bluuebunny/crossref_metadata_2025_split huggingface dataset:
The Non-interacting Fermi Gas
Authors: Ketterson J. B. 
Published: December 2016

Abstract
This chapter first discusses the quantum mechanics of non-interacting electrons in a box. The simplest model of a metal is to assume it consists of free electrons in a box, with their mutual Coulomb repulsion ‘switched off’. The atoms in these materials (Li, Na, K, Rb, and Cs) have low ionization energies, only weakly binding their single valence s electron to the nucleus. It can then be imagined that when assembled as a crystal, each atom contributes one valence electron to the formation of a kind of electron gas or quantum plasma having a number density equal to that of the atoms. On average, the nuclear charge will compensate the free or mobile electronic charge. The remainder of the chapter covers Fermi–Dirac statistics; evaluation of integrals involving the Fermi distribution function; the temperature dependence of the chemical potential; energy of an ideal Fermi gas as a function of temperature; the paramagnetic susceptibility of a Fermi gas; and a qualitative discussion of the behaviour of a Fermi gas. Sample problems are also provided at the end of the chapter.
Lattices and Crystal Structures
Authors: Ketterson J. B. 
Published: December 2016

Abstract
This chapter begins with a definition of space lattice. For most pure materials, the lowest energy state at low temperatures is a crystalline solid, where the atoms or molecules making up the substance bind together in a manner which periodically repeats itself in space. The atoms are not points but have a finite spatial extent, and they execute thermal and quantum mechanical zero-point motions. If the crystal structure involves only one kind of atom and if there is only one atom per unit cell, then we may locate each atom at the origin of a unit cell. However, if there are multiple atoms per unit cell we must specify their location within the unit cell. The collection of atom coordinates is referred to as a basis and together with the lattice defines a crystal structure: lattice + basis = crystal structure. The remainder of the chapter covers point groups, Bravais lattices, and space groups in two dimensions; point groups, Bravais lattices, and space groups in three dimensions; common crystal structures; Miller indices; and the Wigner–Seitz polyhedra and coordination polyhedra.
Augmented Plane Wave and Green’s Function Methods*
Authors: Ketterson J. B. 
Published: December 2016

Abstract
This chapter discusses two techniques for calculating wave functions and energy levels in solids: the augmented plane wave (APW) and Green’s function methods. The APW method is derived using a variational principle based on the Schrödinger differential equation. This is then employed to calculate the band structures of the transition metals platinum and niobium. Green’s function method, also called the scattered wave or Korringa–Kohn–Rostoker (KKR) method, also makes use of a variational principle in which Schrödinger’s equation is recast as an integral equation involving the empty lattice Green’s function. The final section discusses the linearized augmented plane wave (LAPW) and the linearized muffin tin orbital (LMTO) methods. Sample problems are also provided at the end of the chapter.
Piezoelectricity, Pyroelectricity, and Ferroelectricity
Authors: Ketterson J. B. 
Published: December 2016

Abstract
For isotropic (amorphous) and many crystalline dielectrics the internal stresses are proportional to the square of an applied external electric field, a phenomenon called electrostriction, which is discussed in most texts on electricity and magnetism in connection with the Maxwell stress tensor. However, for certain crystal symmetries, strains develop which are linear in the applied electric field. This chapter discusses three such material classes: pyroelectrics, ferroelectrics, and piezoelectrics. Ferroelectrics and pyroelectrics have the property that an external electric field induces a stress. This property is called piezoelectricity. There is a third class of materials that has this property, but does not have a polarization in the absence of a stress; these materials are the piezoelectrics. All three of these materials classes possess an accompanying inverse response: an applied stress produces an electric field. Sample problems are also provided at the end of the chapter.
Superfluid4He
Authors: Ketterson J. B. 
Published: December 2016

