Showing papers by "University of St Andrews published in 2007"
TL;DR: These genome sequences augment the formidable genetic tools that have made Drosophila melanogaster a pre-eminent model for animal genetics, and will further catalyse fundamental research on mechanisms of development, cell biology, genetics, disease, neurobiology, behaviour, physiology and evolution.
Abstract: Comparative analysis of multiple genomes in a phylogenetic framework dramatically improves the precision and sensitivity of evolutionary inference, producing more robust results than single-genome analyses can provide. The genomes of 12 Drosophila species, ten of which are presented here for the first time (sechellia, simulans, yakuba, erecta, ananassae, persimilis, willistoni, mojavensis, virilis and grimshawi), illustrate how rates and patterns of sequence divergence across taxa can illuminate evolutionary processes on a genomic scale. These genome sequences augment the formidable genetic tools that have made Drosophila melanogaster a pre-eminent model for animal genetics, and will further catalyse fundamental research on mechanisms of development, cell biology, genetics, disease, neurobiology, behaviour, physiology and evolution. Despite remarkable similarities among these Drosophila species, we identified many putatively non-neutral changes in protein-coding genes, non-coding RNA genes, and cis-regulatory regions. These may prove to underlie differences in the ecology and behaviour of these diverse species.
2,057 citations
1,239 citations
McGill University1, University of Groningen2, University of Oslo3, University of Michigan4, University of Auckland5, University of St Andrews6, University of Arizona7, University of California, Merced8, University of Alberta9, University of California, Santa Barbara10, University of Chile11, Pontifical Catholic University of Chile12, Michigan State University13, Arizona State University14
TL;DR: Theoretical, empirical and statistical developments in the study of Species abundance distributions are reviewed and it is optimistic that SADs can provide significant insights into basic and applied ecological science.
Abstract: Species abundance distributions (SADs) follow one of ecologys oldest and most universal laws – every community shows a hollow curve or hyperbolic shape on a histogram with many rare species and just a few common species. Here, we review theoretical, empirical and statistical developments in the study of SADs. Several key points emerge. (i) Literally dozens of models have been proposed to explain the hollow curve. Unfortunately, very few models are ever rejected, primarily because few theories make any predictions beyond the hollow-curve SAD itself. (ii) Interesting work has been performed both empirically and theoretically, which goes beyond the hollow-curve prediction to provide a rich variety of information about how SADs behave. These include the study of SADs along environmental gradients and theories that integrate SADs with other biodiversity patterns. Central to this body of work is an effort to move beyond treating the SAD in isolation and to integrate the SAD into its ecological context to enable making many predictions. (iii) Moving forward will entail understanding how sampling and scale affect SADs and developing statistical tools for describing and comparing SADs. We are optimistic that SADs can provide significant insights into basic and applied ecological science.
1,237 citations
TL;DR: In this article, the spectral energy distributions (SEDs) of young stellar objects (YSOs) were analyzed using precomputed two-dimensional (2D) radiation transfer models spanning a large region of parameter space.
Abstract: We present a method to analyze the spectral energy distributions (SEDs) of young stellar objects (YSOs). Our approach is to fit data with precomputed two-dimensional (2D) radiation transfer models spanning a large region of parameter space. This allows us to determine not only a single set of physical parameter values but the entire range of values consistent with the multiwavelength observations of a given source. In this way we hope to avoid any overinterpretation when modeling a set of data. We have constructed spectral energy distributions from optical to submillimeter wavelengths, including new Spitzer IRAC and MIPS photometry, for 30 young and spatially resolved sources in the Taurus-Auriga star-forming region. We demonstrate fitting model SEDs to these sources and find that we correctly identify the evolutionary stage and physical parameters found from previous independent studies, such as disk mass, disk accretion rate, and stellar temperature. We also explore how fluxes at various wavelengths help to constrain physical parameters and show examples of degeneracies that can occur when fitting SEDs. A Web-based version of this tool is available to the community.
952 citations
TL;DR: In this article, the authors present a scheme for the calculation of magnetic response parameters in insulators using ultrasoft pseudopotentials, which uses the gauge-including projector augmented wave method to obtain allelectron accuracy for both finite and infinitely periodic systems.
