bluuebunny/crossref_metadata_2025 huggingface dataset:
Solid-state NMR Study of Ion Adsorption and Charge Storage in Graphene Film Supercapacitor Electrodes
Authors: Li Kecheng , Bo Zheng , Yan Jianhua , Cen Kefa
Published: December 2016

Graphene film has been demonstrated as promising active materials for electric double layer capacitors (EDLCs), mainly due to its excellent mechanical flexibility and freestanding morphology. In this work, the distribution and variation pattern of electrolyte ions in graphene-film based EDLC electrodes are investigated with a 11B magic-angle spinning nuclear magnetic resonance (MAS-NMR) spectroscopy. For neutral graphene films soaked with different amounts of electrolytes (1 M TEABF4/ACN), weakly and strongly adsorbed anions are identified based on the resonances at different 11B chemical shifts. Unlike other porous carbonaceous materials, the strongly adsorbed anions are found as the major electrolyte anions components in graphene films. Further measurements on the ion population upon charging are carried out with applying different charging voltages on the graphene films. Results indicate that the charging process of graphene-film based EDLCs can be divided into two distinct charge storage stages (i.e., ejection of co-ions and adsorption of counter-ions) for different voltages. The as-obtained results will be useful for the design and fabrication of high performance graphene-film based EDLCs.
The levels of the sex hormones are not different between type 1 and type 2 endometrial cancer
Authors: Wan Jiayi , Gao Yifei , Zeng Ke , Yin Yongxiang , Zhao Min , Wei Jia , Chen Qi
Published: December 2016

The involvement of hormonal factors in developing endometrial cancer is well documented. In particular, excess or unopposed estrogen is a major risk factor. Endometrial cancer is divided into estrogen-dependent and estrogen-independent types. Studies suggested that the subtypes of endometrial cancer share many common risk factors. Whether the levels of sex hormones differ between types 1 and 2 endometrial cancer has not been investigated. In this study, levels of estrogen, progesterone, testosterone, follicle stimulating hormone (FSH) and luteinizing hormone (LH) were investigated between type 1 and type 2 endometrial cancer taking into account menopausal status and parity. The sex hormones levels and estrogen and progesterone receptors were measured in 187 women with endometrial cancer. The levels of estradiol (E2), progesterone, testosterone, FSH and LH were not different between the subtypes of endometrial cancer regardless of menopausal status. In addition, the sex hormones were not different between patients of different party regardless of the menopausal status. The majority of type 1 (96%) and type 2 (82%) endometrial cancers were estrogen and progesterone receptor positive. Our data suggest that type 2 endometrial cancer is not completely estrogen independent, and type 1 and type 2 endometrial cancers may have a similar pathogenesis.
Polyaspartamide-based graft copolymers encapsulating iron oxide nanoparticles for imaging and fluorescence labelling of immune cells
Authors: Kim Minsun , Shin Seung Won , Lim Cheol Won , Kim Jaeyun , Um Soong Ho , Kim Dukjoon
Published: December 2016

Iron oxide nanoparticles (NPs) were encapsulated with polyaspartamide derivatives for immune cell binding.
Using chiral ionic liquid additives to enhance asymmetric induction in a Diels–Alder reaction
Authors: Goodrich P. , Nimal Gunaratne H. Q. , Hall L. , Wang Y. , Jin L. , Muldoon M. J. , Ribeiro A. P. C. , Pombeiro A. J. L. , Pârvulescu V. I. , Davey P. , Hardacre C.
Published: December 2016

A bis-oxazoline ligand has been complexed using Cu(ii) and Zn(ii) trifluoromethanesulfonate and a range of chiral ionic liquid (CIL) additives based on natural products were used as a co-catalyst for a Diels–Alder reaction.
Changes in protein expression profiles in bovine endometrial epithelial cells exposed to E. coli LPS challenge
Authors: Piras Cristian , Guo Yongzhi , Soggiu Alessio , Chanrot Metasu , Greco Viviana , Urbani Andrea , Charpigny Gilles , Bonizzi Luigi , Roncada Paola , Humblot Patrice
Published: December 2016

Proteomics of the physiological response of bEECs to LPS challenge to unravel the possible implication of bacterial infection in pregnancy establishment.
Encapsulation of a nitric oxide donor into a liposome to boost the enhanced permeation and retention (EPR) effect
Authors: Tahara Yu , Yoshikawa Takuma , Sato Hikari , Mori Yukina , Zahangir Md Hosain , Kishimura Akihiro , Mori Takeshi , Katayama Yoshiki
Published: December 2016

