bluuebunny/crossref_metadata_2025_split huggingface dataset:
Marker‐Assisted Crop Breeding
Authors: Houston Kelly , Russell Joanne , Ramsey Luke , Bull Hazel , Thomas Bill , Waugh Robbie 
Published: May 2016

Abstract

Molecular genetic markers are tools that provide an opportunity to assist crop breeders in the development of new cultivars. They can be used as a proxy for costly or difficult‐to‐phenotype traits, enabling the screening of germplasm in a more efficient and robust way. The approach of using molecular markers in breeding programs is not new, and the key aim when developing such markers is to identify loci that are in linkage disequilibrium with the trait of interest. However, interesting developments in the technology underpinning contemporary crop genetics, such as next‐generation sequencing and high‐density genotyping platforms, can be translated and applied to crop breeding, potentially improving this process.

Key Concepts

Genetic loci in linkage disequilibrium with a trait of interest can be used to design molecular markers for breeding.

Large numbers of single‐nucleotide polymorphisms (SNPs) enable marker discovery when mapping the trait, with coverage of around one marker per 2 cM to map a trait for marker‐assisted selection (MAS) in crops. A much smaller number can be used for tracking preferred alleles during the breeding process. A denser set of markers than those used in MAS would be needed for genomic selection.
Gene Copy‐Number Changes in Evolution
Authors: Bergthorsson Ulfar , Katju Vaishali 
Published: May 2016

AbstractHigh‐throughput genomics have revealed widespread copy‐number differences within and among populations of species belonging to diverse taxonomic groups. Experimental evolution in model organisms with minimal natural selection demonstrates that genome‐wide empirical estimates of the spontaneous rates of gene duplication and deletion are extremely high and contribute to the abundance of copy‐number variation (CNV). CNVs are, on average, deleterious with respect to fitness, but their high spontaneous rates of origin can also facilitate rapid adaptation to novel environmental challenges. Duplications and deletions constitute opposing forces that shape genome complexity and size. Gene duplications are the ultimate source of new genes that confer novel phenotypes, whereas deletions remove superfluous genetic material. Furthermore, CNVs can contribute to the evolution of genetic incompatibility and speciation. Future challenges for understanding the evolutionary potential of CNVs include elucidating the relative roles of genetic drift and natural selection for the maintenance of CNVs in populations.Key ConceptsGene duplications are naturally occurring mutations within genomes wherein genic material is duplicated, resulting in additional copies of the duplicated gene.Gene deletions are mutations where genic material has been deleted, thereby reducing the number of copies of the deleted gene.Gene duplications and deletions have resulted in extensive gene copy‐number variation (CNV) in populations across all domains of life.The evolution of gene content and genome size is the net result of duplications adding new genetic material and contributing to the evolution of new genes, and deletions, which are continuously removing genetic information.The study of copy‐number variants at single loci has a long history in population genetics, but a systematic analysis of CNVs across whole genomes became possible only after technical breakthroughs in DNA microarray technology and whole‐genome sequencing.The rates of spontaneous gene duplication and deletion per gene are extraordinarily high and usually much higher than the nucleotide substitution rates.Most CNVs in natural populations are deleterious.Both duplications and deletions can contribute to adaptive genetic variation in natural and experimental populations.The long‐term maintenance of duplicated genes, which contribute to the evolution of novel genes, can be achieved by both positive selection on gene copy‐number and subfunctionalisation resulting from the loss of partial functions of complementary gene copies.Gene duplication and subfunctionalisation can contribute to reproductive isolation and speciation.A comprehensive understanding of how CNVs contribute to the evolution of genomes will require a combination of high‐throughput genomics with analysis of the functional and fitness consequences of CNVs in experimental and natural populations.
Blended Wing Body Aircraft: A Historical Perspective
Authors: Torenbeek Egbert 
Published: May 2016