Abstract: We present a scheme for the calculation of magnetic response parameters in insulators using ultrasoft pseudopotentials. It uses the gauge-including projector augmented wave method [C. J. Pickard and F. Mauri, Phys. Rev. B 63, 245101 (2001)] to obtain all-electron accuracy for both finite and infinitely periodic systems. We consider in detail the calculation of NMR chemical shieldings. The approach is successfully validated first for molecular systems by comparing calculated chemical shieldings for a range of molecules with quantum chemistry results and then in the solid state by comparing $^{17}\mathrm{O}$ NMR parameters calculated for silicates with experiment.
804 citations
TL;DR: Ionothermal synthesis, the use of ionic liquids as both solvent and template (structure-directing agent), has been used to prepare zeolites and inorganic-organic hybrids such as metal-organic frameworks.
Abstract: Ionothermal synthesis, the use of ionic liquids as both solvent and template (structure-directing agent), has been used to prepare zeolites and inorganic-organic hybrids such as metal-organic frameworks. The underlying properties of the ionothermal method are discussed, and it is compared with traditional hydrothermal preparative methods. The materials resulting from ionothermal synthesis are described, and any structural features that can be related to the ionic liquid used as the solvent are discussed. Future areas of potential interest are also considered.
761 citations
TL;DR: The physical principles behind the phenomenon of slow light in photonic crystal waveguides, as well as their practical limitations, are discussed and put into context in this paper, including the nature of slow-light propagation, its bandwidth limitation, the scaling of linear and nonlinear interactions with the slowdown factor, issues such as losses, coupling into and the tuning of slow modes.
Abstract: The physical principles behind the phenomenon of slow light in photonic crystal waveguides, as well as their practical limitations, are discussed and put into context This includes the nature of slow light propagation, its bandwidth limitation, the scaling of linear and nonlinear interactions with the slowdown factor as well as issues such as losses, coupling into and the tuning of slow modes Applications in all-optical signal processing appear to be the most promising outcome of the phenomena discussed
627 citations
TL;DR: The case for sexual selection is not as strongly supported as, for example, allopatric speciation, but probably contributes most effectively alongside ecological selection or selection...
Abstract: Sexual selection has a reputation as a major cause of speciation, one of the most potent forces driving reproductive isolation. This reputation arises from observations that species differ most in traits involved with mating success and from successful models of sexual selection–driven speciation. But how well proven is the case? Models confirm that the process can occur, but is strongest in conjunction with ecological or niche specialization. Some models also show that strong sexual selection can act against speciation. Studies using the comparative method are equivocal and often inconclusive, but some phylogeographic studies are more convincing. Experimental evolution and genetic or genomic analyses are in their infancy, but look particularly promising for resolving the importance of sexual selection. The case for sexual selection is not as strongly supported as, for example, allopatric speciation. Sexual selection probably contributes most effectively alongside ecological selection or selection...
609 citations
TL;DR: In this article, a hierarchy of calving processes is defined to distinguish those that exert a fundamental control on the position of the ice margin from more localised processes responsible for individual calving events.
582 citations
TL;DR: The age relations for assembly of Gondwana and Pangea indicate that the timing of collisional orogenesis between amalgamating continental bodies was synchronous with subduction initiation and contractional orogens within accretionary orogens located along the margins of these supercontinents as mentioned in this paper.
567 citations
TL;DR: In this article, the authors explore the influence of the catalysts on the performance of a nonaqueous O 2 electrode on a Li/O 2 cell and find that Co 3 O 4 gives the best compromise between initial capacity (2000 mAhg −1 ) and capacity retention (6.5% per cycle), as well as the lowest charging voltage 4 V.
TL;DR: In this paper, the authors systematically investigated the zero-temperature phase diagram of solid hydrogen using first-principles density functional theory (DFT) electronic-structure methods, including the proton zero-point motion at the harmonic level.