Abstract
Liquid helium is the only substance which, below some temperature-dependent pressure, does not solidify on cooling to absolute zero. The fact that it does not freeze is due to the large quantum zero-point energy and the weak, isotropic, interatomic force. Two isotopes of helium exist, 4He and 3He. Both nuclei have two protons but 4He and 3He have, respectively, two neutrons and one neutron, corresponding to nuclear angular momenta of I = 0 and I = 1/2. This chapter focuses on 4He. It discusses Landau’s phenomenological model for 4He, superfluidity, the two-fluid model, the thermo-mechanical effect, hydrodynamics of superfluids and sound propagation, the Landau–Ginzburg theory of 4He, and quantized vorticity. A sample problem is also provided at the end of the chapter.
Defects and Diffusion in Crystalline Solids
Authors: Ketterson J. B. 
Published: December 2016

Abstract
The previous discussion of crystal lattices has assumed that they are infinite in extent and without any internal defects; i.e., they possess complete translational symmetry. An exception was an alloy, and a dilute concentration of impurities can be regarded as a kind of defect with respect to a host. But other kinds of defects can be present, even in a pure material. Although the word defect is generally used for imperfections in solids they nearly always occur in real materials and their presence cannot be ignored in achieving a realistic understanding of the properties of solids. This chapter focuses on some of the simplest defects. It discusses point defects, the concentration of point defects, point defects in lattices with more than one species, microscopic and macroscopic theories of diffusion, the temperature dependence of the diffusion constant, ionic conduction, and color centres.
Quantum Theory of Electrical Transport in Dilute Alloys
Authors: Ketterson J. B. 
Published: December 2016

Abstract
The discussion of electron transport in Chapter 19 was based on the semi-classical Boltzmann transport equation. Other than implicitly assuming plane-wave-like electron states, as numbered via their wave vectors, k, the primary place where quantum mechanics entered the model was in the use of the Fermi–Dirac distribution function for filling these states, so as to systematically incorporate the Pauli exclusion principle. This chapter begins a quantum mechanical discussion of electrical transport with the relatively simple approach of Mattis and Bardeen. The approach is based on averaging a quantity involving a position-dependent correlation of the single particle wave function that enters the quantum mechanical expression for the current density. After introducing a simple assumption for mathematical form of this correlation, it recovers some results obtained in Chapter 19 that were based on the Boltzmann equation. In particular, it re-derives the Chambers expression for the conductivity.
Strongly Correlated Systems
Authors: Ketterson J. B. 
Published: December 2016

Abstract
This chapter examines strongly correlated systems. The discussions of the quantum mechanics of electrons in solids up to this point have largely involved properties that can be treated within the framework of self-consistent, one-electron, band theory. This approach provides a good description of many metals, including those with d electrons, and various semiconductors with constituents having only s and p valence electrons. But this approach usually fails for the f electrons in rare earth metals, and is problematic for the so-called heavy-fermion inter metallic compounds, formed with certain 4f and 5f elements, as well as a host of chemical compounds containing atoms with d and f electrons, particularly oxides. To understand strongly correlated systems one must directly confront the physics that is left out of the one-electron models. The chapter discusses the following: the Mott insulator and the Mott transition; the local density approximation (LDA) implementation of density functional theory (DFT); strongly correlated electrons in metals; quantum phase transitions and marginal Fermi liquids; and possible mechanisms underlying heavy fermion superconductivity.
Regression analysis: Random effects models
Authors: Biørn Erik , Biørn Erik , Biørn Erik 
Published: December 2016

AbstractThis chapter considers model formulation and interpretation, estimation and testing in regression equations with random intercept heterogeneity. Compared with Chapter 2, assumptions are strengthened and the parametrization made more parsimonious. The chapter also considers one-way and two-way disturbance component models, their relation to variance analysis, and ways of handling disturbance heteroskedasticity and serial correlation.
Unbalanced panel data
Authors: Biørn Erik , Biørn Erik , Biørn Erik , Biørn Erik 
Published: December 2016

