bluuebunny/crossref_metadata_2025 huggingface dataset:
„Rehabilitation NEU denken“: Das 9. Reha-Symposium in Lübeck
Authors: Bethge Matthias , Markus Miriam , Lemke Stella , Stark Michael
Published: April 2018

Am 27.11.2017 fand in Lübeck das 9. Reha-Symposium des Vereins zur Förderung der Rehabilitationsforschung in Hamburg, Mecklenburg-Vorpommern und Schleswig-Holstein (vffr) statt. Der vffr hat das Symposium auch in der 9. Auflage gemeinsam mit der Deutschen Rentenversicherung Nord und dem Institut für Sozialmedizin und Epidemiologie der Universität zu Lübeck geplant und vorbereitet. Knapp 200 Teilnehmer diskutierten unter dem Titel „Rehabilitation NEU denken“ aktuelle rehabilitationswissenschaftliche Forschungsergebnisse.
Giant electrocaloric effect in a cracked ferroelectrics
Authors: Huang Cheng , Yang Hai-Bing , Gao Cun-Fa
Published: April 2018

The electrocaloric effect (ECE) is the temperature change in a material induced by electrical field variation under adiabatic condition. Considering an external electric load applied on a cracked ferroelectric solid, a non-uniform electric field would be induced at the crack tip, and thus, incompatible strain field and local stress concentration would be generated around it. Furthermore, the enormous strain energy and the electrostatic energy would affect the polarization switching of the ferroelectric solid, important for the electrocaloric response. In this paper, the large negative and positive ECEs in a ferroelectric sheet with a conducting crack are investigated by the phase field method with the consideration of time-dependent Ginzburg-Landau equation. The numerical calculations indicated that the polarization field generates a sharp rise during the domain transition from polydomain to monodomain under a certain electric load. Large negative ECEs, about –10.21 K and –7.55 K, are obtained at 135 °C and 85 °C, respectively. The domain transition temperature is much lower than the Curie temperature, which enlarges the existence scope of the large ECE in ferroelectrics. The results also imply that the domain transition from a multi-domain state to a single domain takes place with the minimization of total free energy, which involves the courses of the electric field, stress field, temperature, and polarization interaction. Therefore, the non-uniform distributions of the stress-electric fields induced by the crack play an important role in ECE.
Heavily doped n-type a-IGZO by F plasma treatment and its thermal stability up to 600 °C
Authors: Um Jae Gwang , Jang Jin
Published: April 2018

We report the electrical properties and thermal stability of heavily doped, amorphous indium-gallium-zinc-oxide (a-IGZO) treated with fluorine (F) plasma. When the F doping concentration in a-IGZO is 17.51 × 1021/cm−3, the a-IGZO exhibits a carrier concentration of 6 × 1019 cm−3, a resistivity of 3 × 10−3 Ω cm, and a Hall mobility of 20 cm2/V s. This indicates that F is a suitable n-type dopant in a-IGZO. The similarity of the ionic radius of F to that of oxygen (O) allows substitutional doping by replacing O with F or the occupation of the oxygen vacancy (VO) site by F and consequent reduction in defect density. The semiconducting property of a-IGZO can change into metallic behavior by F doping. The defect passivation by F incorporation is confirmed by the XPS depth profile, which reveals the significant reduction in the VO concentration due to the formation of In-F bonds. The heavily doped a-IGZO exhibits thermally stable conductivity up to 600 °C annealing and thus can be widely used for the ohmic contact of a-IGZO devices.
SU(p,q) coherent states and a Gaussian de Finetti theorem
Authors: Leverrier Anthony
Published: April 2018

We prove a generalization of the quantum de Finetti theorem when the local space is an infinite-dimensional Fock space. In particular, instead of considering the action of the permutation group on n copies of that space, we consider the action of the unitary group U(n) on the creation operators of the n modes and define a natural generalization of the symmetric subspace as the space of states invariant under unitaries in U(n). Our first result is a complete characterization of this subspace, which turns out to be spanned by a family of generalized coherent states related to the special unitary group SU(p, q) of signature (p, q). More precisely, this construction yields a unitary representation of the noncompact simple real Lie group SU(p, q). We therefore find a dual unitary representation of the pair of groups U(n) and SU(p, q) on an n(p + q)-mode Fock space. The (Gaussian) SU(p, q) coherent states resolve the identity on the symmetric subspace, which implies a Gaussian de Finetti theorem stating that tracing over a few modes of a unitary-invariant state yields a state close to a mixture of Gaussian states. As an application of this de Finetti theorem, we show that the n × n upper-left submatrix of an n × n Haar-invariant unitary matrix is close in total variation distance to a matrix of independent normal variables if n3 = O(m).
Self assembled linear polymeric chains with tuneable semiflexibility using isotropic interactions
Authors: Abraham Alex , Chatterji Apratim
Published: April 2018