A blended‐wing‐body aircraft, BWB in short, is an innovative radical configuration applicable to the conceptual design of future large transport aircraft. Realization of the BWB aims at a substantial step in the continuous process of improving their flight performance, reducing atmospheric emissions, and minimizing environmental noise production due to civil aviation. The BWB belongs to the category of flying wings, an airplane layout with high aerodynamic efficiency that until recently has been practiced operationally for long‐range bomber aircraft only. Applications of the BWB are foreseen primarily in high‐subsonic jetliners with a capacity between 250 and 1000 seats. The general arrangement of a BWB does neither feature a discrete fuselage body nor an empennage. The crew, passenger seats, cargo, and luggage compartments are integrated in a thick lift‐generating central wing segment with a large center body chord and approximately equal span. The narrow‐chord outboard wings of recently proposed BWBs together form a conventional moderately loaded high‐aspect ratio swept wing.Advanced designs for a BWB intended for commercial application were developed during the last decennium of the twentieth century in the United States by teams formed by NASA, the industry, and universities. Although various proposed concepts have quite different characteristics, they consistently indicate that a BWB can have acceptable flying qualities, improve the aerodynamic efficiency by 25%, and the fuel efficiency and CO2emissions by 35% relative to the conventional TAW. Further refinements of the concept, wind‐tunnel experiments and low‐speed flights with a remotely controlled flight test vehicle after the year 2000 have confirmed the promises of the advancements obtained by the project study teams.
Advances in Turbofan Engines: AUSPerspective
Authors: Van Zante Dale E. 
Published: May 2016

Turbofan engines have been the mainstay of large aircraft propulsion systems since the first turbofan‐powered commercial airliner was introduced in the late 1960s, replacing the less efficient and noisier turbojets. Engine manufacturers have continually improved the overall engine efficiency by both increasing the propulsive efficiency of the fan system and increasing the thermal efficiency of the core. Combustor technologies have also advanced, resulting in significantly lower emissions even as the overall pressure ratio of the cores has increased. Low operating costs improve aircraft economic competitiveness and motivate the efforts for fuel efficiency/noise reduction, while emissions reduction tends to be regulation driven.The historical improvements in turbofan efficiency, noise, and emissions are reviewed. Current‐generation turbofan systems can still achieve both propulsive and thermal efficiency gains. However, the engine cycle and configuration changes that benefit efficiency can potentially have negative consequences for emissions and noise. Complementary efforts in combustion technology and noise reduction are needed for a balanced approach to engine development. The current development efforts within the United States for next‐generation engines with lower fuel burn, noise, and emissions are summarized. Additionally, research efforts are discussed for generation‐after‐next systems that are typically more electric and/or hybrid.
Impact of Airframe Systems on Green Airliner Operation
Authors: Lawson Craig , Seresinhe Ravinka 
Published: May 2016

This chapter studies the impact of large commercial aircraft trajectories optimized for minimum fuel burn incorporating the on‐board systems. It shows the significant change in the fuel burn due to systems operation and builds up the case as to why a detailed aircraft systems model is required within the optimization loop.
A comparison is also made between conventional power systems and more electric architectures. In the conventional architecture, the environmental control system and the ice protection system are powered by engine bleed air, while actuators and electrics are powered by engine shaft power offtakes. In the more electric architecture, bleed offtake is eliminated, and the environmental control system and ice protection system are also powered electrically through engine shaft power offtakes.
Carbon and Noise Trading in Aviation
Authors: Wadud Zia , Gühnemann Astrid 
Published: May 2016

AbstractGreenhouse gas (GHG) emissions and airport noise are among the key challenges facing the air transportation industry. This chapter looks into emissions trading schemes as a policy tool to mitigate the GHG and noise impacts of aviation. It describes the principles of emissions trading, provides examples of successful trading schemes outside of aviation, lessons learnt from them, and portrays the current status of including aviation in emissions trading. The potential for applying the tradable permit approach to noise is then discussed briefly.
Electric Drives for Propulsion System of Transport Aircraft
Authors: Pornet Clément 
Published: May 2016

