From kinetic-structure analysis to engineering crystalline fiber networks in soft materials

10.1039/c2cp43747cPhysical Chemistry Chemical Physics1593313-3319PPCP

Ontology-Based Data Access and Integration

An ontology-based data integration (OBDI) system is an information management system consisting of three components: an ontology, a set of data sources, and the mapping between the two. The ontology is a conceptual, formal description of the domain of interest to a given organization (or a community of users), expressed in terms of relevant concepts, attributes of concepts, relationships between concepts, and logical assertions characterizing the domain knowledge. The data sources are the repositories accessible by the organization where data concerning the domain are stored. In the general case, such repositories are numerous, heterogeneous, each one managed and maintained independently from the others. The mapping is a precise specification of the correspondence between the data contained in the data sources and the elements of the ontology. The main purpose of an OBDI system is to allow information consumers to query the data using the elements in the ontology as predicates. In the special case where the organization manages a single data source, the term ontology-based data access (ODBA) system is used

First-Order Logic Theorem Proving and Model Building via Approximation and Instantiation

In this paper we consider first-order logic theorem proving and model building via approximation and instantiation. Given a clause set we propose its approximation into a simplified clause set where satisfiability is decidable. The approximation extends the signature and preserves unsatisfiability: if the simplified clause set is satisfiable in some model, so is the original clause set in the same model interpreted in the original signature. A refutation generated by a decision procedure on the simplified clause set can then either be lifted to a refutation in the original clause set, or it guides a refinement excluding the previously found unliftable refutation. This way the approach is refutationally complete. We do not step-wise lift refutations but conflicting cores, finite unsatisfiable clause sets representing at least one refutation. The approach is dual to many existing approaches in the literature because our approximation preserves unsatisfiability

Redundancy, Deduction Schemes, and Minimum-Size Bases for Association Rules

Association rules are among the most widely employed data analysis methods in the field of Data Mining. An association rule is a form of partial implication between two sets of binary variables. In the most common approach, association rules are parameterized by a lower bound on their confidence, which is the empirical conditional probability of their consequent given the antecedent, and/or by some other parameter bounds such as "support" or deviation from independence. We study here notions of redundancy among association rules from a fundamental perspective. We see each transaction in a dataset as an interpretation (or model) in the propositional logic sense, and consider existing notions of redundancy, that is, of logical entailment, among association rules, of the form "any dataset in which this first rule holds must obey also that second rule, therefore the second is redundant". We discuss several existing alternative definitions of redundancy between association rules and provide new characterizations and relationships among them. We show that the main alternatives we discuss correspond actually to just two variants, which differ in the treatment of full-confidence implications. For each of these two notions of redundancy, we provide a sound and complete deduction calculus, and we show how to construct complete bases (that is, axiomatizations) of absolutely minimum size in terms of the number of rules. We explore finally an approach to redundancy with respect to several association rules, and fully characterize its simplest case of two partial premises.Comment: LMCS accepted pape

Oncogenic RIT1 mutations in lung adenocarcinoma

Lung adenocarcinoma is comprised of distinct mutational subtypes characterized by mutually exclusive oncogenic mutations in RTK/RAS pathway members KRAS, EGFR, BRAF and ERBB2, and translocations involving ALK, RET and ROS1. Identification of these oncogenic events has transformed the treatment of lung adenocarcinoma via application of therapies targeted toward specific genetic lesions in stratified patient populations. However, such mutations have been reported in only ∼55% of lung adenocarcinoma cases in the United States, suggesting other mechanisms of malignancy are involved in the remaining cases. Here we report somatic mutations in the small GTPase gene RIT1 in ∼2% of lung adenocarcinoma cases that cluster in a hotspot near the switch II domain of the protein. RIT1 switch II domain mutations are mutually exclusive with all other known lung adenocarcinoma driver mutations. Ectopic expression of mutated RIT1 induces cellular transformation in vitro and in vivo, which can be reversed by combined PI3K and MEK inhibition. These data identify RIT1 as a driver oncogene in a specific subset of lung adenocarcinomas and suggest PI3K and MEK inhibition as a potential therapeutic strategy in RIT1-mutated tumors