We propose a two-body spherically symmetric (isotropic) potential such that particles interacting by the potential self-assemble into linear semiflexible polymeric chains without branching. By suitable control of the potential parameters, we can control the persistence length of the polymer and can even introduce a controlled number of branches. Thus we show how to achieve effective directional interactions starting from spherically symmetric potentials. The self-assembled polymers have an exponential distribution of chain lengths akin to what is observed for worm-like micellar systems. On increasing particle density, the polymeric chains self-organize to an ordered line-hexagonal phase where every chain is surrounded by six parallel chains, the transition is first order. On further increase in monomer density, the order is destroyed and we get a branched gel-like phase. This potential can be used to model semi-flexible equilibrium polymers with tunable semiflexibility and excluded volume. The use of the potential is computationally cheap and hence can be used to simulate and probe equilibrium polymer dynamics with long chains. The potential also gives a plausible method of tuning colloidal interactions in experiments such that one can obtain self-assembling polymeric chains made up of colloids and probe polymer dynamics using an optical microscope. Furthermore, we show how a modified potential leads to the observation of an intermediate nematic phase of self-assembled chains in between the low density disordered phase and the line-ordered hexagonal phase.
Density functional tight-binding and infrequent metadynamics can capture entropic effects in intramolecular hydrogen transfer reactions
Authors: Oliveira Luiz F. L. , Fu Christopher D. , Pfaendtner Jim
Published: April 2018

Infrequent metadynamics uses biased simulations to estimate the unbiased kinetics of a system, facilitating the calculation of rates and barriers. Here the method is applied to study intramolecular hydrogen transfer reactions involving peroxy radicals, a class of reactions that is challenging to model due to the entropic contributions of the formation of ring structures in the transition state. Using the self-consistent charge density-functional based tight-binding (DFTB) method, we applied infrequent metadynamics to the study of four intramolecular H-transfer reactions, demonstrating that the method can qualitatively reproduce these high entropic contributions, as observed in experiments and those predicted by transition state theory modeled by higher levels of theory. We also show that infrequent metadynamics and DFTB are successful in describing the relationship between transition state ring size and kinetic coefficients (e.g., activation energies and the pre-exponential factors).
Improved flexoelectricity in PVDF/barium strontium titanate (BST) nanocomposites
Authors: Hu Xinping , Zhou Yang , Liu Jie , Chu Baojin
Published: April 2018

The flexoelectric effect of polymers is normally much weaker than that of ferroelectric oxides. In order to improve the flexoelectric response of the poly(vinylidene fluoride) (PVDF) ferroelectric polymer, PVDF/Ba0.67Si0.33TiO3 (BST) nanocomposites were fabricated. BST nanofibers were prepared by the electrospinning method, and the fibers were further surface modified with H2O2 to achieve a stronger interfacial interaction between the fibers and polymer matrix. Due to the high dielectric properties and strong flexoelectric effect of the BST, both dielectric constant and flexoelectric response of the composite with 25 vol. % surface modified BST are 3–4 times higher than those of PVDF. The dependence of the dielectric constant and the flexoelectric coefficient on the composition of the nanocomposites can be fitted by the empirical Yamada model, and the dielectric constant and the flexoelectric coefficient are correlated by a linear relationship. This study provides an approach to enhance the flexoelectric response of PVDF-based polymers.
Diffusion of aqueous solutions of ionic, zwitterionic, and polar solutes
Authors: Teng Xiaojing , Huang Qi , Dharmawardhana Chamila Chathuranga , Ichiye Toshiko
Published: April 2018

The properties of aqueous solutions of ionic, zwitterionic, and polar solutes are of interest to many fields. For instance, one of the many anomalous properties of aqueous solutions is the behavior of water diffusion in different monovalent salt solutions. In addition, solutes can affect the stabilities of macromolecules such as proteins in aqueous solution. Here, the diffusivities of aqueous solutions of sodium chloride, potassium chloride, tri-methylamine oxide (TMAO), urea, and TMAO-urea are examined in molecular dynamics simulations. The decrease in the diffusivity of water with the concentration of simple ions and urea can be described by a simple model in which the water molecules hydrogen bonded to the solutes are considered to diffuse at the same rate as the solutes, while the remainder of the water molecules are considered to be bulk and diffuse at almost the same rate as pure water. On the other hand, the decrease in the diffusivity of water with the concentration of TMAO is apparently affected by a decrease in the diffusion rate of the bulk water molecules in addition to the decrease due to the water molecules hydrogen bonded to TMAO. In other words, TMAO enhances the viscosity of water, while urea barely affects it. Overall, this separation of water molecules into those that are hydrogen bonded to solute and those that are bulk can provide a useful means of understanding the short- and long-range effects of solutes on water.
Integrability and correspondence of classical and quantum non-linear three-mode systems
Authors: Odzijewicz A. , Wawreniuk E.
Published: April 2018

