Automatic Extraction of Protein Point Mutations Using a Graph Bigram Association

Protein point mutations are an essential component of the evolutionary and experimental analysis of protein structure and function. While many manually curated databases attempt to index point mutations, most experimentally generated point mutations and the biological impacts of the changes are described in the peer-reviewed published literature. We describe an application, Mutation GraB (Graph Bigram), that identifies, extracts, and verifies point mutations from biomedical literature. The principal problem of point mutation extraction is to link the point mutation with its associated protein and organism of origin. Our algorithm uses a graph-based bigram traversal to identify these relevant associations and exploits the Swiss-Prot protein database to verify this information. The graph bigram method is different from other models for point mutation extraction in that it incorporates frequency and positional data of all terms in an article to drive the point mutation–protein association. Our method was tested on 589 articles describing point mutations from the G protein–coupled receptor (GPCR), tyrosine kinase, and ion channel protein families. We evaluated our graph bigram metric against a word-proximity metric for term association on datasets of full-text literature in these three different protein families. Our testing shows that the graph bigram metric achieves a higher F-measure for the GPCRs (0.79 versus 0.76), protein tyrosine kinases (0.72 versus 0.69), and ion channel transporters (0.76 versus 0.74). Importantly, in situations where more than one protein can be assigned to a point mutation and disambiguation is required, the graph bigram metric achieves a precision of 0.84 compared with the word distance metric precision of 0.73. We believe the graph bigram search metric to be a significant improvement over previous search metrics for point mutation extraction and to be applicable to text-mining application requiring the association of words

Entanglement transformation between sets of bipartite pure quantum states using local operations

Alice and Bob are given an unknown initial state chosen from a set of pure quantum states. Their task is to transform the initial state to a corresponding final pure state using local operations only. We prove necessary and sufficient conditions on the existence of such a transformation. We also provide efficient algorithms that can quickly rule out the possibility of transforming a set of initial states to a set of final states.Comment: 19 pages, 1 figure, minor revision, to appear in J.Math.Phy

DRINKING PATTERNS AMONG MEDICAL IN-PATIENTS WITH REFERENCE TO MAST CATEGORIES: A COMPARATIVE STUDY

The aim of the study was to describe the drinking patterns and alcohol consumption of patients screened by the Michigan Alcoholism Screening Test (MAST) in a sample of medical patients from a general hospital of a French-speaking, wine-drinking country. Data were recorded using a structured interview administered to 103 consecutively admitted 20-75-year-old MAST-positive patients and 103 age-matched and sex-matched MAST-negative controls admitted to the same ward. Relevant differences between MAST-positive and MAST-negative patients included the frequent report of recent and total abstinence in MAST-positive patients (23% versus 4% in controls), their tendency to drink alone, and less often during mealtimes, at home, or with family or friends than MAST-negative patients. Alcohol consumption was significantly higher in MAST-positive patients of both sexes with 250 and 270 g per week being the optimal discriminative cut-off level of consumption for men and women, respectively (kappa coefficient, 0.70 and 0.81, respectively). Regular drinking was the predominant drinking status of both MAST-positive and MAST-negative patients. This study suggests that a screening test such as the MAST, developed in an English-speaking country may be useful in a French-speaking, wine-drinking country. The test identified patients with drinking patterns that are culturally abnormal, yet in certain respects similar to those of alcoholic patients from other drinking cultures. These findings therefore emphasize the worldwide relevance of the concept of the alcohol dependence syndrome in addition to the transcultural usefulness of alcoholism screening test

Reinforcement magnitudes modulate subthalamic beta band activity in patients with Parkinson's disease

