Input-Output Disjointness for Forward Expressions in the Logic of Information Flows

Last year we introduced the logic FLIF (forward logic of information flows) as a declarative language for specifying complex compositions of information sources with limited access patterns. The key insight of this approach is to view a system of information sources as a graph, where the nodes are valuations of variables, so that accesses to information sources can be modeled as edges in the graph. This allows the use of XPath-like navigational graph query languages. Indeed, a well-behaved fragment of FLIF, called io-disjoint FLIF, was shown to be equivalent to the executable fragment of first-order logic. It remained open, however, how io-disjoint FLIF compares to general FLIF . In this paper we close this gap by showing that general FLIF expressions can always be put into io-disjoint form

Distributed Subweb Specifications for Traversing the Web

Link Traversal-based Query Processing (ltqp), in which a sparql query is evaluated over a web of documents rather than a single dataset, is often seen as a theoretically interesting yet impractical technique. However, in a time where the hypercentralization of data has increasingly come under scrutiny, a decentralized Web of Data with a simple document-based interface is appealing, as it enables data publishers to control their data and access rights. While ltqp allows evaluating complex queries over such webs, it suffers from performance issues (due to the high number of documents containing data) as well as information quality concerns (due to the many sources providing such documents). In existing ltqp approaches, the burden of finding sources to query is entirely in the hands of the data consumer. In this paper, we argue that to solve these issues, data publishers should also be able to suggest sources of interest and guide the data consumer towards relevant and trustworthy data. We introduce a theoretical framework that enables such guided link traversal and study its properties. We illustrate with a theoretic example that this can improve query results and reduce the number of network requests. We evaluate our proposal experimentally on a virtual linked web with specifications and indeed observe that not just the data quality but also the efficiency of querying improves. Under consideration in Theory and Practice of Logic Programming (TPLP).Comment: Under consideration in Theory and Practice of Logic Programming (TPLP

Executable First-Order Queries in the Logic of Information Flows

The logic of information flows (LIF) has recently been proposed as a general framework in the field of knowledge representation. In this framework, tasks of a procedural nature can still be modeled in a declarative, logic-based fashion. In this paper, we focus on the task of query processing under limited access patterns, a well-studied problem in the database literature. We show that LIF is well-suited for modeling this task. Toward this goal, we introduce a variant of LIF called "forward" LIF, in a first-order setting. We define FLIFio, a syntactical fragment of forward LIF, and show that it corresponds exactly to the "executable" fragment of first-order logic defined by Nash and Lud\"ascher. Moreover, we show that general FLIF expressions can also be put into io-disjoint form. The definition of FLIFio involves a classification of the free variables of an expression into "input" and "output" variables. Our result hinges on inertia and determinacy laws for forward LIF expressions, which are interesting in their own right. These laws are formulated in terms of the input and output variables.Comment: This paper is the extended version of the two papers presented at ICDT 2020 and ICDT 202

Qatar genome: Insights on genomics from the Middle East

Despite recent biomedical breakthroughs and large genomic studies growing momentum, the Middle Eastern population, home to over 400 million people, is underrepresented in the human genome variation databases. Here we describe insights from Phase 1 of the Qatar Genome Program with whole genome sequenced 6047 individuals from Qatar. We identified more than 88 million variants of which 24 million are novel and 23 million are singletons. Consistent with the high consanguinity and founder effects in the region, we found that several rare deleterious variants were more common in the Qatari population while others seem to provide protection against diseases and have shaped the genetic architecture of adaptive phenotypes. These results highlight the value of our data as a resource to advance genetic studies in the Arab and neighboring Middle Eastern populations and will significantly boost the current efforts to improve our understanding of global patterns of human variations, human history, and genetic contributions to health and diseases in diverse populations.The Qatar Genome Program (QGP) and Qatar Biobank (QBB) are both Research and Development entities within Qatar Foundation for Education, Science and Community Development. The authors are thankful for everyone who contributed to this endeavor including the QGP and QBB team members, in addition to our partners at Hamad Medical Corporation (HMC), Sidra Medicine and other national stakeholders. The authors would like to especially thank all participants in this study for their continuous support

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

Expressiveness within Sequence Datalog

Motivated by old and new applications, we investigate Datalog as a language for sequence databases. We reconsider classical features of Datalog programs, such as negation, recursion, intermediate predicates, and relations of higher arities. We also consider new features that are useful for sequences, notably, equations between path expressions, and "packing". Our goal is to clarify the relative expressiveness of all these different features, in the context of sequences. Towards our goal, we establish a number of redundancy and primitivity results, showing that certain features can, or cannot, be expressed in terms of other features. These results paint a complete picture of the expressiveness relationships among all possible Sequence Datalog fragments that can be formed using the six features that we consider.Comment: This paper is the extended version of a paper presented at PODS 202

Link traversal with distributed subweb specifications

Link Traversal–based Query Processing (ltqp), in which a sparql query is evaluated over a web of documents rather than a single dataset, is often seen as a theoretically interesting yet impractical technique. However, in a time where the hypercentralization of data has increasingly come under scrutiny, a decentralized Web of Data with a simple document-based interface is appealing, as it enables data publishers to control their data and access rights. While ltqp allows evaluating complex queries over such webs, it suffers from performance issues (due to the high number of documents containing data) as well as information quality concerns (due to the many sources providing such documents). In existing ltqp approaches, the burden of finding sources to query is entirely in the hands of the data consumer. In this paper, we argue that to solve these issues, data publishers should also be able to suggest sources of interest and guide the data consumer towards relevant and trustworthy data. We introduce a theoretical framework that enables such guided link traversal and study its properties. We illustrate with a theoretic example that this can improve query results and reduce the number of network requests

Surgical site infection after gastrointestinal surgery in children : an international, multicentre, prospective cohort study

Introduction Surgical site infection (SSI) is one of the most common healthcare-associated infections (HAIs). However, there is a lack of data available about SSI in children worldwide, especially from low-income and middle-income countries. This study aimed to estimate the incidence of SSI in children and associations between SSI and morbidity across human development settings. Methods A multicentre, international, prospective, validated cohort study of children aged under 16 years undergoing clean-contaminated, contaminated or dirty gastrointestinal surgery. Any hospital in the world providing paediatric surgery was eligible to contribute data between January and July 2016. The primary outcome was the incidence of SSI by 30 days. Relationships between explanatory variables and SSI were examined using multilevel logistic regression. Countries were stratified into high development, middle development and low development groups using the United Nations Human Development Index (HDI). Results Of 1159 children across 181 hospitals in 51 countries, 523 (45 center dot 1%) children were from high HDI, 397 (34 center dot 2%) from middle HDI and 239 (20 center dot 6%) from low HDI countries. The 30-day SSI rate was 6.3% (33/523) in high HDI, 12 center dot 8% (51/397) in middle HDI and 24 center dot 7% (59/239) in low HDI countries. SSI was associated with higher incidence of 30-day mortality, intervention, organ-space infection and other HAIs, with the highest rates seen in low HDI countries. Median length of stay in patients who had an SSI was longer (7.0 days), compared with 3.0 days in patients who did not have an SSI. Use of laparoscopy was associated with significantly lower SSI rates, even after accounting for HDI. Conclusion The odds of SSI in children is nearly four times greater in low HDI compared with high HDI countries. Policies to reduce SSI should be prioritised as part of the wider global agenda.Peer reviewe