The relationship between classical and quantum three one-mode systems interacting in a non-linear way is described. We investigate the integrability of these systems by using the reduction procedure. The reduced coherent states for the quantum system are constructed. We find the explicit formulas for the reproducing measure for these states. Examples of some applications of the obtained results in non-linear quantum optics are presented.
Hydrogen intercalation of epitaxial graphene and buffer layer probed by mid-infrared absorption and Raman spectroscopy
Authors: Kunc J. , Rejhon M. , Hlídek P.
Published: April 2018

We have measured optical absorption in mid-infrared spectral range on hydrogen intercalated single layer epitaxial graphene and buffer layer grown on silicon face of SiC. We have used attenuated total reflection geometry to enhance absorption related to the surface and SiC/graphene interface. The Raman spectroscopy is used to show presence of buffer layer and single layer graphene prior to intercalation. We also present Raman spectra of quasi free standing monolayer and bilayer graphene after hydrogen intercalation at temperatures between 790 and 1510°C. We have found that although the Si-H bonds form at as low temperatures as 790°C, the well developed bond order has been reached only for samples intercalated at temperatures exceeding 1000°C. We also study temporal stability of hydrogen intercalated samples stored in ambient air. The optical spectroscopy shows on a formation of silyl and silylene groups on the SiC/graphene interface due to the residual atomic hydrogen left from the intercalation process.
Improved dielectric properties of Ag@TiO2/PVDF nanocomposites induced by interfacial polarization and modifiers with different carbon chain lengths
Authors: Chen Xizi , Liang Fei , Lu Wenzhong , Zhao Yifei , Fan Guifen , Wang Xiaochuan
Published: April 2018

In this study, poly(vinylidene fluoride) (PVDF)-based nanocomposites filled with surface-functionalized Ag@TiO2 core-shell nanoparticles were fabricated in order to achieve high dielectric permittivities. Using two phosphonic acid surfactants with differing carbon chain lengths, octyl and octadecyl phosphonic acid, the filler surfaces were modified to improve the dispersion of the core-shell filler in PVDF. The experimental results showed that the dielectric constant of the composite with fillers modified using octyl phosphonic acid (148 at 1 kHz) was almost three times that of the material with fillers modified using octadecyl phosphonic acid (58 at 1 kHz) at the same filler loading. The mechanisms of interfacial polarization between the modified core-shell filler and the polymer matrix were analyzed by introducing a circuit model based on AC impedance spectroscopy.
Diphenyl diselenide subcutaneous supplementation of dairy sheep: effects on oxidant and antioxidant status, inflammatory response and milk composition
Authors: Biazus Angelisa H. , Cazarotto Chrystian J. , Machado Gustavo , Bottari Nathieli B. , Alves Mariana S. , Morsch Vera M. , Schetinger Maria R. C. , Leal Marta L. R. , Fernandes Natieli F. , Moresco Rafael N. , Baldissera Matheus D. , Da Silva Aleksandro S.
Published: April 2018

Diphenyl diselenide ((PhSe)2) is a organoselenium compound with potent antioxidant properties. Therefore, the aim of the present study was to evaluate whether subcutaneous supplementation of (PhSe)2 in dairy sheep has positive effects on milk composition, as well as on the prevention of oxidative stress and exacerbated inflammatory response. For this, 16 primiparous recently calved sheep were divided into the following two groups, with eight animals in each: Group A, the control group; and Group B, the group subcutaneously supplemented with five doses of (PhSe)2 of 3.0µmol/kg each every 7 days. Blood samples from supplemented animals showed increased concentration of antioxidant enzymes (catalase, superoxide dismutase, glutathione peroxidase and glutathione-S-transferase), and reduced reactive oxygen species and lipid peroxidation, which prevented oxidative damage in the lactation period, as well as increased seric interleukin-10, an anti-inflammatory cytokine. In the sera, supplemented animals showed increased total antioxidant capacity and ferric-reducing ability of plasma compared with the control group. As a consequence, supplemented animals showed increased antioxidant variables, as well as reduced protein oxidation in milk samples. Moreover, milk from supplemented sheep showed a higher fat content, and lower total protein and lactose contents in some periods in the study, than did not-supplemented ewes. Seric concentrations of interleukin-1 were lower on Days 30 and 45 in supplemented animals, as well as the concentrations of tumour necrosis factor α in all periods, than were those in the control group, whereas the interleukin-10 concentrations were higher. Thus, dairy sheep supplementation of (PhSe)2 activated antioxidant and anti-inflammatory responses, and increased milk fat content. Moreover, this protocol increased the antioxidant and, consequently, reduced the oxidant concentration in milk, which is desirable for product quality.
Indirect selection for potential yield in early-generation, spaced plantings of wheat and other small-grain cereals: a review
Authors: Fischer R. A. , Rebetzke G. J.
Published: April 2018

