bluuebunny/crossref_metadata_2025_split huggingface dataset:
Measuring VLDL1-Triglyceride and VLDL2-Triglyceride Kinetics in Men: Effects of Dietary Control on Day-to-Day Variability
Authors: Johansen Rakel , Søndergaard Esben , Sørensen Lars , Jurik Anne , Nielsen Søren 
Published: May 2017

AbstractThe aim of this study was to assess the impact of dietary control on VLDL1- and VLDL2-TG kinetics and associated metabolic parameters. Twelve overweight/obese men were randomized to a provided 3 day isocaloric diet with fixed macronutrient composition (diet group, n=6) or to their regular unrestricted diet (non-diet group, n=6). VLDL1- and VLDL2-TG turnovers were measured twice 2–4 weeks apart, using primed-constant infusion of ex vivo labeled [1-14C]VLDL1-TG and [9,10-3H]VLDL2-TG. Isocaloric diet intervention lowered the difference in the mean of both VLDL2-TG secretion and clearance rate (p<0.01), and the coefficient of variation (CV) of VLDL2-TG clearance rate (p<0.05). The difference in mean and CV of the other kinetic estimates (VLDL1-TG secretion, clearance and oxidation rate) were lowered, but not significantly. The CV’s of total triglyceride, VLDL1-TG, and VLDL2-TG concentrations were significantly lowered by diet intervention compared to regular diet; total triglyceride (31%–5%, p<0.01), VLDL1-TG (42%–9%, p<0.01), and VLDL2-TG (36%–10%, p<0.01). In conclusion, VLDL1- and VLDL2-TG kinetics show great day-to-day variability, which may be diminished by diet intervention. Therefore, standardized macronutrient intake prior to study days improves the probability of demonstrating significant outcomes of cross-sectional and intervention studies of VLDL1-TG and VLDL2-TG kinetics and metabolism.
Macro-heterogeneities in microstructures, concentrations, defects and tensile properties of die cast Al–Mg–Si alloys
Authors: Ji Shouxun , Yang Hailin , Cui Xiaopeng , Fan Zhongyun 
Published: May 2017

The heterogeneities in tensile properties, microstructure, solute concentrations and defects levels were studied for the castings with different thicknesses made by high pressure die cast Al–Mg–Si alloys. For the local mechanical properties, the casting skin provided the highest, whereas the casting centre provided the lowest yield strength, ultimate tensile strength and elongation. The microstructural heterogeneity was characterised by the segregation of coarse fragmented dendrites, the reduction of solute concentrations of Mg and Si, and the increase of porosity level from the surface to the centre of castings. The growth velocities of eutectic α-Al phase estimated using the Jackson–Hunt model confirm that the growth variation is larger in the thin castings than that in thick castings. This paper is part of a thematic issue on Light Alloys.
European Union Law: A Very Short Introduction
Authors: Arnull Anthony 
Published: May 2017

Abstract
European Law: A Very Short Introduction considers the laws and legal system of the European Union and discusses the range of issues that the European Union has been given the power to regulate, including the free movement of goods and people. It considers why an organization based on international treaties has proved capable of having far-reaching effects on both its Member States and on countries that lie beyond its borders, and discusses the effectiveness of its law and legal system in ensuring that Member States respect the commitments they made when they signed the Treaties.
Coping with crises
Authors: Arnull Anthony 
Published: May 2017

Abstract
‘Coping with crises’ describes the eurozone crisis triggered by the 2008 financial crash and the 2015 migration crisis when the EU experienced an influx of over a million migrants from Syria, Afghanistan, and elsewhere. These crises have unmasked an EU apparently devoid of solidarity and riven instead by north–south and east–west divides, where adherence to its ‘values’ is only skin-deep. It has been further weakened by the desire of the UK to withdraw. What does the future hold? Is the solution deeper integration, or should the EU pay more attention to the wishes of its Member States? Either way, the law will have a vital role to play.
GateKeeper: a new hardware architecture for accelerating pre-alignment in DNA short read mapping
Authors: Alser Mohammed , Hassan Hasan , Xin Hongyi , Ergin Oğuz , Mutlu Onur , Alkan Can 
Published: May 2017