Abstract: Hydrogen, being the first element in the periodic table, has the simplest electronic structure of any atom, and the hydrogen molecule contains the simplest covalent chemical bond. Nevertheless, the phase diagram of hydrogen is poorly understood. Determining the stable structures of solid hydrogen is a tremendous experimental challenge1,2,3, because hydrogen atoms scatter X-rays only weakly, leading to low-resolution diffraction patterns. Theoretical studies encounter major difficulties owing to the small energy differences between structures and the importance of the zero-point motion of the protons. We have systematically investigated the zero-temperature phase diagram of solid hydrogen using first-principles density functional theory (DFT) electronic-structure methods4, including the proton zero-point motion at the harmonic level. Our study leads to a radical revision of the DFT phase diagram of hydrogen up to nearly 400 GPa. That the most stable phases remain insulating to very high pressures eliminates a major discrepancy between theory5 and experiment6. One of our new phases is calculated to be stable over a wide range of pressures, and its vibrational properties agree with the available experimental data for phase III.
TL;DR: Gas adsorption experiments have been carried out on a copper benzene tricarboxylate metal-organic framework material and Chemiluminescence and platelet aggregometry experiments indicate that the amount of NO recovered on exposure of the resulting complex to water is enough to be biologically active, completely inhibiting platelet aggregation in platelet rich plasma.
Abstract: Gas adsorption experiments have been carried out on a copper benzene tricarboxylate metal-organic framework material, HKUST-1. Hydrogen adsorption at 1 and 10 bar (both 77 K) gives an adsorption capacity of 11.16 mmol H2 per g of HKUST-1 (22.7 mg g(-)1, 2.27 wt %) at 1 bar and 18 mmol per g (36.28 mg g(-)1, 3.6 wt %) at 10 bar. Adsorption of D2 at 1 bar (77 K) is between 1.09 (at 1 bar) and 1.20(at <100 mbar) times the H2 values depending on the pressure, agreeing with the theoretical expectations. Gravimetric adsorption measurements of NO on HKUST-1 at 196 K (1 bar) gives a large adsorption capacity of approximately 9 mmol g(-1), which is significantly greater than any other adsorption capacity reported on a porous solid. At 298 K the adsorption capacity at 1 bar is just over 3 mmol g(-1). Infra red experiments show that the NO binds to the empty copper metal sites in HKUST-1. Chemiluminescence and platelet aggregometry experiments indicate that the amount of NO recovered on exposure of the resulting complex to water is enough to be biologically active, completely inhibiting platelet aggregation in platelet rich plasma.
TL;DR: In this article, the authors describe how semiconductor quantum-dot structures can provide an efficient means of amplifying and generating ultrafast (of the order of 100 fs), high-power and low-noise optical pulses, with the potential to boost the repetition rate of the pulses to beyond 1 THz.
Abstract: Semiconductor lasers are convenient and compact sources of light, offering highly efficient operation, direct electrical control and integration opportunities. In this review we describe how semiconductor quantum-dot structures can provide an efficient means of amplifying and generating ultrafast (of the order of 100 fs), high-power and low-noise optical pulses, with the potential to boost the repetition rate of the pulses to beyond 1 THz. Such device designs are opening up new possibilities in ultrafast science and technology.
TL;DR: The recent turn to "strategy practice" offers a genuine opportunity for establishing an alternative perspective that is clearly distinct from the traditional strategy process view as discussed by the authors, and the challenge is to clarify and articulate an alternative set of ontological and epistemological premises for founding this new approach to theorizing strategy.
Abstract: The recent turn to ‘strategy practice’ offers a genuine opportunity for establishing an alternative perspective that is clearly distinct from the traditional strategy process view. The challenge is to clarify and articulate an alternative set of ontological and epistemological premises for founding this new approach to theorizing strategy.What has been called the ‘practice turn’ in social theory provides this alternative basis for a ‘post-processual’ approach to theorizing strategy-as-practice. This ‘practice turn’ involves a radical reformulation of the intractable problem of agency and structure that enables us to bypass the ‘micro/macro’ distinction so intimately tied to the social sciences in general and to strategy research in particular. Already, there are signs that the discourse of the strategy-as-practice research community reflects this awareness and are thus straining towards some form of ‘trans-individual’ explanation that is not restricted to the mere ‘activities’ of strategy actors nor to th...
TL;DR: A data set of 19 second-row transition-metal complexes has been collated from sufficiently precise gas-phase electron-diffraction experiments and used for evaluating errors in DFT optimized geometries and the TPSSh hybrid meta-GGA is slightly inferior to the best hybrid GGAs.