Early-generation (e.g. F2–F4) selection for grain yield itself is frustrated in particular by the small amounts of seed available. However, there has long been an interest in traits related to yield and reasonably faithfully expressed in spaced planting arrangements using little seed; these are potentially useful as indirect selection criteria for yield, with the view to increasing genetic progress per unit cost. This subject is revisited in this review, targeting potential yield (yield in the absence of abiotic and biotic stresses) of small-grain cereals. A brief assessment of current breeding systems for self-pollinated crops such as wheat reveals that all have some stage during which selection among visually acceptable spaced plants has to, or could, be practiced. The relative performance of different genotypes in such spaced plantings is then explored, highlighting interactions arising from intergenotypic competition as well as from the extra space itself. The theory of indirect selection is presented, along with some practical examples. After a brief survey of possible selection traits and developments in high-throughput measurement, harvest index, fruiting efficiency and stomatal conductance (and its surrogates) are chosen for in-depth review. All three traits show promise, especially in the light of possible new ways of reducing the cost of their measurement in early generations. Remote sensing of foliage temperature for the detection of genotypic differences in stomatal conductance makes this clearly the most promising trait for thorough testing in commercial breeding populations. Such traits could be used directly or they could complement genomic selection in early generations.
Changes in DNA methylation are associated with heterogeneous cytoplasm suppression of the multi-ovary gene in wheat (Triticum aestivum)
Authors: Guo Jialin , Zhang Gaisheng , Tang Huali , Song Yulong , Ma Shoucai , Niu Na , Wang Junwei
Published: April 2018

Variety DUOII is a multi-ovary line of common wheat (Triticum aestivum L.) that has two or three pistils and three stamens. The multi-ovary trait is controlled by a dominant gene, the expression of which can be suppressed by the special heterogeneous cytoplasm of line TeZhiI (TZI). TZI has the nucleus of common wheat and the cytoplasm of Aegilops. DUOII (♀) × TZI (♂) shows the multi-ovary trait, whereas TZI (♀) × DUOII (♂) shows the mono-ovary trait. DNA methylation affects gene expression and plays a crucial role in organ and tissue differentiation. In order to study the relationship between DNA methylation and the suppression of the multi-ovary gene, we used methylation-sensitive amplification polymorphisms (MSAP) to assess the DNA methylation status of the reciprocal crosses. Genome-wide, 14 584 CCGG sites were detected and the overall methylation levels were 31.10% and 30.76% in the respective crosses DUOII × TZI and TZI × DUOII. Compared with DUOII × TZI, TZI × DUOII showed 672 sites (4.61%) in which methylation–demethylation processes occurred. The results showed that the special heterogeneous cytoplasm significantly changed DNA methylation, and this might have suppressed the multi-ovary gene. The results provide insight into the changing patterns of DNA methylation in the suppression of the multi-ovary gene, and provide essential background for further studies on the underlying mechanisms of heterogeneous cytoplasm suppression of the expression of the multi-ovary gene in wheat.
Making management decisions in the face of uncertainty: a case study using the Burdekin catchment in the Great Barrier Reef
Authors: Kuhnert P. M. , Pagendam D. E. , Bartley R. , Gladish D. W. , Lewis S. E. , Bainbridge Z. T.
Published: April 2018

Modelling and monitoring pollutants entering into the Great Barrier Reef (GBR) lagoon remain important priorities for the Australian and Queensland governments. Uncertainty analysis of pollutant load delivery to the GBR would: (1) inform decision makers on their ability to meet environmental targets; (2) identify whether additional measurements are required to make confident decisions; and (3) determine whether investments into remediation activities are actually making a difference to water quality and the health of the GBR. Using a case study from the Upper Burdekin catchment where sediment concentrations are the focus, herein we explore and demonstrate different ways of communicating uncertainty to a decision maker. In particular, we show how exceedance probabilities can identify hot spots for future monitoring or remediation activities and how they can be used to inform target setting activities. We provide recommendations for water quality specialists that allow them to make more informed and scientifically defensible decisions that consider uncertainty in both the monitoring and modelling data, as well as allowing the calculation of exceedances from a threshold.
Re-assessing the ‘weight’ of translations within the context of translated soap operas
Authors: Okyayuz Şirin
Published: April 2018

In translation studies, investigating translations beyond the implications, realities and difficulties of single texts and single
language combinations, viewing the larger picture surrounding translations and following the translations through to the impacts
they produce wherever they are received, is an integral part of the discipline. The study discussed in this article is an effort
to present food for thought for audiovisual translators of soap operas. Turkish soap operas have been aired in 90 countries around
the world, reaching over 400 million viewers, according to 2014 statistics from the sector. The aim of the study is to indicate
the type of translated soap operas preferred in different regions of the world; to explain, on the basis of feedback from experts,
the public and local and international media, why these are watched; and to investigate the translation modes and strategies used
to market the translations successfully in the receiver markets.
Lugares comunes de la traducción en la Edad Media y Moderna
Authors: García Gavín Santiago
Published: April 2018