Following the hybridization or complete electrification strategy of the electric drive pursued on terrestrial vehicles, the aviation industry is considering with great attention the application of electrical technology and power electronics for transport aircraft. The growing interest toward electric application in transport aircraft is driven by the ambitious targets for aviation declared by Europe and by the United States of America and is motivated by the growing evidence that evolutionary improvement of the technologies might not be sufficient to fulfill these targets. As a result, the introduction of disruptive technologies turns out to be essential. With respect to the progress and perspective in electrical technology, electric drive applications to transport aircraft reveals itself to be a promising field in view of meeting the future goals.The focus of this chapter is the assessment of the electrification of the propulsion system of transport aircraft. While aiming for the ultimate goal of universally electric aircraft, hybrid electric approach will be first necessary to match the requirement of aircraft propulsion system and the development pace of the electrical components technology. The combinatorial variety of hybrid electric and universally electric propulsion system topology considered for transport aircraft application as well as key enabling technologies are first reviewed. A compendium of hybrid electric and universally electric advanced aircraft concepts is then proposed to obtain a notion of the cloud of aircraft configurations and electric drive options investigated up to this point in time. Finally, the integrated prospects of hybrid electric aircraft are investigated to establish the feasibility of hybrid electric aircraft for future market segments.
Metabolic evolution and 13C flux analysis of a succinate dehydrogenase deficient strain of Yarrowia lipolytica
Authors: Yuzbashev Tigran V. , Bondarenko Pavel Yu. , Sobolevskaya Tatiana I. , Yuzbasheva Evgeniya Yu. , Laptev Ivan A. , Kachala Vadim V. , Fedorov Alexander S. , Vybornaya Tatiana V. , Larina Anna S. , Sineoky Sergey P. 
Published: May 2016

ABSTRACTBio‐based succinic acid production can redirect industrial chemistry processes from using limited hydrocarbons to renewable carbohydrates. A fermentation process that does not require pH‐titrating agents will be advantageous to the industry. Previously, a Yarrowia lipolytica strain that was defective for succinate dehydrogenase was constructed and was found to accumulate up to 17.5 g L−1 of succinic acid when grown on glycerol without buffering. Here, a derivative mutant was isolated that produced 40.5 g L−1 of succinic acid in 36 h with a yield of 0.32 g g−1 glycerol. A combination approach of induced mutagenesis and metabolic evolution allowed isolation of another derivative that could utilize glucose efficiently and accumulated 50.2 g L−1 succinic acid in 54 h with a yield of 0.43 g g−1. The parent strain of these isolated mutants was used for [1,6‐13C2]glucose assimilation analysis. At least 35% glucose was estimated to be utilized through the pentose phosphate pathway, while ≥84% succinic acid was formed through the oxidative branch of the tricarboxylic acid cycle. Biotechnol. Bioeng. 2016;113: 2425–2432. © 2016 Wiley Periodicals, Inc.
Cell migration and organization in three‐dimensional in vitro culture driven by stiffness gradient
Authors: Joaquin Danielle , Grigola Michael , Kwon Gubeum , Blasius Christopher , Han Yutao , Perlitz Daniel , Jiang Jing , Ziegler Yvonne , Nardulli Ann , Hsia K. Jimmy 
Published: May 2016

ABSTRACTDurotaxis, a phenomenon that cells move according to changes in stiffness of the extra cellular matrix, has emerged as a crucial parameter controlling cell migration behavior. The current study provides a simple method to generate three‐dimensional continuous stiffness variations without changing other physical characteristics of the extra cellular environment. Using Finite Element simulations, the stiffness and the stiffness gradient variations are evaluated quantitatively, leading to an analysis of the dependence of cell migration behavior on the substrate stiffness parameters. We tested various cell lines on several 3‐D environments. The durotaxis results show that the cell migration velocity does not have any consistency with the stiffness of the substrate, rather it is more related to the stiffness gradient of the substrate. This finding suggests a new mechanism underlying the durotaxis phenomenon, highlighting the importance of the substrate stiffness gradient, rather than the stiffness itself. Biotechnol. Bioeng. 2016;113: 2496–2506. © 2016 Wiley Periodicals, Inc.
Long‐term soy consumption and tumor tissue MicroRNA and gene expression in triple‐negative breast cancer
Authors: Guo Xingyi , Cai Qiuyin , Bao Pingping , Wu Jie , Wen Wanqing , Ye Fei , Zheng Wei , Zheng Ying , Shu Xiao‐Ou 
Published: May 2016