Abstract: A set of 41 metal-ligand bond distances in 25 third-row transition-metal complexes, for which precise structural data are known in the gas phase, is used to assess optimized and zero-point averaged geometries obtained from DFT computations with various exchange-correlation functionals and basis sets. For a given functional (except LSDA) Stuttgart-type quasi-relativistic effective core potentials and an all-electron scalar relativistic approach (ZORA) tend to produce very similar geometries. In contrast to the lighter congeners, LSDA affords reasonably accurate geometries of 5d-metal complexes, as it is among the functionals with the lowest mean and standard deviations from experiment. For this set the ranking of some other popular density functionals, ordered according to decreasing standard deviation, is BLYP > VSXC > BP86 ≈ BPW91 ≈ TPSS ≈ B3LYP ≈ PBE > TPSSh > B3PW91 ≈ B3P86 ≈ PBE hybrid. In this case hybrid functionals are superior to their nonhybrid variants. In addition, we have reinvestigated the previous test sets for 3d- (Buhl M.; Kabrede, H. J. Chem. Theory Comput. 2006, 2, 1282-1290) and 4d- (Waller, M. P.; Buhl, M. J. Comput. Chem. 2007, 28, 1531-1537) transition-metal complexes using all-electron scalar relativistic DFT calculations in addition to the published nonrelativistic and ECP results. For this combined test set comprising first-, second-, and third-row metal complexes, B3P86 and PBE hybrid are indicated to perform best. A remarkably consistent standard deviation of around 2 pm in metal-ligand bond distances is achieved over the entire set of d-block elements.
TL;DR: In this article, the authors show how the structure of the light-emitting dendrimers controls key features such as intermolecular interactions and charge transport, which are important for all OLED materials.
Abstract: Dendrimers are now an important class of light-emitting material for use in organic light-emitting diodes (OLEDs). Dendrimers are branched macromolecules that consist of a core, one or more dendrons, and surface groups. The different parts of the macromolecule can be selected to give the desired optoelectronic and processing properties. The first light-emitting dendrimers were fluorescent but more recently highly efficient phosphorescent dendrimers have been developed. OLEDs containing light-emitting dendrimers have been reported to have external quantum efficiencies of up to 16 %. The solubility of the dendrimers opens the way for simple processing and a new class of flat-panel displays. In this Review we show how the structure of the light-emitting dendrimers controls key features such as intermolecular interactions and charge transport, which are important for all OLED materials. The advantages of the dendrimer architecture for phosphorescent emitters and the way the structure can be varied to enhance materials performance and device design are illustrated.
01 Jan 2007
TL;DR: In this paper, high efficiency grating couplers for coupling between a singlemode fiber and nanophotonic waveguides, fabricated both in silicon-on-insulator (SOI) and InP membranes using BenzoCycloButene wafer bonding, were presented.
Abstract: We present high-efficiency grating couplers for coupling between a single-mode fiber and nanophotonic waveguides, fabricated both in silicon-on-insulator (SOI) and InP membranes using BenzoCycloButene wafer bonding. The coupling efficiency is substantially increased by adding a gold bottom mirror to the structures. The measured coupling efficiency to fiber is 69% for SOI grating couplers and 56% for bonded InP membrane grating couplers
TL;DR: This article examined the relationship between cultural variation and encephalization in a range of vertebrate and invertebrate species, concluding that culture offers a particular confirmation of the Machiavellian intelligence hypothesis that certain kinds of social life (here, culture) select for intelligence: "you need to be smart to sustain culture".
Abstract: Decades-long field research has flowered into integrative studies that, together with experimental evidence for the requisite social learning capacities, have indicated a reliance on multiple traditions (‘cultures’) in a small number of species. It is increasingly evident that there is great variation in manifestations of social learning, tradition and culture among species, offering much scope for evolutionary analysis. Social learning has been identified in a range of vertebrate and invertebrate species, yet sustained traditions appear rarer, and the multiple traditions we call cultures are rarer still. Here, we examine relationships between this variation and both social intelligence—sophisticated information processing adapted to the social domain—and encephalization. First, we consider whether culture offers one particular confirmation of the social (‘Machiavellian’) intelligence hypothesis that certain kinds of social life (here, culture) select for intelligence: ‘you need to be smart to sustain culture’. Phylogenetic comparisons, particularly focusing on our own study animals, the great apes, support this, but we also highlight some paradoxes in a broader taxonomic survey. Second, we use intraspecific variation to address the converse hypothesis that ‘culture makes you smart’, concluding that recent evidence for both chimpanzees and orang-utans support this proposition.
