XP. A Common Lisp Pretty Printing System

XP provides efficient and flexible support for pretty printing in Common Lisp. Its single greatest advantage is that it allows the full benefits of pretty printing to be obtained when printing data structures, as well as when printing program code. XP is efficient, because it is based on a linear time algorithm that uses a small fixed amount of storage. XP is flexible, because users can control the exact form of the output via a set of special format directives. XP can operate on arbitrary data structures, because facilities are provided for specifying pretty printing methods for any type of object.

Monitoring Activities from Multiple Video Streams: Establishing a Common Coordinate Frame

Passive monitoring of large sites typically requires coordination between multiple cameras, which in turn requires methods for automatically relating events between distributed cameras. This paper tackles the problem of self-calibration of multiple cameras which are very far apart, using feature correspondences to determine the camera geometry. The key problem is finding such correspondences. Since the camera geometry and photometric characteristics vary considerably between images, one cannot use brightness and/or proximity constraints. Instead we apply planar geometric constraints to moving objects in the scene in order to align the scene"s ground plane across multiple views. We do not assume synchronized cameras, and we show that enforcing geometric constraints enables us to align the tracking data in time. Once we have recovered the homography which aligns the planar structure in the scene, we can compute from the homography matrix the 3D position of the plane and the relative camera positions. This in turn enables us to recover a homography matrix which maps the images to an overhead view. We demonstrate this technique in two settings: a controlled lab setting where we test the effects of errors in internal camera calibration, and an uncontrolled, outdoor setting in which the full procedure is applied to external camera calibration and ground plane recovery. In spite of noise in the internal camera parameters and image data, the system successfully recovers both planar structure and relative camera positions in both settings.

In Common Cause: The NATO Multilateral Force and Mixed-Manning Demonstration on USS Claude V. Ricketts, 1964-1965

Priest, A. (2005). In Common Cause: The NATO Multilateral Force and Mixed-Manning Demonstration on USS Claude V. Ricketts, 1964-1965. Journal of Military History, 69 (3), 759-789. RAE2008

Comparative proteomics of excretory-secretory proteins released by the liver fluke Fasciola hepatica in sheep host bile and during in vitro culture ex host

Russell M. Morphew, Hazel A. Wright, E. James LaCourse, Debra J. Woods and Peter M. Brophy (2007). Comparative proteomics of excretory-secretory proteins released by the liver fluke Fasciola hepatica in sheep host bile and during in vitro culture ex host. Molecular and Cellular Proteomics, 6 (6), 963-972. Sponsorship: BBSRC / EU RAE2008

Correction to the pathogenic alternative splicing, caused by the common GNB3 c.825C>T allele, using a novel, antisense morpholino

The very common GNB3 c.825C>T polymorphism (rs5443), is present in approximately half of all human chromosomes. Significantly the presence of the GNB3 825T allele has been strongly associated, with predisposition to essential hypertension. Paradoxically the presence of the GNB3 825T allele, in exon 10, introduces a pathogenic alternative RNA splice site into the middle of exon 9. To attempt to correct this pathogenic aberrant splicing, we therefore bioinformatically designed, using a Gene Tools® algorithm, a GNB3 specific, antisense morpholino. It was hoped that this morpholino would behave in vitro as either a potential “ splice blocker and/or exon skipper, to both bind and inhibit/reduce the aberrant splicing of the GNB3, 825T allele. On transfecting a human lymphoblast cell line homozygous for the 825T allele, with this antisense morpholino, we encouragingly observed both a significant reduction (from ~58% to ~5%) in the production of the aberrant smaller GNB3 transcript, and a subsequent increase in the normal GNB3 transcript (from ~42% to ~95%). Our results demonstrate the potential use of a GNB3 specific antisense morpholino, as a pharmacogenetic therapy for essential hypertension.

Depolarization of sperm membrane potential is a common feature of men with subfertility and is associated with low fertilization rate at IVF

