Efficient Spatially Adaptive Convolution and Correlation

Fast methods for convolution and correlation underlie a variety of applications in computer vision and graphics, including efficient filtering, analysis, and simulation. However, standard convolution and correlation are inherently limited to fixed filters: spatial adaptation is impossible without sacrificing efficient computation. In early work, Freeman and Adelson have shown how steerable filters can address this limitation, providing a way for rotating the filter as it is passed over the signal. In this work, we provide a general, representation-theoretic, framework that allows for spatially varying linear transformations to be applied to the filter. This framework allows for efficient implementation of extended convolution and correlation for transformation groups such as rotation (in 2D and 3D) and scale, and provides a new interpretation for previous methods including steerable filters and the generalized Hough transform. We present applications to pattern matching, image feature description, vector field visualization, and adaptive image filtering

Ab initio calculations of the hydrogen bond

Recent x-ray Compton scattering experiments in ice have provided useful information about the quantum nature of the interaction between H$_2$O monomers. The hydrogen bond is characterized by a certain amount of charge transfer which could be determined in a Compton experiment. We use ab-initio simulations to investigate the hydrogen bond in H$_2$O structures by calculating the Compton profile and related quantities in three different systems, namely the water dimer, a cluster containing 12 water molecules and the ice crystal. We show how to extract estimates of the charge transfer from the Compton profiles.Comment: 16 pages, 7 figures, to appear in Phys. Rev.

The development of a program analysis environment for Ada

A unit level, Ada software module testing system, called Query Utility Environment for Software Testing of Ada (QUEST/Ada), is described. The project calls for the design and development of a prototype system. QUEST/Ada design began with a definition of the overall system structure and a description of component dependencies. The project team was divided into three groups to resolve the preliminary designs of the parser/scanner: the test data generator, and the test coverage analyzer. The Phase 1 report is a working document from which the system documentation will evolve. It provides history, a guide to report sections, a literature review, the definition of the system structure and high level interfaces, descriptions of the prototype scope, the three major components, and the plan for the remainder of the project. The appendices include specifications, statistics, two papers derived from the current research, a preliminary users' manual, and the proposal and work plan for Phase 2

Embracing the gut microbiota: the new frontier for inflammatory and infectious diseases

The gut microbiota provides essential signals for the development and appropriate function of the immune system. Through this critical contribution to immune fitness, the gut microbiota has a key role in health and disease. Recent advances in the technological applications to study microbial communities and their functions have contributed to a rapid increase in host–microbiota research. Although it still remains difficult to define a so‐called ‘normal’ or ‘healthy’ microbial composition, alterations in the gut microbiota have been shown to influence the susceptibility of the host to different diseases. Current translational research combined with recent technological and computational advances have enabled in‐depth study of the link between microbial composition and immune function, addressing the interplay between the gut microbiota and immune responses. As such, beneficial modulation of the gut microbiota is a promising clinical target for many prevalent diseases including inflammatory bowel disease, metabolic abnormalities such as obesity, reduced insulin sensitivity and low‐grade inflammation, allergy and protective immunity against infections.Lieke WJ van den Elsen, Hazel C Poyntz, Laura S Weyrich, Wayne Young, Elizabeth E Forbes‐Blo

A framework for digital sunken relief generation based on 3D geometric models

Sunken relief is a special art form of sculpture whereby the depicted shapes are sunk into a given surface. This is traditionally created by laboriously carving materials such as stone. Sunken reliefs often utilize the engraved lines or strokes to strengthen the impressions of a 3D presence and to highlight the features which otherwise are unrevealed. In other types of reliefs, smooth surfaces and their shadows convey such information in a coherent manner. Existing methods for relief generation are focused on forming a smooth surface with a shallow depth which provides the presence of 3D figures. Such methods unfortunately do not help the art form of sunken reliefs as they omit the presence of feature lines. We propose a framework to produce sunken reliefs from a known 3D geometry, which transforms the 3D objects into three layers of input to incorporate the contour lines seamlessly with the smooth surfaces. The three input layers take the advantages of the geometric information and the visual cues to assist the relief generation. This framework alters existing techniques in line drawings and relief generation, and then combines them organically for this particular purpose

