Rare event sampling with stochastic growth algorithms

We discuss uniform sampling algorithms that are based on stochastic growth methods, using sampling of extreme configurations of polymers in simple lattice models as a motivation. We shall show how a series of clever enhancements to a fifty-odd year old algorithm, the Rosenbluth method, led to a cutting-edge algorithm capable of uniform sampling of equilibrium statistical mechanical systems of polymers in situations where competing algorithms failed to perform well. Examples range from collapsed homo-polymers near sticky surfaces to models of protein folding.Comment: First International Conference on Numerical Physic

Cell Migration in the Immune System: the Evolving Inter-Related Roles of Adhesion Molecules and Proteinases

Leukocyte extravasation into perivascular tissue during inflammation and lymphocyte homing to lymphoid organs involve transient adhesion to the vessel endothelium, followed by transmigration through the endothelial cell (EC) layer and establishment of residency at the tissue site for a period of time. In these processes, leukocytes undergo multiple attachments to, and detachments from, the vessel-lining endothelial cells, prior to transendothelial cell migration. Transmigrating leukocytes must traverse a subendothelial basement membrane en route to perivascular tissues and utilize enzymes known as matrix metalloproteinases to make selective clips in the extracellular matrix components of the basement membrane. This review will focus on the evidence for a link between adhesion of leukocytes to endothelial cells, the induction of matrix metalloproteinases mediated by engagement of adhesion receptors on leukocytes, and the ability to utilize these matrix metalloproteinases to facilitate leukocyte invasion of tissues. Leukocytes with invasive phenotypes express high levels of MMPs, and expression of MMPs enhances the migratory and invasive properties of these cells. Furthermore, MMPs may be used by lymphocytes to proteolytically cleave molecules such as adhesion receptors and membrane bound cytokines, increasing their efficiency in the immune response. Engagement of leukocyte adhesion receptors may modulate adhesive (modulation of integrin affinities and expression), synthetic (proteinase induction and activation), and surface organization (clustering of proteolyric complexes) behaviors of invasive leukocytes. Elucidation of these pathways will lead to better understanding of controlling mechanisms in order to develop rational therapeutic approaches in the areas of inflammation and autoimmunity

Slow dynamics of the contact process on complex networks

The Contact Process has been studied on complex networks exhibiting different kinds of quenched disorder. Numerical evidence is found for Griffiths phases and other rare region effects, in Erd˝os Rényi networks, leading rather generically to anomalously slow (algebraic, logarithmic,...) relaxation. More surprisingly, it turns out that Griffiths phases can also emerge in the absence of quenched disorder, as a consequence of sole topological heterogeneity in networks with finite topological dimension. In case of scalefree networks, exhibiting infinite topological dimension, slow dynamics can be observed on tree-like structures and a superimposed weight pattern. In the infinite size limit the correlated subspaces of vertices seem to cause a smeared phase transition. These results have a broad spectrum of implications for propagation phenomena and other dynamical process on networks and are relevant for the analysis of both models and empirical data

Improving the compilation of prolog to C using moded types and determinism information

We describe the current status of and provide performance results for a prototype compiler of Prolog to C, ciaocc. ciaocc is novel in that it is designed to accept different kinds of high-level information, typically obtained via an automatic analysis of the initial Prolog program and expressed in a standardized language of assertions. This information is used to optimize the resulting C code, which is then processed by an off-the-shelf C compiler. The basic translation process essentially mimics the unfolding of a bytecode emulator with respect to the particular bytecode corresponding to the Prolog program. This is facilitated by a flexible design of the instructions and their lower-level components. This approach allows reusing a sizable amount of the machinery of the bytecode emulator: predicates already written in C, data definitions, memory management routines and áreas, etc., as well as mixing emulated bytecode with native code in a relatively straightforward way. We report on the performance of programs compiled by the current versión of the system, both with and without analysis information

