bluuebunny/crossref_metadata_2025_split huggingface dataset:
A Parametric Estimation of Total Factor Productivity and Its Components in U.S. Agriculture
Authors: Plastina Alejandro , Lence Sergio H 
Published: February 2018

AbstractThe present study aims at improving our understanding of the individual contribution of the components of total factor productivity (TFP) change to U.S. agricultural productivity. A novel sequential primal‐dual estimation routine to calculate TFP change is proposed, using a multi‐output input distance function in the first stage, followed by a cost minimization routine in the second stage. TFP change is estimated as the direct sum of the estimates of technical change, technical efficiency change, allocative efficiency change, input price effects, changes in output markup, and changes in returns to scale in each state. The validity of the proposed methodology is supported by the remarkable overlap and high correlation of our annual estimates of TFP change with the USDA's measures of change in TFP by state. Although technical change tends to be the largest contributor to productivity change, it bears a low and statistically insignificant correlation with TFP change on an annual basis, whereas annual changes in the markup effect and returns to scale are highly and significantly correlated with TFP changes. This is the first study to find a slowdown of technical progress in the U.S. farm sector in the 1990s and 2000s, and technical regress during the farm crisis of the 1980s. While technical efficiency shows a positive overall trend, allocative efficiency shows a negative overall trend, and their combined effect (i.e., the overall cost efficiency) slows down TFP growth. The policy recommendations from previous studies on the drivers of TFP should be revised in light of these findings.
50 years of spermatogenesis: Sertoli cells and their interactions with germ cells
Authors: Griswold Michael D 
Published: February 2018

AbstractThe complex morphology of the Sertoli cells and their interactions with germ cells has been a focus of investigators since they were first described by Enrico Sertoli. In the past 50 years, information on Sertoli cells has transcended morphology alone to become increasingly more focused on molecular questions. The goal of investigators has been to understand the role of the Sertoli cells in spermatogenesis and to apply that information to problems relating to male fertility. Sertoli cells are unique in that they are a nondividing cell population that is active for the reproductive lifetime of the animal and cyclically change morphology and gene expression. The numerous and distinctive junctional complexes and membrane specializations made by Sertoli cells provide a scaffold and environment for germ cell development. The increased focus of investigators on the molecular components and putative functions of testicular cells has resulted primarily from procedures that isolate specific cell types from the testicular milieu. Products of Sertoli cells that influence germ cell development and vice versa have been characterized from cultured cells and from the application of transgenic technologies. Germ cell transplantation has shown that the Sertoli cells respond to cues from germ cells with regard to developmental timing and has furthered a focus on spermatogenic stem cells and the stem cell niche. Very basic and universal features of spermatogenesis such as the cycle of the seminiferous epithelium and the spermatogenic wave are initiated by Sertoli cells and maintained by Sertoli-germ cell cooperation.
The developmental transcriptome atlas of the spoon worm Urechis unicinctus (Echiurida: Annelida)
Authors: Park Chungoo , Han Yong-Hee , Lee Sung-Gwon , Ry Kyoung-Bin , Oh Jooseong , Kern Elizabeth M A , Park Joong-Ki , Cho Sung-Jin 
Published: February 2018

Abstract

Background
Echiurida is one of the most intriguing major subgroups of annelida because, unlike most other annelids, echiurids lack metameric body segmentation as adults. For this reason, transcriptome analyses from various developmental stages of echiurid species can be of substantial value for understanding precise expression levels and the complex regulatory networks during early and larval development.

Results
A total of 914 million raw RNA-Seq reads were produced from 14 developmental stages of Urechis unicinctus and were de novo assembled into contigs spanning 63,928,225 bp with an N50 length of 2700 bp. The resulting comprehensive transcriptome database of the early developmental stages of U. unicinctus consists of 20,305 representative functional protein-coding transcripts. Approximately 66% of unigenes were assigned to superphylum-level taxa, including Lophotrochozoa (40%). The completeness of the transcriptome assembly was assessed using benchmarking universal single-copy orthologs; 75.7% of the single-copy orthologs were presented in our transcriptome database. We observed 3 distinct patterns of global transcriptome profiles from 14 developmental stages and identified 12,705 genes that showed dynamic regulation patterns during the differentiation and maturation of U. unicinctus cells.