T granules in human platelets function in TLR9 organization and signaling

Human and murine platelets (PLTs) variably express toll-like receptors (TLRs), which link the innate and adaptive immune responses during infectious inflammation and atherosclerotic vascular disease. In this paper, we show that the TLR9 transcript is specifically up-regulated during pro-PLT production and is distributed to a novel electron-dense tubular system-related compartment we have named the T granule. TLR9 colocalizes with protein disulfide isomerase and is associated with either VAMP 7 or VAMP 8, which regulates its distribution in PLTs on contact activation (spreading). Preincubation of PLTs with type IV collagen specifically increased TLR9 and CD62P surface expression and augmented oligodeoxynucleotide (ODN) sequestration and PLT clumping upon addition of bacterial/viral ODNs. Collectively, this paper (a) tracks TLR9 to a new intracellular compartment in PLTs and (b) describes a novel mechanism of TLR9 organization and signaling in human PLTs

The British Library Big Data Experiment: Experimental Interfaces, Experimental Teaching

Many digital humanities–taught programmes aim to engage undergraduate and postgraduate humanists with computational methods and practices (Hirsch, 2012; Cohen and Scheinfeldt, 2013). It is relatively rare, however, to routinely engage computer scientists with the needs, methods, and worldview of historians, literature scholars, librarians, and related researchers (Spiro, 2012). This poster describes an ongoing collaboration between British Library Digital Research and the UCL Department of Computer Science (UCLCS), facilitated by the UCL Centre for Digital Humanities (UCLDH), that enables and engages students in computer science with humanities research issues as part of their core assessed work. We demonstrate that CS students can provide an experimental test-bed for developing, exploring, and exploiting technical infrastructure and digital content in ways that may benefit humanities researchers within a library context. Encouraging students to develop skills in a new (and often foreign) domain encourages their critical thinking and provides real-world, complex issues that stretch and develop their technical abilities as well as their understanding of user requirements. Furthermore, from the problems, issues, and potentials such collaborative working raises, we learn more about the nature of computational infrastructure we rely on for research, and perceptions of the institutions’ core business in delivering digital content. As the British Library has a vision for transforming access to and research with its digital collections, the British Library Big Data Experiment forms an important complement to the British Library’s ongoing infrastructure activities through enabling the development of experimental services that offer unconventional engagement with its digital collections (Farquhar and Baker, 2014). All taught programmes in UCLCS require students to undertake an industry exchange 4 where they work in teams as clients to an industry partner. Though UCLCS has experience with developing student projects in partnership with digital humanists (Martin et al., 2012), industry partners have tended to come from the financial or manufacturing sectors. The British Library Big Data Experiment is an umbrella for a series of activities where the British Library is the client for assessed UCLCS project work, allowing for a rolling, responsive program of experimental design, development, and testing of infrastructure and systems. At agreed milestones during the project, the British Library provides access to required data, knowledge of data structures, and project requirements. UCLCS and UCLDH jointly provide technical and academic support to the student teams. In June 2014 the first British Library Big Data Experiment team was convened with a dissertation project, submitted in fulfilment of the MSc in Software Systems Engineering (Georgiou, Stavrou) and Computer Science (Alborzpour, Wong), using a collection of circa 68,000 17th- to 19th-century digitised volumes to underpin the design of a research-oriented web-based service. Microsoft Azure 5 APIs were implemented that functionally scale to the data, whilst the students worked in close consultation with humanities researchers who may wish to use the capabilities of such a system. The final public output (http://blpublicdomain.azurewebsites.net/) represents an attempt to capture the complex and multifaceted needs of humanities researchers whilst offering unconventional services such as bulk download of text based on metadata queries, word frequency lists, and OCR text previews. Following this successful pilot, the British Library Big Data Experiment is undertaking further collaborative work, including machine learning and mobile app development strands in autumn/winter 2014 and a second MSc dissertation project in summer 2015. Both UCLCS and its students have an appetite for embedding problems faced by memory institutions within CS learning outcomes. In partaking in such truly interdisciplinary project work, students develop new skill sets, question their assumptions about the role of library and humanities scholars, and provide useful experimental design within the institutional context. In addition, having CS students engage with humanities scholars as a routine part of their degree allows humanists to understand their research needs and institutional structures, from a different perspective. We present the British Library Big Data Experiment as a model ripe for reuse and we argue that the benefits of such collaborative programmes outweigh potential risks. The Big Data Experiment is, then, both an experiment in teaching and an experiment in involving and integrating those undertaking advanced study in computer science into memory institutions and humanities scholarship