A High-Level Implementation of Non-deterministic, Unrestricted, Independent And-Parallelism

The growing popularity of multicore architectures has renewed interest in language-based approaches to the exploitation of parallelism. Logic programming has proved an interesting framework to this end, and there are parallel implementations which have achieved significant speedups, but at the cost of a quite sophisticated low-level machinery. This machinery has been found challenging to code and, specially, to maintain and expand. In this paper, we follow a different approach which adopts a higher level view by raising some of the core components of the implementation to the level of the source language. We briefly present an implementation model for independent and-parallelism which fully supports non-determinism through backtracking and provides flexible solutions for some of the main problems found in previous and-parallel implementations. Our proposal is able to optimize the execution for the case of deterministic programs and to exploit unrestricted and-parallelism, which allows exposing more parallelism among clause literals than fork-join-based proposals. We present performance results for an implementation, including data for benchmarks where and-parallelism is exploited in non-deterministic programs

Antimicrobial resistance among migrants in Europe: a systematic review and meta-analysis

BACKGROUND: Rates of antimicrobial resistance (AMR) are rising globally and there is concern that increased migration is contributing to the burden of antibiotic resistance in Europe. However, the effect of migration on the burden of AMR in Europe has not yet been comprehensively examined. Therefore, we did a systematic review and meta-analysis to identify and synthesise data for AMR carriage or infection in migrants to Europe to examine differences in patterns of AMR across migrant groups and in different settings. METHODS: For this systematic review and meta-analysis, we searched MEDLINE, Embase, PubMed, and Scopus with no language restrictions from Jan 1, 2000, to Jan 18, 2017, for primary data from observational studies reporting antibacterial resistance in common bacterial pathogens among migrants to 21 European Union-15 and European Economic Area countries. To be eligible for inclusion, studies had to report data on carriage or infection with laboratory-confirmed antibiotic-resistant organisms in migrant populations. We extracted data from eligible studies and assessed quality using piloted, standardised forms. We did not examine drug resistance in tuberculosis and excluded articles solely reporting on this parameter. We also excluded articles in which migrant status was determined by ethnicity, country of birth of participants' parents, or was not defined, and articles in which data were not disaggregated by migrant status. Outcomes were carriage of or infection with antibiotic-resistant organisms. We used random-effects models to calculate the pooled prevalence of each outcome. The study protocol is registered with PROSPERO, number CRD42016043681. FINDINGS: We identified 2274 articles, of which 23 observational studies reporting on antibiotic resistance in 2319 migrants were included. The pooled prevalence of any AMR carriage or AMR infection in migrants was 25·4% (95% CI 19·1-31·8; I2 =98%), including meticillin-resistant Staphylococcus aureus (7·8%, 4·8-10·7; I2 =92%) and antibiotic-resistant Gram-negative bacteria (27·2%, 17·6-36·8; I2 =94%). The pooled prevalence of any AMR carriage or infection was higher in refugees and asylum seekers (33·0%, 18·3-47·6; I2 =98%) than in other migrant groups (6·6%, 1·8-11·3; I2 =92%). The pooled prevalence of antibiotic-resistant organisms was slightly higher in high-migrant community settings (33·1%, 11·1-55·1; I2 =96%) than in migrants in hospitals (24·3%, 16·1-32·6; I2 =98%). We did not find evidence of high rates of transmission of AMR from migrant to host populations. INTERPRETATION: Migrants are exposed to conditions favouring the emergence of drug resistance during transit and in host countries in Europe. Increased antibiotic resistance among refugees and asylum seekers and in high-migrant community settings (such as refugee camps and detention facilities) highlights the need for improved living conditions, access to health care, and initiatives to facilitate detection of and appropriate high-quality treatment for antibiotic-resistant infections during transit and in host countries. Protocols for the prevention and control of infection and for antibiotic surveillance need to be integrated in all aspects of health care, which should be accessible for all migrant groups, and should target determinants of AMR before, during, and after migration. FUNDING: UK National Institute for Health Research Imperial Biomedical Research Centre, Imperial College Healthcare Charity, the Wellcome Trust, and UK National Institute for Health Research Health Protection Research Unit in Healthcare-associated Infections and Antimictobial Resistance at Imperial College London