TL;DR: A new chiral coordination polymer, (BMIm)2[Ni(TMA-H)2(H2O)2, was prepared ionothermally from chiral ionic liquid and induces chirality in the resulting solid, despite the fact that the anion is not occluded by the material and that the solid itself is built from only nonchiral building blocks.
Abstract: A new chiral coordination polymer, (BMIm)2[Ni(TMA-H)2(H2O)2], was prepared ionothermally from chiral ionic liquid. The use of l-aspartate as one component of the ionic liquid induces chirality in the resulting solid, despite the fact that the anion is not occluded by the material and that the solid itself is built from only nonchiral building blocks. Without the chiral component, an achiral compound is formed under the same synthesis conditions.
TL;DR: In contrast to mesoporous lithium intercalation compounds, which show superior capacity at high rates compared to bulk materials, mesoporosity does not seem to improve the capacity of conversion reactions on extended cycling.
Abstract: The conversion reactions associated with mesoporous and nanowire Co3O4 when used as negative electrodes in rechargeable lithium batteries have been investigated. Initially, Li is intercalated into Co3O4 up to x
∼ 1.5 Li in LixCo3O4. Thereafter, both materials form a nanocomposite of Co particles imbedded in Li2O, which on subsequent charge forms CoO. The capacities on cycling increase on initial cycles to values exceeding the theoretical value for Co3O4 + 8 Li+ + 8e−
→ 4 Li2O + 3 Co, 890 mAhg−1, and this is interpreted as due to charge storage in a polymer layer that forms on the high surface area of nanowire and mesoporous Co3O4. After 15 cycles, the capacity decreases drastically for the nanowires due to formation of grains that are separated one from another by a thick polymer layer, leading to electrical isolation. In contrast, the mesoporous Co3O4 losses its mesoporosity and forms a morphology similar to bulk Co3O4 (Co particles imbedded in Li2O matrix) with which it exhibits a similar capacity on cycling. In contrast to mesoporous lithium intercalation compounds, which show superior capacity at high rates compared to bulk materials, mesoporosity does not seem to improve the capacity of conversion reactions on extended cycling. If, however, mesoporosity could be retained during the conversion reaction, then higher capacities could be obtained in such systems.
McDonald Institute for Archaeological Research1, University of Leicester2, University of St Andrews3, National University of Singapore4, University of Huddersfield5, Royal Holloway, University of London6, University of Plymouth7, Queen's University Belfast8, University of Oxford9, University of Florida10, Santa Clara University11, University College Dublin12, University of the Philippines Diliman13, University of Bristol14, University of York15, Nottingham Trent University16, University of London17, University of Bradford18, Natural History Museum19, University of Wollongong20
TL;DR: The Niah evidence demonstrates the sophisticated nature of the subsistence behavior developed by modern humans to exploit the tropical environments that they encountered in Southeast Asia, including rainforest.
TL;DR: Using optical long-baseline interferometry, a near-infrared image of the rapidly rotating hot star Altair is constructed with a resolution of <1 milliarcsecond that clearly reveals the strong effect of gravity darkening on the highly distorted stellar photosphere.
Abstract: Spatially resolving the surfaces of nearby stars promises to advance our knowledge of stellar physics. Using optical long-baseline interferometry, we constructed a near-infrared image of the rapidly rotating hot star Altair with a resolution of <1 milliarcsecond. The image clearly reveals the strong effect of gravity darkening on the highly distorted stellar photosphere. Standard models for a uniformly rotating star cannot explain our findings, which appear to result from differential rotation, alternative gravity-darkening laws, or both.
TL;DR: In this article, a simple model for the steady state evolution of debris disks due to collisions is developed and confronted with the properties of the emerging population of seven Sun-like stars that have hot dust at 10 AU (η Corvi and HD 72905); one has three Neptune mass planets at < 1 AU (HD 69830); all exhibit strong mid-IR silicate features.
