bluuebunny/crossref_metadata_2025_split huggingface dataset:
C19ORF66 is an Interferon-Stimulated Gene (ISG) which Inhibits Human Immunodeficiency Virus-1
Authors: Xiong Weidong , Contreras Deisy , Ignatius Irudayam Joseph , Ali Ayub , Yang Otto O. , Arumugaswami Vaithilingaraja 
Published: April 2016

ABSTRACTInnate immunity is the first line of defense against invading microbes1. The type I interferon (IFN) pathway plays a key role in controlling Human Immunodeficiency Virus type 1 (HIV-1) replication2,3. We identified an IFN-α stimulated gene C19ORF66 that we term Suppressor of Viral Activity (SVA). Full length SVA-1 protein inhibits HIV-1 by blocking virion production. SVA splice variants truncated at the C-terminus and/or disrupted at the nuclear export signal (NES) lose antiviral activity and localize to nucleus, while full length SVA-1 co-localizes with HIV-1 p24 protein in the cytoplasmic compartment of infected cells. SVA-1 is structurally and functionally conserved across species, including mouse and chimpanzee. We provide the first description of the effector function of the gene SVA/C190RF66 as an innate immune factor with anti-HIV-1 activity.
Different speciation types meet in a Mediterranean genus: the biogeographic history ofCymbalaria(Plantaginaceae)
Authors: Carnicero Pau , Sáez Llorenç , Garcia-Jacas Núria , Galbany-Casals Mercè 
Published: April 2016

AbstractCymbalariais a Mediterranean genus including ten species and six subspecies growing on rocky habitats. A very fragmented distribution, the different ecologic preferences of partially sympatric species and the presence of different ploidy levels, suggest the role of allopatric, sympatric ecological and polyploid speciation in its evolution. The aims of this study are to verify the monophyly and to reconstruct the phylogenetic relationships ofCymbalaria, to infer its biogeographic history by estimating the lineage divergence dates and the ancestral areas of distribution, and to discuss the role of different types of speciation. To address these issues, we constructed a complete phylogeny of the genus with ITS, 3’ETS,ndhF andrpl32-trnL sequences. A time-calibrated phylogeny and an ancestral-area estimation were obtained from the nrDNA data. The evidence supported the genusCymbalariaas monophyletic. It originated ca. 5 Ma and three lineages segregated rapidly, one with the single extant taxaCymbalaria microcalyxsubsp.microcalyxand the other two corresponding to western and central-eastern species, respectively. The main diversification events occurred after the onset of the Mediterranean climate and during Pleistocene oscillations. Founder-event and sympatric speciation were supported by the biogeographic analyses, and chromosome data combined with our phylogeny supported at least two polyploidization events. We observed that the consequences of physical barriers were different amongst the different species.Supplementary MaterialElectronic Supplement (Figure S1, Table S1) are available in the Supplementary Data section of the online version of this article (http://www.ingentaconnect.com/content/iapt/tax).
Human infants’ understanding of social imitation: Inferences of affiliation from third party observations
Authors: Powell Lindsey J. , Spelke Elizabeth S. 
Published: April 2016

AbstractImitation is ubiquitous in positive social interactions. For adult and child observers, it also supports inferences about the participants in such interactions and their social relationships, but the origins of these inferences are obscure. Do infants attach social significance to this form of interaction? Here we test 4- to 5.5-month-old infants’ interpretation of imitation, asking if the imitative interactions they observe support inferences of social affiliation across 10 experimental conditions that varied the modality of the imitation (movement vs. sound), the roles of specific characters (imitators vs. targets), the number of characters in the displays (3 vs. 5), and the number of parties initiating affiliative test events (1 vs. 2). These experiments, together with one experiment conducted with 12-month-old infants, yielded three main findings. First, infants expect that characters who engaged in imitation will approach and affiliate with the characters whom they imitated. Second, infants show no evidence of expecting that characters who were targets of imitation will approach and affiliate with their imitators. Third, analyzing imitative interactions is difficult for young infants, whose expectations vary in strength depending on the number of characters to be tracked and the number of affiliative actors to be compared. These findings have implications for our understanding of social imitation, and they provide methods for advancing understanding of other aspects of early social cognitive development.
Pan-Retinal Characterisation of Light Responses from Ganglion Cells in the Developing Mouse Retina
Authors: Hilgen Gerrit , Pirmoradian Sahar , Pamplona Daniela , Kornprobst Pierre , Cessac Bruno , Hennig Matthias H. , Sernagor Evelyne 
Published: April 2016