Abstract

Motivation
High throughput DNA sequencing (HTS) technologies generate an excessive number of small DNA segments -called short reads- that cause significant computational burden. To analyze the entire genome, each of the billions of short reads must be mapped to a reference genome based on the similarity between a read and ‘candidate’ locations in that reference genome. The similarity measurement, called alignment, formulated as an approximate string matching problem, is the computational bottleneck because: (i) it is implemented using quadratic-time dynamic programming algorithms and (ii) the majority of candidate locations in the reference genome do not align with a given read due to high dissimilarity. Calculating the alignment of such incorrect candidate locations consumes an overwhelming majority of a modern read mapper’s execution time. Therefore, it is crucial to develop a fast and effective filter that can detect incorrect candidate locations and eliminate them before invoking computationally costly alignment algorithms.

Results
We propose GateKeeper, a new hardware accelerator that functions as a pre-alignment step that quickly filters out most incorrect candidate locations. GateKeeper is the first design to accelerate pre-alignment using Field-Programmable Gate Arrays (FPGAs), which can perform pre-alignment much faster than software. When implemented on a single FPGA chip, GateKeeper maintains high accuracy (on average &gt;96%) while providing, on average, 90-fold and 130-fold speedup over the state-of-the-art software pre-alignment techniques, Adjacency Filter and Shifted Hamming Distance (SHD), respectively. The addition of GateKeeper as a pre-alignment step can reduce the verification time of the mrFAST mapper by a factor of 10.

Availability and implementation
https://github.com/BilkentCompGen/GateKeeper

Supplementary information
Supplementary data are available at Bioinformatics online.
Setting the scene: what did we know before Rosetta?
Authors: Meech K. J. 
Published: May 2017

This paper provides an overview of our state of knowledge about comets prior to the Rosetta mission encounter. Starting with the historical perspective, this paper discusses the development of comet science up to the modern era of space exploration. The extent to which comets are tracers of solar system formation processes or preserve pristine interstellar material has been investigated for over four decades. There is increasing evidence that in contrast with the distinct dynamical comet reservoirs we see today, comet formation regions strongly overlapped in the protoplanetary disc and there was significant migration of material in the disc during the epoch of comet formation. Comet nuclei are now known to be very low-density highly porous bodies, with very low thermal inertia, and have a range of sizes which exhibit a deficiency of very small bodies. The low thermal inertia suggests that comets may preserve pristine materials close to the surface, and that this might be accessible to sample return missions.This article is part of the themed issue ‘Cometary science after Rosetta’.
The composition of cometary ices
Authors: Bockelée-Morvan D. , Biver N. 
Published: May 2017

The chemical composition of cometary ices provides clues for the conditions of formation and evolution of the early Solar System. A large number of molecules have been identified in cometary atmospheres, from both ground-based observations and space, includingin situinvestigations. This includes large organic molecules, which are also observed in star-forming regions. This paper presents a review of molecular abundances measured in cometary atmospheres from remote sensing observations with ground-based and space-based telescopes. The diversity of composition observed in comet populations is presented and discussed.This article is part of the themed issue ‘Cometary science after Rosetta’.
Interaction of the solar wind with comets: a Rosetta perspective
Authors: Glassmeier Karl-Heinz 
Published: May 2017

