Practical implementation of a dependently typed functional programming language

Types express a program's meaning, and checking types ensures that a program has the intended meaning. In a dependently typed programming language types are predicated on values, leading to the possibility of expressing invariants of a program's behaviour in its type. Dependent types allow us to give more detailed meanings to programs, and hence be more confident of their correctness. This thesis considers the practical implementation of a dependently typed programming language, using the Epigram notation defined by McBride and McKinna. Epigram is a high level notation for dependently typed functional programming elaborating to a core type theory based on Lu๙s UTT, using Dybjer's inductive families and elimination rules to implement pattern matching. This gives us a rich framework for reasoning about programs. However, a naive implementation introduces several run-time overheads since the type system blurs the distinction between types and values; these overheads include the duplication of values, and the storage of redundant information and explicit proofs. A practical implementation of any programming language should be as efficient as possible; in this thesis we see how the apparent efficiency problems of dependently typed programming can be overcome and that in many cases the richer type information allows us to apply optimisations which are not directly available in traditional languages. I introduce three storage optimisations on inductive families; forcing, detagging and collapsing. I further introduce a compilation scheme from the core type theory to G-machine code, including a pattern matching compiler for elimination rules and a compilation scheme for efficient run-time implementation of Peano's natural numbers. We also see some low level optimisations for removal of identity functions, unused arguments and impossible case branches. As a result, we see that a dependent type theory is an effective base on which to build a feasible programming language

Fast magnetoacoustic waves in curved coronal loops: II. Tunneling modes

Copyright © 2006 ESO / EDP SciencesAims. Fast magnetoacoustic waves in curved coronal loops are investigated and the role of lateral leakage in wave damping, which includes the mechanism of wave tunneling, is explored. Methods. A coronal loop is modeled as a curved, magnetic slab in the zero plasma- β limit. In this model and for an arbitrary piece-wise continuous power law equilibrium density profile, the wave equation governing linear vertically polarised fast magnetoacoustic waves is solved analytically. An associated dispersion relation is derived and the frequencies and eigenfunctions of the wave modes are characterised. Results. For some equilibria, the waves are shown to be all damped due to lateral leakage. It is demonstrated that waves either leak straight out into the external medium or have to overcome an evanescent barrier, which is linked to wave tunneling. The wave solutions consist of alternating vertically polarised kink and sausage branches. Fast kink oscillations may have a non-zero density perturbation when averaged across the loop. The calculated damping rate of fast magnetoacoustic kink oscillations is shown to be consistent with related numerical simulations and show that lateral leakage may explain the observed damping of (vertically polarised) fast magnetoacoustic kink oscillations

Elaborator reflection : extending Idris in Idris

Many programming languages and proof assistants are defined by elaboration from a high-level language with a great deal of implicit information to a highly explicit core language. In many advanced languages, these elaboration facilities contain powerful tools for program construction, but these tools are rarely designed to be repurposed by users. We describe elaborator reflection, a paradigm for metaprogramming in which the elaboration machinery is made directly available to metaprograms, as well as a concrete realization of elaborator reflection in Idris, a functional language with full dependent types. We demonstrate the applicability of Idris’s reflected elaboration framework to a number of realistic problems, we discuss the motivation for the specific features of its design, and we explore the broader meaning of elaborator reflection as it can relate to other languages.Postprin

Seismology of curved coronal loops with vertically polarised transverse oscillations

Aims. Using a model of vertically polarised fast magnetoacoustic waves in curved coronal loops, the method of coronal seismology is applied to observations of transverse loop oscillations. Methods. A coronal loop is modeled as a curved magnetic slab in the zero plasma-β limit. For an arbitrary piece-wise continuous power law equilibrium density profile, the dispersion relation governing linear vertically polarised fast magnetoacoustic kink waves is derived. The ways in which this model can be used for coronal seismology are explored and applied to two observational examples. Results. The Alfvén speed and equilibrium density profile are determined from observations. It is shown that the mechanism of lateral leakage of fast magnetoacoustic kink oscillations described in this model is efficient. In fact, the damping is so efficient that in order to match predicted values with observational ones, either the loop needs to be highly contrasted or the transverse Alfvén speed profile needs to be close to linear. Possible improvements to make the modeling of lateral wave leakage in loops more realistic, allowing a lower damping efficiency, are discussed

Fast magnetoacoustic waves in curved coronal loops. I, Trapped and leaky modes

A study of vertically polarised fast magnetoacoustic waves in a curved coronal loop is presented. The loop is modeled as a semi-circular magnetic slab in the zero plasma-β limit. The governing equations for linear waves are derived. We show that the wave mode behaviour depends on the slope of the equilibrium density profile, which is modeled as a piece-wise continuous power law curve of index α. For all profiles, except for α = −4, wave modes are not trapped in the loop and leak out into the external medium through wave tunneling. The particular case of α = −4, which corresponds to a linearly increasing Alfvén speed profile, is examined in more detail as this is the only model that can support trapped wave modes. We compare the results with a straight slab model and find similar behaviour. Coupling between sausage and kink wave modes has not been found in the model

The Moving Group Targets of the Seeds High-Contrast Imaging Survey of Exoplanets and Disks: Results and Observations from the First Three Years