AbstractWe have investigated the ontogeny of light-driven responses in mouse retinal ganglion cells (RGCs). Using a large-scale, high-density multielectrode array, we recorded from hundreds to thousands of RGCs simultaneously at pan-retinal level, including dorsal and ventral locations. Responses to different contrasts not only revealed a complex developmental profile for ON, OFF and ON-OFF RGC types, but also unveiled differences between dorsal and ventral RGCs. At eye-opening, dorsal RGCs of all types were more responsive to light, perhaps indicating an environmental priority to nest viewing for pre-weaning pups. The developmental profile of ON and OFF RGCs exhibited antagonistic behavior, with the strongest ON responses shortly after eye-opening, followed by an increase in the strength of OFF responses later on. Further, we found that with maturation receptive field (RF) center sizes decrease, responses to light get stronger, and centers become more circular while seeing differences in all of them between RGC types. These findings show that retinal functionality is not spatially homogeneous, likely reflecting ecological requirements that favour the early development of dorsal retina, and reflecting different roles in vision in the mature animal.
NGS-based assay for frequent newborn inherited diseases: from development to implementation
Authors: Simakova T. , Bragin A. , Zaytseva M. , Clemente C. , Lewicka M. , Machado J.C. , Costa J.L. , Hughes M. , Hertz-Fowler C. , Petrova N. , Polyakov A. , Zinchenko R. , Kondratyeva E. , Pavlov A. 
Published: April 2016

ABSTRACTNGS is a powerful tool for the diagnostics of inherited diseases. A number of studies devoted to the development and validation of targeted NGS panels are published. Here we present not only development and validation of an assay, but report our experience on introduction of a new approach into the real clinical practice. The assay is intended for the diagnostics of frequent newborn inherited diseases: cystic fibrosis, phenylketonuria and galactosemia. The analysis is performed on the Ion PGM™ sequencing platform and allows the detection of single-nucleotide variations as well as copy number variants. We developed the software performing data quality control, providing decision-support variant annotation and generating the medical report that enables clinical application of the assay. Analytical validation of the assay was performed by bi-directional Sanger sequencing of the most part of the targeted region. Clinical validation was performed by multicenter blind testing of clinical and control samples. Sensitivity and specificity of the assay are above 99%. We have developed statements for test ordering, test acquisition form and practical recommendations for the results interpretation. The test has been successfully applied for the confirmatory diagnostics in a clinical laboratory during a year. Thus, the developed assay is a comprehensive ready-to-use CE-IVD solution for clinical diagnostics.
Reconstructing contact network parameters from viral phylogenies
Authors: McCloskey Rosemary M. , Liang Richard H. , Poon Art F.Y. 
Published: April 2016

AbstractModels of the spread of disease in a population often make the simplifying assumption that the population is homogeneously mixed, or is divided into homogeneously mixed compartments. However, human populations have complex structures formed by social contacts, which can have a significant influence on the rate of epidemic spread. Contact network models capture this structure by explicitly representing each contact which could possibly lead to a transmission. We developed a method based on kernel approximate Bayesian computation (kernel-ABC) for estimating structural parameters of the contact network underlying an observed viral phylogeny. The method combines adaptive sequential Monte Carlo for ABC, Gillespie simulation for propagating epidemics though networks, and a kernel-based tree similarity score. We used the method to fit the Barabási-Albert network model to simulated transmission trees, and also applied it to viral phylogenies estimated from five published HIV sequence datasets. On simulated data, we found that the preferential attachment power and the number of infected nodes in the network can often be accurately estimated. On the other hand, the mean degree of the network, as well as the total number of nodes, were not estimable with kernel-ABC. We observed substantial heterogeneity in the parameter estimates on real datasets, with point estimates for the preferential attachment power ranging from 0.06 to 1.05. These results underscore the importance of considering contact structures when performing phylodynamic inference. Our method offers the potential to quantitatively investigate the contact network structure underlying viral epidemics.
AyurvedicAmalaki Rasayanapromotes improved stress tolerance and thus has anti-aging effects inDrosophila melanogaster
Authors: Dwivedi Vibha , Lakhotia Subhash C. 
Published: April 2016