L’objectif de cet article est d'examiner le rôle littéraire de la traduction dans la mesure où elle se réfère à un changement dans
le concept de littérature. Ce paradigme remonte à la légitimité des sources anciennes et s’étend jusqu’à l’exigence de
l’originalité de la création littéraire, qui s’échelonne entre l'époque médiévale et les Temps modernes. Alors qu'à l’époque
médiévale, la traduction était considérée comme un processus productif qui soutenait « l’auctoritas » et faisait partie de la
vérité symbolique, pendant les Temps modernes, son rôle était de préserver la fiction d’authenticité demandée par un auteur.
L’introduction de l’innovation culturelle et littéraire joue également un rôle ici, de même que la distanciation de la fable et la
figure rhétorique paradoxale.
Lost in translation
Authors: Wook-Dong Kim
Published: April 2018

This paper explores how translation of foreign film titles has been carried out in South Korea since foreign films first arrived in
Korea following its emancipation from Japanese colonial rule. With reference to audiovisual translation in general and film or
screen translation in particular, this paper discusses the extent of the mistakes made by Korean translators due to a lack of
thorough contextual knowledge of the source language and culture. Most Korean translations of foreign films result in strange,
surreal, and at best funny adaptations. Discussion regarding “bad,” total, or almost total mistranslations focuses on (1) words
with multiple meanings (homonyms and heteronyms); (2) slang and colloquial expressions; (3) words with culturally specific
features; and (4) proper nouns and common nouns. This paper concludes that in an era of globalization, film title translation in
Korea increasingly shows a trend towards transliteration rather than translation – either literal or liberal.
Neardone;awfulstable;reallychanging
Authors: Tagliamonte Sali A.
Published: April 2018

This paper examines adverb formation with-ly, e.g.,slow/slowly, and uses a large archive of synchronic dialects to uncover the current state and historical trajectory of this process. The results reveal that English adverbs are a variegated system. The intensifying adverbreallyis a frequent form while sentential adverbs appear to be a newer layer in the system. In contrast, manner adverbs are constrained by the semantic interpretation of the adverb as abstract or concrete. These results expose the complexity of the English adverb system and demonstrate that adverb formation is an ideal site for uncovering historical processes in synchronic data.
Irony in a theory of textual meaning
Authors: Jeffries Lesley
Published: April 2018

This chapter attempts to map out different types of irony, using a model of communication which encompasses a range of potential meaning including linguistic, textual, interpersonal and situational meaning. It is argued that the resulting description of potentially ironic examples can help to show where apparently different types have overlap. It also attempts to demonstrate the boundaries of irony in relation to linguistic humour more generally and to articulate some of the distinctions between irony and other forms of apparent clash such as paradox and hypocrisy. The chapter concludes that irony can occur without intention and despite, not because of, an audience, though both intentionality and addressee(s) are needed for the most recognisable forms of verbal irony.
Verbal irony, politeness… and three ironic types
Authors: Simonin Olivier
Published: April 2018

This paper critically examines Leech’s (2014) view that verbal or conversational irony is subsumed by politeness considerations, and proposes a new, threefold account of verbal irony. Although Leech’s pragmatic model of irony is inadequate as a whole, it highlights crucial aspects of irony relating to (im)politeness theory. I propose an alternative account of verbal irony that first recognizes two major types, polar irony and impersonation irony, which have been referred to in the literature under various denominations, including oppositional irony and echoic irony (Simpson 2011). In polar irony, a desirable state of affairs is evoked that is blatantly contradicted by facts; in impersonation irony, the speaker takes up someone else’s viewpoint or an assumed identity to ridicule targets or victims of the irony. Building on Leech’s observations, I argue that a last type should be added,
mock politeness irony, noting that the three types of verbal irony can combine. In the course of the discussion I review psycholinguistic data, other conceptions of irony, and the connection between politeness, irony and banter.
The Rolling Stones promoting Monty Python
Authors: Sorlin Sandrine
Published: April 2018

Based on Text World Theory, this chapter offers a fine-grained analysis of how irony and banter are likely to be processed by viewers watching a promotional video but also highlights the pragmatic functions of such an indirect strategy. It dissects a 1:40 tongue-in-cheek video which served as an introduction to the 2014
Monty Python Live (Mostly) press conference. It features Mick Jagger accusing the coming troupe of being “wrinkly old men trying to relive their youth”, using irony and banter as powerful means of promotion. Bringing together different theoretical frameworks of irony that are usually described as competing, this chapter highlights how expectations are twisted in the “text-world” of the video through the use of (mock) dramatic irony, generating pragmatic paradoxes.
Norwegian Discourse Ellipsis
Authors: Nygård Mari
Published: April 2018