Defect-induced condensation and central peak at elastic phase transitions

Static and dynamical properties of elastic phase transitions under the influence of short--range defects, which locally increase the transition temperature, are investigated. Our approach is based on a Ginzburg--Landau theory for three--dimensional crystals with one--, two-- or three--dimensional soft sectors, respectively. Systems with a finite concentration $n_{\rm D}$ of quenched, randomly placed defects display a phase transition at a temperature $T_c(n_{\rm D})$, which can be considerably above the transition temperature $T_c^0$ of the pure system. The phonon correlation function is calculated in single--site approximation. For $T>T_c(n_{\rm D})$ a dynamical central peak appears; upon approaching $T_c(n_{\rm D})$, its height diverges and its width vanishes. Using an appropriate self--consistent method, we calculate the spatially inhomogeneous order parameter, the free energy and the specific heat, as well as the dynamical correlation function in the ordered phase. The dynamical central peak disappears again as the temperatur is lowered below $T_c(n_{\rm D})$. The inhomogeneous order parameter causes a static central peak in the scattering cross section, with a finite $k$ width depending on the orientation of the external wave vector ${\bf k}$ relative to the soft sector. The jump in the specific heat at the transition temperatur of the pure system is smeared out by the influence of the defects, leading to a distinct maximum instead. In addition, there emerges a tiny discontinuity of the specific heat at $T_c(n_{\rm D})$. We also discuss the range of validity of the mean--field approach, and provide a more realistic estimate for the transition temperature.Comment: 11 pages, 11 ps-figures, to appear in PR

The physics of dynamical atomic charges: the case of ABO3 compounds

Based on recent first-principles computations in perovskite compounds, especially BaTiO3, we examine the significance of the Born effective charge concept and contrast it with other atomic charge definitions, either static (Mulliken, Bader...) or dynamical (Callen, Szigeti...). It is shown that static and dynamical charges are not driven by the same underlying parameters. A unified treatment of dynamical charges in periodic solids and large clusters is proposed. The origin of the difference between static and dynamical charges is discussed in terms of local polarizability and delocalized transfers of charge: local models succeed in reproducing anomalous effective charges thanks to large atomic polarizabilities but, in ABO3 compounds, ab initio calculations favor the physical picture based upon transfer of charges. Various results concerning barium and strontium titanates are presented. The origin of anomalous Born effective charges is discussed thanks to a band-by-band decomposition which allows to identify the displacement of the Wannier center of separated bands induced by an atomic displacement. The sensitivity of the Born effective charges to microscopic and macroscopic strains is examined. Finally, we estimate the spontaneous polarization in the four phases of barium titanate.Comment: 25 pages, 6 Figures, 10 Tables, LaTe

Signal-dependent splicing of tissue factor pre-mRNA modulates the thrombogenecity of human platelets

Tissue factor (TF) is an essential cofactor for the activation of blood coagulation in vivo. We now report that quiescent human platelets express TF pre-mRNA and, in response to activation, splice this intronic-rich message into mature mRNA. Splicing of TF pre-mRNA is associated with increased TF protein expression, procoagulant activity, and accelerated formation of clots. Pre-mRNA splicing is controlled by Cdc2-like kinase (Clk)1, and interruption of Clk1 signaling prevents TF from accumulating in activated platelets. Elevated intravascular TF has been reported in a variety of prothrombotic diseases, but there is debate as to whether anucleate platelets—the key cellular effector of thrombosis—express TF. Our studies demonstrate that human platelets use Clk1-dependent splicing pathways to generate TF protein in response to cellular activation. We propose that platelet-derived TF contributes to the propagation and stabilization of a thrombus