Conclusions
We present the first large-scale developmental transcriptome dataset of U. unicinctus and provide a general overview of the dynamics of global gene expression changes during its early developmental stages. The analysis of time-course gene expression data is a first step toward understanding the complex developmental gene regulatory networks in U. unicinctus and will furnish a valuable resource for analyzing the functions of gene repertoires in various developmental phases.
Draft genome assembly of the Bengalese finch, Lonchura striata domestica, a model for motor skill variability and learning
Authors: Colquitt Bradley M , Mets David G , Brainard Michael S 
Published: February 2018

Abstract

Background
Vocal learning in songbirds has emerged as a powerful model for sensorimotor learning. Neurobehavioral studies of Bengalese finch (Lonchura striata domestica) song, naturally more variable and plastic than songs of other finch species, have demonstrated the importance of behavioral variability for initial learning, maintenance, and plasticity of vocalizations. However, the molecular and genetic underpinnings of this variability and the learning it supports are poorly understood.

Findings
To establish a platform for the molecular analysis of behavioral variability and plasticity, we generated an initial draft assembly of the Bengalese finch genome from a single male animal to 151× coverage and an N50 of 3.0 MB. Furthermore, we developed an initial set of gene models using RNA-seq data from 8 samples that comprise liver, muscle, cerebellum, brainstem/midbrain, and forebrain tissue from juvenile and adult Bengalese finches of both sexes.

Conclusions
We provide a draft Bengalese finch genome and gene annotation to facilitate the study of the molecular-genetic influences on behavioral variability and the process of vocal learning. These data will directly support many avenues for the identification of genes involved in learning, including differential expression analysis, comparative genomic analysis (through comparison to existing avian genome assemblies), and derivation of genetic maps for linkage analysis. Bengalese finch gene models and sequences will be essential for subsequent manipulation (molecular or genetic) of genes and gene products, enabling novel mechanistic investigations into the role of variability in learned behavior.
Single-molecule, full-length transcript sequencing provides insight into the extreme metabolism of the ruby-throated hummingbird Archilochus colubris
Authors: Workman Rachael E , Myrka Alexander M , Wong G William , Tseng Elizabeth , Welch Kenneth C , Timp Winston 
Published: February 2018

Abstract

Background
Hummingbirds oxidize ingested nectar sugars directly to fuel foraging but cannot sustain this fuel use during fasting periods, such as during the night or during long-distance migratory flights. Instead, fasting hummingbirds switch to oxidizing stored lipids that are derived from ingested sugars. The hummingbird liver plays a key role in moderating energy homeostasis and this remarkable capacity for fuel switching. Additionally, liver is the principle location of de novo lipogenesis, which can occur at exceptionally high rates, such as during premigratory fattening. Yet understanding how this tissue and whole organism moderates energy turnover is hampered by a lack of information regarding how relevant enzymes differ in sequence, expression, and regulation.

Findings
We generated a de novo transcriptome of the hummingbird liver using PacBio full-length cDNA sequencing (Iso-Seq), yielding 8.6Gb of sequencing data, or 2.6M reads from 4 different size fractions. We analyzed data using the SMRTAnalysis v3.1 Iso-Seq pipeline, then clustered isoforms into gene families to generate de novo gene contigs using Cogent. We performed orthology analysis to identify closely related sequences between our transcriptome and other avian and human gene sets. Finally, we closely examined homology of critical lipid metabolism genes between our transcriptome data and avian and human genomes.