BACKGROUNDSoy food intake may have protective effects against the risk for breast cancer, including estrogen receptor (ER)–negative breast cancer. However, the underlying molecular mechanisms remain unclear.METHODSTo evaluate the association of soy intake with the expression of microRNAs (miRNAs) and genes in the tumor tissue of patients with triple‐negative breast cancer (TNBC; ie, breast cancer lacking expression of ER, progesterone receptor, and human epidermal growth factor receptor 2), the expression of 800 miRNAs and 302 genes were measured with NanoString nCounter assays in formalin‐fixed, paraffin‐embedded tumor tissue from 272 TNBC patients. Soy intake during the 1‐year period before the cancer diagnosis was assessed with a validated food‐frequency questionnaire. The association of soy intake with the expression of miRNAs and genes was evaluated via linear regression analysis with adjustments for patient age and TNM stage.RESULTSA total of 14 miRNAs and 24 genes were significantly associated with soy food intake (P < .05): Thirteen of the 14 miRNAs (92.9%) and 9 of the 24 genes (37.5%), including tumor suppressors miR‐29a‐3p and IGF1R, showed overexpression for those women with high soy intake, whereas the remaining miRNAs and genes, including oncogenes KRAS and FGFR4, showed underexpression. Furthermore, cell growth–related genes showed a predominantly underexpression pattern according to a comparison of tumor samples from women with high soy food intake and samples from women with lower soy food intake.CONCLUSIONSThis study suggests that long‐term prediagnosis soy intake may lead to increased expression of tumor suppressors and decreased expression of oncogenes, especially cell growth–related genes, in breast tumor tissues. Cancer 2016;122:2544–51. © 2016 American Cancer Society.
Influence of the treatment facility volume on the survival of patients with non‐Hodgkin lymphoma
Authors: Go Ronald S. , Al‐Hamadani Mohammed , Shah Nilay D. , Crowson Cynthia S. , Holton Sara J. , Habermann Elizabeth B. 
Published: May 2016

BACKGROUNDPrior studies have shown that a higher hospital volume or physician caseload is associated with better outcomes for complex and uncommon surgical procedures. Similar studies in the medical management of rare diseases such as hematologic cancers are limited. This retrospective, observational study using the US National Cancer Data Base determined the extent to which the number of new non‐Hodgkin lymphoma (NHL) patients treated annually at a treatment facility affected overall survival (OS).METHODSThere were 278,985 patients treated at 1151 facilities from 1998 to 2006. Treatment facilities were classified by quartiles based on the average number of new NHL patients seen annually: quartile 1 (Q1), 2 to 13 patients; quartile 2 (Q2), 14 to 20 patients; quartile 3 (Q3), 21 to 32 patients; and quartile 4 (Q4), 33 or more patients. The outcome of interest was OS according to facility volume.RESULTSThe unadjusted median OS was 61.8 months for Q1, 65.9 months for Q2, 71.4 months for Q3, and 83.6 months for Q4. A multivariate analysis that was adjusted for demographic (sex, age, race, and ethnicity), socioeconomic (income and insurance type), geographic (area of residence), disease‐specific (NHL subtype and stage), and facility‐specific factors (type and location) showed that the facility volume was associated with OS. Compared with patients at Q4 facilities, patients at lower quartile facilities had higher mortality (hazard ratio for Q3, 1.05 [95% confidence interval, 1.04‐1.06]; hazard ratio for Q2, 1.08 [95% confidence interval, 1.07‐1.10]; hazard ratio for Q1, 1.14 [95% confidence interval, 1.11‐1.17]).CONCLUSIONSNHL patients treated at higher volume facilities may survive longer than those treated at lower volume facilities. Further work is needed to understand the mechanisms of these differences and whether volume should be considered in the determination of referrals for NHL patients. Cancer 2016;122:2552–9. © 2016 American Cancer Society.
Multiplexed imaging of intracellular protein networks
Authors: Grecco Hernán E. , Imtiaz Sarah , Zamir Eli 
Published: May 2016

