Revised 3.99 Report on the Algorithmic Language Scheme

46 pagesThe report gives a defining description of the programming language Scheme. Scheme is a statically scoped and properly tail-recursive dialect of the Lisp programming language invented by Guy Lewis Steele Jr. and Gerald Jay Sussman. It was designed to have an exceptionally clear and simple semantics and few different ways to form · expressions. A wide variety of programming paradigms, including imperative, functional, and message passing styles, find convenient expression in Scheme. The introduction offers a brief history of the language and of the report. The first three chapters present the fundamental ideas of the language and describe the notational conventions used for describing the language· and for writing programs in the language. Chapters 4 and 5 describe the syntax and semantics of expressions, programs, and definitions. Chapter 6 describes Scheme's built-in procedures, which include all of the language's data manipulation and input/ output primitives. Chapter 7 provides a formal syntax for Scheme written in extended BNF, along with a formal denotational semantics. The report concludes with an example of the use of the language and an alphabetic index

Macros That Work

9 pagesThis paper describes a modified form of Kohlbecker's algorithm for reliably hygienic (capture-free) macro expansion in block-structured languages, where macros are source-tos-ource transformations specified using a high-level pattern language. Unlike previous algorithms, the modified algorithm runs in linear instead of quadratic time, copies few constants, does not assume that syntactic keywords ( e.g. if) are reserved words, and allows local (scoped) macros to refer to lexical variables in a referentially transparent manner. Syntactic closures have been advanced as an alternative to hygienic macro expansion. The problem with syntactic closures is that they are inherently low-level and therefore difficult to use correctly, especially when syntactic keywords are not reserved. It is impossible to construct a pattern-based, automatically hygienic macro system on top of syntactic closures because the pattern interpreter must be able to determine the syntactic role of an identifier (in order to close it in the correct syntactic environment) before macro expansion has made that role apparent. may be viewed as a book-keeping technique for deferring such decisions until macro expansion is locally complete. Building on that insight, this paper unifies and extends the competing paradigms of hygienic macro expansion and syntactic closures to obtain an algorithm that combines the benefits of both . Several prototypes of a complete macro system for Scheme have been based on the algorithm presented here

A questionnaire elicitation of surgeons' belief about learning within a surgical trial

PMID: 23145113 [PubMed - indexed for MEDLINE] PMCID: PMC3493499 Free PMC ArticlePeer reviewedPublisher PD

Time-dependence in Relativistic Collisionless Shocks: Theory of the Variable "Wisps" in the Crab Nebula

We describe results from time-dependent numerical modeling of the collisionless reverse shock terminating the pulsar wind in the Crab Nebula. We treat the upstream relativistic wind as composed of ions and electron-positron plasma embedded in a toroidal magnetic field, flowing radially outward from the pulsar in a sector around the rotational equator. The relativistic cyclotron instability of the ion gyrational orbit downstream of the leading shock in the electron-positron pairs launches outward propagating magnetosonic waves. Because of the fresh supply of ions crossing the shock, this time-dependent process achieves a limit-cycle, in which the waves are launched with periodicity on the order of the ion Larmor time. Compressions in the magnetic field and pair density associated with these waves, as well as their propagation speed, semi-quantitatively reproduce the behavior of the wisp and ring features described in recent observations obtained using the Hubble Space Telescope and the Chandra X-Ray Observatory. By selecting the parameters of the ion orbits to fit the spatial separation of the wisps, we predict the period of time variability of the wisps that is consistent with the data. When coupled with a mechanism for non-thermal acceleration of the pairs, the compressions in the magnetic field and plasma density associated with the optical wisp structure naturally account for the location of X-ray features in the Crab. We also discuss the origin of the high energy ions and their acceleration in the equatorial current sheet of the pulsar wind.Comment: 13 pages, 4 figures, accepted to ApJ. High-resolution figures and mpeg movies available at http://astron.berkeley.edu/~anatoly/wisp

"Kludge" gravitational waveforms for a test-body orbiting a Kerr black hole

One of the most exciting potential sources of gravitational waves for low-frequency, space-based gravitational wave (GW) detectors such as the proposed Laser Interferometer Space Antenna (LISA) is the inspiral of compact objects into massive black holes in the centers of galaxies. The detection of waves from such "extreme mass ratio inspiral" systems (EMRIs) and extraction of information from those waves require template waveforms. The systems' extreme mass ratio means that their waveforms can be determined accurately using black hole perturbation theory. Such calculations are computationally very expensive. There is a pressing need for families of approximate waveforms that may be generated cheaply and quickly but which still capture the main features of true waveforms. In this paper, we introduce a family of such "kludge" waveforms and describe ways to generate them. We assess performance of the introduced approximations by comparing "kludge" waveforms to accurate waveforms obtained by solving the Teukolsky equation in the adiabatic limit (neglecting GW backreaction). We find that the kludge waveforms do extremely well at approximating the true gravitational waveform, having overlaps with the Teukolsky waveforms of 95% or higher over most of the parameter space for which comparisons can currently be made. Indeed, we find these kludges to be of such high quality (despite their ease of calculation) that it is possible they may play some role in the final search of LISA data for EMRIs.Comment: 29 pages, 11 figures, requires subeqnarray; v2 contains minor changes for consistency with published versio