Surgical site infection after gastrointestinal surgery in high-income, middle-income, and low-income countries: a prospective, international, multicentre cohort study

Background: Surgical site infection (SSI) is one of the most common infections associated with health care, but its importance as a global health priority is not fully understood. We quantified the burden of SSI after gastrointestinal surgery in countries in all parts of the world. Methods: This international, prospective, multicentre cohort study included consecutive patients undergoing elective or emergency gastrointestinal resection within 2-week time periods at any health-care facility in any country. Countries with participating centres were stratified into high-income, middle-income, and low-income groups according to the UN's Human Development Index (HDI). Data variables from the GlobalSurg 1 study and other studies that have been found to affect the likelihood of SSI were entered into risk adjustment models. The primary outcome measure was the 30-day SSI incidence (defined by US Centers for Disease Control and Prevention criteria for superficial and deep incisional SSI). Relationships with explanatory variables were examined using Bayesian multilevel logistic regression models. This trial is registered with ClinicalTrials.gov, number NCT02662231. Findings: Between Jan 4, 2016, and July 31, 2016, 13 265 records were submitted for analysis. 12 539 patients from 343 hospitals in 66 countries were included. 7339 (58·5%) patient were from high-HDI countries (193 hospitals in 30 countries), 3918 (31·2%) patients were from middle-HDI countries (82 hospitals in 18 countries), and 1282 (10·2%) patients were from low-HDI countries (68 hospitals in 18 countries). In total, 1538 (12·3%) patients had SSI within 30 days of surgery. The incidence of SSI varied between countries with high (691 [9·4%] of 7339 patients), middle (549 [14·0%] of 3918 patients), and low (298 [23·2%] of 1282) HDI (p < 0·001). The highest SSI incidence in each HDI group was after dirty surgery (102 [17·8%] of 574 patients in high-HDI countries; 74 [31·4%] of 236 patients in middle-HDI countries; 72 [39·8%] of 181 patients in low-HDI countries). Following risk factor adjustment, patients in low-HDI countries were at greatest risk of SSI (adjusted odds ratio 1·60, 95% credible interval 1·05–2·37; p=0·030). 132 (21·6%) of 610 patients with an SSI and a microbiology culture result had an infection that was resistant to the prophylactic antibiotic used. Resistant infections were detected in 49 (16·6%) of 295 patients in high-HDI countries, in 37 (19·8%) of 187 patients in middle-HDI countries, and in 46 (35·9%) of 128 patients in low-HDI countries (p < 0·001). Interpretation: Countries with a low HDI carry a disproportionately greater burden of SSI than countries with a middle or high HDI and might have higher rates of antibiotic resistance. In view of WHO recommendations on SSI prevention that highlight the absence of high-quality interventional research, urgent, pragmatic, randomised trials based in LMICs are needed to assess measures aiming to reduce this preventable complication

Cooperative Query Answering for RDF

International audienceThe interest of representing data for the Semantic Web has generated standards for expressing knowledge on the Web. RDF, as one of those standards, has become a recommendation of the W3C. Even if it was designed to be human and machine readable (XML encoding, triples, labeled graphs), RDF was not provided with querying and reasoning services. Most work on querying RDF has concentrated on the use of logic programming evaluation techniques and SQL extensions. We take a new look at the problem of querying and reasoning on RDF statements and find that order-sorted feature (OSF) terms apply to this problem because OSF have been tailored for efficiency and their semantics is compatible with the isomorphic representation (triples) of RDF statements. This transformation allows to compute an ordering on resources and thus provide better answering mechanisms when querying RDF