AbstractEthnopharmacological relevanceAmalaki Rasayana(AR) is a common Ayurvedic herbal formulation ofPhyllanthus emblicafruits and other ingredients and is used for general good health and healthy aging. We earlier reported it to improve life history traits and to suppress neurodegeneration as well as induced apoptosis inDrosophila.Aim of the studyTo examine effects of dietary AR supplement on cell stress responses inDrosophila melanogaster.Materials and methodsLarvae/flies, reared on normal food or on that supplemented with 0.5% (w/v) AR, were exposed to crowding, thermal or oxidative stress and examined for survival, stress tolerance and levels of lipid peroxides, SOD and HSPs.ResultsWild type larvae/flies reared on AR supplemented food survived the various cell stresses much better than those reared on normal food. AR-fed mutantpark13orDJ-1βDelta93(Parkinson’s disease model) larvae, however, showed only partial or no protection, respectively, against paraquat-induced oxidative stress, indicating essentiality ofDJ-1βfor AR mediated oxidative stress tolerance. AR feeding reduced the accumulation of reactive oxygen species (ROS) and lipid peroxidation even in aged (35 day old) wild type flies while enhancing superoxide dismutase (SOD) activity. We show for the first time that while Hsp70 or Hsp83 expression under normal or stress conditions was not differentially affected by AR feeding, Hsp27 levels were elevated in AR fed wild type control as well as heat shocked larvae. Therefore, besides the known anti-oxidant activity ofPhyllanthus emblicafruits, dietary AR also enhances cellular levels of Hsp27.ConclusionIn the context of the reported “anti-aging” and “healthy-aging” effects of AR, the present in vivo study on a model organisms shows that AR feeding significantly improves tolerance to a variety of cell stresses through reduced ROS and lipid peroxidation and enhanced SOD activity and Hsp27. Such improved cellular defences following dietary AR provide better homeostasis and thereby improve the life-span and quality of organism’s life.
Mechanical design, multiple criteria decision making and Pareto optimality gap
Authors: Kaliszewski Ignacy , Kiczkowiak Tomasz , Miroforidis Janusz 
Published: April 2016

Purpose
We present an approach to multiple criteria mechanical design problems, for cases where problem complexity precludes derivation of the whole Pareto front. For such problems we propose to limit search, and hence also derivation, of the Pareto front exclusively to regions of the direct designer’s interest, thus saving on computing efforts and gaining on tractable problem sizes.

Design/methodology/approach
To achieve the purpose, we frame the decision making process (design) into a combination of three specific concepts, namely decision maker's preference capture, local Pareto front search and approximate multiobjective optimization with assessments of the Pareto optimality gap.

We illustrate the approach with two small design problems, namely Pareto optimal round tube beam and Pareto optimal pneumatic high speed machine drive selection. We solve these problems in a setting which can be regarded as representative for problem solving in real environment.

Findings
On the decision making side, the proposed approach has turned out to be a versatile tool for selecting designs from the Pareto suboptimal ones, where each such a Pareto suboptimal design has an explicit assessment of the Pareto optimality gap. On the technical (optimization) side, it has been demonstrated that the approach seamlessly works with evolutionary computations, structured to the specific needs of the approach.

Research limitations/implications
It has been shown that the navigation over the Pareto front can be achieved with limited effort, both on the cognitive and the computing side. Moreover, navigation over the Pareto front can be focused from the very beginning of the design selection process on the regions of the Pareto front which are of the direct designer’s interest. This eliminates the need to derive (or only approximate) the whole Pareto front, a tangible asset as the derivation of that set is the main factor precluding scalability of design selection problems to higher dimensions (to higher problem sizes).

Practical implications
Because of the general formulation of the Pareto optimal design selection problem considered in the paper, the absence of any assumptions on its form and easiness of implementation of the underlying procedure of the proposed approach, the paper offers a clear option to approaches based on classical optimization computations.

Originality/value
The approach offers derivation of Pareto suboptimal designs with assessments of the Pareto optimality gap, whereas currently available multiobjective evolutionary optimization algorithms which derive Pareto suboptimal designs as well, offer no such assessments. Thus, the approach provides a firm ground to valuate designs resulting from approximate multiobjective optimization computations.
Generalized Finite Element Method in linear and nonlinear structural dynamic analyses
Authors: Piedade Neto Dorival , Baroncini Proenca Sergio Persival 
Published: April 2016

PurposeThe purpose of this study is to evaluate the accuracy and numerical stability of the Generalized Finite Element Method (GFEM) for solving structural dynamic problems.Design/methodology/approachThe GFEM is a numerical method based on the Partition of Unity (PU) concept. The method can be understood as an extension of the conventional Finite Element Method (FEM) for which the local approximation provided by the shape functions can be improved by means of enrichment functions. Polynomial enrichment functions are hereby used combined with an implicit time-stepping integration technique for improving the dynamical response of the models. Both consistent and lumped mass matrices techniques are tested. The method accuracy and stability are investigated through linear and nonlinear elastic problems.FindingsThe results indicate that the adopted strategies can provide stable and accurate responses for GFEM in dynamic analyses. Furthermore, the mass lumping technique provided remarkable reductions of the system of equation condition number, therefore leading to more stable numerical models.Originality/valueThe evaluated features of GFEM models for implicit time-stepping integration schemes represent new information of great deal of interest regarding linear and nonlinear dynamic analyses using such a method.
Hydromagnetic flow of heat absorbing and radiating fluid over exponentially stretching sheet with partial slip and viscous and Joule dissipation
Authors: Seth Gauri Shanker , Sharma Rohit , Kumbhakar Bidyasagar , Chamkha Ali J 
Published: April 2016

Purpose
An investigation of hydromagnetic two dimensional boundary layer flow with heat transfer of a viscous, incompressible, electrically conducting, heat absorbing and optically thick heat radiating fluid over a permeable exponentially stretching sheet considering the effects of viscous and Joule dissipations in the presence of velocity and thermal slip is carried out.