The Rosetta mission provides an unprecedented possibility to study the interaction of comets with the solar wind. As the spacecraft accompanies comet 67P/Churyumov–Gerasimenko from its very low-activity stage through its perihelion phase, the physics of mass loading is witnessed for various activity levels of the nucleus. While observations at other comets provided snapshots of the interaction region and its various plasma boundaries, Rosetta observations allow a detailed study of the temporal evolution of the innermost cometary magnetosphere. Owing to the short passage time of the solar wind through the interaction region, plasma instabilities such as ring--beam and non-gyrotropic instabilities are of less importance during the early life of the magnetosphere. Large-amplitude ultra-low-frequency (ULF) waves, the ‘singing’ of the comet, is probably due to a modified ion Weibel instability. This instability drives a cross-field current of implanted cometary ions unstable. The initial pick-up of these ions causes a major deflection of the solar wind protons. Proton deflection, cross-field current and the instability induce a threefold structure of the innermost interaction region with the characteristic Mach cone and Whistler wings as stationary interaction signatures as well as the ULF waves representing the dynamic aspect of the interaction.This article is part of the themed issue ‘Cometary science after Rosetta’.
Asteroid–comet continuum objects in the solar system
Authors: Hsieh Henry H. 
Published: May 2017

In this review presented at the Royal Society meeting, ‘Cometary science after Rosetta’, I present an overview of studies of small solar system objects that exhibit properties of both asteroids and comets (with a focus on so-called active asteroids). Sometimes referred to as ‘transition objects’, these bodies are perhaps more appropriately described as ‘continuum objects’, to reflect the notion that rather than necessarily representing actual transitional evolutionary states between asteroids and comets, they simply belong to the general population of small solar system bodies that happen to exhibit a continuous range of observational, physical and dynamical properties. Continuum objects are intriguing because they possess many of the properties that make classical comets interesting to study (e.g. relatively primitive compositions, ejection of surface and subsurface material into space where it can be more easily studied, and orbital properties that allow us to sample material from distant parts of the solar system that would otherwise be inaccessible), while allowing us to study regions of the solar system that are not sampled by classical comets.This article is part of the themed issue ‘Cometary science after Rosetta’.
Comets: looking ahead
Authors: A’Hearn Michael F. 
Published: May 2017

We outline the key questions about comets that must be answered in order to understand cometary formation in the context of the protoplanetary disc and the role of comets in the formation and evolution of the solar system. We then discuss the new understanding of comets from Rosetta and from other recent advances, including work presented by others at the discussion meeting. Finally, we suggest some key directions for future projects to better address the above questions.This article is part of the themed issue ‘Cometary science after Rosetta’.
Nucleus Specific expression in the multinucleated mushroom-forming fungusAgaricus bisporusreveals different nuclear regulatory programs
Authors: Gehrmann Thies , Pelkmans Jordi F. , Ohm Robin A. , Vos Aurin M. , Sonnenberg Anton S. M. , Baars Johan J. P. , Wösten Han A. B. , Reinders Marcel J. T. , Abeel Thomas 
Published: May 2017

AbstractMotivationFungi are essential in nutrient recycling in nature. They also form symbiotic, commensal, parasitic and pathogenic interactions with other organisms including plants, animals and humans. Many fungi are polykaryotic, containing multiple nuclei per cell. In the case of heterokaryons, there are even different nuclear types within a cell. It is unknown what the different nuclear types contribute in terms of mRNA expression levels in fungal heterokaryons. Each cell of the cultivated, mushroom forming basidiomyceteAgaricus bisporuscontains 2 to 25 nuclei of two nuclear types,P1orP2,that originate from two parental strains. Using RNA-Seq data, we wish to assess the differential mRNA contribution of individual nuclear types in heterokaryotic cells and its functional impact.ResultsWe studied differential expression between genes of the two nuclear types throughout mushroom development ofA. bisporusin various tissue types. The two nuclear types, produced specific mRNA profiles which changed through development of the mushroom. The differential regulation occurred at a gene and multi-gene locus level, rather than the chromosomal or nuclear level. Although the P1 nuclear type dominates the mRNA production throughout development, the P2 type showed more differentially upregulated genes in important functional groups including genes involved in metabolism and genes encoding secreted proteins. Out of 5,090 karyolelle pairs, i.e. genes with different alleles in the two nuclear types, 411 were differentially expressed, of which 246 were up-regulated by the P2 type. In the vegetative mycelium, the P2 nucleus up-regulated almost three-fold more metabolic genes and cazymes than P1, suggesting phenotypic differences in growth. A total of 10% of the differential karyollele expression is associated with differential methylation states, indicating that epigenetic mechanisms may be partly responsible for nuclear specific expression.ConclusionWe have identified widespread transcriptomic variation between the two nuclear types ofA. bisporus. Our novel method enables studying karyollelle specific expression which likely influences the phenotype of a fungus in a polykaryotic stage. This is thus relevant for the performance of these fungi as a crop and for improving this species for breeding. Our findings could have a wider impact to better understand fungi as pathogens. This work provides the first insight into the transcriptomic variation introduced by genomic nuclear separation.
Meta-analysis of sequence-based association studies across three cattle breeds reveals 25 QTL for fat and protein percentages in milk at nucleotide resolution
Authors: Pausch Hubert , Emmerling Reiner , Gredler-Grandl Birgit , Fries Ruedi , Daetwyler Hans D. , Goddard Michael E 
Published: May 2017