Conclusions
We confirmed high levels of sequence divergence within hummingbird lipogenic enzymes, suggesting a high probability of adaptive divergent function in the hepatic lipogenic pathways. Our results leverage cutting-edge technology and a novel bioinformatics pipeline to provide a first direct look at the transcriptome of this incredible organism.
Influence of Supplemental Protein on the Life Expectancy and Reproduction of the Chinese Citrus Fruit Fly, Bactrocera minax (Enderlein) (Tetradacus minax) (Diptera: Tephritidae)
Authors: Wang Fulian , Chambi Consolatha , Li Zaiyuan , Huang Cong , Ma Yuekun , Li Chuanren , Tian Xiaohai , Sangija Frank , Ntambo Mbuya Sylvain , Kankonda Onesime M , Hafeez Sumaira , Anwar Toheed , Sharif Rahat 
Published: February 2018

AbstractBactrocera minax (Enderlein) (Diptera: Tephritidae) is a major citrus pest in China, whose artificial rearing technology of the adult is not well documented to date. In this study, we tried to determine if supplementing proteins to the adult diet could result in the enhancement of some fitness parameters of B. minax. Four feeds with varying protein source were provided as F0 (water), F1 (sucrose), F2 (sucrose + yeast), and F3 (sucrose + peptone). F0 and F1 being the control, F2 and F3 were protein food types. The results showed that adults fed by F2 and F3 lived longer with 40.1 d and 32.8 d, respectively, had reduced death rates (death peaks were delayed for 5.6 d and 4.1 d, respectively), increased mating frequencies (8.1 and 5.3 per females, 4.7 and 7.3 per males, respectively), and longer mating durations (with 42 d and 34 d). In addition, females recorded an increased adult ovary development, more egg load (with 94.8 and 77.3 brood eggs per ovary) and to greater oviposition rates of 63.2 eggs/female and 19.3 eggs/female. Based on our results, protein supplements enhanced B. minax survival, mating, and fecundity. This study does not only provide basic knowledge to implement artificial rearing of B. minax, but also deepens our understanding on its physiology that could be used to enhance the management of the pest.
The diverse density profiles of galaxy clusters with self-interacting dark matter plus baryons
Authors: Robertson Andrew , Massey Richard , Eke Vincent , Tulin Sean , Yu Hai-Bo , Bahé Yannick , Barnes David J , Bower Richard G , Crain Robert A , Dalla Vecchia Claudio , Kay Scott T , Schaller Matthieu , Schaye Joop 
Published: February 2018

Abstract
We present the first simulated galaxy clusters (M200 &gt; 1014 M⊙) with both self-interacting dark matter (SIDM) and baryonic physics. They exhibit a greater diversity in both dark matter and stellar density profiles than their counterparts in simulations with collisionless dark matter (CDM), which is generated by the complex interplay between dark matter self-interactions and baryonic physics. Despite variations in formation history, we demonstrate that analytical Jeans modelling predicts the SIDM density profiles remarkably well, and the diverse properties of the haloes can be understood in terms of their different final baryon distributions.
Interpolation and extrapolation
Authors: Boudreau Joseph F. , Swanson Eric S. 
Published: February 2018

Abstract
This chapter deals with two related problems occurring frequently in the physical sciences: first, the problem of estimating the value of a function from a limited number of data points; and second, the problem of calculating its value from a series approximation. Numerical methods for interpolating and extrapolating data are presented. The famous Lagrange interpolating polynomial is introduced and applied to one-dimensional and multidimensional problems. Cubic spline interpolation is introduced and an implementation in terms of Eigen classes is given. Several techniques for improving the convergence of Taylor series are discussed, including Shank’s transformation, Richardson extrapolation, and the use of Padé approximants. Conversion between representations with the quotient-difference algorithm is discussed. The exercises explore public transportation, human vision, the wine market, and SU(2) lattice gauge theory, among other topics.
Percolation and universality
Authors: Boudreau Joseph F. , Swanson Eric S. 
Published: February 2018