Abstract: In this paper a simple model for the steady state evolution of debris disks due to collisions is developed and confronted with the properties of the emerging population of seven Sun-like stars that have hot dust at 10 AU (η Corvi and HD 72905); one has three Neptune mass planets at <1 AU (HD 69830); all exhibit strong mid-IR silicate features. We consider the most likely origin for this transient dust to be a dynamical instability that scattered planetesimals inward from a more distant planetesimal belt in an event akin to the late heavy bombardment in our own system, the dust being released from such planetesimals in collisions and sublimation.
TL;DR: In this contribution infrared spectroscopy is successfully applied to highlight the positive role played by coordinatively unsaturated Cu2+ ions in HKUST-1, acting as specific interaction sites for molecular adsorption.
Abstract: Among microporous systems metal organic frameworks are considered promising materials for molecular adsorption. In this contribution infrared spectroscopy is successfully applied to highlight the positive role played by coordinatively unsaturated Cu2+ ions in HKUST-1, acting as specific interaction sites. A properly activated material, obtained after solvent removal, is characterized by a high fraction of coordinatively unsaturated Cu2+ ions acting as preferential adsorption sites that show specific activities towards some of the most common gaseous species (NO, CO2, CO, N2 and H2). From a temperature dependent IR study, it has been estimated that the H2 adsorption energy is as high as 10 kJ mol−1. A very complex spectral evolution has been observed upon lowering the temperature. A further peculiarity of this material is the fact that it promotes ortho–para conversion of the adsorbed H2 species.
TL;DR: It is reported that, in the close vicinity of a metamagnetic quantum critical point, high-purity strontium ruthenate Sr3Ru2O7 possesses a large magnetoresistive anisotropy, consistent with the existence of an electronic nematic fluid.
Abstract: In principle, a complex assembly of strongly interacting electrons can self-organize into a wide variety of collective states, but relatively few such states have been identified in practice. We report that, in the close vicinity of a metamagnetic quantum critical point, high-purity strontium ruthenate Sr3Ru2O7 possesses a large magnetoresistive anisotropy, consistent with the existence of an electronic nematic fluid. We discuss a striking phenomenological similarity between our observations and those made in high-purity two-dimensional electron fluids in gallium arsenide devices.
TL;DR: The discovery of a new dwarf galaxy, Leo T, in the Local Group was reported in this paper, which is the smallest, lowest luminosity galaxy found to date with recent star formation.
Abstract: We announce the discovery of a new dwarf galaxy, Leo T, in the Local Group. It was found as a stellar overdensity in the Sloan Digital Sky Survey Data Release 5 (SDSS DR5). The color-magnitude diagram of Leo T shows two well-defined features, which we interpret as a red giant branch and a sequence of young, massive stars. As judged from fits to the color-magnitude diagram, it lies at a distance of ~420 kpc and has an intermediate-age stellar population with a metallicity of [Fe/H] = -1.6, together with a young population of blue stars of age ~200 Myr. There is a compact cloud of neutral hydrogen with mass ~105 M☉ and radial velocity +35 km s-1 coincident with the object visible in the HIPASS channel maps. Leo T is the smallest, lowest luminosity galaxy found to date with recent star formation. It appears to be a transition object similar to, but much lower luminosity than, the Phoenix dwarf.
TL;DR: Right amygdala showed a predicted non-linear response profile with greater responses to highly attractive and unattractive faces compared to middle-ranked faces, independent of task, and was consistent with a role in sensing the value of social stimuli.
TL;DR: In this paper, the authors reviewed the recent academic literature on developments in European banking and concluded that European banking markets have become increasingly integrated in recent years, but barriers to full integration, especially in retail banking, still remain.
Abstract: Against a background of far-reaching structural change in the banking sector, this article reviews the recent academic literature on developments in European banking. European banking markets have become increasingly integrated in recent years, but barriers to full integration, especially in retail banking, still remain. European integration has possible implications for systemic risk, and poses various challenges for the current supervisory framework. The banks’ responses to the changing competitive environment include the pursuit of strategies of diversification, vertical product differentiation and consolidation. European integration has implications for competition in banking markets, for the nature of long-term borrower-lender relationships, and for the relationships between ownership structure, technological change and bank efficiency. The article concludes by reviewing recent literature on the credit channel in the monetary transmission mechanism, and interest rate pass-through.