We present results from the first three years of observations of moving group (MG) targets in the Strategic Exploration of Exoplanets and Disks with Subaru (SEEDS) high-contrast imaging survey of exoplanets and disks using the Subaru telescope. We achieve typical contrasts of (is) approximately10(exp 5) at 1" and (is) approximately 10(exp 6) beyond 2" around 63 proposed members of nearby kinematic MGs. We review each of the kinematic associations to which our targets belong, concluding that five, beta Pictoris ((is) approximately 20 Myr), AB Doradus ((is) approximately 100 Myr), Columba ((is) approximately 30 Myr), Tucana-Horogium ((is) approximately 30 Myr), and TW Hydrae ((is) approximately 10 Myr), are sufficiently well-defined to constrain the ages of individual targets. Somewhat less than half of our targets are high-probability members of one of these MGs. For all of our targets, we combine proposed MG membership with other age indicators where available, including Ca ii HK emission, X-ray activity, and rotation period, to produce a posterior probability distribution of age. SEEDS observations discovered a substellar companion to one of our targets, kappa And, a late B star. We do not detect any other substellar companions, but do find seven new close binary systems, of which one still needs to be confirmed. A detailed analysis of the statistics of this sample, and of the companion mass constraints given our age probability distributions and exoplanet cooling models, will be presented in a forthcoming paper

A New Anti-Depressive Strategy for the Elderly: Ablation of FKBP5/FKBP51

The gene FKBP5 codes for FKBP51, a co-chaperone protein of the Hsp90 complex that increases with age. Through its association with Hsp90, FKBP51 regulates the glucocorticoid receptor (GR). Single nucleotide polymorphisms (SNPs) in the FKBP5 gene associate with increased recurrence of depressive episodes, increased susceptibility to post-traumatic stress disorder, bipolar disorder, attempt of suicide, and major depressive disorder in HIV patients. Variation in one of these SNPs correlates with increased levels of FKBP51. FKBP51 is also increased in HIV patients. Moreover, increases in FKBP51 in the amygdala produce an anxiety phenotype in mice. Therefore, we tested the behavioral consequences of FKBP5 deletion in aged mice. Similar to that of naïve animals treated with classical antidepressants FKBP5−/− mice showed antidepressant behavior without affecting cognition and other basic motor functions. Reduced corticosterone levels following stress accompanied these observed effects on depression. Age-dependent anxiety was also modulated by FKBP5 deletion. Therefore, drug discovery efforts focused on depleting FKBP51 levels may yield novel antidepressant therapies

The James Webb Space Telescope Mission

Twenty-six years ago a small committee report, building on earlier studies, expounded a compelling and poetic vision for the future of astronomy, calling for an infrared-optimized space telescope with an aperture of at least $4m$. With the support of their governments in the US, Europe, and Canada, 20,000 people realized that vision as the $6.5m$ James Webb Space Telescope. A generation of astronomers will celebrate their accomplishments for the life of the mission, potentially as long as 20 years, and beyond. This report and the scientific discoveries that follow are extended thank-you notes to the 20,000 team members. The telescope is working perfectly, with much better image quality than expected. In this and accompanying papers, we give a brief history, describe the observatory, outline its objectives and current observing program, and discuss the inventions and people who made it possible. We cite detailed reports on the design and the measured performance on orbit.Comment: Accepted by PASP for the special issue on The James Webb Space Telescope Overview, 29 pages, 4 figure

Telomerecat: A ploidy-agnostic method for estimating telomere length from whole genome sequencing data.

Telomere length is a risk factor in disease and the dynamics of telomere length are crucial to our understanding of cell replication and vitality. The proliferation of whole genome sequencing represents an unprecedented opportunity to glean new insights into telomere biology on a previously unimaginable scale. To this end, a number of approaches for estimating telomere length from whole-genome sequencing data have been proposed. Here we present Telomerecat, a novel approach to the estimation of telomere length. Previous methods have been dependent on the number of telomeres present in a cell being known, which may be problematic when analysing aneuploid cancer data and non-human samples. Telomerecat is designed to be agnostic to the number of telomeres present, making it suited for the purpose of estimating telomere length in cancer studies. Telomerecat also accounts for interstitial telomeric reads and presents a novel approach to dealing with sequencing errors. We show that Telomerecat performs well at telomere length estimation when compared to leading experimental and computational methods. Furthermore, we show that it detects expected patterns in longitudinal data, repeated measurements, and cross-species comparisons. We also apply the method to a cancer cell data, uncovering an interesting relationship with the underlying telomerase genotype

The impact of COVID-19 vaccination in prisons in England and Wales : a metapopulation model

Background: High incidence of cases and deaths due to coronavirus disease 2019 (COVID-19) have been reported in prisons worldwide. This study aimed to evaluate the impact of different COVID-19 vaccination strategies in epidemiologically semi-enclosed settings such as prisons, where staff interact regularly with those incarcerated and the wider community. Methods: We used a metapopulation transmission-dynamic model of a local prison in England and Wales. Two-dose vaccination strategies included no vaccination, vaccination of all individuals who are incarcerated and/or staff, and an age-based approach. Outcomes were quantified in terms of COVID-19-related symptomatic cases, losses in quality-adjusted life-years (QALYs), and deaths. Results: Compared to no vaccination, vaccinating all people living and working in prison reduced cases, QALY loss and deaths over a one-year period by 41%, 32% and 36% respectively. However, if vaccine introduction was delayed until the start of an outbreak, the impact was negligible. Vaccinating individuals who are incarcerated and staff over 50 years old averted one death for every 104 vaccination courses administered. All-staff-only strategies reduced cases by up to 5%. Increasing coverage from 30 to 90% among those who are incarcerated reduced cases by around 30 percentage points. Conclusions: The impact of vaccination in prison settings was highly dependent on early and rapid vaccine delivery. If administered to both those living and working in prison prior to an outbreak occurring, vaccines could substantially reduce COVID-19-related morbidity and mortality in prison settings