University of St Andrews

About: University of St Andrews is a education organization based out in St Andrews, Fife, United Kingdom. It is known for research contribution in the topics: Population & Laser. The organization has 16260 authors who have published 43364 publications receiving 1636072 citations. The organization is also known as: St Andrews University & University of St. Andrews.

Pan-cancer analysis of whole genomes

Abstract: Cancer is driven by genetic change, and the advent of massively parallel sequencing has enabled systematic documentation of this variation at the whole-genome scale1,2,3. Here we report the integrative analysis of 2,658 whole-cancer genomes and their matching normal tissues across 38 tumour types from the Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium of the International Cancer Genome Consortium (ICGC) and The Cancer Genome Atlas (TCGA). We describe the generation of the PCAWG resource, facilitated by international data sharing using compute clouds. On average, cancer genomes contained 4–5 driver mutations when combining coding and non-coding genomic elements; however, in around 5% of cases no drivers were identified, suggesting that cancer driver discovery is not yet complete. Chromothripsis, in which many clustered structural variants arise in a single catastrophic event, is frequently an early event in tumour evolution; in acral melanoma, for example, these events precede most somatic point mutations and affect several cancer-associated genes simultaneously. Cancers with abnormal telomere maintenance often originate from tissues with low replicative activity and show several mechanisms of preventing telomere attrition to critical levels. Common and rare germline variants affect patterns of somatic mutation, including point mutations, structural variants and somatic retrotransposition. A collection of papers from the PCAWG Consortium describes non-coding mutations that drive cancer beyond those in the TERT promoter4; identifies new signatures of mutational processes that cause base substitutions, small insertions and deletions and structural variation5,6; analyses timings and patterns of tumour evolution7; describes the diverse transcriptional consequences of somatic mutation on splicing, expression levels, fusion genes and promoter activity8,9; and evaluates a range of more-specialized features of cancer genomes8,10,11,12,13,14,15,16,17,18.

Spectropolarimetric observations of active stars

Abstract: This paper reports the results of five years (five runs, 23 nights) of spectropolarimetric observations of active stars with the UCL Echelle Spectrograph of the Anglo-Australian Telescope. 225 circularly (and four linearly) polarized spectra were recorded on 28 objects (21 active stars and seven calibration standards) using the new technique of Zeeman-Doppler imaging. To extract polarization echelle spectra from raw frames, we developed a new dedicated automatic software package (called ESpRIT, which utilizes optimal extraction techniques) whose detailed description is given in the paper. For each recorded spectrum, we extract 'mean' polarized and unpolarized profiles using 'least-squares deconvolution', a technique similar to cross-correlation, which can enhance enormously the sensitivity of Zeeman-Doppler imaging, by up to 7.5 mag in flux with respect to a single average line analysis or by 4.5 mag compared with the older technique of Donati et al. in the particular case of a K1 star. Magnetic field is detected unambiguously on 14 objects, namely the weak-line T Tauri star V410 Tau, the pre-main-sequence binary HD 155555, the ZAMS stars AB Dor and LQ Hya, the dwarf flare star CC Eri, the RS CVn systems HR 1099, EI Eri, TY Pyx, CF Tue, SZ Psc, II Peg, IM Peg and IL Hya, and the FK Com star YY Men. Marginal field detections are also obtained for the weak-line T Tauri star HD 283572 and the Herbig Ae star HD 104237. Except on HR 1099 and II Peg, our results represent the first direct field detections ever reported on these objects, and in particular the first direct field detection on as young a star as V410 Tau. Most of the magnetic signatures we detect on cool stars show several sign reversals throughout the line profile, indicating that the parent field structure is rather complex and must feature (as expected) many small-scale magnetic regions of different polarities. For all stars on which Zeeman detections are recorded with sufficient accuracy (namely LQ Hya, CC Eri, HR 1099, El Eri, II Peg, IL Hya and YY Men), differential least-squares deconvolution from both the blue and the red parts of the spectral domain indicates that the magnetic regions we detect are mostly 500 to 1000 K cooler than, and sometimes at the same temperature as, but never warmer than the surrounding photosphere. Serendipitous results include the first detection (i) of small-amplitude radial velocity variations (1.3 kms -1 peak to peak) of the Herbig Ae star HD 104237 with small enough a period (37.5 ± 1 min) that they must be due to stellar pulsations and (ii) of the solar-like secondary component of the RS CVn system IL Hya.

Model selection: An integral part of inference

Abstract: We argue that model selection uncertainty should be fully incorporated into statistical inference whenever estimation is sensitive to model choice and that choice is made with reference to the data. We consider different philosophies for achieving this goal and suggest strategies for data analysis. We illustrate our methods through three examples. The first is a Poisson regression of bird counts in which a choice is to be made between inclusion of one or both of two covariates. The second is a line transect data set for which different models yield substantially different estimates of abundance. The third is a simulated example in which truth is known.

The superconductivity of Sr 2 RuO 4 and the physics of spin-triplet pairing

Abstract: This review presents a summary and evaluation of the experimental properties of unconventional superconductivity in ${\mathrm{Sr}}_{2}{\mathrm{RuO}}_{4}$ as they were known in the spring of 2002. At the same time, the paper is intended to be useful as an introduction to the physics of spin-triplet superconductivity. First, the authors show how the normal-state properties of ${\mathrm{Sr}}_{2}{\mathrm{RuO}}_{4}$ are quantitatively described in terms of a quasi-two-dimensional Fermi liquid. Then they summarize its phenomenological superconducting parameters in the framework of the Ginzburg-Landau model, and discuss the existing evidence for spin-triplet pairing. After a brief introduction to the vector order parameter, they examine the most likely symmetry of the triplet state. The structure of the superconducting energy gap is discussed, as is the effect of symmetry-breaking magnetic fields on the phase diagram. The article concludes with a discussion of some outstanding issues and desirable future work. Appendixes on additional details of the normal state, difficulty in observing the bulk Fermi surface by angle-resolved photoemission, and the enhancement of superconducting transition temperature in a two-phase ${\mathrm{Sr}}_{2}{\mathrm{RuO}}_{4}\ensuremath{-}\mathrm{Ru}$ system are included.