GBS-SNP-CROP: a reference-optional pipeline for SNP discovery and plant germplasm characterization using variable length, paired-end genotyping-by-sequencing data

Background: With its simple library preparation and robust approach to genome reduction, genotyping-by-sequencing (GBS) is a flexible and cost-effective strategy for SNP discovery and genotyping, provided an appropriate reference genome is available. For resource-limited curation, research, and breeding programs of underutilized plant genetic resources, however, even low-depth references may not be within reach, despite declining sequencing costs. Such programs would find value in an open-source bioinformatics pipeline that can maximize GBS data usage and perform high-density SNP genotyping in the absence of a reference. Results: The GBS SNP-Calling Reference Optional Pipeline (GBS-SNP-CROP) developed and presented here adopts a clustering strategy to build a population-tailored “Mock Reference” from the same GBS data used for downstream SNP calling and genotyping. Designed for libraries of paired-end (PE) reads, GBS-SNP-CROP maximizes data usage by eliminating unnecessary data culling due to imposed read-length uniformity requirements. Using 150 bp PE reads from a GBS library of 48 accessions of tetraploid kiwiberry (Actinidia arguta), GBS-SNP-CROP yielded on average three times as many SNPs as TASSEL-GBS analyses (32 and 64 bp tag lengths) and over 18 times as many as TASSEL-UNEAK, with fewer genotyping errors in all cases, as evidenced by comparing the genotypic characterizations of biological replicates. Using the published reference genome of a related diploid species (A. chinensis), the reference-based version of GBS-SNP-CROP behaved similarly to TASSEL-GBS in terms of the number of SNPs called but had an improved read depth distribution and fewer genotyping errors. Our results also indicate that the sets of SNPs detected by the different pipelines above are largely orthogonal to one another; thus GBS-SNP-CROP may be used to augment the results of alternative analyses, whether or not a reference is available. Conclusions: By achieving high-density SNP genotyping in populations for which no reference genome is available, GBS-SNP-CROP is worth consideration by curators, researchers, and breeders of under-researched plant genetic resources. In cases where a reference is available, especially if from a related species or when the target population is particularly diverse, GBS-SNP-CROP may complement other reference-based pipelines by extracting more information per sequencing dollar spent. The current version of GBS-SNP-CROP is available at https://github.com/halelab/GBS-SNP-CROP.gi

Ground and space based optical analysis of materials degradation in low-Earth-orbit

There is strong interest in being able to accurately and sensitively monitor materials degradation in both ground-based and space-based environments. Two optical techniques for sensitive degradation monitoring are reviewed: spectroscopic ellipsometry and photothermal spectroscopy. These techniques complement each other in that ellipsometry is sensitive to atomically thin surface and subsurface changes, and photothermal spectroscopy is sensitive to local defects, pin-holes, subsurface defects, and delamination. Progress in applying these spectroscopies (both ex situ and in situ) to atomic oxygen degradation of space materials is reviewed

Viral and host factors required for avian H5N1 influenza A virus replication in mammalian cells

Following the initial and sporadic emergence into humans of highly pathogenic avian H5N1 influenza A viruses in Hong Kong in 1997, we have come to realize the potential for avian influenza A viruses to be transmitted directly from birds to humans. Understanding the basic viral and cellular mechanisms that contribute to infection of mammalian species with avian influenza viruses is essential for developing prevention and control measures against possible future human pandemics. Multiple physical and functional cellular barriers can restrict influenza A virus infection in a new host species, including the cell membrane, the nuclear envelope, the nuclear environment, and innate antiviral responses. In this review, we summarize current knowledge on viral and host factors required for avian H5N1 influenza A viruses to successfully establish infections in mammalian cells. We focus on the molecular mechanisms underpinning mammalian host restrictions, as well as the adaptive mutations that are necessary for an avian influenza virus to overcome them. It is likely that many more viral and host determinants remain to be discovered, and future research in this area should provide novel and translational insights into the biology of influenza virus-host interactions

Empowering design practices: exploring relations between architecture, faith, society and community

This paper presents and discusses some key insights derived from a collaborative research project called Empowering Design Practices. The project brought together a multidisciplinary team of academic and non-academic partners to explore the processes, resources and environments that support community-led design practice in the context of historic places of worship. The paper discusses barriers and opportunities surrounding the development and adaptation of historic places of worship as community hubs, and proposes a set of approaches that can help empower those looking after those places to re-imagine and design the future of their places while respecting complex faith, architectural, societal and community values

A condition on delay for differential equations with discrete state-dependent delay

Parabolic differential equations with discrete state-dependent delay are studied. The approach, based on an additional condition on the delay function introduced in [A.V. Rezounenko, Differential equations with discrete state-dependent delay: uniqueness and well-posedness in the space of continuous functions, Nonlinear Analysis: Theory, Methods and Applications, 70 (11) (2009), 3978-3986] is developed. We propose and study a state-dependent analogue of the condition which is sufficient for the well-posedness of the corresponding initial value problem on the whole space of continuous functions $C$. The dynamical system is constructed in $C$ and the existence of a compact global attractor is proved