AbstractCellular functions emerge from the collective action of a large number of different proteins. Understanding how these protein networks operate requires monitoring their components in intact cells. Due to intercellular and intracellular molecular variability, it is important to monitor simultaneously multiple components at high spatiotemporal resolution. However, inherent trade‐offs narrow the boundaries of achievable multiplexed imaging. Pushing these boundaries is essential for a better understanding of cellular processes. Here the motivations, challenges and approaches for multiplexed imaging of intracellular protein networks are discussed. © 2016 International Society for Advancement of Cytometry
Organic carbon inputs, common ions and degassing: rethinking mixing dissolution in coastal eogenetic carbonate aquifers
Authors: Gulley Jason D. , B.Martin Jonathan , Brown Amy 
Published: May 2016

AbstractCaves deliver freshwater from coastal carbonate landscapes to estuaries but how these caves form and grow remains poorly understood. Models suggest fresh and salt water mixing drives dissolution in eogenetic limestone, but have rarely been validated through sampling of mixing waters. Here we assess controls on carbonate mineral saturation states using new and legacy geochemical data that were collected in vertical profiles through three cenotes and one borehole in the Yucatan Peninsula. Results suggest saturation states are primarily controlled by carbon fluxes rather than mixing. Undersaturation predicted by mixing models that rely on idealized end members is diminished or eliminated when end members are collected from above and below actual mixing zones. Undersaturation due to mixing is limited by CO2 degassing from fresh water in karst windows, which results in calcite supersaturation. With respect to saline groundwater, controls on capacity for mixing dissolution were more varied. Oxidation of organic carbon increased pCO2 of saline groundwater in caves (pCO2 = 10–2.06 to 10–0.96 atm) relative to matrix porosity (10–2.39 atm) and local seawater (10–3.12 atm). The impact of increased pCO2 on saturation state, however, depended on the geochemical composition of the saline water and the magnitude of organic carbon oxidation. Carbonate undersaturation due to mixing was limited where gypsum dissolution (Cenote Angelita) or sulfate reduction (Cenote Calica) increased concentrations of common ions (Ca2+ or HCO3−, respectively). Maximum undersaturation was found to occur in mixtures including saline water that had ion concentrations and ratios similar to seawater, but with moderately elevated pCO2 (Cenote Eden). Undersaturation, however, was dominated by the initial undersaturation of the saline end member, mixing was irrelevant. Our results add to a growing body of literature that suggests oxidation of organic carbon, and not mixing dissolution, is the dominant control on cave formation and enlargement in coastal eogenetic karst aquifers. Copyright © 2016 John Wiley & Sons, Ltd.
Comparison and evaluation of pesticide monitoring programs using a process-based mixture model
Authors: Baas Jan , Vijver Martina , Rambohul Justin , Dunbar Mike , van 't Zelfde Maarten , Svendsen Claus , Spurgeon Dave 
Published: May 2016

Abstract

A number of European countries run large-scale pesticide monitoring schemes in watersheds aimed at identifying and evaluating the presence of pesticide residues in the environment. These schemes provide national and regional scale assessments of pesticide concentrations within the context of environmental quality assessment, aiming to ensure some degree of ecological protection. The present study is aimed at evaluating the joint effects of the pesticide mixtures detected in monitoring programs, using a process-based mixture model that was parameterized for Daphnia magna. In total, over 15 000 samples containing over 1 million individual measurements were evaluated for effects. It was found that there are only a small number of places where one can expect to have effects on daphnids, based on measured concentrations. The most polluted samples would cause extinction of a daphnid population within only 30 h. The results show that effects are mostly triggered by a limited number of pesticide residues at locations with high emissions. It was also shown that the analytical detection limits are basically too high to exclude mixture effects. So, despite all the effort that is put into chemical monitoring programs, it remains a challenge to make statements on whether or not the environment is protected. Recommendations are offered for a different setup of monitoring programs to improve this situation. Environ Toxicol Chem 2016;35:3113–3123. © 2016 SETAC