AbstractBackgroundGenotyping and whole-genome sequencing data have been collected in many cattle breeds. The compilation of large reference panels facilitates imputing sequence variant genotypes for animals that have been genotyped using dense genotyping arrays. Association studies with imputed sequence variant genotypes allow characterization of quantitative trait loci (QTL) at nucleotide resolution particularly when individuals from several breeds are included in the mapping populations.ResultsWe imputed genotypes for more than 28 million sequence variants in 17,229 animals of the Braunvieh (BV), Fleckvieh (FV) and Holstein (HOL) cattle breeds in order to generate large mapping populations that are required to identify sequence variants underlying milk production traits. Within-breed association tests between imputed sequence variant genotypes and fat and protein percentages in milk uncovered between six and thirteen QTL (P<1e-8) per breed. Eight of the detected QTL were significant in more than one breed. We combined the association studies across three breeds using meta-analysis and identified 25 QTL including six that were not significant in the within-breed association studies. Closer inspection of the QTL revealed that two well-known causal missense mutations in theABCG2(p.Y581S, rs43702337, P=4.3e-34) andGHR(p.F279Y, rs385640152, P=1.6e-74) genes were the top variants at two QTL on chromosomes 6 and 20. Another true causal missense mutation in theDGAT1gene (p.A232K, rs109326954, P=8.4e-1436) was the second top variant at a QTL on chromosome 14 but its allelic substitution effects were not consistent across three breeds analyzed. It turned out that the conflicting allelic substitution effects resulted from flaws in the imputed genotypes due to the use of a multi-breed reference population for genotype imputation.ConclusionsMany QTL for milk production traits segregate across breeds. Metaanalysis of association studies across breeds has greater power to detect such QTL than within-breed association studies. True causal mutations can be readily detected among the most significantly associated variants at QTL when the accuracy of imputation is high. However, true causal mutations may show conflicting allelic substitution effects across breeds when the imputed sequence variant genotypes contain flaws. Validating the effect of known causal variants is highly recommended in order to assess the ability to detect true causal mutations in association studies with imputed sequence variant genotypes.
Java framework for parametric aircraft design – ground performance
Authors: Trifari Vittorio , Ruocco Manuela , Cusati Vincenzo , Nicolosi Fabrizio , De Marco Agostino 
Published: May 2017

Purpose
This paper aims to introduce the take-off and landing performance analysis modules of the software library named Java toolchain of Programs for Aircraft Design (JPAD), dedicated to the aircraft preliminary design. An overview of JPAD is also presented.

Design/methodology/approach
The calculation of the take-off and landing distances has been implemented using a simulation-based approach. This expects to solve an appropriate set of ordinary differential equations, which describes the aircraft equations of motion during all the take-off and landing phases. Tests upon two aircraft models (ATR72 and B747-100B) have been performed to compare the obtained output with the performance data retrieved from the related flight manuals.