We set out to investigate whether beta oscillations in the human basal ganglia are modulated during reinforcement learning. Based on previous research, we assumed that beta activity might either reflect the magnitudes of individuals' received reinforcements (reinforcement hypothesis), their reinforcement prediction errors (dopamine hypothesis) or their tendencies to repeat versus adapt responses based upon reinforcements (status-quo hypothesis). We tested these hypotheses by recording local field potentials (LFPs) from the subthalamic nuclei of 19 Parkinson's disease patients engaged in a reinforcement-learning paradigm. We then correlated patients' reinforcement magnitudes, reinforcement prediction errors and response repetition tendencies with task-related power changes in their LFP oscillations. During feedback presentation, activity in the frequency range of 14 to 27 Hz (beta spectrum) correlated positively with reinforcement magnitudes. During responding, alpha and low beta activity (6 to 18 Hz) was negatively correlated with previous reinforcement magnitudes. Reinforcement prediction errors and response repetition tendencies did not correlate significantly with LFP oscillations. These results suggest that alpha and beta oscillations during reinforcement learning reflect patients' observed reinforcement magnitudes, rather than their reinforcement prediction errors or their tendencies to repeat versus adapt their responses, arguing both against an involvement of phasic dopamine and against applicability of the status-quo theory

Identifying Metabolomic Profiles of Insulinemic Dietary Patterns

The food-based empirical dietary index for hyperinsulinemia (EDIH) score assesses the insulinemic potential of diet. This cross-sectional study evaluated associations between EDIH scores from food frequency questionnaires with c-peptide concentrations and with 448 metabolites, from fasting plasma samples, in multivariable linear regression analyses. Metabolites were measured with liquid chromatography tandem mass spectroscopy. Using a robust two-stage study design, discovery of metabolite associations was conducted among 1109 Women’s Health Initiative (WHI) Hormone Therapy (HT) trial participants and results replicated in an independent dataset of 810 WHI Observational Study (OS) participants. In both discovery and replication datasets, statistical significance was based on the false-discovery rate adjusted P \u3c 0.05. In the multivariable-adjusted analyses, EDIH was significantly associated with c-peptide concentrations among 919 women (HT & OS) with c-peptide data. On average, c-peptide concentrations were 18% higher (95% CI, 6%, 32%; P-trend \u3c 0.0001) in EDIH quintile 5 compared to quintile 1. Twenty-six metabolites were significantly associated with EDIH in the discovery dataset, and 19 of these were replicated in the validation dataset. Nine metabolites were found to decrease in abundance with increasing EDIH scores and included: C14:0 CE, C16:1 CE, C18:1 CE, C18:3 CE, C20:3 CE, C20:5 CE, C36:1 PS plasmalogen, trigonelline, and eicosapentanoate, whereas the 10 metabolites observed to increase with increasing EDIH scores were: C18:2 SM, C36:3 DAG, C36:4 DAG-A, C51:3 TAG, C52:3 TAG, C52:4, TAG, C54:3 TAG, C54:4 TAG, C54:6 TAG, and C10:2 carnitine. Cholesteryl esters, phospholipids, acylglycerols, and acylcarnitines may constitute circulating metabolites that are associated with insulinemic dietary patterns

Foundations of Digital Arch{\ae}oludology

Digital Archaeoludology (DAL) is a new field of study involving the analysis and reconstruction of ancient games from incomplete descriptions and archaeological evidence using modern computational techniques. The aim is to provide digital tools and methods to help game historians and other researchers better understand traditional games, their development throughout recorded human history, and their relationship to the development of human culture and mathematical knowledge. This work is being explored in the ERC-funded Digital Ludeme Project. The aim of this inaugural international research meeting on DAL is to gather together leading experts in relevant disciplines - computer science, artificial intelligence, machine learning, computational phylogenetics, mathematics, history, archaeology, anthropology, etc. - to discuss the key themes and establish the foundations for this new field of research, so that it may continue beyond the lifetime of its initiating project.Comment: Report on Dagstuhl Research Meeting. Authored/edited by all participants. Appendices by Thierry Depauli