This book develops a grammar model which accounts for discourse ellipses in spoken Norwegian. This is a previously unexplored area, which has also been sparsely investigated internationally. The model takes an exoskeletal view, where lexical items are inserted late and where syntactic structure is generated independently of lexical items. Two major questions are addressed. Firstly, is there active syntactic structure in the ellipsis site? Secondly, how are discourse ellipses licensed? It is argued that both structural and semantic restrictions are required to account for the empirical patterns.
Discourse ellipses can be seen as a contextual adaptation. Ellipsis is only possible in certain contexts. The existence of ellipsis may lead to the impression that syntax is partly destroyed. However, the analysis shows that narrow syntax is not affected. The underlying structure stays intact, as the licensing restrictions concern only phonological realization. Hence, the grammar of discourse ellipses is best characterized as an interface phenomenon.
Machinability Study on Milling Kenaf Fiber Reinforced Plastic Composite Materials using Design of Experiments
Authors: Azmi H. , Haron C. H. C. , Ghani J. A. , Suhaily M. , Yuzairi A. R.
Published: April 2018

The surface roughness (Ra) and delamination factor (Fd) of a milled kenaf reinforced plastic composite materials are depending on the milling parameters (spindle speed, feed rate and depth of cut). Therefore, a study was carried out to investigate the relationship between the milling parameters and their effects on a kenaf reinforced plastic composite materials. The composite panels were fabricated using vacuum assisted resin transfer moulding (VARTM) method. A full factorial design of experiments was use as an initial step to screen the significance of the parameters on the defects using Analysis of Variance (ANOVA). If the curvature of the collected data shows significant, Response Surface Methodology (RSM) is then applied for obtaining a quadratic modelling equation that has more reliable in expressing the optimization. Thus, the objective of this research is obtaining an optimum setting of milling parameters and modelling equations to minimize the surface roughness (Ra) and delamination factor (Fd) of milled kenaf reinforced plastic composite materials. The spindle speed and feed rate contributed the most in affecting the surface roughness and the delamination factor of the kenaf composite materials.
COSSMO: predicting competitive alternative splice site selection using deep learning
Authors: Bretschneider Hannes , Gandhi Shreshth , Deshwar Amit G , Zuberi Khalid , Frey Brendan J
Published: April 2018

Motivation

Alternative splice site selection is inherently competitive and the probability of a given splice site to be used also depends on the strength of neighboring sites. Here, we present a new model named the competitive splice site model (COSSMO), which explicitly accounts for these competitive effects and predicts the percent selected index (PSI) distribution over any number of putative splice sites. We model an alternative splicing event as the choice of a 3′ acceptor site conditional on a fixed upstream 5′ donor site or the choice of a 5′ donor site conditional on a fixed 3′ acceptor site. We build four different architectures that use convolutional layers, communication layers, long short-term memory and residual networks, respectively, to learn relevant motifs from sequence alone. We also construct a new dataset from genome annotations and RNA-Seq read data that we use to train our model.

Results

COSSMO is able to predict the most frequently used splice site with an accuracy of 70% on unseen test data, and achieve an R2 of 0.6 in modeling the PSI distribution. We visualize the motifs that COSSMO learns from sequence and show that COSSMO recognizes the consensus splice site sequences and many known splicing factors with high specificity.

Availability and implementation

Model predictions, our training dataset, and code are available from http://cossmo.genes.toronto.edu.

Supplementary information

Supplementary data are available at Bioinformatics online.
A scalable estimator of SNP heritability for biobank-scale data
Authors: Wu Yue , Sankararaman Sriram
Published: April 2018

Motivation

Heritability, the proportion of variation in a trait that can be explained by genetic variation, is an important parameter in efforts to understand the genetic architecture of complex phenotypes as well as in the design and interpretation of genome-wide association studies. Attempts to understand the heritability of complex phenotypes attributable to genome-wide single nucleotide polymorphism (SNP) variation data has motivated the analysis of large datasets as well as the development of sophisticated tools to estimate heritability in these datasets. Linear mixed models (LMMs) have emerged as a key tool for heritability estimation where the parameters of the LMMs, i.e. the variance components, are related to the heritability attributable to the SNPs analyzed. Likelihood-based inference in LMMs, however, poses serious computational burdens.

Results

We propose a scalable randomized algorithm for estimating variance components in LMMs. Our method is based on a method-of-moment estimator that has a runtime complexity O(NMB) for N individuals and M SNPs (where B is a parameter that controls the number of random matrix-vector multiplications). Further, by leveraging the structure of the genotype matrix, we can reduce the time complexity to O(NMBmax( log⁡3N, log⁡3M)).

We demonstrate the scalability and accuracy of our method on simulated as well as on empirical data. On standard hardware, our method computes heritability on a dataset of 500 000 individuals and 100 000 SNPs in 38 min.

Availability and implementation

The RHE-reg software is made freely available to the research community at: https://github.com/sriramlab/RHE-reg.
AmpUMI: design and analysis of unique molecular identifiers for deep amplicon sequencing
Authors: Clement Kendell , Farouni Rick , Bauer Daniel E , Pinello Luca
Published: April 2018

Motivation

Unique molecular identifiers (UMIs) are added to DNA fragments before PCR amplification to discriminate between alleles arising from the same genomic locus and sequencing reads produced by PCR amplification. While computational methods have been developed to take into account UMI information in genome-wide and single-cell sequencing studies, they are not designed for modern amplicon-based sequencing experiments, especially in cases of high allelic diversity. Importantly, no guidelines are provided for the design of optimal UMI length for amplicon-based sequencing experiments.