Findings
The tool developed has proven to be very reliable and versatile, as it performs the calculation of the required performance with almost no computational effort and with a good accuracy, providing a less than the 5 per cent difference with respect to the statistical trend and a difference from the flight manual or public brochure data around 10 per cent.

Originality/value
The use of a simulation-based approach to have a more accurate estimation of the ground performance with respect to classic semi-empirical equations. Although performing the simulation of the aircraft motion, the approach shown is very time-saving and can be easily implemented in an optimization cycle.
Robust design and optimization of UAV empennage
Authors: Klimczyk Witold Artur , Goraj Zdobyslaw Jan 
Published: May 2017

Purpose
This paper aims to address the issue of designing aerodynamically robust empennage. Aircraft design optimization often narrowed to analysis of cruise conditions does not take into account other flight phases (manoeuvres). These, especially in unmanned air vehicle sector, can be significant part of the whole flight. Empennage is a part of the aircraft, with crucial function for manoeuvres. It is important to consider robustness for highest performance.

Design/methodology/approach
Methodology for robust wing design is presented. Surrogate modelling using kriging is used to reduce the optimization cost for high-fidelity aerodynamic calculations. Analysis of varying flight conditions, angle of attack, is made to assess robustness of design for particular mission. Two cases are compared: global optimization of 11 parameters and optimization divided into two consecutive sub-optimizations.

Findings
Surrogate modelling proves its usefulness for cutting computational time. Optimum design found by splitting problem into sub-optimizations finds better design at lower computational cost.

Practical implications
It is demonstrated, how surrogate modelling can be used for analysis of robustness, and why it is important to consider it. Intuitive split of wing design into airfoil and planform sub-optimizations brings promising savings in the optimization cost.

Originality/value
Methodology presented in this paper can be used in various optimization problems, especially those involving expensive computations and requiring top quality design.
Improving productivity of road surfacing operations using value stream mapping and discrete event simulation
Authors: Aziz Zeeshan , Qasim Rana Muhammad , Wajdi Sahawneh 
Published: May 2017

Purpose
The purpose of this paper is to investigate the integration of discrete event simulation (DES) and value stream mapping (VSM) to enhance the productivity of road surfacing operations by achieving high production rates and minimum road closure times. Highway infrastructure is one of the most valuable assets owned by the public sector. The success of national and local economies as well as quality of life of the general public depend on the efficient operations of highways. Ensuring smooth traffic operations requires maintenance and improvements of the highest standard.

Design/methodology/approach
Research approach involved the use of primary data collected from direct observation, interviews, review of archival records and productivity databases. Based on this, process maps and value stream maps were developed which were subsequently used to produce discrete event simulation models for the exploration of different optimisation scenarios.

Findings
This research highlights the synergistic relationship between VSM and DES in driving innovation in construction processes. Identified factors that affect roadworks process productivity include machine, manpower, material, information, environment and method-related factors. A DES model is presented to optimise the process and increase the production rates. A hybrid DES-VSM approach ensures an integrated approach to process optimisation.

Research limitations/implications
This study is an application of hybrid version of previously published DES-VSM framework in the manufacturing sector. The present study has extended and tested its applicability within road surfacing operations. The different what-if scenarios presented in this paper might not be applicable to other parts of the world owing to various constraints. The study has focused on addressing the waste production inherent in pavement laying process. Even though external variables could possibly influence pavement process, those were ignored to allow for in-depth focus on the process under consideration.

Practical implications
Road users are one of the most important stakeholders that will benefit from the positive implications of this study. Private resurfacing companies and transport departments can optimise their overall process and style of working by comparing their end-to-end process and work plans with the ones mentioned in this paper. It will boost the productivity of equipment like planners, pavers and other machines used for resurfacing operations.

Originality/value
Existing approaches to process modelling such as VSM and process diagrams are constrained by their effectiveness in the analysis of dynamic and complex processes. This study presents a DES-based approach to validate targeted improvements of the current state of road surfacing processes and in exploration of different optimisation scenarios.