Modelling rankings in R: the PlackettLuce package

This paper presents the R package PlackettLuce, which implements a generalization of the Plackett-Luce model for rankings data. The generalization accommodates both ties (of arbitrary order) and partial rankings (complete rankings of subsets of items). By default, the implementation adds a set of pseudo-comparisons with a hypothetical item, ensuring that the underlying network of wins and losses between items is always strongly connected. In this way, the worth of each item always has a finite maximum likelihood estimate, with finite standard error. The use of pseudo-comparisons also has a regularization effect, shrinking the estimated parameters towards equal item worth. In addition to standard methods for model summary, PlackettLuce provides a method to compute quasi standard errors for the item parameters. This provides the basis for comparison intervals that do not change with the choice of identifiability constraint placed on the item parameters. Finally, the package provides a method for model-based partitioning using covariates whose values vary between rankings, enabling the identification of subgroups of judges or settings that have different item worths. The features of the package are demonstrated through application to classic and novel data sets.Comment: In v2: review of software implementing alternative models to Plackett-Luce; comparison of algorithms provided by the PlackettLuce package; further examples of rankings where the underlying win-loss network is not strongly connected. In addition, general editing to improve organisation and clarity. In v3: corrected headings Table 4, minor edit

Self-pulsing dynamics in a cavity soliton laser

The dynamics of a broad-area vertical-cavity surface-emitting laser (VCSEL) with frequency-selective feedback supporting bistable spatial solitons is analyzed experimentally and theoretically. The transient dynamics of a switch-on of a soliton induced by an external optical pulse shows strong self-pulsing at the external-cavity round-trip time with at least ten modes excited. The numerical analysis indicates an even broader bandwidth and a transient sweep of the center frequency. It is argued that mode-locking of spatial solitons is an interesting and viable way to achieve three-dimensional, spatio-temporal self-localization and that the transients observed are preliminary indications of a transient cavity light bullet in the dynamics, though on a non negligible background

Frequency and phase locking of laser cavity solitons

Self-localized states or dissipative solitons have the freedom of translation in systems with a homogeneous background. When compared to cavity solitons in coherently driven nonlinear optical systems, laser cavity solitons have the additional freedom of the optical phase. We explore the consequences of this additional Goldstone mode and analyse experimentally and numerically frequency and phase locking of laser cavity solitons in a vertical-cavity surface-emitting laser with frequency-selective feedback. Due to growth-related variations of the cavity resonance, the translational symmetry is usually broken in real devices. Pinning to different defects means that separate laser cavity solitons have different frequencies and are mutually incoherent. If two solitons are close to each other, however, their interaction leads to synchronization due to phase and frequency locking with strong similarities to the Adler-scenario of coupled oscillators

Spatial correlations in hexagons generated via a Kerr nonlinearity

We consider the hexagonal pattern forming in the cross-section of an optical beam produced by a Kerr cavity, and we study the quantum correlations characterizing this structure. By using arguments related to the symmetry broken by the pattern formation, we identify a complete scenario of six-mode entanglement. Five independent phase quadratures combinations, connecting the hexagonal modes, are shown to exhibit sub-shot-noise fluctuations. By means of a non-linear quantum calculation technique, quantum correlations among the mode photon numbers are demonstrated and calculated.Comment: ReVTeX file, 20 pages, 7 eps figure

Structural transformations and disordering in zirconolite (CaZrTi2O7) at high pressure

There is interest in identifying novel materials for use in radioactive waste applications and studying their behavior under high pressure conditions. The mineral zirconolite (CaZrTi2O7) exists naturally in trace amounts in diamond-bearing deep-seated metamorphic/igneous environments, and it is also identified as a potential ceramic phase for radionuclide sequestration. However, it has been shown to undergo radiation-induced metamictization resulting in amorphous forms. In this study we probed the high pressure structural properties of this pyrochlore-like structure to study its phase transformations and possible amorphization behavior. Combined synchrotron X-ray diffraction and Raman spectroscopy studies reveal a series of high pressure phase transformations. Starting from the ambient pressure monoclinic structure, an intermediate phase with P21/m symmetry is produced above 15.6 GPa via a first order transformation resulting in a wide coexistence range. Upon compression to above 56 GPa a disordered metastable phase III with a cotunnite-related structure appears that is recoverable to ambient conditions. We examine the similarity between the zirconolite behavior and the structural evolution of analogous pyrochlore systems under pressure.<br/

A +1 ribosomal frameshifting motif prevalent among plant amalgaviruses.