We propose a method to improve the enhanced permeability and retention (EPR) effect of nanomedicines based on tumor-specific vasodilation using a nitric oxide (NO) donor-containing PEGylated liposome.
The construction and application of Markov state models for colloidal self-assembly process control
Authors: Tang Xun , Bevan Michael A. , Grover Martha A.
Published: December 2016

Markov state models have been widely applied to study time sequential events in a variety of disciplines.
Constrained evolution of a bispecific enzyme: lessons for biocatalyst design
Authors: Sugrue E. , Scott C. , Jackson C. J.
Published: December 2016

Analysis of the natural evolution of bispecificity in triazine hydrolase highlights the importance of epistasis in protein engineering and evolution.
Copper(ii)-catalyzed Chan–Lam cross-coupling: chemoselective N-arylation of aminophenols
Authors: Siva Reddy A. , Ranjith Reddy K. , Nageswar Rao D. , Jaladanki Chaitanya K. , Bharatam Prasad V. , Lam Patrick Y. S. , Das Parthasarathi
Published: December 2016

Copper(ii)-catalyzed boronic acid promoted chemoselective N-arylation of unprotected aminophenols has been developed.
Controlling self-patterning of acrylate films by photopolymerization
Authors: Lacombe J. , Soulié-Ziakovic C.
Published: December 2016

Acrylate formulations can spontaneously generate surface patterns by UV-curing in open-air.
Controlling the structure and morphology of zinc borate by adjusting the reaction temperature and pH value: formation mechanisms and luminescent properties
Authors: Liang Pan , Tuoheti Zuolaguli , Liu Zhi-Hong
Published: December 2016

Zinc borate micro/nanostructured phosphors with three different compositions and structures have been prepared. When Tb3+ ions were doped into the zinc borate matrix, the three phosphors yielded tunable emissions.
Rectification of current responds to incorporation of fullerenes into mixed-monolayers of alkanethiolates in tunneling junctions
Authors: Qiu Li , Zhang Yanxi , Krijger Theodorus L. , Qiu Xinkai , Hof Patrick van't , Hummelen Jan C. , Chiechi Ryan C.
Published: December 2016

This paper describes the rectification of current through molecular junctions comprising self-assembled monolayers of decanethiolate through the incorporation of C60 fullerene moieties in junctions using eutectic Ga–In (EGaIn) and Au conducting probe AFM top-contacts.
Photoactivatable aggregation-induced emission probes for lipid droplets-specific live cell imaging
Authors: Gao Meng , Su Huifang , Lin Yuhan , Ling Xia , Li Shiwu , Qin Anjun , Tang Ben Zhong
Published: December 2016

Photoactivatable probes for lipid droplets (LDs)-specific live-cell imaging are powerful tools for investigating their biological functions through precise spatial and temporal control.
Photoelectric conversion beyond sunny days: all-weather carbon quantum dot solar cells
Authors: Yang Junxia , Tang Qunwei , Meng Qi , Zhang Zhifang , Li Jinyu , He Benlin , Yang Peizhi
Published: December 2016

All-weather CQD solar cells that can persistently generate electricity at days and nights are built using strawberry powder converted CQDs, yielding a dark efficiency as high as 14.8%.
Effects of a highly lipophilic substituent on the environmental stability of naphthalene tetracarboxylic diimide-based n-channel thin-film transistors
Authors: Zhao Liang , Zhang Dongwei , Zhu Yanan , Sen Peng Sen Peng , Meng Hong , Huang Wei
Published: December 2016

Introduction of highly lipophilic electron withdrawing trifluoromethanesulfenyl (SCF3) group is an effective approach to improve the air stability of n-channel organic thin film transistors.
First-principles study on charge transfer in an actinide-containing superatom from surface-enhanced Raman scattering
Authors: Gao Yang , Jiang Wanrun , Chen Lei , Wang Jia , Wang Zhigang
Published: December 2016

The charge-transfer states (1Dmetal → π*pyridine) can lead to surface-enhanced Raman scattering (SERS) signal enhancement ∼104 for pyridine–Th@Ag14 complexes.
Enhanced and tunable photochromism of MoO3–butylamine organic–inorganic hybrid composites
Authors: Wang Rongguo , Lu Xiaolong , Hao Lifeng , Jiao Weicheng , Liu Wenbo , Zhang Jian , Yuan Feng , Yang Fan
Published: December 2016

Improving the photochromism of MoO3 by n-butylamine intercalation and tuning its discoloration using ethanol as a hole scavenger.
Mumbling: Macho or Morphology?
Authors: Weirich Melanie , Fuchs Susanne , Simpson Adrian , Winkler Ralf , Perrier Pascal
Published: December 2016

Purpose

Mumbling as opposed to clear speech is a typical male characteristic in speech and can be the consequence of a small jaw opening. Whereas behavioral reasons have often been offered to explain sex-specific differences with respect to clear speech, the purpose of this study is to investigate a potential anatomical reason for smaller jaw openings in male than in female speakers.