Clinical effectiveness and cost-effectiveness of open and arthroscopic rotator cuff repair [the UK Rotator Cuff Surgery (UKUFF) randomised trial]

Peer reviewedPublisher PD

Image-Based Cell Profiling Enables Quantitative Tissue Microscopy in Gastroenterology.

Immunofluorescence microscopy is an essential tool for tissue-based research, yet data reporting is almost always qualitative. Quantification of images, at the per-cell level, enables "flow cytometry-type" analyses with intact locational data but achieving this is complex. Gastrointestinal tissue, for example, is highly diverse: from mixed-cell epithelial layers through to discrete lymphoid patches. Moreover, different species (e.g., rat, mouse, and humans) and tissue preparations (paraffin/frozen) are all commonly studied. Here, using field-relevant examples, we develop open, user-friendly methodology that can encompass these variables to provide quantitative tissue microscopy for the field. Antibody-independent cell labeling approaches, compatible across preparation types and species, were optimized. Per-cell data were extracted from routine confocal micrographs, with semantic machine learning employed to tackle densely packed lymphoid tissues. Data analysis was achieved by flow cytometry-type analyses alongside visualization and statistical definition of cell locations, interactions and established microenvironments. First, quantification of Escherichia coli passage into human small bowel tissue, following Ussing chamber incubations exemplified objective quantification of rare events in the context of lumen-tissue crosstalk. Second, in rat jejenum, precise histological context revealed distinct populations of intraepithelial lymphocytes between and directly below enterocytes enabling quantification in context of total epithelial cell numbers. Finally, mouse mononuclear phagocyte-T cell interactions, cell expression and significant spatial cell congregations were mapped to shed light on cell-cell communication in lymphoid Peyer's patch. Accessible, quantitative tissue microscopy provides a new window-of-insight to diverse questions in gastroenterology. It can also help combat some of the data reproducibility crisis associated with antibody technologies and over-reliance on qualitative microscopy. © 2020 The Authors. Cytometry Part A published by Wiley Periodicals LLC. on behalf of International Society for Advancement of Cytometry.UK Medical Research Council (grant number MR/R005699/1) UK Engineering and Physical Sciences Research Council (grant EP/H008683/1) UK Biotechnology and Biological Sciences Research Council (grant number BB/P026818/1

Image-Based Cell Profiling Enables Quantitative Tissue Microscopy in Gastroenterology.

Immunofluorescence microscopy is an essential tool for tissue-based research, yet data reporting is almost always qualitative. Quantification of images, at the per-cell level, enables "flow cytometry-type" analyses with intact locational data but achieving this is complex. Gastrointestinal tissue, for example, is highly diverse: from mixed-cell epithelial layers through to discrete lymphoid patches. Moreover, different species (e.g., rat, mouse, and humans) and tissue preparations (paraffin/frozen) are all commonly studied. Here, using field-relevant examples, we develop open, user-friendly methodology that can encompass these variables to provide quantitative tissue microscopy for the field. Antibody-independent cell labeling approaches, compatible across preparation types and species, were optimized. Per-cell data were extracted from routine confocal micrographs, with semantic machine learning employed to tackle densely packed lymphoid tissues. Data analysis was achieved by flow cytometry-type analyses alongside visualization and statistical definition of cell locations, interactions and established microenvironments. First, quantification of Escherichia coli passage into human small bowel tissue, following Ussing chamber incubations exemplified objective quantification of rare events in the context of lumen-tissue crosstalk. Second, in rat jejenum, precise histological context revealed distinct populations of intraepithelial lymphocytes between and directly below enterocytes enabling quantification in context of total epithelial cell numbers. Finally, mouse mononuclear phagocyte-T cell interactions, cell expression and significant spatial cell congregations were mapped to shed light on cell-cell communication in lymphoid Peyer's patch. Accessible, quantitative tissue microscopy provides a new window-of-insight to diverse questions in gastroenterology. It can also help combat some of the data reproducibility crisis associated with antibody technologies and over-reliance on qualitative microscopy. © 2020 The Authors. Cytometry Part A published by Wiley Periodicals LLC. on behalf of International Society for Advancement of Cytometry.UK Medical Research Council (grant number MR/R005699/1) UK Engineering and Physical Sciences Research Council (grant EP/H008683/1) UK Biotechnology and Biological Sciences Research Council (grant number BB/P026818/1