Design/methodology/approach
Using similarity transform, governing differential equations representing mathematical model of the problem are solved with the help of fourth-order Runge-Kutta method along with shooting technique. Numerical solutions of fluid velocity and fluid temperature are depicted graphically for various values of pertinent flow parameters whereas numerical values of wall velocity gradient and wall temperature gradient are displayed graphically for various values of pertinent flow parameters.

Findings
Numerical results obtained in this paper are compared with earlier published results and are found to be in excellent agreement. Magnetic field and suction tend to enhance the wall velocity gradient whereas dimensionless co-ordinate, injection and velocity slip factor have reverse effect on it. Suction and heat absorption tend to enhance wall temperature gradient whereas magnetic field, velocity slip factor, injection, thermal radiation, thermal slip factor and viscous dissipation have reverse effect on it.

Originality/value
The investigation of this problem may have bearing in several engineering processes such as extrusion of plastic sheet, annealing and tinning of copper wire, paper production, crystal growing and glass blowing, continuous casting of metals and spinning of fibers.
Particle swarm optimization algorithm for suspendome structure under multiple loading cases
Authors: Liu Xuechun , Zhang Ailin , Zhang Xun , Tian Chen 
Published: April 2016

Purpose
The purpose of the paper is to provide an optimization algorithm for a large-span suspendome which is a spatial prestressed structure with complex mechanical characteristics. The algorithm optimizes the cable tension, the dimension of components, the shape parameters of structure simultaneously.

Design/methodology/approach
With the span-to-rise ratio, the length of the strut, the cable tension, the cross-sectional area of the cables and the cross-sectional size of steel members as design variables and the gross mass of entire structure as the objective function, a mathematical optimization method was proposed in the paper based on the hybridization of full stress and particle swarm optimization.

Findings
By using the improved particle swarm optimization algorithm, the coupling problem of the three types of design variables was resolved: the cable tension and the size and shape of the structure were optimized simultaneously for a suspendome. A program was compiled according to this method and was used for a large-span suspendome. The optimization results of the suspendome demonstrates that the method proposed in the paper has the advantages of high efficiency, rapid convergence, and general applicability, which enable it to be used for the optimization of various types of prestressed steel structures.

Originality/value
The optimization program has more general parameters, which can be used to optimize suspendome with different spans, different lattice divisions and different cable-layouts. In addition to the strength of steel and cable, the integral stability of the members, the deformation of the structure and the geometrical and material nonlinearity were considered in this algorithm and program. The optimization result was compared to the design of an actual large-span suspendome engineering project.
Bi-direction multi-surrogate surrogate assisted global optimization
Authors: Wang Hu , Li Enying 
Published: April 2016

Purpose
For global optimization, an important issue is a trade-off between exploration and exploitation within limited number of evaluations. Efficient Global Optimization (EGO) is an important algorithm considering such condition termed as Expected Improvement (EI). One of major bottlenecks of EGO is to keep the diversity of samples. Recently, Multi-Surrogate EGO (MSEGO) uses more samples generated by multiple surrogates to improve the efficiency. However, the total number of samples is commonly large. To overcome this bottleneck, a bi-direction multi-surrogate global optimization is suggested.

Design/methodology/approach
As the name implies, two different ways are used. The first way is to EI criterion to find better samples similar to EGO. The second way is to use the second term of EI to find accurate regions. Sequentially, the samples in these regions should be evaluated by multiple surrogates instead of exact function evaluations. To enhance the accuracy of these samples, Bayesian inference is employed to predicted the performance of each surrogate in each iteration and obtain the corresponding weight coefficients. The predicted response value of a cheap sample is evaluated by the weighted multiple surrogates combination. Therefore, both accuracy and efficiency can be guaranteed based on such frame.

Findings
According to the test functions, it empirically shows that the proposed algorithm is a potentially feasible method for complicated underlying problems.

Originality/value
A bi-direction sampling strategy is suggested. The first way is to use EI criterion to generate samples similar to the EGO. In this way, new samples should be evaluated by real functions or simulations called expensive samples. Another way is to search accurate region according to the second term of EI. To guarantee the reliability of samples, a sample selection scenario based on Bayesian theorem is suggested to select the cheap samples. We hope this strategy help us to construct more accurate model without increasing computational cost.