Method

Articulatory data from 2 data sets (American English and German) were analyzed with respect to jaw opening in low vowels during speech. Particular focus was placed on sex-specific differences, also incorporating potential interactions with different accent conditions in 1 of the data sets. In addition, a modeling study compared the articulatory consequences of similar jaw-opening settings in a typical male and a typical female articulatory model.

Results

Greater jaw openings were found for the female speakers, in particular in the accented condition, where jaw opening was found to be larger. In line with this finding, the modeling study showed that similar jaw-opening settings in male and female speakers led to differences in pharyngeal constriction, resulting in complete radico-pharyngeal closure in the male model.

Conclusion

The empirical and modeling findings suggest a possible physiological component in sex-specific differences in speech clarity for low vowels.
Effect of Domain Initial Strengthening on Vowel Height and Backness Contrasts in French: Acoustic and Ultrasound Data
Authors: Georgeton Laurianne , Antolík Tanja Kocjančič , Fougeron Cécile
Published: December 2016

Purpose

Phonetic variation due to domain initial strengthening was investigated with respect to the acoustic and articulatory distinctiveness of vowels within a subset of the French oral vowel system /i, e, ɛ, a, o, u/, organized along 4 degrees of height for the front vowels and 2 degrees of backness at the close and midclose height levels.

Method

Acoustic and lingual ultrasound data were examined to characterize the production of vowels in intonational phrase initial position, compared with intonational phrase medial position, for 4 speakers.

Results

Formant values and estimates of lingual constriction location and degree differed according to the prosodic position independent of vowel duration, with a higher F1 for /a/, a higher F2 for /ɛ/, a backer constriction for /o/ and /a/ but a fronter constriction for /ɛ/, and a narrower constriction for /e, ɛ, u, o/ but a wider constriction for /a/. For most speakers, these variations enlarge the acoustic and/or articulatory distance between members of the pairs /e-ɛ/, /ɛ-a/, /u-o/, /i-u/, and /e-o/ but reduce the distinction within the pair /i-e/.

Conclusions

These changes in intonational phrase initial position are vowel dependent and frequently contribute to augmenting the phonetic distinctiveness between vowels contrasting along the height and backness dimensions.
Optimised band‐pass filter to ensure accurate ECG‐based identification of exercising human subjects
Authors: Nobunaga T. , Tanaka H. , Tanahashi I. , Watanabe T. , Hattori Y.
Published: December 2016

Waveform distortions generated by exercise cause erroneous predictions in human identification based on the electrocardiogram (ECG). An approach for the ECG‐based identification to achieve accurate predictions while exercising is proposed. In the proposed scheme, passband of a band‐pass filter is optimised to compensate for the distortion. As a result, the proposed scheme archives 100% identification accuracy is revealed when the subject is resting and 99.7% during exercise. The investigation is an important building block in the development of robust ECG‐based identification systems that are consistently accurate despite significant ECG waveform variation due to exercise.
Inorganic nitrogen release from sediment slurry of riverine and estuarine ecosystems located at different river regimes
Authors: Paudel Bhanu , Montagna Paul A. , Besonen Mark , Adams Leslie
Published: December 2016

The purpose of the present study was to compare the nature of dissolved inorganic nitrogen (DIN=ammonium (NH4+) and nitrite+nitrate (NO2+3=(NO2–+NO3–)) release from aerobic sediment slurry at two different hydrologic flow regimes. The watershed of the Guadalupe River–Estuary system receives more freshwater inflow than does the watershed of the Nueces River–Estuary system; thus, the Nueces Estuary is more saline than is the Guadalupe Estuary. Sediment samples were collected using cores, analysed for organic matter and grain size, and used to perform laboratory experiments to measure DIN release. During the experiments, DIN concentrations in overlying water were measured for 48h in five different salinity treatments. Ammonium concentrations were higher in the Nueces River and Estuary treatments than in similarly treated samples from the Guadalupe River and Estuary. An increase in NO2+3 concentrations along salinity gradients of the Nueces Estuary treatments indicated favourable condition for nitrification. The Guadalupe River sediments that were not exposed to salinity had an increase in NH4+ concentration at 7.5ppt. The different DIN release among salinity treatments indicated that hydrologic forcing on organic matter deposition and salinity have an important role on the retention and release of inorganic nitrogen at the sediment–water aerobic layers in rivers and estuaries.
The genera Chiastocaulon, Cryptoplagiochila and Pedinophyllum (Plagiochilaceae) in Australia
Authors: Renner Matt A. M. , Heslewood Margaret M. , Patzak Simon D. F. , Schäfer-Verwimp Alfons , Heinrichs Jochen
Published: December 2016