STUDY QUESTION. Are significant abnormalities in outward (K+) conductance and resting membrane potential (Vm) present in the spermatozoa of patients undertaking IVF and ICSI and if so, what is their functional effect on fertilization success? SUMMARY ANSWER. Negligible outward conductance (≈5% of patients) or an enhanced inward conductance (≈4% of patients), both of which caused depolarization of Vm, were associated with a low rate of fertilization following IVF. WHAT IS KNOWN ALREADY. Sperm-specific potassium channel knockout mice are infertile with defects in sperm function, suggesting that these channels are essential for fertility. These observations suggest that malfunction of K+ channels in human spermatozoa might contribute significantly to the occurrence of subfertility in men. However, remarkably little is known of the nature of K+ channels in human spermatozoa or the incidence and functional consequences of K+ channel defects. STUDY DESIGN, SIZE AND DURATION. Spermatozoa were obtained from healthy volunteer research donors and subfertile IVF and ICSI patients attending a hospital assisted reproductive techniques clinic between May 2013 and December 2015. In total, 40 IVF patients, 41 ICSI patients and 26 normozoospermic donors took part in the study. PARTICIPANTS/MATERIALS, SETTING, METHODS. Samples were examined using electrophysiology (whole-cell patch clamping). Where abnormal electrophysiological characteristics were identified, spermatozoa were further examined for Ca2+ influx induced by progesterone and penetration into viscous media if sufficient sample was available. Full exome sequencing was performed to specifically evaluate potassium calcium-activated channel subfamily M α 1 (KCNMA1), potassium calcium-activated channel subfamily U member 1 (KCNU1) and leucine-rich repeat containing 52 (LRRC52) genes and others associated with K+ signalling. In IVF patients, comparison with fertilization rates was done to assess the functional significance of the electrophysiological abnormalities. MAIN RESULTS AND THE ROLE OF CHANCE. Patch clamp electrophysiology was used to assess outward (K+) conductance and resting membrane potential (Vm) and signalling/motility assays were used to assess functional characteristics of sperm from IVF and ICSI patient samples. The mean Vm and outward membrane conductance in sperm from IVF and ICSI patients were not significantly different from those of control (donor) sperm prepared under the same conditions, but variation between individuals was significantly greater (P< 0.02) with a large number of outliers (>25%). In particular, in ≈10% of patients (7/81), we observed either a negligible outward conductance (4 patients) or an enhanced inward current (3 patients), both of which caused depolarization of Vm. Analysis of clinical data from the IVF patients showed significant association of depolarized Vm (≥0 mV) with low fertilization rate (P= 0.012). Spermatozoa with electrophysiological abnormities (conductance and Vm) responded normally to progesterone with elevation of [Ca2+]i and penetration of viscous medium, indicating retention of cation channel of sperm (CatSper) channel function. LIMITATIONS, REASONS FOR CAUTION. For practical, technical, ethical and logistical reasons, we could not obtain sufficient additional semen samples from men with conductance abnormalities to establish the cause of the conductance defects. Full exome sequencing was only available in two men with conductance defects. WIDER IMPLICATIONS OF THE FINDINGS. These data add significantly to the understanding of the role of ion channels in human sperm function and its impact on male fertility. Impaired potassium channel conductance (Gm) and/or Vm regulation is both common and complex in human spermatozoa and importantly is associated with impaired fertilization capacity when the Vm of cells is completely depolarized.

Towards the identification of the common features of bacterial biofilm development

UPNa. Instituto de Agrobiotecnología. Laboratorio de Biofilms Microbianos

Analysis and Assessment of Conclusions in the White Book regarding Threats and Challenges in EU Common Security and Defence Policy

Among the many issues that were raised in the White Book on National Security of the Republic of Poland (WBNSRP), there were also those related to the functioning of a Common Security and Defence Policy (CSDP). Its importance for the security of Poland was indicated, as well as the need on the part of EU Member States to broaden collaboration in the sphere of security and defence. The key problems occurring in the context of CSDP were also emphasised and their causes indicated. The aim of the article is to present the factors responsible for the weakening of CSDP effectiveness, ones taken into account in the White Book, and subsequently to present a Framework for their analysis in the light of further scholarship.

DSpace How-To Guide: Tips and tricks for managing common DSpace chores

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Efficient Support for Common Relations in Lightweight Formal Reasoning Systems

In work that involves mathematical rigor, there are numerous benefits to adopting a representation of models and arguments that can be supplied to a formal reasoning or verification system: reusability, automatic evaluation of examples, and verification of consistency and correctness. However, accessibility has not been a priority in the design of formal verification tools that can provide these benefits. In earlier work [Lap09a], we attempt to address this broad problem by proposing several specific design criteria organized around the notion of a natural context: the sphere of awareness a working human user maintains of the relevant constructs, arguments, experiences, and background materials necessary to accomplish the task at hand. This work expands one aspect of the earlier work by considering more extensively an essential capability for any formal reasoning system whose design is oriented around simulating the natural context: native support for a collection of mathematical relations that deal with common constructs in arithmetic and set theory. We provide a formal definition for a context of relations that can be used to both validate and assist formal reasoning activities. We provide a proof that any algorithm that implements this formal structure faithfully will necessary converge. Finally, we consider the efficiency of an implementation of this formal structure that leverages modular implementations of well-known data structures: balanced search trees and transitive closures of hypergraphs.

Analysis of institutional arrangements and common pool resources governance: the case of Lake Tana sub-basin, Ethiopia