Results

Based on the total number of DNA fragments and the distribution of allele frequencies, we present a model for the determination of the minimum UMI length required to prevent UMI collisions and reduce allelic distortion. We also introduce a user-friendly software tool called AmpUMI to assist in the design and the analysis of UMI-based amplicon sequencing studies. AmpUMI provides quality control metrics on frequency and quality of UMIs, and trims and deduplicates amplicon sequences with user specified parameters for use in downstream analysis.

Availability and implementation

AmpUMI is open-source and freely available at http://github.com/pinellolab/AmpUMI.
The Kappa platform for rule-based modeling
Authors: Boutillier Pierre , Maasha Mutaamba , Li Xing , Medina-Abarca Héctor F , Krivine Jean , Feret Jérôme , Cristescu Ioana , Forbes Angus G , Fontana Walter
Published: April 2018

Motivation

We present an overview of the Kappa platform, an integrated suite of analysis and visualization techniques for building and interactively exploring rule-based models. The main components of the platform are the Kappa Simulator, the Kappa Static Analyzer and the Kappa Story Extractor. In addition to these components, we describe the Kappa User Interface, which includes a range of interactive visualization tools for rule-based models needed to make sense of the complexity of biological systems. We argue that, in this approach, modeling is akin to programming and can likewise benefit from an integrated development environment. Our platform is a step in this direction.

Results

We discuss details about the computation and rendering of static, dynamic, and causal views of a model, which include the contact map (CM), snaphots at different resolutions, the dynamic influence network (DIN) and causal compression. We provide use cases illustrating how these concepts generate insight. Specifically, we show how the CM and snapshots provide information about systems capable of polymerization, such as Wnt signaling. A well-understood model of the KaiABC oscillator, translated into Kappa from the literature, is deployed to demonstrate the DIN and its use in understanding systems dynamics. Finally, we discuss how pathways might be discovered or recovered from a rule-based model by means of causal compression, as exemplified for early events in EGF signaling.

Availability and implementation

The Kappa platform is available via the project website at kappalanguage.org. All components of the platform are open source and freely available through the authors’ code repositories.
Deep neural networks and distant supervision for geographic location mention extraction
Authors: Magge Arjun , Weissenbacher Davy , Sarker Abeed , Scotch Matthew , Gonzalez-Hernandez Graciela
Published: April 2018

Motivation

Virus phylogeographers rely on DNA sequences of viruses and the locations of the infected hosts found in public sequence databases like GenBank for modeling virus spread. However, the locations in GenBank records are often only at the country or state level, and may require phylogeographers to scan the journal articles associated with the records to identify more localized geographic areas. To automate this process, we present a named entity recognizer (NER) for detecting locations in biomedical literature. We built the NER using a deep feedforward neural network to determine whether a given token is a toponym or not. To overcome the limited human annotated data available for training, we use distant supervision techniques to generate additional samples to train our NER.

Results

Our NER achieves an F1-score of 0.910 and significantly outperforms the previous state-of-the-art system. Using the additional data generated through distant supervision further boosts the performance of the NER achieving an F1-score of 0.927. The NER presented in this research improves over previous systems significantly. Our experiments also demonstrate the NER’s capability to embed external features to further boost the system’s performance. We believe that the same methodology can be applied for recognizing similar biomedical entities in scientific literature.
DeepFam: deep learning based alignment-free method for protein family modeling and prediction
Authors: Seo Seokjun , Oh Minsik , Park Youngjune , Kim Sun
Published: April 2018

Motivation

A large number of newly sequenced proteins are generated by the next-generation sequencing technologies and the biochemical function assignment of the proteins is an important task. However, biological experiments are too expensive to characterize such a large number of protein sequences, thus protein function prediction is primarily done by computational modeling methods, such as profile Hidden Markov Model (pHMM) and k-mer based methods. Nevertheless, existing methods have some limitations; k-mer based methods are not accurate enough to assign protein functions and pHMM is not fast enough to handle large number of protein sequences from numerous genome projects. Therefore, a more accurate and faster protein function prediction method is needed.

Results

In this paper, we introduce DeepFam, an alignment-free method that can extract functional information directly from sequences without the need of multiple sequence alignments. In extensive experiments using the Clusters of Orthologous Groups (COGs) and G protein-coupled receptor (GPCR) dataset, DeepFam achieved better performance in terms of accuracy and runtime for predicting functions of proteins compared to the state-of-the-art methods, both alignment-free and alignment-based methods. Additionally, we showed that DeepFam has a power of capturing conserved regions to model protein families. In fact, DeepFam was able to detect conserved regions documented in the Prosite database while predicting functions of proteins. Our deep learning method will be useful in characterizing functions of the ever increasing protein sequences.