AbstractThis chapter extends some of the models and procedures discussed in Chapters 2 and 3 to handle unbalanced panel data with unobserved heterogeneity. Types of unbalance are discussed and may affect the preferred procedure. Attention is given to the required modifications of the within-, between-, GLS- and OLS-estimators and their relationships. Two kinds of between-estimators are involved. Procedures for estimation of the variance components and joint ML estimation of coefficients and variance components are discussed.
Multi-equation models
Authors: Biørn Erik , Biørn Erik , Biørn Erik , Biørn Erik 
Published: December 2016

AbstractTwo types of models are considered: systems of regression equations and interdependent models. For the former systems, equations with only individual-specific random intercepts and equations with both individual-specific and period-specific random effects and estimation by GLS are considered. For the latter systems, single equation estimation is first considered, and next joint estimation of all equations is explained. The chapter draws on results from earlier chapters regarding within-, between-, and GLS estimation as well as elements from Two-Stage and Three-Stage Least Squares (2SLS, 3SLS). Empirical examples are given.
Approaching the Roman Revolution
Authors: Syme Ronald 
Published: December 2016

Abstract
A collection of twenty-six previously unpublished papers on Roman Republican history by the late Sir Ronald Syme. Titles: The Divorce of Aemilius Paullus; The Predominance of the Fulvii; The Politics of the Marcii; The Abdication of Sulla; The Speech for Roscius of America; M. Aemilius Lepidus (cos. 78 bc); Satellites of Sulla; The Unspeakable Fufidius; Rex Leptasta; Sallust and Bestia; Rome and Arpinum; The Consular Elections, 70–66 bc; Catilina’s Three Marriages; Crassus, Catilina, and the Vestal Virgins; Sallust on Crassus; Sallust’s List of Conspirators; P. Sulla (cos. cand. 66 bc); The Gay Sempronia; The End of the Fulvii; Caesar as Pontifex Maximus; Cicero’s Change of Plan; Nicolaus of Damascus XXVIII and XXXI Virgil’s First Patron; Caesar and Augustus in Virgil; How Many Fasces?; Rome and Umbria.
Editor’s Introduction
Authors: Syme Ronald 
Published: December 2016

Abstract
This Introduction provides an overview of Ronald Syme’s Archive at the Bodleian Library in Oxford. It focuses predominantly on of the papers included in this volume, and aims to provide an assessment of their place within Syme’s scholarly production. Attention is also given to some unpublished studies of Syme that survive in incomplete form, such as a study of the Etruscan elites and the early draft of a book on Julius Caesar, and were not included in this volume. The criteria that have been followed in preparing this edition and in compiling the bibliographical addenda are also set out.
The Divorce of Aemilius Paullus
Authors: Syme Ronald 
Published: December 2016

Abstract
The paper provides a discussion of the divorce of L. Aemilius Paullus (cos. 182, 168 BC) and the role it played in the unfolding of his career. It also sketches a broader treatment of his political trajectory before and after his second marriage and surveys the choices of Aemilius’ sons within the wider context of mid-second century BC politics, as well as the predicament of his first wife and the possible identity of the second one. Some points of wider import are drawn from the specific choices of a prominent individual about the significance of marriage choices to the understanding of Roman Republican politics, and notably on the role that marriages and divorces could have in forging or undoing valuable political connections across the nobility.
The Abdication of Sulla
Authors: Syme Ronald 
Published: December 2016

Abstract
This paper provides a new assessment of the decision of L. Cornelius Sulla to relinquish power; it also provides a full discussion of its chronology and likely motivations, as well as of the wider political context in which it belongs. J. Carcopino’s view that Sulla set out to establish a monarchic regime receives a critical discussion, as well as the evidence of Plutarch and Sallust for some crucial aspects of the political history of the period. Sulla’s relationship with Pompey and Lepidus also receives some consideration, as well as his political connection with the Metelli and other prominent families of the Roman nobility.
Family and Business
Authors: Barker Hannah 
Published: December 2016