On looking into words (and beyond): Structures, Relations, Analyses

On Looking into Words is a wide-ranging volume spanning current research into word structure and morphology, with a focus on historical linguistics and linguistic theory. The papers are offered as a tribute to Stephen R. Anderson, the Dorothy R. Diebold Professor of Linguistics at Yale, who is retiring at the end of the 2016-2017 academic year. The contributors are friends, colleagues, and former students of Professor Anderson, all important contributors to linguistics in their own right. As is typical for such volumes, the contributions span a variety of topics relating to the interests of the honorand. In this case, the central contributions that Anderson has made to so many areas of linguistics and cognitive science, drawing on synchronic and diachronic phenomena in diverse linguistic systems, are represented through the papers in the volume. The 26 papers that constitute this volume are unified by their discussion of the interplay between synchrony and diachrony, theory and empirical results, and the role of diachronic evidence in understanding the nature of language. Central concerns of the volume include morphological gaps, learnability, increases and declines in productivity, and the interaction of different components of the grammar. The papers deal with a range of linked synchronic and diachronic topics in phonology, morphology, and syntax (in particular, cliticization), and their implications for linguistic theory

On looking into words (and beyond): Structures, Relations, Analyses

On Looking into Words is a wide-ranging volume spanning current research into word structure and morphology, with a focus on historical linguistics and linguistic theory. The papers are offered as a tribute to Stephen R. Anderson, the Dorothy R. Diebold Professor of Linguistics at Yale, who is retiring at the end of the 2016-2017 academic year. The contributors are friends, colleagues, and former students of Professor Anderson, all important contributors to linguistics in their own right. As is typical for such volumes, the contributions span a variety of topics relating to the interests of the honorand. In this case, the central contributions that Anderson has made to so many areas of linguistics and cognitive science, drawing on synchronic and diachronic phenomena in diverse linguistic systems, are represented through the papers in the volume. The 26 papers that constitute this volume are unified by their discussion of the interplay between synchrony and diachrony, theory and empirical results, and the role of diachronic evidence in understanding the nature of language. Central concerns of the volume include morphological gaps, learnability, increases and declines in productivity, and the interaction of different components of the grammar. The papers deal with a range of linked synchronic and diachronic topics in phonology, morphology, and syntax (in particular, cliticization), and their implications for linguistic theory

On looking into words (and beyond): Structures, Relations, Analyses

On Looking into Words is a wide-ranging volume spanning current research into word structure and morphology, with a focus on historical linguistics and linguistic theory. The papers are offered as a tribute to Stephen R. Anderson, the Dorothy R. Diebold Professor of Linguistics at Yale, who is retiring at the end of the 2016-2017 academic year. The contributors are friends, colleagues, and former students of Professor Anderson, all important contributors to linguistics in their own right. As is typical for such volumes, the contributions span a variety of topics relating to the interests of the honorand. In this case, the central contributions that Anderson has made to so many areas of linguistics and cognitive science, drawing on synchronic and diachronic phenomena in diverse linguistic systems, are represented through the papers in the volume. The 26 papers that constitute this volume are unified by their discussion of the interplay between synchrony and diachrony, theory and empirical results, and the role of diachronic evidence in understanding the nature of language. Central concerns of the volume include morphological gaps, learnability, increases and declines in productivity, and the interaction of different components of the grammar. The papers deal with a range of linked synchronic and diachronic topics in phonology, morphology, and syntax (in particular, cliticization), and their implications for linguistic theory

On looking into words (and beyond): Structures, Relations, Analyses

On Looking into Words is a wide-ranging volume spanning current research into word structure and morphology, with a focus on historical linguistics and linguistic theory. The papers are offered as a tribute to Stephen R. Anderson, the Dorothy R. Diebold Professor of Linguistics at Yale, who is retiring at the end of the 2016-2017 academic year. The contributors are friends, colleagues, and former students of Professor Anderson, all important contributors to linguistics in their own right. As is typical for such volumes, the contributions span a variety of topics relating to the interests of the honorand. In this case, the central contributions that Anderson has made to so many areas of linguistics and cognitive science, drawing on synchronic and diachronic phenomena in diverse linguistic systems, are represented through the papers in the volume. The 26 papers that constitute this volume are unified by their discussion of the interplay between synchrony and diachrony, theory and empirical results, and the role of diachronic evidence in understanding the nature of language. Central concerns of the volume include morphological gaps, learnability, increases and declines in productivity, and the interaction of different components of the grammar. The papers deal with a range of linked synchronic and diachronic topics in phonology, morphology, and syntax (in particular, cliticization), and their implications for linguistic theory