Availability and implementation

Codes are available at https://bhi-kimlab.github.io/DeepFam.
Unsupervised embedding of single-cell Hi-C data
Authors: Liu Jie , Lin Dejun , Yardımcı Galip Gürkan , Noble William Stafford
Published: April 2018

Motivation

Single-cell Hi-C (scHi-C) data promises to enable scientists to interrogate the 3D architecture of DNA in the nucleus of the cell, studying how this structure varies stochastically or along developmental or cell-cycle axes. However, Hi-C data analysis requires methods that take into account the unique characteristics of this type of data. In this work, we explore whether methods that have been developed previously for the analysis of bulk Hi-C data can be applied to scHi-C data. We apply methods designed for analysis of bulk Hi-C data to scHi-C data in conjunction with unsupervised embedding.

Results

We find that one of these methods, HiCRep, when used in conjunction with multidimensional scaling (MDS), strongly outperforms three other methods, including a technique that has been used previously for scHi-C analysis. We also provide evidence that the HiCRep/MDS method is robust to extremely low per-cell sequencing depth, that this robustness is improved even further when high-coverage and low-coverage cells are projected together, and that the method can be used to jointly embed cells from multiple published datasets.
Gene prioritization using Bayesian matrix factorization with genomic and phenotypic side information
Authors: Zakeri Pooya , Simm Jaak , Arany Adam , ElShal Sarah , Moreau Yves
Published: April 2018

Motivation

Most gene prioritization methods model each disease or phenotype individually, but this fails to capture patterns common to several diseases or phenotypes. To overcome this limitation, we formulate the gene prioritization task as the factorization of a sparsely filled gene-phenotype matrix, where the objective is to predict the unknown matrix entries. To deliver more accurate gene-phenotype matrix completion, we extend classical Bayesian matrix factorization to work with multiple side information sources. The availability of side information allows us to make non-trivial predictions for genes for which no previous disease association is known.

Results

Our gene prioritization method can innovatively not only integrate data sources describing genes, but also data sources describing Human Phenotype Ontology terms. Experimental results on our benchmarks show that our proposed model can effectively improve accuracy over the well-established gene prioritization method, Endeavour. In particular, our proposed method offers promising results on diseases of the nervous system; diseases of the eye and adnexa; endocrine, nutritional and metabolic diseases; and congenital malformations, deformations and chromosomal abnormalities, when compared to Endeavour.

Availability and implementation

The Bayesian data fusion method is implemented as a Python/C++ package: https://github.com/jaak-s/macau. It is also available as a Julia package: https://github.com/jaak-s/BayesianDataFusion.jl. All data and benchmarks generated or analyzed during this study can be downloaded at https://owncloud.esat.kuleuven.be/index.php/s/UGb89WfkZwMYoTn.

Supplementary information

Supplementary data are available at Bioinformatics online.
A space and time-efficient index for the compacted colored de Bruijn graph
Authors: Almodaresi Fatemeh , Sarkar Hirak , Srivastava Avi , Patro Rob
Published: April 2018

Motivation

Indexing reference sequences for search—both individual genomes and collections of genomes—is an important building block for many sequence analysis tasks. Much work has been dedicated to developing full-text indices for genomic sequences, based on data structures such as the suffix array, the BWT and the FM-index. However, the de Bruijn graph, commonly used for sequence assembly, has recently been gaining attention as an indexing data structure, due to its natural ability to represent multiple references using a graphical structure, and to collapse highly-repetitive sequence regions. Yet, much less attention has been given as to how to best index such a structure, such that queries can be performed efficiently and memory usage remains practical as the size and number of reference sequences being indexed grows large.

Results

We present a novel data structure for representing and indexing the compacted colored de Bruijn graph, which allows for efficient pattern matching and retrieval of the reference information associated with each k-mer. As the popularity of the de Bruijn graph as an index has increased over the past few years, so have the number of proposed representations of this structure. Existing structures typically fall into two categories; those that are hashing-based and provide very fast access to the underlying k-mer information, and those that are space-frugal and provide asymptotically efficient but practically slower pattern search. Our representation achieves a compromise between these two extremes. By building upon minimum perfect hashing and making use of succinct representations where applicable, our data structure provides practically fast lookup while greatly reducing the space compared to traditional hashing-based implementations. Further, we describe a sampling scheme for this index, which provides the ability to trade off query speed for a reduction in the index size. We believe this representation strikes a desirable balance between speed and space usage, and allows for fast search on large reference sequences.

Finally, we describe an application of this index to the taxonomic read assignment problem. We show that by adopting, essentially, the approach of Kraken, but replacing k-mer presence with coverage by chains of consistent unique maximal matches, we can improve the space, speed and accuracy of taxonomic read assignment.

Availability and implementation

pufferfish is written in C++11, is open source, and is available at https://github.com/COMBINE-lab/pufferfish.

Supplementary information

Supplementary data are available at Bioinformatics online.