Combined super-/substring and super-/subsequence problems

Super-/substring problems and super-/subsequence problems are well-known problems in stringology that have applications in a variety of areas, such as manufacturing systems design and molecular biology. Here we investigate the complexity of a new type of such problem that forms a combination of a super-/substring and a super-/subsequence problem. Moreover we introduce different types of minimal superstring and maximal substring problems. In particular, we consider the following problems: given a set L of strings and a string S, (i) find a minimal superstring (or maximal substring) of L that is also a supersequence (or a subsequence) of S, (ii) find a minimal supersequence (or maximal subsequence) of L that is also a superstring (or a substring) of S. In addition some non-super-/non-substring and non-super-/non-subsequence variants are studied. We obtain several NP-hardness or even MAX SNP-hardness results and also identify types of "weak minimal" superstrings and "weak maximal" substrings for which (i) is polynomial-time solvable

study on the validation of ring filament winding methods for unidirectional preform ply manufacturing

AbstractRing filament winding enables processing of continuous fibers for manufacturing unidirectional non-crimp unidirectional preform plies on straight-, curved-, or closed-mandrel geometries. However, unidirectional processing of tows can lead to increased lateral tow slippage. The objective of the present study is thus to validate unidirectional winding methods for ring filament winding, performing geodesic and non-geodesic trajectories analytically and experimentally. Implementation of geodesic paths investigates the influence of the tensile force and take-up velocity on the winding angle reproducibility. Non-geodesic winding paths are conducted here dependent on winding methods, slippage coefficients, and the mandrel's surface materials, evidencing the occurrence of lateral tow slippage by measurements of nip-point forces. Findings indicate an excellent reproducibility of geodesic paths independent of the process velocity. Non-geodesic paths were partially validated because of the occurrence of late..

New-age elderly in Germany - how to live better with healthy experiences

This study aims to analyze which potential attributes of anti-ageing experiences (goods, services, and experiences) will tend to be associated with subjective happiness; how cognitive age is associated with mindfulness and the influence of mindfulness on subjective happiness. Senior universities were contacted and approached by the research team to conduct the study. The goals of this study were explained to the managers of the senior universities and the survey collected among the people who participate in the activities and are enrolled in the senior universities. To analyze this theme over two hundred (250) questionnaires were distributed during January 2016 in Hamburg. The findings reveal that (i) mindfulness tend to have a positive effect on subjective happiness among elderly consumers, (ii) cognitive age and chronological age are not overlapped and (iii) the way elderly consumers perceive the anti-aging products and experiences may be correlated with subjective happiness.info:eu-repo/semantics/publishedVersio

Reconstruction of Network Evolutionary History from Extant Network Topology and Duplication History

Genome-wide protein-protein interaction (PPI) data are readily available thanks to recent breakthroughs in biotechnology. However, PPI networks of extant organisms are only snapshots of the network evolution. How to infer the whole evolution history becomes a challenging problem in computational biology. In this paper, we present a likelihood-based approach to inferring network evolution history from the topology of PPI networks and the duplication relationship among the paralogs. Simulations show that our approach outperforms the existing ones in terms of the accuracy of reconstruction. Moreover, the growth parameters of several real PPI networks estimated by our method are more consistent with the ones predicted in literature.Comment: 15 pages, 5 figures, submitted to ISBRA 201

A classification-based framework for predicting and analyzing gene regulatory response

BACKGROUND: We have recently introduced a predictive framework for studying gene transcriptional regulation in simpler organisms using a novel supervised learning algorithm called GeneClass. GeneClass is motivated by the hypothesis that in model organisms such as Saccharomyces cerevisiae, we can learn a decision rule for predicting whether a gene is up- or down-regulated in a particular microarray experiment based on the presence of binding site subsequences ("motifs") in the gene's regulatory region and the expression levels of regulators such as transcription factors in the experiment ("parents"). GeneClass formulates the learning task as a classification problem — predicting +1 and -1 labels corresponding to up- and down-regulation beyond the levels of biological and measurement noise in microarray measurements. Using the Adaboost algorithm, GeneClass learns a prediction function in the form of an alternating decision tree, a margin-based generalization of a decision tree. METHODS: In the current work, we introduce a new, robust version of the GeneClass algorithm that increases stability and computational efficiency, yielding a more scalable and reliable predictive model. The improved stability of the prediction tree enables us to introduce a detailed post-processing framework for biological interpretation, including individual and group target gene analysis to reveal condition-specific regulation programs and to suggest signaling pathways. Robust GeneClass uses a novel stabilized variant of boosting that allows a set of correlated features, rather than single features, to be included at nodes of the tree; in this way, biologically important features that are correlated with the single best feature are retained rather than decorrelated and lost in the next round of boosting. Other computational developments include fast matrix computation of the loss function for all features, allowing scalability to large datasets, and the use of abstaining weak rules, which results in a more shallow and interpretable tree. We also show how to incorporate genome-wide protein-DNA binding data from ChIP chip experiments into the GeneClass algorithm, and we use an improved noise model for gene expression data. RESULTS: Using the improved scalability of Robust GeneClass, we present larger scale experiments on a yeast environmental stress dataset, training and testing on all genes and using a comprehensive set of potential regulators. We demonstrate the improved stability of the features in the learned prediction tree, and we show the utility of the post-processing framework by analyzing two groups of genes in yeast — the protein chaperones and a set of putative targets of the Nrg1 and Nrg2 transcription factors — and suggesting novel hypotheses about their transcriptional and post-transcriptional regulation. Detailed results and Robust GeneClass source code is available for download from

A compact and light-weight refractive telescope for the observation of extensive air showers

A general purpose instrument for imaging of Cherenkov light or fluorescence light emitted by extensive air showers is presented. Its refractive optics allows for a compact and light-weight design with a wide field-of-view of 12{\deg}. The optical system features a 0.5 m diameter Fresnel lens and a camera with 61 pixels composed of Winston cones and large-sized 6x6 mm photo sensors. As photo sensors, semi conductor light sensors (SiPMs) are utilized. The camera provides a high photon detection efficiency together with robust operation. The enclosed optics permit operation in regions of harsh environmental conditions. The low price of the telescope allows the production of a large number of telescopes and the application of the instrument in various projects, such as FAMOUS for the Pierre Auger Observatory, HAWC's Eye for HAWC or IceAct for IceCube. In this paper the novel design of this telescope and first measurements are presented.Comment: Submitted to JINST, second (minor) revisio

Analysis of collection of hemolytic uremic syndrome-associated enterohemorrhagic Escherichia coli

Multilocus sequence typing of 169 non-O157 enterohemorrhagic Escherichia coli (EHEC) isolated from patients with hemolytic uremic syndrome (HUS) demonstrated 29 different sequence types (STs); 78.1% of these strains clustered in 5 STs. From all STs and serotypes identified, we established a reference panel of EHEC associated with HUS (HUSEC collection).</p

Dynamics of an antibiotic oligopeptide

Neutron time-of-flight spectra were measured for an HO-hydrated and a nominally dry sample of a 15-residue antibacterial oligopeptide from 99 to 271 K. Proton mobilities, quasielastic broadenings, and changes in low-frequency inelastic intensities characterise the evolution of the peptide energy landscape as a function of momentum transfer and temperature