Molecular and morphological data support the recognition of seven species of Chiastocaulon in Australia, of which four, namely C. braunianum and C. geminifolium comb. nov. from tropical north-eastern Queensland and C. proliferum and C. flamabilis sp. nov. from Tasmania (and New Zealand), represent new records. The other three species accepted for Australia are C. biserialis, C. dendroides and C. oppositum. Chiastocaulon conjugatum is excluded from the Australian flora, because previous Australian records are based on misidentifications of C. braunianum and Plagiochila retrospectans. Pedinophyllum monoicum, reported for Australia from a single locality in Victoria, is excluded from the Australian flora because all credible records are based on misidentifications of Syzygiella tasmanica. The Papua New Guinean Chiastocaulon takakii comb. nov. is reinstated from synonymy under C. dendroides on the basis of morphological evidence. Descriptions and illustrations of all Australian species, and dichotomous keys to species of the Chiastocaulon lineage in Australia and New Zealand, are provided.
Statistical Catch-Free Age-Structured Assessment to Estimate Year-Class Strength for Inland Recreational Fisheries: A Largemouth Bass Example
Authors: Feltz Nicholas G. , Catalano Matthew J.
Published: December 2016

Statistical catch-at-age analysis (SCAA) is commonly used to estimate recruitment and mortality for large-scale, economically important fish stocks, but fishery-dependent catch-at-age data are often unavailable for smaller-scale inland fisheries, thus limiting the use of SCAA. In these systems, a catch-free approach to age-structure modeling may be useful for estimating recruitment and mortality rates solely from a time series of survey age composition and catch rate data by estimating recruitment as a relative index of year-class strength (Rt). Here, we demonstrate a statistical catch-free age-structured assessment (SCFASA) model for small-scale inland fish stocks as an alternative to traditional catch curve approaches by using Largemouth Bass Micropterus salmoides as an example. We fitted the SCFASA to fishery-independent survey age composition and catch-per-effort data from Largemouth Bass stocks in three Alabama reservoirs to estimate Rt, annual fishing mortality rates, and age-specific electrofishing survey vulnerability; we compared Rt to catch curve residual estimates and performed a sensitivity analysis under a variety of model assumptions. Model estimates of Rt and temporal trends in fishing mortality were robust to changes in assumptions about the effective sample size of multinomial age samples, natural mortality rate, and temporal variability in fishing mortality. However, the magnitude of instantaneous fishing mortality rates at two of the three reservoirs was somewhat higher than empirical estimates for similar stocks and was sensitive to model assumptions. Our application of the SCFASA to survey data sets routinely collected by management agencies for Largemouth Bass potentially provides a comprehensive approach to estimating Rt, mortality, and sampling vulnerability for these stocks without increasing sampling effort. Future investigations of SCFASA's utility for small-scale inland stocks should address the potential for bias in the magnitude of fishing mortality estimates due to incorrectly specified vulnerability schedules.

Received October 5, 2015; accepted September 19, 2016 Published online December 21, 2016
An analytical model to calculate the peak temperature for friction stir welding
Authors: Qian Jinwen , Ou Yan , Li Jinglong , Xiao Yifeng , Wu Liang , Xu Yanfei
Published: December 2016

The peak temperature and temperature profile greatly affect the defect formation and the joint strength during the friction stir welding processing. An analytical model is proposed and tested to estimate the peak temperature based on the common constitutive equation of inverse hyperbolic sine function and the fundamentals of continuum mechanics. The calculated results of the peak temperature are consistent with the literature data of several aluminium alloys.
Oviposition-site mimicry
Authors: Johnson Steven D. , Schiestl Florian P.
Published: December 2016

Of all the floral mimicry systems covered in this book, oviposition-site mimicry is probably the most widespread (in terms of geography and the number of plant species and lineages represented) and the most diverse (in terms of floral signals). It is also the most under-appreciated system of floral mimicry and is certainly less well known than floral sexual mimicry. The widespread phenomenon of floral oviposition-site mimicry includes mimicry of fruit, carrion, feces and fungal substrates that are used by insects as brood sites. Chemical signals are key in all of these systems, but there is also evidence for combined effects of chemical and visual signals (in other words multimodal signals).
Special cases
Authors: Johnson Steven D. , Schiestl Florian P.
Published: December 2016

