Computing and Visualizing Dynamic Time Warping Alignments in R: The dtw Package

Dynamic time warping is a popular technique for comparing time series, providing both a distance measure that is insensitive to local compression and stretches and the warping which optimally deforms one of the two input series onto the other. A variety of algorithms and constraints have been discussed in the literature. The dtw package provides an unification of them; it allows R users to compute time series alignments mixing freely a variety of continuity constraints, restriction windows, endpoints, local distance definitions, and so on. The package also provides functions for visualizing alignments and constraints using several classic diagram types.

Exploring the Role of Interdisciplinarity in Physics: Success, Talent and Luck

Although interdisciplinarity is often touted as a necessity for modern research, the evidence on the relative impact of sectorial versus to interdisciplinary science is qualitative at best. In this paper we leverage the bibliographic data set of the American Physical Society to quantify the role of interdisciplinarity in physics, and that of talent and luck in achieving success in scientific careers. We analyze a period of 30 years (1980-2009) tagging papers and their authors by means of the Physics and Astronomy Classification Scheme (PACS), to show that some degree of interdisciplinarity is quite helpful to reach success, measured as a proxy of either the number of articles or the citations score. We also propose an agent-based model of the publication-reputation-citation dynamics reproduces the trends observed in the APS data set. On the one hand, the results highlight the crucial role of randomness and serendipity in real scientific research; on the other, they shed light on a counter-intuitive effect indicating that the most talented authors are not necessarily the most successful ones.Comment: 21 pages, 19 figure

Adaptable dialogue architecture and runtime engine (AdaRTE): A framework for rapid prototyping of health dialog systems

International audienceSpoken dialog systems have been increasingly employed to provide ubiquitous access via telephone to information and services for the non-Internet-connected public. They have been successfully applied in the health care context; however, speech technology requires a considerable development investment. The advent of VoiceXML reduced the proliferation of incompatible dialog formalisms, at the expense of adding even more complexity. This paper introduces a novel architecture for dialogue representation and interpretation, AdaRTE, which allows developers to lay out dialog interactions through a high-level formalism, offering both declarative and procedural features. AdaRTE's aim is to provide a ground for deploying complex and adaptable dialogs whilst allowing experimentation and incremental adoption of innovative speech technologies. It enhances augmented transition networks with dynamic behavior, and drives multiple back-end realizers, including VoiceXML. It has been especially targeted to the health care context, because of the great scale and the need for reducing the barrier to a widespread adoption of dialog systems

Identification of slow molecular order parameters for Markov model construction

A goal in the kinetic characterization of a macromolecular system is the description of its slow relaxation processes via (i) identification of the structural changes involved in these processes and (ii) estimation of the rates or timescales at which these slow processes occur. Most of the approaches to this task, including Markov models, master-equation models, and kinetic network models, start by discretizing the high-dimensional state space and then characterize relaxation processes in terms of the eigenvectors and eigenvalues of a discrete transition matrix. The practical success of such an approach depends very much on the ability to finely discretize the slow order parameters. How can this task be achieved in a high-dimensional configuration space without relying on subjective guesses of the slow order parameters? In this paper, we use the variational principle of conformation dynamics to derive an optimal way of identifying the “slow subspace” of a large set of prior order parameters – either generic internal coordinates or a user-defined set of parameters. Using a variational formulation of conformational dynamics, it is shown that an existing method—the time-lagged independent component analysis—provides the optional solution to this problem. In addition, optimal indicators—order parameters indicating the progress of the slow transitions and thus may serve as reaction coordinates—are readily identified. We demonstrate that the slow subspace is well suited to construct accurate kinetic models of two sets of molecular dynamics simulations, the 6-residue fluorescent peptide MR121-GSGSW and the 30-residue intrinsically disordered peptide kinase inducible domain (KID). The identified optimal indicators reveal the structural changes associated with the slow processes of the molecular system under analysis

Genetic studies of abdominal MRI data identify genes regulating hepcidin as major determinants of liver iron concentration

Background & Aims: Excess liver iron content is common and is linked to hepatic and extrahepatic disease risk. We aimed to identify genetic variants influencing liver iron content and use genetics to understand its link to other traits and diseases. Methods: First, we performed a genome-wide association study (GWAS) in 8,289 individuals in UK Biobank with MRI quantified liver iron, and validated our findings in an independent cohort (n=1,513 from IMI DIRECT). Second, we used Mendelian randomisation to test the causal effects of 29 predominantly metabolic traits on liver iron content. Third, we tested phenome-wide associations between liver iron variants and 770 anthropometric traits and diseases. Results: We identified three independent genetic variants (rs1800562 (C282Y) and rs1799945 (H63D) in HFE and rs855791 (V736A) in TMPRSS6) associated with liver iron content that reached the GWAS significance threshold (p<5x10-8). The two HFE variants account for ~85% of all cases of hereditary haemochromatosis. Mendelian randomisation analysis provided evidence that higher central obesity plays a causal role in increased liver iron content. Phenome-wide association analysis demonstrated shared aetiopathogenic mechanisms for elevated liver iron, high blood pressure, cirrhosis, malignancies, neuropsychiatric and rheumatological conditions, while also highlighting inverse associations with anaemias, lipidaemias and ischaemic heart disease. Conclusion: Our study provides genetic evidence that mechanisms underlying higher liver iron content are likely systemic rather than organ specific, that higher central obesity is causally associated with higher liver iron, and that liver iron shares common aetiology with multiple metabolic and non-metabolic diseases

Quality of life and treatment satisfaction in adults with Type 1 diabetes: A comparison between continuous subcutaneous insulin infusion and multiple daily injections

Aims: The aim of this case-control study was to compare quality of life (QoL) and treatment satisfaction in adults with Type 1 diabetes (T1DM) treated with either continuous subcutaneous insulin infusion (CSII) or multiple daily injections (MDI). Methods: Consecutive patients aged between 18 and 55 years, and attending diabetes clinics for a routine visit, completed the Diabetes-Specific Quality-of-Life Scale (DSQOLS), the Diabetes Treatment Satisfaction Questionnaire (DTSQ) and the SF-36 Health Survey (SF-36). Case (CSII) and control subjects (MDI) were recruited in a 1 : 2 ratio. Results: Overall, 1341 individuals were enrolled by 62 diabetes clinics; 481 were cases and 860 control subjects. Cases had a longer diabetes duration and were more likely to have eye and renal complications. Age, school education, occupation and HbA1c were similar. Of control subjects, 90% followed glargine-based MDI regimens and 10% used NPH-based MDI regimens. On multivariate analysis, after adjusting for socioeconomic and clinical characteristics, scores in the following areas of the DSQOLS were higher in cases than control subjects: diet restrictions (β = 5.96; P &lt; 0.0001), daily hassles (β = 3.57; P = 0.01) and fears about hypoglycaemia (β = 3.88; P = 0.006). Treatment with CSII was also associated with a markedly higher DTSQ score (β = 4.13; P &lt; 0.0001) compared with MDI. Results were similar when CSII was compared separately with glargine- or NPH-based MDI regimens. Conclusions: This large, non-randomized, case-control study suggests quality of life gains deriving from greater lifestyle flexibility, less fear of hypoglycaemia, and higher treatment satisfaction, when CSII is compared with either glargine-based or NPH-based MDI regimens. © 2008 The Authors