Abstract
Percolation deals with global properties of random configurations of local objects. While simple to implement in models, understanding percolation requires skill in pattern recognition and analysis. A cluster recognition algorithm is developed to obtain properties of percolation models. The fractal nature of a percolating system is discussed, along with general features of fractals. Scaling laws and critical exponents, which are central features of modern approaches to complex systems, are also introduced and illustrated with percolating systems. The important concept of a correlation function is also used to characterize these systems. Finally, the insensitivity of large classes of model systems with respect to short range dynamics, known as universality, is discussed in the context of percolation. This is illustrated with the modern concepts of coarse graining and the renormalization group.
Simulation
Authors: Boudreau Joseph F. , Swanson Eric S. 
Published: February 2018

Abstract
This chapter is devoted to Monte Carlo simulation of stochastic processes, both fundamental processes and those involving radiation transport through macroscopic material. The computation of fundamental processes builds on the treatment of rotations and Lorentz transformations from the previous chapter and expands it with a discussion of computational techniques for the evaluation of Feynman diagrams. The simulation of radiation transport covers electromagnetic processes such as ionization energy loss, bremsstrahlung, and pair production. A discussion of real-life challenges in the simulation of radiation transport is included, as well as a brief discussion of simulation toolkits that are available for solving industrial-strength problems. The discussion is intended to give an overview of some of the principal computational and numerical techniques enabling these toolkits.
Classical spin systems
Authors: Boudreau Joseph F. , Swanson Eric S. 
Published: February 2018

Abstract
The thermodynamic properties of spin systems are evaluated with Monte Carlo methods. A review of classical thermodynamics is followed by a discussion of critical exponents. The Monte Carlo method is then applied to the two-dimensional Ising model with the goal of determining the phase diagram for magnetization. Boundary conditions, the reweighting method, autocorrelation, and critical slowing down are all explored. Cluster algorithms for overcoming critical slowing down are developed next and shown to dramatically reduce autocorrelation. A variety of spin systems that illustrate first, second, and infinite order (topological) phase transitions are explored. Finally, applications to random systems called spin glasses and to neural networks are briefly reviewed.
Quantum mechanics II–many body systems
Authors: Boudreau Joseph F. , Swanson Eric S. 
Published: February 2018

Abstract
Chapter 23 develops formalism relevant to atomic and molecular electronic structure. A review of the product Ansatz, the Slater determinant, and atomic configurations is followed by applications to small atoms. Then the self-consistent Hartree-Fock method is introduced and applied to larger atoms. Molecular structure is addressed by introducing an adiabatic separation of scales and the construction of molecular orbitals. The use of specialized bases for molecular computations is also discussed. Density functional theory and its application to complicated molecules is introduced and the local density approximation and the Kohn-Sham procedure for solving the functional equations are explained. Techniques for moving beyond the local density approximation are briefly reviewed.
Quantum field theory
Authors: Boudreau Joseph F. , Swanson Eric S. 
Published: February 2018

Abstract
Markov chain Monte Carlo techniques are developed to compute properties of a variety of quantum field theories. The method is introduced with a simple scalar field theory and used to evaluate the particle spectrum and phase diagram for parity symmetry breaking. The technique of micorcanonical updating is introduced to increase efficiency. The important topic of gauge theory is then introduced via the gauged Z2 model. Development of the gauge theory formalism continues with Abelian gauge theory in two dimensions. The interaction between static charges is computed and compared to the exact result. The string tension in nonableian SU(2) gauge theory is explored with the aid of the renormalization group, which gives an entrée to a discussion of the Higgs mechanism. Finally, the formalism for including fermions is briefly reviewed.
The European Court of Justice and the Policy Process
Authors: Schmidt Susanne K. 
Published: February 2018