Although Common Pool Resources (CPRs) make up a significant share of total income for rural households in Ethiopia and elsewhere in developing world, limited access to these resources and environmental degradation threaten local livelihoods. As a result, the issues of management, governance of CPRs and how to prevent their over-exploitation are of great importance for development policy. This study examines the current state and dynamics of CPRs and overall resource governance system of the Lake Tana sub-basin. This research employed the modified form of Institutional Analysis and Development (IAD) framework. The framework integrates the concept of Socio-Ecological Systems (SES) and Interactive Governance (IG) perspectives where social actors, institutions, the politico-economic context, discourses and ecological features across governance and government levels were considered. It has been observed that overexploitation, degradation and encroachment of CPRs have increased dramatically and this threatens the sustainability of Lake Tana ecosystem. The stakeholder analysis result reveals that there are multiple stakeholders with diverse interest in and power over CPRs. The analysis of institutional arrangements reveals that the existing formal rules and regulations governing access to and control over CPRs could not be implemented and were not effective to legally bind and govern CPR user’s behavior at the operational level. The study also shows that a top-down and non-participatory policy formulation, law and decision making process overlooks the local contexts (local knowledge and informal institutions). The outcomes of examining the participation of local resource users, as an alternative to a centralized, command-and-control, and hierarchical approach to resource management and governance, have called for a fundamental shift in CPR use, management and governance to facilitate the participation of stakeholders in decision making. Therefore, establishing a multi-level stakeholder governance system as an institutional structure and process is necessary to sustain stakeholder participation in decision-making regarding CPR use, management and governance.

The relevance of bacterial isoprenoid biosynthetic pathways for host-microbe interactions

This thesis was undertaken to investigate the relevance of two bacterial isoprenoid biosynthetic pathways (Mevalonate (MVAL) and 2-C-methyl-D-erythritol 4-phosphate (MEP)) for host-microbe interactions. We determined a significant reduction in microbial diversity in the murine gut microbiota (by next generation sequencing) following oral administration of a common anti-cholesterol drug Rosuvastatin (RSV) that targets mammalian and bacterial HMG-CoA reductase (HMG-R) for inhibition of MVAL formation. In tandem we identified significant hepatic and intestinal off-target alterations to the murine metabolome indicating alterations in inflammation, bile acid profiles and antimicrobial peptide synthesis with implications on community structure of the gastrointestinal microbiota in statin-treated animals. However we found no effect on local Short Chain Fatty Acid biosynthesis (metabolic health marker in our model). We demonstrated direct inhibition of bacterial growth in-vitro by RSV which correlated with reductions in bacterial MVAL formation. However this was only at high doses of RSV. Our observations demonstrate a significant RSV-associated impact on the gut microbiota prompting similar human analysis. Successful deletion of another MVAL pathway enzyme (HMG-CoA synthase (mvaS)) involved in Listeria monocytogenes EGDe isoprenoid biosynthesis determined that the enzyme is non-essential for normal growth and in-vivo pathogenesis of this pathogen. We highlight potential evidence for alternative means of synthesis of the HMG-CoA substrate that could render mvaS activity redundant under our test conditions. Finally, we showed by global gene expression analysis (Massive Analysis of cDNA Ends (MACE RNA-seq) a significant role for the penultimate MEP pathway metabolite (E)-4-hydroxy-3-methyl-2-but-2-enyl pyrophosphate (HMBPP) in significant up regulation of genes of immunity and antigen presentation in THP-1 cells at nanomolar levels. We infected THP-1 cells with wild type or HMBPP under/over-producing L. monoctyogenes EGDe mutants and determined subtle effects of HMBPP upon overall host responses to Listeria infection. Overall our findings provide greater insights regarding bacterial isoprenoid biosynthetic pathways for host-microbe/microbe-host dialogue.

Equity trading volume and volatility: Latent information arrivals and common long-run dependencies

This article examines the behavior of equity trading volume and volatility for the individual firms composing the Standard & Poor's 100 composite index. Using multivariate spectral methods, we find that fractionally integrated processes best describe the long-run temporal dependencies in both series. Consistent with a stylized mixture-of-distributions hypothesis model in which the aggregate "news"-arrival process possesses long-memory characteristics, the long-run hyperbolic decay rates appear to be common across each volume-volatility pair.

How common are common mental disorders? Evidence that lifetime prevalence rates are doubled by prospective versus retrospective ascertainment.

BACKGROUND: Most information about the lifetime prevalence of mental disorders comes from retrospective surveys, but how much these surveys have undercounted due to recall failure is unknown. We compared results from a prospective study with those from retrospective studies. METHOD: The representative 1972-1973 Dunedin New Zealand birth cohort (n=1037) was followed to age 32 years with 96% retention, and compared to the national New Zealand Mental Health Survey (NZMHS) and two US National Comorbidity Surveys (NCS and NCS-R). Measures were research diagnoses of anxiety, depression, alcohol dependence and cannabis dependence from ages 18 to 32 years. RESULTS: The prevalence of lifetime disorder to age 32 was approximately doubled in prospective as compared to retrospective data for all four disorder types. Moreover, across disorders, prospective measurement yielded a mean past-year-to-lifetime ratio of 38% whereas retrospective measurement yielded higher mean past-year-to-lifetime ratios of 57% (NZMHS, NCS-R) and 65% (NCS). CONCLUSIONS: Prospective longitudinal studies complement retrospective surveys by providing unique information about lifetime prevalence. The experience of at least one episode of DSM-defined disorder during a lifetime may be far more common in the population than previously thought. Research should ask what this means for etiological theory, construct validity of the DSM approach, public perception of stigma, estimates of the burden of disease and public health policy.