Discovery and saturation analysis of cancer genes across 21 tumour types

Although a few cancer genes are mutated in a high proportion of tumours of a given type (>20%), most are mutated at intermediate frequencies (2–20%). To explore the feasibility of creating a comprehensive catalogue of cancer genes, we analysed somatic point mutations in exome sequences from 4,742 human cancers and their matched normal-tissue samples across 21 cancer types. We found that large-scale genomic analysis can identify nearly all known cancer genes in these tumour types. Our analysis also identified 33 genes that were not previously known to be significantly mutated in cancer, including genes related to proliferation, apoptosis, genome stability, chromatin regulation, immune evasion, RNA processing and protein homeostasis. Down-sampling analysis indicates that larger sample sizes will reveal many more genes mutated at clinically important frequencies. We estimate that near-saturation may be achieved with 600–5,000 samples per tumour type, depending on background mutation frequency. The results may help to guide the next stage of cancer genomics

An automatic critical care urine meter

Nowadays patients admitted to critical care units have most of their physiological parameters measured automatically by sophisticated commercial monitoring devices. More often than not, these devices supervise whether the values of the parameters they measure lie within a pre-established range, and issue warning of deviations from this range by triggering alarms. The automation of measuring and supervising tasks not only discharges the healthcare staff of a considerable workload but also avoids human errors in these repetitive and monotonous tasks. Arguably, the most relevant physiological parameter that is still measured and supervised manually by critical care unit staff is urine output (UO). In this paper we present a patent-pending device that provides continuous and accurate measurements of patient’s UO. The device uses capacitive sensors to take continuous measurements of the height of the column of liquid accumulated in two chambers that make up a plastic container. The first chamber, where the urine inputs, has a small volume. Once it has been filled it overflows into a second bigger chamber. The first chamber provides accurate UO measures of patients whose UO has to be closely supervised, while the second one avoids the need for frequent interventions by the nursing staff to empty the containe

The microaerophilic microbiota of de-novo paediatric inflammatory bowel disease: the BISCUIT study

<p>Introduction: Children presenting for the first time with inflammatory bowel disease (IBD) offer a unique opportunity to study aetiological agents before the confounders of treatment. Microaerophilic bacteria can exploit the ecological niche of the intestinal epithelium; Helicobacter and Campylobacter are previously implicated in IBD pathogenesis. We set out to study these and other microaerophilic bacteria in de-novo paediatric IBD.</p> <p>Patients and Methods: 100 children undergoing colonoscopy were recruited including 44 treatment naïve de-novo IBD patients and 42 with normal colons. Colonic biopsies were subjected to microaerophilic culture with Gram-negative isolates then identified by sequencing. Biopsies were also PCR screened for the specific microaerophilic bacterial groups: Helicobacteraceae, Campylobacteraceae and Sutterella wadsworthensis.</p> <p>Results: 129 Gram-negative microaerophilic bacterial isolates were identified from 10 genera. The most frequently cultured was S. wadsworthensis (32 distinct isolates). Unusual Campylobacter were isolated from 8 subjects (including 3 C. concisus, 1 C. curvus, 1 C. lari, 1 C. rectus, 3 C. showae). No Helicobacter were cultured. When comparing IBD vs. normal colon control by PCR the prevalence figures were not significantly different (Helicobacter 11% vs. 12%, p = 1.00; Campylobacter 75% vs. 76%, p = 1.00; S. wadsworthensis 82% vs. 71%, p = 0.312).</p> <p>Conclusions: This study offers a comprehensive overview of the microaerophilic microbiota of the paediatric colon including at IBD onset. Campylobacter appear to be surprisingly common, are not more strongly associated with IBD and can be isolated from around 8% of paediatric colonic biopsies. S. wadsworthensis appears to be a common commensal. Helicobacter species are relatively rare in the paediatric colon.</p&gt

Metabolic Networks Analysis using Convex Optimization

Metabolic networks map the biochemical reactions in a living cell to the flow of various chemical substances in the cell, which are called metabolites. A standard model of a metabolic network is given as a linear map from the reaction rates to the change in metabolites concentrations. We study two problems related to the analysis of metabolic networks, the minimal network problem and the minimal knockout problem

Microbiota of De-Novo Pediatric IBD : Increased Faecalibacterium Prausnitzii and Reduced Bacterial Diversity in Crohn's But Not in Ulcerative Colitis

ACKNOWLEDGMENTS We are grateful for the expertise of our sequencing provider NewGene and in particular for the support and help of Dr Jonathan Coxhead.Mrs Karen McIntyre and Dr Dagmar Kastner were invaluable in identifying patients for recruitment in Dundee. Mrs Ann Morrice provided administrative support in Aberdeen. Dr Paul Henderson gave helpful comments on the manuscript. We appreciate the generosity of the families who freely gave their time and samples to make this study possible and the theatre staff of all centers who allowed time for sample collection during busy endoscopy lists.Peer reviewedPublisher PD