as to liquid−liquid equilibria. Simple mixing and combining rules were adopted for mixtures with more than one associating compound, introducing no additional binary interaction parameter. The simultaneous description of liquid−liquid and vapor−liquid equilibrium was also possible with a single kij parameter.