This chapter deals with topics that are contentious, difficult to categorize, or fall somewhat outside the mainstream of floral mimicry research. The concept of Müllerian mimicry has been applied to resemblance among rewarding flowers, but this chapter shows that the evidence that this reflects a process of mimicry remains tenuous. Intersexual resemblance of flowers of dioecious plants is clearly not mimicry in the classical sense, but selection does appear to maintain similarity, particularly in cases where only one sex offers a reward. These special cases illustrate the potentially ubiquitous nature of mimicry phenomena and also the fact that many mimicry systems involve more species than just a single mimic, model, and operator.
Future directions in floral mimicry research
Authors: Johnson Steven D. , Schiestl Florian P.
Published: December 2016

More than 200 years after the discovery of floral mimicry by Sprengel many questions about this fascinating natural phenomenon remain unanswered. Floral mimicry has traditionally been a relatively small field of research compared with animal mimicry; however, floral mimicry studies now account for almost a third of all studies dealing with mimicry among organisms. This chapter looks to the future of mimicry research and focuses on molecular approaches and their potential to answer unresolved questions about speciation. The inclusion of this chapter does not mean that the future of mimicry research is purely molecular rather than ecological. However, it can be considered that molecular approaches are not specific to a particular type of mimicry system, and it therefore makes more sense to deal with this topic in a single chapter and to discuss ecological approaches in the chapters that focus on each type of floral mimicry.
The Non-interacting Fermi Gas
Authors: Ketterson J. B.
Published: December 2016

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

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

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

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

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

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

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

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

This 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

This 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

Two 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

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

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

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

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.
Multiple Denotation
Authors: Priest Graham
Published: December 2016

Chapter 8 replies to an argument against noneism based on a paradox of denotation, due essentially to Hilbert and Bernays. The solution proceeds in terms of a theory of multiple-denotation.
Possibility, Impossibility, and Conceivability
Authors: Priest Graham
Published: December 2016

Chapter 9 returns to the question of impossible worlds, and discusses their structure in its own right (independent of questions of intentionality). It then discusses conceivability, and argues that everything is conceivable, whether or not it is possible.
SeinLanguage
Authors: Priest Graham
Published: December 2016

Chapter 17 provides an analysis of how the verb ‘to be’ behaves in English. Matters are much more complicated than is often presumed. Sometimes, ‘being’ means ‘existence’; sometimes it does not.
Family and Business
Authors: Barker Hannah
Published: December 2016

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

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

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

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

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

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

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.
Surgical Trainee Feedback-Seeking Behavior in the Context of Workplace-Based Assessment in Clinical Settings
Authors: Gaunt Anne , Patel Abhilasha , Fallis Simon , Rusius Victoria , Mylvaganam Seni , Royle T. James , Almond Max , Markham Deborah H. , Pawlikowska Teresa R.B.
Published: December 2016

Purpose

To investigate surgical trainee feedback-seeking behaviors—directly asking for feedback (inquiry) and observing and responding to situational clues (monitoring)—in the context of workplace-based assessment (WBA).

Method

A hypothetical model of trainee feedback-seeking behavior was developed using existing literature. A questionnaire, incorporating previously validated instruments from organizational psychology, was distributed to general surgical trainees at 23 U.K. hospitals in 2012–2013. Statistical modeling techniques compared the data with 12 predetermined hypothetical relationships between feedback-seeking behaviors and predictive variables (goal orientation, supervisory style) through mediating variables (perceptions of personal benefits and costs of feedback) to develop a final model.

Results

Of 235 trainees invited, 178 (76%) responded. Trainees completed 48 WBAs/year on average, and 73% reported receiving feedback via WBA. The final model was of good fit (chi-square/degree of freedom ratio = 1.620, comparative fit index = 0.953, root mean square error of approximation = 0.059). Modeled data showed trainees who perceive personal benefits to feedback use both feedback inquiry and monitoring to engage in feedback interactions. Trainees who seek feedback engage in using WBA. Trainees’ goal orientations and perceptions of trainers’ supervisory styles as supportive and instrumental are associated with perceived benefits and costs to feedback.

Conclusions

Trainees actively engage in seeking feedback and using WBA. Their perceptions of feedback benefits and costs and supervisory style play a role in their feedback-seeking behavior. Encouraging trainees to actively seek feedback by providing specific training and creating a supportive environment for feedback interactions could positively affect their ability to seek feedback.