Flexoelectricity and pattern formation in nematic liquid crystals

We present in this paper a detailed analysis of the flexoelectric instability of a planar nematic layer in the presence of an alternating electric field (frequency $\omega$), which leads to stripe patterns (flexodomains) in the plane of the layer. This equilibrium transition is governed by the free energy of the nematic which describes the elasticity with respects to the orientational degrees of freedom supplemented by an electric part. Surprisingly the limit $\omega \to 0$ is highly singular. In distinct contrast to the dc-case, where the patterns are stationary and time-independent, they appear at finite, small $\omega$ periodically in time as sudden bursts. Flexodomains are in competition with the intensively studied electro-hydrodynamic instability in nematics, which presents a non-equilibrium dissipative transition. It will be demonstrated that $\omega$ is a very convenient control parameter to tune between flexodomains and convection patterns, which are clearly distinguished by the orientation of their stripes

Biomimetic heterogenous elastic tissue development

There is an unmet need for artificial tissue to address current limitations with donor organs and problems with donor site morbidity. Despite the success with sophisticated tissue engineering endeavours, which employ cells as building blocks, they are limited to dedicated labs suitable for cell culture, with associated high costs and long tissue maturation times before available for clinical use. Direct 3D printing presents rapid, bespoke, acellular solutions for skull and bone repair or replacement, and can potentially address the need for elastic tissue, which is a major constituent of smooth muscle, cartilage, ligaments and connective tissue that support organs. Thermoplastic polyurethanes are one of the most versatile elastomeric polymers. Their segmented block copolymeric nature, comprising of hard and soft segments allows for an almost limitless potential to control physical properties and mechanical behaviour. Here we show direct 3D printing of biocompatible thermoplastic polyurethanes with Fused Deposition Modelling, with a view to presenting cell independent in-situ tissue substitutes. This method can expeditiously and economically produce heterogenous, biomimetic elastic tissue substitutes with controlled porosity to potentially facilitate vascularisation. The flexibility of this application is shown here with tubular constructs as exemplars. We demonstrate how these 3D printed constructs can be post-processed to incorporate bioactive molecules. This efficacious strategy, when combined with the privileges of digital healthcare, can be used to produce bespoke elastic tissue substitutes in-situ, independent of extensive cell culture and may be developed as a point-of-care therapy approach

O marco legal da mediação no Brasil : comentários à Lei nº 13.140, de 26 de junho de 2015

- Divulgação dos SUMÁRIOS das obras recentemente incorporadas ao acervo da Biblioteca Ministro Oscar Saraiva do STJ. Em respeito à lei de Direitos Autorais, não disponibilizamos a obra na íntegra.- Localização na estante: 347.925(81)(094) M321

Monitoring a PGD solver for parametric power flow problems with goal-oriented error assessment

This is the peer reviewed version of the following article: [García-Blanco, R., Borzacchiello, D., Chinesta, F., and Diez, P. (2017) Monitoring a PGD solver for parametric power flow problems with goal-oriented error assessment. Int. J. Numer. Meth. Engng, 111: 529–552. doi: 10.1002/nme.5470], which has been published in final form at http://onlinelibrary.wiley.com/doi/10.1002/nme.5470/full. This article may be used for non-commercial purposes in accordance with Wiley Terms and Conditions for Self-Archiving.The parametric analysis of electric grids requires carrying out a large number of Power Flow computations. The different parameters describe loading conditions and grid properties. In this framework, the Proper Generalized Decomposition (PGD) provides a numerical solution explicitly accounting for the parametric dependence. Once the PGD solution is available, exploring the multidimensional parametric space is computationally inexpensive. The aim of this paper is to provide tools to monitor the error associated with this significant computational gain and to guarantee the quality of the PGD solution. In this case, the PGD algorithm consists in three nested loops that correspond to 1) iterating algebraic solver, 2) number of terms in the separable greedy expansion and 3) the alternated directions for each term. In the proposed approach, the three loops are controlled by stopping criteria based on residual goal-oriented error estimates. This allows one for using only the computational resources necessary to achieve the accuracy prescribed by the end- user. The paper discusses how to compute the goal-oriented error estimates. This requires linearizing the error equation and the Quantity of Interest to derive an efficient error representation based on an adjoint problem. The efficiency of the proposed approach is demonstrated on benchmark problems.Peer ReviewedPostprint (author's final draft

Scalable scheme for entangling multiple ququarts using linear optical elements

We report a scalable linear optical scheme for generating entangled states of multiple ququarts in which the individual single-ququart state is prepared with the biphoton polarization state of frequency-nondegenerate spontaneous parametric down-conversion. The output state is calculated with the full consideration of the higher order effect (double-pair events) of spontaneous parametric down-conversion. Scalability to multiple-ququart entanglement is demonstrated with examples: linear optical entanglement of three and four individual biphoton ququarts