Abstract
The European Court of Justice is one of the most important actors in the process of European integration. Political science still struggles to understand its significance, with recent scholarship emphasizing how closely rulings reflect member states’ preferences. In this book, I argue that the implications of the supremacy and direct effect of the EU law have still been overlooked. As it constitutionalizes an intergovernmental treaty, the European Union has a detailed set of policies inscribed into its constitution that are extensively shaped by the Court’s case law. If rulings have constitutional status, their impact is considerable, even if the Court only occasionally diverts from member states’ preferences. By focusing on the four freedoms of goods, services, persons, and capital, as well as citizenship rights, the book analyses how the Court’s development of case law has ascribed a broad meaning to these freedoms. The constitutional status of this case law constrains policymaking at the European and member-state levels. Different case studies show how major pieces of EU legislation cannot move beyond case law but have to codify its principles. Judicialization is important in the EU. It also directly constrains member-state policies. Court rulings oriented towards individual disputes are difficult to translate into general policies, and into administrative practices. Policy options are thereby withdrawn from majoritarian decision-making. As the Court cannot be overruled, short of a Treaty change, its case law casts a long shadow over policymaking in the European Union and its member states, undermining the legitimacy of this political order.
Reaching Beyond the Market into State Responsibilities
Authors: Schmidt Susanne K. 
Published: February 2018

Abstract
Chapter 5 addresses policies that are more sensitive to sovereignty. The Citizenship Directive and the Patient Mobility Directive were both highly influenced by case-law development, although member states have largely reserved the right to define citizenship and the shape of their welfare states. The Court, however, consistently holds that member states have to respect the four freedoms also in areas of exclusive competence. Neither did existing secondary law inhibit the Court from partly designing an alternative policy. Regulation through case law is susceptible to creating inequalities, as it is difficult for private actors to understand. By codifying case law, member states wanted to signal their preferences to the Court. However, existing case law does not guarantee the necessary majorities for a common policy. Corporate tax policy is an example of an area where there is a lack of agreement in the face of a great deal of case law.
Interacting Systems far from Equilibrium
Authors: Morawetz Klaus 
Published: February 2018

AbstractIn quantum statistics based on many-body Green’s functions, the effective medium is represented by the selfenergy. This book aims to discuss the selfenergy from this point of view. The knowledge of the exact selfenergy is equivalent to the knowledge of the exact correlation function from which one can evaluate any single-particle observable. Complete interpretations of the selfenergy are as rich as the properties of the many-body systems. It will be shown that classical features are helpful to understand the selfenergy, but in many cases we have to include additional aspects describing the internal dynamics of the interaction. The inductive presentation introduces the concept of Ludwig Boltzmann to describe correlations by the scattering of many particles from elementary principles up to refined approximations of many-body quantum systems. The ultimate goal is to contribute to the understanding of the time-dependent formation of correlations. Within this book an up-to-date most simple formalism of nonequilibrium Green’s functions is presented to cover different applications ranging from solid state physics (impurity scattering, semiconductor, superconductivity, Bose–Einstein condensation, spin-orbit coupled systems), plasma physics (screening, transport in magnetic fields), cold atoms in optical lattices up to nuclear reactions (heavy-ion collisions). Both possibilities are provided, to learn the quantum kinetic theory in terms of Green’s functions from the basics using experiences with phenomena, and experienced researchers can find a framework to develop and to apply the quantum many-body theory straight to versatile phenomena.
Scattering on a Single Impurity
Authors: Morawetz Klaus 
Published: February 2018

AbstractEvolution of a many-body system consists of permanent collisions among particles. Looking at the motion of a single particle, one can identify encounters by which a particle abruptly changes the direction of flight, these are seen as true collisions, and small-angle encounters, which in sum act as an applied force rather than randomising collisions. The scattering on impurities is used to introduce the mentioned mechanisms and, in particular, to show how they affect each other. Point impurities are assumed, i.e. impurities the potential of which is restricted to a single atomic site of the crystal lattice. In this case interaction potentials never overlap and many-body effects are due to nonlocal character of the quantum particle. To introduce elementary components of the formalism, in this chapter we first describe the interaction of an electron with a single impurity. Lippman–Schwinger equations are derived and the physics behind the collision delay, dissipativeness and optical theorems is explored.