Abstract
This chapter explores the concept of ‘family strategy’ among those in trade, particularly concerning business. Although it shows that internal dynamics within families might sometimes be difficult, and that the possibility of unseemly fallings-out between individuals was very real, it also demonstrates the pervasive belief that familial relationships should be based on duty, love and trust and that family members should work together to ensure a shared prosperity. Using court records, the chapter explores a variety of forms of familial disharmony and struggles over resources, but it also presents examples of cooperation within families where members worked together to ensure mutual economic benefit as part of a joint business strategy, as well as the existence of strong emotional ties between family members.
Family and Household
Authors: Barker Hannah 
Published: December 2016

Abstract
This chapter explores individual experiences of space by examining personal testimony. Hierarchies within trading households were often expressed in terms of access to different interior spaces. Though gender was a powerful organizational concept among those in trade, generational hierarchies seem more important in terms of the control of space. Variations between households were linked both to different understandings of the family, and to the physical constraints of the households concerned. Privacy does not seem to have been conceived in terms of personal space but it was clearly important in small business households in terms of upholding certain standards of respectability. Ensuring this sort of privacy meant that individuals had to abide by sets of unwritten rules about behaviour and conduct. Failure to do so, or the appearance of family battles over power and/or resources, could mean that the break-up of household relations, which also affected businesses.
Marine Geochemistry
Authors: Roy-Barman Matthieu , Jeandel Catherine 
Published: December 2016

Abstract
Marine geochemistry uses chemical elements and their isotopes to study how the ocean works. It brings quantitative answers to questions such as: What is the deep ocean mixing rate? How much atmospheric CO2 is pumped by the ocean? How fast are pollutants removed from the ocean? How do ecosystems react to the anthropogenic pressure? The book provides a simple introduction to the concepts (environmental chemistry, isotopes), the methods (field approach, remote sensing, modeling) and the applications (ocean circulation, carbon cycle, climate change) of marine geochemistry with a particular emphasis on isotopic tracers. Marine geochemistry is not an isolated discipline: numerous openings on physical oceanography, marine biology, climatology, geology, pollutions and ecology are proposed and provide a global vision of the ocean. It includes new topics based on ongoing research programs such as GEOTRACES, Global Carbon Project, Tara Ocean. It provides a complete outline for a course in marine geochemistry. To favor a hands-on approach, application exercises are worked out throughout the book and each chapter concludes with a set of problems based on the recent scientific literature (with solutions given at the end of the book).
Ocean History and Climate Evolution
Authors: Roy-Barman Matthieu , Jeandel Catherine 
Published: December 2016

Abstract
Over Earth history, there has been an interplay between the ocean and the climate evolution and this will continue in the future. Elemental and isotopic tracers called proxies are used to reconstruct environmental changes over timescales from billions of years to decades. Over the long term, the ocean acts on the climate through the carbon cycle (in relation with life evolution and carbon storage in marine sediments) and plate tectonics (ocean circulation changes with continental masses location, isthmus opening or closing). Studying the past climate variability during the last interglacial/glacial cycle highlights some of the mechanisms and retroactions controlling the ongoing climate change. Global warming impacts such as warmer sea surface temperature, Arctic sea-ice decrease or shifts in plankton phenology are already observed. Other forecast impacts such as the meridional overturning circulation slow-down or changes of the ocean biological productivity have not yet clearly emerged from the natural variability.
The Use of Metabolomics to Identify Biological Signatures of Manganese Exposure
Authors: Baker Marissa G , Simpson Christopher D , Lin Yvonne S , Shireman Laura M , Seixas Noah 
Published: December 2016

Abstract

Objectives
Manganese (Mn) is a known neurotoxicant, and given its health effects and ubiquitous nature in metal-working settings, identification of a valid and reproducible biomarker of Mn exposure is of interest. Here, global metabolomics is utilized to determine metabolites that differ between groups defined by Mn exposure status, with the goal being to help inform a potential metabolite biomarker of Mn exposure.

Methods
Mn exposed subjects were recruited from a Mn steel foundry and Mn unexposed subjects were recruited from crane operators at a metal recycling facility. Over the course of a work day, each subject wore a personal inhalable dust sampler (IOM), and provided an end of shift urine sample that underwent global metabolomics profiling. Both exposed and unexposed subjects were divided into a training set and demographically similar validation set. Using a two-sided adjusted t-test, relative abundances of all metabolites found were compared between Mn exposed and unexposed training sets, and those with a false discovery rates (FDR) <0.1 were further tested in the validation sets.