Sequence accessions attributable to novel plant amalgaviruses have been found in the Transcriptome Shotgun Assembly database. Sixteen accessions, derived from 12 different plant species, appear to encompass the complete protein-coding regions of the proposed amalgaviruses, which would substantially expand the size of genus Amalgavirus from 4 current species. Other findings include evidence for UUU_CGN as a +1 ribosomal frameshifting motif prevalent among plant amalgaviruses; for a variant version of this motif found thus far in only two amalgaviruses from solanaceous plants; for a region of α-helical coiled coil propensity conserved in a central region of the ORF1 translation product of plant amalgaviruses; and for conserved sequences in a C-terminal region of the ORF2 translation product (RNA-dependent RNA polymerase) of plant amalgaviruses, seemingly beyond the region of conserved polymerase motifs. These results additionally illustrate the value of mining the TSA database and others for novel viral sequences for comparative analyses.M.L.N. was supported in part by a subcontract from NIH grant 5R01GM033050-33. J.D.P. completed his work on this project during a lab rotation for the Ph.D. Training Program in Virology at Harvard University, Cambridge, MA, USA and was supported in part by NIH grant 2T32AI007245-31. A.E.F. was supported in part by the Wellcome Trust (grant 106207).This is the final version of the article. It first appeared from Elsevier via https://doi.org/10.1016/j.virol.2016.07.00

Optical pattern formation with a 2-level nonlinearity

We present an experimental and theoretical investigation of spontaneous pattern formation in the transverse section of a single retro-reflected laser beam passing through a cloud of cold Rubidium atoms. In contrast to previously investigated systems, the nonlinearity at work here is that of a 2-level atom, which realizes the paradigmatic situation considered in many theoretical studies of optical pattern formation. In particular, we are able to observe the disappearance of the patterns at high intensity due to the intrinsic saturable character of 2-level atomic transitions.Comment: 5 pages, 4 figure

Frequency selection by soliton excitation in nondegenerate intracavity downconversion

We show that soliton excitation in intracavity downconversion naturally selects a strictly defined frequency difference between the signal and idler fields. In particular, this phenomenon implies that if the signal has smaller losses than the idler then its frequency is pulled away from the cavity resonance and the idler frequency is pulled towards the resonance and {\em vice versa}. The frequency selection is shown to be closely linked with the relative energy balance between the idler and signal fields.Comment: 5 pages, 3 figures. To appear in Phys Rev Let

Imaginary companions in childhood: Relations to imagination skills and autobiographical memory in adults

The presence of a childhood imaginary companion (IC) has been proposed to reflect heightened imaginative abilities. This study hypothesized that adults who reported having a childhood IC would score higher on a task requiring the imaginative construction of visual scenes. Additionally, it was proposed that individuals who produced more vivid and detailed scenes would also report richer autobiographical memories, due to a shared reliance on imaginative abilities in construction and recollection. Sixty participants (20 with an IC), completed an adapted scene construction procedure and an autobiographical memory questionnaire. Participants reporting a childhood IC scored significantly higher on scene construction and rated themselves as more imaginative. Scene construction scores were also moderately related to the richness of autobiographical memories, although this was almost entirely due to scores on the thought/emotion/action component of scene construction. Autobiographical memory was unrelated to the presence of an IC. Implications for overlapping and dissociable aspects of imagination and memory are discussed