Results
Fifteen ions were found to be significantly different (FDR < 0.1) between the exposed and unexposed training sets, and nine of these ions remained significantly different between the exposed and unexposed validation set as well. When further dividing exposure status into ‘lower exposure’ and ‘higher exposure’, several of these nine ions exhibited an apparent exposure–response relationship.

Conclusions
This is the first time that metabolomics has been used to distinguish between Mn exposure status in an occupational cohort, though additional work should be done to replicate these findings with a larger cohort. With metabolite identification by name, empirical formula, or pathway, a better understanding of the relationship between Mn exposure and neurotoxic effects could be elucidated, and a potential metabolite biomarker of Mn exposure could be determined.
A pipeline for local assembly of minisatellite alleles from single-molecule sequencing data
Authors: Ogeh Denye , Badge Richard 
Published: December 2016

Abstract

Motivation
The advent of Next Generation Sequencing (NGS) has led to the generation of enormous volumes of short read sequence data, cheaply and in reasonable time scales. Nevertheless, the quality of genome assemblies generated using NGS technologies has been greatly affected, compared to those generated using Sanger DNA sequencing. This is largely due to the inability of short read sequence data to scaffold repetitive structures, creating gaps, inversions and rearrangements and resulting in assemblies that are, at best, draft forms. Third generation single-molecule sequencing (SMS) technologies (e.g. Pacific Biosciences Single Molecule Real Time (SMRT) system) address this challenge by generating sequences with increased read lengths, offering the prospect to better recover these complex repetitive structures, concomitantly improving assembly quality.

Results
Here, we evaluate the ability of SMS data (specifically human genome Pacific Biosciences SMRT data) to recover poorly represented repetitive sequences (specifically, GC-rich human minisatellites). To do this we designed a pipeline for the collection, processing and local assembly of single-molecule sequence data to form accurate contiguous local reconstructions. Our results show the recovery of an allele of the non-coding minisatellite MS1 (located on chromosome 1 at 1p33-35) at greater than 97% identity to reference (GRCh38) from the unprocessed sequence data of a haploid complete hydatidiform mole (CHM1) cell line. Furthermore, our assembly revealed an allele of over 500 repeat units; much larger than the reference (GRCh38), but consistent in structure with naturally occurring alleles that are segregating in human populations. This local assembly’s reconstruction was validated with the release of the whole genome assemblies GCA_001297185.1 and GCA_000772585.3, where this allele occurs. Additionally, application of this pipeline to coding minisatellites in the PRDM9 and ZNF93 genes enabled recovery of high identity allele structures for these sequence regions whose length was confirmed by PCR from cell line genomic DNA. The internal repeat structure of the PRDM9 allele recovered was consistent with common human-specific alleles.

Availability and Implementation
Code available at https://github.com/ndliberial/smrt_pipeline
The null hypothesis of GSEA, and a novel statistical model for competitive gene set analysis
Authors: Debrabant Birgit 
Published: December 2016

Abstract

Motivation
Competitive gene set analysis intends to assess whether a specific set of genes is more associated with a trait than the remaining genes. However, the statistical models assumed to date to underly these methods do not enable a clear cut formulation of the competitive null hypothesis. This is a major handicap to the interpretation of results obtained from a gene set analysis.

Results
This work presents a hierarchical statistical model based on the notion of dependence measures, which overcomes this problem. The two levels of the model naturally reflect the modular structure of many gene set analysis methods. We apply the model to show that the popular GSEA method, which recently has been claimed to test the self-contained null hypothesis, actually tests the competitive null if the weight parameter is zero. However, for this result to hold strictly, the choice of the dependence measures underlying GSEA and the estimators used for it is crucial.

Supplementary information
Supplementary material is available at Bioinformatics online.